commit 9992d844099c3df81d9499519ffeb7f93a201dc6
Author: Shreyas Ananthan <shreyas@umd.edu>
Date:   Sun Oct 4 18:19:24 2020 -0600

    Hypre IJ interface: Enable access to additional solvers and preconditioners available in Hypre (#1437)
    
    This PR extends the AMReX _hypre_ IJ interface to allow access to additional solvers and preconditioners available in _hypre_.
    
    - Refactored `HypreABecLap3` and `HypreNodeLap` (IJ matrix/vector ParCSR interfaces) and created a new IJ interface class that provides a unified way to access Hypre ParCSR solvers.
    - In addition to BoomerAMG, adds support for 7 other [ParCSR solvers](https://hypre.readthedocs.io/en/latest/ch-solvers.html) (GMRES (4 variants), PCG, BiCGSTAB, and Hybrid). Also adds support for BoomerAMG and Euclid as preconditioners for solvers that can use a preconditioner.
    - Adds support to parse user options to configure hypre library via AMReX ParmParse interface and input file, using a custom namespace (default is `hypre`)
    - Adds `MLMG::setHypreOptionsNamespace` that allow applications to customize the namespace for different types of linear solvers (e.g., `mac_proj.hypre.<option>`, `nodal_proj.hypre.<option>`, etc.)
    - Add option to skip solver/preconditioner setup step `recompute_preconditioner` for cases where the matrix coefficients do not change.
    - Add option to dump linear system in _hypre_ `IJ{Matrix,Vector}` format for debugging.
    
    ## Additional background
    
    The extensions to _hypre_ interface supports [ExaWind AMR-Wind](https://github.com/exawind/amr-wind) overset and RANS applications.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [X] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreIJIface.H
Src/Extern/HYPRE/AMReX_HypreIJIface.cpp
Src/Extern/HYPRE/AMReX_HypreNodeLap.H
Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp
Src/Extern/HYPRE/CMakeLists.txt
Src/Extern/HYPRE/Make.package
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit ce70a325264f77dcdda362e3b6aae598ae60972d
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Sat Oct 3 18:52:56 2020 -0700

    Fix CPU version of uninitailiedFillNImpl in PODVector (#1435)

Src/Base/AMReX_PODVector.H

commit 362f23ded9cac059fc5f224094545b04832409c6
Author: Shreyas Ananthan <shreyas@umd.edu>
Date:   Sat Oct 3 13:06:46 2020 -0600

    CMake: Fix missing compile time definitions for HYPRE/PETSc (#1436)

Tools/CMake/AMReX_Config.H.in

commit 984f471222394ce2a46dc4972d00019470bafe20
Author: drangara <69211175+drangara@users.noreply.github.com>
Date:   Fri Oct 2 16:42:04 2020 -0400

    Fix bug in EB extdir slopes (#1434)

Src/EB/AMReX_EB_slopes_K.H

commit 00123ce623f70c6ebf70bab8fdc6fc66cd1d7128
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 1 17:09:25 2020 -0700

    Make the id and cpu members of amrex_particle private, as they should… (#1433)
    
    … no longer be accessed directly
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90

commit 5cb09218dbd69357081aa162d10c71282288c570
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Thu Oct 1 13:46:41 2020 -0700

    Disable OpenMPI C++ binding in GNU make system (#1398)
    
    This should fix the warning reported in #1397.  Note that C++ binding has
    been removed from the MPI-3 standard.

Tools/GNUMake/sites/Make.unknown

commit 3e2dbdaf7348ce92c04b3932ae5288108a7c6ca9
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Thu Oct 1 10:49:11 2020 -0700

    fix a long standing bug in eb levelset (#1432)
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/EB/AMReX_EB_utils.cpp

commit 40744a9c8e18fff72a9121a8c46b7b2414634374
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Thu Oct 1 08:49:37 2020 -0700

    update CHANGES for 20.10 (#1431)

CHANGES

commit 3371d5208cfa6c6edeb9195cfc9b25372c8b90d3
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Sep 30 22:57:59 2020 -0700

    CMake: fix ENABLE_PROFPARSER and ENABLE_SENSEI options (#1428)
    
    * CMake: fix incorrect option
    
    * CMake: fix ENABLE_SENSEI option

Docs/sphinx_documentation/source/BuildingAMReX.rst
Src/CMakeLists.txt
Src/Extern/amrdata/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReXThirdPartyLibraries.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake

commit c43b88a85571a7a829d71c094f6675b8151112e8
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 30 19:50:37 2020 -0700

    Tulip mpi (#1430)
    
    * Update mpi setup on tulip
    
    * More information on the number of devices for HIP

Src/Base/AMReX_GpuDevice.cpp
Tools/GNUMake/sites/Make.frontier-coe

commit d446c6a4ee04ba61468c8b023469092c8c7b5e01
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 30 18:00:36 2020 -0700

    Remove EB LSCore and levelset (#1429)
    
    ## Summary
    They are no longer supported.  To fill a MultiFab with signed distance
    function, amrex::FillSignedDistance can be used.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Docs/sphinx_documentation/source/EB.rst
Docs/sphinx_documentation/source/EB/loc_ls_ex.png
Src/EB/AMReX_EB_F.H
Src/EB/AMReX_EB_LSCore.H
Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_LSCore_F.H
Src/EB/AMReX_EB_Tagging.F90
Src/EB/AMReX_EB_bc_fill_nd.F90
Src/EB/AMReX_EB_geometry.F90
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_levelset_F.F90
Src/EB/AMReX_EB_utils.H
Src/EB/AMReX_EB_utils.cpp
Src/EB/AMReX_WriteEBSurface.cpp
Src/EB/AMReX_compute_normals.F90
Src/EB/CMakeLists.txt
Src/EB/Make.package
Tutorials/EB/Donut/CMakeLists.txt
Tutorials/EB/Donut/Exec/GNUmakefile
Tutorials/EB/Donut/Exec/inputs
Tutorials/EB/Donut/Src/Make.package
Tutorials/EB/Donut/Src/main.cpp
Tutorials/EB/LevelSet/CMakeLists.txt
Tutorials/EB/LevelSet/Exec/GNUmakefile
Tutorials/EB/LevelSet/Exec/inputs
Tutorials/EB/LevelSet/Exec/inputs_eb2
Tutorials/EB/LevelSet/Src/Make.package
Tutorials/EB/LevelSet/Src/main.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp
Tutorials/EB/LevelSet/Src/make_poly.cpp
Tutorials/EB/LevelSet/Src/make_shapes.H

commit 61734d3da08b88a5c35a7c57c20644e122fa5e36
Author: Pedro Costa <p.simoes.costa@gmail.com>
Date:   Wed Sep 30 16:43:17 2020 +0000

    typo fixes (#1427)

Docs/sphinx_documentation/source/AmrCore.rst
Docs/sphinx_documentation/source/AmrLevel.rst
Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/Fortran.rst
Docs/sphinx_documentation/source/GridCreation.rst
Docs/sphinx_documentation/source/IO.rst
Docs/sphinx_documentation/source/LinearSolvers.rst
Docs/sphinx_documentation/source/LoadBalancing.rst

commit c75c4a65ec50580504f87e6ea7cbd4d314644a17
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 29 21:55:31 2020 -0700

    Signed distance function (#1425)
    
    ## Summary
    * Add FillImpFunc to fill MultiFab with the value of implicit function
    
    * average_down_nodal: optional argument to specify the safety of mfiter
    
    * Add FillSignedDistance to fill MultiFab with signed distance.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_MultiFabUtil.H
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EB_utils.H
Src/EB/AMReX_EB_utils.cpp

commit ea9f8208cd820326cbd38d65307ae7f1181b48fb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Sep 29 14:53:33 2020 -0700

    Call sync at the end of the particle transformation functions. (#1424)
    
    The `ParticleTransformations` test was broken on Tulip. The problem was missing `synchronize` statements in the test code itself. However, it is safer if these functions perform the synchronization internally.
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Particle/AMReX_ParticleTransformation.H

commit 23f2eb2dc97b56038d38b4079ee161800c8e40c2
Author: mic84 <mrosso@lbl.gov>
Date:   Tue Sep 29 12:41:26 2020 -0700

    Doc: update documentation on CMake+CUDA (#1421)
    
    * Doc: update documentation on CMake+CUDA
    
    * Update Docs/sphinx_documentation/source/GPU.rst
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
    
    * Update Docs/sphinx_documentation/source/GPU.rst
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
    
    * CMake: bump up minimum required CUDA version
    
    * Doc: update doc
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

Docs/sphinx_documentation/source/BuildingAMReX.rst
Docs/sphinx_documentation/source/GPU.rst
Tools/CMake/AMReX_SetupCUDA.cmake

commit f9a441ae372198bf6efe3af6eaca3b967ee3291c
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 29 09:16:03 2020 -0700

    Fix 1D CUDA compilation failure due to #1332 (#1423)
    
    The most vexing parse in C++ strikes again.
    
    This closes #1422.

Src/Base/AMReX_GpuLaunchMacrosG.H

commit b7ef5a650d7e3accb9f698b7ec929c87cbf24711
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 29 08:24:51 2020 -0700

    Remove the call to set device flags. (#1417)
    
    ## Summary
    This is no longer needed and may result in failure due to that the device
    has already been set and initialized in another code.
    
    ## Additional background
    Exa-Wind has a code that uses both Kokkos and AMReX.  It seems that
    the call to cudaSetDeviceFlags fails because of that.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_GpuDevice.cpp

commit ef6789d593814c78ce1de0456fb5fa524a1f9c13
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Sep 28 17:30:23 2020 -0700

    Fix new bug in clearNeighhborsGPU (#1420)
    
    * Fix new bug in clearNeighhborsGPU
    
    * fix typo

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit c4116b67f7f176229a749bc818b7610a61a9a2f8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Sep 28 14:17:55 2020 -0700

    these functions need to be marked __host__ __device__ to compile with HIP (#1419)

Src/Particle/AMReX_ParticleUtil.H

commit e4f0bcd12845e81daa8c13d9839e9662c26bfd08
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Sep 28 13:11:30 2020 -0700

    Define ParticleTile in AddParticles (#1409)
    
    * Remove GetPosition and SetPosition from ParIter
    
    * define the particle tile before adding particles to it

Src/Particle/AMReX_ParticleContainerI.H

commit aadf8eb8711b816d3234745a98c6170918bca7c3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Sep 28 13:09:33 2020 -0700

    Generalize clearNeighbors for multiple levels and remove faulty assertions. (#1418)
    
    * Generalize clearNeighbors for multiple levels and remove faulty assertions.
    
    * also fix cpu version

Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 3a9381141a1fe78180be578e7b0e1b24a7532171
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 25 14:15:18 2020 -0700

    fix decltype for the case where have a random engine (#1414)

Src/Particle/AMReX_ParticleTransformation.H

commit d7ed0d7a41d92ecfb0a4cee2ff023597e5e9f875
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 25 14:15:09 2020 -0700

    always clear neighbor particles before calling Redistribute() (#1415)

Src/Particle/AMReX_NeighborParticles.H

commit 4a4d585621b0fa34980464baab0466b5e09bc781
Author: asalmgren <asalmgren@lbl.gov>
Date:   Fri Sep 25 09:50:37 2020 -0700

    1) remove flags setCGVerbose and setCGMaxIter since those are more accurately called (#1413)
    
    setBottomVerbose and setBottomMaxIter.   The "setCG..." flags are misleading since
    they actually apply to non-CG bottom solvers as well.
    2) add documentation in the Linear Solvers section about "maxorder" -- this was not previously documented.

Docs/sphinx_documentation/source/LinearSolvers.rst
Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Tests/LinearSolvers/MLMG/inputs
Tests/LinearSolvers/MLMG/inputs.boxes
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp
Tutorials/Basic/HeatEquation_EX3_C/Source/advance.cpp
Tutorials/LinearSolvers/ABecLaplacian_F/inputs
Tutorials/LinearSolvers/ABecLaplacian_F/inputs-rt-abeclap-lev
Tutorials/LinearSolvers/ABecLaplacian_F/inputs-rt-poisson-com
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90
Tutorials/LinearSolvers/MAC_Projection_EB/inputs_3d
Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp
Tutorials/LinearSolvers/MultiComponent/inputs
Tutorials/LinearSolvers/MultiComponent/main.cpp
Tutorials/LinearSolvers/Nodal_Projection_EB/inputs_3d
Tutorials/LinearSolvers/Nodal_Projection_EB/main.cpp
Tutorials/SDC/MISDC_ADR_2d/Source/main.cpp

commit bd7c2b8db69b4a3cdb40bf3f23bf8eea952d5071
Author: Pedro Costa <p.simoes.costa@gmail.com>
Date:   Fri Sep 25 16:13:23 2020 +0000

    typo fixes (#1411)
    
    ## Summary
    some small typos I found while reading the documentation
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate
    
    
    Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>

Docs/sphinx_documentation/source/Basics.rst

commit 9499db8a1f406d1691b845f203c3a15c5f28c744
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 25 08:43:04 2020 -0700

    Remove GetPosition and SetPosition from ParIter (#1408)
    
    These were added for WarpX, but they are not used any more.
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Particle/AMReX_ParIter.H

commit 9f43ecbb0df8e37e4d0aa9511f76cc5e91c52d9d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Sep 24 13:58:32 2020 -0700

    filterParticles and filterAndTransformParticles need to take callables with and without RNG (#1407)
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [x] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Particle/AMReX_ParticleTransformation.H
Src/Particle/AMReX_ParticleUtil.H
Src/Particle/AMReX_WriteBinaryParticleData.H

commit 605e276d42d660eaf28e8a7f68636d30f624738f
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Sep 24 08:10:29 2020 -0700

    ParallelDescriptor: Check MPI If Self (#1406)
    
    ## Summary
    
    Only check the requested MPI Threading level if AMReX also initialized MPI.
    
    Follow-up to #1351
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_ParallelDescriptor.cpp

commit 3cad68f7a504044186d0caa20649197d2794aa8b
Author: Donald E. Willcox <dwillcox@users.noreply.github.com>
Date:   Wed Sep 23 18:02:34 2020 -0700

    Enable compilation on Cori interactive nodes (#1405)
    
    ## Summary
    
    This enables compilation in Cori interactive jobs.
    
    Previously, in interactive jobs on Cori Haswell and KNL, `hostname -f` returned a string like `nid00018` so we were loading `Make.unknown`, causing compilation failure.
    
    @WeiqunZhang suggested checking the `NERSC_HOST` environment variable instead, which is defined on Cori login, interactive (Haswell & KNL), and GPU nodes.
    
    This PR moves the check in `Make.machines` for Cori to follow the logic for Cori GPU, and we check if `NERSC_HOST` is set to `cori`.
    
    I've tested this works on Haswell & KNL interactive jobs and that we are still setting `which_computer` correctly on Cori GPU.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [X] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/GNUMake/Make.machines

commit 2b31386adec5efda010ff08261d5f0658027e96c
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 23 17:23:48 2020 -0700

    DPCPP: use C++17 and disable mkl warnings (#1404)
    
    * DPCPP: use C++17 and disable mkl warnings
    
    * Explicitly use C++17 because MKL contains C++17 codes.
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

Src/Base/AMReX_Random.H
Src/Base/AMReX_RandomEngine.H
Tools/GNUMake/comps/dpcpp.mak

commit 766a2385cf37e97291f7e0d4fa5ebe1ed55f7fe5
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Sep 23 16:32:19 2020 -0700

    Docs: C++17 & Particle SP (#1403)
    
    Update the build docs for GNUmake:
    - single precision for particles
    - typo in `USE_DPCPP` option
    - add C++17 option
    
    Equivalent CMake options are up-to-date, so no change is needed.

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit fbee3e3a3b1ebd912dbe6c1b6bb29d36d10ab153
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Sep 23 16:16:11 2020 -0700

    CMake: enforce C++17 as minimum C++ standard for ENABLE_DPCPP=ON (#1402)

Tools/CMake/AMReX_Config.cmake

commit 577c8221804b5a2185c0356d6ab46e538722b9d1
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 23 14:47:56 2020 -0700

    Use RNG in Particle I/O filter (#1401)
    
    In order to support the use of RNG in particle I/O filters, we need to be
    able to call two types of filter functions.  The new type has a
    RandomEngine argument.

Src/Particle/AMReX_WriteBinaryParticleData.H

commit e9007d6832efe63e94ff180d97f2212cad9e13ac
Author: Pedro Costa <p.simoes.costa@gmail.com>
Date:   Wed Sep 23 17:58:05 2020 +0000

    nitpicking :) (#1400)
    
    ## Summary
    typo fix
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Docs/sphinx_documentation/source/Basics.rst

commit 5f85756e8523423913bd46a7d318def6f1889103
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 23 10:31:10 2020 -0700

    Update dpcpp flags (#1399)
    
    * -fsycl-unnamed-lambda is enabled by default now.  So we do not need to
       pass the flag anymore.
    
    * Early optimizations are enabled by default in beta09.  This makes a lot of
      tests crash.  So we disable it with -fno-sycl-early-optimizations.

Tools/CMake/AMReXSYCL.cmake
Tools/GNUMake/comps/dpcpp.mak

commit f75ae5897d699a0fa4835818b5d5ab83535e5be8
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Sep 23 08:09:22 2020 -0700

    NodalProjector: fix comments (#1396)

Src/LinearSolvers/Projections/AMReX_NodalProjector.H
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 804f844b0634e5fde9fd52a36c12fcb3069fcc66
Author: kngott <30483578+kngott@users.noreply.github.com>
Date:   Tue Sep 22 15:11:36 2020 -0700

    Fix inaccurate assertion. (#1395)

Src/Base/AMReX_BoxList.cpp

commit a18b88f27ca0b5c69cd935d7af3011d954322d9a
Author: mic84 <mrosso@lbl.gov>
Date:   Tue Sep 22 13:47:12 2020 -0700

    CMake: remove LinearSolvers/MultiComponent from tutorials (#1394)

Tutorials/LinearSolvers/MultiComponent/CMakeLists.txt

commit 784f23144d3edda49ff812e6c601ca3ec1468372
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 22 13:33:25 2020 -0700

    Fix function type for HIP (#1393)
    
    Currently in HIP we do not have a way to do SNFINAE based on whether the
    function is callable on host or not.  So we have to replace the device
    lambda with host and device lambda.

Src/Base/AMReX_MultiFab.cpp

commit 9198b1b9a7f7f77ff04261aada6284301db77391
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Mon Sep 21 21:08:18 2020 -0700

    DPCPP support for mulitple GPUs (#1392)

Src/Base/AMReX_GpuDevice.cpp

commit d6eadf8c32ae211febeaa2aa1e6e1df5a70807cb
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Mon Sep 21 20:21:53 2020 -0700

    Intall intel-oneapi-mkl-devel in CI (#1391)

.github/workflows/dependencies/dependencies_dpcpp.sh

commit 9a272a1701dbedd1f0b993720f157cf340d12f33
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Mon Sep 21 13:52:33 2020 -0700

    Random Number Generation on Device (#1363)
    
    In order to support RNG on device with DPC++, we have to change the API
    because DPC++ does not support global device variables.  We introduce a new
    ParallelForRNG function that takes a device lambda with an extra
    RandomEngine argument.  Random numbers can be generated by calling
    amrex::Random(RandomEngine const&).  To maintain backward compatibility in
    the short term, the old way of calling `amrex::Random()` on device is kept.
    But it will be removed soon because no locking is needed in the new way
    unlike in `Random()`.  Note that only the device version of
    `amrex::Random()` is deprecated.

Src/Base/AMReX_Extension.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_Random.H
Src/Base/AMReX_Random.cpp
Src/Base/AMReX_RandomEngine.H
Src/Base/AMReX_Reduce.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tests/AsyncOut/multifab/main.cpp
Tests/GPU/RandomNumberGeneration/inputs
Tests/GPU/RandomNumberGeneration/main.cpp
Tests/Particles/ParallelContext/main.cpp
Tests/Particles/Redistribute/main.cpp
Tutorials/GPU/ParallelReduce/main.cpp

commit 3c8dad86006c5ef256884733bff99b9806be46d4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Sep 21 13:51:30 2020 -0700

    Remove redundant particle test (#1389)
    
    The same functionality is already tested in `Tests/Particles/Redistribute`.
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tests/Particles/GNUmakefile
Tests/Particles/Make.package
Tests/Particles/main.cpp
Tests/Particles/test.py

commit 1e35d0d50287bc32a02a94b03466a750c9e491d1
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Mon Sep 21 10:24:23 2020 -0700

    CMake & DPC++: Avoid Flag Deduplication (#1388)
    
    ## Summary
    
    Avoid deduplication of `-mlong-double-64 -Xclang -mlong-double-64` into `-mlong-double-64 -Xclang`.
    
    Update the apt package name, which was changed by upstream for beta09.
    
    Refs.:
    - https://gitlab.kitware.com/cmake/cmake/-/issues/15826
    - https://gitlab.kitware.com/cmake/cmake/-/merge_requests/1841
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

.github/workflows/dependencies/dependencies_dpcpp.sh
Tools/CMake/AMReXSYCL.cmake

commit 1cec808bc2f814033350b09f01f4b64a9112f2cd
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Mon Sep 21 08:33:10 2020 -0700

    More on Gpu kernel fusing (#1332)
    
    ## Summary
    
    * Add Gpu::KernelInfo argument to ParallelFor to allow the user to indicate
      whether the kernel is an candidate for fusing.
    
    * For MFIter, if the local size is less or equal to 3, the fuse region is
      turned on and small kernels marked fusable will be fused.
    
    * Add launch macros for fusing.
    
    * Add fusing to a number of functions used by linear solvers.  Note that
      there are a lot more amrex functions need to be updated for fusing.
    
    * Optimize reduction for bottom solve.
    
    * Consolidate memcpy in communication functions.
    
    * Option to use device memory in communication kernels for packing and
      unpacking buffers.  But it's currently turned off because the performance
      was not improved in testing.  In fact, it was worse than using pinned
      memory.  But this might change in the future.  So the option is kept.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [x] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX.cpp
Src/Base/AMReX_FBI.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuFuse.H
Src/Base/AMReX_GpuFuse.cpp
Src/Base/AMReX_GpuKernelInfo.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuLaunchMacrosG.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_Reduce.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 626b5f55c1c3d143e918f5e5e95cb231e497e896
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Mon Sep 21 08:29:39 2020 -0700

    Make max GPU streams runtime parameter (#1386)
    
    ## Summary
    
    Add a new runtime parameter, amrex.max_gpu_streams.
    
    ## Additional background
    
    This can be used to work around a HIP compiler bug by setting `amrex.max_gpu_streams=1`.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [x] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp

commit 50e3994bb3cb3d4fdd1a680ae10176bc99dcd4d5
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Sun Sep 20 13:40:05 2020 -0700

    Switch to `use mpi` from `include 'mpif.h'` (#1385)

Src/F_Interfaces/Base/AMReX_parallel_mod.F90

commit 816ef0b6d37580fc86c5c1119ecdfa7288cf83e5
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Sun Sep 20 13:31:59 2020 -0700

    Fix a typo in Advection_F make file (#1384)
    
    ## Summary
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tutorials/FortranInterface/Advection_F/Source/Src_3d/Make.package

commit 35a0533f8726e3741a5bc7cadc68d9e6926a6893
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Sun Sep 20 13:31:24 2020 -0700

    Fix tensor solver with periodic boundaries (#1383)
    
    ## Summary
    
    Remove erroneous calls to EnforcePeriodicity.  When coarse/fine boundary
    meets periodic boundary with fine grids form an L-shape, the uncovered fine
    ghost cell at the corner is actually "multi-valued". That is the cells with
    the same indices has different values in different boxes.  That's why
    calling EnforcePeriodicity is erroneous.  For CPU runs, this bug introduces
    deterministic errors, but the solver still converges.  For GPU runs, this
    causes convergence issues too because EnforcePeriodicity is not
    deterministic when the values inside domain are not consistent.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [x] changes answers in the test suite to more than roundoff level
    - [x] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 7c5cce3687a5b663355b1a367f0734760dcb4a0b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 18 17:15:53 2020 -0700

    Remove old / obsolete / non-test tests. (#1381)

Tests/Algoim/CMakeLists.txt
Tests/Algoim/GNUmakefile
Tests/Algoim/Make.package
Tests/Algoim/main.cpp
Tests/BBIOBenchmark/BBIOTest.cpp
Tests/BBIOBenchmark/BBIOTestDriver.cpp
Tests/BBIOBenchmark/CMakeLists.txt
Tests/BBIOBenchmark/GNUmakefile
Tests/BBIOBenchmark/README
Tests/BaseFabTesting/CMakeLists.txt
Tests/BaseFabTesting/GNUmakefile
Tests/BaseFabTesting/Make.package
Tests/BaseFabTesting/inputs
Tests/BaseFabTesting/main.cpp
Tests/C_BaseLib/AMRPROFTEST_F.H
Tests/C_BaseLib/AMRProfTestBL.cpp
Tests/C_BaseLib/CMakeLists.txt
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/TPROFILER.F
Tests/C_BaseLib/TPROFILER_F.H
Tests/C_BaseLib/fillfab.f
Tests/C_BaseLib/mt19937int.out
Tests/C_BaseLib/t8BIT.cpp
Tests/C_BaseLib/tBA.cpp
Tests/C_BaseLib/tCArena.cpp
Tests/C_BaseLib/tDM.cpp
Tests/C_BaseLib/tDir.cpp
Tests/C_BaseLib/tFAC.cpp
Tests/C_BaseLib/tFB.cpp
Tests/C_BaseLib/tFillFab.cpp
Tests/C_BaseLib/tMF.cpp
Tests/C_BaseLib/tMFcopy.cpp
Tests/C_BaseLib/tParmParse.cpp
Tests/C_BaseLib/tProfiler.cpp
Tests/C_BaseLib/tRABcast.cpp
Tests/C_BaseLib/tRan.cpp
Tests/C_BaseLib/tUMap.cpp
Tests/C_BaseLib/tVisMF.cpp
Tests/C_BaseLib/tVisMF2.cpp
Tests/C_BaseLib/tread.cpp
Tests/DataServicesTest0/CMakeLists.txt
Tests/DataServicesTest0/DataServicesTest0.cpp
Tests/DataServicesTest0/GNUmakefile
Tests/GPU/CudaGraphs/BuildingGraphs/GNUmakefile
Tests/GPU/CudaGraphs/BuildingGraphs/Make.package
Tests/GPU/CudaGraphs/BuildingGraphs/inputs_3d
Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp
Tests/GPU/CudaGraphs/BuildingGraphs/run.corigpu
Tests/GPU/CudaGraphs/CrazyGraphs/GNUmakefile
Tests/GPU/CudaGraphs/CrazyGraphs/main.cpp
Tests/GPU/CudaGraphs/CrazyGraphs/run.corigpu
Tests/GPU/CudaGraphs/GraphBoundary/GNUmakefile
Tests/GPU/CudaGraphs/GraphBoundary/Make.package
Tests/GPU/CudaGraphs/GraphBoundary/Prob.H
Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d
Tests/GPU/CudaGraphs/GraphBoundary/main.cpp
Tests/GPU/CudaGraphs/GraphBoundary/profile.sh
Tests/GPU/CudaGraphs/GraphBoundary/run.corigpu
Tests/GPU/CudaGraphs/GraphBoundary/run.summit
Tests/GPU/CudaGraphs/GraphInitTest/GNUmakefile
Tests/GPU/CudaGraphs/GraphInitTest/Make.package
Tests/GPU/CudaGraphs/GraphInitTest/inputs_3d
Tests/GPU/CudaGraphs/GraphInitTest/main.cpp
Tests/GPU/CudaGraphs/GraphReuseCopy/GNUmakefile
Tests/GPU/CudaGraphs/GraphReuseCopy/Make.package
Tests/GPU/CudaGraphs/GraphReuseCopy/inputs_3d
Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp
Tests/GPU/CudaGraphs/GraphReuseCopy/run.corigpu
Tests/GPU/CudaGraphs/GraphWithMemcpy/GNUmakefile
Tests/GPU/CudaGraphs/GraphWithMemcpy/Make.package
Tests/GPU/CudaGraphs/GraphWithMemcpy/inputs_3d
Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp
Tests/GPU/CudaGraphs/GraphWithMemcpy/run.corigpu
Tests/GPU/CudaGraphs/Readme.txt
Tests/GPU/CuptiTest/Exec/CUDA/GNUmakefile
Tests/GPU/CuptiTest/Exec/CUDA/Make.package
Tests/GPU/CuptiTest/Exec/CUDA/myfunc.H
Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp
Tests/GPU/CuptiTest/Exec/CUDA/mykernel.H
Tests/GPU/CuptiTest/Make.CUPTI
Tests/GPU/CuptiTest/Source/Make.package
Tests/GPU/CuptiTest/Source/main.cpp
Tests/GPU/Locking/GNUmakefile
Tests/GPU/Locking/Make.package
Tests/GPU/Locking/inputs
Tests/GPU/Locking/main.cpp
Tests/GPU/libamrex_CUDA/GNUmakefile
Tests/GPU/libamrex_CUDA/README.md
Tests/GPU/libamrex_CUDA/main.cpp
Tests/IOBenchmark/GNUmakefile
Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/IOBenchmark/README
Tests/IOBenchmark/inputs
Tests/IOBenchmark/inputs.dirname
Tests/IOBenchmark/inputs.dss
Tests/IOBenchmark/inputs.dssmf
Tests/IOBenchmark/inputs.nft
Tests/IOBenchmark/inputs.small
Tests/MKDir/GNUmakefile
Tests/MKDir/MKDir.cpp
Tests/NoFort/GNUmakefile
Tests/NoFort/Make.package
Tests/NoFort/main.cpp
Tests/PnetCDFBenchmark/GNUmakefile
Tests/PnetCDFBenchmark/Make.package
Tests/PnetCDFBenchmark/ReadMe
Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.H
Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp
Tests/PnetCDFBenchmark/inputs
Tests/PnetCDFBenchmark/main.cpp
Tests/ProfTests/HeatEquation_EX1_C/Exec/GNUmakefile
Tests/ProfTests/HeatEquation_EX1_C/Exec/inputs_2d
Tests/ProfTests/HeatEquation_EX1_C/Exec/inputs_3d
Tests/ProfTests/HeatEquation_EX1_C/Source/Make.package
Tests/ProfTests/HeatEquation_EX1_C/Source/advance.cpp
Tests/ProfTests/HeatEquation_EX1_C/Source/advance_2d.f90
Tests/ProfTests/HeatEquation_EX1_C/Source/advance_3d.f90
Tests/ProfTests/HeatEquation_EX1_C/Source/init_phi_2d.f90
Tests/ProfTests/HeatEquation_EX1_C/Source/init_phi_3d.f90
Tests/ProfTests/HeatEquation_EX1_C/Source/main.cpp
Tests/ProfTests/HeatEquation_EX1_C/Source/myfunc.H
Tests/ProfTests/HeatEquation_EX1_C/Source/myfunc_F.H
Tests/ProfTests/ThirdParty/Exec/GNUmakefile
Tests/ProfTests/ThirdParty/Exec/inputs_2d
Tests/ProfTests/ThirdParty/Exec/inputs_3d
Tests/ProfTests/ThirdParty/Source/Make.package
Tests/ProfTests/ThirdParty/Source/advance.cpp
Tests/ProfTests/ThirdParty/Source/advance_2d.f90
Tests/ProfTests/ThirdParty/Source/advance_3d.f90
Tests/ProfTests/ThirdParty/Source/init_phi_2d.f90
Tests/ProfTests/ThirdParty/Source/init_phi_3d.f90
Tests/ProfTests/ThirdParty/Source/main.cpp
Tests/ProfTests/ThirdParty/Source/myfunc.H
Tests/ProfTests/ThirdParty/Source/myfunc_F.H
Tests/SinglePrecision/GNUmakefile
Tests/SinglePrecision/Make.package
Tests/SinglePrecision/main.cpp
Tests/Slice/GNUmakefile
Tests/Slice/Make.package
Tests/Slice/inputs
Tests/Slice/main.H
Tests/Slice/main.cpp
Tests/SliceWithInterp/inputs
Tests/SliceWithInterp/main.cpp
Tests/Stream/GNUmakefile
Tests/Stream/Make.package
Tests/Stream/inputs
Tests/Stream/main.cpp
Tests/ThirdPartyLib/GNUmakefile
Tests/ThirdPartyLib/Readme
Tests/ThirdPartyLib/bar.F90
Tests/ThirdPartyLib/foo.cpp
Tests/ThirdPartyLib/main.c
Tests/TypeCheck/GNUmakefile
Tests/TypeCheck/Make.package
Tests/TypeCheck/f.f90
Tests/TypeCheck/f_F.H
Tests/Vectorization/GNUmakefile
Tests/Vectorization/Make.package
Tests/Vectorization/kc.H
Tests/Vectorization/kc.cpp
Tests/Vectorization/kdecl.H
Tests/Vectorization/kf.F90
Tests/Vectorization/main.cpp

commit 28a454d7ea1f696dd721834b9b4e668294bf50b5
Author: mic84 <mrosso@lbl.gov>
Date:   Fri Sep 18 16:23:04 2020 -0700

    CMake: enable testing via CTest. (#1362)

.github/workflows/linux.yml
CMakeLists.txt
Tests/Algoim/CMakeLists.txt
Tests/AsyncOut/multifab/CMakeLists.txt
Tests/BBIOBenchmark/CMakeLists.txt
Tests/BaseFabTesting/CMakeLists.txt
Tests/CMakeLists.txt
Tests/C_BaseLib/CMakeLists.txt
Tests/DataServicesTest0/CMakeLists.txt
Tests/FillBoundaryComparison/CMakeLists.txt
Tests/Particles/NeighborParticles/CMakeLists.txt
Tests/Particles/ParticleMesh/CMakeLists.txt
Tests/Particles/ParticleReduce/CMakeLists.txt
Tests/Particles/ParticleTransformations/CMakeLists.txt
Tests/Particles/Redistribute/CMakeLists.txt
Tests/complementIn/CMakeLists.txt

commit 9831ee93eb844ce43a37c8b3af138cc57e893964
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 18 15:58:59 2020 -0700

    Remove reliance on managed memory from AMReX_ParticleCommunication.H/.cpp (#1380)

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit eb2b7fd5419a4b2e89d32c6ec0ac8e7bfd59df69
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 18 10:25:48 2020 -0700

    fix signed vs. unsigned issue in AMReX_ParticleCommunication.cpp (#1379)

Src/Particle/AMReX_ParticleCommunication.cpp

commit 6fbd2868a38396391260c0ac61f23c5eac5d6d6b
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Fri Sep 18 07:24:18 2020 -0700

    Fix #1375 (#1378)
    
    A Bug was introduced in #1375.  The host vector should have an initial size.

Src/Particle/AMReX_ParticleTile.H

commit 6ce92531fd1fb5fce70506ddd214aacf0db06501
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Thu Sep 17 19:09:33 2020 -0700

    DPC++ & HIP: NumberOfParticles on device (#1377)
    
    ## Summary
    
    For DPC++ and HIP, we have to run NumberOfParticles on device.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Particle/AMReX_ParticleContainerI.H

commit e4023270d871f6850f9fe8ff744745e7d74fdaac
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Thu Sep 17 18:30:12 2020 -0700

    Put static constexpr members back to ParticleTile (#1376)
    
    ## Summary
    
    They should not be removed in #1375.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Particle/AMReX_ParticleTile.H

commit 4b2f5fa1fc7d13c150a41f74ff33b5fbe4395bdf
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Thu Sep 17 17:21:44 2020 -0700

    Avoid accessing device memory directly on host (#1375)
    
    ## Summary
    
    ParticleLocator and ParticleTile contain vectors using device memory.  To
    remove the dependency on unified memory we avoid accessing them directly on
    the host.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Particle/AMReX_ParticleLocator.H
Src/Particle/AMReX_ParticleReduce.H
Src/Particle/AMReX_ParticleTile.H

commit 39f32bd4f9f6d9f0a9455f7f1790337a780a1e09
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Sep 17 11:34:21 2020 -0700

    Add explicit syncs to InitParticles in the Test routines. (#1374)
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tests/Particles/AsyncIO/main.cpp
Tests/Particles/NeighborParticles/MDParticleContainer.cpp
Tests/Particles/ParallelContext/main.cpp
Tests/Particles/ParticleReduce/main.cpp
Tests/Particles/ParticleTransformations/main.cpp
Tests/Particles/Redistribute/main.cpp

commit 3cf2461f97ba66b8da5d62cacf35b43ab6584b67
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Thu Sep 17 09:48:48 2020 -0700

    User defined literals in DPC++ (#1366)
    
    It is now supported in beta09 with `-Xclang -mlong-double-64`.

Src/Base/AMReX_REAL.H
Tools/CMake/AMReXSYCL.cmake
Tools/GNUMake/comps/dpcpp.mak

commit 5a2d460801039b79a9d90ac2bf116c186d1220f9
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Sep 16 19:02:22 2020 -0700

    GNUMake: remove unused define for HIP compilation (#1372)
    
    * GNUMake: remove unused AMREX_HIP_PLATFORM define
    
    * GNUMake: rename HIP_PLATFORM to HIP_COMPILER for consistency

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/hip.mak

commit 59036167c676ae1acc31b18e061f99573af36111
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Sep 16 17:09:11 2020 -0700

    .gitignore: build/ (#1373)
    
    ## Summary
    
    besides our currently assumed temporary build directories, a temporar build/ directory is quite common in CMake (although discouraged to build inside the tree at all, but this is safe enough).
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

.gitignore

commit ea27c4008901d88fa41af08592bbd2355f23f569
Author: Mark Meredith <mwm126@pm.me>
Date:   Wed Sep 16 17:38:46 2020 -0400

    Fix uninitialized compiler warnings for: xslope yslope zslope (#1371)
    
    ## Summary
    
    Getting compiler warnings when building MFiX-Exa file that includes `AMReX_EB_slopes_K.H`
    
    ## Additional background
    
    Building with GCC 7.5.0:
    ```
    ../src/convection/mfix_slopes.cpp: In member function 'void mfix::mfix_compute_slopes(int, amrex::Real, amrex::MultiFab&, const amrex::Vector<amrex::MultiFab*>&, const amrex::Vector<amrex::MultiFab*>&, const amrex::Vector<amrex::MultiFab*>&, int, std::map<std::__cxx11::basic_string<char>, amrex::PODVector<int, std::allocator<int> > >&)':
    ../src/convection/mfix_slopes.cpp:235:52: error: 'zslope' may be used uninitialized in this function [-Werror=maybe-uninitialized]
                            zs_fab(i,j,k,slopes_comp+n) = eb_slopes[2];
    ../src/convection/mfix_slopes.cpp:216:52: error: 'yslope' may be used uninitialized in this function [-Werror=maybe-uninitialized]
                            ys_fab(i,j,k,slopes_comp+n) = eb_slopes[1];
    ../src/convection/mfix_slopes.cpp:197:52: error: 'xslope' may be used uninitialized in this function [-Werror=maybe-uninitialized]
                            xs_fab(i,j,k,slopes_comp+n) = eb_slopes[0];
    ```
    
    ## Checklist
    
    The proposed changes:
    - [X] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate
    
    
    Co-authored-by: Mark Meredith <mark.meredith@netl.doe.gov>

Src/EB/AMReX_EB_slopes_K.H

commit 7aacbd10c8b6b0cf463d04d3418783587090467f
Author: mic84 <mrosso@lbl.gov>
Date:   Tue Sep 15 17:41:31 2020 -0700

    CMake: remove duplicate sources (#1370)

Src/Base/CMakeLists.txt

commit 940a9499bb7c5c4f1aa209d4e501d34e20eeafff
Author: mic84 <mrosso@lbl.gov>
Date:   Tue Sep 15 14:50:59 2020 -0700

    CMake: re-organize tutorials (#1333)
    
    * CMake: begin refactoring tutorials
    * CMake: refactor Tutorials/Basic
    * CMake: setup_tutorials is now able to figure out include paths by itself
    * CMake: add optional arguments ot setup_tutorial
    * CMake: refactor Tutorials/Amr
    * CMake: refactor Tutorials/LinearSolvers
    * CMake: add tutorials in Tutorials/EB
    * Tutorials: change name of file for consistency with 2D case
    * CMake: refactor Tutorials/FortranInterface
    * CMake: refactor Tutorials/Particles
    * CMake: forgot to refactor Tutorials/LinearSolvers/NodeTensorLap/
    * CMake: update CI
    * CMake: some clean-up
    * CMake: forgot to update the CI for win and mac
    * CMake: add missing F_interfaces sources to build set
    * CMake: 2D setup for tutorials
    * CMake: 1D setup for tutorials
    * CMake: EB is made avaialble only if DIM>1
    * CMake: exclude MPI-only tutorials from build if ENABLE_MPI=OFF
    * CMake: some turotorials need Fortran enabled
    * CMake: exclude CUDA-unaware tutorials from CUDA builds
    * CMake: this should fix the Windows CI
    * CMake: add tutorials in Tutorials/ForkJoin
    * CMake: fix mispelled variable
    * CMAke: Particles/CellSortedParticles tutorial is not CUDA-ready
    * CMake: change naming scheme for tutorials target to avoid conflicts
    * CMake: add tutorials in Tutorials/Blueprint
    * CMake: replace option ENABLE_TUTORIALS with AMReX_BUILD_TUTORIALS
    * Update Tools/CMake/AMReX_Options.cmake
    * Update Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt
    * CMake: this is not needed anymore
    * CMake: must use setup_target_for_cuda_compilation
    * CMake: fix build setup for Particles/ElectromagneticPIC
    * CMake: add tutorials in Tutorials/GPU
    * Fix EBCNS particles tutorials.
    The syntax for reductions has changed since itwas written.
    * CMake: improvements to setup_tutorials()
    * CMake: document how to build tutorials
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

.github/workflows/linux.yml
.github/workflows/macos.yml
.github/workflows/windows.yml
CMakeLists.txt
Docs/sphinx_documentation/source/BuildingAMReX.rst
Src/F_Interfaces/CMakeLists.txt
Tools/CMake/AMReX_Options.cmake
Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX1_CF/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX1_F/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX2_C/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX2_CF/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX3_C/CMakeLists.txt
Tutorials/Basic/HelloWorld_C/CMakeLists.txt
Tutorials/Basic/HelloWorld_F/CMakeLists.txt
Tutorials/Basic/PrefixSum_MultiFab/CMakeLists.txt
Tutorials/Basic/main_C/CMakeLists.txt
Tutorials/Basic/main_F/CMakeLists.txt
Tutorials/Blueprint/AssignMultiLevelDensity/CMakeLists.txt
Tutorials/Blueprint/CellSortedParticles/CMakeLists.txt
Tutorials/Blueprint/HeatEquation_EX1_C/CMakeLists.txt
Tutorials/CMakeLists.txt
Tutorials/EB/CNS/CMakeLists.txt
Tutorials/EB/Donut/CMakeLists.txt
Tutorials/EB/GeometryGeneration/CMakeLists.txt
Tutorials/EB/LevelSet/CMakeLists.txt
Tutorials/EB/MacProj/CMakeLists.txt
Tutorials/EB/Poisson/CMakeLists.txt
Tutorials/ForkJoin/MLMG/CMakeLists.txt
Tutorials/ForkJoin/Simple/CMakeLists.txt
Tutorials/FortranInterface/Advection_F/CMakeLists.txt
Tutorials/FortranInterface/Advection_F/Source/Src_3d/Make.package
Tutorials/FortranInterface/Advection_F/Source/Src_3d/advect_3d_mod.F90
Tutorials/FortranInterface/Advection_octree_F/CMakeLists.txt
Tutorials/FortranInterface/Advection_octree_F2/CMakeLists.txt
Tutorials/GPU/CNS/CMakeLists.txt
Tutorials/GPU/EBCNS/CMakeLists.txt
Tutorials/GPU/EBCNS/Source/CNS.cpp
Tutorials/GPU/EBCNS/Source/CNS_K.H
Tutorials/GPU/Launch/CMakeLists.txt
Tutorials/GPU/ParallelReduce/CMakeLists.txt
Tutorials/GPU/ParallelScan/CMakeLists.txt
Tutorials/LinearSolvers/ABecLaplacian_C/CMakeLists.txt
Tutorials/LinearSolvers/ABecLaplacian_F/CMakeLists.txt
Tutorials/LinearSolvers/MAC_Projection_EB/CMakeLists.txt
Tutorials/LinearSolvers/MultiComponent/CMakeLists.txt
Tutorials/LinearSolvers/NodalPoisson/CMakeLists.txt
Tutorials/LinearSolvers/Nodal_Projection_EB/CMakeLists.txt
Tutorials/LinearSolvers/NodeTensorLap/CMakeLists.txt
Tutorials/Particles/CellSortedParticles/CMakeLists.txt
Tutorials/Particles/ElectromagneticPIC/CMakeLists.txt
Tutorials/Particles/ElectrostaticPIC/CMakeLists.txt
Tutorials/Particles/NeighborList/CMakeLists.txt

commit a2284e9368e079dd4030ec9e0c41512f191848cf
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Sep 15 08:31:16 2020 -0700

    Reorder struct (#1368)
    
    This reverts a breaking change introduced in 1337.
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_Particle.H

commit 8929086e08058ac61d096414363341485afec34b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Sep 14 08:30:11 2020 -0700

    Implement Particle in a way that does not involve UB. (#1337)

Src/Particle/AMReX_Particle.H
Tests/Particles/Redistribute/main.cpp

commit 6fa3cc67ed0997e12877cdf3b5baf6d594d1c538
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Sep 14 07:56:41 2020 -0700

    Updates for oneAPI beta09 (#1365)

Src/Base/AMReX_GpuQualifiers.H
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/dpcpp.mak

commit 82339abdc742453d076d0bfeca7d9ed4e479eb0c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Sep 12 18:24:06 2020 -0700

    Revert "DPCPP Beta09: Package Broken (#1361)" (#1364)
    
    This reverts commit 198a4958cc2cbfd5a7e1d639d5ff750489104df6.
    
    The workaround does not work with #1363 because of mkl.  We have now
    temporarily removed dpc++ from the list of required checks.  So we can
    revert this change now.  Once the packages are fixed, we will make the check
    require again.

.github/workflows/linux.yml

commit 5175acf9efc2e8aeb37fc581480aba034a1fbb3f
Author: Candace Gilet <cgilet@users.noreply.github.com>
Date:   Fri Sep 11 12:55:43 2020 -0400

    amrex::EB_average_down(): Fix indexing error. (#1360)

Src/EB/AMReX_EBMultiFabUtil.cpp

commit 198a4958cc2cbfd5a7e1d639d5ff750489104df6
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri Sep 11 07:55:44 2020 -0700

    DPCPP Beta09: Package Broken (#1361)
    
    ## Summary
    
    The Ubuntu packages seem to forget the `env/var.sh` activation
    scripts for the compiler packages for beta09.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

.github/workflows/linux.yml

commit de4aab4f20ebffa862a0f9c29daa2717d8abcbd3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Sep 10 17:00:08 2020 -0700

    only add one copy of the ghost particle regardless of how many isects we have (#1359)

Src/Particle/AMReX_ParticleContainerI.H

commit fe4c98e749e40c65f03046a3efc9df5f948ced69
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Sep 10 13:47:36 2020 -0700

    SetBoxArray (#1310)
    
    If SetBoxArray is called in Level 0's MakeNewLevelFromScrach, the set
    BoxArray will be used.  This makes it consistent with the behavior of
    SetDistributionMap.

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit b1fcd62bd7f98fce1be98313307697d61320687d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Sep 10 13:46:42 2020 -0700

    Remove duplicated alias. (#1311)

Src/Base/AMReX_GpuAllocators.H

commit a1eafe7ab57324e7b574ab5b636ba0fc98ea7635
Author: asalmgren <asalmgren@lbl.gov>
Date:   Wed Sep 9 19:36:15 2020 -0700

    Logic wasn't quite right for the calculation in amrex_calc_slopes_ext… (#1358)
    
    …dir_eb routine
    
    of slope not seeing EB cells that is adjacent to and tangential to ext_dir boundary
    
    ## Summary
    Previous commit of AMReX_EB_slopes.cpp had messed up the logic for calcluation of the slope in amrex_calc_slopes_extdir_eb routine in cells not seeing any EB but next to ext_dir bondary and tangential to boundary
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [X] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/EB/AMReX_EB_slopes_K.H

commit 27c21a0c56623022a9b012c0ec2ec837e4971366
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 9 19:03:25 2020 -0700

    Gpu::single_task (#1357)
    
    Add a new version that uses the current default stream.

Src/Base/AMReX_GpuLaunchFunctsG.H

commit 6b032b4188e77e2b089e21c74586f5a2e6c1e5d2
Author: asalmgren <asalmgren@lbl.gov>
Date:   Wed Sep 9 08:48:34 2020 -0700

    Add non-EB slopes and extend the generality of EB slope routines in 2D and 3D (#1350)
    
    ## Summary
    This commit adds a file with the non-EB slope routines, and updates the EB-aware routines to correctly compute slopes where an EB boundary intersects an hoextrap/extdir face, e.g. inflow.  This does not assume the geometry intersects without a slant.   This has been tested in 2D and 3D (with a function f(x,y,z) = 10 + 5 x + 2 y + 3 z specified at cell centroids) and with slanted cylinders intersecting inflow in each coordinate direction.
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [x] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_Slopes_K.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/EB/AMReX_EB_slopes_K.H

commit 7cc452c65185efbb07e6503cb79206d10c0dc35c
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Sep 9 08:40:32 2020 -0700

    Async IO: Check Runtime Threading (#1351)
    
    ##  Summary
    
    Even if `AMREX_MPI_THREAD_MULTIPLE` is defined at compile time, applications might provide their own MPI init routines and/or MPI implementations, runtime arguments or environment arguments can influence the actually provided MPI thread safety level at runtime.
    
    Therefore, we need to check the MPI thread safety level again at runtime where we require a certain minimum.
    
    ## Additional background
    
    WarpX PR: https://github.com/ECP-WarpX/WarpX/pull/1298
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_AsyncOut.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit f542f98d72c2cd651a0eae4d092c12239976db3f
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Sep 9 08:31:53 2020 -0700

    Docs: MPI_THREAD_MULTIPLE (#1355)
    
    ## Summary
    
    Add GNUmake and CMake docs about control of `MPI_THREAD_MULTIPLE`.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [x] are described in the proposed changes to the AMReX documentation, if appropriate

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit a9aa65cc3841375b762324fe79516f5cfdee7364
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Sep 8 17:17:57 2020 -0700

    also use atomics in the particle_dx != dx case (#1356)

Src/Particle/AMReX_Particle_mod_K.H

commit c59619f5ff32a78494b0b2328914fe108254844c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Sep 8 15:53:07 2020 -0700

    Fix EM pic tutorial - the syntax for reductions has changed since it was written. (#1354)

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H

commit 96d1381e1f20adf48df84ff4f16601c887dac239
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 8 12:34:35 2020 -0700

    USE_EB (#1349)
    
    Changes to make AMR codes compiled with EB but not building any Geometry
    work as if it is all regular.

Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_FillPatchUtil_I.H

commit a2aebd24854b5d375899a44156603f4bc9c85a64
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Sep 8 10:49:03 2020 -0700

    Always recompute offset, dx, and inv_dx, and the roundoff_domain when either the ProbDomain or Domain is changed. (#1353)

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp

commit cd075c81967aca29a17a52af3f41310a8426b121
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Tue Sep 8 08:13:49 2020 -0700

    Fallthrough: ICC Warning (#1352)
    
    ## Summary
    
    `gnu::fallthrough` is not defined with ICC 20.2.1.20200602 and throws a warning at compile-time in ParamsParse.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_Extension.H

commit 9ec96e6f9b286ccd26a61a910f0fb97a08a377fe
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Sep 6 09:19:33 2020 -0700

    bcf/hpcsdk-updates (#1348)
    
    ## Summary
    
    This PR fixes two wrong compile/link flags in the NVIDIA HPC SDK which are documented in #1347.
    
    ## Additional background
    
    The wrong/missing flags are documented in #1347.
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/GNUMake/comps/hpcsdk.mak

commit 31421f70c3cf73ae2cc9aaa4e7e024f554a69e20
Author: asalmgren <asalmgren@lbl.gov>
Date:   Fri Sep 4 17:35:28 2020 -0700

    Add slopes routines (#1346)
    
    * Add the calculation of slopes using a least squares fit when the values in each cell
    are defined to be at cell centroids.
    
    * Add to the description of each routine
    
    * EB_SLOPES_K_H --> AMREX_EB_SLOPES_K_H

Src/EB/AMReX_EB_slopes_K.H
Src/EB/CMakeLists.txt
Src/EB/Make.package

commit 7e0d7196dd1e8ac91625030622b360cbcafa21ce
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Sep 4 17:27:40 2020 -0700

    No inline for assertion (#1345)
    
    It is recommended that assertion calls on device are not inlined because
    of performance issues.

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_Extension.H
Src/Base/AMReX_GpuDevice.cpp

commit a7166b92dc0b58b1ed96110ed2a43341513dcdd3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Sep 4 16:21:32 2020 -0700

    Fix mkconfig.py (#1344)
    
    ## Summary
    
    In the script, Intel, Cray and PGI should be quoted as string.
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/libamrex/mkconfig.py

commit de8a23ac50146b732aeaadf874ead2cae93753c8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 4 14:43:29 2020 -0700

    Add -Xcudafe --diag_suppress=esa_on_defaulted_function_ignored to suppress spurious warnings from nvcc. (#1342)

Tools/CMake/AMReX_SetupCUDA.cmake
Tools/GNUMake/comps/nvcc.mak

commit d8747f753f9f5524aba04e1a70fee3d1665654bd
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri Sep 4 13:39:44 2020 -0700

    CI: Move DPC++ dependencies (#1336)
    
    Move install script into unified location.
    
    ## Summary
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

.github/workflows/dependencies/dependencies_dpcpp.sh
.github/workflows/linux.yml

commit b9e746e447e896aa0df049845d573e11f7db10ab
Author: Rajeev Jain <rajeeja@gmail.com>
Date:   Fri Sep 4 15:36:46 2020 -0500

    Update AMReX_multifab_mod.F90 (#1339)
    
    #1338
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 2ae64e7f472e81000c25ca97eb7587f4d43d0960
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 4 13:35:18 2020 -0700

    PR 1324 did not account for runtime-added components (#1341)
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Particle/AMReX_ParticleContainerI.H

commit e34912f3bc26d532fa9c3ee608ec5e50c4ce26f9
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Sep 3 10:29:23 2020 -0700

    update CHANGES for 20.09 (#1334)

CHANGES

commit c7cef052978eb509972a8f2c6b43771f22cf4fff
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Sep 2 19:11:10 2020 -0700

    Add support for extended particle range to the Fortran interfaces (#1331)
    
    * add support for extended particle range to the Fortran interfaces
    
    * replace c_long -> amrex_long for Windows support

Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90
Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/Prob_2d.f90
Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/Prob_3d.f90

commit 64e772795b9f9b09db11e4fbdf30552331850965
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 2 16:43:45 2020 -0700

    Avoid divide-by-zero in 2D EB (#1319)

Src/EB/AMReX_EB2_2D_C.cpp
Src/EB/AMReX_EB2_3D_C.cpp

commit 3d65510d12ef10fe2a7d4b0d0bf9164615689597
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 2 16:34:45 2020 -0700

    EB smoother (#1330)
    
    * EB smoother
    
    In #1327, the interpolation coefficients for EB stencil in cell-centered
    linear solvers were fixed.  Here, the EB smoother is also updated to use the
    correct coefficients.
    
    * fix order in interpolation coefficient
    
    * Reduce max order to 2 for cut cells.
    
    * If using hypre or petsc for EB solver, reduce order to 2.

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 4128f25ffa247802ab93e8fae7133b80a5e3d59f
Author: Roberto Porcu <53792251+rporcu@users.noreply.github.com>
Date:   Wed Sep 2 14:21:45 2020 -0400

    Gpu synchronization is needed to avoid deadlock situations (#1328)

Src/Particle/AMReX_ParticleCommunication.H

commit 65f25c7db1ba2f88654cff8e91d24cf3ff45b075
Author: OscarAntepara <52221614+OscarAntepara@users.noreply.github.com>
Date:   Tue Sep 1 17:26:10 2020 -0700

    Fix bug to correctly compute the interp_coeff array (#1327)

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H

commit d5e29d965070a36c6e232ef114d1f5bd88b701e3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 1 17:02:51 2020 -0700

    EB extend_domain_face (#1321)
    
    ## Summary
    
    When there are a lot of ghost cells, extend_domain_face option could fail in
    the current development branch.  This PR fixes it.
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Docs/sphinx_documentation/source/Basics.rst
Src/EB/AMReX_EB2_Level.H

commit e4444fa80264ae716f9cadd4d7e8847fcf3d833b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Sep 1 17:02:26 2020 -0700

    Add explicit default copy ctors for ParticleIDWrapper and ParticleCPUWrapper (#1323)
    
    This should fix a warning with DPC++.

Src/Particle/AMReX_Particle.H

commit 98b73e64bfcc839ba168b3e423d4d2f8e4914c28
Author: Klaus <kweide@users.noreply.github.com>
Date:   Tue Sep 1 19:01:42 2020 -0500

    Add parameter that stores OpenMP support version (#1325)
    
    ## Summary
    
    Add a parameter to `AMReX_omp_mod` that can be used by Fortran code to check whether AMReX was built with OpenMP support, and, if yes, what the version number (_OPENMP) was at the time AMReX was compiled.
    
    ## Additional background
    The name of the parameter is `amrex_omp_support`, the type is (default kind) integer.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [x] add new **(mini)**-capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate
    
    
    Co-authored-by: Klaus Weide <>

Src/Base/AMReX_omp_mod.F90

commit 1ffbfc1caab2dae19db0e7fa27202938300f9ced
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Sep 1 17:00:43 2020 -0700

    Use Long for maxnextid in plot and checkfiles to accomodate the expanded range. (#1326)
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Particle/AMReX_ParticleHDF5.H
Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_WriteBinaryParticleData.H

commit 57d5bfeb97b03ce037714a08260d78660b6774be
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 1 16:46:23 2020 -0700

    ParticleContainer: communicate_real_comp and commuicate_int_comp (#1324)
    
    Having both host and device copies of these two so that we do not rely on
    unified memory.

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit b7479f0a662a9b256f1e42d1cd3c628457a53c1c
Author: mic84 <mrosso@lbl.gov>
Date:   Tue Sep 1 11:15:35 2020 -0700

    CMake: re-write genex evaluation functions (#1287)
    
    * CMake: start adding genex evaluation functions
    
    * CMake: more genex evaluation functions
    
    * CMake: add support for more genex types
    
    * CMake: finalize new function to evaluate genex
    
    * CMake: slighly change the interface of function eval_genex
    
    * CMake: deploy eval_genex.
    
    * CMake: set MSVC required flags using regex
    
    * CMake: final improvements to new genex evaluation helpers

Tools/CMake/AMReXBuildInfo.cmake
Tools/CMake/AMReXGenexHelpers.cmake
Tools/CMake/AMReXInstallHelpers.cmake
Tools/CMake/AMReXTargetHelpers.cmake
Tools/CMake/AMReXTypecheck.cmake
Tools/CMake/AMReX_Config.cmake

commit 6dd02ab17f06478d7fbea8e91ba274f932004801
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 27 19:08:59 2020 -0700

    Need another overload of the operator= for ParticleIDWrapper and ParticleCPUWrapper. (#1317)
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Particle/AMReX_Particle.H

commit 5e9dbc1dd2fb8675de53bc42bd8b3d13f9eacb88
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 27 11:12:18 2020 -0700

    Extend the number of unique particles per cpu we can have at once. (#1315)
    
    Currently, we use two signed integers to store id numbers for each particle as well as the rank it was generated on. This allows unique combinations of 'id', and 'cpu' numbers to be generated without any communication between ranks. However, this does waste some space, since it's unlikely that 2**31-1 MPI ranks will be used any time soon, while the same limit for the id has actually been overflowed in real-world WarpX simulations. To address this, in this PR, we still use 64 bits to represent the combination of (id, cpu), but we devote 40 bits to the id and only 24 to the cpu. This allows ~0.5 trillion unique particles on each of 16.7 million MPI ranks, which should be good enough for the foreseeable future.
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [x] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_ParticleContainerI.H

commit d48f68f1a641084009e597d955ce3036d36b1755
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Aug 26 09:00:42 2020 -0700

    Add ParmParse parameters to Tutorials/GPU/Launch (#1314)

Tutorials/GPU/Launch/main.cpp

commit 655f10afbc68b5c4279d2ca78c7add8b449f71e4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 25 15:57:40 2020 -0700

    HIP: printf works now on device (#1312)
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [x] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_GpuPrint.H

commit 02530bc8a600e2a3589b875208f372dd2e462a31
Author: Klaus <kweide@users.noreply.github.com>
Date:   Tue Aug 25 15:44:05 2020 -0500

    Add get_pmap method to amrex_distromap (Fortran) (#1307)
    
    ## Summary
    Add a new method to the `amrex_distromap` type in F_Interfaces. `get_pmap` fills a caller-owned array of PEs.
    
    Changes to make this more elegant are welcome.
    
    ## Additional background
    We need something like this in order to actually look into a distribution mapping computed by AMReX from Fortran code.
    (Currently this functionality is desired for Implementing a parallel restart capability from FLASH checkpoint files in FLASH.)
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [x] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate
    
    
    Co-authored-by: Klaus Weide <>

Src/F_Interfaces/Base/AMReX_distromap_fi.cpp
Src/F_Interfaces/Base/AMReX_distromap_mod.F90

commit 7b72e38bbbe63d2039a5e0ef7a4833792c99beff
Author: kngott <30483578+kngott@users.noreply.github.com>
Date:   Tue Aug 25 12:04:39 2020 -0700

    Nsight documentation fix. (#1309)
    
    * Fix Nsight docs.
    
    * Missing syntax.

Docs/sphinx_documentation/source/External_Profiling_Tools.rst

commit 51c4a990b42e37d84cc0c2b8055403d351febbb2
Author: Klaus <kweide@users.noreply.github.com>
Date:   Tue Aug 25 12:25:42 2020 -0500

    Fix instruction for local development branch (#1305)
    
    ## Summary
    Just a simple one-word doc change
    
    ## Additional background
    I tried to follow instructions in `CONTRIBUTING.md` and found that the `git pull` command as documented before this change resulted in an error message.
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug in AMReX documentation
    
    
    Co-authored-by: Klaus Weide <>

CONTRIBUTING.md

commit a34e8e42d52b7725552ea97e5e089a90b96833cc
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Aug 24 19:22:19 2020 -0700

    Modify the use of HOST and HOSTNAME in make system (#1303)
    
    ## Summary
    
    PR #1275 fixed a bug in the use of `HOST` and `HOSTNAME` in the make system.
    However, the fix broke on Summit because `HOSTNAME` on Summit login nodes
    is set to something like `login1`.  We now set `host_name` to `hostname -f` and
    `host_name_short` to `hostname -s` command, which is the behavior before the fix
    in #1275.  We add a new make variable `host_name_env` that is set to
    `HOSTNAME` and `HOST` from the environment and use it for tulip.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/GNUMake/Make.machines

commit e82080e322f238435f925da35fb8bae36365269d
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Aug 24 18:00:46 2020 -0700

    Move declaration of Array4 object (#1302)
    
    ## Summary
    
    The autogen function for refinement tagging on physical box doesn't make use of a field, but the controller was trying to make an Array4 using the field that doesn't exist in this case.  This fix moves the declaration down into a place where the data is guaranteed to exist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/AmrCore/AMReX_ErrorList.cpp

commit 21269eff092d0a03aff9269b1200c0e408fde90e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 24 12:31:26 2020 -0700

    Remove early exit for the 1 box case in RedistributeGPU. (#1301)
    
    This early exit had a bug in that it did not properly remove invalid particles.
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit bb831b49bbb3b853a18ee0e16d955aafe251da7d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Aug 22 21:04:40 2020 -0700

    add Scan::InclusiveSum and ExclusiveSum for CPU (#1299)
    
    ## Summary
    
    Add Scan::InclusiveSum and ExclusiveSum for CPU to avoid ifdef.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_Scan.H

commit 91f387dad9f57dfa884b4e5d03b88ff18f7b8c12
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Aug 22 16:00:51 2020 -0700

    Turn on AsyncOut by default for HIP (#1298)
    
    ## Summary
    
    Currently for HIP, The_Arena allocates device memory.  We turn on AsyncOut
    by default so that we can write plotfiles and VisMF files.  In the long term, we
    should also fix VisMF::Write so that it can work with device memory.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_AsyncOut.cpp

commit ba556dfe28afaa6704ea049f8200a8b53cffd888
Author: mxxw <marcus.wagner@hpe.com>
Date:   Sat Aug 22 09:29:21 2020 -0700

    removed AMREX_NOEXCEPT from main.cpp:L139 to avoid 'error: expected b… (#1297)
    
    removed AMREX_NOEXCEPT from main.cpp:L139 to avoid 'error: expected body of lambda expression'
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tutorials/GPU/ParallelReduce/main.cpp

commit ab300111b705486f10782f1966020907d9f66b66
Author: jmsexton03 <jmsexton@lbl.gov>
Date:   Fri Aug 21 14:58:25 2020 -0400

    Add check for empty probin_file in Amr::restart (#1295)
    
    ## Summary
    This adds the same empty check in Amr::restart that is used in Amr::InitializeInit
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Amr/AMReX_Amr.cpp

commit a70adecd122ef1a4441cabd0f6356f53389e606b
Author: mic84 <mrosso@lbl.gov>
Date:   Fri Aug 21 11:33:50 2020 -0700

    CMake: fix typo in source file name (#1296)

Tutorials/Basic/HeatEquation_EX1_F/CMakeLists.txt

commit 373cb8ac3143e1252ccd9b181280d355e9399f8a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Aug 21 08:06:10 2020 -0700

    Fix a few warnings (#1293)

Src/Base/AMReX_FBI.H
Src/Base/AMReX_GpuPrint.H
Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_Reduce.H
Src/Particle/AMReX_ParticleContainerI.H

commit 1aef797d0dd5a701c696d02165237c2c8e39771c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Aug 20 20:19:30 2020 -0700

    Extern HIP device function (#1294)
    
    ## Summary
    
    We now need to use __attribute__((weak)) for extern HIP device function,
    otherwise we get undefined hidden symbol error.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_GpuQualifiers.H

commit ce5e0d4bf4b27a88fc3eb6a2dab137b6b25e2bbb
Author: jmsexton03 <jmsexton@lbl.gov>
Date:   Thu Aug 20 23:19:02 2020 -0400

    Update Sundials interface, documentation, and build to be version agnostic (#1289)
    
    ## Summary
    
    Updates the make system to use SUNDIALS_ROOT and USE_SUNDIALS
    Updates the documentation regarding sundials and tutorials
    Removes some CVODE/SUNDIALS tutorials
    This will require applications to update their make variables
    
    ## Additional background
    Co-authored-by: Balos, Cody Joe <balos1@llnl.gov>
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [x] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate
    
    Co-authored-by: Balos, Cody Joe <balos1@llnl.gov>
    Co-authored-by: Michele Rosso <mrosso@lbl.gov>

Docs/sphinx_documentation/source/CVODE_top.rst
Docs/sphinx_documentation/source/External_Frameworks_Chapter.rst
Docs/sphinx_documentation/source/SUNDIALS.rst
Docs/sphinx_documentation/source/SUNDIALS3.rst
Docs/sphinx_documentation/source/SUNDIALS_CVODE.rst
Docs/sphinx_documentation/source/SUNDIALS_top.rst
Docs/sphinx_tutorials/source/CVODE_Tutorial.rst
Docs/sphinx_tutorials/source/SUNDIALS_Tutorial.rst
Src/CMakeLists.txt
Src/Extern/SUNDIALS/CMakeLists.txt
Src/Extern/SUNDIALS/Make.package
Src/Extern/SUNDIALS/arkode_interface.f90
Src/Extern/SUNDIALS/cvode_interface.f90
Src/Extern/SUNDIALS3/CMakeLists.txt
Src/Extern/SUNDIALS3/Make.package
Src/Extern/SUNDIALS3/arkode_interface.f90
Src/Extern/SUNDIALS3/cvode_interface.f90
Src/Extern/SUNDIALS3/farkode.f90
Src/Extern/SUNDIALS3/fcvode.f90
Src/Extern/SUNDIALS3/fnvector_serial.f90
Src/Extern/SUNDIALS3/fnvector_serial_fprefix.f90
Src/Extern/SUNDIALS3/fsunlinsol_dense.f90
Src/Extern/SUNDIALS3/fsunmat_dense.f90
Src/Extern/SUNDIALS4/CMakeLists.txt
Src/Extern/SUNDIALS4/Make.package
Src/Extern/SUNDIALS4/arkode_interface.f90
Src/Extern/SUNDIALS4/cvode_interface.f90
Src/Extern/SUNDIALS4/farkode_arkstep_mod.f90
Src/Extern/SUNDIALS4/farkode_mod.f90
Src/Extern/SUNDIALS4/fcvode_mod.f90
Src/Extern/SUNDIALS4/fnvector_mod.f90
Src/Extern/SUNDIALS4/fnvector_serial_mod.f90
Src/Extern/SUNDIALS4/fsundials_types_mod.f90
Src/Extern/SUNDIALS4/fsunlinsol_dense_mod.f90
Src/Extern/SUNDIALS4/fsunlinsol_mod.f90
Src/Extern/SUNDIALS4/fsunmatrix_dense_mod.f90
Src/Extern/SUNDIALS4/fsunmatrix_mod.f90
Tools/CMake/AMReXThirdPartyLibraries.cmake
Tools/CMake/FindSUNDIALS.cmake
Tools/GNUMake/Make.defs
Tools/GNUMake/packages/Make.sundials
Tools/GNUMake/packages/Make.sundials3
Tools/GNUMake/packages/Make.sundials4
Tutorials/CVODE/EX1_F/GNUmakefile
Tutorials/CVODE/EX1_F/Make.package
Tutorials/CVODE/EX1_F/inputs
Tutorials/CVODE/EX1_F/integrate_ode.f90
Tutorials/CVODE/EX1_F/main.cpp
Tutorials/CVODE/EX1_F/myfunc_F.H
Tutorials/CVODE/EX1_F/ode_mod.f90
Tutorials/CVODE/EX2_F/GNUmakefile
Tutorials/CVODE/EX2_F/Make.package
Tutorials/CVODE/EX2_F/inputs
Tutorials/CVODE/EX2_F/integrate_ode_no_jac.f90
Tutorials/CVODE/EX2_F/integrate_ode_with_jac.f90
Tutorials/CVODE/EX2_F/main.cpp
Tutorials/CVODE/EX2_F/myfunc_F.H
Tutorials/CVODE/EX2_F/ode_mod.f90
Tutorials/CVODE/SUNDIALS3_finterface/EX1/CMakeLists.txt
Tutorials/CVODE/SUNDIALS3_finterface/EX1/main.cpp
Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/Make.package
Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/ark_analytic_fp.f90
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/Make.package
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/cv_analytic_fp.f90
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/cv_analytic_fp.out
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/Make.package
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/cv_analytic_sys_dns.f90
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/cv_analytic_sys_dns.out
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/Make.package
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/cv_analytic_sys_dns_jac.f90
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/cv_analytic_sys_dns_jac.out
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/Make.package
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/cv_brusselator_dns.f90
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/cv_brusselator_dns.out
Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/GNUmakefile
Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/Make.package
Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/ark_analytic_f2003.f90
Tutorials/SUNDIALS/EX-CUSOLVER/GNUmakefile
Tutorials/SUNDIALS/EX-CUSOLVER/Make.CVODE
Tutorials/SUNDIALS/EX-CUSOLVER/Make.package
Tutorials/SUNDIALS/EX-CUSOLVER/README.md
Tutorials/SUNDIALS/EX-CUSOLVER/extern_probin.template
Tutorials/SUNDIALS/EX-CUSOLVER/inputs
Tutorials/SUNDIALS/EX-CUSOLVER/inputs_128
Tutorials/SUNDIALS/EX-CUSOLVER/inputs_256
Tutorials/SUNDIALS/EX-CUSOLVER/inputs_32
Tutorials/SUNDIALS/EX-CUSOLVER/inputs_64
Tutorials/SUNDIALS/EX-CUSOLVER/main.cpp
Tutorials/SUNDIALS/EX-CUSOLVER/make_cuda.sh
Tutorials/SUNDIALS/EX-CUSOLVER/make_cuda_cusolver.sh
Tutorials/SUNDIALS/EX-CUSOLVER/make_serial.sh
Tutorials/SUNDIALS/EX-CUSOLVER/react_cuda.cpp
Tutorials/SUNDIALS/EX-CUSOLVER/react_cuda_cusolver.cpp
Tutorials/SUNDIALS/EX-CUSOLVER/react_serial.cpp
Tutorials/SUNDIALS/EX-CUSOLVER/react_system.F90
Tutorials/SUNDIALS/EX-CUSOLVER/react_utils.F90
Tutorials/SUNDIALS/EX-CUSOLVER/test_react.H
Tutorials/SUNDIALS/EX-CUSOLVER/test_react_F.H
Tutorials/SUNDIALS/EX1_C/CMakeLists.txt
Tutorials/SUNDIALS/EX1_C/GNUmakefile
Tutorials/SUNDIALS/EX1_C/Make.package
Tutorials/SUNDIALS/EX1_C/SetIC.f90
Tutorials/SUNDIALS/EX1_C/inputs
Tutorials/SUNDIALS/EX1_C/inputs_2box
Tutorials/SUNDIALS/EX1_C/inputs_non_vectorized
Tutorials/SUNDIALS/EX1_C/main.cpp
Tutorials/SUNDIALS/EX1_C/myfunc_F.H
Tutorials/SUNDIALS/EX1_CUDA/GNUmakefile
Tutorials/SUNDIALS/EX1_CUDA/Make.package
Tutorials/SUNDIALS/EX1_CUDA/SetIC.f90
Tutorials/SUNDIALS/EX1_CUDA/inputs
Tutorials/SUNDIALS/EX1_CUDA/main.cpp
Tutorials/SUNDIALS/EX1_CUDA/myfunc_F.H
Tutorials/SUNDIALS/EX1_CUDA/ode_mod.f90
Tutorials/SUNDIALS/EX1_F/GNUmakefile
Tutorials/SUNDIALS/EX1_F/Make.package
Tutorials/SUNDIALS/EX1_F/inputs
Tutorials/SUNDIALS/EX1_F/integrate_ode.f90
Tutorials/SUNDIALS/EX1_F/main.cpp
Tutorials/SUNDIALS/EX1_F/myfunc_F.H
Tutorials/SUNDIALS/EX1_F/ode_mod.f90
Tutorials/SUNDIALS/EX2_F/GNUmakefile
Tutorials/SUNDIALS/EX2_F/Make.package
Tutorials/SUNDIALS/EX2_F/inputs
Tutorials/SUNDIALS/EX2_F/integrate_ode_no_jac.f90
Tutorials/SUNDIALS/EX2_F/integrate_ode_with_jac.f90
Tutorials/SUNDIALS/EX2_F/main.cpp
Tutorials/SUNDIALS/EX2_F/myfunc_F.H
Tutorials/SUNDIALS/EX2_F/ode_mod.f90

commit 418f90d6f6620008edc0385ce6f487cb555ae1fb
Author: Candace Gilet <cgilet@users.noreply.github.com>
Date:   Thu Aug 20 21:15:56 2020 -0400

    Fix typo (#1292)
    
    ## Summary
    Fix a typo in AMReX_extrapolater_3D_K.H
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Amr/AMReX_extrapolater_3D_K.H

commit f38919982f59b25f49b9b2a4c948f20677f144e7
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Aug 20 16:26:04 2020 -0700

    Un-comment lines which should not have been commented (#1291)
    
    ## Summary
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tests/LinearSolvers/EBTensor/MyTest.cpp

commit df022f23e57792da09feed9b9db74dc60e6d4847
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Aug 20 14:14:12 2020 -0700

    Skip MPI checking when doing make clean etc. (#1290)
    
    ## Summary
    
    When we do `make clean`, `make realclean` etc., we do not need to check MPI.  This can avoid unnecessary errors.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/GNUMake/sites/Make.unknown

commit 924ec34c858335848b9514590f41d221990f209d
Author: kngott <30483578+kngott@users.noreply.github.com>
Date:   Thu Aug 20 13:55:11 2020 -0700

    Get rid of incorrect comment. (#1288)
    
    ## Summary
    
    Just deleting this old, spurious comment before I forget about it.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/GNUMake/Make.defs

commit 7c35abbcdf3882d0b83c5746a23c5f2eca24a2dc
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Aug 20 10:20:27 2020 -0700

    Physical locations in pltofiles (#1286)
    
    Normally, the integer index of a Geometry's Domain starts with 0.  But if
    not, the physical location of boxes stored in plotfiles is incorrect,
    because the RealBox constructor we use takes the physical location of index
    0.  So we need to shift the box before using RealBox.

Src/Base/AMReX_PlotFileUtil.cpp

commit 0748356f06fadf2f6caef6542f48d15c3e9391bc
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Aug 20 08:20:26 2020 -0700

    Misc. updates for ROCm 3.6.0 (#1285)
    
    ## Summary
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_Dim3.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_GpuAssert.H
Src/Base/AMReX_GpuComplex.H
Src/Base/AMReX_GpuPrint.H
Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_GpuUtility.H
Src/Base/AMReX_Math.H
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_PlotFileDataImpl.H
Src/Base/AMReX_Random.cpp
Src/Base/AMReX_RealVect.H
Tools/GNUMake/comps/hip.mak
Tutorials/Basic/HeatEquation_EX2_C/Source/mykernel.H
Tutorials/GPU/CNS/Source/CNS_K.H

commit e33b6cd8b866c2f8f34a16491316f912960922c0
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Aug 19 17:56:11 2020 -0700

    Add section to Make.unknown for intel mpi (#1284)
    
    ## Summary
    
    Avoid another site-specific make setting by adding generic id for Intel MPI - seems to work for UT Austin's TACC center computer, Stampede2, for example.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [x] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/GNUMake/sites/Make.unknown

commit c35f7aad31ec34f55f3dcfab9b42f19a31224a18
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Aug 19 15:55:31 2020 -0700

    CMake: re-factor third party libraries setup (#1252)
    
    ## Summary
    Centralize setup of all parallel backends dependencies.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/CMakeLists.txt
Src/Extern/Conduit/CMakeLists.txt
Src/Extern/HYPRE/CMakeLists.txt
Src/Extern/PETSc/CMakeLists.txt
Src/Extern/SENSEI/CMakeLists.txt
Src/Extern/SUNDIALS4/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReXThirdPartyLibraries.cmake
Tools/CMake/AMReX_Config.cmake

commit 547e0f040a8ec6c03b73a4a001eaa34fd369121e
Author: asalmgren <asalmgren@lbl.gov>
Date:   Wed Aug 19 12:43:32 2020 -0700

    1) replace gpu_regtest flag by plot_error flag (which can be used on … (#1283)
    
    …CPU or GPU)
    
    2) add analogous 2D test problem  -- also with analytical solution
    
    ## Summary
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [X] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tests/LinearSolvers/EBTensor/Make.package
Tests/LinearSolvers/EBTensor/MyTest.cpp
Tests/LinearSolvers/EBTensor/MyTestPlotfile.cpp
Tests/LinearSolvers/EBTensor/MyTest_2D_K.H
Tests/LinearSolvers/EBTensor/MyTest_3D_K.H
Tests/LinearSolvers/EBTensor/inputs
Tests/LinearSolvers/EBTensor/inputs.rt.2d

commit 5a81f883ec4d83fbe4c31c8e18db023deade5623
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Wed Aug 19 10:36:34 2020 -0600

    Add use of CUDA_HOME to Make.nrel. (#1282)
    
    ## Summary
    We set `CUDA_HOME` on machines at NREL so this adds its use to `Make.nrel`. This is mostly so that `-lnvToolsExt` will happen automatically for us when using the tiny profiler.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [x] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/GNUMake/sites/Make.nrel

commit 192f638662e02c660e98bca5970c5e75b4c535b5
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Aug 19 06:58:12 2020 -0700

    fcompare (#1281)
    
    ## Summary
    
    Remove unimplemented option from help message.  Print more information on
    which files have NaNs if there are.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/Plotfile/fcompare.cpp

commit 33fdf6bbc80eacca651766697e991c21bae8d32d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 18 19:55:11 2020 -0700

    HIP: exp (#1280)
    
    ## Summary
    
    ROCm 3.6 has fixed std::exp.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tutorials/Basic/HeatEquation_EX1_C/Source/mykernel.H

commit 2d258baa734c8929035a1a2523d87695881c2008
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 18 19:54:47 2020 -0700

    Fix a bug in VisMF::AsyncWrite (#1279)
    
    ## Summary
    
    When not writing ghost cells, we need to make sure the header has the
    correct number of ghost cells that is zero.
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_VisMF.cpp

commit cb2cdfafde7c00f62e951d7060552c71167856b1
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 18 17:21:46 2020 -0700

    Updates for Tulip (#1278)
    
    ## Summary
    
    * Force DEBUG=FALSE for HIP to avoid a compiler bug.
    
    * Modify makefile so that the dependency files are not dumped in the current
      directory.
    
    * Add support for MPI.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/GNUMake/sites/Make.frontier-coe

commit ce38e4b385fdd54f8bb67f254904802ceacc4079
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 18 15:15:54 2020 -0700

    OMP CI (#1277)
    
    Add an OMP CI test.

.github/workflows/linux.yml

commit 8688f76e033b5868762c178fe4dc20ef2930032a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 18 14:57:39 2020 -0700

    Fix typo for OMP (#1276)
    
    The typo was introduced in #1274.

Src/AmrCore/AMReX_TagBox.cpp

commit b0735b5e604305f226b42816d9f0d3c882ff3c4c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 18 14:34:07 2020 -0700

    Fix Make.machines (#1275)
    
    The tests on environment variables HOSTNAME and HOST were incorrect.

Tools/GNUMake/Make.machines

commit f71d122d0ed6831ae946e108116a88bee9b563d7
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 18 14:02:54 2020 -0700

    TagBoxArray::hasTags (#1274)
    
    In #1258, TagBoxArray::numtags was removed.  However, IAMR still needs it.
    So a new function, hasTags, is added for IAMR.

Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp

commit 6478336784067131d857a3f219220b6b00127751
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Aug 17 21:19:11 2020 -0700

    TagBoxArray on GPU (#1258)
    
    # Summary
    
    TagBoxArray functions can now run on GPU now.  We no longer rely on unified memory for TagBoxArray functions.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [x] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_AsyncOut.cpp
Src/Base/AMReX_GpuAtomic.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_Scan.H

commit 3235db6b295923ed454cc1bbdfe6ce3b6964e93c
Author: mxxw <marcus.wagner@hpe.com>
Date:   Mon Aug 17 16:36:17 2020 -0700

    Make.machines (#1273)
    
    ## Summary
    ensure host_name_short is always defined in Tools/GNUMake/Make.machines
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/GNUMake/Make.machines

commit 8b66f47e906c53cd0127531d97fd65508d8eb9f9
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Aug 17 10:32:21 2020 -0700

    DPC++: Missing synchronize() (#1268)
    
    Missing Gpu::synnhronize() call after host to device memcpy.

Src/Base/AMReX_Reduce.H

commit addfc7d6f35604f43893d836c891138b373757d2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Aug 17 10:02:25 2020 -0700

    Should use std::forward. (#1267)

Src/Base/AMReX_FabArrayUtility.H

commit 2c45e058537a3bffd212e13968e6df6562f01bc3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Aug 17 09:51:32 2020 -0700

    Advection_AmrCore Tutorial (#1266)
    
    Remove redundant MPI_Allreduce and cleanup.

Tutorials/Amr/Advection_AmrCore/Source/AdvancePhiAtLevel.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 2d16fa694c4e08cc6ce922d31da730d4ab116985
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Aug 17 09:03:24 2020 -0700

    amrex::Math::abs for beta8 on DG1 (#1271)
    
    ## Summary
    
    Due to a compiler bug (I believe), we have to modify amrex::Math::abs for
    beta8 on DG1.
    
    ## Additional background
    
    After spending many hours debugging Tutorial/Amr/Adevection_AmrCore/
    on DG1, it is found that `MultiFab::norm0` does not return the correct
    result, because of the use of `amrex::Math::abs`.  After making the change
    in this PR, the test now produces correct results with AMR.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_Math.H

commit b4128deaff6e9ec9a91b605271f1aa972a1d3809
Author: mxxw <marcus.wagner@hpe.com>
Date:   Sun Aug 16 18:21:43 2020 -0700

    add support for additional AMD GPU SKUs and incl. poplar and redwood … (#1270)
    
    #1168  Summary
    Changed Tools/GNUMake/sites/Make.frontier-coe to
    1. add support for additional AMD GPU SKUs;
    2. include poplar and redwood in the list of frontier-coe machines
    
    ## Additional background
    Changed
       ifeq ($(which_computer),$(filter $(which_computer),tulip))
         ifeq ($(USE_HIP),TRUE)
           CXXFLAGS += --amdgpu-target=gfx906
           HIPCC_FLAGS += --amdgpu-target=gfx906
         endif
       endif
    to
       ifeq (,$(filter $(which_computer),poplar redwood tulip))
         $(error Unknown Frontier CoE computer, $(which_computer))
       else
         ifeq ($(USE_HIP),TRUE)
           CXXFLAGS += --amdgpu-target=gfx906,gfx908
           HIPCC_FLAGS += --amdgpu-target=gfx906,gfx908
         endif
       endif
    For AMD GPUs, the compile target should be exact to avoid runtime errors,
    i.e., one should generally not assume that a binary targeting an older GPU
    will always run correctly on a newer GPU.  However, building "fat binaries"
    is possible, so that one does, typically, not need one separate binary
    specifically built for each AMD GPU SKU available on the platform.
    
    
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/GNUMake/sites/Make.frontier-coe

commit cf4e666a7268d83dffcbb8559c1608fbee067b7c
Author: mxxw <marcus.wagner@hpe.com>
Date:   Sun Aug 16 18:21:02 2020 -0700

    updated Make.machines to include new frontier-coe machines and change… (#1265)
    
    …d 'hostname -f' command to 'hostname'
    
    ## Summary
    updated Make.machines:
    1. added poplar and redwood to frontier-coe machines;
    2. changed name string matching for frontier-coe to only
        yield exact matches (filter); hence, !="" means exact match;
    3. changed `hostname -f` command (which includes the domain) to `hostname` to
        avoid false negatives, e.g., not recognizing `hostname -f`==tulip.cm.cluster as tulip;
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [x] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/GNUMake/Make.machines

commit bfaa57db45438d795293032609286d5c3146d8a3
Author: mxxw <marcus.wagner@hpe.com>
Date:   Sun Aug 16 16:58:39 2020 -0700

    fixed bug in matching of COMP_VERSION to correctly treat CCE > 9 (#1269)
    
    ## Summary
    changed Tools/GNUMake/comps/cray.mak to fix bugs in the matching of $(COMP_VERSION) in order to correctly treat CCE version > 9
    
    ## Additional background
    Starting with version 9, the Cray CCE C and C++ compilers changed to being clang/LLVM based
    which makes it necessary to change some flags compared to CCE versions <=8.
    (This change does not apply to the Cray Fortran compiler versions.)
    However, the original version check of
        COMP_VERSION = $(shell echo $(CRAY_CC_VERSION) | cut -f 1 -d .)
    in combination with the tests of  "ifeq ($(COMP_VERSION),9)"
    differentiated only between V9 and non-V9, which it assumed to be V8.
    Howerver, now, we have V10 while V11 is being tested, all of which would
    be treated like V8, which is incorrect.
    To address this issue the compiler version classification is now done with
         ifeq ($(shell expr $(COMP_VERSION) \>= 9), 1)
                CCE_GE_V9 := TRUE
         else
                CCE_GE_V9 := FALSE
         endif
    and it is tested with
         ifeq ($(CCE_GE_V9),TRUE)
    
    ## Checklist
    
    The proposed changes:
    - [X] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/GNUMake/comps/cray.mak

commit 3896fae0158d1456e238845250bda4264d5980d7
Author: asalmgren <asalmgren@lbl.gov>
Date:   Sun Aug 16 16:17:37 2020 -0700

    Change default max_level in AmrCore tutorial from 0 to 2. (#1264)

Tutorials/Amr/Advection_AmrCore/Exec/inputs

commit ac2128cc218ea5ba8124f2c78c808cccf1fab1f9
Author: asalmgren <asalmgren@lbl.gov>
Date:   Fri Aug 14 17:33:32 2020 -0700

    Replace amrcore tutorial (#1253)
    
    ## Summary
    
    This replaces the existing tutorial with the more general, all C++ one developed for ATPESC 2020.  This version works for CPU and GPU (compile-time option), in 2D and 3D (compile-time option), with and without subcycling (run-time option).
    A .md file is also included in the directory which walks a new user through how to run this code and what to experiment with to understand AMR.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [x] are described in the proposed changes to the AMReX documentation, if appropriate
    
    
    Co-authored-by: Weiqun Zhang <weiqunzhang@lbl.gov>

Docs/sphinx_tutorials/source/AMR_Tutorial.rst
Src/Base/AMReX_Box.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_DistributionMapping.cpp
Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/Amr/Advection_AmrCore/Exec/GNUmakefile
Tutorials/Amr/Advection_AmrCore/Exec/GNUmakefile_movie
Tutorials/Amr/Advection_AmrCore/Exec/Make.Adv
Tutorials/Amr/Advection_AmrCore/Exec/Make.package
Tutorials/Amr/Advection_AmrCore/Exec/Prob.H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Make.package
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Prob.f90
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_AmrCore/Exec/inputs
Tutorials/Amr/Advection_AmrCore/Exec/inputs_for_scaling
Tutorials/Amr/Advection_AmrCore/Exec/paraview_amr101.py
Tutorials/Amr/Advection_AmrCore/README
Tutorials/Amr/Advection_AmrCore/README.md
Tutorials/Amr/Advection_AmrCore/Source/AdvancePhiAllLevels.cpp
Tutorials/Amr/Advection_AmrCore/Source/AdvancePhiAtLevel.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/Amr/Advection_AmrCore/Source/DefineVelocity.cpp
Tutorials/Amr/Advection_AmrCore/Source/Kernels.H
Tutorials/Amr/Advection_AmrCore/Source/Make.package
Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Make.package
Tutorials/Amr/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_2d/slope_2d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Make.package
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/slope_3d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_K/Adv_K.H
Tutorials/Amr/Advection_AmrCore/Source/Src_K/Make.package
Tutorials/Amr/Advection_AmrCore/Source/Src_K/compute_flux_2D_K.H
Tutorials/Amr/Advection_AmrCore/Source/Src_K/compute_flux_3D_K.H
Tutorials/Amr/Advection_AmrCore/Source/Src_K/slope_K.H
Tutorials/Amr/Advection_AmrCore/Source/Src_nd/Make.package
Tutorials/Amr/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90
Tutorials/Amr/Advection_AmrCore/Source/Tagging.H
Tutorials/Amr/Advection_AmrCore/Source/bc_fill.H
Tutorials/Amr/Advection_AmrCore/Source/bc_fill_nd.F90
Tutorials/Amr/Advection_AmrCore/Source/face_velocity.H
Tutorials/Amr/Advection_AmrCore/Source/main.cpp
Tutorials/GPU/Advection_AmrCore/CMakeLists.txt
Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs
Tutorials/GPU/Advection_AmrCore/README
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/GPU/Advection_AmrCore/Source/Kernels_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src_2d/Adv_2d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src_2d/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src_2d/slope_2d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H
Tutorials/GPU/Advection_AmrCore/Source/bc_fill.H
Tutorials/GPU/Advection_AmrCore/Source/main.cpp

commit 192fa35ab4195456ba122bce5585e901d51e4b6d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Aug 14 16:12:46 2020 -0700

    Rocm36 (#1263)
    
    ## Summary
    
    Update make system for hip-clang.  Remove some hip workarounds.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFabUtility.H
Src/Base/AMReX_Extension.H
Src/Base/AMReX_GpuAsyncArray.H
Src/Base/AMReX_GpuAsyncArray.cpp
Src/Base/AMReX_GpuElixir.cpp
Src/Base/AMReX_GpuError.H
Src/Base/AMReX_GpuLaunch.H
Tools/GNUMake/Make.defs
Tools/GNUMake/comps/hip.mak

commit 6c36b5ffcf2c7fb97a9cf2ee7a2d6951c5dc1064
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Aug 14 10:32:50 2020 -0700

    Tensor solver and extension of EB domain face (#1262)
    
    ## Summary
    
    ParmParse parameter eb2.extend_domain_face is now true by default.  The
    reason for the change is that for most applications it's hard to imagine one
    would want it to be false.  It will also solve the EB tensor solver issue
    when there is a cut cell just outside the domain abutting a covered valid
    cell.
    
    Recent changes to the tensor solvers are incorrect and are reverted here.
    They are incorrect because the ghost cells in the modified functions
    actually have values at the cell centered.  Although the users put domain
    face values in the ghost cells, that is not what the solver does.  The
    solver stores the boundary values in boundary registers.  Before the stencil
    is being applied, bc function is called to fill the ghost cells with
    properly interpolated or extrapolated values so that the stencil operations
    are just like working on normal interior cells.
    
    Revert "Correcting tensor cross terms computation for periodic bcs (#1254)"
    This reverts commit 1197adc5be6144bae9e362c114ca16b879006180.
    
    Revert "Changing computation at inflow/outflow for tensor solve (#1235)"
    This reverts commit b391885e918d63fa1741f954d2792e31426a6204.
    
    Revert "Changing computation at outflow for the EBTensor (#1187)"
    This reverts commit 9cd538802ea5b3ab7e6db10d6046933e937aa449.
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [x] changes answers in the test suite to more than roundoff level
    - [x] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/EB/AMReX_EB2.cpp
Src/EB/AMReX_EB2_Level.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit 5f7a29477108d74834fc0d19ca966e8ea7b6a16f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 13 13:25:13 2020 -0700

    reuse the tiling machinary in SortParticlesByBin. (#1257)

Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleUtil.H

commit 1652a9da291f96dfa8c1f522a6ddf281b2ad252c
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Aug 13 10:26:44 2020 -0700

    Fix formatting (1261)
    
    ## Summary
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Docs/sphinx_documentation/source/Basics.rst

commit 4c6040c0a3f5c96a2f26592d54f0284dfb524b8b
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Aug 13 08:34:56 2020 -0700

    Add text about how to set default value in the code by passing name (#1260)
    
    of routine to amrex::Initialize(...)

Docs/sphinx_documentation/source/Basics.rst

commit 04d0eecf4a09bcdb584368d89e931fb7a1978580
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Aug 12 17:36:04 2020 -0700

    nvcc -MM (#1259)
    
    ## Summary
    
    `-MM` is not supported for nvcc <= 10.0.
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tools/GNUMake/comps/nvcc.mak

commit e915f9e20be15cc070d4aa023474c8cc2f92840c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 12 12:16:23 2020 -0700

    Domain precision (#1209)
    
    Due to issues with pointing point precision, there are points inside the `ProbDomain()` that do not map to cells inside the `Domain()` box when binned using something like the `getParticleCell` function. This PR adds an additional domain, the "RoundoffDomain()", to the Geometry object. Points inside the roundoff domain are always sure to map to cells inside `Domain()`. The bounds are calculated when the Geometry object is constructed using bisection.
    
    This helps solve a number of issues that can happen when you have particles very close to the domain boundaries.
    
    While I have tested this with Nyx and WarpX, there is a chance that there could be a downstream effect on other codes. If the bisection fails when setting the roundoff domain on some problem, then we may need to adjust some tolerances.

Src/Base/AMReX_Algorithm.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit 19db258fdd76dd5631d8205d8078623c6b97037b
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Aug 12 10:40:28 2020 -0700

    CI: Fix oneAPI Activation (#1208)
    
    now located at `/opt/intel/oneapi/setvars.sh`

Tools/CMake/AMReXSYCL.cmake
Tools/GNUMake/comps/dpcpp.mak

commit 4d4ef3e9b950639f2da9cafe2ee7fa3d572e227c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 12 10:27:34 2020 -0700

    Give HDF5 benchmark option to read in a set of realistic grids. (#1236)
    
    This should lead to more useful measurements for Castro.
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [x] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Tests/HDF5Benchmark/inputs
Tests/HDF5Benchmark/main.cpp

commit d89d48026e077f251408c2652c6ee2e5c5f80d51
Author: Mu-Hua Chien <b94209002@gmail.com>
Date:   Wed Aug 12 13:26:02 2020 -0400

    fix semicoarsening bugs for nodal solver (#1255)
    
    ## Summary
    Fix a semicoarsening bug for nodal solver.
    ## Additional background
    In avgdown coefficient, there is a place use coarsen ratio instead of the mg_coarsen_ratio_vec. Also, build the semi_avgdown for nodal solver.
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 1628d314b33143c6747bd2b44a99426bd1ac3d09
Author: kngott <30483578+kngott@users.noreply.github.com>
Date:   Wed Aug 12 10:22:46 2020 -0700

    Fixes for Amrvis warnings from gcc 7.5 with DEBUG=TRUE, DIM=2 and DIM=3. (#1256)
    
    ## Summary
    
    Warnings from compiling Amrvis using GCC 7.5 with DEBUG=TRUE, DIM=2 and DIM=3. (Build on dogora). Primarily ignore_unused, commenting out function parameter declarations and a few manual type casts. Some unique warning adjustments as well (e.g. a shadowed BL_PROFILER).
    
    To be paired with a matching PR in the Amrvis repo.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_BoxList.cpp
Src/Extern/ProfParser/AMReX_BLProfStats.H
Src/Extern/ProfParser/AMReX_BLProfStats.cpp
Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp
Src/Extern/ProfParser/AMReX_CommProfStats.H
Src/Extern/ProfParser/AMReX_CommProfStats.cpp
Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp
Src/Extern/ProfParser/AMReX_RegionsProfStats.H
Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp
Src/Extern/ProfParser/BLProfParser.y
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/Extern/amrdata/AMReX_DataServices.cpp

commit 1197adc5be6144bae9e362c114ca16b879006180
Author: OscarAntepara <52221614+OscarAntepara@users.noreply.github.com>
Date:   Tue Aug 11 14:02:22 2020 -0700

    Correcting tensor cross terms computation for periodic bcs (#1254)
    
    ## Summary
    Correcting tensor cross terms computation for periodic bcs
    
    ## Additional background
    Fixing a bug introduced in PR #1235. Now it computes in the correct way the cross terms in the tensor solve for problems with periodic bcs.
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [x] changes answers in the test suite to more than roundoff level
    - [x] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit a4ab677faf1279d20d7feb6f42263bcc7b1468f4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Aug 10 17:35:07 2020 -0700

    Fix bug in FPinfo for EB (#1241)
    
    PR #1224 introduced a bug that affects FillPatch on nodal grids for EB.
    When there is only one ghost cell, the fine patch grids might be degenerate
    in the sense that some boxes are only 1 node wide.  In that case, we cannot
    build cell-centered EBCellFlags unless there are ghost cells.

Src/Base/AMReX_FabArrayBase.cpp

commit 46b75867f5106fa363563a230e64a078a3cacc00
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 10 14:00:15 2020 -0700

    Fix curly brace warning with clang (#1251)

Src/Base/AMReX_Machine.cpp

commit a1c997e6ca9d3ad58b18881ef9f319334a2db161
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 10 14:00:05 2020 -0700

    fix some warnings that arise in the redistribute test (#1250)

Tests/Particles/Redistribute/main.cpp

commit c99e8ac4af561a960b98e7995d8fbb291aa70865
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 10 13:49:52 2020 -0700

    Remove _rt and _prt from the particle code, for reasons explained in PR 1243. (#1249)

Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_Particle_mod_K.H
Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 480d1fffe7c7ff7bddcca356ce656f1cecd7f308
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Aug 10 13:41:07 2020 -0700

    Remove Perilla (#1248)
    
    Remove Perilla because it's incompatible with our GPU strategy and it's no
    longer being maintained.

Docs/Doxygen/doxygen.conf
Docs/sphinx_documentation/make_api.py
Docs/sphinx_documentation/source/AsyncIter.rst
Docs/sphinx_documentation/source/AsyncIter_Chapter.rst
Docs/sphinx_documentation/source/index.rst
Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AsyncFillPatch.cpp
Src/Amr/Make.package
Src/AmrTask/AMFIter/AMReX_AmrTask.H
Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H
Src/AmrTask/AMFIter/AMReX_AsyncMFIter.cpp
Src/AmrTask/AMFIter/AMReX_Connections.H
Src/AmrTask/AMFIter/Makefile
Src/AmrTask/Amr/AMReX_AmrLevelTask.H
Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Src/AmrTask/Amr/Make.package
Src/AmrTask/Amr/Makefile
Src/AmrTask/AmrCore/AMReX_FillPatchUtil.H
Src/AmrTask/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrTask/Makefile
Src/AmrTask/arch.common
Src/AmrTask/arch/arch.mpi.generic
Src/AmrTask/arch/arch.serial
Src/AmrTask/graph/AMReX_AbstractTask.H
Src/AmrTask/graph/AMReX_AbstractTask.cpp
Src/AmrTask/graph/AMReX_Affinity.H
Src/AmrTask/graph/AMReX_Affinity.cpp
Src/AmrTask/graph/AMReX_DataTypes.H
Src/AmrTask/graph/AMReX_TaskGraph.H
Src/AmrTask/graph/AMReX_TaskGraph.cpp
Src/AmrTask/graph/Makefile
Src/AmrTask/graph/RTS.H
Src/AmrTask/make_defaults/Cori
Src/AmrTask/make_defaults/Edison
Src/AmrTask/make_defaults/Summit-dev
Src/AmrTask/rts_impls/MPI_Generic/Makefile
Src/AmrTask/rts_impls/MPI_Generic/README
Src/AmrTask/rts_impls/MPI_Generic/mylock.h
Src/AmrTask/rts_impls/MPI_Generic/rts.C
Src/AmrTask/rts_impls/MPI_Generic/rts_graphimpl.H
Src/AmrTask/rts_impls/MPI_Generic/rts_taskimpl.H
Src/AmrTask/rts_impls/README
Src/AmrTask/rts_impls/Serial/Makefile
Src/AmrTask/rts_impls/Serial/rts.C
Src/AmrTask/rts_impls/Serial/rts_graphimpl.H
Src/AmrTask/rts_impls/Serial/rts_taskimpl.H
Src/AmrTask/rts_impls/Utils/dl_malloc.c
Src/AmrTask/rts_impls/Utils/dl_malloc.h
Src/AmrTask/rts_impls/Utils/sysInfo.C
Src/AmrTask/rts_impls/Utils/sysInfo.H
Src/AmrTask/rts_impls/mpi/Make.package
Src/AmrTask/rts_impls/mpi/PackageQueue.H
Src/AmrTask/rts_impls/mpi/PackageQueue.cpp
Src/AmrTask/rts_impls/mpi/Perilla.H
Src/AmrTask/rts_impls/mpi/Perilla.cpp
Src/AmrTask/rts_impls/mpi/PerillaConfig.H
Src/AmrTask/rts_impls/mpi/PerillaRts.H
Src/AmrTask/rts_impls/mpi/PerillaRts.cpp
Src/AmrTask/rts_impls/mpi/perilla.mak
Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/mpi_omp/Barrier.H
Src/AmrTask/rts_impls/mpi_omp/Barrier.cpp
Src/AmrTask/rts_impls/mpi_omp/LocalConnection.H
Src/AmrTask/rts_impls/mpi_omp/Make.package
Src/AmrTask/rts_impls/mpi_omp/PackageQueue.H
Src/AmrTask/rts_impls/mpi_omp/PackageQueue.cpp
Src/AmrTask/rts_impls/mpi_omp/Perilla.H
Src/AmrTask/rts_impls/mpi_omp/Perilla.cpp
Src/AmrTask/rts_impls/mpi_omp/PerillaConfig.H
Src/AmrTask/rts_impls/mpi_omp/PerillaRts.H
Src/AmrTask/rts_impls/mpi_omp/PerillaRts.cpp
Src/AmrTask/rts_impls/mpi_omp/RGIter.H
Src/AmrTask/rts_impls/mpi_omp/RGIter.cpp
Src/AmrTask/rts_impls/mpi_omp/RegionGraph.H
Src/AmrTask/rts_impls/mpi_omp/RegionGraph.cpp
Src/AmrTask/rts_impls/mpi_omp/RegionQueue.H
Src/AmrTask/rts_impls/mpi_omp/RegionQueue.cpp
Src/AmrTask/rts_impls/mpi_omp/RemoteConnection.H
Src/AmrTask/rts_impls/mpi_omp/WorkerThread.H
Src/AmrTask/rts_impls/mpi_omp/WorkerThread.cpp
Src/AmrTask/rts_impls/mpi_omp/perilla.mak
Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/runtime_common/Barrier.H
Src/AmrTask/rts_impls/runtime_common/Barrier.cpp
Src/AmrTask/rts_impls/runtime_common/LocalConnection.H
Src/AmrTask/rts_impls/runtime_common/Make.package
Src/AmrTask/rts_impls/runtime_common/PerillaMemCheck.H
Src/AmrTask/rts_impls/runtime_common/PerillaMemCheck.cpp
Src/AmrTask/rts_impls/runtime_common/Perilla_common.cpp
Src/AmrTask/rts_impls/runtime_common/RGIter.H
Src/AmrTask/rts_impls/runtime_common/RGIter.cpp
Src/AmrTask/rts_impls/runtime_common/RegionGraph.H
Src/AmrTask/rts_impls/runtime_common/RegionGraph.cpp
Src/AmrTask/rts_impls/runtime_common/RegionQueue.H
Src/AmrTask/rts_impls/runtime_common/RegionQueue.cpp
Src/AmrTask/rts_impls/runtime_common/RemoteConnection.H
Src/AmrTask/rts_impls/runtime_common/WorkerThread.H
Src/AmrTask/rts_impls/runtime_common/WorkerThread.cpp
Src/AmrTask/rts_impls/runtime_common/mylock.h
Src/AmrTask/rts_impls/runtime_common/perilla.mak
Src/AmrTask/rts_impls/upcxx/Make.package
Src/AmrTask/rts_impls/upcxx/PackageQueue.H
Src/AmrTask/rts_impls/upcxx/PackageQueue.cpp
Src/AmrTask/rts_impls/upcxx/Perilla.H
Src/AmrTask/rts_impls/upcxx/Perilla.cpp
Src/AmrTask/rts_impls/upcxx/PerillaConfig.H
Src/AmrTask/rts_impls/upcxx/PerillaRts.H
Src/AmrTask/rts_impls/upcxx/PerillaRts.cpp
Src/AmrTask/rts_impls/upcxx/perilla.mak
Src/AmrTask/todolist
Src/Base/AMReX.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil_Perilla.H
Src/Base/AMReX_MultiFabUtil_Perilla.cpp
Src/Base/Make.package
Tools/CMake/AMReX_Defines.cmake
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.upcxx
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/Make.package
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/Prob.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/inputs
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/probin
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/Make.package
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/Prob.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/inputs
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/probdata.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/probin
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/README
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv.H
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv.cpp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/AdvBld.cpp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv_F.H
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv_advance.cpp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv_dt.cpp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv_io.cpp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv_setup.cpp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Make.package
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_2d/Adv_2d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_2d/Make.package
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_2d/compute_flux_2d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_2d/slope_2d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_3d/Adv_3d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_3d/Make.package
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_3d/compute_flux_3d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_3d/slope_3d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Adv_nd.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Make.package
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Tagging_nd.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_nd/tagging_params.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/main.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/Make.Adv.upcxx
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/Prob.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/inputs
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/probin
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/Prob.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/inputs
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/probdata.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/probin
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/README
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv.H
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/AdvBld.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv_F.H
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv_dt.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv_io.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv_setup.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_2d/Adv_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_2d/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_2d/compute_flux_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_2d/slope_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_3d/Adv_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_3d/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_3d/compute_flux_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_3d/slope_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_nd/Adv_nd.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_nd/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_nd/Tagging_nd.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_nd/tagging_params.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/main.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/Prob.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/inputs
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/probin
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/Prob.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/inputs
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/probdata.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/probin
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/README
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv.H
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/AdvBld.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv_F.H
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv_advance.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv_dt.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv_io.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv_setup.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/Adv_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/compute_flux_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/slope_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/Adv_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/compute_flux_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/slope_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Adv_nd.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Tagging_nd.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/tagging_params.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/main.cpp

commit b391885e918d63fa1741f954d2792e31426a6204
Author: OscarAntepara <52221614+OscarAntepara@users.noreply.github.com>
Date:   Mon Aug 10 11:17:32 2020 -0700

    Changing computation at inflow/outflow for tensor solve (#1235)
    
    ## Summary
    Computation at inflow boundaries for the MLEBTensor and inflow/outflow for MLTensor has been changed.
    
    ## Additional background
    At outflow the tensor solve uses extrapolated values from the interior cell to the outflow face. At inflow, the tensor solve uses boundary data, evaluated at the face, that has been stored in the ghost cell next to the inflow face.
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [x] changes answers in the test suite to more than roundoff level
    - [x] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit ad1b75d9557fddf126f67be4b802327c1a4415e5
Author: asalmgren <asalmgren@lbl.gov>
Date:   Mon Aug 10 10:46:17 2020 -0700

    Remove sensei tutorials (#1247)
    
    * Remove SENSEI tutorials.
    
    * Update tutorial documentation since we no longer have SENSEI tutorials

Docs/sphinx_tutorials/source/SENSEI_Tutorial.rst
Docs/sphinx_tutorials/source/index.rst
Tutorials/SENSEI/Advection_AmrCore/CMakeLists.txt
Tutorials/SENSEI/Advection_AmrCore/Exec/Make.Adv
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/Make.package
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/Prob.f90
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/inputs
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/histogram.py
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/histogram_python.xml
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_catalyst.py
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml
Tutorials/SENSEI/Advection_AmrCore/README
Tutorials/SENSEI/Advection_AmrCore/README_SENSEI.md
Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/SENSEI/Advection_AmrCore/Source/Make.package
Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/Adv_2d.f90
Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/Make.package
Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90
Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/slope_2d.f90
Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/Adv_3d.f90
Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/Make.package
Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90
Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/slope_3d.f90
Tutorials/SENSEI/Advection_AmrCore/Source/Src_nd/Make.package
Tutorials/SENSEI/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90
Tutorials/SENSEI/Advection_AmrCore/Source/bc_fill_nd.F90
Tutorials/SENSEI/Advection_AmrCore/Source/main.cpp
Tutorials/SENSEI/Advection_AmrLevel/CMakeLists.txt
Tutorials/SENSEI/Advection_AmrLevel/Exec/Make.Adv
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/Make.package
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/Prob.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/probin
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/histogram.py
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/histogram_python.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/iso_extract.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/read_adios2_bp4_default.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/read_adios2_sst_default.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_catalyst.py
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.session
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.session
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_libsim.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/write_adios2_bp4.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/write_adios2_sst.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/write_vtk.xml
Tutorials/SENSEI/Advection_AmrLevel/README
Tutorials/SENSEI/Advection_AmrLevel/README_SENSEI.md
Tutorials/SENSEI/Advection_AmrLevel/Source/Adv_F.H
Tutorials/SENSEI/Advection_AmrLevel/Source/AmrLevelAdv.H
Tutorials/SENSEI/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Tutorials/SENSEI/Advection_AmrLevel/Source/LevelBldAdv.cpp
Tutorials/SENSEI/Advection_AmrLevel/Source/Make.package
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/Make.package
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/slope_2d.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/Make.package
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/slope_3d.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Make.package
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/tagging_params.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/main.cpp
Tutorials/SENSEI/README.md

commit 63d386514d5167d5849d11e0cc6dbb146c46a37b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun Aug 9 20:22:25 2020 -0700

    oneAPI Beta 8 (#1243)
    
    In beta8, C++11 user defined literals are broken because of the use of long
    double.  We have implemented a workaround by overloading operator "" _rt
    with `const char*` argument and our own `atof`.  But, because Clang does not
    evaluate the new version of the operator at compile time, we now avoid using
    `_rt` in AMReX.  In the long term, we may have to remove it entirely if the
    long double issue is not resolved in DPC++.
    
    With the workaround, we can enable the DPC++ CI test again.

.github/workflows/linux.yml
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_extrapolater_2D_K.H
Src/Amr/AMReX_extrapolater_3D_K.H
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_ErrorList.cpp
Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Src/Base/AMReX_Dim3.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil_nd_C.H
Src/Base/AMReX_REAL.H
Src/Base/AMReX_Random.cpp
Src/Base/AMReX_Scan.H
Src/Boundary/AMReX_InterpBndryData_2D_K.H
Src/Boundary/AMReX_InterpBndryData_3D_K.H
Src/EB/AMReX_algoim_K.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H
Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/Source/mykernel.H
Tutorials/Basic/HeatEquation_EX1_CF/Source/main.cpp
Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX2_CF/Source/main.cpp
Tutorials/Basic/HeatEquation_EX3_C/Source/main.cpp
Tutorials/GPU/CNS/Exec/RT/cns_prob.H
Tutorials/GPU/CNS/Exec/RT/cns_prob_parm.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob_parm.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/CNS_parm.H
Tutorials/GPU/CNS/Source/CNS_parm.cpp
Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H
Tutorials/GPU/CNS/Source/main.cpp

commit e3f25aa6b9ed74229d203110fa59fb2d0e815bdf
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun Aug 9 20:21:44 2020 -0700

    Fix a bug in Tutorials/GPU/CNS (#1245)
    
    Fix a bug in deriving velocity and a number of warnings for
    Tutorials/GPU/CNS.

Src/Base/AMReX_FBI.H
Tutorials/GPU/CNS/Exec/RT/cns_prob.cpp
Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/CNS_derive.cpp

commit cd0a8034f389b40882900b3faa92d84beed13201
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun Aug 9 20:21:04 2020 -0700

    FPE trap in DPC++ (#1244)
    
    Due to a bug in DPC++ compiler, we disable fpe trapping.

Src/Base/AMReX.cpp

commit a2eecef9c2efab1548ad14d6b5083f14451441bb
Author: drangara <69211175+drangara@users.noreply.github.com>
Date:   Sun Aug 9 16:34:44 2020 -0400

    Small volfrac (#1228)
    
    ## Summary
    
    When extend_domain_face is set to true we do the following: If we set a cell that lies on one of the 6 faces of the domain as covered because its volfrac is less than the small_volfrac , we are forcing the corresponding ghost cells on that face to also be covered.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [x] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/EB/AMReX_EB2_2D_C.cpp
Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EB2_C.H
Src/EB/AMReX_EB2_Level.H

commit d8d270056e953904c04d3ae3221006389128531e
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Sun Aug 9 10:30:38 2020 -0600

    Remove error message for unknown MPI in Make.nrel since we want to be able to use MPT for MPI. (#1242)

Tools/GNUMake/sites/Make.nrel

commit 09db04bf308dbfe797baa19b9118466f545ee16c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 7 16:39:17 2020 -0700

    fix some warnings that arise when USE_SINGLE_PRECISION_PARTICLES=TRUE but PRECISION=DOUBLE (#1240)

Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleUtil.H
Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 881397d57f8fee10dc24db747e07a7bb3685d4ec
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Aug 7 16:23:35 2020 -0700

    GNU Make dependency (#1239)
    
    Use `-MM` instead of `-M` to generate dependency in GNU Make system, because
    we do not need to include dependency on headers in the system header
    directories.

Tools/GNUMake/Make.defs

commit b4ba4429672be4589d535b7e6c83272fee5fdfe3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Aug 7 13:51:41 2020 -0700

    Oversetmask (#1232)
    
    Switch the overset mask convention to that 1 means unknown and 0 means
    known.  The new convention is more convenient for AMR-Wind.

Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H
Tests/LinearSolvers/CellOverset/MyTest.cpp
Tests/LinearSolvers/NodalOverset/MyTest.cpp
Tests/LinearSolvers/TensorOverset/MyTest.cpp

commit cd71ce08c17edb1aeeaa89d00bb9b072713c26a8
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Aug 7 13:40:39 2020 -0700

    Remove old solvers (#1238)
    
    Src/LinearSolvers/C_CellMG and C_TensorMG are removed.  They have been
    superseded by Src/LinearSolvers/MLMG.

Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H
Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_F.H
Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_F.H
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_F.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp
Src/LinearSolvers/C_CellMG/AMReX_lo_bctypes.fi
Src/LinearSolvers/C_CellMG/Make.package
Src/LinearSolvers/C_CellMG/OpenSource.txt
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F90
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F90
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F90
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F90
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H
Src/LinearSolvers/C_CellMG4/Make.package
Src/LinearSolvers/C_CellMG4/OpenSource.txt
Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F
Src/LinearSolvers/C_TensorMG/AMReX_DV_3D1.F
Src/LinearSolvers/C_TensorMG/AMReX_DV_3D2.F
Src/LinearSolvers/C_TensorMG/AMReX_DV_3D3.F
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_2D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_3D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_2D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_3D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp
Src/LinearSolvers/C_TensorMG/DV_2D.mF
Src/LinearSolvers/C_TensorMG/DV_3D1.mF
Src/LinearSolvers/C_TensorMG/DV_3D2.mF
Src/LinearSolvers/C_TensorMG/DV_3D3.mF
Src/LinearSolvers/C_TensorMG/DV_3D4.mF
Src/LinearSolvers/C_TensorMG/Format.m
Src/LinearSolvers/C_TensorMG/Make.package
Src/LinearSolvers/C_TensorMG/OpenSource.txt
Src/LinearSolvers/C_TensorMG/Optimize.m
Src/LinearSolvers/C_TensorMG/amrex_tmg_util.F90
Src/LinearSolvers/C_TensorMG/visc2d.m
Src/LinearSolvers/C_TensorMG/visc2d.ma
Src/LinearSolvers/C_TensorMG/visc2d.nb
Src/LinearSolvers/C_TensorMG/visc3d.m
Src/LinearSolvers/C_TensorMG/visc3d.ma
Src/LinearSolvers/C_TensorMG/visc3d.nb
Tests/LinearSolvers/C_CellMG/COEF_2D.F
Tests/LinearSolvers/C_CellMG/COEF_3D.F
Tests/LinearSolvers/C_CellMG/COEF_F.H
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile.dumpi
Tests/LinearSolvers/C_CellMG/MACOPERATOR_2D.F
Tests/LinearSolvers/C_CellMG/MACOPERATOR_3D.F
Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H
Tests/LinearSolvers/C_CellMG/MACPROJ_2D.F
Tests/LinearSolvers/C_CellMG/MACPROJ_3D.F
Tests/LinearSolvers/C_CellMG/MacOpMacDrivers.H
Tests/LinearSolvers/C_CellMG/MacOperator.H
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/C_CellMG/Make.package
Tests/LinearSolvers/C_CellMG/Palette
Tests/LinearSolvers/C_CellMG/amrvis.defaults
Tests/LinearSolvers/C_CellMG/dumpi/NOTE
Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.4096core
Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.512core
Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.64core
Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.8core
Tests/LinearSolvers/C_CellMG/inputs.2d
Tests/LinearSolvers/C_CellMG/inputs.3d
Tests/LinearSolvers/C_CellMG/macprojTest.cpp
Tests/LinearSolvers/C_CellMG/main.cpp
Tests/LinearSolvers/C_CellMG/vpramps.dat
Tests/LinearSolvers/C_TensorMG/GNUmakefile
Tests/LinearSolvers/C_TensorMG/Make.package
Tests/LinearSolvers/C_TensorMG/Palette
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp
Tests/LinearSolvers/C_TensorMG/amrvis.defaults
Tests/LinearSolvers/C_TensorMG/inputs
Tests/LinearSolvers/C_TensorMG/inputs2D
Tests/LinearSolvers/C_TensorMG/inputs3D
Tests/LinearSolvers/C_TensorMG/inputs8
Tests/LinearSolvers/C_TensorMG/main_2D.F
Tests/LinearSolvers/C_TensorMG/main_3D.F
Tests/LinearSolvers/C_TensorMG/main_F.H
Tests/LinearSolvers/C_TensorMG/probin
Tests/LinearSolvers/C_TensorMG/testVI.cpp
Tests/LinearSolvers/C_TensorMG/vpramps.dat
Tools/CompileTesting/compiletesting.py

commit 6de33d5b79d614dcdd3c7f4923676c7e8ad503dd
Author: mic84 <mrosso@lbl.gov>
Date:   Fri Aug 7 12:25:10 2020 -0700

    MacProjector: allow for re-use of the object and enhance multi-level algorithm. (#1225)
    
    * MacProjector: build RHS each time project() is called
    
    * MacProjector: average down velocities before and after projection

Src/LinearSolvers/Projections/AMReX_MacProjector.H
Src/LinearSolvers/Projections/AMReX_MacProjector.cpp

commit b9ed579c052acac1fb73ced3ac2e9e63b17b3046
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 7 11:59:09 2020 -0700

    Fix unused variable warnings in AMReX_LinOp.* (#1237)
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp

commit 53d32def6b48c00270f97f4efd6251aa55cb6e7a
Author: Candace Gilet <cgilet@users.noreply.github.com>
Date:   Thu Aug 6 17:06:06 2020 -0400

    Fix typo. (#1234)
    
    ## Summary
    Fix a typo in AMReX_extrapolater_3D_K.H
    
    ## Additional background
    Some IAMR runs were crashing with out of bounds errors. This fixes those, and brings this C version in agreement with what the old F90 version was doing.
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Amr/AMReX_extrapolater_3D_K.H

commit fe8cc5f3facab97cd39df5c06f6a3e2cc43ab378
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Aug 6 11:15:56 2020 -0700

    Fix AMREX_HOME in Tests and Tutorials only (#1233)
    
    * 1) Replace all instances of "AMREX_HOME ?=" by "AMREX_HOME =" in Tests and Tutorials only.
       Since these exist within the amrex directory structure the default should be that they
       always use the amrex they are part of, not the one set by the user's environment variable
    2) Replace all instances of BoxLib/BOXLIB/boxlib by AMReX.

Tests/Algoim/GNUmakefile
Tests/AsyncOut/multifab/GNUmakefile
Tests/BBIOBenchmark/GNUmakefile
Tests/BaseFabTesting/GNUmakefile
Tests/GPU/CudaGraphs/BuildingGraphs/GNUmakefile
Tests/GPU/CudaGraphs/GraphBoundary/GNUmakefile
Tests/GPU/CudaGraphs/GraphInitTest/GNUmakefile
Tests/GPU/CudaGraphs/GraphReuseCopy/GNUmakefile
Tests/GPU/CudaGraphs/GraphWithMemcpy/GNUmakefile
Tests/GPU/CuptiTest/Exec/CUDA/GNUmakefile
Tests/GPU/Fuse/GNUmakefile
Tests/GPU/Locking/GNUmakefile
Tests/GPU/RandomNumberGeneration/GNUmakefile
Tests/GPU/Vector/GNUmakefile
Tests/GPU/libamrex_CUDA/GNUmakefile
Tests/HDF5Benchmark/GNUmakefile
Tests/LinearSolvers/CellEB/GNUmakefile
Tests/LinearSolvers/CellEB2/GNUmakefile
Tests/LinearSolvers/CellOverset/GNUmakefile
Tests/LinearSolvers/EBConvergenceTest/GNUmakefile
Tests/LinearSolvers/EBTensor/GNUmakefile
Tests/LinearSolvers/EBflux_grad/GNUmakefile
Tests/LinearSolvers/MLMG/GNUmakefile
Tests/LinearSolvers/NodalOverset/GNUmakefile
Tests/LinearSolvers/NodeEB/GNUmakefile
Tests/LinearSolvers/TensorOverset/GNUmakefile
Tests/MKDir/GNUmakefile
Tests/NoFort/GNUmakefile
Tests/Particles/AssignDensity/GNUmakefile
Tests/Particles/AssignMultiLevelDensity/GNUmakefile
Tests/Particles/AsyncIO/GNUmakefile
Tests/Particles/GNUmakefile
Tests/Particles/GhostsAndVirtuals/GNUmakefile
Tests/Particles/InitFromAscii/GNUmakefile
Tests/Particles/Intersection/GNUmakefile
Tests/Particles/NeighborParticles/GNUmakefile
Tests/Particles/ParallelContext/GNUmakefile
Tests/Particles/ParticleIterator/GNUmakefile
Tests/Particles/ParticleMesh/GNUmakefile
Tests/Particles/ParticleReduce/GNUmakefile
Tests/Particles/ParticleTransformations/GNUmakefile
Tests/Particles/Redistribute/GNUmakefile
Tests/Particles/SparseBins/GNUmakefile
Tests/Particles/TypeDescriptor/GNUmakefile
Tests/PnetCDFBenchmark/GNUmakefile
Tests/ProfTests/HeatEquation_EX1_C/Exec/GNUmakefile
Tests/ProfTests/ThirdParty/Exec/GNUmakefile
Tests/SinglePrecision/GNUmakefile
Tests/Slice/GNUmakefile
Tests/Stream/GNUmakefile
Tests/TypeCheck/GNUmakefile
Tests/Vectorization/GNUmakefile
Tests/complementIn/GNUmakefile
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/README
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_2d/Adv_2d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_3d/Adv_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/README
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_2d/Adv_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_3d/Adv_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/README
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/Adv_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/Adv_3d.f90
Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_CF/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_F/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_F/inputs
Tutorials/Basic/HeatEquation_EX2_C/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX2_CF/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX3_C/Exec/GNUmakefile
Tutorials/Basic/HelloWorld_C/GNUmakefile
Tutorials/Basic/HelloWorld_F/GNUmakefile
Tutorials/Basic/PrefixSum_MultiFab/GNUmakefile
Tutorials/Basic/main_C/GNUmakefile
Tutorials/Basic/main_F/GNUmakefile
Tutorials/Blueprint/AssignMultiLevelDensity/GNUmakefile
Tutorials/Blueprint/CellSortedParticles/GNUmakefile
Tutorials/Blueprint/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/CVODE/SUNDIALS2_finterface/EX1/GNUmakefile
Tutorials/CVODE/SUNDIALS2_finterface/EX2/GNUmakefile
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/GNUmakefile
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX1/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/GNUmakefile
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/GNUmakefile
Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/GNUmakefile
Tutorials/EB/GeometryGeneration/GNUmakefile
Tutorials/EB/MacProj/GNUmakefile
Tutorials/EB/Poisson/GNUmakefile
Tutorials/ForkJoin/MLMG/GNUmakefile
Tutorials/ForkJoin/Simple/GNUmakefile
Tutorials/FortranInterface/Advection_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/FortranInterface/Advection_F/Source/Src_3d/Adv_3d.f90
Tutorials/FortranInterface/Advection_octree_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/GPU/Launch/GNUmakefile
Tutorials/GPU/ParallelReduce/GNUmakefile
Tutorials/GPU/ParallelScan/GNUmakefile
Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile
Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile
Tutorials/LinearSolvers/MAC_Projection_EB/GNUmakefile
Tutorials/LinearSolvers/MultiComponent/GNUmakefile
Tutorials/LinearSolvers/NodalPoisson/GNUmakefile
Tutorials/LinearSolvers/Nodal_Projection_EB/GNUmakefile
Tutorials/LinearSolvers/NodeTensorLap/GNUmakefile
Tutorials/MUI/Exec_01/GNUmakefile
Tutorials/MUI/Exec_02/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile
Tutorials/SDC/MISDC_ADR_2d/Exec/GNUmakefile
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90

commit 888e804b77fad6754368396bb728e3ec491ed610
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 5 13:23:09 2020 -0700

    use rvalues for functions that take callables (#1231)

Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_NeighborList.H
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_SparseBins.H

commit 30fe5a59e9730683a28f7291ae96310d9560d917
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Aug 5 12:32:34 2020 -0400

    add asserts for bounds checking to Array1D and Array2D (#1230)
    
    ## Summary
    
    Array1D and Array2D did not check if the index was in bounds.  This adds an `AMREX_ASSERT` that catches out of bounds issues when compiled with `DEBUG = TRUE`.
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_Array.H

commit e2dac9c4e6fa2a4163ec778b4958af843077069c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 4 16:12:50 2020 -0700

    Optimization of the construction of SFC (#1227)
    
    ## Summary
    
    The Morton numbers are explicitly computed and stored in SFCTokens.  This
    speeds up the sorting in making space filling curve significantly.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_Print.H

commit 9d76c3732bd03111c0279630761e5439e70c9b49
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Aug 4 15:00:39 2020 -0700

    Refactoring of particle buffer map (#1229)

Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_ParticleBufferMap.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleLocator.H
Src/Particle/AMReX_ParticleUtil.H

commit d570a8c6647abc85a32cbcbe4af886fa2dde3782
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 4 11:13:27 2020 -0700

    Ignore unused indices in AMREX_LOOP_3D and 4D (#1226)

Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_Loop.H

commit f706d8aceb4272eb3e8f700cf77150cf4967aa20
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 4 09:20:57 2020 -0700

    Optimization of FPinfo and complementIn (#1224)
    
    ## Summary
    
    Use simplified BoxArray in FPinfo and parallelize FPinfo.  Add parallel version of
    BoxList::parallelComplementIn and use it in AmrMesh::MakeNewGrids.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_FillPatchUtil_I.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxDomain.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 99d2227371a6a47e40b8175ee0f73f97ecf3aa59
Author: Lucas Esclapez <13371051+esclapez@users.noreply.github.com>
Date:   Tue Aug 4 08:41:54 2020 -0700

    Feature extrapolator gpu (#1222)
    
    ## Summary
    Move the Amr/Extrapolater used in IAMR/PeleLM to C++/GPU compliant.
    
    ## Additional background
    The Extrapolater allows to fill ghost cells with first order extrapolation from interior cells.
    
    ## Checklist
    The C++ version does not introduce any changes to the results and passed CI compilation tests.
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [X] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Amr/AMReX_Extrapolater.cpp
Src/Amr/AMReX_extrapolater_1D_K.H
Src/Amr/AMReX_extrapolater_1d.f90
Src/Amr/AMReX_extrapolater_2D_K.H
Src/Amr/AMReX_extrapolater_2d.f90
Src/Amr/AMReX_extrapolater_3D_K.H
Src/Amr/AMReX_extrapolater_3d.f90
Src/Amr/AMReX_extrapolater_K.H
Src/Amr/CMakeLists.txt
Src/Amr/Make.package

commit 294435b79bddc3106249a15c64bd7b4322c19024
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 3 14:11:17 2020 -0700

    Less surprising behavior for the ok() method of FabArray. (#1223)
    
    This makes the `ok()` method of FabArray return `false` instead of crashing if the `define()` method has yet to be called.
    
    We allow FabArray and its derived classes to be default constructed, which places them in a unusable state until the the `define` method has been called. We also provide an `ok()` method, which according to its doxygen strings returns whether the FabArray is well-defined. Currently, this method will crash with a not-particularly instructive error message if it is called on a default-constructed-but-not-defined FabArray. This pull request changes it to return `false` instead, which I'd argue is more intuitive - if it's legal to construct a FabArray and define it later, then it should be legal to test whether that has been done or not. I have also updated the doxygen string for the method in question.
    
    Even if we want this to crash instead of returning `false`, it should do so with its own assertion and a clear error message.
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [x] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_FabArray.H

commit a918cdabf2bd5f5991fe69494593634f1fced2b4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Aug 3 13:16:49 2020 -0700

    Optimization of regrid (#1199)
    
    ## Summary
    
    New BoxList::maxSize function that keeps Boxes after chopping in an order that is easy to merge them
    back into original Box.
    
    New BoxList::order_simplify function that assumes the BoxList is in the order that we only need to
    search the next Box in the list.
    
    Cache simplified BoxList inside BoxArray.
    
    Use simplified BoxArray in FPinfo.
    
    This commit will make most regression tests fail because it changes the grids.  But if the comparison is
    done with `fcompare....ex -a`, it should only change answers at roundoff level unless the test is very
    sensitive.

Src/AmrCore/AMReX_AmrMesh.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_FabArrayBase.cpp

commit 4c50993ce86e8f6c54c50b93cbbb1aab92d42edd
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Mon Aug 3 12:29:18 2020 -0600

    Fillboundary (#1171)
    
    This pull request fixes the problem of edge nodes not getting filled properly when filling multiple layers of ghost nodes. This occurs when there are overlapping ghost nodes on a coarse/fine boundary. (See issue #568)
    
    Summary of changes to AMreX:
    - Added a `BoxArray::complementIn` function that takes a box _list_ and returns the complement box list.
    - Added an additional boolean argument `multi_ghost` to all `FillBoundary` functions that gets passed (eventually) to `define_fb`. In all cases, a default value of `false` is supplied.
    - Modified `define_fb` to include the missing ghost nodes in the list of `send_tags`. (This uses the new `complementIn` function.)
    
    Summery of changes to `LinearSolver/MultiComponent` tutorial:
    - Removed the `realFillBoundary` function, replaced with `FillBoundary(false,true)
    - Modified `main.cpp` so that it can be compiled and run (non-trivially) in 2D as well as 3D.
    
    Diagram of the problem that this PR fixes:
    ![FillBoundaryIllustration](https://user-images.githubusercontent.com/6371567/88218141-d9982980-cc1c-11ea-84f7-194934dfed73.png)

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.H
Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp
Tutorials/LinearSolvers/MultiComponent/inputs
Tutorials/LinearSolvers/MultiComponent/main.cpp

commit 28ceb92eae33e7b7797831bed85ad6242fdcf317
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Aug 3 11:25:41 2020 -0700

    Tools: add NVIDIA HPC SDK as a compiler (#1131)
    
    HPC SDK replaced PGI after PGI 20.4, so we should get it working now.

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/hpcsdk.mak

commit 273cf0cc0c2b26d1f81147a5a00ceb26bd17184c
Author: asalmgren <asalmgren@lbl.gov>
Date:   Sun Aug 2 14:09:09 2020 -0700

    The average_down_faces calls between AMR levels in the linear solvers need to see periodicity (#1221)
    
    The average_down_faces calls between AMR levels need to use the interfaces that sees the periodicity.  This requires adding that functionality to EB_average_down_faces (it has already been added to non-EB average_down_faces.)
    
    ## Summary
    Recently we added the functionality for an average_down_faces call to average fine data from one side to average not only onto the face under it but also onto the face on the other side of the domain if periodic in that direction.  This PR 1) extends that functionality to the EB_average_down_faces call and 2) uses this new functionality when averaging down face-based coefficients between AMR levels in the cell-centered linear solvers.
    
    ## Checklist
    
    The proposed changes:
    - [X] fix a bug or incorrect behavior in AMReX
    - [X] add new capabilities to AMReX
    - [X] changes answers in the test suite to more than roundoff level
    - [X] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 9cd538802ea5b3ab7e6db10d6046933e937aa449
Author: OscarAntepara <52221614+OscarAntepara@users.noreply.github.com>
Date:   Sun Aug 2 14:00:12 2020 -0700

    Changing computation at outflow for the EBTensor (#1187)
    
    Computation at outflow boundaries for the EBTensor has been changed to not take into account cells outside the domain.

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit ccaebccf710600e2e28510f8ba43b760a10a918b
Author: asalmgren <asalmgren@lbl.gov>
Date:   Sun Aug 2 13:16:56 2020 -0700

    Fix the calculation of divu at inflow face in nodal projection so that it does not use tangential velocities on an inflow face (#1219)
    
    ## Summary
    Mathematically the nodal projection should only see the normal velocity at inflow faces, but it was coded so that it would use non-zero tangential velocities at inflow in the calculation of divu.  Most users never set tangential velocities to anything but zero, but if they did, this would give an incorrect divergence.
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [X] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [X] changes answers in the test suite to more than roundoff level
    - [X] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 9ed2833df8a110f0ea43e901da96a93f0686a031
Author: Marc Day <MSDay@lbl.gov>
Date:   Sat Aug 1 18:48:08 2020 -0700

    Remove instructions....not needed and clutters Slack notices (#1218)
    
    ## Summary
    
    Although the instructions were commented out in the formatted PR text, they clutter up the Slack notices, and aren't really necessary anyway.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

.github/pull_request_template.md

commit 20d9b4a451bc2ee8a9133fa618e46ffd479c6807
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Aug 1 12:58:03 2020 -0700

    20.08 (#1220)
    
    ## Summary
    
    Update CHANGES for 20.08
    
    ## Additional background
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

CHANGES

commit 2dad6e2975931107be98205086eb11969e937ed1
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jul 30 22:53:09 2020 -0700

    Average down faces (#1216)
    
    New average_down_faces functions that take coarse Geometry and average down periodically.

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 1476ea3ef4a3dc6bae80b241d85657c0fc5d9d31
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jul 29 18:30:43 2020 -0700

    fix angle brackets pr template (#1215)
    
    ## Summary
    
    The `-->` in the html comment part of the PR template closes the comment and leaves the words after that and before the actual closing `-->` visible.  This is fixed.
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

.github/pull_request_template.md

commit d8cdfd9eda11126954ac549c57eec8723e97f21b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jul 29 18:26:27 2020 -0700

    Fix warnings for DPC++ (#1214)
    
    ## Summary
    
    - Add more warnings flags to dpcpp.
    - Fix warnings for DPC++.
    - Fix a bug in DPC++ version of ReduceLogicalOr.
    
    ## Checklist
    
    The proposed changes:
    - [x] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

Src/Base/AMReX_BlockMutex.H
Src/Base/AMReX_BlockMutex.cpp
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_GpuAtomic.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuUtility.H
Src/Base/AMReX_Random.cpp
Src/Base/AMReX_Reduce.H
Src/Base/AMReX_parstream.cpp
Tools/GNUMake/comps/dpcpp.mak
Tools/GNUMake/comps/llvm.mak

commit 2dc11c2ffd58a4e3f50d691a856446db0dfde8c5
Author: kngott <30483578+kngott@users.noreply.github.com>
Date:   Wed Jul 29 09:01:50 2020 -0700

    Update the documentation for NSight tools. (#1163)
    
    Created a skeleton in External Profiling for documenting AMReX specific implementations of the NSight package.
    
    Also updated the run.corigpu script with new data from the Hackathon.

Docs/sphinx_documentation/source/External_Profiling_Tools.rst
Docs/sphinx_documentation/source/External_Profiling_Tools_Chapter.rst
Tutorials/GPU/run.corigpu
Tutorials/GPU/run.script
Tutorials/GPU/run.summit

commit 94961adbaf07c228eaae7c3ee3536f1ee338a3ce
Author: Houjun <houj.tang@gmail.com>
Date:   Tue Jul 28 17:12:15 2020 -0700

    Fix a bug with HDF5 boxcenter data (#1213)
    
    * Fix a bug that causes wrong value assignment for the boxcenter dataset
    
    Co-authored-by: Houjun Tang <htang4@lbl.gov>

Src/Base/AMReX_PlotFileUtil.cpp

commit 1a4780d8ef5fb2fa7948ab926c942ea551690e60
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jul 28 14:25:29 2020 -0700

    Add PR template file (#1211)
    
    ## Sumary
    
    Following CASTRO's lead, this template for PRs will pre-fill PR messages with suggested text.  Hitting "Preview" in the PR window will format the message nicely.
    
    ## Checklist
    
    The proposed changes:
    - [ ] fix a bug or incorrect behavior in AMReX
    - [ ] add new capabilities to AMReX
    - [ ] changes answers in the test suite to more than roundoff level
    - [ ] are likely to significantly affect the results of downstream AMReX users
    - [ ] are described in the proposed changes to the AMReX documentation, if appropriate

.github/pull_request_template.md

commit 97a6fa2f59f2985a4f67adbd8d431a50f8a35590
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 28 13:14:02 2020 -0700

    Turn off CI for DPC++ right now, since it's currently broken. (#1210)
    
    * turn off the DPC++ CI workflow for now, as it is broken in beta 8
    
    * note that this is borked right now

.github/workflows/linux.yml

commit e4da66c8e01efa09257e6362688c8a7c4e3bd1dd
Author: asalmgren <asalmgren@lbl.gov>
Date:   Mon Jul 27 17:27:16 2020 -0700

    Docs hypre fix (#1207)

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 9db726812c87a2138ee2b2a831d3363824f1c633
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Mon Jul 27 12:59:33 2020 -0700

    CMake: NVCC/cudafe Error Numbers (#1206)
    
    Activate this fancy, undocumented flag to show error numbers in NVCC.
    This is great if one wants to suppress (or report) them and should be
    standard.

Tools/CMake/AMReX_SetupCUDA.cmake

commit ffe8d2e06bf276cbe382b658223ea3b4d78b89e7
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jul 27 11:16:17 2020 -0700

    fix periodic boundary bug in #1204 (#1205)

Src/AmrCore/AMReX_TagBox.cpp

commit d731f8ba3a26c74febfae7d42862617e01112534
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun Jul 26 18:05:50 2020 -0700

    EB outside domain (#1201)
    
    * EB outside domain
    
    Add a runtime parameter `eb2.extend_domain_face` to control EB generation outside the domain.  The
    default is false.  That is the implicit function will be used for cells outside the domain.  This
    preserves the current behavior.  If it is set to true, the geometry information is then extrapolated
    from domain faces.
    
    * fix fillFab for EB_levelset

Src/Base/AMReX_Algorithm.H
Src/EB/AMReX_EB2.H
Src/EB/AMReX_EB2.cpp
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EB2_IndexSpaceI.H
Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_EB_levelset.H

commit 931ac6fb4a03faed44918731ecb383368ba0cfe2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun Jul 26 15:06:25 2020 -0700

    Fix bug in #1156 (#1204)
    
    In #1156, newly generated grids were not always properly nested because the tags in ghost cells were
    discarded.  This is fixed and an assertion is added.

Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp

commit 6812ea39f6739eae11d4cfaf9ac28940e77df0ae
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jul 26 09:22:22 2020 -0700

    Fix CellConservativeProtected bug from #1184 (#1203)
    
    * Fix CellConservativeProtected bug from #1184
    
    * Fix comment

Src/AmrCore/AMReX_Interpolater.cpp

commit 1dbf5d7a5939e2b9bdb41627716fe392f168c5e0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Jul 25 20:43:52 2020 -0700

    GNU Make option to turn warnings into errors (#1198)
    
    Add `WARN_ERROR` (with default of `FALSE`) to the GNU Make system to turn warnings into errors for
    GCC and Clang.  Add `WARN_ERROR` to the 2d and 3d CIs using GNU Make.

.github/workflows/linux.yml
Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/GNUMake/Make.defs
Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/llvm.mak

commit b9b0196728b93353a34f1152337f88a701ff6fde
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Jul 25 16:14:04 2020 -0700

    udpate branch name due to regression_testing branch name change (#1200)

Docs/Doxygen/doxygen.conf
Docs/sphinx_documentation/source/Testing.rst

commit 8ce4756814f2064eae003a5c414e914f60a69960
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 24 19:12:29 2020 -0700

    Fix some more clang warnings (#1197)

Src/AmrCore/AMReX_ErrorList.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_Array.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_Machine.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_ParallelReduce.H
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PlotFileDataImpl.cpp
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_linop_fi.cpp
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_TracerParticles.cpp

commit c013c29ad1e9e7da23431a6f4b5c1ab47cc059a4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jul 24 18:27:53 2020 -0700

    Gcc7 no array bounds (#1196)
    
    * Wno-array-bounds for gcc 7
    
    * [[gnu::fallthrought]] is available for gcc >= 7 only.  Test the result of dynamic_cast.

Src/Base/AMReX_Extension.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tools/GNUMake/comps/gnu.mak

commit c9ca46b45b96ce1507e74a0bcafe545de802e5c0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 24 16:24:55 2020 -0700

    Remove anonymous struct, which is not standard. Note that this is a b… (#1191)

Src/Particle/AMReX_Particle.H

commit 660da8bb839c47a6aa530b9611006c1d3fb8c50f
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jul 24 14:42:28 2020 -0700

    fix a wrong clang flag (#1194)
    
    * fix a wrong clang flag
    
    * fix a warning

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tools/GNUMake/comps/llvm.mak

commit 572648806d3aeaac06406637b13802c975171b24
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jul 24 12:45:45 2020 -0700

    fix clang warnings (#1193)

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_StateDescriptor.cpp
Src/AmrCore/AMReX_FillPatchUtil_I.H
Src/AmrCore/AMReX_Interpolater.H
Src/Base/AMReX_Array.H
Src/Base/AMReX_Extension.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_GpuRange.H
Src/Base/AMReX_PODVector.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_Tuple.H
Src/Boundary/AMReX_Mask.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/Projections/AMReX_MacProjector.H
Src/LinearSolvers/Projections/AMReX_NodalProjector.H
Src/Particle/AMReX_BinIterator.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Tools/GNUMake/comps/llvm.mak

commit a4947448f775cbc027a9b0b6a639e70a74caae9f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 24 11:49:35 2020 -0700

    fix a parameter shadowing warning coming from VisMF::RemoveFiles with gcc (#1192)

Src/Base/AMReX_VisMF.cpp

commit 1fe53cb2852b162a9d7f37a2147e4e4e651d1c2f
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jul 24 11:07:38 2020 -0700

    fix more warnings and add CI for building 3d with configure (#1184)
    
    * fix more warnings and add CI for building 3d with configure
    
    * make ignore_unused constexpr and force inline
    
    * add AMREX_FALLTHROUGH
    
    * fix more warnings
    
    * enable xsdk in ci and test no_fortran
    
    * remove constexpr from ignore_unused for C++11
    
    * use Clang for 2d ci
    
    * disable mpi for the 2d ci with clang

.github/workflows/linux.yml
Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateDescriptor.cpp
Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX.H
Src/Base/AMReX_Array4.H
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_BlockMutex.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_Extension.H
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabConv.cpp
Src/Base/AMReX_FilCC_1D_C.H
Src/Base/AMReX_FilCC_2D_C.H
Src/Base/AMReX_Machine.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.H
Src/Base/AMReX_NFiles.cpp
Src/Base/AMReX_ParallelContext.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ParallelReduce.H
Src/Base/AMReX_ParmParse.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_Reduce.H
Src/Base/AMReX_Utility.H
Src/Base/AMReX_VisMF.cpp
Src/Base/AMReX_iMultiFab.cpp
Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_InterpBndryData_1D_K.H
Src/Boundary/AMReX_YAFluxRegister_1D_K.H
Src/EB/AMReX_EB2_2D_C.cpp
Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EB2_IF_AllRegular.H
Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_EB2_Level.cpp
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_2D_C.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_utils.cpp
Src/EB/AMReX_algoim.cpp
Src/EB/AMReX_distFcnElement.cpp
Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp
Src/F_Interfaces/Base/AMReX_FPhysBC.cpp
Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp
Src/F_Interfaces/Base/AMReX_init_fi.cpp
Src/F_Interfaces/Base/AMReX_parallel_mod.F90
Src/F_Interfaces/Octree/AMReX_octree_fi.cpp
Src/F_Interfaces/Octree/AMReX_octree_mod.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/Projections/AMReX_MacProjector.cpp
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleIO.H

commit 5dbcd14861f7656df4e2b2d5a588a00b7ad5c8ef
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 24 11:03:38 2020 -0700

    rewrite these loops in a way that silences a gcc warning about potential null deferences (#1190)

Src/Particle/AMReX_ParticleTile.H

commit fb413521ab2ebd9fa7614c1434a4c913a3516b06
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 24 09:38:49 2020 -0700

    Make aggregation type and buffer static member data of ParticleContainer. This silences a warning about unused variables. (#1189)

Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 2acea22a9390f3a691d7c2b721aa0b03c5f44129
Author: asalmgren <asalmgren@lbl.gov>
Date:   Fri Jul 24 09:38:04 2020 -0700

    D_DECL --> AMREX_D_DECL (#1188)

Src/AmrCore/AMReX_ErrorList.cpp

commit 0c180badf2333e18101fefbe900794fb24964e51
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri Jul 24 09:32:02 2020 -0700

    CI: Clang 6 C++17 SP NOMPI (#1181)
    
    Add a Clang build to CI that also covers single precision (SP).

.github/workflows/dependencies/dependencies_clang6.sh
.github/workflows/linux.yml

commit 92418c3a0256c66a365a6ee4f61510a4308348a9
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jul 23 22:23:50 2020 -0700

    Communication buffers (#1186)
    
    Use The_Cpu_Arena (BArena) instead of The_Pinned_Arena (CArena) for communication buffers to avoid
    the CArena fragmentation issue with the type of problems that allocate increasingly larger memory in
    a contiguous chunk during simulation.  CArena then cannot effective use previous allocation chunks
    because they are slightly smaller.  The fix is for CPU build only.  We still need to have a strategy
    for this for GPU build.

Src/Base/AMReX_FabArrayBase.cpp

commit 9f29a86876fb1c8ada03cb121a10869211ea9bba
Author: Mu-Hua Chien <b94209002@gmail.com>
Date:   Fri Jul 24 00:42:19 2020 -0400

    Fix a bug for Nodal semicoarsening (#1185)
    
    * set up starting point
    
    * Fix the problem of semicoarsening in yz direction and restore MyTest.cpp and input-rt
    
    * fix a bug in 2d
    
    * commit for debuggin failure in tridiagonal solve
    
    * fix a bug when doing semicoarsening with short x
    
    Co-authored-by: Kan Bok-Hua <mhc431@nyu.edu>

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp

commit 84276f6176ca64a8df617b33c9e82a5915d72396
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jul 23 20:28:15 2020 -0700

    Add some supports for nghost vector in Fortran multifab (#1099)
    
    * Support nghost vector in Fortran multifab
    
    * nghost vector version of amrex_multifab%copy

Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit e010fa881d837acd0824156323c1ff8aa44d67c5
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Jul 23 19:55:28 2020 -0700

    Wreorder: ErrorList (#1182)
    
    Fix:
    ```
    AMReX_ErrorList.H:434:47: warning: field 'm_ngrow' will be initialized after field 'm_info' [-Wreorder]
    ```

Src/AmrCore/AMReX_ErrorList.H

commit 370bccc3f3b148bde0ec9377697d5db31b4bb946
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Jul 23 15:21:08 2020 -0700

    Fix c++11 float narrowing (#1180)
    
    Fix a compile issue with DPC++ (SP) and AppleClang (DP):
    ```
    Src/AmrCore/AMReX_ErrorList.cpp:318:52: error: non-constant-expression cannot be narrowed from type 'double' to 'float' in initializer list [-Wc++11-narrowing]
    ```

Src/AmrCore/AMReX_ErrorList.cpp

commit 3b0aec5d0286b533835d1a245acd4afbc0a3067a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 23 14:06:11 2020 -0700

    reimplement SortParticlesByCell() in terms of SortParticlesByBin(), reducing code duplication. (#1172)

Src/Particle/AMReX_ParticleContainerI.H

commit e1b7a288e50553150610baeabca3d6fe12e29d58
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 23 14:05:10 2020 -0700

    Test for ghost and virtual particles (#1179)

Tests/Particles/GhostsAndVirtuals/GNUmakefile
Tests/Particles/GhostsAndVirtuals/Make.package
Tests/Particles/GhostsAndVirtuals/inputs
Tests/Particles/GhostsAndVirtuals/main.cpp

commit bba8d3fa1c0bba29289caeb314ec19d6188ab84e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jul 23 13:41:09 2020 -0700

    Switch to nvtxRangePush() and nvtxRangePop() in TinyProfiler (#1177)

Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp

commit 2abcbb8bd30239dc4278cf8bbd717e1af5ab13d1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 23 13:35:27 2020 -0700

    fix enable_if and typedef (#1178)

Src/Particle/AMReX_ParticleTile.H

commit f031488e07d10d409f7fbffe52f073de055eafc9
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jul 23 12:00:46 2020 -0700

    Fused GPU kernel launches (#1135)
    
    * First pass of fused launches
    
    * fuse 4D kernels too
    
    * fuse 1D kernels too
    
    * consolidate cudaMemcpy
    
    * Fuser singleton
    
    * add a test for fuse
    
    * add more assertion on not in omp parallel region
    
    * move the varidic version of launch_global back to GpuLaunch.H because it depends on other funcitons not in GpuLaunchGlobal.H
    
    * fix comment
    
    * fix a couple of bugs
    
    * do the not-in-omp-parallel assertion only if there are fused kernels to launch
    
    * add recommended threshold for kernel fusing
    
    * missing include guard

Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuFuse.H
Src/Base/AMReX_GpuFuse.cpp
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchGlobal.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tests/GPU/Fuse/GNUmakefile
Tests/GPU/Fuse/Make.package
Tests/GPU/Fuse/main.cpp

commit 685886a14096b5180dbb9f3e039f0d44272c8be2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jul 23 11:56:17 2020 -0700

    update DPC++ wishlist (#1175)

Docs/Notes/DPCPPWishlist.md

commit 411ea9b9467f9443b8d455a98deca43b1f7233ce
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jul 23 11:55:49 2020 -0700

    WARN_ALL (#1176)
    
    * WARN_ALL
    
    Add WARN_ALL option to GNUMake system to turn on more compiler warnings for gcc and clang.  The
    default is FALSE.  Fix a couple of bugs found by the warning and a number of warnings.
    
    * add WARN_ALL to documentation

Docs/sphinx_documentation/source/BuildingAMReX.rst
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_Interp_3D_C.H
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_EArena.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FBI.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_FabConv.cpp
Src/Base/AMReX_FilCC_C.cpp
Src/Base/AMReX_FilND_C.cpp
Src/Base/AMReX_GpuAsyncArray.cpp
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuElixir.cpp
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_MFCopyDescriptor.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_PODVector.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_Random.cpp
Src/Base/AMReX_Reduce.H
Src/Base/AMReX_TinyProfiler.cpp
Src/Base/AMReX_VisMF.cpp
Src/Boundary/AMReX_InterpBndryData.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleUtil.H
Tools/GNUMake/Make.defs
Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/llvm.mak

commit 38e3dfb14e30c6ed05a5335185fd746d0b23ba4b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jul 23 08:58:17 2020 -0700

    fix documentation format (#1174)

Docs/sphinx_documentation/source/Basics.rst

commit e1cffba53407ce934add479ea73145e0ee815024
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jul 22 20:49:28 2020 -0700

    Add alternative error tagging class (#1166)
    
    * Add alternative error tagging class
    
    * Address PR comments

Src/AmrCore/AMReX_ErrorList.H
Src/AmrCore/AMReX_ErrorList.cpp

commit 8e535d480ab2eb3f180aeb5078d6525ec24d8a21
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 22 13:41:35 2020 -0700

    Make ghost particles support soa data (#1053)

Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_ParIter.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_ParticleTransformation.H
Src/Particle/AMReX_Particles.H

commit 5fa8dc1d70d58c04c7170dfbe85a02c954a8c071
Author: jmsexton03 <jmsexton@lbl.gov>
Date:   Wed Jul 22 16:07:27 2020 -0400

    Fix HDF5 dataset id precision for single precision particles (#1173)
    
    Fixes segfault in amrex/Tests/HDF5Benchmark for
    USE_HDF5=TRUE USE_CUDA=TRUE USE_SINGLE_PRECISION_PARTICLES=TRUE

Src/Particle/AMReX_ParticleHDF5.H

commit 39d03b864f3bad3de32988eb5351000447075344
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jul 22 10:49:16 2020 -0700

    update CONTRIBUTING.md on how to fix git commits to have a clean history (#1164)
    
    * update CONTRIBUTING.md on how to fix git commits to have a clean history
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

CONTRIBUTING.md

commit 5fa55019e580a70aa8c1a8f3f9c908f2d24ed5c2
Author: Mu-Hua Chien <b94209002@gmail.com>
Date:   Wed Jul 22 12:24:24 2020 -0400

    Semicoarsening nodal (#1158)

Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tutorials/LinearSolvers/NodalPoisson/MyTest.H

commit ecb5c574f5eebd2c63080b0f561f44db9fd27581
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jul 22 08:06:01 2020 -0700

    Fix bug in #1159 (#1168)

Src/Base/AMReX_DistributionMapping.cpp

commit f87409ca66f212fa81315fcb77318f4a9131f63d
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Jul 22 00:58:15 2020 -0700

    CMake: implement ability to export build tree (#1149)
    
    * CMake: define C++ required flags as a property of target amrex
    
    * CMake: fix handling of typechecker.
    
    Just found out that:
      1) We did not install typechecker
      2) We do not need the typechecker path in the config file anymore
    
    * CMake: enable exporting of build-tree
    
    * CMake: linking against Flags_CXX_REQUIRED not needed anymore
    
    * CMake: MSVC preprocessor flags must the public
    
    * CMake: one more instance of Flags_CXX_REQUIRED to get rid of
    
    * CMake: clean-up and add some comments
    
    * Update Tools/CMake/AMReXInstallHelpers.cmake
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

Src/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReXFlagsTargets.cmake
Tools/CMake/AMReXInstallHelpers.cmake
Tools/CMake/AMReX_Config.cmake

commit cc05b20149176b6260a903d84e89e5c073f49759
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jul 21 19:43:13 2020 -0700

    add comments to hash version of RemoveDuplicates (#1162)

Src/Base/AMReX_Vector.H

commit a8db2cdf5be4e62e901b68913f1b192dde6fea8c
Author: Neil Carlson <nnc@lanl.gov>
Date:   Tue Jul 21 19:54:57 2020 -0600

    Reset amrex_geometry_module initialization state when finalizing (#1165)

Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Src/F_Interfaces/Base/AMReX_init_mod.F90

commit 3d6877fb2dbb81de5ae048f8995065b8ff0fc9e0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jul 21 15:56:05 2020 -0700

    Remove Long version of Gatherv and reimplement AllGatherBoxes (#1161)

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_ParallelDescriptor.H

commit a44b32f2d3aa92ddd33624361a60b85a2ae6f883
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jul 21 15:16:15 2020 -0700

    GatherLayoutDataToVector and DistributionMapping (#1159)
    
    Use int version of gatherv because the long version is not scalable.  Use GatherLayoutDataToVector
    in DistributionMapping because it is faster than ReduceSum.

Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_ParallelDescriptor.H

commit e2da3ce40ab41cae399207e21e80df22584303c3
Author: Zach Jibben <zjibben@gmail.com>
Date:   Mon Jul 20 14:50:41 2020 -0600

    Add interfaces for bottom solve Hypre configuration (#1150)
    
    * Add interfaces for bottom solve Hypre configuration
    
    * Remove preserve_hypre_solver flag
    
    This commit moves the Hypre and Petsc solver reset calls inside the
    needsUpdate if statement, removing the need for the flag.

Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 27ac069c768ae5b90bbcdd6394d3070edb9b9c13
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jul 20 13:02:35 2020 -0700

    Optimization of TagBoxArray::collate (#1156)
    
    Use a new way to remove duplicated tags.  Instead of removing duplicated from vector, we remove
    duplicates when tags are still stored in FabArray.  Because they are in FabArray with a BoxArray
    that has no overlapped valid cells, we can use ParallelAdd to remove duplicates due to the overlap
    of valid cells with ghost cells.
    
    Assertion in AmrCore on blocking factor to make sure that there are no overlapped valid cells in
    TagBoxArray after coarsening.
    
    Use int version of Gatherv.  The long version is not scalable.
    
    Broadcast pre-maxsized BoxList instead of tags.  In most cases, this should reduce the amount of
    data to be broadcasted.

Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp

commit 9a48873f0addaeeac3fff323c5feb3554bf3e260
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Jul 18 14:16:36 2020 -0700

    Combine two functions for periodically shifting particles into one and re-use (#1152)
    
    * combine periodic shifts into one and re-use
    
    * fix assertion

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleUtil.H

commit ba534dcd5f7b09285c95ed6bbcd18f49fe3922ea
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Jul 18 13:47:19 2020 -0700

    remove the sumParticleMass function, which has been deprecated in favor of the generic reduction functions that also work on the GPU (#1153)

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit d7de3d65aeea07683ecd698228925e505e2b8065
Author: jmsexton03 <jmsexton@lbl.gov>
Date:   Fri Jul 17 15:33:54 2020 -0400

    Change hdf5 make syntax (#1151)

Tools/GNUMake/packages/Make.hdf5

commit fedc596633f0f2c52f5b9de7349adf30873d0f04
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jul 16 19:55:26 2020 -0700

    add github action for 1D and 2D using configure (#1147)

.github/workflows/linux.yml

commit 62bee904a589df82e835da2a41a909955ff78db8
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jul 16 16:54:26 2020 -0700

    Error on implicit capture of this by extended lambda by default (#1148)

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/nvcc.mak

commit 824b23f6b26b787d86d6c67a5b55be1d00b574f5
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Jul 16 11:58:42 2020 -0700

    CMake: More NVCC Controls (#1095)
    
    * CMake: More NVCC Controls
    
    Add control for more debug and warning flags with NVCC.
    
    - [x] ptx debug infos: performance neutral and good
    - [x] compilation timer: useful for interactions with Nvidia engineers
    - [x] keep files: good for inspecting generated PTX code
    - [x] warnings: accidental capture of this (CUDA11+)
    - [x] device LTO: awesome new feature to try (CUDA11+)
    - [x] unknown flags: just forward to host, make build more robust (CUDA10.2+)
    
    * Docs: New CMake CUDA Options

Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/CMake/AMReX_SetupCUDA.cmake

commit 3efc8a9fe5aed2b82d5199dedf26baf772f40579
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jul 16 09:31:53 2020 -0700

    fix 1d compilation error in #1109 (#1144)

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 97ca27aa8a3b704309eaa92343ac8d99dedbad60
Author: Mu-Hua Chien <b94209002@gmail.com>
Date:   Wed Jul 15 19:15:18 2020 -0400

    update semicoarsening for agglomeration (#1109)
    
    Co-authored-by: Kan Bok-Hua <mhc431@nyu.edu>

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 878143a8cfb2e94fef4a769719c794e1c71314dd
Author: Mark Meredith <mwm126@gmail.com>
Date:   Wed Jul 15 18:50:35 2020 -0400

    Fix warnings (#1123)
    
    * nxm possibly uninitialized
    
    * psize possibly unused
    
    * m_runtime_r_ptrs.size() comparison of signed and unsigned types
    
    * Fix indentation
    
    Co-authored-by: Mark Meredith <mark.meredith@netl.doe.gov>

Src/EB/AMReX_EB2_3D_C.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleTile.H

commit de3fa02f2e8415458ba11e8f0f409b44dbab779a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 15 15:49:25 2020 -0700

    fix the redistribute test for single precision (#1141)

Tests/Particles/Redistribute/main.cpp

commit a3132f373219c14cc9637b3d9f28ff57f10d94a8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 15 15:40:42 2020 -0700

    fix clamping in enforcePeriodic (#1142)

Src/Particle/AMReX_ParticleUtil.H

commit e991cc91c4b5db6cd9d751f485f70c61c7626968
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 15 15:32:07 2020 -0700

    Fix indexing error in initial conditions for EM PIC Tutorial (#1143)

Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp

commit 4b182a4f608796beb37c07697599b7a0d6fc7925
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Jul 15 15:24:34 2020 -0700

    Fix line lenght issues in fixed-form Fortran sources (#1139)

Src/CMakeLists.txt
Src/Extern/ProfParser/AMReX_AVGDOWN_2D.F
Src/Extern/ProfParser/AMReX_AVGDOWN_3D.F
Src/Extern/amrdata/AMReX_FABUTIL_2D.F
Src/Extern/amrdata/AMReX_FABUTIL_3D.F
Tools/CMake/AMReXFlagsTargets.cmake

commit 7666b346859276821a0fddcc022cf014afea4e26
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Jul 15 13:51:42 2020 -0700

    CMake: re-factor parallel backends setup (#1103)
    
    * CMake: start reordering parallel backends setup
    
    * CMake: forgot to add the parallel backend setup file
    
    * CMake: finalize re-organization of parallel backends setup
    
    * CMake: forgot to commit a comment

Src/Base/CMakeLists.txt
Src/CMakeLists.txt
Src/F_Interfaces/CMakeLists.txt
Tools/CMake/AMReXParallelBackends.cmake
Tools/CMake/AMReX_Config.cmake

commit 6f2e60118d757a374b8a8e93da195cfe244ee4cc
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Jul 15 13:02:49 2020 -0700

    CMake: fix missing PETSc setup in Config file (#1134)

Tools/CMake/AMReXConfig.cmake.in

commit bb17d53ada8c76203d8aedc90e3742d63a69b659
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Jul 15 11:02:06 2020 -0700

    work with ax3l: fail when fortran c interface could not be found -- and fail (#1140)

Tools/CMake/AMReX_Defines.cmake

commit 4bd7976676539d015ef1aeb6a82f45ee677fd5dd
Author: mic84 <mrosso@lbl.gov>
Date:   Tue Jul 14 15:14:06 2020 -0700

    Add missing AMREX_D_DECL (#1138)

Src/Extern/ProfParser/AMReX_CommProfStats.cpp

commit d307624f8451a18da755a6cb1b5a3c31a42cdd48
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Mon Jul 13 19:16:17 2020 -0700

    FORTLINK: Guess if Unknown (#1126)
    
    * FORTLINK: Guess of Unknown
    
    Guess the FORTLINK API convention is `UNDERSCORE` for unknown values,
    unless it's the classic (non-clang) IBM Fortran compiler, where it's
    `LOWERCASE`.
    
    * add edge case where FORTLINK couldn't be determined by CMake
    
    Co-authored-by: Johannes Blaschke <jpblaschke@lbl.gov>

Tools/CMake/AMReX_Defines.cmake

commit a8ad3ad4dab830e5e425df064a8c2ca59d50ca74
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jul 10 13:14:02 2020 -0700

    remove ifdef AMREX_USE_GPU from nodal GpuBndryFunc so that it works for CPU build (#1133)

Src/Base/AMReX_PhysBCFunct.H
Tutorials/GPU/CNS/Source/CNS_bcfill.cpp

commit cbbe896e9ab20375c8f1cc9b93f663d329fda3fb
Author: mic84 <mrosso@lbl.gov>
Date:   Thu Jul 9 17:22:59 2020 -0700

    CMake: allow an application to use a different compiler than the one used to build AMReX (#1130)
    
    * CMake: an application to use a different compiler than the one used to build AMReX
    
    * CMake/mkconfig.py: more info in error message
    
    * mkconfig.py: change error message
    
    * Update mkconfig.py

Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/CMake/AMReXInstallHelpers.cmake
Tools/CMake/AMReX_Config.H.in
Tools/CMake/AMReX_Options.cmake
Tools/libamrex/mkconfig.py

commit 2be81a2ff2571fbed90a81741bb01c45748539b5
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jul 9 15:26:39 2020 -0700

    BndryFunc for nodal data (#1116)

Src/Base/AMReX_FilND_C.H
Src/Base/AMReX_FilND_C.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 1fd999f073b2a052732dc9bf4014895785e5b3c5
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Jul 9 13:57:34 2020 -0700

    AppleClang, MSVC: Avoid Malformed Config.H (#1127)
    
    * AppleClang, MSVC: Avoid Malformed Config.H
    
    Identify AppleClang as LLVM for AMReX compiler defines.
    Also add a fallback to avoid malforming the config header file on
    new/unknown/experimental compilers.
    
    * Update Tools/CMake/AMReXInstallHelpers.cmake
    
    Co-authored-by: mic84 <mrosso@lbl.gov>

Tools/CMake/AMReXInstallHelpers.cmake

commit 03bfa214aa5fe0ea0f31968f935f8e128fd703ea
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Jul 9 13:08:46 2020 -0700

    Update path for tutorials that were moved (#1128)

Tutorials/FortranInterface/Advection_F/Exec/Make.Adv
Tutorials/FortranInterface/Advection_octree_F/Exec/Make.Adv
Tutorials/FortranInterface/Advection_octree_F2/Exec/Make.Adv

commit c2a57a21bee0e80b16db46babbd3c723c2d2efa7
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jul 9 09:32:50 2020 -0700

    Retain old timestep data during post-timestep regrid (#1122)

Src/Amr/AMReX_Amr.cpp

commit 0d45d8c407236d5e542b6a57e348def385f488a8
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jul 9 09:04:56 2020 -0700

    FaceLinear Interpolater for face data (#1118)
    
    It's linear in the nodal direction and constant in others.  This preserves the divergence, but it's only first-order.

Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_Interpolater.cpp

commit fd4e0d1078a489fe9f07f0d4aa9de77f1680ed2c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 8 21:23:02 2020 -0700

    revert 1073, which introduces a subtle bug (#1121)

Src/Particle/AMReX_ParticleContainerI.H

commit d30a61ffbd5e0d0171242c0827ca2470c9a54d40
Author: asalmgren <asalmgren@lbl.gov>
Date:   Wed Jul 8 19:10:27 2020 -0700

    Move several tutorials from Tutorials/Amr to Tutorials/FortranInterface (#1120)

Tutorials/FortranInterface/Advection_F/CMakeLists.txt
Tutorials/FortranInterface/Advection_F/Exec/Make.Adv
Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/GNUmakefile
Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/Make.package
Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/Prob_2d.f90
Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/Prob_3d.f90
Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/face_velocity_2d.F90
Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/face_velocity_3d.F90
Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/inputs
Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/inputs.physbc
Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/inputs.rt
Tutorials/FortranInterface/Advection_F/README
Tutorials/FortranInterface/Advection_F/Source/Make.package
Tutorials/FortranInterface/Advection_F/Source/Src_2d/Make.package
Tutorials/FortranInterface/Advection_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/FortranInterface/Advection_F/Source/Src_2d/compute_flux_2d.f90
Tutorials/FortranInterface/Advection_F/Source/Src_2d/slope_2d.f90
Tutorials/FortranInterface/Advection_F/Source/Src_3d/Adv_3d.f90
Tutorials/FortranInterface/Advection_F/Source/Src_3d/Make.package
Tutorials/FortranInterface/Advection_F/Source/Src_3d/compute_flux_3d.f90
Tutorials/FortranInterface/Advection_F/Source/Src_3d/slope_3d.f90
Tutorials/FortranInterface/Advection_F/Source/amr_data_mod.F90
Tutorials/FortranInterface/Advection_F/Source/averagedown_mod.F90
Tutorials/FortranInterface/Advection_F/Source/bc_mod.F90
Tutorials/FortranInterface/Advection_F/Source/compute_dt_mod.F90
Tutorials/FortranInterface/Advection_F/Source/evolve_mod.F90
Tutorials/FortranInterface/Advection_F/Source/fillpatch_mod.F90
Tutorials/FortranInterface/Advection_F/Source/fmain.F90
Tutorials/FortranInterface/Advection_F/Source/initdata.F90
Tutorials/FortranInterface/Advection_F/Source/my_amr_mod.F90
Tutorials/FortranInterface/Advection_F/Source/plotfile_mod.F90
Tutorials/FortranInterface/Advection_F/Source/tagging_mod.F90
Tutorials/FortranInterface/Advection_octree_F/CMakeLists.txt
Tutorials/FortranInterface/Advection_octree_F/Exec/Make.Adv
Tutorials/FortranInterface/Advection_octree_F/Exec/SingleVortex/GNUmakefile
Tutorials/FortranInterface/Advection_octree_F/Exec/SingleVortex/Make.package
Tutorials/FortranInterface/Advection_octree_F/Exec/SingleVortex/Prob.f90
Tutorials/FortranInterface/Advection_octree_F/Exec/SingleVortex/face_velocity_2d.F90
Tutorials/FortranInterface/Advection_octree_F/Exec/SingleVortex/inputs
Tutorials/FortranInterface/Advection_octree_F/Exec/SingleVortex/inputs.rt
Tutorials/FortranInterface/Advection_octree_F/README
Tutorials/FortranInterface/Advection_octree_F/Source/Make.package
Tutorials/FortranInterface/Advection_octree_F/Source/Src_2d/Make.package
Tutorials/FortranInterface/Advection_octree_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/FortranInterface/Advection_octree_F/Source/Src_2d/compute_flux_2d.f90
Tutorials/FortranInterface/Advection_octree_F/Source/Src_2d/slope_2d.f90
Tutorials/FortranInterface/Advection_octree_F/Source/amr_data_mod.F90
Tutorials/FortranInterface/Advection_octree_F/Source/averagedown_mod.F90
Tutorials/FortranInterface/Advection_octree_F/Source/bc_mod.F90
Tutorials/FortranInterface/Advection_octree_F/Source/compute_dt_mod.F90
Tutorials/FortranInterface/Advection_octree_F/Source/evolve_mod.F90
Tutorials/FortranInterface/Advection_octree_F/Source/fillpatch_mod.F90
Tutorials/FortranInterface/Advection_octree_F/Source/fmain.F90
Tutorials/FortranInterface/Advection_octree_F/Source/initdata.F90
Tutorials/FortranInterface/Advection_octree_F/Source/my_amr_mod.F90
Tutorials/FortranInterface/Advection_octree_F/Source/plotfile_mod.F90
Tutorials/FortranInterface/Advection_octree_F/Source/tagging_mod.F90
Tutorials/FortranInterface/Advection_octree_F2/Exec/Make.Adv
Tutorials/FortranInterface/Advection_octree_F2/Exec/SingleVortex/GNUmakefile
Tutorials/FortranInterface/Advection_octree_F2/Exec/SingleVortex/Make.package
Tutorials/FortranInterface/Advection_octree_F2/Exec/SingleVortex/Prob.f90
Tutorials/FortranInterface/Advection_octree_F2/Exec/SingleVortex/face_velocity_2d.F90
Tutorials/FortranInterface/Advection_octree_F2/Exec/SingleVortex/inputs
Tutorials/FortranInterface/Advection_octree_F2/README
Tutorials/FortranInterface/Advection_octree_F2/Source/Make.package
Tutorials/FortranInterface/Advection_octree_F2/Source/Src_2d/Make.package
Tutorials/FortranInterface/Advection_octree_F2/Source/Src_2d/advect_2d_mod.F90
Tutorials/FortranInterface/Advection_octree_F2/Source/Src_2d/compute_flux_2d.f90
Tutorials/FortranInterface/Advection_octree_F2/Source/Src_2d/slope_2d.f90
Tutorials/FortranInterface/Advection_octree_F2/Source/amr_data_mod.F90
Tutorials/FortranInterface/Advection_octree_F2/Source/averagedown_mod.F90
Tutorials/FortranInterface/Advection_octree_F2/Source/bc_mod.F90
Tutorials/FortranInterface/Advection_octree_F2/Source/compute_dt_mod.F90
Tutorials/FortranInterface/Advection_octree_F2/Source/evolve_mod.F90
Tutorials/FortranInterface/Advection_octree_F2/Source/fillpatch_mod.F90
Tutorials/FortranInterface/Advection_octree_F2/Source/fmain.F90
Tutorials/FortranInterface/Advection_octree_F2/Source/initdata.F90
Tutorials/FortranInterface/Advection_octree_F2/Source/my_amr_mod.F90
Tutorials/FortranInterface/Advection_octree_F2/Source/plotfile_mod.F90
Tutorials/FortranInterface/Advection_octree_F2/Source/tagging_mod.F90

commit c4c271bc5468e9b0c0c49b6b05f07682e0dda312
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jul 8 17:25:11 2020 -0700

    fix BCRec vector in Fortran fillpatch thanks to @tpg2114. (#1117)

Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp

commit 5d82195e36511970b7a957cfafe9fb20d7576609
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 8 12:04:51 2020 -0700

    remove another unused variable from the particle io routines (#1115)

Src/Particle/AMReX_WriteBinaryParticleData.H

commit 8ce63fbe9ff71287507d396dd38a85523aea8261
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 8 10:09:36 2020 -0700

    remove unused variable (#1114)

Src/Particle/AMReX_WriteBinaryParticleData.H

commit 3af57db43e1c68a072903bd7068fab1e195978fc
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jul 7 23:33:43 2020 -0700

    add AMREX_NO_INLINE attribute (#1111)

Src/Base/AMReX_Extension.H

commit 201f6e86fc95b2a7dccd328a59181544ed52dcad
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Tue Jul 7 22:58:07 2020 -0700

    Tutorials: Build System Race Condition (#1112)
    
    Fix a naming collision in generated Fortran modules: with enough
    build parallelism (N>1), a race condition could lead to sporadically
    failing builds.

Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt
Tutorials/SENSEI/Advection_AmrLevel/CMakeLists.txt

commit c42df3e4ce635aec781dfb1a6a6a8bfcc188203d
Author: mic84 <mrosso@lbl.gov>
Date:   Tue Jul 7 17:05:22 2020 -0700

    CMake: get rid of soon-to-be deprecated CUDA Fortran defines (#1110)

Tools/CMake/AMReX_Defines.cmake

commit de150caec585325aa540e95c36cfc01c6f7c48dc
Author: asalmgren <asalmgren@lbl.gov>
Date:   Tue Jul 7 11:05:21 2020 -0700

    Mlmg hypre fix (#1105)
    
    * When the operator is singular and we are solving with hypre, subtract
    off the average value of the solution -- hypre seems to want to add
    a very large constant to the solution for singular problems ...

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit e354f1d2f9c2255ba5c332c528498b610cc09980
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jul 6 22:12:53 2020 -0700

    update DPC++ wishlist (#1106)

Docs/Notes/DPCPPWishlist.md

commit 6564cfa7c107e08bd8eb043eac71869dba6b38a9
Author: mic84 <mrosso@lbl.gov>
Date:   Mon Jul 6 15:03:52 2020 -0700

    CMake: HYPRE and PETSc support don't need Fortran anymore (#1102)

Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake

commit a5fe6eaee216cf42758612b04528d6fcdbec1afe
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Mon Jul 6 15:00:20 2020 -0700

    CMake: Fix CUDA Host Check (#1081)
    
    The check did only write a regular message due to a typo of the
    message type.
    
    Then checking the test, I realized it is not save:
    - false negatives are raised if e.g. CXX is set to g++ while
      CUDAHOSTCXX defaults to c++
    - checking only env variables is not sufficient to validate user
      intent: setting explicitly off compilers with -DCMAKE_...
      variables slips through
    
    The only save check we can implement is checking compiler name
    and ID, but that one is blocked by a missing upstream feature:
      https://gitlab.kitware.com/cmake/cmake/-/issues/20901
    
    All in all: fallback now to (flawed) env-logic but only throw a
    warning.

Tools/CMake/AMReX_SetupCUDA.cmake

commit e02489e5ed8044210a449550c96b7b838bc08d1f
Author: mic84 <mrosso@lbl.gov>
Date:   Mon Jul 6 13:39:24 2020 -0700

    CMake: forgot to print option ENABLE_MPI_THREAD_MULTIPLE (#1101)

Tools/CMake/AMReX_Options.cmake

commit 579a0c4418e0025b5e781f4b209c9f2b0bd336b0
Author: OscarAntepara <52221614+OscarAntepara@users.noreply.github.com>
Date:   Mon Jul 6 13:07:48 2020 -0700

    Porting fortran files to cpp in Src/Extern/HYPRE (#1049)

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_Habec_2D_K.H
Src/Extern/HYPRE/AMReX_Habec_3D_K.H
Src/Extern/HYPRE/AMReX_Habec_K.H
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H
Src/Extern/HYPRE/AMReX_HypreNodeLap.H
Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp
Src/Extern/HYPRE/AMReX_Hypre_fort_mod.F90
Src/Extern/HYPRE/CMakeLists.txt
Src/Extern/HYPRE/Make.package
Src/Extern/PETSc/AMReX_PETSc.H
Src/Extern/PETSc/AMReX_PETSc.cpp
Src/Extern/PETSc/AMReX_PETSc_fort_mod.F90
Src/Extern/PETSc/CMakeLists.txt
Src/Extern/PETSc/Make.package

commit cc1f9d44fccd3e1dcdb921e24f52add3400a026e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 6 13:06:18 2020 -0700

    Document GPUS_PER_SOCKET and GPUS_PER_NODE (#1097)
    
    * Document GPUS_PER_SOCKET and GPUS_PER_NODE
    
    * Update Docs/sphinx_documentation/source/GPU.rst
    
    Co-authored-by: WeiqunZhang <WeiqunZhang@lbl.gov>

Docs/sphinx_documentation/source/GPU.rst

commit 454e55a94cb9bc85323a0f7497f9659b80ead1ed
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jul 6 13:05:46 2020 -0700

    Clarify how load is measured in DistributionMapping generation. (#1100)

Docs/sphinx_documentation/source/LoadBalancing.rst

commit 6175b18620ede1f7a735306b3ef22133d273e4cd
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jul 3 23:49:39 2020 -0700

    For nvcc >= 10.2, tell it to forward unknowns to host compiler, and we… (#1094)
    
    * For nvcc >= 10.2, tell it to forward unknowns to host compiler, and we no longer need to sanitize options for nvcc.
    
    * fix -pthread for using cuda and pgfortran

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/nvcc.mak
Tools/GNUMake/comps/pgi.mak

commit 53bdc7c1d9109ba880874ea7539a5cbcc96b4935
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 2 21:43:02 2020 -0700

    Add copy filter (#1089)
    
    * reimplement NumberOfParticlesInGrid
    
    * some works towards filter for add and copy
    
    * add option to filter particles when copying and adding them to the container
    
    * add trailing return type

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleTransformation.H
Src/Particle/AMReX_Particles.H
Tests/Particles/ParticleTransformations/main.cpp

commit 115bdf23eed3499228508c696488126fb73fc047
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Jul 2 21:41:30 2020 -0700

    Nodal overset fix (#1091)
    
    * For nodal solves now -- test on whether we have an overset (masked) region with Dirichlet bc's -- and if so, don't set is_singular to true

Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 9808be202fa3fddd724aa26b2309c3626be50e13
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Jul 2 21:37:04 2020 -0700

    Cc overset fix (#1090)
    
    * When we have an interior overset (masked) region with Dirichlet bc's, we don't set
    is_singular to true even if the domain bc's are all Neumann/periodic

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp

commit 33fecca07f1e8533eed7fea6daa3e3b99820041a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jul 2 19:58:29 2020 -0700

    fix rereflux at domain boundary: ghost cells outside non-periodic domain should not participate rereflux (#1088)

Src/EB/AMReX_EBFluxRegister.cpp

commit 37a7986b8ca114a183ec4d0ac05367a69f9c6cbc
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 2 17:05:41 2020 -0700

    Add back the levelDirectoriesCreated routine, which is used by Nyx (#1087)
    
    * add back the levelDirectoriesCreated routine, which is used by Nyx
    
    * missed async version

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleHDF5.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_WriteBinaryParticleData.H

commit 78ceea62b6dfff644a335ae84b731b14693ea0be
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Jul 2 16:43:18 2020 -0600

    Fixed error in grownnodaltilebox (#1086)

Src/Base/AMReX_MFIter.cpp

commit 0e09a85064b04df316db9633ff3e95a69ced59de
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 2 14:38:33 2020 -0700

    GCC 81 workaround for Async IO (#1085)
    
    * Workaround for GCC 8.1 in particle async IO
    
    * ifdef this to only happen in 8.1

Src/Particle/AMReX_WriteBinaryParticleData.H

commit a19fb05e6cb95d403e6609ffe4e1798ee6892635
Author: Mu-Hua Chien <b94209002@gmail.com>
Date:   Thu Jul 2 14:04:59 2020 -0400

    Semicoarsening  (#1072)
    
    Co-authored-by: Kan Bok-Hua <mhc431@nyu.edu>
    Co-authored-by: Weiqun Zhang <weiqunzhang@lbl.gov>

Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp

commit 1390da59e7992653390b1cd10b22fdfc1ea1c77b
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Jul 2 10:58:03 2020 -0700

    Mlmg abort fix (#1083)
    
    * Abort the MLMG iterations if the residual becomes greater than 1e20 times the initial
    rhs (or initial resid)

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit e33845666a19c0c11904bdf2e2a72fa48e30b7d3
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Jul 2 09:43:01 2020 -0700

    Nodal hypre fix  (#1082)
    
    * Allow 2d nodal solver to use hypre at mglev > 0

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 600d31dd401b05326e7449d9b217d2d5e9712b4d
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Jul 2 08:44:29 2020 -0700

    Mac projector fix (#1080)
    
    1) Allow MAC projector to take overset mask
    2) have MacProjector's setVerbose not just reset local variable but also reset LinOp's verbosity

Src/LinearSolvers/Projections/AMReX_MacProjector.H
Src/LinearSolvers/Projections/AMReX_MacProjector.cpp

commit 0f1dfb3e12505a6912e7f7838a9e8b0ea0bedb8a
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Jul 1 18:39:35 2020 -0700

    CMake: add support for MPI multiple threads (#1079)

Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Config.H.in
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake

commit 9d9d06a91ce3bb7d7b2411a63f1d5cd5ce54f477
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jul 1 15:12:53 2020 -0700

    class BackgroundThread and use it for AsyncOut (#1078)
    
    * add BackgroundThread class
    
    * use BackgroundThread in AsyncOut
    
    * fix for Windows

Src/Base/AMReX_AsyncOut.H
Src/Base/AMReX_AsyncOut.cpp
Src/Base/AMReX_BackgroundThread.H
Src/Base/AMReX_BackgroundThread.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit a5ba208b4a2c5aec85551ef1fd40e08263b0b7ce
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 1 14:05:44 2020 -0700

    reimplement NumberOfParticlesInGrid (#1077)

Src/Particle/AMReX_ParticleContainerI.H

commit 12190b20114393254b689e7456857e734a7b566a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 1 11:06:01 2020 -0700

    reimplement NumParticlesAtLevel (#1073)
    
    * reimplement NumParticlesAtLevel
    
    * I guess this needs to be host / device

Src/Particle/AMReX_ParticleContainerI.H

commit 443fad731bd28291c3d03b58cb521a339b40852b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 1 11:01:31 2020 -0700

    Async IO for Particles (#1058)

Src/Base/AMReX_GpuAllocators.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleHDF5.H
Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_ParticleReduce.H
Src/Particle/AMReX_ParticleTransformation.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_WriteBinaryParticleData.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package
Tests/Particles/AsyncIO/GNUmakefile
Tests/Particles/AsyncIO/Make.package
Tests/Particles/AsyncIO/inputs
Tests/Particles/AsyncIO/main.cpp

commit 2e188a7500bc84572d91410b92bbe9c1a1b6c7e5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 1 10:34:22 2020 -0700

    Restore nl tutorial (#1075)
    
    * add back in this tutorial
    
    * update for levels
    
    * use parallelfor instead of the macro for some reason
    
    * move this tutorial to Particles

Src/Particle/AMReX_DenseBins.H
Tutorials/Particles/NeighborList/CMakeLists.txt
Tutorials/Particles/NeighborList/CheckPair.H
Tutorials/Particles/NeighborList/Constants.H
Tutorials/Particles/NeighborList/GNUmakefile
Tutorials/Particles/NeighborList/MDParticleContainer.H
Tutorials/Particles/NeighborList/MDParticleContainer.cpp
Tutorials/Particles/NeighborList/Make.package
Tutorials/Particles/NeighborList/README.md
Tutorials/Particles/NeighborList/inputs
Tutorials/Particles/NeighborList/main.cpp
Tutorials/Particles/NeighborList/script.sh

commit ca12febf19571d51a4cb7f164f25ed2a17f194ca
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jul 1 09:18:49 2020 -0700

    update CHANGES (#1076)

CHANGES

commit a2f432016158000b797d4a6b7f5c72879be505f1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jun 30 15:54:43 2020 -0700

    bugs in documenation pointed out by Mark Sussman (#1074)

Docs/sphinx_documentation/source/Particle.rst

commit 6558075e444749af7021ecda9abe7c1c25cc2e46
Author: OscarAntepara <52221614+OscarAntepara@users.noreply.github.com>
Date:   Tue Jun 30 11:12:41 2020 -0700

    Updating external solvers doc (#1068)
    
    * Updating external solvers doc
    
    * Fixing couple of lines in the doc

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 8117ed5e33f35b77de2b96396709c581ed59c1dc
Author: asalmgren <asalmgren@lbl.gov>
Date:   Mon Jun 29 16:57:49 2020 -0700

    Nodal hypre fix (#1069)

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit d93db0a9500dda2d1964abac5e0f1d8a29f0d59c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Jun 27 13:42:20 2020 -0700

    Manage memory (#1066)
    
    * add runtime parameter to not use managed memory for The_Arena
    
    * udpate documentation

Docs/sphinx_documentation/source/GPU.rst
Src/Base/AMReX_Arena.cpp

commit ef8ac4a78d4ee45b50ffc7dcc7731163d8887cb3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 27 13:41:55 2020 -0700

    Set backtrace threadprivate exception for PGI (#1067)

Src/Base/AMReX_BLBackTrace.H

commit 38572ef1ff1da8fe89482183f66bf5ba6b91813d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jun 26 17:36:25 2020 -0700

    Gpu stream thread safety (#1064)
    
    * Make gpu streams omp cpu thread safe.  Add OpenMP namespace for convenience.
    
    * use the new OpenMP:: functions
    
    * fix typo

Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_OpenMP.H
Src/Base/AMReX_Random.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 0f17d07b66aa1a80de8384f7b8b55316fef2f630
Author: kngott <30483578+kngott@users.noreply.github.com>
Date:   Fri Jun 26 13:23:47 2020 -0700

    GPU + OMP documentation adjustment. (#1065)

Docs/sphinx_documentation/source/GPU.rst

commit d1ce22a7c19948363adb1d3af97b2a57ce6b688e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jun 26 10:57:39 2020 -0700

    Add mpi reduction to fix a bug in overset linear solver (#1061)

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp

commit 116ff2a98f40ac1b742b7d2bc6d930b312f1dc62
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jun 26 10:02:38 2020 -0700

    MFIter reducer belongs only to AMREX_USE_GPU_PRAGMA (#1063)
    
    * MFIter reducer belongs only to AMREX_USE_GPU_PRAGMA
    
    * Simplify logic for operator++

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 385a0a5c8881deabeb469f38d1a8399f39be0731
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 25 15:02:09 2020 -0700

    Only add generic GNU flags to F compiler when appropriate (#1060)
    
    * Only add generic GNU flags to F compiler when appropriate
    
    * Remove redundant flags

Tools/GNUMake/comps/gnu.mak

commit 62619cc04a0795fdd8def9e94f3698b660e12a5b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jun 25 14:24:38 2020 -0700

    fix the version of tilebox that takes index type and grow cells (#1059)

Src/Base/AMReX_MFIter.cpp

commit 7e5c619d5ce21907e6f4dbcff17fef3c3a10d992
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jun 25 13:39:01 2020 -0700

    remove compile time BACKTRACE flag for simplicity (#1055)
    
    * remove compile time BACKTRACE flag for simplicity
    
    * update documentation on backtrace

.github/workflows/linux.yml
.github/workflows/macos.yml
Docs/Notes/Readme.backtrace
Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/BuildingAMReX.rst
Src/Base/AMReX_BLBackTrace.H
Src/Base/AMReX_BLBackTrace.cpp
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Config.H.in
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/GNUMake/Make.defs

commit a3924af54d4ae1825d1d3a5462e614c4f547726c
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Thu Jun 25 12:30:59 2020 -0700

    fix const issue with blueprint particle wrapping (#1057)

Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H

commit 26d8bf04ef87c3090d8e68e63fbcfe776c4b3bc1
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Thu Jun 25 10:37:45 2020 -0700

    blueprint: wrap amr nesting info for use in ascent (#1051)
    
    * this is the magic
    
    * populate  nestset
    
    * get the nesting correct
    
    * cleanup
    
    * remove more debugging statements
    
    * restore file
    
    * make a uniform data set
    
    * only add nestsets to more than 1 level
    
    * don't add nestset unless there are children or parents
    
    * change the order of find packages for conduit
    
    * have ENABLE_ASCENT trigger the conduit path
    
    Co-authored-by: Matt Larsen <larsen30@llnl.gov>

Src/CMakeLists.txt
Src/Extern/Conduit/AMReX_Conduit_Blueprint.H
Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp
Src/Extern/Conduit/CMakeLists.txt

commit 87c998acd4004796090ffad5285345ef3f725d79
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 24 17:15:02 2020 -0700

    fix Abs for FabArray (#1004)

Src/Base/AMReX_FabArrayUtility.H

commit dc2a02a30555986af0f6825b490d18a59e39bd8d
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Jun 24 17:04:08 2020 -0700

    CMake: print out only the enabled configuration options (#1052)

Tools/CMake/AMReX_Options.cmake

commit 32d2e44041cc0cc113ea66a3cce4526b114b0a4c
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Jun 24 15:57:16 2020 -0700

    CMake: add HDF5 support (#1048)

Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/CMake/AMReX_Config.H.in
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake

commit df3e65beac99290a0d9d1e0753b06e29f1002940
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 24 06:52:55 2020 -0700

    Fix Allocator comparison operator (#1050)
    
    * Remove allocator comparison operators, because they are too generic.
    
    * fix bug in PODVector
    
    * fix PloymorphicAllocator
    
    * fix cast in PODVector
    
    * fix return

Src/Base/AMReX_GpuAllocators.H
Src/Base/AMReX_PODVector.H

commit a8b4d5c95b74e6e87fa8ddf119b246f58f76e718
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jun 23 18:21:37 2020 -0700

    put USE_HDF5 in the GNUMake build system (#1047)

Tests/HDF5Benchmark/GNUmakefile
Tests/Slice/GNUmakefile
Tools/GNUMake/Make.defs
Tools/GNUMake/packages/Make.hdf5

commit 5ad4ae219e76730d009319b516de6a635f5d4164
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jun 23 08:34:52 2020 -0700

    fix bug in arguments passed to derFuncFab in one of the derive functions (#1045)

Src/Amr/AMReX_AmrLevel.cpp

commit 9b2172017f8aa6aea00bda090e7c93e7919ff6eb
Author: asalmgren <asalmgren@lbl.gov>
Date:   Sun Jun 21 16:19:47 2020 -0700

    Fix for hypre (#1044)
    
    * When using hypre, limit number of possible multigrid levels by how much the EB can be coarsened
    
    * Remove assertion that hypre can only be called when number of mg levels = 1 now that
    we restrict the building of levels based on coarsening of the EB.

Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit d6a28508104c2a22a6075c0e68c95d6efec35e37
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Jun 20 21:56:36 2020 -0700

    dpc++: unless explicitly specified, use default standard, which is c+… (#1043)
    
    * dpc++: unless explicitly specified, use default standard, which is c++ 17 in beta 7
    
    * CMake: enforce c++17 for dpc++ builds
    
    Co-authored-by: Michele Rosso <mrosso@lbl.gov>

Tools/CMake/AMReXSYCL.cmake
Tools/GNUMake/comps/dpcpp.mak

commit 82ec2dc54fd2a8bd21d79291d8bbf7ca91f8b8a8
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jun 19 17:50:58 2020 -0700

    fix 2d initializaton of linear solver tutorials (#1042)

Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H
Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90

commit 8be36ee57c5d4ab4ad810d0898dc79c2fa9f3d5b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jun 19 17:46:54 2020 -0700

    Initialize MPI_Wtime (#1041)

Src/Base/AMReX_ParallelDescriptor.cpp

commit 123970a7dd6a6a066121e3bacae365c47d0e1f73
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jun 19 13:38:09 2020 -0700

    Since DPC++ beta7, we can use link time flag -device-math-lib (#1040)

Tools/GNUMake/comps/dpcpp.mak

commit ca2138c3853e9232f1f8fa81afaa3edd17c00547
Author: mic84 <mrosso@lbl.gov>
Date:   Fri Jun 19 12:31:54 2020 -0700

    CMake: disable 'run' test when ENABLE_DPCPP=ON (#1039)

Tutorials/Basic/HeatEquation_EX1_CF/CMakeLists.txt

commit e16f97e878fefe544917caf5f0566048ad933d04
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jun 19 11:36:31 2020 -0700

    fix a tutorial for dpc++ (and cuda) (#1038)
    
    * fix a tutorial for dpc++ (and cuda)
    
    * Fix code block alignment
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp

commit cc65bd6f21d65e6d3183ebc8b875252b67b23a15
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri Jun 19 09:02:00 2020 -0700

    CI: DPC++ (#943)
    
    Prepares Intel DPC++ CI builds.

.github/workflows/cmake/dependencies_dpcpp.sh
.github/workflows/linux.yml

commit b3609f062ea6fb968be05ab7a2415d7e1e841a57
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Jun 18 20:44:24 2020 -0700

    CMake Summary: No Fortran (#1037)
    
    Disable Fortran summary details if Fortran is not used.

Tools/CMake/AMReX_Config.cmake

commit 4b4719ab7be2d5b7c8669df32e69b2226c66544c
Author: Houjun <houj.tang@gmail.com>
Date:   Thu Jun 18 15:53:05 2020 -0700

    Update HDF5 particle write and benchmark codes (#1035)
    
    * Update HDF5 related code for better write performance
    
    * Update Makefile for HDF5Benchmark
    
    * Update GNUmakefile
    
    * Update inputs
    
    * Use correct MPI datatype from AMReX
    
    Co-authored-by: Houjun Tang <htang4@lbl.gov>

Src/Base/AMReX_PlotFileUtil.cpp
Src/Particle/AMReX_ParticleHDF5.H
Tests/HDF5Benchmark/GNUmakefile
Tests/HDF5Benchmark/inputs
Tests/HDF5Benchmark/main.cpp

commit dfa064a3547e643f3dbc1a6317794dc943e85ee2
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Jun 18 14:55:44 2020 -0700

    Remove CCSE-specific info from Tools/GNUMake. (#1036)

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.ccse

commit 67a96b8b3f50633b9c8d00bdcf8bd40485d9f2f2
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Jun 17 21:16:15 2020 -0700

    Conduit: Work-Around Missing Const (#1032)
    
    This is a work-around for missing `const` qualifier overloads in
    Conduit's `node::set_external()`.

Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H

commit 1816b9cd1936ba737d438ee43edfd88ad01513d5
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Jun 17 13:45:43 2020 -0700

    CMake: create SYCL target to handle dpcpp builds (#1034)
    
    * CMake: get rid of dpc++ flags -fsycl-unnamed-lambda at link time
    
    * CMake: create SYCL target to handle dpcpp builds
    
    * CMake: treat libsycl-glibc.o as link object rather than an interface source
    
    * Add SYCL AOT Comment
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

Src/CMakeLists.txt
Tools/CMake/AMReXSYCL.cmake
Tools/CMake/AMReX_Config.H.in
Tools/CMake/AMReX_Config.cmake

commit 6e99321e9a49c5a1899c8ca7b8034fd4b4dd79e8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jun 17 10:20:12 2020 -0700

    Allow customization of the allocator used for ParticleTile (#1026)
    
    * add ability to specify allocator for a particle tile
    
    * fix ifdef
    
    * missed a few places where the default allocator was used

Src/Base/AMReX_GpuAllocators.H
Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_StructOfArrays.H

commit a9a2e82e3972e991df03bd71578827b1f2344f20
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 17 08:12:33 2020 -0700

    remove reference to master branch.  change terminology in StateDescriptor. (#1033)

CONTRIBUTING.md
Docs/sphinx_documentation/source/GettingStarted.rst
Docs/sphinx_documentation/source/index.rst
Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StateDescriptor.H
Src/Amr/AMReX_StateDescriptor.cpp

commit 8f94577b219700a5117d0fd67c6e8a198c79ebf3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jun 16 20:38:59 2020 -0700

    overset support for tensor solver (#1029)

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H
Tests/LinearSolvers/TensorOverset/GNUmakefile
Tests/LinearSolvers/TensorOverset/Make.package
Tests/LinearSolvers/TensorOverset/MyTest.H
Tests/LinearSolvers/TensorOverset/MyTest.cpp
Tests/LinearSolvers/TensorOverset/MyTest_K.H
Tests/LinearSolvers/TensorOverset/main.cpp

commit 5ed64778cdca5134248b3055db037a4f25a14a8d
Author: mic84 <mrosso@lbl.gov>
Date:   Tue Jun 16 17:42:10 2020 -0700

    CMake: get rid of AMReX_Machines.cmake (#1028)
    
    * CMake: remove AMReX_Machines.cmake
    
    * CMake: get system info via native CMake tools rather than uname

CMakeLists.txt
Tools/CMake/AMReXBuildInfo.cmake
Tools/CMake/AMReX_Machines.cmake
Tools/CMake/AMReX_ThirdPartyProfilers.cmake

commit 99a008f7c094d177946f9a297568076051d767cc
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Tue Jun 16 17:42:01 2020 -0700

    Conduit: Fix CMake Target Typo (#1031)
    
    Add a missing : in the `conduit::conduit` target.

Src/Extern/Conduit/CMakeLists.txt

commit 467dc1cc53d5745bb2382afff001057da4cb5976
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Jun 16 17:39:27 2020 -0700

    Tools: remove Make.cscs since Piz Daint is not used anymore (#1027)

Tools/GNUMake/sites/Make.cscs

commit 747e5cf57faaf93b416998596b01968e529a2fc4
Author: asalmgren <asalmgren@lbl.gov>
Date:   Tue Jun 16 10:54:19 2020 -0700

    Update how we write out EB data so it correctly handles problo !=0 (#1024)
    
    * Update how we write out EB data so it correctly handles the case when problo is not 0.
    
    * replace real(lo) and real(llc) by real(lo,amrex_real) and real(llc,amrex_real)

Src/EB/AMReX_WriteEBSurface.cpp
Src/EB/AMReX_WriteEB_F.H
Src/EB/AMReX_eb_to_pvd.F90

commit df7729dc498e81cb366ed874a3cd613bd2a5e567
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jun 15 18:13:23 2020 -0700

    Support for overset in cell-centered MLABecLaplacian (#1023)
    
    * cell-centered ABecLaplacian linear solver for overset
    
    * At coarse MG levels, we rescale the b coefficient at the overset boundary so that the overset points are essentially at fixed location.  This is important for convergence.
    
    * set overset region's rhs to zero inside the solver
    
    * clean up

Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/CellOverset/GNUmakefile
Tests/LinearSolvers/CellOverset/Make.package
Tests/LinearSolvers/CellOverset/MyTest.H
Tests/LinearSolvers/CellOverset/MyTest.cpp
Tests/LinearSolvers/CellOverset/main.cpp

commit bc6134dfdf464b40bef483c05c28644a1d540b2d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jun 15 17:27:54 2020 -0700

    Fix conduit for changes to particles (#1010)

Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H
Src/Particle/AMReX_ArrayOfStructs.H

commit 65d60c442e95498239f18d47fc64d0082124b774
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jun 12 17:58:27 2020 -0700

    add assertion on EB statck (#1020)

Src/EB/AMReX_EB2.H

commit c397ad30b72d7ce6af1045c4572984c297a729f8
Author: mic84 <mrosso@lbl.gov>
Date:   Fri Jun 12 17:11:50 2020 -0700

    CMake: add support for DPCPP (#1016)
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake

commit 6a5131cbbae227f6af07e0efc93bd95df0ac81c7
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jun 12 16:44:23 2020 -0700

    These files need to be included even when Fortran is off. (#1019)

Src/Base/CMakeLists.txt

commit 9a40723c7846191aac6288db996a20450b6d2b5a
Author: mic84 <mrosso@lbl.gov>
Date:   Fri Jun 12 14:50:33 2020 -0700

    CMake: set minimum C++ standard to 17 for Windows builds (#1017)
    
    * CMake: set minimum C++17 for Windows builds
    
    * CMake CI: no need to set C++ standard for windows CI

.github/workflows/windows.yml
Tools/CMake/AMReX_Config.cmake

commit 1d75ba05f084cd3c1d91dacefdfedc6c2e85ab7f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jun 12 08:15:06 2020 -0700

    fix typo introduced in #995 (#1013)

Src/Particle/AMReX_NeighborParticlesI.H

commit d59c1a8b8bdc58b435b9281072afc3ecf51c2a45
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri Jun 12 06:26:11 2020 -0700

    Single Precision: INVALID_TIME Value OoR (#1011)
    
    * SinglePrecision: INVALID_TIME Value OoR
    
    AppleClang 11.0.3 in single precision build errors with on WarpX:
    ```
    error: constexpr variable 'INVALID_TIME' must be initialized by a
           constant expression
    static constexpr Real INVALID_TIME = -1.0e200;
                          ^              ~~~~~~~~
    WarpX/build_sp/_deps/fetchedamrex-src/Src/Amr/AMReX_StateData.cpp:17:38:
      note: value -1.0E+200 is outside the range of representable values of
            type 'const amrex::Real' (aka 'const float')
    static constexpr Real INVALID_TIME = -1.0e200;
    ```
    
    This changes the numeric value of this constant to the minimum in the
    supported range of the underlying data type.
    
    * INVALID_TIME: Only change for Float

Src/Amr/AMReX_StateData.cpp

commit ba9be262a0fa5d493e8193f253a5b219244536bb
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Jun 11 21:46:47 2020 -0700

    CI: Verbose Make (#1012)
    
    Although we build with `-j2` to speed up CI on all available cores,
    this can improve understanding if things fail.

.github/workflows/linux.yml
.github/workflows/macos.yml
.github/workflows/windows.yml

commit 33a35a8ff4af38924c2c54fb53f8fdceab8f18e8
Author: mic84 <mrosso@lbl.gov>
Date:   Thu Jun 11 17:09:54 2020 -0700

    CMake: fix bug introduced in PR #996 (#1009)

Tools/CMake/AMReXFlagsTargets.cmake

commit c69e431ed9bfe71d13c2c00dd39ac9f75f420650
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jun 11 14:32:21 2020 -0700

    add -DNDEBUG for non-debug build (#1006)
    
    * add -DNDEBUG for non-debug build
    
    * Don't define NDEBUG if USE_ASSERTION is TRUE

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit d73c9d180b0e4e485473a121ddf0bda04103ab87
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jun 11 13:50:43 2020 -0700

    use launch function instead of macro so that we can have ifdef inside (#1008)

Src/Base/AMReX_Scan.H

commit 6cfdc9f634273953b5b6e9f51db2bfd2134d4431
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jun 11 11:51:46 2020 -0700

    use iso646 to provide alternative operator names for Windows (#1003)

Src/Base/AMReX.H
Src/Base/AMReX_Extension.H
Tools/CMake/AMReXFlagsTargets.cmake

commit cccc96a37de6098316069fb5ada5839d8e5526b4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jun 11 11:18:58 2020 -0700

    update comments on abs function (#1005)

Src/Base/AMReX_Math.H

commit 607d36634d331425f0f433913af601b4cba7433d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jun 11 11:03:56 2020 -0700

    reduce duplication in indexFromValue (#1002)

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.cpp

commit 2d4ad87b5f30f33768c91a307151a54c111a2cfe
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jun 11 08:55:46 2020 -0700

    Particle parallel context (#995)

Src/Base/AMReX_ParallelDescriptor.H
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleBufferMap.cpp
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleMPIUtil.cpp
Src/Particle/AMReX_ParticleUtil.H
Src/Particle/AMReX_ParticleUtil.cpp
Src/Particle/AMReX_TracerParticles.cpp
Tests/Particles/ParallelContext/GNUmakefile
Tests/Particles/ParallelContext/Make.package
Tests/Particles/ParallelContext/inputs.rt
Tests/Particles/ParallelContext/main.cpp

commit 2e15ac4b042b8154bb05733636824b3543a8266f
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 10 13:36:43 2020 -0700

    Remove this OutOfMemory that is never defined. (#999)

Src/Base/AMReX.H

commit 9550f73aa21a04c243d3617b1cc1ece0acc1955d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 10 13:35:55 2020 -0700

    fix unused variable warning (#1000)

Src/Base/AMReX_AsyncOut.cpp

commit 231990f61bcde4946d1dae23080496e5fa5f632e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 10 13:35:23 2020 -0700

    No need to make subcommunicator if neither agglomeration nor consolidation is done (#998)

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit fd03d74ea9df3b081e667bb9b82773dec5391666
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 10 13:17:10 2020 -0700

    fix nvcc version for Cuda 11 (#997)

Tools/GNUMake/comps/nvcc.mak

commit 3bee52740bf4201a870e5b418f13e0613851686f
Author: Robert Maynard <robert.maynard@kitware.com>
Date:   Wed Jun 10 16:07:24 2020 -0400

    CMake: improve MSVC+CUDA support (#996)
    
    The primary issue now is that nvcc doesn't seem to be parsing with
    /Za enabled, so alternate tokens are causing compile failures.

Tools/CMake/AMReXFlagsTargets.cmake
Tools/CMake/AMReX_SetupCUDA.cmake

commit 37224d307ab7baa32b6eea666a981a9758ab06f4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jun 10 10:29:44 2020 -0700

    Non const iterator neighbor list (#994)
    
    * build non-const iterator for neighbor lists
    
    * build non-const iterator for neighbor lists
    
    * implement non-const iterators for neighbor list
    
    * remove second access operator for Neighbors<ParticleType>::iterator
    
    * const
    
    Co-authored-by: Johannes Blaschke <jpblaschke@lbl.gov>

Src/Particle/AMReX_NeighborList.H
Tests/Particles/NeighborParticles/MDParticleContainer.cpp

commit 399917f45ac0502ebf2247dd2ac182e1705e33ca
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jun 9 07:34:29 2020 -0700

    Make PrintToFile() and AllPrintToFile() work with ParallelContext (#991)

Src/Base/AMReX_Print.H

commit 1eff033385765a49110b9cea681bdaa619e4e298
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jun 8 22:13:21 2020 -0700

    remove some testing code I checked in by mistake (#992)

Tests/Particles/Redistribute/main.cpp

commit db9e1d25230331869aed5abf0e4fb2b121718efe
Author: mic84 <mrosso@lbl.gov>
Date:   Mon Jun 8 22:11:12 2020 -0700

    CMake: improve MSVC support (#989)
    
    * CMake: do not force 64bit CUDA builds on Windows
    
    CUDA only supports 64bit builds on windows ( 32bit builds are deprecated ).
    Thus the option "--machine 64", AKA "-m64" is set by the msbuild configuration
    automatically.
    
    * CMake: new interface library Flags_CXX_REQUIRED
    
    * CMake: always use C++ required flags in the build
    
    * CMake: remove wrong definition of compile options for MSVC.
    
    The new Flags_CXX_REQUIRED will take care of MSVC correctly.
    
    * CMake: pass required C++ flags to CUDA compiler.
    
    * CMake: fix bug in setting CXX required flags for CUDA target
    
    * CMake: update required MSVC flags
    
    * CMake: add comment
    
    * CMake: modify MSVC flags to account for compiler version
    
    * CMake CI: force verbosity during MS build
    
    * Revert "CMake CI: force verbosity during MS build"
    
    This reverts commit 8f6148ab70df1dac9627a9e4aae32fa9daed57bc.
    
    * CMake: make sure C++ compiler version for GNU and MSVC > minimum.

CMakeLists.txt
Src/CMakeLists.txt
Tools/CMake/AMReXFlagsTargets.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_SetupCUDA.cmake
Tools/CMake/AMReX_Utils.cmake

commit 3a1915e324ffcd170473ae690b1411703b76b42b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 8 14:39:59 2020 -0700

    Compare single-level plotfiles; diff and norms; all nodalities (#983)
    
    * new utility to compare plotfiles and take norms.  goal is to work for any nodality
    
    * begin new functionality for ComparePlotfiles routine
    
    * ComparePlotfiles.cpp WIP
    
    * saving progress
    
    * periodicity fix
    
    * fix a bug in norm2 where there are overlaps
    
    * first draft of ComparePlotfiles, including PrintUsage
    
    * plotfile diff and norm utility
    
    * consolidated all cases into 1 loop
    
    * more comments
    
    * remove debugging statement
    
    * option to point to data directly, rather than plotfile base
    this is useful for warpx when using "plot_raw_fields"; where the nodal data is output to a non-standard directory
    
    * implement Weiqun's suggestions
    
    Co-authored-by: Weiqun Zhang <weiqunzhang@lbl.gov>

Tools/C_util/Convergence/ComparePlotfiles.cpp
Tools/C_util/Convergence/GNUmakefile

commit a2961b1e2b91ad2bc9801ac85a655cb5915e5a9a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jun 8 12:15:06 2020 -0700

    use __CUDACC_VER_MAJOR__ instead of AMREX_NVCC_MAJOR_VERSION, which is gone (#988)

Src/Base/AMReX_GpuDevice.cpp

commit 8eb5b5e6859f4e0a0ff9cec75811cf871ed1a2b0
Author: kngott <30483578+kngott@users.noreply.github.com>
Date:   Mon Jun 8 10:51:16 2020 -0700

    Modify HeatEquation dts to account for non-cubic cases. (#977)

Src/Base/AMReX_SPACE.H
Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX1_CF/Source/main.cpp
Tutorials/Basic/HeatEquation_EX1_F/Make.package
Tutorials/Basic/HeatEquation_EX1_F/fmain.F90
Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX2_CF/Source/main.cpp
Tutorials/Basic/HeatEquation_EX3_C/Source/main.cpp

commit 86a361c8856bdda455e3fe7d2c01b4d7ce35261a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jun 8 08:58:56 2020 -0700

    Fix a missing semicolon (#986)

Src/Base/AMReX_GpuLaunchFunctsG.H

commit 70afa5a814a16fdeba7b18f03115f6ece5b8b5a2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Jun 6 16:58:01 2020 -0700

    fix a bug in norm2 where there are overlaps (#982)

Src/Base/AMReX_MultiFab.cpp

commit f52f7beeb1c47b30ebd15830c1f3c25e3a025c89
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Jun 6 15:48:42 2020 -0700

    Make: use -M to generate dependencies (#980)
    
    * Make: use -M to generate dependencies
    
    * use > to save output because pgi does not support -o
    
    * remove redundant flag
    
    * comment out some cray flags that generate compile information we usually don't need
    
    * use -o for dpcpp because it does not put output of -M in stdout

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/cray.mak
Tools/GNUMake/comps/nvcc.mak

commit 6d76716ef6d108f2f66ae918e7d80976331cc4c5
Author: mic84 <mrosso@lbl.gov>
Date:   Sat Jun 6 09:40:50 2020 -0700

    Remove compiler version defines from compile definitions (#981)

Tools/CMake/AMReX_Config.H.in
Tools/CMake/AMReX_Config.cmake
Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/llvm-flang.mak
Tools/GNUMake/comps/llvm.mak
Tools/GNUMake/comps/nag.mak
Tools/GNUMake/comps/nvcc.mak

commit f889ad3b6081e188ead46a14927517e26f08df5a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 3 17:21:45 2020 -0700

    add a macro so that it's easy to reproduce the issue (#976)

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 1132127817d4b5edfd6130853a16f4df44452624
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 3 17:21:26 2020 -0700

    This earlier stopgap for EB tensor solver with DPC++ is no longer needed. (#974)

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit c69e4409ae3fad6f285ab173a23ea6c79acfb092
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 3 15:20:44 2020 -0700

    Option to add extra CPPFLAGS from command line (#975)

Tools/GNUMake/Make.defs

commit 1841a87f9531e3c6f29887e1f79ee2d521ff97c0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 3 14:01:52 2020 -0700

    fix DPC++ bug introduced in 8272ea8b84f3027f1d (#973)

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit befabe69319379658510d47896f4e79e27c28db0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 3 09:55:54 2020 -0700

    update documentation for Windows (#972)

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit d462130220d51d44ea406b7fd33ed246dd89acb3
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Jun 3 09:05:33 2020 -0700

    CI: Mainly Debug (#971)
    
    Enable debug builds for most CI builds. Easier to catch errors and
    enables more checks.

.github/workflows/linux.yml
.github/workflows/macos.yml
.github/workflows/windows.yml

commit a3a1e8fe5174dc84cc1f4e4e415fba085f7904aa
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jun 2 17:03:59 2020 -0700

    remove moveKick, which is not used any more (#970)

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 294066686c92f5a2d11687c188824c6fb8a5d808
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Tue Jun 2 12:52:13 2020 -0700

    CMake CUDA: Cleanups & CCache (#964)
    
    * CMake CUDA: Cleanups & CCache
    
    - gencode: use no-space syntax; this confuses CCache<4.0
      (all available releases today) and is complicating deduplication
      operations on lists
    - min CXX standard in CUDA: technically the right thing to set
      this as well for the CMake CUDA C++ language
    
    * Update AMReX_Config.cmake
    
    CUDA meta-features were introduced with CMake 3.17, see: [https://blog.kitware.com/cmake-3-17-0-rc3-is-ready-for-testing/](https://blog.kitware.com/cmake-3-17-0-rc3-is-ready-for-testing/).
    
    Co-authored-by: mic84 <mrosso@lbl.gov>

Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_SetupCUDA.cmake

commit d74a1c95a41438ea77c2e3c320b567607fb1e562
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jun 2 12:29:15 2020 -0700

    remove WriteCoarsenedAsciiFile method (#968)

Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_Particles.H

commit 3aaa8b67f6bf18b291e0136db57c659da719d9d8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jun 2 12:28:32 2020 -0700

    fix new bug I just introduced (#969)

Src/Particle/AMReX_ParticleInit.H

commit 0950e22ac4433f98642f43afa25d4508d43e03c0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jun 2 11:38:01 2020 -0700

    Remove directly accessing the m_idata and m_rdata structs internally (#963)

Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H
Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleHDF5.H
Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 33d534b2c021355f4eaaf643cba97b2a3588c84a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jun 2 09:29:14 2020 -0700

    make sure we enable particles in cmake CI (#966)

.github/workflows/linux.yml
.github/workflows/macos.yml

commit bfdf479f1092ca75677f8431e812efa58178fc79
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jun 2 09:21:50 2020 -0700

    ifdef out htod_memcpy (#967)

Src/EB/AMReX_EB2_IF_Polynomial.H

commit 98663ccab011d20a5f0ec54359f4a2d262b8eab2
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Tue Jun 2 06:35:34 2020 -0700

    ParticleIO: Update Arg Signature Usage (#965)
    
    Follow-up to new function signature.

Src/Particle/AMReX_ParticleIO.H

commit 8272ea8b84f3027f1d78746006c62f570f3cadb0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jun 1 22:41:55 2020 -0700

    Windows (#947)
    
    * If it's Windows, use C++17 for files system operations, and avoid posix functions.
    
    * Avoid gcc extension that allows embedded prepressor directive in function macro.
    
    * Get around some MSVC template argument deduction issues.
    
    * Rename amrex::USleep to amrex:Sleep and use C++ thread for sleep. The reason for renaming is it would be very confusing that usleep in unistd sleeps for given microseconds whereas amrex::USleep sleep for given seconds.
    
    * Windows CI
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

.github/workflows/windows.yml
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AsyncFillPatch.cpp
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_Array4.H
Src/Base/AMReX_BLBackTrace.H
Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Extension.H
Src/Base/AMReX_FPC.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_FileSystem.H
Src/Base/AMReX_FileSystem.cpp
Src/Base/AMReX_GpuAsyncArray.H
Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuMemory.H
Src/Base/AMReX_GpuRange.H
Src/Base/AMReX_MemProfiler.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_SPACE.H
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EB2_IF_Complement.H
Src/EB/AMReX_EB2_IF_Difference.H
Src/EB/AMReX_EB2_IF_Extrusion.H
Src/EB/AMReX_EB2_IF_Intersection.H
Src/EB/AMReX_EB2_IF_Lathe.H
Src/EB/AMReX_EB2_IF_Rotation.H
Src/EB/AMReX_EB2_IF_Scale.H
Src/EB/AMReX_EB2_IF_Translation.H
Src/EB/AMReX_EB2_IF_Union.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EB_utils.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/Particle/AMReX_ParticleIO.H
Tests/AsyncOut/multifab/main.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/MKDir/MKDir.cpp
Tools/AMRProfParser/TestCodes/AMRProfTest0.cpp
Tools/AMRProfParser/TestCodes/ProfWaitTest.cpp
Tools/CMake/AMReXFlagsTargets.cmake
Tools/CMake/AMReX_Config.cmake

commit 2d2dbf423b2977460f19aac2f108b72932c4d875
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jun 1 22:40:07 2020 -0700

    remove the RealDescriptor args, which aren't used anyway (#962)

Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_Particles.H

commit baaed44ccff92c696503e800c3cb913cc65737ce
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jun 1 15:33:30 2020 -0700

    handle more unused variables (#961)

Src/AmrCore/AMReX_Interpolater.H
Src/Base/AMReX_FilCC_3D_C.H
Src/Base/AMReX_PhysBCFunct.H

commit dfa5023c9237476a4fb770740959f5ce6ea53fb6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jun 1 15:03:37 2020 -0700

    only define these functions if AMREX_USE_GPU is true (#960)

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_PODVector.H

commit b6ea3e816af7a32709079ff695689d281506dc0a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jun 1 15:03:17 2020 -0700

    avoid embedded macro directive in macro function argument because it's not portable (#959)

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_GpuAsyncArray.H
Src/Base/AMReX_GpuAsyncArray.cpp
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuElixir.cpp
Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_Random.cpp
Src/Base/AMReX_Scan.H
Tests/GPU/Locking/main.cpp

commit 79d62bebd471442d8aa638f2ff38f28c26f6d4c7
Author: Shreyas Ananthan <shreyas@umd.edu>
Date:   Mon Jun 1 14:43:14 2020 -0600

    DistributionMapping::makeSFC - distribute to user-defined procs (#957)
    
    Extends the makeSFC method to take an additional argument where the user
    can override the number of processes a BoxArray is distributed to.

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit 6612258dcd4f4bfb1d1539539ed626ddc0a9eeff
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jun 1 13:42:00 2020 -0700

    remove unused variables from tutorials (#956)

Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/Basic/HeatEquation_EX1_CF/Source/advance.cpp
Tutorials/Basic/HeatEquation_EX2_CF/Source/advance.cpp
Tutorials/LinearSolvers/MultiComponent/main.cpp

commit 54ea99efa50b9765979ace6541ca5ab7ea685de2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jun 1 13:40:24 2020 -0700

    fix a few unused / uninitialized variable warnings (#955)

Src/Base/AMReX_FabArrayBase.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Src/F_Interfaces/Octree/AMReX_octree_fi.cpp

commit 3a9341800b675c09f793229d618d960c400ea916
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jun 1 13:38:46 2020 -0700

    add cuda test script from cuda to the repo (#954)

Tools/RegressionTesting/AMReX-cuda-tests.ini

commit 3e7366503edb5dcbabdf2b22d4c7417b22f52995
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jun 1 13:37:29 2020 -0700

    turn tiling off by default for gpu (#953)

Src/Base/AMReX_FabArrayBase.cpp

commit af68380aa4b23ce7f01223d696aafa82cfa5e06c
Author: mic84 <mrosso@lbl.gov>
Date:   Mon Jun 1 12:27:45 2020 -0700

    CMake: improve handling of options (#946)
    
    * CMake: move general setup operations out of AMReX_Options.cmake
    
    * CMake: better handling of option inter-dependencies via cmake_dependent_option
    
    * CMake: refactor AMReX_Options.cmake
    
    * Update Tools/CMake/AMReX_Options.cmake
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
    
    * Update CMakeLists.txt
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
    
    * Update Tools/CMake/AMReX_Options.cmake
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

CMakeLists.txt
Src/Extern/SUNDIALS4/CMakeLists.txt
Tools/CMake/AMReX_Options.cmake

commit 227bf82812793dc942fa8472974bcdd3d3e60ad3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jun 1 10:04:01 2020 -0700

    use explicit casts to silence compiler warnings (#952)

Src/Particle/AMReX_Particle_mod_K.H

commit b83904febeb29df3901f9f46e94ca3204944ccf6
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun May 31 22:04:16 2020 -0700

    set up DPC++ regression test suite (#951)

Tools/GNUMake/Make.defs
Tools/RegressionTesting/AMReX-dpcpp-tests.ini

commit e6a312fc09f534fbefaebf1d96e70165fc27cb49
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun May 31 17:55:05 2020 -0700

    update CHANGES (#950)

CHANGES

commit 1b30da66e7f7c9fe7b66905c9d6a9fb1e82fe574
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri May 29 15:38:43 2020 -0700

    C++20 Compatibility: GCC 10.1 (#949)

.github/workflows/dependencies/dependencies.sh
.github/workflows/dependencies/dependencies_gcc10.sh
.github/workflows/dependencies/dependencies_mac.sh
.github/workflows/linux.yml

commit 4e051cdebf11fb8b31a4162e16e5040383180c7f
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri May 29 14:06:16 2020 -0700

    GH Action CI: Restructure (#948)
    
    Restructure the CI dirs and workflow names: split by OS.
    Preparation for Windows.

.github/workflows/dependencies/dependencies.sh
.github/workflows/dependencies/dependencies_mac.sh
.github/workflows/dependencies/dependencies_nofortran.sh
.github/workflows/dependencies/dependencies_nvcc.sh
.github/workflows/linux.yml
.github/workflows/macos.yml

commit 5738a0a334d581473ea2986a8875e52da103496e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 27 09:38:55 2020 -0700

    remove const for compare_exchange_strong (#941)

Src/Base/AMReX_GpuAtomic.H

commit f96af7af7c11a1c29658464764f39fd2a69650af
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed May 27 07:09:05 2020 -0700

    Atomics: Constify Wrapper (#927)

Src/Base/AMReX_GpuAtomic.H

commit d4e2a30df8bb086b4583e991837c926083b1ba31
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue May 26 18:08:55 2020 -0700

    Unused warnings (#940)
    
    * silence unused variable warnings in Src/Base
    
    * silence unused variable warnings in Src/Particle
    
    * silence unused variable warnings in Src/LinearSolvers

Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_EArena.cpp
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_GpuUtility.cpp
Src/Base/AMReX_Machine.cpp
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/Projections/AMReX_MacProjector.cpp
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particle_mod_K.H

commit f25de11b41cedcdbc25010c00e5b89211d7a8645
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue May 26 12:58:28 2020 -0700

    add cstdlib header to AMReX_MATH.H (#939)

Src/Base/AMReX_Math.H

commit fadf58ef77be62e832b528e15e7c996af1791c55
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Tue May 26 11:38:45 2020 -0700

    CMAKE_INSTALL_PREFX: Only Toplevel (#936)
    
    Set a non-default CMAKE_INSTALL_PREFIX only if AMReX is the top-level
    CMake project. Otherwise, the default of a downstream project using
    AMReX as subproject will be placed in a quite confusing, temporary
    directory.

CMakeLists.txt

commit 38f9ee12c68022eca233c79f219361537eb93cbf
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 25 11:45:14 2020 -0700

    C order support for Array2D and Array3D (#934)

Src/Base/AMReX_Array.H

commit 6c877f0884d03d40e9b993cac5b39a591fbefaff
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 25 11:15:38 2020 -0700

    disable unqualified abs function with amrex namespace (#938)

Src/Base/AMReX.H
Src/Base/AMReX_Math.H

commit b055d9aa331f5498b21283235e5f208f69b022b9
Author: Burlen Loring <bloring@lbl.gov>
Date:   Mon May 25 09:54:16 2020 -0700

    updates for SENSEI 3.2 release (#929)
    
    * updates for SENSEI 3.0
    
    * The data adaptor for amrex::Amr is working with SENSEI 3.0.
    
    * The adaptor for amrex::AmrMesh has new SENSEI 3.0 API's in place
      and compiles but is not filling all metadata.
    
    * The bridge code has been updated for SENSEI 3.0 and is working
    
    * updates to the SENSEI tutorial
    
    * Added a Python example.
    * Added an ADIOS2 example.
    * Updated ParaView Catalyst scripts for use with PareView 5.7.
    * Added a README describing tutorial layout in the root dir.
    * Cleaned up the make files.
    
    * updates for SENSEI 3.2
    
    * Adds per-array per-block range metadata calculations. For cell
      centered data, the cells covered by those in refined levels are
      skipped. This lets one be more precise about which blocks are
      needed for iso-surfacing. For other centerings ranges include
      all cells.
    
    * finish updates to AmrMesh data adaptor for SENSEI 3.2
    
    * finish updates to Amr data adaptor for SENSEI 3.2

Src/Extern/SENSEI/AMReX_AmrDataAdaptor.H
Src/Extern/SENSEI/AMReX_AmrDataAdaptor.cpp
Src/Extern/SENSEI/AMReX_AmrInSituBridge.cpp
Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.H
Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp
Src/Extern/SENSEI/AMReX_AmrMeshInSituBridge.cpp
Src/Extern/SENSEI/AMReX_InSituBridge.cpp
Src/Extern/SENSEI/AMReX_InSituUtils.H
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/inputs
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/histogram.py
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/histogram_python.xml
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py
Tutorials/SENSEI/Advection_AmrCore/README_SENSEI.md
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/histogram.py
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/histogram_python.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/iso_extract.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/read_adios2_bp4_default.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/read_adios2_sst_default.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.session
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/write_adios2_bp4.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/write_adios2_sst.xml
Tutorials/SENSEI/README.md

commit e3ad694e2fa924a6fc80bf84b6c99d521f9c39e6
Author: mic84 <mrosso@lbl.gov>
Date:   Sun May 24 19:45:48 2020 -0700

    CMake: link to OpenMP::Fortran only when needed (#935)

Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Config.cmake

commit 019617c097a5aa35f7f1c03bf8b9ce6dff718cc7
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat May 23 17:05:17 2020 -0700

    DPC++: disable gpu launch for mlndlap because the compiler hangs (#932)

Docs/Notes/DPCPPWishlist.md
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit cbd2effff3b228dfa60fa3db4df363fbe0bac4ca
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat May 23 17:04:34 2020 -0700

    more kernel size reduction in MLEBABecLap (#933)

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 02b21fa0c28c0c345359065fc24fa9ad72b8a0a7
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat May 23 16:39:07 2020 -0700

    more on reducing dpc++ kernel parameter size (#917)
    
    * more on reducing dpc++ kernel parameter size
    
    * In order to reduce kernel parameter size, launch separate kernels with DPC++
    
    * dpc++: disable launch region in tensor bc. reduce kernel size.

Src/Base/AMReX_GpuLaunchFunctsG.H
Src/EB/AMReX_EB2_Level.cpp
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit da9036d5f9fe23d48c37b8e4e5f627015e1c2654
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 22 23:04:28 2020 -0700

    add non-const data() to GpuArray (#931)

Src/Base/AMReX_Array.H

commit d425eb7668d231d1b114f9f54404172bd90486ab
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 22 10:40:55 2020 -0700

    Hip/scan (#920)
    
    * hip version of scan
    
    * use ::exp for HIP

Src/Base/AMReX_Scan.H
Tutorials/Basic/HeatEquation_EX1_C/Source/mykernel.H
Tutorials/Basic/HeatEquation_EX2_C/Source/mykernel.H

commit b759012b2c3bbbfa373f5b59c45907e35109734c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu May 21 22:10:09 2020 -0700

    Return immediately from memcpy if size is zero. (#928)

Src/Base/AMReX_GpuDevice.H

commit 528b74ab46b36ddae74791b2217903edb6e32b0a
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu May 21 17:16:59 2020 -0700

    Aa/more docs (#926)
    
    * Add EB stuff to Linear Solvers in addition to Linear Solvers stuff in EB
    
    * Update documentation to describe how to set homogeneous or inhomogeneous
    bc's on EB faces in a cell-centered solve

Docs/sphinx_documentation/source/EB.rst
Docs/sphinx_documentation/source/LinearSolvers.rst

commit 9e4d718e579bca6be82be54b17a4c829e4bd40ee
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu May 21 16:45:32 2020 -0700

    move operator<< for pair from neighbor particles test into amrex print so that dpcpp does not have ADL issue (#925)

Src/Base/AMReX_Print.H
Tests/Particles/NeighborParticles/main.cpp

commit c5c9907b0c8c4c7cdca1a55db4719472167d867c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu May 21 16:41:38 2020 -0700

    typo (#923)

CONTRIBUTING.md

commit bede80010c37c0fb46e88704f4c59642b56992b1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 21 16:01:45 2020 -0700

    silence some unused parameter warnings (#921)

Src/AmrCore/AMReX_AmrMesh.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabFactory.H
Src/Base/AMReX_GpuRange.H
Src/Base/AMReX_GpuUtility.H
Src/Particle/AMReX_ParGDB.H
Src/Particle/AMReX_Particles.H

commit 7a1812da68bcb409afa48a48fba1ef7d30fd41c2
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu May 21 15:29:09 2020 -0700

    Update the section about EB Linear solvers to reflect (#922)
    
    1) what bc's on EB faces are supported,
    2) how to set center vs centroid locations for solution variable and for face-based coefficients

Docs/sphinx_documentation/source/EB.rst

commit 2e2bb92415dac28552249e94886ca107cf3c6ca0
Author: mic84 <mrosso@lbl.gov>
Date:   Thu May 21 13:48:53 2020 -0700

    CMake: do not set Fortran properties when Fortran is disabled. (#919)
    
    In particular, do not specify Fortran module files path when
    Fortran is off, else superbuilds will fail.

Src/CMakeLists.txt

commit e2079f703fd483b54f7c07991a8bfdb287f25294
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu May 21 09:30:02 2020 -0700

    Fix new bug in mlebabeclap.  Forgot about the change in index order when I switched from 2d C Array to Array2D. (#918)

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H

commit 97b888bcfb9282e7b788e2c11a76f68e35e5979d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 20 11:11:20 2020 -0700

    document JIT fpe (#916)

Docs/Notes/DPCPPWishlist.md

commit f2940620f73a3373dbb605ec1c83f1ca4955f25e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 20 10:58:11 2020 -0700

    get around dpc++ kernel parameter size issue in EB build_cells (#914)

Src/EB/AMReX_EB2_3D_C.cpp

commit d4773e7585ae53292be8bf235736b5ef7d99ad37
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 20 10:40:38 2020 -0700

    fix new bug in 2675b0915d0b11d6e: Array2D does not have operator[] (#915)

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H

commit f5cdf22b9251eba96b07cb3854d83818a55553ce
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 20 10:07:20 2020 -0700

    add HIP issues we have (#913)

Docs/Notes/HIPIssues.md

commit 2283b88487ed2798e2fd3efbceb76a56dd624a33
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 20 10:07:00 2020 -0700

    reorganize DPC++ wishlist in terms of severity (#912)

Docs/Notes/DPCPPWishlist.md

commit 2675b0915d0b11d6e897db04bc77003e6c41674d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 20 10:06:44 2020 -0700

    Dpcpp/debug/mlmg (#911)
    
    * DPC++: manually copy ABecLapLacian gsrb kernel arguments to get around size limit
    
    * minor: remove unused capture
    
    * use GpuArray and initialization to get around DPC++ bug

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H

commit 2e8aa8d90945611b7f10215336729cacb87d7b91
Author: Mark Meredith <mwm126@gmail.com>
Date:   Tue May 19 19:41:01 2020 -0400

    Fix sign-compare warnings (#910)
    
    Co-authored-by: Mark Meredith <mark.meredith@netl.doe.gov>

Src/Particle/AMReX_NeighborList.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleTile.H

commit 4f11dbb113304bb119c07c1e657c3b6b5b9cfa5d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue May 19 10:47:07 2020 -0700

    No longer fall back to the CPU when calling Redistribute with ngrow != 0 (#909)
    
    * no longer fall back on cpu implementation when ngrow != 0
    
    * change the assert at the end of redistribute to account for nGrow
    
    * fix assertions
    
    * make sure we replicate exactly the behavior of the CPU locate
    
    * make sure we correctly search the gpu map structure for the boxes with ngrow

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleLocator.H
Src/Particle/AMReX_ParticleUtil.H

commit 4809ebef8a417b2629cc36bfdff665eae7b5cdd9
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue May 19 10:24:34 2020 -0700

    make device version random compile with dpc++, though it doesn't work yet. (#906)

Src/Base/AMReX_GpuQualifiers.H
Src/Base/AMReX_Random.H
Src/Base/AMReX_Random.cpp

commit 520f154e54a29a2b75a8371489340d9688322362
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue May 19 10:24:25 2020 -0700

    add synchronize statements to UpdateNeighbors (#908)

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 1aa23e9a5334b01fe11fa0168bab9719bc621384
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue May 19 10:06:47 2020 -0700

    replace cuda specific code (#907)

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleUtil.H

commit d8fe45c4fae04663a90adc2924a2ef927ac6cdf0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue May 19 07:45:06 2020 -0700

    Allow zero-length GpuArray. This fixes zero-length array, a gcc extension, in ParticleTile that is not allowed by the standard (#903)

Src/Base/AMReX_Algorithm.H
Src/Base/AMReX_Array.H
Src/Base/AMReX_Dim3.H

commit 31f46837f0af9e4a97f0fa4e71869533ecea8d93
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue May 19 07:44:47 2020 -0700

    directive inside macro argument is non-standard (#905)

Src/Base/AMReX_MultiFabUtil.cpp

commit 18d87ed313cf9a7c0806f1ee89cd3b8394f09023
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue May 19 07:43:57 2020 -0700

    fix data type (#904)

Src/Base/AMReX_DistributionMapping.cpp

commit ff4669b940fe5406fdee5fd1e0c5a62c0198f70b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 18 17:30:36 2020 -0700

    Avoid new line in ParmParse's Fortran namelist for PGI and IBM (#902)

Src/Base/AMReX_ParmParse.cpp

commit 43e281ae862c9e1cb3f27afc1ca05cfc137f8c8b
Author: mic84 <mrosso@lbl.gov>
Date:   Mon May 18 17:28:22 2020 -0700

    CMake: add helper function setup_target_for_cuda_compilation() (#866)
    
    * CMake: add helper function setup_target_for_cuda_compilation()
    
    This function ensures that the CUDA compilation of a dependent
    target is consistent with amrex CUDA build.
    
    * Update Tools/CMake/AMReXTargetHelpers.cmake
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
    
    * Leave default value for CUDA_RESOLVE_DEVICE_SYMBOLS
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
    
    * CMake: deploy setup_target_for_cuda_compilation()
    
    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

Src/CMakeLists.txt
Tools/CMake/AMReXTargetHelpers.cmake
Tools/CMake/AMReX_Config.cmake

commit 7d88e64f656dc1b522eb4bef6412841d492cfa1d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 18 16:40:44 2020 -0700

    add BL_NO_FORT to hip makefile (#901)

Tools/GNUMake/comps/hip.mak

commit ce8e12f49ac6d15c0c38f082419805bdc677440c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 18 16:23:08 2020 -0700

    DPC++: add fortran support (#900)

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/dpcpp.mak

commit 0aadce3d0713de3ec87bb33bf16d86b1a76d4fbf
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 18 16:22:49 2020 -0700

    ParticleMesh test: std::floor -> amrex::Math::floor for DPC++ (#899)

Tests/Particles/ParticleMesh/main.cpp

commit 9a1957ae1c273d53b283198ca3f497dc6a65b0d4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 18 13:55:06 2020 -0700

    fix EB MacProj tutorial due to interface change (#898)

Tutorials/EB/MacProj/main.cpp

commit beb6beb76d830f3df01f802be1a6509b804c3555
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 18 10:15:39 2020 -0700

    fix the logic of setting USE_MPI when MPI_THREAD_MULTIPLE is defined (#896)

Tools/GNUMake/Make.defs

commit f836e77216d5573182ebcfe87da829dd2d46e3f0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 18 10:15:01 2020 -0700

    tulip: add amdgpu-target only if USE_HIP=TRUE (#895)

Tools/GNUMake/sites/Make.frontier-coe

commit 197d77678fdad597883cb2052642d33a2a08aa8c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 18 07:24:25 2020 -0700

    fix bug in 16e256420f2e34c8d0d8 (#894)

Src/Base/AMReX_FBI.H

commit 72ef88ee6a1df083cbb32609cc417ce735a5fb5c
Author: asalmgren <asalmgren@lbl.gov>
Date:   Sun May 17 09:51:53 2020 -0700

    "single_vauled_bits" --> "single_valued_bits" (#893)

Src/EB/AMReX_EBCellFlag.H

commit 16e256420f2e34c8d0d8c3e56d18ab100c0f8a80
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat May 16 22:48:08 2020 -0700

    * add user defined constructors to Dim3 for hip (#892)
    
    * add amrex::Math::sqrt for hip
    * both heat equation and cns compile with hip, but crash at runtime

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Dim3.H
Src/Base/AMReX_FBI.H
Src/Base/AMReX_GpuComplex.H
Src/Base/AMReX_Math.H
Src/Base/AMReX_RealVect.H
Src/Base/AMReX_iMultiFab.cpp
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H

commit d040966d15540893563367f8769b68e3e0826e34
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat May 16 21:02:52 2020 -0700

    get HelloWorld to compile on tulip (#891)

Src/Base/AMReX_GpuUtility.H
Src/Base/AMReX_Math.H
Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.frontier-coe

commit 43bcd0cf01333e2638313bd98c16211f113e189c
Author: Eloise Yang <55457939+eloisejyang@users.noreply.github.com>
Date:   Sat May 16 10:58:34 2020 -0700

    Heat Equation 2 to GPU (#884)
    
    * Converting Heat Equation 2 to GPU
    
    * Putting HeatEquation2_CF Back

Tutorials/Basic/HeatEquation_EX2_C/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs
Tutorials/Basic/HeatEquation_EX2_C/Source/Make.package
Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc.H
Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc.cpp
Tutorials/Basic/HeatEquation_EX2_C/Source/mykernel.H
Tutorials/Basic/HeatEquation_EX2_CF/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX2_CF/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX2_CF/Exec/inputs_2d
Tutorials/Basic/HeatEquation_EX2_CF/Exec/inputs_3d
Tutorials/Basic/HeatEquation_EX2_CF/Source/Make.package
Tutorials/Basic/HeatEquation_EX2_CF/Source/advance.cpp
Tutorials/Basic/HeatEquation_EX2_CF/Source/advance_2d.f90
Tutorials/Basic/HeatEquation_EX2_CF/Source/advance_3d.f90
Tutorials/Basic/HeatEquation_EX2_CF/Source/init_phi_2d.f90
Tutorials/Basic/HeatEquation_EX2_CF/Source/init_phi_3d.f90
Tutorials/Basic/HeatEquation_EX2_CF/Source/main.cpp
Tutorials/Basic/HeatEquation_EX2_CF/Source/myfunc.H
Tutorials/Basic/HeatEquation_EX2_CF/Source/myfunc_F.H

commit d05946a9d30faf7f3a348dd8438bce89d9928495
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 15 19:27:04 2020 -0700

    fix division by zero (#890)

Src/EB/AMReX_algoim_K.H

commit af9dd8431835c6e83bc98731d7472be7d2a85879
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 15 17:58:38 2020 -0700

    increase the maximal depth of backtrace stack to 64 (#889)

Src/Base/AMReX_BLBackTrace.cpp

commit 78fad8e0b9a06204864a4af0608216da3b72326e
Author: kngott <30483578+kngott@users.noreply.github.com>
Date:   Fri May 15 16:59:22 2020 -0700

    The Invisible PR (#888)
    
    * Remove non-ASCII characters from the docs.
    
    * Remove non-ASCII characters from the doc tutorials.
    
    * Remove non-ASCII characters from paper.md
    
    * Remove non-ASCII characters from SWFFT.
    
    * Fix warning in docs of identically named tables.

Docs/sphinx_documentation/source/AMReX_Profiling_Tools.rst
Docs/sphinx_documentation/source/AmrCore.rst
Docs/sphinx_documentation/source/AmrLevel.rst
Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/Basics_Chapter.rst
Docs/sphinx_documentation/source/BuildingAMReX.rst
Docs/sphinx_documentation/source/CVODE.rst
Docs/sphinx_documentation/source/CVODE_top.rst
Docs/sphinx_documentation/source/EB.rst
Docs/sphinx_documentation/source/External_Profiling_Tools.rst
Docs/sphinx_documentation/source/Fortran.rst
Docs/sphinx_documentation/source/Fortran_Chapter.rst
Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_documentation/source/GettingStarted.rst
Docs/sphinx_documentation/source/GettingStarted_Chapter.rst
Docs/sphinx_documentation/source/IO.rst
Docs/sphinx_documentation/source/IO_Chapter.rst
Docs/sphinx_documentation/source/LoadBalancing.rst
Docs/sphinx_documentation/source/Particle.rst
Docs/sphinx_documentation/source/SUNDIALS3.rst
Docs/sphinx_documentation/source/Visualization.rst
Docs/sphinx_documentation/source/Visualization_Chapter.rst
Docs/sphinx_tutorials/source/CVODE_Tutorial.rst
Src/Extern/SWFFT/AlignedAllocator.h
Src/Extern/SWFFT/COPYING
Src/Extern/SWFFT/CheckDecomposition.c
Src/Extern/SWFFT/Dfft.H
Src/Extern/SWFFT/DfftC.cpp
Src/Extern/SWFFT/Distribution.H
Src/Extern/SWFFT/DistributionC.cpp
Src/Extern/SWFFT/Error.h
Src/Extern/SWFFT/TimingStats.h
Src/Extern/SWFFT/complex-type.h
Src/Extern/SWFFT/distribution.c
Src/Extern/SWFFT/distribution_c.h
paper/paper.md

commit a017d599f4d11898b43246f3ab6240a0e397d86b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu May 14 17:46:25 2020 -0700

    fix interp functions for single precison (#887)

Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H

commit e5d0c103cdbc6a1a8e53143f838bf7182ab453a4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu May 14 17:46:06 2020 -0700

    update DPC++ wishlist (#886)

Docs/Notes/DPCPPWishlist.md

commit a595fc350b7c610799233b46f0f7aa0347d57404
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu May 14 14:55:09 2020 -0700

    valid_cells_only option in VisMF::AsyncWrite (#878)

Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp
Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs

commit aa9a2acefe565186ddac24985a998182725e2c39
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu May 14 15:53:48 2020 -0600

    Templating FillPatch and Interpolator (#883)
    
    * updated so that setdomainbndry does not create template issues
    
    * templating the nodebilin interpolator functions

Src/AmrCore/AMReX_FillPatchUtil_I.H
Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/AmrCore/AMReX_Interpolater.cpp

commit 4d9c627d1d5ff8483c2f1207cf9d17ce457460dc
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 14 10:51:27 2020 -0700

    Fix bug I introduced in PR 882 and add an assertion

Src/Particle/AMReX_NeighborList.H

commit 780fd94cb7502118eeb28f187fb475ce81693a91
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 13 15:40:11 2020 -0700

    FillPatch: use factory only if FAB is FArrayBox (#879)

Src/AmrCore/AMReX_FillPatchUtil_I.H

commit 80631854f4dba8d9138f1c7e9f787715d1c1293c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 13 15:23:26 2020 -0700

    PhysBCFunct: no longer need to be virtual (#872)
    
    * PhysBCFunct: no longer need to be virtual
    
    * Fix typo in AmrCore.rst
    
    Co-authored-by: Andrew Myers <atmyers2@gmail.com>

Docs/sphinx_documentation/source/AmrCore.rst
Docs/sphinx_documentation/source/Basics.rst
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/F_Interfaces/Base/AMReX_FPhysBC.H
Src/F_Interfaces/Base/AMReX_FPhysBC.cpp

commit 0c4606cf624aebe2ab6072ed91086281747f0a41
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 13 12:58:39 2020 -0700

    MLMG::apply: need to apply inhomogeneous Neumann BC (#875)

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 1eed01cedff56af6c38a388c152720d4f39d9fd3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed May 13 12:28:50 2020 -0700

    use explicit casts to silence warnings (#882)
    
    * use explicit casts to silence warnings

Src/Particle/AMReX_NeighborList.H

commit ac9cd4ca023c2df78bd8ecebc5dda568b999a927
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed May 13 08:46:41 2020 -0700

    set the tiling options at runtime rather than hard-coding them (#880)
    
    * set the tiling options at runtime rather than hard-coding them

Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit 04725d6a5de3d0f3e72a73cd87d9e548678e8852
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue May 12 16:30:50 2020 -0700

    Teach the gpu particle locators about lev_min, lev_max, and ngrow (#877)
    
    * teach the gpu particle locators about lev_min, lev_max, and ngrow
    
    * missed an nGrow

Src/Particle/AMReX_ParticleLocator.H

commit ce38af7239fd44d58755890dfbc52fe4c84204d5
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue May 12 12:20:19 2020 -0700

    Mpi thread multiple (#873)
    
    * MPI_MULTIPLE -> MPI_THREAD_MULTIPLE for clarity
    
    * check mpi thread support level too when we does not initialize mpi

Src/Base/AMReX_AsyncOut.cpp
Src/Base/AMReX_ParallelDescriptor.cpp
Tests/AsyncOut/multifab/GNUmakefile
Tools/GNUMake/Make.defs
Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs

commit 874b65e914751464418987982c1a04604c3fd6f3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue May 12 10:37:10 2020 -0700

    remove profiler from WriteGenericPlotfileHeader because it's not async safe (#871)

Src/Base/AMReX_PlotFileUtil.cpp

commit d1484d49c1505d9883cbcb0f02b03efbc55102a2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue May 12 10:36:32 2020 -0700

    Async cleanup (#863)
    
    * remove superseded functions
    
    * update test

Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp
Tests/AsyncOut/multifab/GNUmakefile
Tests/AsyncOut/multifab/Make.package
Tests/AsyncOut/multifab/inputs
Tests/AsyncOut/multifab/main.cpp
Tests/VELOC/multifab/GNUmakefile
Tests/VELOC/multifab/Make.package
Tests/VELOC/multifab/Readme
Tests/VELOC/multifab/inputs
Tests/VELOC/multifab/main.cpp
Tests/VELOC/multifab/veloc.cfg
Tests/VELOC/pltfile_mpi/GNUmakefile
Tests/VELOC/pltfile_mpi/Make.package
Tests/VELOC/pltfile_mpi/inputs
Tests/VELOC/pltfile_mpi/main.cpp

commit c11bbc9bec2762299447402c6ca6f5aa4389a0c4
Author: MaxThevenet <mthevenet@lbl.gov>
Date:   Mon May 11 22:16:23 2020 -0700

    Fix bug in GpuComplex substraction (#870)

Src/Base/AMReX_GpuComplex.H

commit 8d573c62bd4c95bde0853c65370e34d150806685
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 11 19:21:35 2020 -0700

    add inline namespace literals and use in CNS and Heat Equation tutorials (#869)

Src/Base/AMReX_REAL.H
Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.H
Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.cpp
Tutorials/Basic/HeatEquation_EX1_C/Source/mykernel.H
Tutorials/GPU/CNS/Exec/RT/cns_prob.H
Tutorials/GPU/CNS/Exec/RT/cns_prob_parm.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob_parm.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/CNS_parm.H
Tutorials/GPU/CNS/Source/CNS_parm.cpp
Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H
Tutorials/GPU/CNS/Source/main.cpp

commit 6efe80c0c19dd0c11a6785a594250ad2dd871da9
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Mon May 11 17:28:17 2020 -0600

    Templating the PhysBCBase class  (#867)
    
    * Added () operator to PhysBCFunctBase and templated the FillPatchUtil functions to take a BC functor

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil_I.H
Src/Base/AMReX_PhysBCFunct.H

commit 0a92755c0e43b29e1c8386cf454ed2eff6a4fc4e
Author: mic84 <mrosso@lbl.gov>
Date:   Mon May 11 15:46:29 2020 -0700

    GNUMake: fix mispelled header name (#868)

Src/EB/Make.package

commit a15e9be68b1bb853a176cce013a42fa864443386
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Mon May 11 12:40:17 2020 -0700

    DPCPP Makefile: Fix CC Typo (#865)
    
    Typo: treat C as C++ code for now. We can also use a shipped `clang` instead with DPC++ installs.

Tools/GNUMake/comps/dpcpp.mak

commit 57eccd045f9d7770dd86af04be7c4a36434cec3b
Author: mic84 <mrosso@lbl.gov>
Date:   Mon May 11 12:24:21 2020 -0700

    CMake: add HeatEquation tutorials (#864)

Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX1_F/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX2_C/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX3_C/CMakeLists.txt

commit ef2a119c08d3cb52d631cdc0b340ff81978327b0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 11 09:34:32 2020 -0700

    DPC++: add device api of rng to wishlist (#862)

Docs/Notes/DPCPPWishlist.md

commit 0547aa88bb0e3f13335ab5ef96691e3bd69dbcea
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 11 09:34:06 2020 -0700

    use more relaxed memory order for BaseFab stats because we need them to be atomic but we do not require a specific synchronization order across threads (#860)

Src/Base/AMReX_BaseFab.cpp

commit 1a7f32f7cb8cd16691b45bf017ed9116aa33e8b2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 11 09:30:16 2020 -0700

    restore tutorial of the traditional hybrid C++/Fortran way (#861)

Tutorials/Basic/HeatEquation_EX1_CF/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX1_CF/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_CF/Exec/inputs_2d
Tutorials/Basic/HeatEquation_EX1_CF/Exec/inputs_3d
Tutorials/Basic/HeatEquation_EX1_CF/Source/Make.package
Tutorials/Basic/HeatEquation_EX1_CF/Source/advance.cpp
Tutorials/Basic/HeatEquation_EX1_CF/Source/advance_2d.f90
Tutorials/Basic/HeatEquation_EX1_CF/Source/advance_3d.f90
Tutorials/Basic/HeatEquation_EX1_CF/Source/init_phi_2d.f90
Tutorials/Basic/HeatEquation_EX1_CF/Source/init_phi_3d.f90
Tutorials/Basic/HeatEquation_EX1_CF/Source/main.cpp
Tutorials/Basic/HeatEquation_EX1_CF/Source/myfunc.H
Tutorials/Basic/HeatEquation_EX1_CF/Source/myfunc_F.H

commit 390f32d233d7679bab460639a2189e058456aa4e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 11 09:19:39 2020 -0700

    HeatEquation_Ex1_C: add missing files (#859)

Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.cpp
Tutorials/Basic/HeatEquation_EX1_C/Source/mykernel.H

commit f9131627f9096b95a3ab6bf089230ab11fe7ef8b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat May 9 09:06:43 2020 -0700

    asyncout in AmrLevel::checkPoint() (#858)

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_StateData.cpp
Src/Boundary/AMReX_FabSet.cpp

commit fa82c15ea6b5959bc59a058e8bc566e716a906eb
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat May 9 09:06:02 2020 -0700

    extract common code in writePlotFile and writeSmallPlotfile into a private function (#857)

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp

commit 3c115e68bea60f8567ab03b3516bb722ef7aed0d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 8 17:08:28 2020 -0700

    Update heat equation tutorial to our currently preferred style. (#853)
    
    * HeatEquation_EX1_C -> HeatEquation_EX1_CF and move gpu version of heat equation to basic
    
    * update documentation for the change in heat equation tutorial

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_tutorials/source/GPU_Tutorial.rst
Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs
Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs_2d
Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs_3d
Tutorials/Basic/HeatEquation_EX1_C/Source/Make.package
Tutorials/Basic/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/Basic/HeatEquation_EX1_C/Source/advance_2d.f90
Tutorials/Basic/HeatEquation_EX1_C/Source/advance_3d.f90
Tutorials/Basic/HeatEquation_EX1_C/Source/init_phi_2d.f90
Tutorials/Basic/HeatEquation_EX1_C/Source/init_phi_3d.f90
Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.H
Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc_F.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile.libamrex
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc_F.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/mykernel.F90
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/run.summitdev
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc_F.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/mykernel.F90
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/run.summitdev
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/inputs_3d_hip
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/myfunc.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/mykernel.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.ascent
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.nocuda.script
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.summit
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.summitdev
Tutorials/GPU/HeatEquation_EX1_C/Make.HEAT
Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit be8104b25776036ac741da7c72d31bd1292ded13
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 8 16:16:05 2020 -0700

    DPC++: add max parameter size to device properties (#856)

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp

commit e7b91ef94801aaf3afa7b9d7070526137830a937
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 8 15:03:03 2020 -0700

    DPC++: currently allocating too much memory might fail, so we set the initial arena size to 1GB. (#855)

Src/Base/AMReX_Arena.cpp

commit 01aaa928d4da6c9dc48aae758e41a942a21350ac
Author: mic84 <mrosso@lbl.gov>
Date:   Fri May 8 14:33:13 2020 -0700

    CMake: link against OpenMP_Fortran only when Fortran is enabled (#851)
    
    * CMake: link against OpenMP_Fortran only when Fortran is enabled
    
    * CMake: fix if() statement

Tools/CMake/AMReX_Config.cmake

commit 52e11a11b8ee4d3a6b19f20ddef723a23fbe72f6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri May 8 13:49:51 2020 -0700

    Particle locator fix (#854)
    
    * fix logic for re-building the particle locator
    
    * if the entry isn't in the map, then the number of copies is 0

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleLocator.H

commit 8194c10004aae594e2d120d79c5e30aa7b2dce3e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu May 7 18:20:37 2020 -0700

    some updates on Chapter Basic of the documentaion (#849)
    
    * some updates on Chapter Basic of the documentaion
    
    * Minor proofreading changes to Basics.rst
    
    Co-authored-by: Andrew Myers <atmyers2@gmail.com>

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/GPU.rst

commit 72fe04903c6a67ce901c9350f58a9f565d9fa6a2
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu May 7 17:41:25 2020 -0700

    Add nodal_proj.num_pre_smooth, nodal_proj.num_post_smooth, mac_proj.num_pre_smooth and (#850)
    
    mac_proj.num_post_smooth options -- these can be used to pass the parameters through to the
    MLMG.

Src/LinearSolvers/Projections/AMReX_MacProjector.cpp
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 1c24f8a94c482ff79d401e1226502a98394e5ad2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu May 7 08:22:45 2020 -0700

    Async out (#845)
    
    * AsyncOut using a background thread.  This is based on our previous
    implementations of async output.
    
    In our first implementation, we use std::async to launch a thread for
    the output job.  There are two issues with that first implementation.
    First, it does not scale to a large number of MPI processes.  We do
    not want every MPI process to write to disk simultaneously.  To avoid
    that, the first implementation writes a small file to the disk and
    uses that to coordinate.  This way of message passing using file does
    not scale.  The second issue is it is hard to manage multiple jobs.
    Ideally we would like the second job to start after the first job is
    finish to avoid launching too many threads writing to the disk.
    
    In our second implementation, MPI is initialized with support for
    multiple threads.  This solves the first issue above.  However, the
    second issue still exists.  To write a plotfile with multiple
    MultiFabs like the functions in AMReX_PlotFileUtil, the second
    implementation has a new function to manually merge multiple
    MultiFabs' data into one contiguous chunk of memory for a std::async
    job.  However this cannot be easily extended to AmrLevel's
    WritePlotfile function.
    
    In this third implementation, we launch a background thread
    specifically for async output.  The thread persists during the run
    waiting on a C++ conditional variable.  The thread is woke up when a
    job is submitted to the async job queue.  As in the second
    implementation, MPI_THREAD_MULTIPLE is used.  The use of a background
    thread and a job queue provides flexibility.  For example, writing
    plotfile in AmrLevel requires only a few lines of changes.  One can
    submit multiple jobs to the queue, as long as there is enough memory,
    without worrying about launching too many threads.

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp
Src/Base/AMReX.cpp
Src/Base/AMReX_AsyncOut.H
Src/Base/AMReX_AsyncOut.cpp
Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabConv.cpp
Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tests/VELOC/mf_mpi/inputs
Tests/VELOC/multifab/main.cpp
Tools/GNUMake/Make.defs

commit a9d1c7649200f186419be0b1e07114ff3b5ddb56
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 6 13:53:20 2020 -0700

    fix a corner case in which the object is fully contained within a coarse cell without touching its surface.  this could happen during the coarsening of fine geometry. (#847)

Src/EB/AMReX_EB2_2D_C.H
Src/EB/AMReX_EB2_3D_C.H

commit fc08afe8327f96d507cda7f9f9a6423787381b2b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue May 5 14:35:06 2020 -0700

    For cuda > 10, use cudaLaunchHostFunc instead of cudaStreamAddCallback, which has been marked as deprecated (#844)

Src/Base/AMReX_GpuAsyncArray.H
Src/Base/AMReX_GpuAsyncArray.cpp
Src/Base/AMReX_GpuElixir.cpp

commit d555fcad06bfc4e7d3fb076a819064664deb92a4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue May 5 12:46:33 2020 -0700

    Move prefetch from AmrLevel WritePlotfile to VisMF::Write.  Avoid unn… (#843)
    
    * Move prefetch from AmrLevel WritePlotfile to VisMF::Write.  Avoid unnecessary work if no ghost cells.
    
    * If not manged memory, we do not need to start MFIter

Src/Amr/AMReX_AmrLevel.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_VisMF.cpp
Tutorials/GPU/EBCNS/Source/CNS_io.cpp

commit 0dbb88eb067149d719fa1eaf2f46d0b38385b466
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 4 20:30:54 2020 -0700

    prefetch only if it's managed memory (#842)

Src/Base/AMReX_BaseFab.H

commit 46000d3312a926242b9dd328982dfe5be1ea836b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon May 4 13:13:07 2020 -0700

    User literals: add a space before _ to make gcc 4.8 happy (#841)

Src/Base/AMReX_REAL.H

commit a718d8f90da3299a686a7aab6f84ec9b88518b7a
Author: mic84 <mrosso@lbl.gov>
Date:   Mon May 4 13:11:32 2020 -0700

    CMake: make AMReX_buildInfo.cpp always out of date (#835)
    
    * CMake: make AMReX_buildInfo.cpp always out of date.
    
    buildInfoGetBuildDate() will now return the date and time of the
    build. Before this change, it returned the date and time of the
    CMake configuration step.
    
    * CMake: allow user to set build date and time.
    
    This is meant to facilitate reproducible builds.

Tools/CMake/AMReXBuildInfo.cmake
Tools/CMake/AMReX_buildInfo.cpp.in

commit cb069a03468a4d5e33a9a93cad087f3e9801c248
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon May 4 12:24:27 2020 -0700

    Particle hdf5 move (#840)
    
    * fix some indentation
    
    * move all the HDF5 particle routines to a separate file

Src/Particle/AMReX_ParticleHDF5.H
Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 0d9dcf511355d59900b97eca468edb649e28d073
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon May 4 11:24:07 2020 -0700

    Do not explicitly reset the device on finalize (#839)

Src/Base/AMReX_GpuDevice.cpp

commit cc04525912bd71264cb879780bb5fdc28e56236a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sun May 3 19:45:44 2020 -0700

    Add a short section to the docs about runtime particle components (#838)
    
    * Add a short section to the docs about runtime particle components
    
    * add some more detail about how and when to call DefineAndReturnParticleTile
    
    * add in some missing style markers

Docs/sphinx_documentation/source/Particle.rst

commit 53490404d74eb49e8a833cc5b1e0f7b84d78c166
Author: mic84 <mrosso@lbl.gov>
Date:   Sat May 2 23:01:52 2020 -0700

    CMake: do not install Fortran modules directory if Fortran is not enabled. (#833)

Tools/CMake/AMReXInstallHelpers.cmake

commit ad63449780e4d2a7c428937dfb0476624fefa569
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat May 2 13:15:21 2020 -0700

    DPC++ scan (#837)
    
    * DPC++ scan
    
    * ParallelScan tutorial: add std version and put thrust version unside ifdef AMREX_USE_CUDA

Src/Base/AMReX_FBI.H
Src/Base/AMReX_Scan.H
Tutorials/GPU/ParallelScan/main.cpp

commit d4970bb0db316234a93969a1564df275f64e6ea7
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat May 2 12:09:16 2020 -0700

    remove -g so that dpcpp beta6 doesn't generate warnings at runtime (#836)

Tools/GNUMake/comps/dpcpp.mak

commit 39d51cb631fd1916ac182a7f0e787eb3acf66a91
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri May 1 20:36:12 2020 -0700

    InitFromAsciiFile Improvements (#831)
    
    * GPU-friendly init from ascii file
    
    * add test for InitFromAscii
    
    * make InitFromAscii handle SoA data

Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Tests/Particles/InitFromAscii/GNUmakefile
Tests/Particles/InitFromAscii/Make.package
Tests/Particles/InitFromAscii/inputs
Tests/Particles/InitFromAscii/main.cpp
Tests/Particles/InitFromAscii/particles.txt

commit a9b8d6c16ff3b5eed92b0c0f0b79c2862fc0b393
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri May 1 17:30:44 2020 -0700

    catch the case that the message size is too big. (#834)

Src/Base/AMReX_FabArrayBase.cpp

commit aa16f495770661ac14ca9d8b8865e720f150261e
Author: kngott <30483578+kngott@users.noreply.github.com>
Date:   Fri May 1 15:10:09 2020 -0700

    Async I/O (#808)

Src/Base/AMReX.cpp
Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp
Tests/VELOC/mf_mpi/GNUmakefile
Tests/VELOC/mf_mpi/Make.package
Tests/VELOC/mf_mpi/inputs
Tests/VELOC/mf_mpi/main.cpp
Tests/VELOC/pltfile_mpi/GNUmakefile
Tests/VELOC/pltfile_mpi/Make.package
Tests/VELOC/pltfile_mpi/inputs
Tests/VELOC/pltfile_mpi/main.cpp
Tools/GNUMake/Make.defs
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit 2e66e12f94e2e9b0bcf09c3a423f47110004a892
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 1 08:21:04 2020 -0700

    update CHANGES (#829)

CHANGES

commit 47882ba850b9876c61943d5160df9fe7ee518958
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Apr 30 13:58:54 2020 -0700

    Add a suggestion about not merging pr branch into development (#830)

CONTRIBUTING.md

commit 72b2ad1efce53d176da22b374c660b1bdcce12a4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Apr 30 06:46:45 2020 -0700

    fix VisMF::min and max when they are not in the header (#828)

Src/Base/AMReX_VisMF.cpp

commit dccaf5b22f1462a98aea8215a31e7b394b31f084
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Apr 29 20:05:04 2020 -0700

    DPC++: add link to unsupported math functions (#827)

Src/Base/AMReX_Math.H

commit 6973ef43e6d21fbcff6fea27ea656c18b1e38d51
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Apr 29 17:06:09 2020 -0700

    DPC++: replace order_queue, subgroup all and any that are deprecated in beta6 (#825)

Src/Base/AMReX_FBI.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuTypes.H

commit 013bfe6843f40a98c46ae8f83e10fa2a42c71715
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 29 16:23:13 2020 -0700

    fix a new-ish bug I introduced with tiling + neighbor lists (#826)

Src/Particle/AMReX_NeighborParticlesI.H

commit f96a7bd6d445864d4dc2c2ac41425ae722562210
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Apr 29 13:50:26 2020 -0700

    split sycl device code per kernel be default (#824)

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Tools/GNUMake/comps/dpcpp.mak

commit ad3619d745727a814fdbfc74118387702cb520bc
Author: Candace Gilet <cgilet@users.noreply.github.com>
Date:   Wed Apr 29 14:41:03 2020 -0400

    Macproj fix eb set bcoeffs (#823)
    
    * Pass m_beta_loc in call to setBCoeffs
    
    * MacProjector:: Remove unneeded local copies of phi_loc and beta_loc

Src/LinearSolvers/Projections/AMReX_MacProjector.H
Src/LinearSolvers/Projections/AMReX_MacProjector.cpp

commit 45f2c8f9a4ae6f6f977ed67623c516fedb0b0fa9
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Apr 29 09:18:23 2020 -0700

    CI: GitHub Checkout Action v2 (#822)
    
    Just updates to the latest stable release of the checkout action.
    
    I saw some problems with the old v1 version in other projects
    recently, so proactively migrating this.

.github/workflows/cmake.yml

commit bce44ba71508f8bd8bd0accfe8d8c6da6635938b
Author: asalmgren <asalmgren@lbl.gov>
Date:   Tue Apr 28 21:25:57 2020 -0700

    Move m_phi_loc from MLCellLinOP to MLABecLap and (#821)
    
    1) set default to Location::CellCenter
    2) create setPhiOnCentroids()
    3) allow call to setPhiOnCentroids from AMREX_MacProjector

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/Projections/AMReX_MacProjector.cpp

commit 2f0c802e52c365a8e0273cd2f4961e9487764a6f
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Apr 28 17:04:07 2020 -0700

    add links to oneapi-spec issues (#817)

Docs/Notes/DPCPPWishlist.md

commit eff6aa113fef06786b9c74316ec13e4ed855950d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Apr 28 16:38:04 2020 -0700

    add non-mpi github action (#819)

.github/workflows/cmake.yml

commit b77d1dfe45ff9d12330d2e87f6443395e308be04
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Apr 28 16:15:04 2020 -0700

    remove extra explicit qualificaton (#820)

Src/Base/AMReX_ParallelDescriptor.H

commit bd1ed4ed8aa9046a82e3d2999cb6d3e6b1bcc976
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Apr 28 15:40:14 2020 -0700

    add non-MPI version of GatherLayoutDatatoVector (#818)

Src/Base/AMReX_ParallelDescriptor.H

commit 587a39d54c83a5c0343220fdb1dc7c0cdb5dd496
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Tue Apr 28 12:29:18 2020 -0700

    Add LayoutData overload for makeKnapSack and makeSFC (#805)

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_ParallelDescriptor.H

commit 778ff85a222f248f62832784d4fd9cc2f0a70d57
Author: mic84 <mrosso@lbl.gov>
Date:   Tue Apr 28 12:05:36 2020 -0700

    CMake: fix some minor bugs in AMReX_Options.cmake (#812)

Tools/CMake/AMReX_Options.cmake

commit 37e0d28c074316717038b2bb0e0d4822991dc0e0
Author: asalmgren <asalmgren@lbl.gov>
Date:   Tue Apr 28 11:54:26 2020 -0700

    Bug fix in AMReX_MacProjector.cpp (#816)

Src/LinearSolvers/Projections/AMReX_MacProjector.cpp

commit 96a2dbab1f169d45f2bb69eed8ab0fcf5b9590c8
Author: asalmgren <asalmgren@lbl.gov>
Date:   Tue Apr 28 10:17:47 2020 -0700

    EB Linear Solver Test/Tutorials fix (#815)

Tests/LinearSolvers/EBTensor/MyTest.cpp
Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp

commit d04999c60f76c86a664bc60b1f98bc39bb3552d6
Author: asalmgren <asalmgren@lbl.gov>
Date:   Mon Apr 27 20:10:57 2020 -0700

    Modify the EB-aware cell-centered solvers to distinguish between the coefficients on face centers vs face centroids; similarly distinguish between solution variable and RHS on cell centers vs cell centroids (#810)

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/Projections/AMReX_MacProjector.H
Src/LinearSolvers/Projections/AMReX_MacProjector.cpp

commit d74624d7b800488590d23f7711cbdf7fab286286
Author: mic84 <mrosso@lbl.gov>
Date:   Mon Apr 27 17:58:29 2020 -0700

    CMake: must build source files erroneusly excluded from build when ENABLE_FORTRAN=OFF. (#813)

Src/Base/CMakeLists.txt

commit 445ca73ad93a7aac52a188ebf72de7de5d39e47a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun Apr 26 19:49:43 2020 -0700

    explicitly construct Array to avoid overload error (#811)

Tutorials/ForkJoin/MLMG/main.cpp

commit 17500c6090396367ac07857a0b3745d7930bafb0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun Apr 26 16:26:52 2020 -0700

    EB_utils: add new interfaces and deprecate the old ones (#802)
    
    Co-authored-by: asalmgren <asalmgren@lbl.gov>

Src/EB/AMReX_EB_utils.H
Src/EB/AMReX_EB_utils.cpp

commit ee96dee9864a40624eeba43bd4c4c37e51ce7abd
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Apr 26 10:17:02 2020 -0700

    neighbor lists are stored per level (#807)

Tests/Particles/NeighborParticles/MDParticleContainer.cpp

commit efae0bd0964e98753255e9dd90f1170cf91d1a94
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Apr 25 16:47:02 2020 -0700

    make sure these loops only go over the valid particles (#806)

Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_TracerParticles.cpp

commit f24bfd7805b80978fa4e6b9199eaa7774d5f32d7
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Apr 24 15:07:05 2020 -0700

    EnableIf for ParticleContainer plotfile methods (#803)

Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_Particles.H

commit a56106e4855bab7df8691ca5b09caf0f8b1bb878
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Apr 24 14:29:04 2020 -0700

    Call the same code for building neighbor lists whether we are on the CPU or GPU (#799)
    
    * start to unify GPU and CPU versions of neighbor particle / neighbor list implementations
    
    * allow for checking > 1 neighboring bin in GPU implementation of NeighborList::build

Src/Particle/AMReX_NeighborList.H
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParIter.H
Src/Particle/AMReX_ParticleContainerI.H
Tutorials/GPU/NeighborList/CMakeLists.txt
Tutorials/GPU/NeighborList/CheckPair.H
Tutorials/GPU/NeighborList/Constants.H
Tutorials/GPU/NeighborList/GNUmakefile
Tutorials/GPU/NeighborList/MDParticleContainer.H
Tutorials/GPU/NeighborList/MDParticleContainer.cpp
Tutorials/GPU/NeighborList/Make.package
Tutorials/GPU/NeighborList/README.md
Tutorials/GPU/NeighborList/inputs
Tutorials/GPU/NeighborList/main.cpp
Tutorials/GPU/NeighborList/script.sh
Tutorials/Particles/NeighborList/GNUmakefile
Tutorials/Particles/NeighborList/Make.package
Tutorials/Particles/NeighborList/NeighborListParticleContainer.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborList/inputs
Tutorials/Particles/NeighborList/inputs.mr
Tutorials/Particles/NeighborList/main.cpp
Tutorials/Particles/NeighborList/neighbor_list_2d.f90
Tutorials/Particles/NeighborList/neighbor_list_3d.f90
Tutorials/Particles/NeighborList/neighbor_list_F.H

commit df00a0bf2ef7217ae0f8d861d433058c93d07b97
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 24 13:51:54 2020 -0700

    make ParallelFor work for functors (#804)

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_TypeTraits.H

commit a516406c25c5df90d7e4426394bfa2cb92e9acf7
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 24 09:41:20 2020 -0700

    For CPU, GpuArray is no longer an alias to std::array (#801)
    
    * For CPU, GpuArray is no longer an alias to std::array
    
    * fix Tutorials/LinearSolvers/MultiComponent

Src/Base/AMReX_Array.H
Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp

commit 77a1b9b189a022e6390d06864a7a2f12795bedf0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 24 08:53:06 2020 -0700

    add semicolon due to change in TinyProfiler macros (#800)

Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_utils.cpp

commit 445d25e26667ac96b71f59050930678726eb0cf5
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 24 06:49:38 2020 -0700

    use enableif in various parallel for functions (#790)

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_TypeTraits.H

commit 0f2e7aae8713b697ce4679a2a1d2d1ba82558e6c
Author: Abhishek Bagusetty <59661409+abagusetty@users.noreply.github.com>
Date:   Thu Apr 23 19:12:01 2020 -0500

    Support for DPCPP USM prefetch and mem_advise (#793)
    
    * Support for DPCPP USM prefetch and mem_advise
    
    * addressing PR comments for prefetch and mem_advise

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp

commit 86dab656439481c20a1ffcfb1707afcbafc675f5
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Apr 23 09:42:50 2020 -0700

    remove some semincolons in TinyProfiler macros to avoid warning about extra semicolons (#798)

Src/Base/AMReX_BLProfiler.H

commit 9c9699f7387709cea7baafba8129688deb3e75b5
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Apr 22 16:03:15 2020 -0700

    add host device for functions (#789)

Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_GpuLaunchFunctsG.H

commit c02f8124c3a3bfbd24c03e69803dde079d7dceca
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Apr 22 15:05:04 2020 -0700

    CMake: get rid of zero size arrays in AMReX_buildInfo.cpp (#794)

Tools/CMake/AMReXBuildInfo.cmake

commit 285b06832e3a446ce6529f36a0e4574467c813ba
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 22 14:33:21 2020 -0700

    Fix a couple of minor typos in Contributing.md (#796)
    
    * replace ';' with '.'
    
    * fix capitalization

CONTRIBUTING.md

commit e0658315005f4521b73a530d53fc6c47fce93cba
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 22 13:30:28 2020 -0700

    Some long -> amrex::Long (#792)

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_ParticleTransformation.H

commit 6e59367c8fad3005d1cebe28afe0ac7e728c4aab
Author: asalmgren <asalmgren@lbl.gov>
Date:   Tue Apr 21 18:26:58 2020 -0700

    Remove calls to std::min in eb_interp_centroid2facecent in Src/EB/AMReX_EBMultiFab_3D_C.H (#791)
    
    * Don't use std::min on the gpu!

Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit e8cac4c8e754be4391c219ef4d3b584b85c04763
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Apr 21 11:54:15 2020 -0700

    Make 1d launch macro consistent with 3d and 4d in terms of return and continue.  That is continue will fail to compile and return will return from the lambda not the enclosed funciton. (#788)

Src/Base/AMReX_GpuLaunchMacrosG.H

commit 49fc0fed1cd3ce4648b1c66e2ca353b672e9f739
Author: mic84 <mrosso@lbl.gov>
Date:   Tue Apr 21 10:57:13 2020 -0700

    CMake: set CMake minimum required version in package config file. (#787)

Tools/CMake/AMReXConfig.cmake.in

commit 67e5c6d94bd7cedcade1dc9722ee22e07118fa31
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Apr 21 10:01:58 2020 -0700

    add note about deleting feature branches when they are done (#786)

CONTRIBUTING.md

commit 70e9b1cb70d08ebc445d4962de3b943fe87a272c
Author: mic84 <mrosso@lbl.gov>
Date:   Mon Apr 20 18:49:12 2020 -0700

    CMake: generate AMReX_Config.H the CMake way (#785)
    
    * CMake: fix issue with installation of AMReX_Config.H

Tools/CMake/AMReXInstallHelpers.cmake
Tools/CMake/AMReX_Config.H.in

commit f54a9f4f61ba3d129e82df5117d79dc8861f9004
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Apr 20 17:40:56 2020 -0700

    CNS tutorial: make [GC]puBndryFuncFab local instead of static (#784)

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/bc_fill.H
Tutorials/GPU/CNS/Source/CNS_bcfill.cpp
Tutorials/GPU/EBCNS/Source/CNS_bcfill.cpp

commit a496d6aff094a50818a3c091fc25be2e5a7e6cc2
Author: mic84 <mrosso@lbl.gov>
Date:   Mon Apr 20 17:13:35 2020 -0700

    CMake: update defines list. (#783)

Tools/CMake/AMReX_Defines.cmake

commit a9c3122cd4528df5b34b193b0fc7d4bf5c1552cb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Apr 20 14:43:50 2020 -0700

    Bugfix after PR#780 (#782)
    
    * use return instead of continue to break out of AMREX_PARALLEL_FOR, which does not work now that PR#780 is merged.
    
    * avoid return altogether in these launch macros

Src/Particle/AMReX_ParticleCommunication.H

commit 319aa0e1f408781a314ac8125d47bd3cf851a782
Author: mic84 <mrosso@lbl.gov>
Date:   Mon Apr 20 13:48:54 2020 -0700

    CMake: make generation of AMReX_buildInfo.cpp more robust. (#781)
    
    This commit improves the handling of quotes escaping.

Tools/CMake/AMReXBuildInfo.cmake

commit 527094da45e54820f9ed583e5dea1ff058fb611c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Apr 20 13:34:37 2020 -0700

    Simplify launch macros by calling launch functions (#780)

Src/Base/AMReX_GpuLaunchMacrosG.H

commit c23a44085bee6fa5acd79b1d9b7a54fae17feb0f
Author: asalmgren <asalmgren@lbl.gov>
Date:   Mon Apr 20 11:26:09 2020 -0700

    Remove print statements accidentally left in (#779)
    
    * Fix logic for 3D interpolation of cell centroids to face centroids
    
    * Remove print statement that I left in by accident

Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit cb74aed183813f826d9571d402a8a73bb27ac9f7
Author: asalmgren <asalmgren@lbl.gov>
Date:   Mon Apr 20 09:56:04 2020 -0700

    Fix logic for 3D interpolation of cell centroids to face centroids (#778)

Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit 82bd805ef145a2cfedd52e812680e694cdcd4cf2
Author: Revathi  Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Date:   Sun Apr 19 22:00:58 2020 -0700

    fixing minor typos (#777)

Docs/Notes/DPCPPWishlist.md
Docs/sphinx_documentation/source/GettingStarted.rst

commit cc48e0e3e033275f7dc167f734126b4f65a1839d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun Apr 19 20:50:39 2020 -0700

    DPC++ kernel too big (#776)
    
    * This kernel's parameters are too big for DPCPP on Gen9 that has a limit of 1KB.
    
    * sqrt -> std::sqrt

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H

commit 500e4e8cb0f3141a7aef1548d8b573dd95c4ce7b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 19 16:55:41 2020 -0700

    add support for DPC++ Ahead of Time compilation

Tools/GNUMake/comps/dpcpp.mak

commit 87300a943d4967292eeda6c9791c370af8ae0ee7
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun Apr 19 11:30:16 2020 -0700

    fix instruction in CONTRIBUTING.md (#774)

CONTRIBUTING.md

commit c0c4b6293f7683dc9a633e20d6e6027d47f7e158
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Apr 19 14:08:36 2020 -0400

    fix Stony Brook spelling (#773)

CONTRIBUTING.md

commit 6ff71302e7e092e1b3fcf0aff23a54f27362b108
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun Apr 19 10:58:41 2020 -0700

    fix link to amrex github page (#771)

CONTRIBUTING.md

commit 571b72cb4b2b06c2aaa2aa3c6202ecbd4f9e2b55
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Apr 18 21:24:07 2020 -0700

    Add a CONTRIBUTING.md (#770)
    
    * add a CONTRIBUTING.md file explaining how to use forks and pull requests.
    
    * merge discussion of branch structure and core contributors into CONTRIBUTING.md
    
    * all caps
    
    * advise users to set their development branches to track the upstream one instead of their forks
    
    * use draft PRs instead of a [WIP] tag in the PR title.
    
    * add link to CONTRIBUTING.md from README.md
    
    * add a 'cd' and a 'fetch' to the instructions
    
    * also add note to set master to track upstream
    
    * instruct people to set the push url for upstream to their fork
    
    * add a note about re-forking

CONTRIBUTING.md
README.md

commit ae38db0d088bf1978d149c16f0f885a717fc8e3c
Merge: 95de5f025 8c07fd8c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 17 21:04:31 2020 -0700

    Merge branch 'master' into development

commit 95de5f0251c9b616ddfbfdead9fdf09f35bb0335
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 17 21:00:09 2020 -0700

    Merge master back to development for consitence (#769)
    
    * "maxorder" is an unused variable when doing the nodal projection.
    
    * remove large grids files (#763)
    
    * remove more grids files (#765)
    
    * remove timestramp files from Tools (#764)
    
    * Weiqun/rm eps pdf (#766)
    
    * remove large grids files
    
    * remove timestramp files from Tools
    
    * remove more grids files
    
    * remove unused eps and pdf files
    
    * remove these sensi files because there is already Tutorials/SENSEI (#768)
    
    Co-authored-by: Ann Almgren <asalmgren@lbl.gov>

Docs/sphinx_documentation/source/Visualization/ParaView.png
Docs/sphinx_documentation/source/Visualization/ParaView.png.REMOVED.git-id
Docs/sphinx_documentation/source/Visualization/ParaView_particles.png
Docs/sphinx_documentation/source/Visualization/ParaView_particles.png.REMOVED.git-id
Docs/sphinx_documentation/source/Visualization/rt_2048_paraview_000500.png
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Docs/sphinx_documentation/source/_static/theme_overrides.css
Docs/sphinx_tutorials/source/_static/theme_overrides.css
Docs/sphinx_tutorials/source/figs/mf_remap_hires.png
Docs/sphinx_tutorials/source/figs/mf_remap_hires.png.REMOVED.git-id
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 8c07fd8c0e36475b309f5cd365f0e20ccf856b78
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 17 19:49:57 2020 -0700

    remove these sensi files because there is already Tutorials/SENSEI (#768)

Docs/sphinx_documentation/source/Visualization/ParaView.png
Docs/sphinx_documentation/source/Visualization/ParaView.png.REMOVED.git-id
Docs/sphinx_documentation/source/Visualization/ParaView_particles.png
Docs/sphinx_documentation/source/Visualization/ParaView_particles.png.REMOVED.git-id
Docs/sphinx_documentation/source/Visualization/rt_2048_paraview_000500.png
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Docs/sphinx_documentation/source/Visualization/rt_2048_visit_000500.png
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Docs/sphinx_documentation/source/_static/theme_overrides.css
Docs/sphinx_tutorials/source/_static/theme_overrides.css
Docs/sphinx_tutorials/source/figs/mf_remap_hires.png
Docs/sphinx_tutorials/source/figs/mf_remap_hires.png.REMOVED.git-id
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_catalyst.py
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.session
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.session
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_libsim.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/write_vtk.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_catalyst.py
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml
Tutorials/GPU/Advection_AmrCore/README_SENSEI.md

commit ac0e50721b599f3311ec47d2eeed7a3e2658cb27
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 17 17:50:26 2020 -0700

    Weiqun/rm eps pdf (#766)
    
    * remove large grids files
    
    * remove timestramp files from Tools
    
    * remove more grids files
    
    * remove unused eps and pdf files

Docs/sphinx_documentation/source/AmrCore/figs/Adv1.pdf
Docs/sphinx_documentation/source/AmrCore/figs/Adv2.pdf
Docs/sphinx_documentation/source/AmrCore/figs/Adv3.pdf
Docs/sphinx_documentation/source/AmrCore/figs/Adv4.pdf
Docs/sphinx_documentation/source/AmrCore/figs/Adv5.pdf
Docs/sphinx_documentation/source/AmrCore/figs/flowchart.pdf
Docs/sphinx_documentation/source/AmrCore/figs/subcycling.pdf
Docs/sphinx_documentation/source/AmrLevel/figs/flowchart.pdf
Docs/sphinx_documentation/source/Basics/amrgrids.pdf
Docs/sphinx_documentation/source/Basics/cc_growbox.pdf
Docs/sphinx_documentation/source/Basics/cc_tilebox.pdf
Docs/sphinx_documentation/source/Basics/cc_validbox.pdf
Docs/sphinx_documentation/source/Basics/ec_growbox.pdf
Docs/sphinx_documentation/source/Basics/ec_tilebox.pdf
Docs/sphinx_documentation/source/Basics/ec_validbox.pdf
Docs/sphinx_documentation/source/Basics/figs/flowchart.pdf
Docs/sphinx_documentation/source/Basics/indextypes.pdf
Docs/sphinx_documentation/source/EB/EB_example.eps
Docs/sphinx_documentation/source/EB/EB_example.pdf
Docs/sphinx_documentation/source/EB/areas_and_volumes.eps
Docs/sphinx_documentation/source/EB/areas_and_volumes.pdf
Docs/sphinx_documentation/source/EB/eb_fluxes.eps
Docs/sphinx_documentation/source/EB/eb_fluxes.pdf
Docs/sphinx_documentation/source/EB/graph.pdf
Docs/sphinx_documentation/source/EB/multidivide.pdf
Docs/sphinx_documentation/source/EB/redist.eps
Docs/sphinx_documentation/source/EB/redist.pdf
Docs/sphinx_documentation/source/EB/volume.pdf
Docs/sphinx_documentation/source/GPU/Streams.pdf
Docs/sphinx_documentation/source/GPU/gpu_1.pdf
Docs/sphinx_documentation/source/GPU/gpu_2.pdf
Docs/sphinx_documentation/source/GPU/gpu_3.pdf
Docs/sphinx_documentation/source/LinearSolvers/refluxfreecoarsefine.pdf
Docs/sphinx_documentation/source/Particle/neighbor_list.pdf
Docs/sphinx_documentation/source/Particle/neighbor_particles.pdf
Docs/sphinx_documentation/source/Particle/particle_arrays.pdf
Docs/sphinx_documentation/source/Visualization/Amrvis_2d.eps
Docs/sphinx_documentation/source/Visualization/Amrvis_2d.pdf
Docs/sphinx_documentation/source/Visualization/Amrvis_3d.eps
Docs/sphinx_documentation/source/Visualization/Amrvis_3d.pdf
Docs/sphinx_documentation/source/Visualization/ParaView.eps
Docs/sphinx_documentation/source/Visualization/ParaView.pdf
Docs/sphinx_documentation/source/Visualization/ParaView_particles.eps.REMOVED.git-id
Docs/sphinx_documentation/source/Visualization/ParaView_particles.pdf
Docs/sphinx_documentation/source/Visualization/VisIt_2D.eps
Docs/sphinx_documentation/source/Visualization/VisIt_2D.pdf
Docs/sphinx_documentation/source/Visualization/VisIt_3D.eps
Docs/sphinx_documentation/source/Visualization/VisIt_3D.pdf

commit 71623c0c255945c24bd7e07ba9fc2a5f49e97ee6
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 17 17:50:06 2020 -0700

    remove timestramp files from Tools (#764)

Tools/Postprocessing/python/timestamp_00.REMOVED.git-id
Tools/Postprocessing/python/timestamp_02.REMOVED.git-id

commit dd60d07a9015ab0aabbc313c8baf8abf783ce208
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 17 17:31:43 2020 -0700

    remove more grids files (#765)

Tests/C_BaseLib/ba.15456.REMOVED.git-id
Tests/C_BaseLib/ba.15784.REMOVED.git-id
Tests/C_BaseLib/ba.213
Tests/C_BaseLib/ba.23925.REMOVED.git-id
Tests/C_BaseLib/ba.25600.REMOVED.git-id
Tests/C_BaseLib/ba.3865
Tests/C_BaseLib/ba.5034
Tests/C_BaseLib/ba.60
Tests/C_BaseLib/ba.95860.REMOVED.git-id
Tests/C_BaseLib/ba.mac.294

commit 3b3b27fba21c08135c6a99a46b55932644272cfe
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 17 17:29:29 2020 -0700

    remove large grids files (#763)

Tests/LinearSolvers/C_CellMG/grids/gr.2_19boxes
Tests/LinearSolvers/C_CellMG/grids/gr.2_256squared
Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_c
Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_c
Tests/LinearSolvers/C_CellMG/grids/gr.2_3x2
Tests/LinearSolvers/C_CellMG/grids/gr.2_big
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_d
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_e
Tests/LinearSolvers/C_CellMG/grids/gr.2_small_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_small_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_c
Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_d
Tests/LinearSolvers/C_CellMG/grids/gr.3_128cubed
Tests/LinearSolvers/C_CellMG/grids/gr.3_256cubed
Tests/LinearSolvers/C_CellMG/grids/gr.3_2boxes_a
Tests/LinearSolvers/C_CellMG/grids/gr.3_2x3x4
Tests/LinearSolvers/C_CellMG/grids/gr.3_512cubed
Tests/LinearSolvers/C_CellMG/grids/gr.3_big
Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/gr.3_mac_tst
Tests/LinearSolvers/C_CellMG/grids/gr.3_shiftedUp
Tests/LinearSolvers/C_CellMG/grids/gr.3_small_a
Tests/LinearSolvers/C_CellMG/grids/gr.3_stack_a
Tests/LinearSolvers/C_CellMG/grids/grids.15456.REMOVED.git-id
Tests/LinearSolvers/C_CellMG/grids/grids.213
Tests/LinearSolvers/C_CellMG/grids/grids.25600.REMOVED.git-id
Tests/LinearSolvers/C_CellMG/grids/grids.5034
Tests/LinearSolvers/C_CellMG/grids/in.2_19boxes
Tests/LinearSolvers/C_CellMG/grids/in.2_256squared
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_a
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_b
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_c
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_a
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_b
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_c
Tests/LinearSolvers/C_CellMG/grids/in.2_3x2
Tests/LinearSolvers/C_CellMG/grids/in.2_big
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_d
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_e
Tests/LinearSolvers/C_CellMG/grids/in.2_small_a
Tests/LinearSolvers/C_CellMG/grids/in.2_small_b
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_a
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_b
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_c
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_d
Tests/LinearSolvers/C_CellMG/grids/in.2per_2x2_c
Tests/LinearSolvers/C_CellMG/grids/in.3_128cubed
Tests/LinearSolvers/C_CellMG/grids/in.3_256cubed
Tests/LinearSolvers/C_CellMG/grids/in.3_2boxes_a
Tests/LinearSolvers/C_CellMG/grids/in.3_2x3x4
Tests/LinearSolvers/C_CellMG/grids/in.3_512cubed
Tests/LinearSolvers/C_CellMG/grids/in.3_big
Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/in.3_mac_tst
Tests/LinearSolvers/C_CellMG/grids/in.3_shiftedUp
Tests/LinearSolvers/C_CellMG/grids/in.3_small_a
Tests/LinearSolvers/C_CellMG/grids/in.3_stack_a
Tests/LinearSolvers/C_CellMG/grids/in.3per_2x3x4
Tests/LinearSolvers/C_CellMG/grids/in.grids.15456
Tests/LinearSolvers/C_CellMG/grids/in.grids.213
Tests/LinearSolvers/C_CellMG/grids/in.grids.25600
Tests/LinearSolvers/C_CellMG/grids/in.grids.5034
Tests/LinearSolvers/C_TensorMG/grids/gr.3_2x3x4
Tests/LinearSolvers/C_TensorMG/grids/gr16.dog
Tests/LinearSolvers/C_TensorMG/grids/gr16x8.dog
Tests/LinearSolvers/C_TensorMG/grids/gr2D
Tests/LinearSolvers/C_TensorMG/grids/gr32.dog
Tests/LinearSolvers/C_TensorMG/grids/gr32x8.dog
Tests/LinearSolvers/C_TensorMG/grids/gr64.dog
Tests/LinearSolvers/C_TensorMG/grids/gr8.dog
Tests/LinearSolvers/MLMG/grids/gr.3_128cubed
Tests/LinearSolvers/MLMG/grids/gr.3_256cubed
Tests/LinearSolvers/MLMG/grids/gr.3_2boxes_a
Tests/LinearSolvers/MLMG/grids/gr.3_2x3x4
Tests/LinearSolvers/MLMG/grids/gr.3_512cubed
Tests/LinearSolvers/MLMG/grids/gr.3_big
Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_a
Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_b
Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_c
Tests/LinearSolvers/MLMG/grids/gr.3_mac_tst
Tests/LinearSolvers/MLMG/grids/gr.3_shiftedUp
Tests/LinearSolvers/MLMG/grids/gr.3_small_a
Tests/LinearSolvers/MLMG/grids/gr.3_stack_a
Tests/LinearSolvers/MLMG/grids/grids.15456.REMOVED.git-id
Tests/LinearSolvers/MLMG/grids/grids.213
Tests/LinearSolvers/MLMG/grids/grids.25600.REMOVED.git-id
Tests/LinearSolvers/MLMG/grids/grids.5034
Tests/complementIn/grids/grids_1
Tests/complementIn/grids/grids_10.REMOVED.git-id
Tests/complementIn/grids/grids_2
Tests/complementIn/grids/grids_3.REMOVED.git-id
Tests/complementIn/grids/grids_4.REMOVED.git-id
Tests/complementIn/grids/grids_5.REMOVED.git-id
Tests/complementIn/grids/grids_6
Tests/complementIn/grids/grids_7
Tests/complementIn/grids/grids_8.REMOVED.git-id
Tests/complementIn/grids/grids_9.REMOVED.git-id

commit 86cf441f037a80ab6fa3ddd1933b7e06f556eef3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 17 19:49:57 2020 -0700

    remove these sensi files because there is already Tutorials/SENSEI (#768)

Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_catalyst.py
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.session
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.session
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_libsim.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/write_vtk.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_catalyst.py
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml
Tutorials/GPU/Advection_AmrCore/README_SENSEI.md

commit 3be8f0daaaba6c897f2e95eeefaae6214a0c0f93
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 17 17:50:26 2020 -0700

    Weiqun/rm eps pdf (#766)
    
    * remove large grids files
    
    * remove timestramp files from Tools
    
    * remove more grids files
    
    * remove unused eps and pdf files

Docs/sphinx_documentation/source/AmrCore/figs/Adv1.pdf
Docs/sphinx_documentation/source/AmrCore/figs/Adv2.pdf
Docs/sphinx_documentation/source/AmrCore/figs/Adv3.pdf
Docs/sphinx_documentation/source/AmrCore/figs/Adv4.pdf
Docs/sphinx_documentation/source/AmrCore/figs/Adv5.pdf
Docs/sphinx_documentation/source/AmrCore/figs/flowchart.pdf
Docs/sphinx_documentation/source/AmrCore/figs/subcycling.pdf
Docs/sphinx_documentation/source/AmrLevel/figs/flowchart.pdf
Docs/sphinx_documentation/source/Basics/amrgrids.pdf
Docs/sphinx_documentation/source/Basics/cc_growbox.pdf
Docs/sphinx_documentation/source/Basics/cc_tilebox.pdf
Docs/sphinx_documentation/source/Basics/cc_validbox.pdf
Docs/sphinx_documentation/source/Basics/ec_growbox.pdf
Docs/sphinx_documentation/source/Basics/ec_tilebox.pdf
Docs/sphinx_documentation/source/Basics/ec_validbox.pdf
Docs/sphinx_documentation/source/Basics/figs/flowchart.pdf
Docs/sphinx_documentation/source/Basics/indextypes.pdf
Docs/sphinx_documentation/source/EB/EB_example.eps
Docs/sphinx_documentation/source/EB/EB_example.pdf
Docs/sphinx_documentation/source/EB/areas_and_volumes.eps
Docs/sphinx_documentation/source/EB/areas_and_volumes.pdf
Docs/sphinx_documentation/source/EB/eb_fluxes.eps
Docs/sphinx_documentation/source/EB/eb_fluxes.pdf
Docs/sphinx_documentation/source/EB/graph.pdf
Docs/sphinx_documentation/source/EB/multidivide.pdf
Docs/sphinx_documentation/source/EB/redist.eps
Docs/sphinx_documentation/source/EB/redist.pdf
Docs/sphinx_documentation/source/EB/volume.pdf
Docs/sphinx_documentation/source/GPU/Streams.pdf
Docs/sphinx_documentation/source/GPU/gpu_1.pdf
Docs/sphinx_documentation/source/GPU/gpu_2.pdf
Docs/sphinx_documentation/source/GPU/gpu_3.pdf
Docs/sphinx_documentation/source/LinearSolvers/refluxfreecoarsefine.pdf
Docs/sphinx_documentation/source/Particle/neighbor_list.pdf
Docs/sphinx_documentation/source/Particle/neighbor_particles.pdf
Docs/sphinx_documentation/source/Particle/particle_arrays.pdf
Docs/sphinx_documentation/source/Visualization/Amrvis_2d.eps
Docs/sphinx_documentation/source/Visualization/Amrvis_2d.pdf
Docs/sphinx_documentation/source/Visualization/Amrvis_3d.eps
Docs/sphinx_documentation/source/Visualization/Amrvis_3d.pdf
Docs/sphinx_documentation/source/Visualization/ParaView.eps
Docs/sphinx_documentation/source/Visualization/ParaView.pdf
Docs/sphinx_documentation/source/Visualization/ParaView_particles.eps.REMOVED.git-id
Docs/sphinx_documentation/source/Visualization/ParaView_particles.pdf
Docs/sphinx_documentation/source/Visualization/VisIt_2D.eps
Docs/sphinx_documentation/source/Visualization/VisIt_2D.pdf
Docs/sphinx_documentation/source/Visualization/VisIt_3D.eps
Docs/sphinx_documentation/source/Visualization/VisIt_3D.pdf

commit 6a52f407bc6edbfdfe2498d64cddb7e37ea426d1
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 17 17:50:06 2020 -0700

    remove timestramp files from Tools (#764)

Tools/Postprocessing/python/timestamp_00.REMOVED.git-id
Tools/Postprocessing/python/timestamp_02.REMOVED.git-id

commit 5710b81dec26ee1935ed9f4e8cfca9660792f490
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 17 17:31:43 2020 -0700

    remove more grids files (#765)

Tests/C_BaseLib/ba.15456.REMOVED.git-id
Tests/C_BaseLib/ba.15784.REMOVED.git-id
Tests/C_BaseLib/ba.213
Tests/C_BaseLib/ba.23925.REMOVED.git-id
Tests/C_BaseLib/ba.25600.REMOVED.git-id
Tests/C_BaseLib/ba.3865
Tests/C_BaseLib/ba.5034
Tests/C_BaseLib/ba.60
Tests/C_BaseLib/ba.95860.REMOVED.git-id
Tests/C_BaseLib/ba.mac.294

commit 1aba0fdb287760db3b4d6b4d7a2cd69cbd6f8dff
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 17 17:29:29 2020 -0700

    remove large grids files (#763)

Tests/LinearSolvers/C_CellMG/grids/gr.2_19boxes
Tests/LinearSolvers/C_CellMG/grids/gr.2_256squared
Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_c
Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_c
Tests/LinearSolvers/C_CellMG/grids/gr.2_3x2
Tests/LinearSolvers/C_CellMG/grids/gr.2_big
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_d
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_e
Tests/LinearSolvers/C_CellMG/grids/gr.2_small_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_small_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_c
Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_d
Tests/LinearSolvers/C_CellMG/grids/gr.3_128cubed
Tests/LinearSolvers/C_CellMG/grids/gr.3_256cubed
Tests/LinearSolvers/C_CellMG/grids/gr.3_2boxes_a
Tests/LinearSolvers/C_CellMG/grids/gr.3_2x3x4
Tests/LinearSolvers/C_CellMG/grids/gr.3_512cubed
Tests/LinearSolvers/C_CellMG/grids/gr.3_big
Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/gr.3_mac_tst
Tests/LinearSolvers/C_CellMG/grids/gr.3_shiftedUp
Tests/LinearSolvers/C_CellMG/grids/gr.3_small_a
Tests/LinearSolvers/C_CellMG/grids/gr.3_stack_a
Tests/LinearSolvers/C_CellMG/grids/grids.15456.REMOVED.git-id
Tests/LinearSolvers/C_CellMG/grids/grids.213
Tests/LinearSolvers/C_CellMG/grids/grids.25600.REMOVED.git-id
Tests/LinearSolvers/C_CellMG/grids/grids.5034
Tests/LinearSolvers/C_CellMG/grids/in.2_19boxes
Tests/LinearSolvers/C_CellMG/grids/in.2_256squared
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_a
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_b
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_c
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_a
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_b
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_c
Tests/LinearSolvers/C_CellMG/grids/in.2_3x2
Tests/LinearSolvers/C_CellMG/grids/in.2_big
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_d
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_e
Tests/LinearSolvers/C_CellMG/grids/in.2_small_a
Tests/LinearSolvers/C_CellMG/grids/in.2_small_b
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_a
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_b
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_c
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_d
Tests/LinearSolvers/C_CellMG/grids/in.2per_2x2_c
Tests/LinearSolvers/C_CellMG/grids/in.3_128cubed
Tests/LinearSolvers/C_CellMG/grids/in.3_256cubed
Tests/LinearSolvers/C_CellMG/grids/in.3_2boxes_a
Tests/LinearSolvers/C_CellMG/grids/in.3_2x3x4
Tests/LinearSolvers/C_CellMG/grids/in.3_512cubed
Tests/LinearSolvers/C_CellMG/grids/in.3_big
Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/in.3_mac_tst
Tests/LinearSolvers/C_CellMG/grids/in.3_shiftedUp
Tests/LinearSolvers/C_CellMG/grids/in.3_small_a
Tests/LinearSolvers/C_CellMG/grids/in.3_stack_a
Tests/LinearSolvers/C_CellMG/grids/in.3per_2x3x4
Tests/LinearSolvers/C_CellMG/grids/in.grids.15456
Tests/LinearSolvers/C_CellMG/grids/in.grids.213
Tests/LinearSolvers/C_CellMG/grids/in.grids.25600
Tests/LinearSolvers/C_CellMG/grids/in.grids.5034
Tests/LinearSolvers/C_TensorMG/grids/gr.3_2x3x4
Tests/LinearSolvers/C_TensorMG/grids/gr16.dog
Tests/LinearSolvers/C_TensorMG/grids/gr16x8.dog
Tests/LinearSolvers/C_TensorMG/grids/gr2D
Tests/LinearSolvers/C_TensorMG/grids/gr32.dog
Tests/LinearSolvers/C_TensorMG/grids/gr32x8.dog
Tests/LinearSolvers/C_TensorMG/grids/gr64.dog
Tests/LinearSolvers/C_TensorMG/grids/gr8.dog
Tests/LinearSolvers/MLMG/grids/gr.3_128cubed
Tests/LinearSolvers/MLMG/grids/gr.3_256cubed
Tests/LinearSolvers/MLMG/grids/gr.3_2boxes_a
Tests/LinearSolvers/MLMG/grids/gr.3_2x3x4
Tests/LinearSolvers/MLMG/grids/gr.3_512cubed
Tests/LinearSolvers/MLMG/grids/gr.3_big
Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_a
Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_b
Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_c
Tests/LinearSolvers/MLMG/grids/gr.3_mac_tst
Tests/LinearSolvers/MLMG/grids/gr.3_shiftedUp
Tests/LinearSolvers/MLMG/grids/gr.3_small_a
Tests/LinearSolvers/MLMG/grids/gr.3_stack_a
Tests/LinearSolvers/MLMG/grids/grids.15456.REMOVED.git-id
Tests/LinearSolvers/MLMG/grids/grids.213
Tests/LinearSolvers/MLMG/grids/grids.25600.REMOVED.git-id
Tests/LinearSolvers/MLMG/grids/grids.5034
Tests/complementIn/grids/grids_1
Tests/complementIn/grids/grids_10.REMOVED.git-id
Tests/complementIn/grids/grids_2
Tests/complementIn/grids/grids_3.REMOVED.git-id
Tests/complementIn/grids/grids_4.REMOVED.git-id
Tests/complementIn/grids/grids_5.REMOVED.git-id
Tests/complementIn/grids/grids_6
Tests/complementIn/grids/grids_7
Tests/complementIn/grids/grids_8.REMOVED.git-id
Tests/complementIn/grids/grids_9.REMOVED.git-id

commit 273b9d0c132f5259d71f7a564e143ff1feff0cf9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Apr 17 13:25:49 2020 -0700

    Add EB_interp_CellCentroid_to_FaceCentroid routines in 2D and 3D...

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit 64728fa54c01aa9307dd31ee129b15a7c4a62aed
Merge: 8adea484f 2d2d0c02f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 17 12:50:49 2020 -0700

    merging development into atmyers/mpi_datatype

commit 2d2d0c02f6363820ac92cf596b15656a2660fbd0
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 16 19:12:46 2020 -0700

    Add sort argument for makeKnapSack (#761)
    
    Co-authored-by: WeiqunZhang <WeiqunZhang@lbl.gov>

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit a6e68d7731d35a55fd5d16a4bf0a602a236bd5ae
Merge: 1cac20f21 61f751eb1
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 16 18:53:40 2020 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 1cac20f21344412c4b99cd09290a5020262be1eb
Merge: 87e7f603e eda314ad8
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 16 18:53:21 2020 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 61f751eb10fec682cc67e1f0f4d0e5a12753cc60
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 16 18:53:14 2020 -0700

    replace pow with *

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit 87e7f603ec9651b27952917fe051cb695fa7905f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 16 18:51:10 2020 -0700

    CMake: use native CMake tools to generate AMReX_buildInfo.cpp.
    
    This commit removes the dependency on python to generate
    AMReX_buildInfo.cpp.
    AMReX_buildInfo.cpp is now generated from AMReX_buildInfo.cpp.in
    using CMake native configure_file().

Tools/CMake/AMReXBuildInfo.cmake
Tools/CMake/AMReX_buildInfo.cpp.in

commit eda314ad8a5c37e3f6f8c7a890bbb2858471b8db
Merge: 92136adf2 8ee9bcad5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 16 18:51:04 2020 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8ee9bcad53cac04d4625819096134cfe16cf6373
Merge: f4802fe5d 4f671cebd
Author: mic84 <mrosso@lbl.gov>
Date:   Thu Apr 16 18:43:55 2020 -0700

    Merge pull request #762 from ax3l/topic-ciMacOS
    
    CI: macOS

commit 4f671cebd64bff8a84ce16d72c60e4c2f3e6b03e
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Apr 16 17:58:16 2020 -0700

    CI: macOS
    
    Since more than half of our developers use macOS for development,
    its time to check how well we support native compilers.

.github/workflows/cmake.yml
.github/workflows/cmake/dependencies_mac.sh

commit 92136adf2791a92689702fc2321eb75356813571
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 16 17:13:17 2020 -0700

    long -> amrex::Long in Tools

Tools/Plotfile/AMReX_PPMUtil.cpp
Tools/Plotfile/fboxinfo.cpp
Tools/Postprocessing/C_Src/PlotfileToMatLab.cpp

commit 2667bfdec8537194fc219330b6fcaec57b4f7a65
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 16 17:04:21 2020 -0700

    long -> amrex::Long in Tutorials

Tutorials/Basic/PrefixSum_MultiFab/main.cpp
Tutorials/GPU/Launch/main.cpp
Tutorials/GPU/ParallelReduce/main.cpp
Tutorials/GPU/ParallelScan/main.cpp
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90
Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp

commit f71ca214f4700ee0c931c5398d5323a69eb76fb5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 16 16:56:54 2020 -0700

    long -> amrex::Long in Src/Extern

Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp
Src/Extern/PETSc/AMReX_PETSc.cpp
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/Extern/amrdata/AMReX_DataServices.cpp

commit 19be07bb06ac55a7dfb101c053444853206cb5f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 16 10:00:46 2020 -0700

    long -> amrex::Long in Particle/ and F_Interfaces

Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_ccse-mpi.H
Src/F_Interfaces/Base/AMReX_box_mod.F90
Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_fab_mod.F90
Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90
Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_ParticleMPIUtil.H
Src/Particle/AMReX_ParticleMPIUtil.cpp
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_SparseBins.H

commit 80f30c5675e04fa2ec870bc8e3a0b972c4119354
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 16 09:46:24 2020 -0700

    more long -> amrex::Long

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_Cluster.H
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H

commit 082e714c5d7fbf05f99f610ba54f522723e38bf2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 15 17:34:04 2020 -0700

    long -> amrex::Long in Base/

Docs/sphinx_documentation/source/BuildingAMReX.rst
Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_Array4.H
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CudaGraph.H
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FPC.H
Src/Base/AMReX_FPC.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabConv.H
Src/Base/AMReX_FabConv.cpp
Src/Base/AMReX_GpuAtomic.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuMemory.H
Src/Base/AMReX_GpuRange.H
Src/Base/AMReX_GpuUtility.H
Src/Base/AMReX_INT.H
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_MemProfiler.H
Src/Base/AMReX_MemProfiler.cpp
Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ParmParse.H
Src/Base/AMReX_ParmParse.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_Random.H
Src/Base/AMReX_Random.cpp
Src/Base/AMReX_Scan.H
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Vector.H
Src/Base/AMReX_VectorIO.H
Src/Base/AMReX_VectorIO.cpp
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp
Src/Base/AMReX_ccse-mpi.H
Src/Base/AMReX_fort_mod.F90
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp

commit f4802fe5d08f4473a0750d88ce43ae089804768c
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Wed Apr 15 16:41:49 2020 -0700

    porting CompVelGrad to EB world to allow compilation of IAMR and PeleLM with EB=TRUE

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit 23a8c3516f5dcb98df87155607c2b193661d0861
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Wed Apr 15 16:39:38 2020 -0700

    Add profiling to makeSFC routines (#760)

Src/Base/AMReX_DistributionMapping.cpp

commit a95520e59aeabb730bc8858aef7dc93d15951504
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 15 16:19:57 2020 -0700

    typo

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit b48397202fb3458877f75b35958c35231ee42930
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 15 15:56:18 2020 -0700

    update documentaion

Docs/sphinx_documentation/source/BuildingAMReX.rst
Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst
Docs/sphinx_documentation/source/GettingStarted.rst
Docs/sphinx_documentation/source/Introduction.rst

commit 26e07326c33254149039db52d2ffb373b3ef60fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 15 15:50:23 2020 -0700

    set DIM=3 by default for consistence with cmake

Tools/GNUMake/Make.defs

commit a66374e07ac48de468e7ab519c2d64721a9cf92b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 15 15:45:23 2020 -0700

    no longer print arean usage for cpu build by default

Src/Base/AMReX_Arena.cpp

commit a877627493379151aacd52ebe6183ef35c81cb57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 15 15:44:52 2020 -0700

    add .hpp to vpath

Tools/GNUMake/Make.rules

commit 20f103825e33a39324d254797834c91d76acb922
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 15 15:44:30 2020 -0700

    make DEBUG=FALSE the default to be consistent with cmake

Tools/GNUMake/Make.defs

commit b70dc0fffce1dfe733d3e88e475736a77005af41
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 15 12:35:26 2020 -0700

    "maxorder" is an unused variable when doing the nodal projection.

Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 3f2b4bf022fdedae4e67dd411ccf989e2263a4f5
Merge: 43e10a6c5 5ab5fd398
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 15 11:33:53 2020 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 43e10a6c5ce4cd50a0b5b186137c7273e871e836
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 15 10:19:54 2020 -0700

    fix deprecated defeatures

Src/EB/AMReX_EB2_GeometryShop.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/Particle/AMReX_ArrayOfStructs.H
Tools/GNUMake/comps/gnu.mak
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/GPU/EBCNS/Source/CNS.cpp
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp

commit 5ab5fd39834a44e560d94becd961cd29ae07a873
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Apr 15 10:10:48 2020 -0700

    CMake: consider case of empty CMAKE_BUILD_TYPE in AMReXBuildInfo.cmake

Tools/CMake/AMReXBuildInfo.cmake

commit 3c341becd024cfc86b277003ffa402932e3d2b09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 15 09:39:02 2020 -0700

    option to add -Werror=deprecated

Tools/GNUMake/comps/gnu.mak

commit 8adea484f13b8faaa8c955832fe5466caee558aa
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Apr 14 20:24:38 2020 -0400

    (more) use long to avoid overflow issues

Src/Particle/AMReX_ParticleTile.H

commit 16c28e6a09fe8f83ce00a764a42d24efca5e94cb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Apr 14 20:24:07 2020 -0400

    use long to avoid overflow issues

Src/Particle/AMReX_ParticleCommunication.H

commit cdbb701a5986ad32b00421027f95b7f8350d510a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Apr 14 20:23:20 2020 -0400

    make sure the host and device copies of the level offsets have the same size

Src/Particle/AMReX_ParticleBufferMap.cpp

commit c4252f5bbf535cac03075298421461c69da85540
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 14 15:07:04 2020 -0700

    fix shadow warning in some cases

Src/Base/AMReX_BLProfiler.H

commit b7630cb2b70ebaa648664f8166281140d9171a25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 14 14:33:39 2020 -0700

    fix reorder

Src/Base/AMReX_TinyProfiler.H

commit ad8330be0fa0894b071ff9222941c217520a4d59
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 14 11:08:59 2020 -0700

    minor optimization by avoiding copy

Src/Base/AMReX_MultiFabUtil.cpp

commit 479f5c0abd6ab2d12a88566dca0cd8c2f2f170da
Merge: 0982acd9c f0822e8c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 13 20:25:29 2020 -0700

    Merge branch 'dpcpp' into development

commit 0982acd9c6bf7e613601a60efcadbb2cbd1745d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 13 19:29:41 2020 -0700

    GpuBndryFunc: special cases for single box and cpu

Src/Base/AMReX_PhysBCFunct.H

commit 9cbd8a63ac276075968e3e3eb6d0da68a54404f4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 13 17:13:05 2020 -0700

    get rid of a bunch of ___

Src/Base/AMReX_BLProfiler.H
Tutorials/Blueprint/HeatEquation_EX1_C/Source/myfunc_F.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc_F.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc_F.H
Tutorials/SDC/MISDC_ADR_2d/Source/myfunc_F.H

commit 938db17c0a61b7f40af4a1ddb17ab9aa77f512a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 13 16:48:01 2020 -0700

    some cleanup of cputitrace

Src/Base/AMReX.cpp
Src/Base/AMReX_CuptiTrace.H
Src/Base/AMReX_CuptiTrace.cpp

commit cd24b951778e36f4051ee867f36f8fc911263724
Merge: 7d0b93a31 83c63f2ea
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 13 19:17:54 2020 -0400

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 83c63f2eac8bbf63f3c215e35a9b46539f8679ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 13 15:54:36 2020 -0700

    fix for pgi on cori gpu

Tools/GNUMake/sites/Make.nersc

commit 7d0b93a31a43cd4a36c90b871a146d27b13d4427
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 13 18:42:42 2020 -0400

    CMake: disable target run_HeatEquation_EX1_C.exe if ENABLE_CUDA=ON

Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt

commit e7ee45e4ca1805aaeebd4b98be21a05299c1b00b
Merge: c336311bd 26fb102e1
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 13 18:10:03 2020 -0400

    Merge branch 'development' into mr/cmake-bl-no-fort

commit 26fb102e1c4d8ded5d1d384cef442329da44d517
Merge: cd8fd3314 2fb140db3
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 13 17:56:41 2020 -0400

    Merge branch 'mr/cmake-cuda-tutorials' into development

commit cd8fd331432fb10cef3ed1cb2777c20c477ddedb
Merge: 8e84e8f97 3b1b92e36
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Apr 13 14:46:00 2020 -0700

    Merge pull request #616 from mrowan137/mrowan/CUPTI_trace
    
    Add CUPTI trace feature for GPU kernel timing

commit 2fb140db316c4f096b8ce54beda46b2ef0d95fe6
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 13 17:28:05 2020 -0400

    CMake: set language of amrex sources via set_cpp_sources_to_cuda_language

Src/CMakeLists.txt

commit 8761f5018ecd83843617d6d2598ab9341994027a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 13 17:16:54 2020 -0400

    CMake: CUDA-fy tutorials

Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt
Tutorials/LinearSolvers/ABecLaplacian_C/CMakeLists.txt
Tutorials/LinearSolvers/MultiComponent/CMakeLists.txt
Tutorials/LinearSolvers/NodalPoisson/CMakeLists.txt
Tutorials/LinearSolvers/NodeTensorLap/CMakeLists.txt

commit 702f293072cc86cf8b564769d418a903c1dc89fb
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 13 17:16:27 2020 -0400

    CMake: add helper function to mark C++ source files as CUDA

Tools/CMake/AMReXTargetHelpers.cmake

commit f0822e8c424ecc0de39836ab78dd78bd4614a5f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 13 13:17:25 2020 -0700

    make Tutorials/GPU/CNS work with DPC++ by avoiding global variables

Tutorials/GPU/CNS/Exec/RT/cns_prob.H
Tutorials/GPU/CNS/Exec/RT/cns_prob.cpp
Tutorials/GPU/CNS/Exec/RT/cns_prob_parm.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp
Tutorials/GPU/CNS/Exec/Sod/cns_prob_parm.H
Tutorials/GPU/CNS/Source/CNS.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/CNS_derive.cpp
Tutorials/GPU/CNS/Source/CNS_parm.H
Tutorials/GPU/CNS/Source/CNS_parm.cpp
Tutorials/GPU/CNS/Source/CNS_setup.cpp
Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H

commit 0780ea0e8fb0ff7d92aad16facb9a09cf70d5785
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 13 12:05:07 2020 -0700

    operator delete: for safety test the pointer first

Src/Base/AMReX_GpuMemory.H

commit 0af0f99a72777960e56a3666b692009745e03043
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 13 09:41:23 2020 -0700

    reorganize various ParalleFor functions

Src/Base/AMReX_GpuLaunchFunctsG.H

commit cf0b059c96b0e307872d06b334a547d75a7734b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 13 09:10:34 2020 -0700

    add amrex::IsHostDeviceLambda

Src/Base/AMReX_TypeTraits.H

commit 8e84e8f97ea8205214be04a7a205ed5b6f6cd3f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 12 20:15:06 2020 -0700

    fix link to mpi on Cori gpu

Tools/GNUMake/sites/Make.nersc

commit 1699c94d4364fc3b09a0e8d82d6f2b986bf1a726
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 12 13:13:19 2020 -0700

    Copy beta from host to GPU when beta is Vector<Real> not just Real -- in setEBDirichlet and setEBHomogDirichlet

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit fa6530436ba95b67313218a54f0204e27c2e089c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 12 12:00:00 2020 -0700

    For setting the beta coefficients for a multicomponent CC solve in EB and non-EB versions,
    1) we now allow the user to pass an array of scalars as an alternative to a single scalar
    2) when a MultiFab is passed in, we assert that there is either 1 component or the same number
    of components as the solution so either copy component by component or just from the one component
    as appropriate.
    These changes are in the setBCoeffs, setEBDirichlet and setEBHomogDirichlet calls
    of AMReX_MLABecLaplacian.* and AMReX_MLEBABecLap.*.

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit ae9b193116606101ca9ebfd47447c12af1a53a1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 10 14:02:07 2020 -0700

    update wishlist

Docs/Notes/DPCPPWishlist.md

commit c336311bdb1407b43a4674f5027d2a2a8d91cd97
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 9 17:23:01 2020 -0700

    CMake: don't build tutorials with Fortran sources if ENABLE_FORTRAN=OFF

Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt

commit a6b5acda22cb651ce76eb969b1a6ff7c9e565306
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 9 17:05:27 2020 -0700

    CI: add make command to build tutorials

.github/workflows/cmake.yml

commit 96b1117e36d3c49495310bfd005391256a8e4e78
Merge: 15220b232 7c3b2698a
Author: mic84 <mrosso@lbl.gov>
Date:   Thu Apr 9 17:01:09 2020 -0700

    Merge pull request #759 from ax3l/fix-cmakeVersionMatch
    
    CMake: Regex Version Validator

commit 7c3b2698a13094d702a92820d2649a52c1da154b
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Apr 9 16:49:39 2020 -0700

    CMake: Regex Version Validator
    
    If what we get from `git describe` does not match
    `<Number>.<Number>[.<Number>][-something]` then we treat that
    as not a proper version.

CMakeLists.txt

commit 15220b232aca637c27a644f70ecb72a3acf37d96
Author: jmsexton03 <jmsexton@lbl.gov>
Date:   Thu Apr 9 10:52:55 2020 -0700

    Cori-gpu make update for testing USE_MPI=TRUE USE_CUDA=FALSE (#753)
    
    Building with USE_CUDA=TRUE on Cori login nodes is now disallowed; CUDA builds must be done from cgpu nodes. We now uniformly support OpenMPI, MVAPICH, and MPICH. The Make.nersc file is cleaned up a bit as a result.

Src/Base/AMReX_Machine.cpp
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.nersc

commit 570844d3d2bc9bbf71392813f2a3afc555681f04
Merge: effc622d2 f918ae798
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Apr 8 21:04:26 2020 -0700

    Merge branch 'mr/cmake-bl-no-fort' of https://github.com/AMReX-Codes/amrex into mr/cmake-bl-no-fort

commit effc622d2f89093c5f32414e507d3acff8e52469
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Apr 8 21:04:08 2020 -0700

    CMake: implement ENABLE_FORTRAN (BL_NO_FORT) option

CMakeLists.txt
Docs/sphinx_documentation/source/BuildingAMReX.rst
Src/Amr/CMakeLists.txt
Src/AmrCore/CMakeLists.txt
Src/Base/CMakeLists.txt
Src/Boundary/CMakeLists.txt
Src/EB/CMakeLists.txt
Src/LinearSolvers/CMakeLists.txt
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake

commit 30314de4f19256b7736dc7389771d335586fbf97
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 8 20:51:47 2020 -0700

    loop on cpu instead

Tools/Plotfile/fsnapshot.cpp

commit f918ae7982cf1415abdf4f8eb25a47d0c489d35e
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Apr 8 19:13:28 2020 -0700

    CI: Remove gfortran for No-Fortran Build

.github/workflows/cmake.yml
.github/workflows/cmake/dependencies_nofortran.sh

commit 64edb83bbccfee00572b59de83dbf39cd2807a52
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Apr 8 19:11:16 2020 -0700

    CI: Add a Fortran-Free CMake Build

.github/workflows/cmake.yml

commit 206a3c9c816a7ca6fe2dab72a21aa4f533656e07
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Apr 8 18:29:58 2020 -0700

    No need to define Fortran functions if BL_NO_FORT is TRUE

Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_Random.cpp

commit 5fb3be52571d82d2252d2ca6e86bd42bf262737f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Apr 8 17:16:06 2020 -0400

    CMake: add CUDA-support to plotfile tools build. It fixes issue #748

Tools/Plotfile/CMakeLists.txt

commit a82d6303a607ae6c372881e86184ec80e6a6bbff
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 8 10:28:21 2020 -0700

    add some missing AMREX_GPU_HOST_DEVICE

Tools/Plotfile/fsnapshot.cpp

commit 84265ea5db97cbee1342da22e957c6976a631530
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 7 20:01:47 2020 -0700

    fix multiple exectuables build for CUDA

Tools/GNUMake/Make.rules

commit 09f9cb751a43e8d4c4163e59e2c84c69ba6f5c1c
Merge: 53b056f40 524fd6e71
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Apr 7 17:41:43 2020 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/cmake-bl-no-fort

commit 524fd6e7136517311dbd8f9a04d4628c21b8cd35
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 7 17:35:03 2020 -0700

    No need to define BL_FORT_USE_ if BL_NO_FORT is TRUE

Src/Base/AMReX_BLFort.H

commit 53b056f4065daf70f2e8dafbb79ba6d225498270
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Apr 7 11:36:34 2020 -0700

    CMake: add native include guard to AMReX_Options.cmake

Tools/CMake/AMReX_Options.cmake

commit 7c77e104e653d1b1e29c4fab2ffe3ade98ce2f50
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 6 22:08:20 2020 -0700

    fix some warnings

Src/Amr/AMReX_Amr.cpp
Src/Base/AMReX_FabConv.cpp
Src/Base/AMReX_ForkJoin.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_nd_C.H
Src/Base/AMReX_Random.cpp
Src/Base/AMReX_Utility.cpp
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_distFcnElement.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_ParticleUtil.H
Src/Particle/AMReX_TracerParticle_mod_K.H
Tools/GNUMake/comps/gnu.mak
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp

commit 9bf2d4be00eae70313480f5b72268c788d8cd515
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 6 20:12:13 2020 -0700

    static_cast to avoid warning

Src/Base/AMReX_MultiFabUtil_nd_C.H

commit 49ea587bcab6e373062efd13ff8e0b9e4cb62120
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 6 18:22:42 2020 -0700

    fcompare: always return

Tools/Plotfile/fcompare.cpp

commit 95375ec320b2250b6aef731ed3d131aff36487fb
Merge: 0ec72262d 3fda5d099
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Apr 6 14:24:12 2020 -0700

    Merge pull request #758 from MaxThevenet/ixtype
    
    add function IndexType::toIntVect

commit 3fda5d0990aeccaf3df906df89c8b274baa52382
Author: MaxThevenet <mthevenet@lbl.gov>
Date:   Mon Apr 6 13:54:19 2020 -0700

    add function IndexType::toIntVect

Src/Base/AMReX_IndexType.H

commit 0ec72262d86817ec06a9d61fa865f689adc70131
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 6 13:10:39 2020 -0700

    allow evaluation of f on the gpu for particle filtering

Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_Particles.H

commit ff2634d4ff0d97cd7cfaff54f38d438e96022d71
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 4 16:09:07 2020 -0700

    fix namespace

Src/Base/AMReX_Utility.H

commit 810480b2b4bae1834b079885c68abfba426df479
Merge: 5aa5c3e45 2425a7894
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Apr 4 09:26:03 2020 -0700

    Merge pull request #746 from AMReX-Codes/writeplotfile_eb
    
    Writeplotfile eb

commit 5aa5c3e45aefb093b74ea5b41e047a93f05df500
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 3 21:51:17 2020 -0700

    add trim and is_it function for string

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit 2774693d0b43e710f2e5d02995aabe4cfabce98c
Merge: ff4bc0009 4305a7677
Author: mic84 <mrosso@lbl.gov>
Date:   Fri Apr 3 18:48:10 2020 -0700

    Merge pull request #755 from ax3l/fix-cmakeInvalidGitVersions
    
    CMake: Discard Invalid Git Versions

commit 4305a76772b720214752dc4238a4935d4b794c42
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri Apr 3 18:39:28 2020 -0700

    CMake: Discard Invalid Git Versions
    
    In case a user only performed a shallow copy of the git repo,
    `git describe` will not find a latest tag and return only a hash.
    Hashes are not valid `VERSION` attributes in CMake and crash the
    configuration stage.
    
    This fix just discards invalid versions and tries the fallback of
    parsing the change log file.
    
    Fix #731 (continued)
    
    Ref.: https://github.com/AMReX-Codes/amrex/issues/731#issuecomment-596077396

CMakeLists.txt

commit ff4bc0009cca362d4b9349787e38f735ceafcbc7
Merge: d13c2a662 14f0634ae
Author: mic84 <mrosso@lbl.gov>
Date:   Fri Apr 3 18:28:21 2020 -0700

    Merge pull request #749 from ax3l/topic-cmakePropsCUDA
    
    Default CMake CXX Standard Control

commit 14f0634ae7e6480f35cec5c0fb6ab902cc2b51c7
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri Apr 3 18:07:03 2020 -0700

    Finalize Build: Docs & Labels

.github/workflows/cmake.yml
CMakeLists.txt
Docs/sphinx_documentation/source/BuildingAMReX.rst

commit 3a8c0402a2405e34e720ca1dc43960e69a3fe977
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri Apr 3 17:39:08 2020 -0700

    Library CMake Build: C++17

.github/workflows/cmake.yml
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake

commit d13c2a662c330b528d4bc5027f07defe05efa017
Merge: 597cf62af 89ff6e88c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 3 17:38:01 2020 -0700

    Merge pull request #754 from rporcu/development
    
    substitute RunOn::Device with RunOn::Host in copyTo function

commit 507366d5b5b82a6ec8ab39be9e7ac66449739dc0
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Mon Mar 30 18:19:43 2020 -0700

    Add CMAKE_C_COMPILER: gcc-4.8
    
    Otherwise the system-wide 7.5.0 GCC is picked up for C sources
    (and potentially some linking).

.github/workflows/cmake.yml

commit 9adf70a3b80f9244915b434f2646bee76b6c85c5
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri Apr 3 17:09:13 2020 -0700

    Skip CMake Install
    
    Is there some recent CMake laying around??

.github/workflows/cmake.yml
.github/workflows/cmake/dependencies.sh
.github/workflows/cmake/dependencies_nvcc.sh

commit 2efd03550f49e65e957d97aeaf3ac28d26f6d963
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Mon Mar 30 17:20:35 2020 -0700

    CMake: Std only via Compile Feature

.github/workflows/cmake.yml
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake

commit 89ff6e88c5d78083a1eda1ece22a720af58dde02
Author: rporcu <robertoporcu@lbl.gov>
Date:   Fri Apr 3 19:38:04 2020 -0400

    substitute RunOn::Device with RunOn::Host in copyTo function

Src/Base/AMReX_FabArrayCommI.H

commit 1eb6f5334ae54c0e49011dd22530a71f5ceadd90
Merge: 3859780d8 597cf62af
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Apr 3 17:42:04 2020 -0400

    Merge branch 'development' into atmyers/mpi_datatype

commit 597cf62afa2d9f8b483eb19f7cfc97186dad363e
Merge: 193adb277 b31826feb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 3 08:25:41 2020 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 3b1b92e36306a070a8df846153a1cd3ac4bf23e8
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Thu Apr 2 10:41:37 2020 -0700

    [WIP] Formatting

Src/Base/AMReX_TinyProfiler.cpp
Tests/GPU/CuptiTest/Source/main.cpp

commit 8a6b318c7cf686ade56e8243cfa0a98f6ec7f646
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:23:25 2020 -0700

    Update main.cpp

Tests/GPU/CuptiTest/Source/main.cpp

commit e219285438a724e7efc0796e32a380ed24f40678
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:22:31 2020 -0700

    Update nvcc.mak

commit 36d3435e5d70036464387807c5914cad3838eb03
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:21:51 2020 -0700

    Update nvcc.mak

commit 7d809db8de008ddf00963c63ecae600db1e6c2a5
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:21:19 2020 -0700

    Update Make.defs

commit 315890077cda14e849a3d5933ccb3317cd05b34a
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:20:43 2020 -0700

    Update Make.package

commit 2ac2a2d9cefc9b96bfaa905ac2bc484ce94cc8c9
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:20:08 2020 -0700

    Update Make.CUPTI

commit cf3e95cf2f3a0bc38eb3016e9f970ae49735eab0
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:19:36 2020 -0700

    Update myfunc.cpp

commit b949602b310524e6b1982e3115b7dfb71f210c90
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:19:00 2020 -0700

    Update myfunc.H

commit 427baec4c9cce5272438951a95fee86a5d1ecb51
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:18:32 2020 -0700

    Update Make.package

commit 8e424e71853f9df2adff16cf328bb433f5bdabf1
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:18:00 2020 -0700

    Update GNUmakefile

commit 2bceefda93480fe2ced6c037fb839c86768024c0
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:17:24 2020 -0700

    Update Make.package

Src/Base/Make.package

commit ffbad9a336b2d3aa8301c092b9ce5b771004dc92
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:15:10 2020 -0700

    Update AMReX_TinyProfiler.H

commit 93e307f7c35e6374c2dc90889e77e6e9531c8803
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:14:44 2020 -0700

    Update AMReX_CuptiTrace.cpp

Src/Base/AMReX_CuptiTrace.cpp

commit 32e94fa2f4ceb0339934604652d16567004f1156
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:13:48 2020 -0700

    Update AMReX_CuptiTrace.H

commit ebc22600d34c1422bf68691e7afa15f1750da0a1
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:13:22 2020 -0700

    Update AMReX_BLProfiler.H

commit d7954ce34f8299fda95350f555eed97c97188f34
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Thu Apr 2 10:05:30 2020 -0700

    Update AMReX_CuptiTrace.cpp

Src/Base/AMReX_CuptiTrace.cpp

commit c40835214cbd88aaf3745777efdaaa37a084a7ba
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Thu Apr 2 10:00:56 2020 -0700

    [WIP] formatting mykernel.H

Tests/GPU/CuptiTest/Exec/CUDA/mykernel.H

commit ecde67289e6935ab282db55e904bf670dc016280
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Thu Apr 2 02:31:19 2020 -0700

    [WIP] Review fixes

Src/Base/AMReX_CuptiTrace.H
Src/Base/AMReX_CuptiTrace.cpp

commit c7caac2b81d7a0c28ff6713e0cae803455adb3e5
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Thu Apr 2 02:20:30 2020 -0700

    [WIP] Review fixes

Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp

commit 6a2d004ddb8324f18e66ab9831081da6128adb3a
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Thu Apr 2 02:02:14 2020 -0700

    [WIP] Review fixes

Src/Base/AMReX_CuptiTrace.H
Src/Base/AMReX_CuptiTrace.cpp
Src/Base/AMReX_TinyProfiler.cpp
Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp

commit 5ee7327e76cabc781b5ccb16ac838a2524975323
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Wed Apr 1 20:06:33 2020 -0400

    [WIP] review changes

Src/Base/AMReX_CuptiTrace.H
Src/Base/AMReX_CuptiTrace.cpp
Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp

commit b31826feb6b76b584d1f7c4a231abb17875a657f
Merge: 6eac633c8 a782eba56
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 1 13:43:56 2020 -0700

    Merge branch 'master' into development

commit 193adb277cd44ff117a3e81f58454b0ac470a032
Merge: 7075f2575 6eac633c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 1 13:42:28 2020 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit e4502c77de6d65ee75816eee565eed8dab86fe86
Merge: 0a813f20a 6eac633c8
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Wed Apr 1 15:36:38 2020 -0400

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mrowan/CUPTI_trace

commit 6eac633c8c4388ccd31eac3acee9a85fefb169af
Merge: 2fcea2a1d bef840955
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Apr 1 09:21:18 2020 -0700

    Merge pull request #750 from mwm126/patch-1
    
    Fix warning maybe-uninitialized for: the_send_data

commit 7075f25758cd1e79a2bcc2db4ed98339b89e17c6
Merge: b7e78115e a782eba56
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 1 09:08:46 2020 -0700

    Merge branch 'development' into dpcpp

commit a782eba56e024d3c6743a0953302eac21d1a2d17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 1 09:07:33 2020 -0700

    update CHANGES

CHANGES

commit bef840955be84fe9ce2ca826e1af62c8708d31d4
Author: Mark Meredith <mwm126@gmail.com>
Date:   Wed Apr 1 10:43:45 2020 -0400

    Fix warning maybe-uninitialized for: the_send_data
    
    Compiler warning with GCC 9.3:
    
    .../Src/Base/AMReX_FabArrayCommI.H: In member function 'void amrex::FabArray<FAB>::ParallelCopy(const amrex::FabArray<FAB>&, int, int, int, const amrex::IntVect&, const amrex::IntVect&, const amrex::Periodicity&, amrex::FabArrayBase::CpOp, const amrex::FabArrayBase::CPC*) [with FAB = amrex::FArrayBox]':
    .../Src/Base/AMReX_FabArrayCommI.H:611:40: error: 'the_send_data' may be used uninitialized in this function [-Werror=maybe-uninitialized]
                 amrex::The_FA_Arena()->free(the_send_data);
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~

Src/Base/AMReX_FabArrayCommI.H

commit b7e78115e8e1ed37ea66fd40e09b90225f81fee4
Merge: 7a8cbfcc2 2fcea2a1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 21:50:11 2020 -0700

    Merge branch 'development' into dpcpp

commit 2fcea2a1d574031189416f86a056ed2760720663
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 21:49:49 2020 -0700

    remove an ifdef AMREX_USE_CUDA meant for HIP

Tutorials/GPU/HeatEquation_EX1_C/Exec/default/mykernel.H

commit 7a8cbfcc2fc5442279e24f7f392c10ef74b4989b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 21:43:22 2020 +0000

    update wishlist

Docs/Notes/DPCPPWishlist.md

commit 02d043ad38da27557340164ad74e05ad90ba6562
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 21:28:20 2020 +0000

    add -fsycl

Tools/GNUMake/comps/dpcpp.mak

commit fd6219895658c835fb94bb8a379da195a248dbf9
Author: kngott <kngott@lbl.gov>
Date:   Sun Mar 29 12:59:01 2020 -0700

    Missed a {

Src/Base/AMReX_GpuLaunch.H

commit 6df41cdd76cd6dbc07ee15a559a94ccf980d4659
Author: kngott <kngott@lbl.gov>
Date:   Sun Mar 29 12:36:00 2020 -0700

    Few strays.

Src/Base/AMReX_FArrayBox.cpp
Src/Boundary/AMReX_Mask.H

commit 44d9bc1486b35162712c36ad55f8f0072cef4f54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 19:12:18 2020 +0000

    udpate DPC++ wishlist

Docs/Notes/DPCPPWishlist.md

commit 7858e3b28c46e8fc9404738cad8c55bbc8e5642f
Author: kngott <kngott@lbl.gov>
Date:   Sun Mar 29 12:11:55 2020 -0700

    How'd I miss BaseFab?

Src/AmrCore/AMReX_Interpolater.cpp
Src/Base/AMReX_BaseFab.H

commit 2d69ab8cb932d3b9833fb5ec58fa3a9a7037b0b7
Author: kngott <kngott@lbl.gov>
Date:   Sun Mar 29 11:18:54 2020 -0700

    Change FLAG based launches from bool to RunOn.

Src/AmrCore/AMReX_Interpolater.cpp
Src/Base/AMReX_GpuLaunch.H
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBInterpolater.cpp

commit ddcdbf99a17150c3d08ce7d1a7f6b02b94151bc3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 17:35:11 2020 +0000

    Revert "more amrex::Math for broken dpc++"
    Revert "fix sycl::pow so that it works for pow(double,int) like c++ standard does"
    Revert "use amrex::Math for dpc++"
    Revert "dpc++: use amrex::Math"
    Revert "some math functions are broken in dpc++ beta5"
    
    No longer needed after we link to libsycl-fp64.

Src/Base/AMReX_COORDSYS_2D_C.H
Src/Base/AMReX_GpuComplex.H
Src/Base/AMReX_Math.H
Src/Base/AMReX_RealVect.H
Src/EB/AMReX_EB2_2D_C.H
Src/EB/AMReX_EB2_2D_C.cpp
Src/EB/AMReX_EB2_3D_C.H
Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EB2_IF_Base.H
Src/EB/AMReX_EB2_IF_Lathe.H
Src/EB/AMReX_EB2_IF_Polynomial.H
Src/EB/AMReX_EB2_IF_Rotation.H
Src/EB/AMReX_EB2_IF_Torus.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Tests/LinearSolvers/CellEB/MyEB.H
Tests/LinearSolvers/CellEB/MyTest.cpp
Tests/LinearSolvers/CellEB/initEB.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/mykernel.H

commit b38324d6a544809b59c13bc1dcac294a7e41e57d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 17:33:24 2020 +0000

    dpc++: we now have to link to libsycl-cmath-fp64 for double precision math

Tools/GNUMake/comps/dpcpp.mak

commit b93a02069cdf4b438c8ac43316df149e569bf162
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 07:45:13 2020 -0700

    more amrex::Math for broken dpc++

Src/Base/AMReX_COORDSYS_2D_C.H
Src/Base/AMReX_GpuComplex.H
Src/Base/AMReX_RealVect.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H

commit 49a92c2d412f576d654acd2c3b014daba5f33972
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 07:27:01 2020 -0700

    fix sycl::pow so that it works for pow(double,int) like c++ standard does

Src/Base/AMReX_Math.H

commit 713d5d104f547dcb53cb32ebe1f80b7acb668f8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 07:10:22 2020 -0700

    use amrex::Math for dpc++

Src/EB/AMReX_EB2_2D_C.H
Src/EB/AMReX_EB2_2D_C.cpp
Src/EB/AMReX_EB2_3D_C.H
Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EB2_IF_Base.H
Src/EB/AMReX_EB2_IF_Lathe.H
Src/EB/AMReX_EB2_IF_Polynomial.H
Src/EB/AMReX_EB2_IF_Rotation.H
Src/EB/AMReX_EB2_IF_Torus.H
Tests/LinearSolvers/CellEB/MyEB.H
Tests/LinearSolvers/CellEB/MyTest.cpp
Tests/LinearSolvers/CellEB/initEB.cpp

commit 36185dcc018e5d3bb1a674f1373c3f524d44c853
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 06:57:27 2020 -0700

    remove trivial dtor from a number of EB implicit functions so that they are trivially destructible and thus can work with DPC++

Src/EB/AMReX_EB2_IF_Complement.H
Src/EB/AMReX_EB2_IF_Difference.H
Src/EB/AMReX_EB2_IF_Extrusion.H
Src/EB/AMReX_EB2_IF_Intersection.H
Src/EB/AMReX_EB2_IF_Lathe.H
Src/EB/AMReX_EB2_IF_Polynomial.H
Src/EB/AMReX_EB2_IF_Rotation.H
Src/EB/AMReX_EB2_IF_Scale.H
Src/EB/AMReX_EB2_IF_Spline.H
Src/EB/AMReX_EB2_IF_Translation.H
Src/EB/AMReX_EB2_IF_Union.H
Tests/LinearSolvers/CellEB/MyEB.H
Tests/LinearSolvers/CellEB2/MyEB.H
Tests/LinearSolvers/EBConvergenceTest/MyEB.H
Tests/LinearSolvers/EBflux_grad/MyEB.H

commit 42f5cc87b35564b5b5cf0bcac89f494a187e05b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 06:47:30 2020 -0700

    dpc++: use amrex::Math

Tutorials/GPU/HeatEquation_EX1_C/Exec/default/mykernel.H

commit 61dd1d04896675ceb04da08f99a870ea5e12da8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 04:55:31 2020 +0000

    dpc++: explicitly access id so that it works for beta4 too

Src/Base/AMReX_GpuReduce.H

commit 3424240b792fdadb06b6ade328ab28b943f675bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 29 02:05:18 2020 +0000

    some math functions are broken in dpc++ beta5

Src/Base/AMReX_Math.H

commit 7d8be7c461454922365141c5e5ee0f6f23a6e68a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 28 21:10:50 2020 +0000

    dpc++: use 16 as subgroup size because shuffle_down does not work otherwise

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuReduce.H

commit 1bdc1d077489de6860f57f18a7e9c470f8fc4783
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 28 19:24:38 2020 +0000

    dpc++ use sub_group methods to get land and warp id and comment out unsupported code

Src/Base/AMReX_GpuReduce.H

commit 33bd5149cb9a45dd073736a5069e459494b84082
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 28 18:11:55 2020 +0000

    dppc++: use subgroup shuffle_down for reduction

Src/Base/AMReX_GpuReduce.H

commit 242cb2e23c7576b35f079c273ed37e901bb3fb33
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 28 17:31:57 2020 +0000

    dpc++: allocate local memory for reduction

Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_Reduce.H

commit 492172f433dd7508c8427e2649564296b2d3add7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 28 03:32:31 2020 +0000

    add Gpu::Handler for DPC++

Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_GpuTypes.H
Src/Base/AMReX_Reduce.H

commit f396e29cfc8e20b71689b8c2cf8377cfca9b606b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 27 18:25:16 2020 -0700

    turn on AMREX_REQUIRE_SUBGROUP_SIZE for dpc++

Src/Base/AMReX_GpuQualifiers.H

commit 3eb820a7c5b7fee54882f2fa5a661a2c8f92b8fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 27 17:02:53 2020 +0000

    use sycl::isnan

Src/Base/AMReX_GpuUtility.H

commit daf78c4e33512f46e48da55123febda6725996a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 27 16:28:11 2020 +0000

    update Make file for jlse

Tools/GNUMake/Make.defs

commit 26c22d5ca7b8fe95374ffc70835627c1cbd21e22
Merge: 73c70e4e4 9e9f7b8f6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Mar 27 11:15:54 2020 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 73c70e4e4ae48569b09dced609a73ac5053f05e1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Mar 27 11:15:13 2020 -0400

    always sync at the end of redistribute

Src/Particle/AMReX_ParticleContainerI.H

commit 0a813f20af8c5530913132a27e11eead37e76a8a
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Thu Mar 26 19:39:29 2020 -0400

    Review changes

Src/Base/AMReX_CuptiTrace.cpp

commit 39f3553f07eb43b202b8fea572bec0fae1056b01
Merge: ab3930c6e 9e9f7b8f6
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Thu Mar 26 19:38:02 2020 -0400

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mrowan/CUPTI_trace

commit f8619663ac2ab54fd6b73f42e19ab944596774ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 26 16:21:16 2020 -0700

    update wording

Docs/Notes/DPCPPWishlist.md

commit 232aa130b39f579fe9c512685f9a7cc891330414
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 26 16:18:29 2020 -0700

    update format

Docs/Notes/DPCPPWishlist.md

commit ef3fc32850627f75eb5c3918abd067d6db24a832
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 26 16:12:44 2020 -0700

    add DPC++ wishlish

Docs/Notes/DPCPPWishlist.md
Docs/Notes/Readme.dpcpp

commit 2425a78944298cf18589b876901c854c856825f7
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Mar 26 15:12:45 2020 -0700

    left out an important part of that

Src/Amr/AMReX_AmrLevel.cpp

commit 78426326fd55b13693f066166b8b5508f6b53205
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Mar 26 14:50:48 2020 -0700

    add eb information to AMRLevel's writePlotFile routine

Src/Amr/AMReX_AmrLevel.cpp
Tutorials/EB/CNS/Source/CNS_io.cpp

commit ab3930c6e46d01bb52cb3ec0adc771323a2dca6f
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Wed Mar 25 21:48:12 2020 -0400

    Remove unneeded ActivityTraceAsync file

Src/Base/AMReX_ActivityTraceAsync.H
Src/Base/AMReX_ActivityTraceAsync.cpp

commit 8ff5b565ad49ddced6ae7c04b52f003d3d894983
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Wed Mar 25 18:44:12 2020 -0700

    Review changes

Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_CuptiTrace.H
Src/Base/AMReX_CuptiTrace.cpp
Src/Base/AMReX_TinyProfiler.H
Tools/GNUMake/comps/nvcc.mak

commit 8d1f6715212edaf9980d7934a7c6f7478accfbac
Merge: 1ed6ec669 34c5d391e
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Wed Mar 25 17:02:38 2020 -0700

    Merge conflict

commit 1ed6ec669f185ddd4aa304a653337bd248a037c9
Merge: 8432d8d24 e348a5f7b
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Wed Mar 25 16:46:17 2020 -0700

    Merge branch 'master' of https://github.com/AMReX-Codes/amrex into mrowan/CUPTI_trace

commit 9e9f7b8f63f1fdb7eb765a699d3a18fd2340fab0
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Mar 25 15:32:39 2020 -0700

    make sure we are using the float version of abs in AMReX_EBMultiFabUtil_?D_C.H

Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit d1affc0bfd0cfa9680c6a9a5bb292032feb7e2a3
Merge: 2c7c61fab 2f9e8b17f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 24 21:21:00 2020 -0700

    Merge branch 'weiqun/bat' into development

commit 2f9e8b17fece1fdec01ffed0fa995890bf0f1620
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 24 18:38:23 2020 -0400

    BoxArray BATransformer: optimization

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit a5da328a37e12b4586b2a1889e6c01185004faf3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 24 10:23:18 2020 -0700

    fix a couple of new bugs

Src/Base/AMReX_BoxArray.H

commit 07ffa91b18b2048ae3b8d5666ed990699ba686c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 17 21:13:18 2020 -0700

    get rid of virtual transformer in BoxArray

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_MultiMask.cpp

commit 2c7c61fab9e9a91f737b44f138f1fff8d601fc39
Merge: 5369e707b e02e0a971
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Mar 21 17:19:55 2020 -0700

    Merge pull request #744 from AMReX-Codes/setphysboundaryvalues_fab
    
    Use Fab interface in setPhysBoundaryValues if available

commit e02e0a9719a3caa08a988d2daeb564cd77478630
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Mar 20 22:01:56 2020 -0700

    Use Fab interface in setPhysBoundaryValues if available

Src/Amr/AMReX_AmrLevel.cpp

commit 5369e707b4c57ffd06433752c51b02547077695f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 20 11:33:05 2020 -0700

    add template keyword otherwise Clang does not like it

Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleContainerI.H

commit 7955ceb5a071b7bb19d94f51f30f167da34de39f
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Mar 19 23:01:17 2020 -0700

    fix several of the WritePlotFile methods for runtime components

Src/Particle/AMReX_ParticleIO.H

commit 123ba3aa2aec03e8e33faecfc135fe1bca5314df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 19 14:15:54 2020 -0700

    fix pthread for nvcc by default in Make.unknown

Tools/GNUMake/sites/Make.ccse
Tools/GNUMake/sites/Make.unknown

commit 87c6428bcbb599e0e1da988bf13fa0b71d5b59ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 19 14:14:42 2020 -0700

    make sure mpi_cxx is linked when nvcc is used for linking

Tools/GNUMake/sites/Make.unknown

commit 1f1351dcaa85a517d7da5fc16271e7c70c4c7293
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 19 10:54:07 2020 -0700

    fix some BaseFab RunOn

Src/Base/AMReX_BaseFab.H

commit afddf068f1b4067d48878043551d2416ca75de6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 19 10:22:11 2020 -0700

    fix FabArray:copyTo RunOn

Src/Base/AMReX_FabArrayCommI.H

commit 0ffb4eb5852d9c0c19344cc44b4db0045cfdab4b
Merge: cbd85536b 7edab7812
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Mar 18 11:01:14 2020 -0700

    Merge pull request #741 from jrood-nrel/update_nrel_site
    
    Update makefiles for NREL site

commit 7edab7812053047f3d0c842a8376026b8596752a
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Wed Mar 18 11:51:03 2020 -0600

    Update makefiles for NREL site to remove Peregrine machine and allow building with CUDA.

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.nrel

commit cbd85536b64d887670984267ac16163d8c8ff6e5
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Mar 17 15:55:22 2020 -0700

    CMake: only install required subfolders within Tools directory

Tools/CMake/AMReXInstallHelpers.cmake

commit 3d0788c0fe27c0d4e840b5e2f9986951c4aaf000
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Mar 17 15:07:34 2020 -0700

    CMake: remove ENABLE_CUDA option duplicate

Tools/CMake/AMReX_Options.cmake

commit 7de60498d064ffaa2b67957343555fb0015ca483
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 17 14:24:12 2020 -0700

    fix Arena test in FArrayBox and IArrayBox

Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_IArrayBox.cpp

commit 38f25e08f7803c39b79da425362e509f6c040ba1
Merge: b938fad38 b99f08366
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 16 16:35:02 2020 -0700

    Merge branch 'development' into weiqun/dev

commit b99f08366d904df9f2adb22f329ddd75724a23bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 16 15:38:17 2020 -0700

    fix a new bug in FluxRegister::SumReg

Src/AmrCore/AMReX_FluxRegister.cpp

commit b938fad38ac7f26dc4b51878d684ce47a04bdedc
Merge: c63c131bf 2db7bf32a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 16 10:19:00 2020 -0700

    Merge branch 'development' into weiqun/dev

commit 2db7bf32a5955fe7af8c977aff26adb23e227ab6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 16 10:17:06 2020 -0700

    remove some temporary variables

Src/Base/AMReX_FilCC_3D_C.H

commit 2724030e1628bf6370dabb450383ae32f293c375
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 16 09:20:29 2020 -0700

    use DeviceVector instead of AsyncArray because it does not need to be async safe

Src/EB/AMReX_EBMultiFabUtil.cpp

commit b9f76a6a0beddf9aa7e3d1ac491a1db0d14439f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 16 09:10:27 2020 -0700

    no need to be virtual

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H

commit 81192d9d2417e844aefbfc91d629316bc2ded767
Merge: c6f8b693d ccd483e79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 16 08:24:35 2020 -0700

    Merge branch 'development' into dpcpp

commit c63c131bf23705f34e42c136663b6d7972c4ba34
Merge: ccd483e79 c6f8b693d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 16 08:23:35 2020 -0700

    Merge branch 'dpcpp' into weiqun/dev

commit ccd483e791d456c9275c559742099fb919aee6f4
Merge: 3830a2435 69651f46d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 16 08:21:43 2020 -0700

    Merge branch 'development' into basefab_runon

commit 69651f46d9307acd5190583c44542838c91f0de7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 15 17:03:15 2020 -0700

    EB: optional to build coarse level from GeometryShop when coarsening fails.  This could be used for hyperbolic system with EB resolved to the finest level

Src/EB/AMReX_EB2.H
Src/EB/AMReX_EB2.cpp
Src/EB/AMReX_EB2_IndexSpaceI.H

commit 2b08d7a7901eb8ac927fc65b5a4a2e21971e8858
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 15 09:31:19 2020 -0700

    fix warning when BL_NO_FORT is true

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit 3d44d648c4c6e214b569a83e1ceee5a639e5c6a9
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Mar 13 15:21:14 2020 -0700

    silence missing braces warning in clang, which is too aggressive

Tools/GNUMake/comps/llvm.mak

commit 3efe0e4887f0715fdcf07a0b8f1c948e11593037
Merge: 39e619cdd 755a332fd
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Mar 13 15:13:29 2020 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 39e619cdd5c26266ac6eb522e45fbc510e253f10
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Mar 13 15:12:25 2020 -0700

    some casts to silence warnings when doing mixed precision

Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_Particle_mod_K.H

commit 755a332fde7f8b16358c33110ff89b83e5d33f18
Merge: df479eab6 0fdcc4969
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Mar 13 15:09:03 2020 -0700

    Merge pull request #740 from AMReX-Codes/Emmanuel/velocity_gradients_for_LES
    
    Emmanuel/velocity gradients for les

commit 1f8383f4f39891652ffb5c03e311746e6cb1c1ce
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Mar 13 14:42:35 2020 -0700

    fix 'default initialization of an object of const type without a user-provided default constructor'

Src/Base/AMReX_GpuContainers.H

commit c4152373c029739162040663d9547a55d47d82ec
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Mar 13 14:38:31 2020 -0700

    fix some narrowing conversion warnings in Particle_mod_K.H

Src/Particle/AMReX_Particle_mod_K.H

commit c6f8b693d1eb8077ad3e18749d764237074523c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 13 08:44:40 2020 -0700

    update Advection_AmrCore tutorial for DPC++

Src/Base/AMReX_FBI.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H

commit 5711bb6d122e3d0e66e38fd73eaa5d4d242053c2
Merge: f849352bb 3830a2435
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 20:17:03 2020 -0700

    Merge branch 'basefab_runon' into dpcpp

commit 3830a243592ddacb36108c19169c3eaa53e112be
Merge: 25f87f90d df479eab6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 20:14:10 2020 -0700

    Merge branch 'development' into basefab_runon

commit df479eab6f15e94b66e5f1da0155cd5456879929
Merge: ba8d2ec4f 4d8da23b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 20:12:24 2020 -0700

    Merge branch 'weiqun/dev' into development

commit f849352bb76d3c78f1d41de707cb5cd9eeb49af0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 20:11:23 2020 -0700

    implement DPC++ version of fab to fab op with mask in communcation

Src/Base/AMReX_FBI.H

commit 32758a85e7e66d159fcaec6fb5c955d0e9442978
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 20:08:17 2020 -0700

    update GPU/Launch tutorial for basefab_runon

Tutorials/GPU/Launch/CMakeLists.txt
Tutorials/GPU/Launch/Make.package
Tutorials/GPU/Launch/MyKernel.H
Tutorials/GPU/Launch/main.cpp

commit ba8d2ec4f070dbcb4564f89206eb87b7478c3b05
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Mar 12 18:34:08 2020 -0700

    CMake: add C++ 17 among valid options for AMREX_CXX_STANDARD

Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/CMake/AMReX_Options.cmake

commit 76898f1ae14cfaa3219f5f03ce6ff5b0fcba9d59
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Mar 12 17:36:00 2020 -0700

    CMake: allow user to specify C++ standard

.github/workflows/cmake.yml
Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake

commit 6c96edb32bc6dd0087b420f2a97e09a95d7fca2b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 15:32:36 2020 -0700

    cmake: change C++ standard target to 11 so that cuda build in github workflow works

Tools/CMake/AMReX_Config.cmake

commit fef0ebb0be99abc02a3e04ec76aa4b2fe1c4db9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 13:15:11 2020 -0700

    use gcc-4.8 for build build in github workflow

.github/workflows/cmake.yml
.github/workflows/cmake/dependencies.sh
.github/workflows/cmake/dependencies_nvcc.sh

commit 8eae0cd11bc65e5cb94d7fecdf30ff26da0d08c8
Merge: ab9704b1c 25f87f90d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 12:33:42 2020 -0700

    Merge branch 'basefab_runon' into dpcpp

commit 25f87f90dd0a253510f8b7499467dbdce38d1488
Merge: 5e26513bb 0153dc0af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 12:32:45 2020 -0700

    Merge branch 'development' into basefab_runon

commit 4d8da23b016eee8e27c1632fba20558f05154868
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 09:17:39 2020 -0700

    template FillPatch* so that they can work on any FabArray

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FillPatchUtil_I.H
Src/AmrCore/CMakeLists.txt
Src/AmrCore/Make.package
Src/Base/AMReX_MultiFab.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp

commit 0fdcc4969dd7aabf5d515a7495a214ada636464f
Merge: a5f80946d 0153dc0af
Author: emotheau <emotheau@lbl.gov>
Date:   Wed Mar 11 18:13:31 2020 -0700

    Merge remote-tracking branch 'origin/development' into Emmanuel/velocity_gradients_for_LES

commit 9a8c4c3a8736c14a07a4cd28eff2dadf81439957
Merge: 4c5a93a3c 0153dc0af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 11 17:02:43 2020 -0700

    Merge branch 'development' into weiqun/dev

commit a5f80946db73aa9bfa66fd80f61d291e7e9f6937
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Wed Mar 11 16:02:15 2020 -0700

    some cleaning

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 0153dc0afc19b48464321be1700e0d7939808044
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 11 15:25:48 2020 -0700

    add option to set fixed number of iterations in the Fortran interface of linear solver

Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90

commit 2f52133decf2c0138fe26ae4997565275b20bbdd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 11 14:58:11 2020 -0700

    Create alias Fab in FabArray using factory so that the EB information can be carried over

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabFactory.H
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_MultiCutFab.H

commit 77f4264c2d72d56f8829de7122de94208773aa49
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Wed Mar 11 14:41:11 2020 -0700

    bug fix in 3D

Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit 2ae0257baebeb2d927ea6fbaac1062dc10f5f07f
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Wed Mar 11 14:23:29 2020 -0700

    routines are now available in 3D

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit 81ec27925d84a6f3393dcc6ce1ec9b84929d6ef8
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Mar 11 11:36:27 2020 -0700

    add missing include guard

Src/Particle/AMReX_ParIter.H

commit 1b704499778d372b08687423f061d0acf2ed4be8
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Mar 11 11:34:41 2020 -0700

    unused variable

Src/Base/AMReX_Arena.cpp

commit ab9704b1c3a6880a6e3fb6f4714972ad7d68d9d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 10 15:45:36 2020 -0700

    add DPC++ flag to relax SYCL restriction

Tools/GNUMake/comps/dpcpp.mak

commit 3fdabfe9d432a6c3ece36b1505cc47bfddd3d82e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 10 11:07:39 2020 -0700

    update GPU limitations

Docs/sphinx_documentation/source/GPU.rst

commit 3859780d834256225f5b489806830470dd47d3e9
Merge: 3075027b1 cd00f209b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Mar 9 16:18:37 2020 -0700

    Merge branch 'development' into atmyers/mpi_datatype

commit 3075027b140364819f9676627d058dacf8a48ce6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Mar 9 15:52:23 2020 -0700

    another fix for the corner case where we don't do any sends

Src/Particle/AMReX_ParticleCommunication.H

commit 9f108ab53882b49399769ffff07c430f55c617bf
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Mar 9 13:43:43 2020 -0700

    add switch based on message size

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit cd00f209b4b482890561b985580bc91bb37d5fce
Merge: d21cc21eb 1a01fda0a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Mar 9 12:40:35 2020 -0700

    Merge pull request #736 from rporcu/development
    
    Implementation of  operator *= (Real) was missing

commit d21cc21ebf50c6048c70e60937a0c6c493cbe24d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Mar 9 11:21:23 2020 -0700

    fix index error in interpolate_cic

Src/Particle/AMReX_Particle_mod_K.H

commit 5e26513bb6783ab36c545ebe19cfd9b019317655
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 7 19:12:39 2020 -0800

    fix FArrayBox and IArrayBox template function operator=

Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IArrayBox.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit 0ec556a436236aedbb2e667c9ac1743c5997d5da
Merge: 866654b34 bcd9ade9c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 7 18:20:41 2020 -0800

    Merge branch 'development' into basefab_runon

commit 1a01fda0ad182d984055bd3b6e5f6245c8f5330c
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Sat Mar 7 18:08:28 2020 -0800

    Implementation of *=(Real) was missing

Src/Base/AMReX_RealVect.H

commit f4803821418b25f5a9962cbeb6f9dc25ea73c4b9
Merge: 0c7787b48 bcd9ade9c
Author: emotheau <emotheau@lbl.gov>
Date:   Sat Mar 7 16:00:16 2020 -0800

    Merge remote-tracking branch 'origin/development' into Emmanuel/velocity_gradients_for_LES

commit 0c7787b489741cef73b01d714f09a3f6bce3f3d5
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Sat Mar 7 15:58:40 2020 -0800

    new routine in TensorOP to compute gradients of velocity at each face. Only in 2d and no EB for now

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H

commit bcd9ade9ca6e015ba7afa31e045c62e653b510de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 7 10:59:48 2020 -0800

    fix some warnings

Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_VisMF.cpp

commit 4a11a0279fa7d744258c16673a175deae59f3187
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 23:02:27 2020 -0800

    add AMREX_LOOP_3D and 4D

Src/Base/AMReX_Loop.H

commit 866654b3404eb4d3ebf89f4ca0e795aedcbcf955
Merge: 4e573e47d b93348cb3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 22:26:06 2020 -0800

    Merge branch 'basefab_runon_nodefault' into basefab_runon

commit b93348cb31bd2a996abf6ad79e9a3d3051329e0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 22:25:43 2020 -0800

    fix makeFineMask_doit template

Src/Base/AMReX_MultiFabUtil.cpp

commit 4e573e47d3b6d539df7eef75d9d251fdafd44a9b
Merge: b5db926d1 1e597b7fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 21:37:32 2020 -0800

    Merge branch 'basefab_runon_nodefault' into basefab_runon

commit 1e597b7fde5eedb9b49a2155a57072d331ae99d2
Merge: ed99f7e7e d0b98e963
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 21:37:00 2020 -0800

    Merge branch 'development' into basefab_runon_nodefault

commit d0b98e9636337f67dd85e96d04288e6beb458420
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 21:34:20 2020 -0800

    add a new makeFineMask function that returns MultiFab

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 92a025bd6bad1dfc3ebfba855360bee75545f3a6
Merge: 31f42022f 56b1ea5b7
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Mar 6 16:47:50 2020 -0800

    Merge pull request #734 from Alpine-DAV/task/2020_03_bp_particle_mesh_name_opt
    
    conduit blueprint: add topo name option to particle container wrapper

commit 56b1ea5b76bdb8ed355eed18ecc307d640c9e09b
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Fri Mar 6 15:55:02 2020 -0800

    add comment about new  topology_name arg

Src/Extern/Conduit/AMReX_Conduit_Blueprint.H

commit b5db926d1bf63dd9c4dc7380ab96092344d5bb2d
Merge: bcd64e203 ed99f7e7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 15:49:52 2020 -0800

    Merge branch 'basefab_runon_nodefault' into basefab_runon

commit ed99f7e7ea9fafd8092e269fc7d237a7763fc5cf
Merge: 88a3a4000 31f42022f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 15:48:45 2020 -0800

    Merge branch 'development' into basefab_runon_nodefault

commit bcd64e203ba001a8034e3418ba5b2a225a8d88eb
Merge: a8054fca4 88a3a4000
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 15:47:06 2020 -0800

    Merge branch 'basefab_runon_nodefault' into basefab_runon

commit 88a3a40002531442964e23e3481e3c3cd8d9e89f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 15:46:27 2020 -0800

    fix the new DistributionMapping functions

Src/Base/AMReX_DistributionMapping.cpp

commit 0a2830d20868bb767b708fbeeead81eff417bfa0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 6 15:44:09 2020 -0800

    fix sign error in pad offset computation, add some useful assertions

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit a8054fca4ff924296005c528420f544d490534bf
Merge: 51cd1dc3b 8dcbb083a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 15:29:05 2020 -0800

    Merge branch 'basefab_runon_nodefault' into basefab_runon

commit 8dcbb083a2553b29ac8a09e09a7c162e2d73dcb5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 15:28:43 2020 -0800

    remove device code from ~BaseFab

Src/Base/AMReX_BaseFab.H

commit 9254908d30993e0da79ca40fea0f818d6d16b32c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 6 13:53:17 2020 -0800

    more debug code

Src/Particle/AMReX_ParticleCommunication.H

commit 99de5f9b8eb7ebfd032627729ce168adce96ae78
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 6 13:47:38 2020 -0800

    remove debug prints

Src/Particle/AMReX_ParticleCommunication.H

commit 012e83223ab37abc2c02802e158388d871785a93
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 6 13:41:12 2020 -0800

    add missing header

Src/Base/AMReX_ParallelDescriptor.cpp

commit 1ada983a94618490e08e9d8b182045417899cb52
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 6 13:39:06 2020 -0800

    using unsigned long long as the datatype for particle mpi comms

Src/Particle/AMReX_ParticleCommunication.H

commit 76ecf6939ca20c1ecdbb74738e16ccc24cf8e210
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 6 13:29:40 2020 -0800

    refactr the alignment / comm_type functions so they can be used outside of FabArra

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit 083fbeb22006e0c611fe86fcb006b08d8455378b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 6 13:13:01 2020 -0800

    remove some commented out code

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit f76e83861b380f3aa74e3f20221934a8e23a12be
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Fri Mar 6 13:04:52 2020 -0800

    allow explicit name for particle mesh topos

Src/Extern/Conduit/AMReX_Conduit_Blueprint.H
Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H

commit 0532ce148829071dbf27081c9c20850c5c30258e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 6 12:46:18 2020 -0800

    add ability to pad mpi messages by an alignment size

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit 0d24b8aa157ed3d4e64041422c4b7bc640129361
Merge: 21ef1d8d6 31f42022f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 6 12:08:18 2020 -0800

    Merge branch 'development' into atmyers/mpi_datatype

commit 31f42022f8193aeb48fa9b415ad2c7341a9bbe0f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 6 12:07:43 2020 -0800

    remove kdtree

Src/Particle/AMReX_KDTree_1d.F90
Src/Particle/AMReX_KDTree_2d.F90
Src/Particle/AMReX_KDTree_3d.F90
Src/Particle/AMReX_KDTree_F.H
Src/Particle/AMReX_LoadBalanceKD.H
Src/Particle/AMReX_LoadBalanceKD.cpp
Src/Particle/CMakeLists.txt
Src/Particle/Make.package
Tests/Particles/LoadBalance/GNUmakefile
Tests/Particles/LoadBalance/Make.package
Tests/Particles/LoadBalance/create_binary_particle_file.py
Tests/Particles/LoadBalance/inputs
Tests/Particles/LoadBalance/main.cpp
Tests/Particles/LoadBalance/visualize_output.ipynb

commit 51cd1dc3b8929ad35d4fb248b69089ddbada0e55
Merge: a87d84dfe f3e870010
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 11:34:09 2020 -0800

    Merge branch 'basefab_runon_nodefault' into basefab_runon

commit f3e870010bd1ab7430062e3d2d68091991902693
Merge: b63ba2ece ea755eb94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 11:33:23 2020 -0800

    Merge branch 'development' into basefab_runon_nodefault

commit a87d84dfef1845d42f95cb868ef947961bfc8341
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 11:31:12 2020 -0800

    add RunOn::Host as default when not using GPU

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Boundary/AMReX_Mask.H

commit b63ba2eced14efa1c4bd95612ccfed439396118c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 11:04:46 2020 -0800

    fix tutorial for RunOn

Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H

commit cc524566d15132b8ae3bbba937290330ed828c32
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 10:47:07 2020 -0800

    rm old tests

Tests/GPU/FusedLaunches/GNUmakefile
Tests/GPU/FusedLaunches/Make.package
Tests/GPU/FusedLaunches/inputs_3d
Tests/GPU/FusedLaunches/main.cpp
Tests/GPU/FusedLaunches/run.corigpu
Tests/GPU/Particles/Redistribute/Constants.H
Tests/GPU/Particles/Redistribute/GNUmakefile
Tests/GPU/Particles/Redistribute/Make.package
Tests/GPU/Particles/Redistribute/TestParticleContainer.H
Tests/GPU/Particles/Redistribute/TestParticleContainer.cpp
Tests/GPU/Particles/Redistribute/inputs
Tests/GPU/Particles/Redistribute/main.cpp
Tests/GPU/Particles/Redistribute/test_3d.F90
Tests/GPU/Particles/Redistribute/test_F.H
Tests/GPU/Partition/GNUmakefile
Tests/GPU/Partition/Make.package
Tests/GPU/Partition/inputs
Tests/GPU/Partition/main.cpp
Tests/GPU/ScratchPad/GNUmakefile
Tests/GPU/ScratchPad/Make.package
Tests/GPU/ScratchPad/inputs_3d
Tests/GPU/ScratchPad/main.cpp
Tests/GPU/ScratchPad/run.script
Tests/GPU/Test/GNUmakefile
Tests/GPU/Test/Make.package
Tests/GPU/Test/main.cpp
Tests/GPU/Test/run.exitcode
Tests/GPU/Test/run.script
Tests/GPU/TestB/GNUmakefile
Tests/GPU/TestB/Make.package
Tests/GPU/TestB/main.cpp
Tests/GPU/TestB/return_test.F90
Tests/GPU/TestC/GNUmakefile
Tests/GPU/TestC/Make.package
Tests/GPU/TestC/main.cpp
Tests/GPU/TestC/run.summit
Tests/GPU/TestC/run.summitdev
Tests/GPU/buildHybrid/GNUmakefile
Tests/GPU/buildHybrid/MyKernel.H
Tests/GPU/buildHybrid/MyKernel.cpp
Tests/GPU/buildHybrid/MyKernelB.H
Tests/GPU/buildHybrid/MyKernelB.cpp
Tests/GPU/buildHybrid/MyKernel_F.F90
Tests/GPU/buildHybrid/MyKernel_F.H
Tests/GPU/buildHybrid/Readme
Tests/GPU/buildHybrid/main.cpp
Tests/GPU/buildHybrid/run.script
Tests/GPU/buildNotused/Extern.H
Tests/GPU/buildNotused/GNUmakefile
Tests/GPU/buildNotused/MyKernel.H
Tests/GPU/buildNotused/MyKernel.cpp
Tests/GPU/buildNotused/MyKernelB.H
Tests/GPU/buildNotused/MyKernelB.cpp
Tests/GPU/buildNotused/Notused.H
Tests/GPU/buildNotused/Notused.cpp
Tests/GPU/buildNotused/Readme
Tests/GPU/buildNotused/main.cpp
Tests/GPU/buildTest/GNUmakefile
Tests/GPU/buildTest/MyKernel.H
Tests/GPU/buildTest/MyKernel.cpp
Tests/GPU/buildTest/MyKernelB.H
Tests/GPU/buildTest/MyKernelB.cpp
Tests/GPU/buildTest/Readme
Tests/GPU/buildTest/main.cpp
Tests/GPU/buildTest/run.script

commit 7165d47d896932ebbe3308f76849adb8332502cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 09:42:18 2020 -0800

    add more RunOns

Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/PETSc/AMReX_PETSc.cpp
Src/Particle/AMReX_ParticleContainerI.H
Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp

commit ea755eb94d4f6991995453faa59f7fd8a4614579
Merge: de3e8972b 7aeef1811
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Mar 6 09:21:52 2020 -0800

    Merge pull request #725 from mrowan137/mrowan/loadbalance
    
    Add efficiency argument to makeSFC, makeKnapSack

commit 1eb7bbfdb946e763da1f4855bb39c8408392875e
Merge: 32f74b8cb de3e8972b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 08:19:06 2020 -0800

    Merge branch 'development' into basefab_runon

commit 32f74b8cbb55017d61fb1584604b03c294853726
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 6 08:15:02 2020 -0800

    add RunOn to a test

Tutorials/Basic/PrefixSum_MultiFab/main.cpp

commit cc0a00dfd8a735c65177865844cfd36666359307
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 5 21:06:42 2020 -0800

    clean up

Src/Base/AMReX_IArrayBox.cpp

commit 21ef1d8d6ecc2f44a994a094e4d425a96d6e6edd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 5 16:44:16 2020 -0800

    remove some variables I ended up not using

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit 4f6a83f633478bb541c73d7b96005c51882fd55f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 5 16:36:22 2020 -0800

    fix for one proc case

Src/Particle/AMReX_ParticleCommunication.H

commit c9e0e4778b70e558a0b0331f0ab37111b8fe47b8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 5 16:22:33 2020 -0800

    also adding the rcv padding

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit 8bc6a7a05e7bfc0d7457973b12677b3c6da732d3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 5 15:29:36 2020 -0800

    also use the snd buffer functor in unpack

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleTile.H

commit de3e8972b47e37b2b6c6cb9902ea5eea727c2c3f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 5 15:08:20 2020 -0800

    allow nodal solver to coarsen more

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 188634614b2b3c2ac5cb6dc9f7da99e39bf043ef
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 5 14:59:21 2020 -0800

    forgot to copy to device

Src/Particle/AMReX_ParticleCommunication.H

commit 450637088236fa8f0a8a6f6d2e06093acd0f76d4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 5 14:54:52 2020 -0800

    also compute rcv pad

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit eae6110e4df027a3059f091c094fbc6143c6bca7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 5 14:18:53 2020 -0800

    combine send buffer offset calculation into single functor

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit e2e9c4741f8ad23953f8452e0bee8d740c10f06d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 5 13:37:57 2020 -0800

    change pack to work in terms of address

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleTile.H

commit ac984c0208a18566d634b3f0c25ce0e04978c949
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 5 13:33:19 2020 -0800

    need to include self in neighbor procs for this to work

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleUtil.cpp

commit a2b5b13e5fabd99962825a11d0524b74a614cc05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 5 11:48:07 2020 -0800

    remove old tutorials

INSTALL
OldTutorials/.gitignore
OldTutorials/MeshRefinement/GNUmakefile
OldTutorials/MeshRefinement/Make.package
OldTutorials/MeshRefinement/MyAmr.H
OldTutorials/MeshRefinement/MyAmr.cpp
OldTutorials/MeshRefinement/main.cpp
OldTutorials/MultiColor_C/GNUmakefile
OldTutorials/MultiColor_C/Make.package
OldTutorials/MultiColor_C/ff.f90
OldTutorials/MultiColor_C/inputs
OldTutorials/MultiColor_C/main.cpp
OldTutorials/MultiFabTests_C/GNUmakefile
OldTutorials/MultiFabTests_C/Make.package
OldTutorials/MultiFabTests_C/MultiFabFillBoundary.cpp
OldTutorials/MultiFabTests_C/MultiFabReadWrite.cpp
OldTutorials/PIC_C/GNUmakefile
OldTutorials/PIC_C/Make.package
OldTutorials/PIC_C/README
OldTutorials/PIC_C/inputs
OldTutorials/PIC_C/main.cpp
OldTutorials/PIC_C/single_level.cpp
OldTutorials/PIC_C/solve_for_accel.cpp
OldTutorials/PIC_C/solve_with_mlmg.cpp
OldTutorials/PIC_C/two_level.cpp
OldTutorials/README_C
OldTutorials/Tiling_C/GNUmakefile
OldTutorials/Tiling_C/Make.package
OldTutorials/Tiling_C/main.cpp
OldTutorials/Tiling_C/work.f90
OldTutorials/Tiling_Heat_C/GNUmakefile
OldTutorials/Tiling_Heat_C/Make.package
OldTutorials/Tiling_Heat_C/advance_3d.f90
OldTutorials/Tiling_Heat_C/init_phi_3d.f90
OldTutorials/Tiling_Heat_C/inputs_3d
OldTutorials/Tiling_Heat_C/main.cpp
OldTutorials/Tiling_Heat_C/results/results.org
OldTutorials/Tiling_Heat_C/results/run-babbage.sh
OldTutorials/Tiling_Heat_C/results/run-edison.sh
OldTutorials/Tiling_Heat_C/writePlotFile.H
OldTutorials/Tiling_Heat_C/writePlotFile.cpp
OldTutorials/TwoGrid_PIC_C/GNUmakefile
OldTutorials/TwoGrid_PIC_C/Make.package
OldTutorials/TwoGrid_PIC_C/main.cpp
OldTutorials/TwoGrid_PIC_C/solve_for_accel.cpp
OldTutorials/TwoGrid_PIC_C/solve_with_mlmg.cpp
OldTutorials/TwoGrid_PIC_C/split_boxes.cpp
OldTutorials/WaveEquation_C/GNUmakefile
OldTutorials/WaveEquation_C/Make.package
OldTutorials/WaveEquation_C/advance_2d.f90
OldTutorials/WaveEquation_C/advance_3d.f90
OldTutorials/WaveEquation_C/init_data_2d.f90
OldTutorials/WaveEquation_C/init_data_3d.f90
OldTutorials/WaveEquation_C/inputs_2d
OldTutorials/WaveEquation_C/inputs_3d
OldTutorials/WaveEquation_C/main.cpp
OldTutorials/WaveEquation_C/writePlotFile.H
OldTutorials/WaveEquation_C/writePlotFile.cpp
Tools/CompileTesting/compiletesting.py
Tutorials/Basic/Build_with_libamrex/GNUmakefile

commit 99cdacd7c6e4c0d6b878a059319497db3334b4e5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 5 11:39:25 2020 -0800

    refactor slightly to compute and reuse snd sizes and offsets

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit eef7ea4bfdf5a5de840c8a9e8e9b1743c73f89ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 5 11:15:36 2020 -0800

    update Mask for RunOn

Src/Boundary/AMReX_Mask.H

commit c54388b16811745feaf5a30eb5db6e395155124b
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Mar 5 10:24:48 2020 -0800

    CMake: use CMAKE_CURRENT_LIST_DIR instead of CMAKE_SOURCE_DIR when
    retrieving version info. This fixes issue #731.

CMakeLists.txt

commit 2179dc8dfbc18d51eb148a227cfebc188585b0a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 5 10:20:29 2020 -0800

    update IArrayBox for RunOn

Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_IArrayBox.cpp
Src/EB/AMReX_EB_LSCoreBase.cpp

commit 07f0c6151263efbfaeb1c5c9f2765791aaad339f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 5 10:10:32 2020 -0800

    update FArrayBox for RunOn

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_GpuLaunch.H

commit 6a69bf762b0def4905d394f927597f4055cd05ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 20:02:07 2020 -0800

    fix for gpu

Src/Base/AMReX_BaseFab.H

commit 7aeef181117102fa54bcc64e074e086f47e13011
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Wed Mar 4 20:48:56 2020 -0800

    Remove tab

Src/Base/AMReX_DistributionMapping.cpp

commit 111ac9d60c2e7530347d5dba57471b03ea827d93
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Wed Mar 4 20:45:29 2020 -0800

    Remove print statement

Src/Base/AMReX_DistributionMapping.cpp

commit c1196da64a04fc36a5be3f87a6fbc49ac3b4e52b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 19:53:53 2020 -0800

    prepare for default parameter

Src/Base/AMReX_BaseFab.H

commit 83edb3cf65eeed2abced0c7594ff7477122d511b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 19:25:56 2020 -0800

    add a number of <RunOn::Host>

Src/Base/AMReX_FabArray.H
Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp
Src/Extern/ProfParser/AMReX_CommProfStats.cpp
Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/Extern/amrdata/AMReX_DataServices.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp
Src/Particle/AMReX_LoadBalanceKD.cpp
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleMesh.H
Tests/C_BaseLib/tUMap.cpp
Tests/IOBenchmark/IOTest.cpp
Tests/LinearSolvers/C_CellMG/main.cpp
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit 0ab577a9c29686916f0253eddc85f9fa9b83ec0f
Merge: dd5f85f81 abbc81dee
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Mar 4 17:30:16 2020 -0800

    Merge pull request #733 from AMReX-Codes/fix_EB_setCoveredFace
    
    Fix EB_set_covered_face: now use the input value. Also duplicate

commit abbc81deecb505a32b5770a6294e5eaa690e2904
Author: Lucas Esclapez <lesclapez@lbl.gov>
Date:   Wed Mar 4 16:39:14 2020 -0800

    Fix EB_set_covered_face: now use the input value. Also duplicate
    function to set a range of the MF component.

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit 7b602fe8b628a53ec0f7acb90f740e0441920e83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 16:20:22 2020 -0800

    template more BaseFab functions with RunOn

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_PCI.H
Tutorials/EB/CNS/Source/CNS_advance.cpp

commit dd5f85f81b580efe6efde233f16825ff10bb56cb
Merge: ace0e084e f75989fdf
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Mar 4 15:57:33 2020 -0800

    Merge pull request #732 from AMReX-Codes/jmsexton/particle_bounds
    
    Fix for single-precision RedistributeCPU PeriodicShift particle loss

commit ace0e084e42b57963e2d46f5138f7919e4824232
Merge: 5907f0f85 522ae3d2b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Mar 4 15:53:44 2020 -0800

    Merge pull request #724 from Alpine-DAV/task/2020_03_bp_fix_particle_type
    
    Conduit Blueprint: fix case needed for single prec particles

commit f75989fdf1e33924f6f259c108d6bf14e04afe6e
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Wed Mar 4 15:06:16 2020 -0800

    Update fix for case where ProbLo is not 0

Src/Particle/AMReX_ParticleContainerI.H

commit 82c03f5e4cb6a90e6550f51a80aebc4433bf4015
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Wed Feb 12 15:03:39 2020 -0800

    Fix for single precision mis-match by testing using particle typename

Src/Particle/AMReX_ParticleContainerI.H

commit 5907f0f85e9a6cfa31b76bfb6e377ecae467d02a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 12:56:41 2020 -0800

    In computing RHS, we always double at Neumann boundary as before.

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit e7e2b05976528a9d18caeccbbf309d9ee1f14e3f
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Tue Mar 3 18:01:31 2020 -0500

    Add efficiency argument to makeSFC, makeKnapSack
    
    Additional variant of FlashFluxRegister load method (untested)
    
    1. Add another variant of load method, amrex_flash_fluxregister_load_1_area,
       Since we will frequently use this for FLASH. This is for when we
       have area factors, but do not use an additional (cflux) input as in
       amrex_flash_fluxregister_load_2_area. It turns out we never need a
       separate scalar scaling factor in this case, so I also removed that.
    
    2. Rename previous
         amrex_flash_fluxregister_load_area -> amrex_flash_fluxregister_load_2_area
       and
         amrex_fi_flash_fluxregister_load_area -> amrex_fi_flash_fluxregister_load_2_area
    
    3. Fix: Replace sf_f -> my_sf_f, sf_c -> my_sf_c in a couple
       amrex_fi_flash_fluxregister_load_foo calls, as apparently intended.
    
    fix for amrex_flash_fluxregister_load_FOO procedure names
    
    fix typo
    
    fixed comment
    
    now random() returns numbers in [0.0,1.0) for both CPU and GPU
    
    Fix minor typo Tools/libamrex/configure.py
    
    Add efficiency argument to makeSFC, makeKnapSack
    
    Cleanup
    
    Cleanup
    
    Minor
    
    Logic fix
    
    Add efficiency argument to makeSFC, makeKnapSack
    
    Additional variant of FlashFluxRegister load method (untested)
    
    1. Add another variant of load method, amrex_flash_fluxregister_load_1_area,
       Since we will frequently use this for FLASH. This is for when we
       have area factors, but do not use an additional (cflux) input as in
       amrex_flash_fluxregister_load_2_area. It turns out we never need a
       separate scalar scaling factor in this case, so I also removed that.
    
    2. Rename previous
         amrex_flash_fluxregister_load_area -> amrex_flash_fluxregister_load_2_area
       and
         amrex_fi_flash_fluxregister_load_area -> amrex_fi_flash_fluxregister_load_2_area
    
    3. Fix: Replace sf_f -> my_sf_f, sf_c -> my_sf_c in a couple
       amrex_fi_flash_fluxregister_load_foo calls, as apparently intended.
    
    fix for amrex_flash_fluxregister_load_FOO procedure names
    
    fix typo
    
    fixed comment
    
    now random() returns numbers in [0.0,1.0) for both CPU and GPU
    
    Fix minor typo Tools/libamrex/configure.py
    
    Add efficiency argument to makeSFC, makeKnapSack
    
    Cleanup
    
    Cleanup
    
    Minor
    
    Logic fix
    
    Add efficiency argument to makeSFC, makeKnapSack
    
    Additional variant of FlashFluxRegister load method (untested)
    
    1. Add another variant of load method, amrex_flash_fluxregister_load_1_area,
       Since we will frequently use this for FLASH. This is for when we
       have area factors, but do not use an additional (cflux) input as in
       amrex_flash_fluxregister_load_2_area. It turns out we never need a
       separate scalar scaling factor in this case, so I also removed that.
    
    2. Rename previous
         amrex_flash_fluxregister_load_area -> amrex_flash_fluxregister_load_2_area
       and
         amrex_fi_flash_fluxregister_load_area -> amrex_fi_flash_fluxregister_load_2_area
    
    3. Fix: Replace sf_f -> my_sf_f, sf_c -> my_sf_c in a couple
       amrex_fi_flash_fluxregister_load_foo calls, as apparently intended.
    
    fix for amrex_flash_fluxregister_load_FOO procedure names
    
    fix typo
    
    fixed comment
    
    now random() returns numbers in [0.0,1.0) for both CPU and GPU
    
    Fix minor typo Tools/libamrex/configure.py
    
    Add efficiency argument to makeSFC, makeKnapSack
    
    Cleanup
    
    Cleanup
    
    Minor
    
    Logic fix
    
    Add efficiency argument to makeSFC, makeKnapSack
    
    Additional variant of FlashFluxRegister load method (untested)
    
    1. Add another variant of load method, amrex_flash_fluxregister_load_1_area,
       Since we will frequently use this for FLASH. This is for when we
       have area factors, but do not use an additional (cflux) input as in
       amrex_flash_fluxregister_load_2_area. It turns out we never need a
       separate scalar scaling factor in this case, so I also removed that.
    
    2. Rename previous
         amrex_flash_fluxregister_load_area -> amrex_flash_fluxregister_load_2_area
       and
         amrex_fi_flash_fluxregister_load_area -> amrex_fi_flash_fluxregister_load_2_area
    
    3. Fix: Replace sf_f -> my_sf_f, sf_c -> my_sf_c in a couple
       amrex_fi_flash_fluxregister_load_foo calls, as apparently intended.
    
    fix for amrex_flash_fluxregister_load_FOO procedure names
    
    fix typo
    
    fixed comment
    
    now random() returns numbers in [0.0,1.0) for both CPU and GPU
    
    Fix minor typo Tools/libamrex/configure.py
    
    Add efficiency argument to makeSFC, makeKnapSack
    
    Cleanup
    
    Cleanup
    
    Minor
    
    Logic fix

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit 542bde669824916da6d51c8ad4085d52bbdadedc
Merge: f2cbed89f 284618dc1
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Wed Mar 4 13:36:41 2020 -0500

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex

commit 284618dc1a33a00a38af11558b15fcec4de8e408
Merge: db1d028bd ff75afc26
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Mar 4 10:36:23 2020 -0800

    Merge pull request #729 from cselab/fabian/pullreq
    
    Fix minor typo Tools/libamrex/configure.py

commit db1d028bd03204120b3f624f49648d78e26e3112
Merge: ee6dde591 0c2574f50
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 10:34:49 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ee6dde591ab9a0a4c4ddd96168a5435ca78f2d81
Merge: 1604c0262 e137ef417
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 10:31:07 2020 -0800

    Merge branch 'development' into FlashFluxRegister

commit 0c2574f500a3e911a59ad9893e35c1e6b6b83c80
Merge: e137ef417 575af1b7c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Mar 4 10:31:06 2020 -0800

    Merge pull request #726 from lucafedeli88/fix_doc_random
    
    Make amrex::Random() return numbers in the same interval for both CPU and GPU: [0:1)

commit e137ef41706e81143bb59aa24dfc6900124714dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 10:30:28 2020 -0800

    fix typo

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 1604c0262f87953d1c5f404d76d734fbb1c879b6
Merge: e97431df1 54be23e8e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Mar 4 10:29:50 2020 -0800

    Merge pull request #728 from kweide/FlashFluxRegister
    
    Additional variant of FlashFluxRegister load method (untested)

commit ff75afc2603aff502dce5e1b08bb81f380166605
Author: Fabian Wermelinger <fabianw@mavt.ethz.ch>
Date:   Wed Mar 4 10:16:00 2020 -0800

    Fix minor typo Tools/libamrex/configure.py

Tools/libamrex/configure.py

commit f2cbed89f6b15dc377fd701e3b22044539d685f7
Merge: 332ae3119 1bd08c21b
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Wed Mar 4 13:16:13 2020 -0500

    Merge branch 'master' of https://github.com/mrowan137/amrex

commit 332ae3119f6ffd7db5d3c2e6bc9d37b7300aaf4f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 09:31:59 2020 -0800

    fix Neumann for divu too

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 54be23e8e677ce6481f5282372a13c0169bb484f
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Wed Mar 4 11:52:22 2020 -0600

    fix for amrex_flash_fluxregister_load_FOO procedure names

Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90

commit e96e5da37fdbfe7684aa479fa8c07664572ffa16
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Wed Mar 4 09:36:55 2020 -0600

    Additional variant of FlashFluxRegister load method (untested)
    
    1. Add another variant of load method, amrex_flash_fluxregister_load_1_area,
       Since we will frequently use this for FLASH. This is for when we
       have area factors, but do not use an additional (cflux) input as in
       amrex_flash_fluxregister_load_2_area. It turns out we never need a
       separate scalar scaling factor in this case, so I also removed that.
    
    2. Rename previous
         amrex_flash_fluxregister_load_area -> amrex_flash_fluxregister_load_2_area
       and
         amrex_fi_flash_fluxregister_load_area -> amrex_fi_flash_fluxregister_load_2_area
    
    3. Fix: Replace sf_f -> my_sf_f, sf_c -> my_sf_c in a couple
       amrex_fi_flash_fluxregister_load_foo calls, as apparently intended.

Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H
Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp
Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90

commit 575af1b7c68964afed9ea013a004b8e3c8fe9505
Author: Luca Fedeli <luca.fedeli.88@gmail.com>
Date:   Wed Mar 4 16:06:02 2020 +0100

    now random() returns numbers in [0.0,1.0) for both CPU and GPU

Src/Base/AMReX_Random.cpp

commit 6cbd0cb6e46081bacac754565c6f32617d5ad990
Author: Luca Fedeli <luca.fedeli.88@gmail.com>
Date:   Wed Mar 4 16:05:20 2020 +0100

    fixed comment

Src/Base/AMReX_Random.H

commit 1bd08c21b93438ba1473425e6e19325b9bea8061
Merge: dcea782fb 59ea39584
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Tue Mar 3 20:19:04 2020 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex

commit 59ea39584d84764da76ef49bd6583d6f7c08559e
Merge: 8a2378ef8 6268db578
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 3 19:25:16 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8a2378ef8bc1039e78878e9c9efe0639f42561b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 3 19:25:09 2020 -0800

    should not multiple by 2 at Neumann BC when using RAP

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit dcea782fbb2307b585da9bc5e2bca7d11808e7a6
Merge: 6268db578 c275ccc2f
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Tue Mar 3 16:25:01 2020 -0800

    Merge branch 'mrowan/loadbalance' of https://github.com/mrowan137/amrex

commit 6268db5787b3c631c796b5e5938b62dcae487204
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Mar 3 15:43:15 2020 -0800

    decrease max buffer size

Src/Particle/AMReX_ParticleUtil.H

commit 6659bcf4849f0283c4dfe5f77e9589840e708056
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Mar 3 15:42:35 2020 -0800

    can exit early from the no particle case

Src/Particle/AMReX_ParticleUtil.H

commit d33b926f241f0a25e89a662bf49815185cf43258
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Mar 3 15:42:11 2020 -0800

    make sure to handle the invalid particle case here

Src/Particle/AMReX_ParticleContainerI.H

commit c275ccc2ff6e7f3ee3496b0dbb417b5e5114a928
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Tue Mar 3 18:01:31 2020 -0500

    Add efficiency argument to makeSFC, makeKnapSack

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit 522ae3d2b5cf310a5fecd1dbb4736d44c65df394
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Tue Mar 3 12:44:43 2020 -0800

    fix particle case where ParticleReal is needed

Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H

commit f7d989ca12c0a1dcfae0897c12d5e2e842d51b00
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Mar 3 11:54:20 2020 -0800

    prevent overflow error

Src/Particle/AMReX_ParticleUtil.H

commit dc915e981a702818a6439485b82df22a4ad02d54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 2 16:22:36 2020 -0800

    disable cl::intel_reqd_sub_group_size for now because it causes CL_INVALID_KERNEL_NAME failure

Src/Base/AMReX_GpuQualifiers.H

commit fd522194c913a043102d252c64e7883312aafce2
Merge: f521886e7 495c398dc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Mar 2 15:52:08 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f521886e767e4ff831a7ab75a267001eff57127f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Mar 2 15:51:57 2020 -0800

    another tweak to particle_compare

Tools/Postprocessing/C_Src/particle_compare.cpp

commit 495c398dc816eb8e30cbba55ff0daeddde882b8f
Merge: a2b6859ba 35e0b44bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 2 14:25:12 2020 -0800

    Merge branch 'development' into dpcpp

commit a2b6859baabb2452f741db440ddbbf4429bdb5b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 2 14:22:18 2020 -0800

    add cl::intel_reqd_sub_group_size and get rid of compiler warnings

Src/Base/AMReX_FBI.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuLaunchMacrosG.H
Src/Base/AMReX_GpuQualifiers.H
Src/Base/AMReX_Machine.cpp
Src/Base/AMReX_Reduce.H

commit 35e0b44bc929fc7dbbf15952be9fdedec0578797
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 2 14:11:53 2020 -0800

    update DPC++ notes

Docs/Notes/Readme.dpcpp

commit 6c6c9df46ad02737539c2cb7e7a75dacefbcb0d9
Merge: ccc4b5c66 50595a480
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 2 14:05:41 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 50595a480ef53880aa83d7376ec36c4578fa01ea
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Mar 2 13:38:36 2020 -0800

    need to do this at run time instead of compile time

Tools/Postprocessing/C_Src/particle_compare.cpp

commit a9b771f3ecbf48909ec9ba5a81ef1993b0381a24
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Mar 2 13:16:43 2020 -0800

    make particle_compare respect single precision

Tools/Postprocessing/C_Src/particle_compare.cpp

commit ccc4b5c66e7021d943c3142b5407b6f5fedf9183
Merge: e348a5f7b 6a4f8d868
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 2 10:23:32 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6a4f8d868d51e3fd5ffeb7c5e3c2af5a63c5645e
Merge: 645e5cc9e f5fc91130
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Mar 2 10:19:49 2020 -0800

    Merge branch 'atmyers/memopt' into development

commit e348a5f7b6f036b3ed9f7bcc55ebbc64d4cc1fb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 2 09:12:22 2020 -0800

    update CHANGES

CHANGES

commit 2a31c2a6a5d7fde098790bb25e6cd2025b33517b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 1 18:30:45 2020 -0800

    fix typo

Src/Base/AMReX_BaseFab.H

commit 29ae52325be9f8ee5b83f9dfe7a26984d89abbaa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 1 14:31:38 2020 -0800

    template BaseFab::sum with RunOn

Src/AmrCore/AMReX_FluxRegister.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_DistributionMapping.cpp

commit b8cd05f729a5e5f7a4c6292c998417b224995e75
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 1 13:50:50 2020 -0800

    remove device code from BaseFab::minIndex and maxIndex

Src/Base/AMReX_BaseFab.H

commit 756ea9312cfbb5043620cc858648a27583b4d9cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 1 13:40:24 2020 -0800

    rm BaseFab::indexFromValue

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.cpp

commit 2ad2f906f0b6ee8b5104c5ff4ce371ae58fbccdd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 1 13:09:34 2020 -0800

    template BaseFab::min, max and norm with RunOn

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_VisMF.cpp
Src/Base/AMReX_iMultiFab.cpp
Src/EB/AMReX_EB_LSCoreBase.cpp

commit 96dd9739562626361ee49d556be34da96397b7be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 29 20:18:13 2020 -0800

    template BaseFab::copyToMem, copyFromMem and addFromMem with RunOn

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_FBI.H
Src/EB/AMReX_MultiCutFab.H

commit 8380ebf4b815887c15a0a83d20b92b1c2871cbcc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 29 20:06:42 2020 -0800

    template BaseFab::copy with RunOn

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_FBI.H
Src/Base/AMReX_MFCopyDescriptor.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_PCI.H
Src/Base/AMReX_PlotFileDataImpl.cpp
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/EB/AMReX_MultiCutFab.H

commit 25a293d08b91ba4220cf1b03cdcfa613953501dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 29 19:14:19 2020 -0800

    setVal: pass by const&

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_IArrayBox.H

commit a26cca5b5c7c136dcc725217d9fe70f384e5ce46
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 29 19:08:26 2020 -0800

    template setVal with RunOn

Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_IArrayBox.cpp
Src/Base/AMReX_Loop.H
Src/Base/AMReX_MFCopyDescriptor.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_VisMF.cpp
Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/EB/AMReX_EB2_Level.cpp
Src/EB/AMReX_EB_levelset.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp

commit f5fc911308d2dc386a5001475aac3888cc8377e9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Feb 29 16:22:43 2020 -0800

    ability to do a 'chunked' partition

Src/Particle/AMReX_ParticleUtil.H

commit 0a5da0d2e9197651e9baf3ce3c40720a0ca76596
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Feb 29 16:22:28 2020 -0800

    swap particle routine

Src/Particle/AMReX_ParticleTransformation.H

commit 34c5d391e85ec79bf64b472416353e2412eaa444
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Sat Feb 29 14:22:21 2020 -0500

    CUDAPATH --> SYSTEM_CUDA_PATH

Tools/GNUMake/comps/nvcc.mak

commit 8f2fba619699c842a0b55d15bc29dbf360e4fb17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 29 10:51:42 2020 -0800

    move ~T() calls to a function

Src/Base/AMReX_BaseFab.H

commit 98d1d279450e5e93651a3c911cdc927409f4ed80
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 29 10:39:57 2020 -0800

    add RunOn to operator= and change the parameter to const&

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_IArrayBox.cpp

commit 8d8f8b1b8f20ac0b533c8130a229cd2cebd61a05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 29 08:47:27 2020 -0800

    remove AMREX_GPU_HOST_DEVICE qualifier from BaseFab functions

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_IArrayBox.H
Src/Boundary/AMReX_Mask.H

commit 8b612f61d27d2e1cd05ba2a32f9f6b8370cc57e7
Merge: 4c5a93a3c 645e5cc9e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 28 21:34:34 2020 -0800

    Merge branch 'development' into weiqun/dev

commit 645e5cc9e2e60e29b9acb9729caa983bebc6a29f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Feb 28 17:38:55 2020 -0800

    CMake: set versioning variables before project()

CMakeLists.txt
Tools/CMake/AMReXInstallHelpers.cmake

commit f0467fdcc44775b47ce7ef68059d6fdc30f11417
Merge: 44ceea24c 26fbe3874
Author: mic84 <mrosso@lbl.gov>
Date:   Fri Feb 28 14:44:40 2020 -0800

    Merge pull request #721 from ax3l/topic-ciTutorials
    
    CI: Make Tutorials

commit 26fbe387440ca1fc0b1be408b34d73f61ae11130
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri Feb 28 14:33:07 2020 -0800

    CI: Make Tutorials
    
    Remove demonstrator `CMakeLists.txt` files from tutorials
    as they confuse the tutorial superbuild.
    
    Build tutorials with and without CUDA.

.github/workflows/cmake.yml
.github/workflows/cmake/dependencies_nvcc.sh
Tutorials/Basic/HelloWorld_C/CMakeLists.txt
Tutorials/Particles/CellSortedParticles/CMakeLists.txt

commit 44ceea24cb6dd6ea90940e0944c78bd4b7a9e5bf
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Feb 28 12:49:13 2020 -0800

    CMake: add defines for Clang version

Tools/CMake/AMReX_Config.cmake

commit 64cb1fc7e9435daff9a19a34c88afb2683e14056
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Feb 28 12:47:15 2020 -0800

    CMake: allow building with Cray compiler
    
    Partially fixes issue #719

Tools/CMake/AMReX_Config.cmake

commit 5d5b8d33b4f7cf4fdcc7663939638d8d8b31d486
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Feb 28 12:45:49 2020 -0800

    CMake: update flags target + add Clang flags

Tools/CMake/AMReXFlagsTargets.cmake

commit 092d417cf35a96790d64ce7e0faa3358443b01c1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 28 12:31:53 2020 -0800

    ifdef out function if no GPU

Src/Particle/AMReX_ParticleUtil.H

commit de5a297a66a4eb8797b72879b3726ab849c499b2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 28 15:20:08 2020 -0500

    add missing header

Src/Particle/AMReX_ParticleUtil.H

commit 8031fbd79466ebdffd247f5c8fde487a0a08c1ce
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 28 15:13:17 2020 -0500

    move partition step into its own function

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_ParticleUtil.H

commit 59b27bae370c573b8a34ed9273874bbde1cea041
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 28 14:10:59 2020 -0500

    move lev, grid calculations to be on-the-fly

Src/Particle/AMReX_ParticleContainerI.H

commit 4c5a93a3c151466630452e2de0234c2cea4ac349
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 28 10:47:37 2020 -0800

    set ghost cells to zero to avoid fpe

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit e4091e882d79dc339d77520258c4bb01fc13153f
Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Date:   Fri Feb 28 10:42:22 2020 -0800

    Formatting

Src/Base/AMReX_TinyProfiler.cpp

commit 88ee09c2e4ad55294fb53a02202f8306327b402f
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Fri Nov 8 12:30:38 2019 -0800

    Add CUPTI trace feature for GPU kernel timing
    
    Cleanup CUPTI GPU timer
    
    Save more kernel stats to activity record
    
    Cleanup; eliminate unneeded functions
    
    Cleanup

Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_CuptiTrace.H
Src/Base/AMReX_CuptiTrace.cpp
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp
Src/Base/Make.package
Tests/GPU/CuptiTest/Exec/CUDA/GNUmakefile
Tests/GPU/CuptiTest/Exec/CUDA/Make.package
Tests/GPU/CuptiTest/Exec/CUDA/myfunc.H
Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp
Tests/GPU/CuptiTest/Exec/CUDA/mykernel.H
Tests/GPU/CuptiTest/Make.CUPTI
Tests/GPU/CuptiTest/Source/Make.package
Tests/GPU/CuptiTest/Source/main.cpp
Tools/GNUMake/Make.defs
Tools/GNUMake/comps/nvcc.mak

commit 7943502fe23ed86b0e986f51a5d4f37ae1d7f820
Merge: 787f0de5e a2ce2acee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 28 09:48:20 2020 -0800

    Merge branch 'dpcpp' into weiqun/dev

commit a2ce2aceef149ced0aac7cc7114a0d05f056335d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 28 09:40:23 2020 -0800

    fix gpu race conditions in YAFluxRegister::FineAdd

Src/Boundary/AMReX_YAFluxRegister_1D_K.H
Src/Boundary/AMReX_YAFluxRegister_2D_K.H
Src/Boundary/AMReX_YAFluxRegister_3D_K.H

commit 787f0de5edcf0b4ea6a67f1671b70f38fc49668f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 27 22:00:45 2020 -0800

    IntVect::coarsen optimization

Src/Base/AMReX_IntVect.H

commit 737b607a0462d6157b0e87603d18b95bd4e96861
Merge: f42684ca7 4e3aa38c0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 27 21:41:41 2020 -0800

    Merge pull request #718 from AMReX-Codes/empic-offset
    
    Initialize the particles in the first cell of each tile for EM PIC tutorial

commit f42684ca71b8a0dcfd0186b71ad4b4b1c52ec08b
Merge: 8c5dbb6a4 599ccf16a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Feb 27 21:29:36 2020 -0500

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8c5dbb6a4ac930390cd66738c400a1592bc3c0fa
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Feb 27 21:26:12 2020 -0500

    CMake: do not enable CUDA via AMReX_SetupCUDA.
    
    From now on, application codes will need to enable CUDA directly instead of
    relying on AMReX_SetupCUDA.
    However, AMReX_SetupCUDA must still be included by application codes
    to setup the CUDA build environment for linking to AMReX.

CMakeLists.txt
Tools/CMake/AMReX_SetupCUDA.cmake

commit 4e3aa38c00542e3f5d96e7abdb93079234c0b247
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Thu Feb 27 17:41:50 2020 -0800

    Subtract the number of particles in the first cell of each tile to get the offset index for the first particle in each cell.

Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp

commit 599ccf16a721a09091a02d43154844cbb41348fd
Merge: d9b1fffa8 7627071b9
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Feb 27 13:42:29 2020 -0800

    Merge pull request #705 from ax3l/fix-warnExpansionToDefined
    
    Fix Warning in AMREX_DEVICE_COMPILE

commit 7627071b99be332c27c6d8ad36e4d8e714420229
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Feb 26 14:12:31 2020 -0800

    Remove defines in AMREX_DEVICE_COMPILE
    
    Adding `defined()` in a macro is raising warnings
    of undefined behavior (clang) or non-portable
    behavior (gcc).
    
    This patch seems to work on for CUDA, DPC++ and non-gpu.
    (HIP untested.)
    
    Co-authored-by: Weiqun Zhang <weiqunzhang@lbl.gov>

Src/Base/AMReX_GpuQualifiers.H

commit 49666bba776bb1cf242756353c0385cc067bbd55
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Tue Feb 25 23:36:36 2020 -0800

    Fix Warning in AMREX_DEVICE_COMPILE
    
    Calling the macro `AMREX_DEVICE_COMPILE` with `()` in pre-processor
    calls seams to be an alternative, non-portable way of checking
    `defined()`.
    Modern versions of GCC issue a `-Wexpansion-to-defined` warning on
    this.
    
    Remove the `()` from `AMREX_DEVICE_COMPILE()` calls since they
    should not be needed.

Src/Base/AMReX.H
Src/Base/AMReX_Array4.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_GpuAtomic.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuRange.H
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EB2_IF_Polynomial.H

commit d9b1fffa8b78b23ca800e65da60181593605ad1d
Merge: 529a74151 fd4a5b6af
Author: mic84 <mrosso@lbl.gov>
Date:   Thu Feb 27 12:38:21 2020 -0800

    Merge pull request #716 from ax3l/fix-enableFortranCmake
    
    CMake: CXX Downstream Transitive Fortran

commit fd4a5b6af482ce9b02f18023207f265c902aa62d
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Feb 27 10:45:11 2020 -0800

    CMake: Fix Transtive Fortran Libs
    
    CMake currently has the bug that some transitive, implicit language
    dependencies as not commuted downstream if the downstream project
    does not `enable_language` the same lang. as upstream.
    
    This is mostly visible in missing `-lgfortran` links.
    
    This adds a useful work-around by just exposing these implicit
    Fortran "standard" libraries as explicit link dependencies.

Src/CMakeLists.txt

commit 529a74151350da4f7fa6d5ae48917a761ada97e2
Merge: 288c14646 989ee2242
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 27 10:39:04 2020 -0800

    Merge pull request #713 from ax3l/topic-ciBadges
    
    Readme: Add CI Badges

commit 1249afd1e9a499192dce96302da0b2a17380796d
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Feb 27 10:37:39 2020 -0800

    CMake: CXX Downstream Transtive Fortran
    
    CMake currently has the bug that some transitive, implicit language
    dependencies as not commuted downstream if the downstream project
    does not `enable_language` the same lang. as upstream.
    
    This is mostly visible in missing `-lgfortran` links.
    
    This triggers this bug.

Tutorials/Basic/HelloWorld_C/CMakeLists.txt

commit 288c14646bced8e90247f02645030f51833104ca
Merge: e6aa32068 742ecd37c
Author: mic84 <mrosso@lbl.gov>
Date:   Thu Feb 27 10:29:14 2020 -0800

    Merge pull request #714 from ax3l/fix-offWarningClangGfortran
    
    CMake Tools: Fix CXX Host Compiler Check

commit 742ecd37cb020e17a2ebeb85ac7f2eb40513b9a4
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Feb 26 23:38:10 2020 -0800

    CMake Tools: Fix CXX Host Compiler Check
    
    False Warning with Clang+Gfortran builds.

Tools/CMake/AMReX_Config.cmake

commit 989ee2242c351d770c18ee978d23d8cc704396e9
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Feb 26 22:28:58 2020 -0800

    Readme: Add CI Badges
    
    Add Travis-CI and GitHub Action status badges for the
    `development` branch.

README.md

commit e6aa32068caa8cb45c714b446ab8b7f3c00d5665
Merge: 1425839ff 563b7242a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 26 19:33:33 2020 -0800

    Merge pull request #712 from ax3l/topic-ghActionCMake
    
    CI: Add GitHub Workflow for CMake

commit 563b7242af14ddfc6c0ec3d63652ad15383f7e15
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Feb 26 16:12:40 2020 -0800

    CI: Add GitHub Workflow for CMake
    
    Add a CI job via GitHub actions to ensure CMake builds are
    not breaking.

.github/workflows/cmake.yml
.github/workflows/cmake/dependencies.sh
Tutorials/Basic/HelloWorld_C/CMakeLists.txt
Tutorials/Particles/CellSortedParticles/CMakeLists.txt

commit 1425839ffb5d7c2f215571445f45b41d5b87c923
Merge: d57f56875 f9e9fc33b
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Feb 26 17:27:48 2020 -0800

    Merge pull request #711 from ax3l/fix-newFortranInterfaceFile
    
    CMake: New Fortran Interface File

commit d57f568754fe5f32c903058e68c6d0478d395ccc
Merge: 415a09e22 cc4330cd7
Author: mic84 <mrosso@lbl.gov>
Date:   Wed Feb 26 17:24:29 2020 -0800

    Merge pull request #710 from ax3l/topic-cmakeAlias
    
    CMake: AMReX::amrex Alias

commit f9e9fc33bdfc0a0efa1d73d79d0b9033ffd888d4
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Feb 26 16:06:02 2020 -0800

    CMake: New Fortran Interface File
    
    Add a new Fortran file to the F_Interface sources.
    Fixes a compile issue.

Src/F_Interfaces/CMakeLists.txt

commit cc4330cd771fe848cfcfc064a2199a1efbf47939
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Feb 26 14:44:47 2020 -0800

    CMake Targets: More Namespace Aliases
    
    Add installed namespace alias to all public AMReX targets.

Tools/CMake/AMReXFlagsTargets.cmake

commit 1f05c40dfe5897afd5cf4938ee9862666e233464
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Feb 26 14:41:10 2020 -0800

    CMake: AMReX::amrex Alias
    
    Adding a project alias on `CMakeLists.txt` level that is
    identical to the installed CMake namespace.
    
    This is a community-convention in CMake and makes sure that
    both `add_subdirectory(AMReX_DIR)` as well as `find_package(AMReX)`
    targets can just be accessed as `AMReX::amrex` in all cases in
    user code.

Src/CMakeLists.txt

commit 415a09e22df63723587aa5a3ed290f64736d622c
Merge: f3958d151 f68c92290
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Feb 26 12:14:13 2020 -0800

    Merge pull request #709 from AMReX-Codes/load_balance_api
    
    Load balance api

commit f3958d151830a1a6a01a3a33fa3aad253b696c12
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 26 12:04:39 2020 -0800

    make

Tools/GNUMake/comps/gnu.mak

commit f68c92290f7d90f09795cd5e0f66f697e5efd688
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 26 12:01:23 2020 -0800

    Add rcost version of makeSFC

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit 5373dabb441de43f253ab6f803f96bfd847fe37c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 26 11:46:55 2020 -0800

    add nmax argument to rcost version of makeKnapSack

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit dcb3da2a63f77360428d1986e04ff3453f2e41f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 26 09:12:14 2020 -0800

    fix USE_CUDA=TRUE BL_NO_FORT=TRUE

Tools/GNUMake/sites/Make.unknown

commit 9e5adaac2b8f67330a339f2354f672c28e07c794
Merge: e883ebf89 334d2b7ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 25 21:13:40 2020 -0500

    Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development

commit e883ebf8916016c628255f6a026fdf16e19bad24
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 25 21:13:27 2020 -0500

    strings should not be gpu managed

Tools/F_scripts/write_probin.py

commit 334d2b7ba63c954414a7da04435f7b88ecb207b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 25 11:39:03 2020 -0800

    make some Macs even more happier with make

Tools/GNUMake/sites/Make.unknown

commit f125809d61f36d1da2336648cfc55d1258bf6ca5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 25 11:13:14 2020 -0800

    make some Macs happy with make

Tools/GNUMake/sites/Make.unknown

commit 63f4e2248ed3181319a757c200924fc20759dd64
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 25 08:53:19 2020 -0800

    fix for hip

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/gnu.mak

commit 1ba6c22f27058b02ac056b19b3a293480cb49e34
Merge: f45019991 be5232a9c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 25 01:47:08 2020 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f45019991709df63f9bba670c184d26464e8e40a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 25 01:46:49 2020 -0500

    use Send instead of Asend in particle communication

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit be5232a9c51ab4641c75e2373aeb767aa28eb029
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 24 16:08:06 2020 -0800

    If one compiles with NVCC_CCBIN=gcc-x, it will be used as the nvcc host compiler

Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/nvcc.mak

commit a8b60a3b0a6a12059cc89753a53bb013778949d2
Merge: 7d1eb6004 f9c81ed9b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 24 16:37:22 2020 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 7d1eb600495e816a8ab00701c4dde73cd13ac1f0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 24 16:23:39 2020 -0500

    make these temporary instead of member data

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 15ccf23ea44027e9c10b73a7658cb63d78d1a822
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 24 16:23:04 2020 -0500

    shrink to fit and capacity methods for ParticleTile

Src/Particle/AMReX_ParticleTile.H

commit f9c81ed9b1b08b5e76f617b7b2c817cbef1519b2
Merge: 487366bed b1c8ce10b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 24 12:36:45 2020 -0800

    Merge branch 'dpcpp' into development

commit 487366bed987a7c2478562e33bc2a3bda0ca09d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 24 11:26:16 2020 -0800

    add CArena::heap_space_actually_used

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp

commit 7f1bf0a7a1afec98ed1959169d53d5e2ee0ca7c2
Merge: f5d8735ad 771e143d3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Feb 24 10:24:51 2020 -0800

    Merge pull request #701 from AMReX-Codes/cgilet_dev
    
    Cgilet dev

commit f5d8735ad032b8a772270c7e76845da66c8dfda1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 24 10:17:25 2020 -0800

    add CArena::sizeOf to return the size of momory held by a pointer

Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp

commit b1c8ce10b852b646040397321b179dd2ba462860
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 24 09:45:37 2020 -0800

    cannot use sycl::abs directly because it returns unsigned int given int.

Src/Base/AMReX_Math.H

commit 55a396c4d72217599b28d19b49426c8fdf64703f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 24 09:37:14 2020 -0800

    FBI: we can assume thread safety if not using OpenMP.

Src/Base/AMReX_FabArrayBase.cpp

commit 771e143d3b48abd77d0520dd85b52cb37ab332ba
Author: cgilet <cgilet@gmail.com>
Date:   Mon Feb 24 08:16:57 2020 -0500

    Allow EBFabFactories with Basic EB support to use boxArray() and DistributionMap()

Src/EB/AMReX_EBFabFactory.cpp

commit f1d2244bcea147128790efbc7e20d101e5f8445b
Merge: b11160ac8 185b2d4cd
Author: cgilet <cgilet@gmail.com>
Date:   Mon Feb 24 08:13:25 2020 -0500

    Merge remote-tracking branch 'origin/development' into cgilet_dev

commit 135c9ea682a2b101579c25d4d2cf3706185e55c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 23 13:29:49 2020 -0800

    make the heat equation problem bigger and there is no need to create plotmf

Tutorials/GPU/HeatEquation_EX1_C/Exec/default/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit 185b2d4cd61969379a629092e7ef7cf1da07a816
Merge: db72de3d0 0b512f363
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Feb 23 16:06:59 2020 -0500

    Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development

commit db72de3d04afa17bb027ba6412e520ab6932e4a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Feb 23 16:04:19 2020 -0500

    add character support

Tools/F_scripts/write_probin.py

commit d28a52e37fead82a1974cc3c8cf2f54853d1383e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 23 09:35:57 2020 -0800

    set USE_CUDA=FALSE when USE_HIP=TRUE

Tools/GNUMake/Make.defs

commit 7f002a20184705ad23496f4d2e6571968b751a58
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 23 09:33:43 2020 -0800

    Heat equation tutorial: merge CUDA and HIP

Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/myfunc.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/mykernel.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/inputs_3d_hip
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/myfunc.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/mykernel.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.ascent
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.nocuda.script
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.summit
Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.summitdev

commit 8c929d513c9ad75464ca03b724ded617e1b1ca00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 23 09:12:30 2020 -0800

    remove enable_if for non-DPC++

Src/Base/AMReX_Reduce.H

commit 2d70f51fc09bac602efc8c89e1ac572646f40621
Merge: 75cc8040e 0b512f363
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 23 09:08:02 2020 -0800

    Merge branch 'development' into dpcpp

commit 0b512f3630779f632f18d001d9a47f904064fc86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 22 22:38:38 2020 -0800

    one more int -> long

Src/Base/AMReX_FabArrayBase.H

commit 75cc8040ea9b158aea089dcec098ace139dce4a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 22 21:28:20 2020 -0800

    update DPC++ notes

Docs/Notes/Readme.dpcpp

commit 872a3a677cb52b70410948dc52bc4414a49c2773
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 22 20:59:11 2020 -0800

    get around DPC++ bug?

Src/Base/AMReX_Reduce.H

commit 738ca166f23f93ecae5dafbacd44d4b697dfd202
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 22 19:52:53 2020 -0800

    make GpuTuple's default ctor host device function

Src/Base/AMReX_Tuple.H

commit a5d3676c74e3e8ad7ffddcdb1eae53afe34c9255
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 22 18:13:39 2020 -0800

    update ParallelReduce tutorial

Tutorials/GPU/ParallelReduce/main.cpp

commit 98524153e355c97cdc59ffbf903ff4ff37de008a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 22 18:13:12 2020 -0800

    fix a typo

Src/Base/AMReX_GpuLaunchFunctsG.H

commit b736f2ea84215a9494f1613c4b4fe673f03916e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 22 18:12:12 2020 -0800

    avoid capture GpuTuple by value in reduction because dpc++ does like it's not standard layout

Src/Base/AMReX_Reduce.H

commit 312bd157995f4ada0fb00a264aa1b7772996e129
Merge: 784a199aa 560e11ff2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 22 17:30:23 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 784a199aa0560ebaddf8e73cb1dccf46644bf4e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 22 17:30:03 2020 -0800

    int -> long to avoid overflow

Src/Base/AMReX_FabArrayBase.H

commit 560e11ff292f5b7c303dbe76adb0c40a8d1fa878
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Feb 22 19:17:02 2020 -0500

    ManagedVector -> DeviceVector throughout ParticleContainer

Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_NeighborList.H
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleLocator.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_StructOfArrays.H

commit 715face89aaaa6b89dc5a5b8a291a6ffa480abdb
Merge: f63d9af67 04ac0df52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 21 21:32:35 2020 -0800

    Merge branch 'dpcpp' into development

commit 04ac0df524c922fda5d057bc96c6524901e3d8fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 21 21:32:11 2020 -0800

    note to GpuTuple and DPC++

Docs/Notes/Readme.dpcpp

commit f63d9af676b6c261ba6b75cef3fdb7ff3266cd17
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Feb 21 20:40:33 2020 -0800

    Deal with the case where extern is in a subdirectory

Tools/F_scripts/write_probin.py

commit 87686a7ee1bd07087172d8b1d9ab4f7394d98b19
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 21 16:04:51 2020 -0800

    fix DPCPP launch macros

Src/Base/AMReX_GpuLaunchMacrosG.H
Tutorials/GPU/Launch/Make.package

commit 319385afff27bceea60e48d6cf6b9df84a127cf3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 21 14:59:03 2020 -0800

    DPCPP: abort in amrex::launch if shared memory is asked

Src/Base/AMReX_GpuLaunchFunctsG.H

commit b54644026d649070dd0180762d253e919c0417d0
Merge: a54971835 2d6772c93
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Feb 21 14:12:46 2020 -0800

    Merge pull request #700 from ax3l/fix-FBIConstr
    
    FAB: Fix Constructor Calls

commit 2d6772c930120385ecb791557fd4df0a3a84b366
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri Feb 21 13:38:53 2020 -0800

    FAB: Fix Constructor Calls
    
    This fixes a bug in `Array4CopyTag` construction while pushing back
    to a vector. The current call does not what one expects to do, as
    hinted by the nvcc warning:
    ```
    Src/Base/AMReX_FBI.H(920): warning: variable "zero" was set but never used
              detected during:
                instantiation of "void amrex::FabArray<FAB>::FBEP_nowait(int, int, const amrex::IntVect &, const amrex::Periodicity &, __nv_bool, __nv_bool) [with FAB=amrex::FArrayBox, F=amrex::FArrayBox, <unnamed>=void]"
    Src/Base/AMReX_FabArray.H(1993): here
                instantiation of "void amrex::FabArray<FAB>::FillBoundary_nowait(int, int, const amrex::IntVect &, const amrex::Periodicity &, __nv_bool) [with FAB=amrex::FArrayBox]"
    Src/Base/AMReX_FabArray.H(1870): here
                instantiation of "void amrex::FabArray<FAB>::FillBoundary(const amrex::Periodicity &, __nv_bool) [with FAB=amrex::FArrayBox]"
    
    Src/Base/AMReX_FBI.H(955): warning: variable "zero" was set but never used
              detected during:
                instantiation of "void amrex::FabArray<FAB>::FillBoundary_finish() [with FAB=amrex::FArrayBox, F=amrex::FArrayBox, <unnamed>=void]"
    Src/Base/AMReX_FabArray.H(1871): here
                instantiation of "void amrex::FabArray<FAB>::FillBoundary(const amrex::Periodicity &, __nv_bool) [with FAB=amrex::FArrayBox]"
    ```
    
    Basically the last arguments were not passed to object construction of
    `amrex::Array4CopyTag`.
    
    Further fixes:
    - add missing includes
    - move created r-values in (`emplace_back`)

Src/Base/AMReX_FBI.H

commit a5497183578cd5d6c2b77910c12e06fbb1a72dc1
Merge: 5b535ee5c 556438f6d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 21 13:21:57 2020 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 556438f6d4e72d0460748d7fa61cf0af75f5105e
Merge: e13001f2c 052c5cc6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 21 13:21:44 2020 -0800

    Merge branch 'dpcpp' into development

commit 052c5cc6a260466ba0be47460a000b403faec7e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 21 13:21:19 2020 -0800

    notes on DPC++

Docs/Notes/Readme.dpcpp

commit 5b535ee5c8e59425ab410686becf7fb5f6d330d9
Merge: e13001f2c 1a3fc7cbf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 21 13:19:45 2020 -0800

    Merge branch 'dpcpp' into development

commit 1a3fc7cbf78848f006ab9ea2e76b8da094771f20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 21 13:08:49 2020 -0800

    wait and throw

Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuReduce.H

commit ddfcd77d3b83166de8d9f6b1f689d9943bc9118a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 21 12:52:32 2020 -0800

    update comments

Src/Base/AMReX_GpuDevice.cpp

commit e13001f2c92d5fdfac8dff6c107251d85f5d392e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Feb 21 15:29:20 2020 -0500

    CMake+CUDA: no need to specify libcuda manually

Tools/CMake/AMReX_Config.cmake

commit 8266379fa4b4cfe42077b525bdc41cb084b0909e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Feb 21 15:13:07 2020 -0500

    CMake:add missing sources from Extern/ProfParser

Src/Extern/ProfParser/CMakeLists.txt

commit 3d976f4c33859a8993df596ad390efa0eb6cecc6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 21 09:48:44 2020 -0800

    do not define dim3 for non-dpcpp

Src/Base/AMReX_GpuTypes.H

commit 3237a58d1edd575645e4c0b1d99c89d063cefa1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 21 09:40:41 2020 -0800

    remove shared_mem_bytes option from FabReduce and VecReduce

Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_Reduce.H

commit e1fa142531608ffdd5b4c437f18c339ed999bd3a
Merge: 73ac4da6d cb0f385fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 21 09:18:18 2020 -0800

    Merge branch 'development' into dpcpp

commit 73ac4da6d61f50c17936ba1239f513f1de1f4f8a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 20 21:55:33 2020 -0800

    DPC++: implement AnyOf

Src/Base/AMReX_Reduce.H

commit 10db5b5993d6db903b4233a34c324a0f7986f2e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 20 21:42:19 2020 -0800

    DPC++: implement some functions used by FillBoundary

Src/Base/AMReX_FBI.H

commit 5d0429f0f605febedfb3e3cda1cb5bd3991da75a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 20 21:11:47 2020 -0800

    fix a number of cmath functions with hack

Src/Base/AMReX_IntVect.H
Src/Base/AMReX_RealVect.H
Src/EB/AMReX_EB2_2D_C.cpp
Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H
Src/EB/AMReX_algoim_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/Particle/AMReX_Particle_mod_K.H
Src/Particle/AMReX_TracerParticle_mod_K.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_tagging.H
Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H

commit ecceecffb5bb06187bd0a3079c9034a253263d6d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 20 18:50:57 2020 -0800

    update dpcpp todo comments

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuMemory.H
Src/Base/AMReX_GpuUtility.H

commit b4d40eaf6d2ddf98281cfd2777b5731c4b204ef3
Merge: e9d333ee4 1b17c9671
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 20 18:39:59 2020 -0800

    Merge branch 'development' into dpcpp

commit e9d333ee4b6f9606e4109f5bb0c468cbc7c8f97c
Merge: 6dd56834d 102e00216
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 20 18:39:51 2020 -0800

    Merge branch 'dpcpp2' into dpcpp

commit cb0f385fac872f6023432aafd10790853621c6a8
Merge: 90201e7af 1b17c9671
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Feb 20 18:28:22 2020 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 90201e7afec3ba02e3044d4291b9bc27222e8037
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Feb 20 18:28:08 2020 -0800

    CMake: fix how ProfParser is built

Src/CMakeLists.txt
Src/Extern/ProfParser/CMakeLists.txt

commit 102e0021642b13e6c1fce4d08613cc3ea9623ba3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 20 17:35:03 2020 -0800

    link to libsycl-cmath

Src/Base/AMReX_COORDSYS_2D_C.H
Src/Base/AMReX_GpuComplex.H
Src/Base/AMReX_Math.H
Src/Base/AMReX_MultiFabUtil_nd_C.H
Tools/GNUMake/Make.defs
Tools/GNUMake/comps/dpcpp.mak

commit fb95fdb0465866252c15f42e10888cd1575eaf0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 20 16:47:23 2020 -0800

    link to libsycl-glibc

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/dpcpp.mak

commit 1b17c9671fdf0d50c9a7226b073f781791a35484
Merge: ce9419a88 e97431df1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 20 15:43:36 2020 -0800

    Merge branch 'FlashFluxRegister' into development

commit ce9419a8848d8f56950703cdd9fbe77c2a63ad3f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Feb 20 15:15:03 2020 -0800

    CMake+CUDA: link to nvToolsExt when ENABLE_BASE_PROFILE is on

Tools/CMake/AMReX_Config.cmake

commit e97431df18279c182186a8f3cfc89708cb98da56
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 20 09:12:41 2020 -0800

    Optimization thanks to Klaus's suggestion

Src/AmrCore/AMReX_AmrCore.cpp

commit 730cd6a58aa0e6e5688f29a7fdf3aa2dbb1bd146
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 19 15:52:44 2020 -0800

    NodalOverset test: use sigma strategy

Tests/LinearSolvers/NodalOverset/MyTest.cpp

commit 20b4130ef13ee8917d38b4733d709de670c7fb93
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 19 15:22:38 2020 -0800

    AmrCore::regrid: if coarse level changes, we need to remake fine level so that flux register can be updated

Src/AmrCore/AMReX_AmrCore.cpp

commit 098de322f613c8b9e9ba0aba89a70d195671ff6f
Merge: cf83828e2 3b3a210e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 19 14:17:26 2020 -0800

    Merge branch 'weiqun/dev' into development

commit 3b3a210e604bcee88e2bde8964dbbc998a510b00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 19 13:34:10 2020 -0800

    missing Make.package

Tests/LinearSolvers/NodalOverset/Make.package

commit 4872d803030a7b8e76956704db64ebecdc1682c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 19 13:32:24 2020 -0800

    let user set nodal solver Dirichlet mask

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 1afcf8bc06ed4a9a54750eff1f5d7f079367b2b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 19 13:30:44 2020 -0800

    template average_down_nodes

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.H
Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H

commit e73d62fb72521249c31e99b96aaa7833889bb59a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 19 13:28:43 2020 -0800

    move is_nodal and is_cell_centered from MultiFab to FabArrayBase

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit f578bf9747038bc58fd92f14b65bb04feff16cec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 19 13:27:21 2020 -0800

    add new test NodalOverset

Tests/LinearSolvers/NodalOverset/GNUmakefile
Tests/LinearSolvers/NodalOverset/MyTest.H
Tests/LinearSolvers/NodalOverset/MyTest.cpp
Tests/LinearSolvers/NodalOverset/main.cpp

commit cf83828e2bde3114e3bb8b03f1e6cd72d4cd935c
Merge: c7a1ff788 d02402f4e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 19 10:19:25 2020 -0800

    Merge branch 'development' into sort_particles_bin

commit c7ae49a5195fa16277f418f48564adfd0e83af66
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 19 09:15:43 2020 -0800

    FlashFluxRegister: isFluxDensity

Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H
Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp
Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90

commit 987148a246030ee10efb44016c050c6118128f2c
Merge: aaf960090 d02402f4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 18 14:00:20 2020 -0800

    Merge branch 'development' into FlashFluxRegister

commit d02402f4e2d239f2c98c6880fda2bd70a8371405
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 18 09:46:03 2020 -0800

    fix index error in mac tracer advection

Src/Particle/AMReX_TracerParticle_mod_K.H

commit 88372ce588c7cbdf1858e3dc09ea32b3741cf754
Merge: d5d0404fe a7dd3eeea
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 18 09:31:34 2020 -0800

    Merge branch 'particle_io_filter' into development

commit c7a1ff78823f55a4bb79091b414fcd457ee8a87f
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Feb 17 14:44:28 2020 -0800

    bugfix

Src/Particle/AMReX_ParticleContainerI.H

commit f9aab1755ad13d0295b647dddcc29fdd1dda3598
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Feb 17 14:26:51 2020 -0800

    Add SortParticlesByBin

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit a7dd3eeeadc249a562f5716f5c2b7475734d0c2a
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Feb 17 13:38:47 2020 -0800

    fix the io filter

Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_Particles.H

commit 9eb898d60921fef103b9b53ed1a2fb97822f9b0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 16 18:59:09 2020 -0800

    more detail in abort message

Src/Base/AMReX_FBI.H
Src/Base/AMReX_MultiFabUtil_nd_C.H
Src/Base/AMReX_Reduce.H

commit 6dd56834d2f494fa64898409b6f67828beb213be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 16 13:20:31 2020 -0800

    remove abort in DPC++ reduce

Src/Base/AMReX_GpuReduce.H

commit 2a81f457608a4faeb81bc4351118485ae982f771
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 16 13:20:31 2020 -0800

    remove abort in DPC++ reduce

Src/Base/AMReX_GpuReduce.H

commit 883f1a8d312e4ee8f315dad7609046ed1744b36a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 16 11:35:19 2020 -0800

    clean up

Tools/GNUMake/comps/dpcpp.mak

commit 35d1932dfbd73ae0bdde9ae036d94f3af6fdabc0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 16 10:03:36 2020 -0800

    amrex::Math

Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_COORDSYS_1D_C.H
Src/Base/AMReX_COORDSYS_2D_C.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_GpuComplex.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_Math.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_RealVect.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H

commit dccd99da140b3319693d92c7e801bc7f156afb15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 16 08:43:48 2020 -0800

    Revert "use scyl::abs and sycl::copysign. This commit should be reverted once they are in std:: in future version of DPC++"
    
    This reverts commit fe39b7a09ab4089c3f48953bd708e4a555d8356d.

Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/Base/AMReX_BaseFab.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H

commit 720d281c234f2e9f3b50f6baeb74d232e8020501
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 16 08:43:19 2020 -0800

    Revert "missing using sycl::abs.  This should be reverted too eventually."
    
    This reverts commit b182bd57042761dcab6aac1f2300772ca309d027.

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H

commit f6d6a3c899113f10b833365b05ce84d8f16d40d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 16 08:42:04 2020 -0800

    always add -DNDEBUG to get around compiler bug

Tools/GNUMake/Make.defs

commit 0feb4e34fa68aef6354c595e4a82a27a35067745
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 15 21:29:54 2020 -0800

    avoid NDEBUG

Src/Base/AMReX_Machine.cpp

commit b219a3d57902bb95d200f6076e08f39a0dfc4aa8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 15 21:21:42 2020 -0800

    use amrex::Abort and ASSERT

Src/Base/AMReX.H
Src/Base/AMReX_Machine.cpp

commit 47454df66dc3279b429b12a54f872063ac86c8e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 15 20:41:56 2020 -0800

    more detail in abort message

Src/Base/AMReX_GpuAssert.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuLaunchMacrosG.H

commit d5d0404fe1860fe653b66b375276545db3a45a0d
Merge: 88c5e3186 1803fa5c6
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Feb 15 15:30:34 2020 -0800

    Merge pull request #696 from AMReX-Codes/stream
    
    Add stream benchmark

commit a7a27ab3cb3669e4ae69d1007604b8a136f4e096
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 15 15:13:15 2020 -0800

    wait and throw

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp

commit 1803fa5c668dd90207986129686653a655b8e16d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 15 13:32:38 2020 -0800

    Add stream benchmark

Tests/Stream/GNUmakefile
Tests/Stream/Make.package
Tests/Stream/inputs
Tests/Stream/main.cpp

commit 1747d8936095282354a7f816d0dc6e5ace793bb5
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Feb 14 23:31:39 2020 -0800

    particle type -> superparticletype

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleIO.H

commit 3376fe9989d7d5d1cef988e7aa16c9f2472c2c9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 14 19:56:29 2020 -0800

    add placeholders for deviceReduce

Src/Base/AMReX_GpuReduce.H

commit 0782fda17ebe2a3c7c1f1676f463bffc23e51774
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 14 19:19:15 2020 -0800

    use abort() instead of assert(0)

Src/Base/AMReX_GpuAssert.H

commit 5e79c491fefbbfc038dcfdacd145abc168e5633e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 14 16:38:08 2020 -0800

    no need for __SYCL_DEVICE_ONLY__

Src/Base/AMReX_BaseFab.H

commit 23cc995636bb2a98bf0a2fcb7d966c180b0d61be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 13 21:54:34 2020 -0800

    remove shared memory from paralle for because it may be unsafe

Src/Base/AMReX_GpuLaunchFunctsG.H

commit a7be1bc354cb4a982349099878602a420f5c1369
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 13 19:42:08 2020 -0800

    DPC++: start reduction

Src/Base/AMReX_BlockMutex.cpp
Src/Base/AMReX_FBI.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_Reduce.H

commit b182bd57042761dcab6aac1f2300772ca309d027
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 13 19:41:06 2020 -0800

    missing using sycl::abs.  This should be reverted too eventually.

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H

commit fe39b7a09ab4089c3f48953bd708e4a555d8356d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 13 15:13:50 2020 -0800

    use scyl::abs and sycl::copysign. This commit should be reverted once they are in std:: in future version of DPC++

Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/Base/AMReX_BaseFab.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H

commit f4cf306c1ece8321702cfc5ce4a1620c2c75e1e0
Merge: f3fce75e1 88c5e3186
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Feb 13 15:10:25 2020 -0800

    Merge branch 'development' into particle_io_filter

commit 5442903068d33a472e0f6980c35e8128f25c3dc5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 13 15:09:20 2020 -0800

    fix some issue in launch macros

Src/Base/AMReX_GpuLaunchMacrosG.H

commit 0df9e1075926a6ec5f020aaaf1339989467a0faf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 13 15:09:02 2020 -0800

    add override

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H

commit f3fce75e10e534b8fe4506805d51a75b4d88dfc2
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Feb 13 14:56:26 2020 -0800

    add a filter to control which particles get written out

Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_Particles.H

commit 88c5e318674a79096df9ad43c089159ac5acce36
Merge: 1ba9b1e05 075602eda
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Feb 13 14:29:55 2020 -0800

    Merge pull request #695 from maikel/feature/VirtualMakeBaseGrids
    
    Feature/virtual make base grids

commit 53fec0ca63f47b551d8e81c103ed073c9cc70488
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 13 14:04:31 2020 -0800

    fix launch macros

Src/Base/AMReX_GpuLaunchMacrosG.H

commit 075602eda011f8e27bc4066249c118d21249b1a8
Author: Maikel Nadolski <maikel.nadolski@gmail.com>
Date:   Thu Feb 13 22:24:59 2020 +0100

    Add const qualifier to PostProcessBaseGrids

Src/AmrCore/AMReX_AmrMesh.H

commit 250a6e8981ef90a75f69c7df3ab7a8a3de173211
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 13 13:19:16 2020 -0800

    DPC++: for now streamSynchronize in Elixir and AsyncArray clear()

Src/Base/AMReX_GpuAsyncArray.H
Src/Base/AMReX_GpuElixir.cpp

commit 4e5dee69716a08f0176d46ce1bea14fb88e7d383
Author: Maikel Nadolski <maikel.nadolski@gmail.com>
Date:   Thu Feb 13 22:16:10 2020 +0100

    Add a virtual member function to AmrMesh
    
    This commit adds a PostProcessBaseGrids member function.
    This makes it possible to alter the box array for the coarsest level
    before it is  being used.

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit e1ff734fdc632b196a4d0e6ef8ee3f075c3d3895
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 13 12:38:19 2020 -0800

    Gpu::Atomic: add missing features and cleanup

Src/Base/AMReX_GpuAtomic.H

commit 8f1b48f4c89dc3ea2ef21602a03b9cb11a9ebb0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 13 05:18:31 2020 -0800

    put Gpu::Atomic in a new file

Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuAtomic.H
Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_GpuUtility.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit bd47346656c109731b48e2b47c46420bb3271289
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 12 20:02:47 2020 -0800

    DPC++: Gpu::Atomic::Add

Src/Base/AMReX_GpuUtility.H

commit b32c81e370148ebdc4b402991545525c557786ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 12 16:31:09 2020 -0800

    DPC++ add async error handler

Src/Base/AMReX_GpuDevice.cpp

commit a6c0fed6f4c471348e78bce61853700ba650f7a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 12 16:11:50 2020 -0800

    some minor changes

Src/Base/AMReX_BaseFab.H
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EB2_IF_Polynomial.H

commit a0ee6756ad8430eb568d41b0e4a9f07b17b37d96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 12 15:01:04 2020 -0800

    DPC++: always wait after memcpy

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuLaunchFunctsG.H

commit ddbc17c824b5dffa735fea9b00474fdf62ae6097
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 12 14:28:11 2020 -0800

    redefined AMREX_DEVICE_COMPILE as a macro

Src/Base/AMReX.H
Src/Base/AMReX_Array4.H
Src/Base/AMReX_GpuAssert.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuPrint.H
Src/Base/AMReX_GpuQualifiers.H
Src/Base/AMReX_GpuRange.H

commit 80cbc3587811509ee5adde3013151c30efe24a8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 12 13:40:58 2020 -0800

    DPC++: assert

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_Array4.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuAssert.H
Src/Base/AMReX_GpuPrint.H
Src/Base/AMReX_MultiFabUtil_nd_C.H
Src/Base/AMReX_TypeTraits.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit aa630dbe1b5c28296710a74a61a189562d1b6bef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 12 12:33:26 2020 -0800

    DPC++: printf

Src/Base/AMReX_Array4.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuPrint.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit b1969f3ec6f739856891fea1ae53a3f984bd0650
Merge: 98707e1d2 6d947f3e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 12 12:03:43 2020 -0800

    Merge branch 'dpcpp' of https://github.com/AMReX-Codes/amrex into dpcpp

commit 6d947f3e73418936a311054c61e4e7728dae54d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 12 12:03:15 2020 -0800

    have to use sycl::floor

Src/Base/AMReX_MultiFabUtil_nd_C.H

commit 98707e1d269edd62103919d29c719fe41f86d063
Merge: 9434b3573 0ad0a706d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 12 11:47:05 2020 -0800

    Merge branch 'dpcpp' of https://github.com/AMReX-Codes/amrex into dpcpp

commit 0ad0a706da151991509dddd26e6c034b9ddf3ef7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 12 11:46:40 2020 -0800

    make sure sycl doesn't see virtual funcitons

Src/Base/AMReX.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_GpuRange.H
Src/Base/AMReX_ParmParse.H

commit a4a0d3029df21bc1a7a9a34660db3436a2488d9c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 12 05:59:18 2020 -0800

    launch macros in DPC++

Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuLaunchMacrosC.H
Src/Base/AMReX_GpuLaunchMacrosG.H
Src/Base/AMReX_GpuRange.H
Src/Base/AMReX_PODVector.H
Src/Base/AMReX_Random.cpp

commit f949fed83d29080cc4e71ab21d15d2e59c4fde85
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 11 13:04:28 2020 -0800

    launch functions in DPC++

Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuRange.H

commit 6bafe7679bbb11328dbe8296ae69d22293bcb7de
Merge: c94a089be 1ba9b1e05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 11 10:31:39 2020 -0800

    Merge branch 'development' into dpcpp

commit 1ba9b1e05fcdd83162ce03ce1d4318b29096ebf6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 11 10:31:08 2020 -0800

    add Gpu::synchronize

Src/EB/AMReX_EBMultiFabUtil.cpp

commit 9434b3573641f2055e03479f9d95effe812705b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 11 10:29:05 2020 -0800

    IsDeviceLambda always return true for DPC++

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_TypeTraits.H

commit c94a089beb350b7eca24a158ae8048c8b133eb94
Merge: 81ad9c561 a427c460d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 11 08:54:35 2020 -0800

    Merge branch 'dpcpp' of https://github.com/AMReX-Codes/amrex into dpcpp

commit 81ad9c561c6ab53a3a50ce4d1425d7a8e2bcde3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 11 08:54:28 2020 -0800

    more place holders

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Random.H

commit a427c460d0345ca5e9db38e15ec14c7413e46069
Merge: 6a833ce49 8a4093562
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 11 08:53:06 2020 -0800

    Merge branch 'development' into dpcpp

commit 8a40935623817e52ed0714bcfa9516bb3e3f94d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 11 08:50:08 2020 -0800

    use __CUDA_ARCH__ and __HIP_DEVICE_COMPILE__ directly in preparation for DPC++

Src/Base/AMReX.cpp
Src/Base/AMReX_Array4.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuRange.H
Src/Base/AMReX_GpuUtility.H
Src/Base/AMReX_Random.cpp
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EB2_IF_Polynomial.H

commit f6b892db407122d89ab6113cf9a04ac42d9fd2dc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 10 22:36:55 2020 -0800

    need to skip the size-0 entries in this loop, if we are going to do this in the one-box case

Src/Particle/AMReX_ParticleCommunication.H

commit d000aaa3ec2c84770b729a19e50e99e8dc06a5cb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 10 18:49:54 2020 -0800

    remove these early exits from the particle communication code

Src/Particle/AMReX_ParticleCommunication.H

commit d040ef87f8c7f4e170238721a2943e79b9f6ace2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 10 10:43:32 2020 -0800

    add variadic version of std::is_same

Src/Base/AMReX_TypeTraits.H

commit 08562ec0240554a7dfeffdd75d77182401b799c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 9 07:12:08 2020 -0800

    implicit conversion for 1d

Src/Base/AMReX_Box.H

commit fc9c503744ad2ed3aec78193b382e7fd545bcbc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 8 20:13:16 2020 -0800

    move some RealVect functions from cpp to H file

Src/Base/AMReX_IntVect.H
Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp

commit 77ef0f95f68f5e9991289311bc18e2ef0d3411d4
Merge: 1e29dfcba 1e47b1f2b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Feb 8 20:14:33 2020 -0800

    Merge pull request #690 from AMReX-Codes/write_probin
    
    simplify write_probin + add C++ parameter support

commit 1e47b1f2b17d54d2149a4e2e89b03e68bc523bd3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 8 19:54:27 2020 -0800

    Add __managed__ attribute to extern parameters

Tools/F_scripts/write_probin.py

commit 45abae9ac500cecc34dc198e040522aa1870b92e
Merge: b292551bf 1e29dfcba
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 8 19:19:07 2020 -0800

    Merge branch 'development' into write_probin

commit 6a833ce49c59d7371db729cfa652673c58e6b609
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 8 16:36:29 2020 -0800

    make sure all queues use the same context with an empty async handler

Src/Base/AMReX_GpuDevice.cpp

commit 1e29dfcbae2180ecf270abad4b79ef3810614854
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 8 10:30:11 2020 -0800

    Add AMREX_GPU_CONSTANT and AMREX_GPU_MANAGED

Src/Base/AMReX_GpuQualifiers.H

commit f1ed2b4c6590d983a435fee9b739f6e4bf8600c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 8 06:56:01 2020 -0800

    placeholder in Array4 assert

Src/Base/AMReX_Array4.H
Src/Base/AMReX_GpuUtility.H

commit b3cb68507249c714042eb04c1843066766fab7f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 7 16:30:44 2020 -0800

    store subgroup size

Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuLaunchFunctsG.H

commit e9d4577e6a2ddbe34a67e06b4735adbe0c668fb0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 7 15:00:41 2020 -0800

    fix some ifdefs

Src/Base/AMReX_GpuDevice.H

commit 2f68f73b1e18696285dd0dc9c4b42b16512a8c62
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 7 14:54:38 2020 -0800

    minor change to make

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/dpcpp.mak

commit 5af4b7785c0533ce31f1f68a63a1addf286ceabc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 7 13:33:47 2020 -0800

    ParalleFor inside MFIter works

Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuTypes.H
Tools/GNUMake/Make.defs

commit 2d75132396dcb86e67dd80161c774b9308c1c6c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 7 12:59:32 2020 -0800

    ParallelFor works for a simple example

Src/Base/AMReX_Array4.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuLaunchFunctsG.H
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/dpcpp.mak

commit f4bb2905278deb4d535b3095feba0e54505c7097
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 7 10:24:31 2020 -0800

    update Arena

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp

commit ef075785130a4aded995048167d47c2c7e47239d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 6 21:38:49 2020 -0800

    place holders and device properties

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BlockMutex.H
Src/Base/AMReX_BlockMutex.cpp
Src/Base/AMReX_FBI.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuAsyncArray.H
Src/Base/AMReX_GpuAsyncArray.cpp
Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuElixir.cpp
Src/Base/AMReX_GpuError.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuLaunchMacrosG.H
Src/Base/AMReX_GpuMemory.H
Src/Base/AMReX_GpuQualifiers.H
Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_GpuUtility.H
Src/Base/AMReX_Random.cpp
Src/Base/AMReX_Reduce.H
Src/Base/AMReX_Scan.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tools/GNUMake/Make.defs

commit 13f6b479f07875826d934dd6048a3651b21b6213
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 6 16:24:35 2020 -0800

    compile with dpcpp

Src/Base/AMReX_GpuTypes.H

commit e39a8c15236ccb6ee8133eae9f0c13f46d581928
Merge: 0e71c1e5b 79360ad04
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 6 11:52:41 2020 -0800

    Merge branch 'development' into dpcpp

commit aaf960090453d2b4a11ec299664975d4370b1a5c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 6 11:24:20 2020 -0800

    FlashFluxRegister: add addition load/store with area argument

Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H
Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp
Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90

commit 6d3cf34cee07b60edf6e7a6cf38abdf80d5d0f31
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 6 10:55:36 2020 -0800

    FlashFluxRegister: add addition load

Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H
Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp
Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90

commit 79360ad04143dc06d1ac14ad28b79a1ab15861f0
Merge: 8744e4ab3 2cd152353
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Feb 6 09:20:01 2020 -0800

    Merge pull request #684 from lucafedeli88/add_poisson_random_distribution
    
    Add Poisson random distribution

commit 8744e4ab303afcd1b1663a8aa3a0e9db6c85c3bf
Merge: fec9bc974 73637768c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Feb 6 08:53:25 2020 -0800

    Merge pull request #687 from Alpine-DAV/task/2020_02_blueprint_multi_topo
    
    Conduit Blueprint Update to support Multiple Topologies

commit fec9bc9742265ff858dc9ba7fd97c27b384f05e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 5 14:31:04 2020 -0800

    fix bug in nodal solver bc

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H

commit 73637768cbf34e4a897e898c5a764a66a0e1f78c
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Wed Feb 5 15:23:59 2020 -0600

    blueprint: dont reset output node when wrapping data

Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp
Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H

commit c9fd1ef4d02ee4cd024c0b512875aabe794f23ca
Merge: cb90c0a31 2e675c7b2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 5 10:08:39 2020 -0800

    Merge pull request #686 from AMReX-Codes/jmsexton/hdf5
    
    Fix for USE_CUDA=TRUE case

commit 2e675c7b22f5a7ed4b051b3e83f9406c467dffe1
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Wed Feb 5 12:58:03 2020 -0500

    Fix for USE_CUDA=TRUE case

Tests/HDF5Benchmark/GNUmakefile

commit 2cd1523531db6f39194cfd3ee22d6e80f2745980
Author: Luca Fedeli <luca.fedeli.88@gmail.com>
Date:   Wed Feb 5 02:10:41 2020 +0100

    add Poisson random distribution

Src/Base/AMReX_Random.H
Src/Base/AMReX_Random.cpp

commit cb90c0a31969b33062bc583c890fee089ad28459
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 5 03:09:02 2020 -0500

    remove some timers I don't need anymore

Src/Particle/AMReX_ParticleCommunication.cpp

commit 498823e15dbc528d48a8cb35814d210b87e553cd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 5 02:54:10 2020 -0500

    an optmization for ParticleCopyPlan::buildMPI start in the local case

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit 11f456f7b41c3abd64193460d8a0b309fb3b3307
Merge: d58c8adfd 86b29ea71
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Feb 4 16:16:28 2020 -0800

    Merge pull request #656 from AMReX-Codes/kngott/hip
    
    [WIP] First draft of Changes for HIP

commit 86b29ea71d7cce6518f88c6f43e68eaa4080be08
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 4 16:15:49 2020 -0800

    fix typo

Tests/GPU/RandomNumberGeneration/GNUmakefile

commit c26406b24e6633f24b52047287cffe290ce53d4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 4 15:32:28 2020 -0800

    change DEBUG

Tutorials/GPU/ParallelReduce/GNUmakefile

commit 5a20b0e3d819ee9cd913e75b915dd82f32da4537
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 4 15:24:49 2020 -0800

    restore USE_CUDA=TRUE

Tests/GPU/RandomNumberGeneration/GNUmakefile

commit 5dfff1935f1f32abf4e1002858403f6710c6b2cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 4 14:58:07 2020 -0800

    add amrex:: because macros doesn't know namespace

Src/Base/AMReX_GpuLaunch.H

commit 112e26a1cb3c5df4cf86f1f4e39ef8f7930b77b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 4 14:44:18 2020 -0800

    fix for USE_MPI and CUDA >= 10

Src/Base/AMReX_GpuDevice.cpp

commit 26a272419990e07ef21864f9b78f57c5432bf19e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 4 13:32:35 2020 -0800

    use gcc in HelloWorld

Tutorials/Basic/HelloWorld_C/GNUmakefile

commit 6c90e33162763ed5861a6e6d47fe5191b2d173bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 4 13:31:27 2020 -0800

    disable USE_HIP in tutorials by default

Tutorials/Basic/HelloWorld_C/GNUmakefile
Tutorials/GPU/Launch/GNUmakefile
Tutorials/GPU/ParallelReduce/GNUmakefile

commit 1b1cd65154736bfd83a50954c5c90b57629e11d1
Merge: dcade0429 d58c8adfd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 4 13:27:06 2020 -0800

    Merge branch 'development' into kngott/hip

commit d58c8adfd46c9acab809a2a13f3774328c28a689
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 4 13:08:08 2020 -0800

    fix setBndry for 1d and 2d. update setDomainBndry

Src/Base/AMReX_FabArray.H

commit 886c4e240283325310d332b05ae9bbc9fade975c
Merge: 46c807c7e 87461f3db
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Feb 4 12:54:31 2020 -0800

    Merge pull request #673 from AMReX-Codes/kngott/newBndry
    
    New version of setBndry for GPUs.

commit 46c807c7ebb2c2e507915af6d96226fc480ceacb
Merge: cdca9338e 998c6d79e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Feb 4 12:27:56 2020 -0800

    Merge pull request #653 from AMReX-Codes/ebtensor_flux
    
    Ebtensor flux

commit cdca9338e2f6d0c2e285939905777bb640d32a69
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 4 11:55:50 2020 -0800

    Tutorials/Amr: remove duplicated code

Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/Amr/Advection_octree_F/Source/Src_2d/advect_2d_mod.F90

commit 1fada34e00d22ffd3f89582b6b93bdfe249e7078
Merge: 5f3e48732 0aadeb423
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 4 11:54:44 2020 -0800

    Merge branch 'FlashFluxRegister' into development

commit 5f3e487329b3def0300d2980836949da208e2e80
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 4 11:50:14 2020 -0800

    FillPatch: no need to do interpolation of the time is exact

Src/AmrCore/AMReX_FillPatchUtil.cpp

commit a67d5fb68f3311e7dd1a259a8d13561f9c330c2f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 4 11:49:36 2020 -0800

    if Cluster::new_chop fails, switch to Cluster::chop

Src/AmrCore/AMReX_Cluster.cpp

commit b1abf0be45d0b4064f3e9a709608711cd88b86f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 3 15:18:44 2020 -0800

    Option to specify number of ghost cells in fill coarse patch

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp

commit d0efe05ac7a235d58a9d4b3d0435074c1ab4fb42
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Feb 3 18:44:21 2020 -0800

    update caption of advection tutorial figs

Docs/sphinx_documentation/source/AmrCore.rst

commit 90445ea2a13b24fa99ba075926b705a675dada9e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 3 15:49:40 2020 -0800

    fix docstrings

Src/Particle/AMReX_ParticleTransformation.H

commit 2ed901095b8455c20760e4555640180f684abb36
Merge: bbca1d6ed a26d08210
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Feb 3 09:30:07 2020 -0800

    Merge pull request #657 from kcdodd/development
    
    Change cell bilinear to work with odd refinement ratio

commit bbca1d6ed839e73368f89af03fba8bdc661376cc
Merge: 0650a0779 334c134ae
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Feb 3 09:27:51 2020 -0800

    Merge pull request #674 from ax3l/fix-shadowVisMF
    
    VisMF: Remove Shadow Warning

commit 0650a077998e3242e185a3e8b6083a4da250e24f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 3 09:20:40 2020 -0800

    update CHANGES

CHANGES

commit e96621d7f73fd707c88782d84f6dfe2734d01472
Merge: 26a67533b 4093c8dbc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 3 09:17:33 2020 -0800

    Merge branch 'weiqun/AmrInfo' into development

commit 26a67533b00e5aebe4b050c169c1b92afcc4ce80
Merge: e149db520 8e744786c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 3 09:17:05 2020 -0800

    Merge branch 'weiqun/bl_no_fort' into development

commit e149db520688a2f532ff82343c5ab1408dc581af
Merge: 6ca35b031 5d36be589
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 3 09:16:16 2020 -0800

    Merge branch 'weiqun/mfiter' into development

commit 6ca35b031a421b2960245d071be6a88f87003731
Merge: b84aecdfa 41a552fb8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 3 09:13:53 2020 -0800

    Merge branch 'master' into development

commit 41a552fb8429f637c1396818057b359284813c5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 3 09:12:48 2020 -0800

    update CHANGES

CHANGES

commit b84aecdfa5106c7a9bbf805b2adbb7b376879a40
Merge: 71dd0ddd3 bd470e49d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Feb 1 21:57:05 2020 -0800

    Merge pull request #683 from ax3l/fix-floatBuild
    
    Fix Build With Single Precision

commit b292551bf8832d69e02bb388cff24051ab30dd33
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 1 20:55:18 2020 -0500

    add to the C++ header

Tools/F_scripts/write_probin.py

commit 031696034ee3c220b7cbce8aab2c803f972c1bd5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 1 20:13:32 2020 -0500

    fix python

Tools/F_scripts/write_probin.py

commit 2785e150bc4b08f4e04d6808197547d65229df65
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 1 20:08:45 2020 -0500

    revert parameter name:

Tools/F_scripts/write_probin.py

commit b50bfd4cb0481dd844d8327d7837955363da8cb6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 1 19:50:41 2020 -0500

    fix comment

Tools/F_scripts/write_probin.py

commit f09b3a83c926c263426f22ac58658e9ea2308fa6
Merge: bb0550b18 4ae6d4962
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 1 19:47:35 2020 -0500

    Merge branch 'write_probin' of ssh://github.com/AMReX-Codes/AMReX into write_probin

commit bb0550b188ee5c4ecd1c2e33d0a3376f7c50d0ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 1 19:47:20 2020 -0500

    get rid of the option of 2 different parameter lists

Tools/F_scripts/write_probin.py

commit 4ae6d496240149cbf2fddb7344271e91c9e454c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 1 19:46:49 2020 -0500

    add the C++ code

Tools/F_scripts/write_probin.py

commit 9559307bfe4ef5fa7b27f15f479bd7f95363cfa3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 1 19:09:26 2020 -0500

    add the Fortran -> C++ headers

Tools/F_scripts/write_probin.py

commit 2566433edf5dda20e5a6c96d721b727bbc39ea59
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 1 18:43:29 2020 -0500

    automagically write the functions that will send F90 to C++

Tools/F_scripts/write_probin.py

commit abf1056ae8969b8faca9716be2edc5b409f8fc3e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 1 18:07:52 2020 -0500

    some cleaning / linting

Tools/F_scripts/write_probin.py

commit bd470e49d5c565e18b49b9a954137de5aad3bb5b
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Sat Feb 1 14:03:15 2020 -0800

    Fix Build With Single Precision
    
    With float builds (mismatched types in `max()`).

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 0e71c1e5b0c4b590e06b16b8fc33ae528e1471a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 31 12:35:26 2020 -0800

    add dpcpp.mak

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/dpcpp.mak

commit 2460a719e270413e2f2e126e933b4925568cc37a
Merge: 71dd0ddd3 8e744786c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 31 11:07:20 2020 -0800

    Merge branch 'weiqun/bl_no_fort' into dpcpp

commit 0aadeb4234db0d4442c7291d6ad30cf4d70a0c4a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 31 10:20:53 2020 -0800

    BoxArray: this is probably better than the previous fix because it is more backward compatible

Src/Base/AMReX_BoxArray.cpp

commit 71dd0ddd357896d7a0c54fab73152ea1ad942aaf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 31 09:22:52 2020 -0800

    create a local device copy of BCRec vector before using it on GPU

Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit 00f4d824b4a0586c9e18f01d97aaae8651873d82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 30 21:33:33 2020 -0800

    FlashFluxRegister tutorial: communicate only for fine levels

Tutorials/Amr/Advection_octree_F2/Source/evolve_mod.F90

commit cb5edf1c52d2b1f016495622c5ed238725911797
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 30 21:23:29 2020 -0800

    fix a corner case in building BoxArray hash map

Src/Base/AMReX_BoxArray.cpp

commit 7cf662696f16333c829b2c1471ca6f16eb40d202
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 30 21:22:10 2020 -0800

    FlashFluxRegister: bugs fixed

Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp
Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90
Tutorials/Amr/Advection_octree_F/Source/evolve_mod.F90
Tutorials/Amr/Advection_octree_F2/Source/evolve_mod.F90

commit 264c194db809e27fb7d541de9c80cd90fb2bac14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 30 15:07:52 2020 -0800

    Tutorial using FlashFluxRegister

Tutorials/Amr/Advection_octree_F2/Exec/Make.Adv
Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/Make.package
Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/Prob.f90
Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/face_velocity_2d.F90
Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_octree_F2/README
Tutorials/Amr/Advection_octree_F2/Source/Make.package
Tutorials/Amr/Advection_octree_F2/Source/Src_2d/Make.package
Tutorials/Amr/Advection_octree_F2/Source/Src_2d/advect_2d_mod.F90
Tutorials/Amr/Advection_octree_F2/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/Advection_octree_F2/Source/Src_2d/slope_2d.f90
Tutorials/Amr/Advection_octree_F2/Source/amr_data_mod.F90
Tutorials/Amr/Advection_octree_F2/Source/averagedown_mod.F90
Tutorials/Amr/Advection_octree_F2/Source/bc_mod.F90
Tutorials/Amr/Advection_octree_F2/Source/compute_dt_mod.F90
Tutorials/Amr/Advection_octree_F2/Source/evolve_mod.F90
Tutorials/Amr/Advection_octree_F2/Source/fillpatch_mod.F90
Tutorials/Amr/Advection_octree_F2/Source/fmain.F90
Tutorials/Amr/Advection_octree_F2/Source/initdata.F90
Tutorials/Amr/Advection_octree_F2/Source/my_amr_mod.F90
Tutorials/Amr/Advection_octree_F2/Source/plotfile_mod.F90
Tutorials/Amr/Advection_octree_F2/Source/tagging_mod.F90

commit f1479f8db81b6478ccb29b68c3b3aef144e0ab77
Merge: 724d88e4f 33aa5ccd1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 30 14:51:56 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 724d88e4f92d489194ebe01c5614696e0d3ff613
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 30 14:51:45 2020 -0800

    fix circular dependency

Src/Particle/AMReX_ParticleLocator.H

commit b85a8ed9961814f01d28bb788561ddaf22301655
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 30 14:23:56 2020 -0800

    FlashFluxRegister: fix BoxList index type

Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp

commit faaf49ec62f8ab92c9dbe1535b93e3c0e580eb14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 30 14:18:40 2020 -0800

    octree iterator for a given level

Src/F_Interfaces/Octree/AMReX_octree_fi.cpp
Src/F_Interfaces/Octree/AMReX_octree_mod.F90

commit 70bd030767650008a6c3e7da810e2dd007e6d14b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 30 13:43:23 2020 -0800

    pass boxarray and distributionmap when building amrex_flash_fluxregister

Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H
Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp
Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90
Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90
Src/F_Interfaces/AmrCore/Make.package
Src/F_Interfaces/Octree/AMReX_octree_mod.F90
Src/F_Interfaces/Octree/Make.package

commit 2119a99191bdc07e6d17d78306c7c6aec2fbedf9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 30 13:18:05 2020 -0800

    amrex_flash_fluxregister

Src/F_Interfaces/Octree/AMReX_FlashFluxRegister.H
Src/F_Interfaces/Octree/AMReX_FlashFluxRegister.cpp
Src/F_Interfaces/Octree/AMReX_flash_fluxregister_fi.cpp
Src/F_Interfaces/Octree/AMReX_flash_fluxregister_mod.F90
Src/F_Interfaces/Octree/AMReX_octree_mod.F90
Src/F_Interfaces/Octree/Make.package

commit 998c6d79e3a97ee8815a0dae7395bbd8beeb9b97
Author: cgilet <cgilet@gmail.com>
Date:   Thu Jan 30 12:28:14 2020 -0800

    Remove unused variable

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit a81396306020655ff0e184e028169d1d96d46142
Merge: e71750713 33aa5ccd1
Author: cgilet <cgilet@gmail.com>
Date:   Thu Jan 30 12:20:43 2020 -0800

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit e71750713b97a39109e03d6dcbc7f051ebf2d516
Author: cgilet <cgilet@gmail.com>
Date:   Thu Jan 30 12:20:37 2020 -0800

    Clean up.

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit bb32431fc5ff26fa0220a6e615a2033a405e816e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 30 11:25:37 2020 -0800

    FlashFluxRegister

Src/F_Interfaces/Octree/AMReX_FlashFluxRegister.H
Src/F_Interfaces/Octree/AMReX_FlashFluxRegister.cpp
Src/F_Interfaces/Octree/Make.package

commit 4093c8dbcd27706765eca2b70585fc7d462a4632
Merge: aa7dbf181 cd68ff50d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jan 30 09:45:11 2020 -0800

    Merge pull request #680 from maikel/weiqun/AmrInfo
    
    Make AmrMesh destructor default

commit cd68ff50d580f42633e16fefac16ebf96db1d3b4
Author: Maikel Nadolski <maikel.nadolski@gmail.com>
Date:   Thu Jan 30 18:32:56 2020 +0100

    Make AmrMesh destructor default

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit aa7dbf1810accf9b64e54b1fa36f5154d1a53cff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 30 09:01:20 2020 -0800

    remove Initialize and Finalize from AmrCore and AmrMesh

Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit aa8bf562aac19590eeb152471ef4c1ace5c89067
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 30 08:58:59 2020 -0800

    AmrMesh: protect AmrInfo and friend operator<<

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit 33aa5ccd17bce31a7429d7d8394f88e0dc491579
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 29 21:28:09 2020 -0800

    fix periodic bug in tensor solver

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit f025a39445aac82027ef030155c1ba078e10c30e
Merge: f2723677f 9322c69e3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jan 29 20:01:21 2020 -0800

    Merge pull request #679 from houjun/development
    
    Add support to restart from HDF5 particle checkpoint file

commit 1e6af4d3a729e5d0db9367e9e575a333ac89d4f5
Author: cgilet <cgilet@gmail.com>
Date:   Wed Jan 29 18:50:48 2020 -0800

    WIP debugging corner fill issue

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit 05c8af14f1912e0a1bd1c6d64fb9858cc9fb5ee4
Merge: 2b303c3c1 f2723677f
Author: cgilet <cgilet@gmail.com>
Date:   Wed Jan 29 14:59:05 2020 -0800

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 8432d8d2424e8d3f97a7a7f790c2d2cd8bb5de60
Merge: 50a5fbe68 3ffe33d38
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Wed Jan 29 13:05:46 2020 -0800

    Merge branch 'mrowan/CUPTI_trace' of https://github.com/mrowan137/amrex into mrowan/CUPTI_trace

commit 9322c69e3bd20d9f68e056324d99df8d8a86cd2c
Merge: 054c1758c f2723677f
Author: Houjun Tang <htang4@lbl.gov>
Date:   Wed Jan 29 13:04:38 2020 -0800

    Merge remote-tracking branch 'upstream/development' into development

commit 054c1758cbec88d8b93b6387b8053110f6eca90d
Author: Houjun Tang <htang4@lbl.gov>
Date:   Wed Jan 29 13:02:20 2020 -0800

    Add support to restart from checkpointed HDF5 particle file

Src/Base/AMReX_PlotFileUtil.cpp
Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_Particles.H
Tests/HDF5Benchmark/main.cpp

commit 50a5fbe68f099cc23dc81ac62a3eb9d630e25c61
Merge: 3b97486ee f2723677f
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Wed Jan 29 12:58:01 2020 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mrowan/CUPTI_trace

commit eaffc15cf63523bb51ce3061cddf46b25e085a72
Merge: cc71abae5 f2723677f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 29 09:29:29 2020 -0800

    Merge branch 'development' into weiqun/AmrInfo

commit cc71abae5b784e2fee7424d4ee65462bee6a3b5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 29 09:28:55 2020 -0800

    New constructor for AmrMesh and AmrCore that does not use ParmParse

Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit f2723677f35398f863c3c2d245c1312a892c3d67
Author: cgilet <cgilet@gmail.com>
Date:   Wed Jan 29 11:12:44 2020 -0500

    Some clean up.

Src/EB/AMReX_EB_utils.cpp

commit b11160ac81dea11c06bc64dd5717b569f801a0a9
Author: cgilet <cgilet@gmail.com>
Date:   Wed Jan 29 10:55:00 2020 -0500

    Some clean up.

Src/EB/AMReX_EB_utils.cpp

commit a09659e435bd23f2ea052b4e1dbbc0c3772be4b6
Merge: 3fbf12606 af7c69380
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jan 29 07:46:15 2020 -0800

    Merge pull request #678 from AMReX-Codes/cgilet_dev
    
    Fix apply_eb_redistrubution() to work in 3D.

commit af7c69380d826c13afa53db80a8358b26ec51e9d
Author: cgilet <cgilet@gmail.com>
Date:   Wed Jan 29 09:56:01 2020 -0500

    Fix apply_eb_redistrubution() to work in 3D.

Src/EB/AMReX_EB_utils.cpp

commit 3fbf126063c19cfc4500aaac7a1e006efa80bd2b
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Tue Jan 28 16:05:58 2020 -0800

    Some changes in eb_redistribution to avoid evaluating the redistribution near physical boundaries with data outside of the domain

Src/EB/AMReX_EB_utils.cpp

commit 459c725e12d10b071335100f6ea77edb6cd4d18a
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Tue Jan 28 18:45:40 2020 -0500

    Update summit MPS command -- is now a bsub command

Tutorials/GPU/run.summit

commit 8e744786c36f13d5e7719072768a991ce38c995a
Merge: 563e61899 2e871a1b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 28 15:30:48 2020 -0800

    Merge branch 'development' into weiqun/bl_no_fort

commit 2e871a1b9f5e551d8046d9cd3a70d1c57d52f692
Merge: e4bb42235 41d775e65
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 28 13:25:47 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 563e61899cf8b9535baf86380480bf45274915c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 28 12:59:27 2020 -0800

    no need to link to libgfortran

Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/llvm.mak

commit 41d775e6569dc258b29104d1308b8e7f5050c24c
Merge: 4f2a7d1f9 14b8c797b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jan 28 12:52:52 2020 -0800

    Merge pull request #676 from AMReX-Codes/jmsexton/particle
    
    Added check for RedistributeCPU edge case

commit e4bb42235ed116c7e4600b13a67d65778b6e0fbb
Merge: d44dfdbff 4f2a7d1f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 28 11:55:07 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9b1e83cdc880898649088c05fd7243be9cabf8ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 28 11:45:33 2020 -0800

    update configure for BL_NO_FORT

Tools/libamrex/configure.py

commit 4a22ce45f46ed3f02d19652325bd1774619edd3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 28 11:22:10 2020 -0800

    BL_NO_FORT: EB

Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EB_utils.H
Src/EB/AMReX_EB_utils.cpp
Src/EB/Make.package

commit 96d83f3f3eacbe6a6fd8c580c8a916b97ed51b8b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 28 10:40:52 2020 -0800

    BL_NO_FORT in Amr

Src/Amr/Make.package
Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv
Tutorials/GPU/CNS/Exec/Make.CNS

commit edb32eb669d4101fb3a0b947ce342aae1776e5e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 28 10:21:51 2020 -0800

    BL_NO_FORT in AmrCore

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrCore/Make.package
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile

commit f544c44da602766422066a2076f3703a595b0ae6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 28 09:49:39 2020 -0800

    BL_NO_FORT in Particle

Src/Particle/Make.package

commit 7a2f3d33ad971f321def54d3cdd518d77c892013
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 28 09:41:35 2020 -0800

    BL_NO_FORT in MLMG

Src/Boundary/Make.package
Src/Boundary/OpenSource.txt
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/Make.package
Tests/NoFort/GNUmakefile
Tools/GNUMake/Make.defs
Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile

commit 0a425059e053666f9e29ead7f2169a1db0bb5b52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 27 20:25:18 2020 -0800

    port fab_filcc to C++

Src/Base/AMReX_Box.H
Src/Base/AMReX_FilCC_C.H
Src/Base/AMReX_FilCC_C.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 22984d214f378fb3aa460ab1e72592f8ce77250d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 27 20:01:15 2020 -0800

    add more fortran free files to BL_NO_FORT build

Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_MFCopyDescriptor.cpp
Src/Base/Make.package

commit 5d36be5893712a475960e97ed43478839d18140e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 27 09:10:39 2020 -0800

    make MFIter(BoxArray const&, DistributionMapping,...) omp safe

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 2b303c3c1b6f42913798dd40fd09d497ea43be6f
Merge: 5517a2e2b 4f2a7d1f9
Author: cgilet <cgilet@gmail.com>
Date:   Mon Jan 27 07:31:05 2020 -0800

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 334c134ae4a4d2be03313abe36dca92ec119395b
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri Jan 24 17:19:01 2020 -0800

    VisMF: Remove Shadow Warning
    
    Change a private static interface to use the only-usage, same-class
    static control variable it passes to avoid variable name shadowing.

Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp

commit 4f2a7d1f94cfd3bfcac61322fbccd0ee67fdfb80
Merge: 7a0f6f1f3 4babed47c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jan 24 16:41:18 2020 -0800

    Merge pull request #672 from ax3l/fix-shadowTilingPC
    
    ParticleContainer: Fix Warnings

commit 7a0f6f1f3426f9c71485af7acb9808791626a1d5
Merge: efabff7b6 c701bd89b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 24 16:42:21 2020 -0800

    Merge branch 'development' into atmyers/sparse_bins

commit c701bd89bfd1865d2e43301acbc48d4941f5567f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 24 16:26:21 2020 -0800

    add missing include

Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 87461f3db39bb769c9590d980aa63d37aa596bf9
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Jan 24 19:25:18 2020 -0500

    New version of setBndry.

Src/Base/AMReX_FabArray.H

commit 4babed47cefed437aeed9fe88b4dc0b9c2901ed1
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Fri Jan 24 15:38:06 2020 -0800

    ParticleContainer: Fix Warnings
    
    Remove shadowed variable and unused local variable warnings.

Src/Particle/AMReX_ParticleContainerI.H

commit efabff7b61089f8a94512f69ad9dae9c96747e32
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 24 15:19:55 2020 -0800

    reset default to the 'dense' binning strategy for now

Src/Particle/AMReX_Particles.H

commit e95ba6bdb50a64cf762523557a577a1a7c5fb6e0
Merge: 5d9ad8845 ce0fc37e3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 24 15:19:07 2020 -0800

    Merge branch 'development' into atmyers/sparse_bins

commit 132672b0c12684d351997209d3814fff873f25c9
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jan 24 15:02:56 2020 -0800

    NodalProjector: some minor cleaning/tweaks

Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 823126a2752ebc20536dcb9bd4a21f60ba97f936
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jan 24 15:00:48 2020 -0800

    NodalProjector: print norm0(RHS) after projection

Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 26ca00a613f2538dbbc4fe234b35eb10730ef9f7
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jan 24 14:57:55 2020 -0800

    NodalProjector: add code to handle fine->coarse averaging of velocity and fluxes

Src/LinearSolvers/Projections/AMReX_NodalProjector.H
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 5d9ad88452276763ef3a42ba3e7ff2bd60c0ad1a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 24 12:03:41 2020 -0800

    typo

Src/Particle/AMReX_SparseBins.H

commit 39cb0f1122ec981ced9bdc3ac42e3cea96ffb993
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 24 12:01:58 2020 -0800

    getIndex needs to handle the corner case where there is only 1 bin

Src/Particle/AMReX_SparseBins.H

commit d44dfdbff17e14f81800e3a3acb7fa8d8f2af10f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 24 08:49:42 2020 -0800

    simply using amrex_long = int64_t

Src/Base/AMReX_INT.H

commit ce0fc37e3541473194af571f18bb20bd25b2267a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 24 08:42:28 2020 -0800

    long -> unsigned int

Src/AmrCore/AMReX_AmrMesh.H

commit 273e1feff1feee7f7bac32f2a9c3776fe4f6c328
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 24 08:22:55 2020 -0800

    fix compilation

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 60d1c72b71fe33e9dd94efea5806f431d7d7bad1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 24 05:59:05 2020 -0800

    LinOp: use m_factory because a_factory might be empty

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 6085a6f2c0e92fcfb3080fc046ecebcfd635f385
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 23 18:59:21 2020 -0800

    more robust way of detecting if SetDistributionMapping has been called

Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit a5ed6ec58ff3d7d90fc8b941b612c4f150c900d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 23 18:37:23 2020 -0800

    fix my recent mistake

Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_AmrMesh.cpp

commit efc2de046df58d0e1ba25289fe18ee585b7c8f6d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 23 16:47:36 2020 -0800

    Nodal sovler sigma: use EB_average_down

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit fa7d503d9d3aba68fbe297623d1fd6636dbaaed4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 23 15:05:13 2020 -0800

    forgot to set m_items

Src/Particle/AMReX_ParticleLocator.H
Src/Particle/AMReX_SparseBins.H

commit 3a331a9595c50a3fe791f6e745290f7bac2fb519
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 23 14:48:29 2020 -0800

    fix potential overflow

Src/Particle/AMReX_BinIterator.H

commit 156377ef58dd9d25fa72fb73bf66957cb9140df0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 23 14:46:27 2020 -0800

    fix CPU compile

Src/Particle/AMReX_BinIterator.H
Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_SparseBins.H

commit baa486268d8c2b49f3d2bd1d1116e466d9f0cc2e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 23 14:24:06 2020 -0800

    attempting to use SparseBins in the particle locator

Src/Particle/AMReX_BinIterator.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_SparseBins.H

commit 488cd61291ce4552f9c01029ae8f27c48a99bb8c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 23 14:10:19 2020 -0800

    a convenient typedef

Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_SparseBins.H

commit 5ec2f016ba91f9190a7ff0ccf06606637c7b5a8d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 23 14:06:36 2020 -0800

    implement sparse bins search

Src/Particle/AMReX_ParticleLocator.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_SparseBins.H

commit 5e8bc61503e7372e6e396f21ba9c1dc45d463098
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 23 13:07:43 2020 -0800

    Within a bin, DenseBins and SparseBins can use the same iterator type

Src/Particle/AMReX_BinIterator.H
Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_SparseBins.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 2401ce8f978fb0fa01672be7dde5b320a25a8fea
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 23 13:00:27 2020 -0800

    adding SparseBinIteratorFactory

Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_SparseBins.H

commit db6f8489cae17150c4b648a838aed26c9f46343d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 23 12:52:18 2020 -0800

    forgot to check in SparseBins

Src/Particle/AMReX_SparseBins.H

commit 23577ec7910a869c7963a672a7e78319ba7fc509
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 23 12:52:00 2020 -0800

    some useful typedefs

Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_ParticleLocator.H
Src/Particle/AMReX_Particles.H

commit 6998a7d95602e80834156ef107313699cf562773
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 23 11:16:30 2020 -0800

    AmrCore: allow MakeNewLevelFromScratch to ignore DistribitionMapping provided

Src/AmrCore/AMReX_AmrMesh.cpp

commit 3dd3cf18c9bc70857fa8f58f3153dac07d6478c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 23 10:13:22 2020 -0800

    AmrCore: allow users to ignore the DistributionMapping provided

Src/AmrCore/AMReX_AmrCore.cpp

commit dfb28ffe035a8fd283629484a662369a0058b19d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 22 20:10:44 2020 -0800

    FillPatchTwoLevels: option to specify number of ghost cells

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp

commit 961c3479ea5ae1cefd8fd8f26d48a58f6e6daed2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jan 22 16:15:44 2020 -0800

    refactor dense bins to make it easier to incorporate sparse

Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_ParticleLocator.H
Src/Particle/AMReX_Particles.H
Tests/Particles/SparseBins/main.cpp

commit 2142c1b2bd78c037f494137451b9c24ab7838a7e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jan 22 14:21:11 2020 -0800

    code to compute a sparse binning structure

Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/CMakeLists.txt
Src/Particle/Make.package
Tests/Particles/SparseBins/GNUmakefile
Tests/Particles/SparseBins/Make.package
Tests/Particles/SparseBins/inputs
Tests/Particles/SparseBins/main.cpp

commit cf1f2083ed8a6f1ae2e973898753c0a21026e77e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 22 09:54:37 2020 -0800

    no need to use D_TERM

Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit a6e519d0c712880ade4d6a2714f80e254d85264b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 22 09:49:59 2020 -0800

    D_DECL -> AMREX_D_DECL

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit 57e381f6094f49e7607daace4c45f10ad5b496eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 22 09:10:02 2020 -0800

    fix warning

Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit a74381db392566d4e8f855ce121e8fc365e1be73
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Wed Jan 22 09:02:50 2020 -0800

    minor cosmetic cleaning

Src/EB/AMReX_EBMultiFabUtil.cpp

commit 5e332397d6a53a84938eb227c23244dfdd7bdc83
Merge: 79a6365f6 8f0ab38fd
Author: emotheau <emotheau@lbl.gov>
Date:   Wed Jan 22 09:01:15 2020 -0800

    Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines

commit 8f0ab38fd70497ba5ef545a91f6be64e9d6ee282
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 21 20:43:39 2020 -0800

    MacProjector: no ghost cells needed if mac velocity is already on centroid

Src/LinearSolvers/Projections/AMReX_MacProjector.cpp

commit 3ffe33d382d2f63df73c7a6837633a652efc200e
Merge: 3897a3f53 c55b4f48d
Author: Michael Rowan <mrowan@batch4.summit.olcf.ornl.gov>
Date:   Tue Jan 21 17:29:54 2020 -0500

    Get most recent.
    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mrowan/CUPTI_trace

commit 79a6365f612ac78a72e3ed4ec9ef0bf4936d46b7
Author: emotheau <emotheau@lbl.gov>
Date:   Tue Jan 21 12:47:47 2020 -0800

    Revert "fix to fill the ghost cells"
    
    This reverts commit 37c60739ede6399f9e523eae722d4c78a610af61.

Src/EB/AMReX_EBMultiFabUtil.cpp

commit 654fc82ce5d54bd80bde2e2cd7ad9d4fce0b74db
Merge: 37c60739e c55b4f48d
Author: emotheau <emotheau@lbl.gov>
Date:   Tue Jan 21 12:47:26 2020 -0800

    Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines

commit c55b4f48d0219d96b5b9d09bf248cccf93165408
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Tue Jan 21 12:39:33 2020 -0800

    Fix run script comment to use absolute path

Tutorials/GPU/run.corigpu

commit ae5f600b1268a4d532ff7f9dcbaa15b89b5607d8
Merge: e800f66d3 4f86c5a59
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 21 12:23:19 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit e800f66d32f264e6e6831d8af4c9da53bf8d64a3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 21 12:23:10 2020 -0800

    make USE_CUDA=FALSE on this test by default

Tests/GPU/Vector/GNUmakefile

commit 4f86c5a5902e6878695526b2e0d7c102e32f6594
Merge: 2e62c191c fb14dd295
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jan 21 14:24:21 2020 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2e62c191c3be1ec519d8768d30602047008f655f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jan 21 14:23:46 2020 -0500

    this IO proc check is redundant and also wrong

Tests/Particles/Redistribute/main.cpp

commit fb14dd29591640f71e415485336a37e29881f5b5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 21 11:08:52 2020 -0800

    tweak test

Tests/GPU/Vector/main.cpp

commit fc3f1f0d273ec40023f77ca0fa0b59ce345573d5
Merge: 46c137a17 87dcbc4d7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 21 11:06:50 2020 -0800

    Merge branch 'device_vector_refactor' into development

commit 87dcbc4d76dd5186eaf13286232967cd3cd17617
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 21 10:58:19 2020 -0800

    adding tests of the various host / device vectors

Tests/GPU/Vector/GNUmakefile
Tests/GPU/Vector/Make.package
Tests/GPU/Vector/inputs
Tests/GPU/Vector/main.cpp

commit 3d90bb9ca4c1b5be8e0ccc1020cbc2404f7b4169
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 21 10:48:54 2020 -0800

    add missing const_cast

Src/Base/AMReX_PODVector.H

commit 6387d30064fed30698faf932db0271efc3f62cbf
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 17 20:01:06 2020 -0800

    these function signatures need to be consistent

Src/Base/AMReX_PODVector.H

commit df4763e2cc84c58ccc3842361056e2c5952327fc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 17 17:18:51 2020 -0800

    do memmove

Src/Base/AMReX_PODVector.H

commit 965c98649e30dbeac3cbeea85fca4f6de9da249b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 17 16:32:32 2020 -0800

    add missing streamSync here

Src/Base/AMReX_PODVector.H

commit 1a012c621eda3af616e6fe59ba61919522ce8767
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 17 16:13:07 2020 -0800

    fixing a couple of bugs

Src/Base/AMReX_PODVector.H

commit 6e9ac4d9fd57c0238b38f21f58f837da875d40c5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 17 15:17:20 2020 -0800

    handling initializer list

Src/Base/AMReX_PODVector.H
Tests/Particles/Redistribute/main.cpp

commit b83894deaf462a70fc974700dd702201771043dd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 17 14:57:55 2020 -0800

    also do memcpy

Src/Base/AMReX_PODVector.H

commit 46c137a171c00576a5e17265ec3d2310930c98c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 17 14:52:51 2020 -0800

    ParmParse: private -> protected

Src/Base/AMReX_ParmParse.H

commit 0a6c0bcbe5d051b978209cb4f2e9bcc07774f0d8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 17 13:54:22 2020 -0800

    adding uninitializedFillNImpl

Src/Base/AMReX_GpuAllocators.H
Src/Base/AMReX_PODVector.H

commit 78932f81c1450073a0aa31fccfdf3cba659268eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 17 12:29:27 2020 -0800

    fix typo

Src/Base/AMReX_GpuLaunchFunctsG.H

commit e5511d3e4b71049580b3b6b432009e17f4219472
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 17 12:14:16 2020 -0800

    some indentation fixes

Src/Base/AMReX_PODVector.H

commit 6904104e24423b50b56e92c436e175ec01b78957
Merge: 2a971c636 57e644e66
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 16 18:25:51 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2a971c636db67a873c9ea574f1f9a43d95f5b5b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 16 18:25:42 2020 -0800

    fix constexpr

Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp

commit 57e644e6627e5ef3dba45b3e3eb6d53cfb3f7372
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Thu Jan 16 15:38:56 2020 -0800

    Updating job scripts

Tutorials/GPU/run.corigpu
Tutorials/GPU/run.summit

commit dcade0429a5a4b743ef6bbdc037cd9483ae7fb65
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Jan 16 12:33:27 2020 -0800

    Forgot about those pesky non-GPU cases.

Src/Base/AMReX_Random.cpp

commit 71fa5bddb950229db05e87cd56bfed9a566a691e
Merge: b1e25fd24 4f2b90adb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 16 12:30:39 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b1e25fd24accf3a43e681c6d5a79f6f4b3f971ca
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 16 12:30:29 2020 -0800

    docstrings for amrex::Partition and amrex::StablePartition

Src/Base/AMReX_Partition.H

commit 7eb05de1d60d3cd3a358f16f9c9c22262a33c7ba
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 16 12:16:00 2020 -0800

    remove call to deprecated function

Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp

commit 4a1a72cd46796f181286ed7f67eba3fd37e6ccf3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 16 12:15:50 2020 -0800

    change default compiler for Cuda version to gcc

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/GNUmakefile

commit 2b2d09f88b44a6fb1c5fa3da415e80a3b53bc43c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 16 12:15:22 2020 -0800

    docstrings for GpuComplex

Src/Base/AMReX_GpuComplex.H

commit 4f2b90adbf5fd9cf00875c91cc7dd0c6f61f2fde
Merge: 51110e91e dc6afb510
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 16 09:48:19 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 51110e91e914c477ac17437b21f8a8f745392af1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 16 09:48:13 2020 -0800

    fix launch region test

Tests/GPU/CudaGraphs/GraphBoundary/Prob.H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H

commit dc6afb510247358d28fd5c580e67683385a8d151
Merge: 1e3fac6a4 bf430fdce
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 16 09:47:42 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit bf430fdce902f679eebec6d0995c8450130087bc
Merge: 8a6dc6412 567e83f98
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jan 16 08:46:19 2020 -0800

    Merge pull request #661 from rporcu/development
    
    Added 'TheZeroVector', 'TheUnitVector' and 'floor' functions to class RealVect

commit 8a6dc6412030a5cf25906725a0b52af409f4e66d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 15 21:20:53 2020 -0800

    add explicit

Src/Base/AMReX_Box.H

commit 5517a2e2b87092a1955d0324e3c9eb254ad8c150
Author: cgilet <cgilet@gmail.com>
Date:   Wed Jan 15 18:43:10 2020 -0800

    Fix const qualifier so compiles with CUDA

Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 5ab66d52057430eb249eafe44097ea8cdf826ef6
Author: cgilet <cgilet@gmail.com>
Date:   Wed Jan 15 18:42:03 2020 -0800

    Remove unused variable

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit 37c60739ede6399f9e523eae722d4c78a610af61
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Wed Jan 15 17:53:34 2020 -0800

    fix to fill the ghost cells

Src/EB/AMReX_EBMultiFabUtil.cpp

commit 6215e492ac2bac2bea8aca3d3a2946ea2fd0b7f0
Author: cgilet <cgilet@gmail.com>
Date:   Wed Jan 15 17:53:44 2020 -0500

    In MLTensorOp::compFlux(), surroundingnodes -> nodaltilebox

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 121e683978466d04be16583ca9af9b470a4c311b
Author: cgilet <cgilet@gmail.com>
Date:   Wed Jan 15 17:52:02 2020 -0500

    Create MLEBTensorOp::compCrossTerms() for use in apply() and compFlux(). This fixes a bug in compFlux.

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit 3304459a97075257626abc386e5a6ccd26cc4225
Author: kngott <kngott@lbl.gov>
Date:   Wed Jan 15 12:32:07 2020 -0800

    Fix the portable Random.

Src/Base/AMReX_BlockMutex.cpp
Src/Base/AMReX_Random.cpp

commit 567e83f98be91dc5c4f12434a9e102adaf1e5316
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Wed Jan 15 11:51:06 2020 -0800

    Add constructor from Real pointer for class RealVect

Src/Base/AMReX_RealVect.H

commit 4d5eaf6a1e6bbc7354ebc7e53fbc32d69368bf91
Merge: ebd002093 d10f51425
Author: cgilet <cgilet@gmail.com>
Date:   Wed Jan 15 09:28:57 2020 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit d29da0478da3ecaa069cb9ffee347a95c90e427e
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Tue Jan 14 18:12:56 2020 -0800

    Added functions 'ceil' and 'round' to class RealVect

Src/Base/AMReX_RealVect.H

commit 0f591d744ddf85a3a81dc5a5b9217f3f875a5537
Merge: 30d0ce285 d10f51425
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Tue Jan 14 17:59:53 2020 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 507a087c6649fc92c2575323ba71e72cacd7d621
Merge: 610b468c1 d10f51425
Author: emotheau <emotheau@lbl.gov>
Date:   Tue Jan 14 10:33:48 2020 -0800

    Merge remote-tracking branch 'origin/mr/projections' into Emmanuel/new_EB_interpolation_routines

commit 1e3fac6a4bd980c61dffa797e55fbb91685791f5
Merge: 4056d41fa d10f51425
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 13 17:06:54 2020 -0800

    Merge branch 'development' into atmyers/no_thrust

commit 4056d41fa28ae62e80ccf1f32bd0fde67f5a8442
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 13 16:55:29 2020 -0800

    fix typo

Src/Base/AMReX_Partition.H

commit d10f514255a535ed149c5c614e647753b9a8f7fe
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jan 13 15:41:25 2020 -0800

    CMake: add all tutorials in Tutorials/LinearSolvers

Tutorials/LinearSolvers/ABecLaplacian_F/CMakeLists.txt
Tutorials/LinearSolvers/MAC_Projection_EB/CMakeLists.txt
Tutorials/LinearSolvers/MultiComponent/CMakeLists.txt
Tutorials/LinearSolvers/NodalPoisson/CMakeLists.txt
Tutorials/LinearSolvers/Nodal_Projection_EB/CMakeLists.txt
Tutorials/LinearSolvers/NodeTensorLap/CMakeLists.txt

commit 30d0ce285484bcea9697952dff2a0b5bc0a440e8
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Mon Jan 13 14:32:39 2020 -0800

    Fix a bug in 'floor' function of class RealVect

Src/Base/AMReX_RealVect.H

commit dd9ac8e367172f1e439aadfa625f44230bb0604e
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Mon Jan 13 14:05:37 2020 -0800

    Added 'TheZeroVector', 'TheUnitVector' and 'floor' functions to class RealVect

Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp

commit 49fcc4d19617de43a4a617572ab8f5766ff91a33
Merge: 497387e09 593d2fa8a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jan 13 13:57:31 2020 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections

commit 593d2fa8aae135e02ef4141824c30d5787b45d60
Merge: 069fbc974 14efdb227
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jan 13 11:18:37 2020 -0800

    Merge pull request #660 from rporcu/development
    
    Fix a bug which can give errors when compiling

commit 14efdb2275a2dd0a0ca8d4efafe9fda48a7d8a2d
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Mon Jan 13 10:56:29 2020 -0800

    Fix a bug which can give errors when compiling

Src/Particle/AMReX_Particle.H

commit 019047e19e2c7d7093f11aa901c4325db5b567f3
Merge: 55d15b766 069fbc974
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 13 10:14:46 2020 -0800

    Merge branch 'development' into atmyers/no_thrust

commit 610b468c1fc6329836d62b5f1c9eeaa900bb2fef
Merge: ac47ee1ab 069fbc974
Author: emotheau <emotheau@lbl.gov>
Date:   Sun Jan 12 09:46:16 2020 -0800

    Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines

commit 497387e098d840871d2b622e67e71ff9ac6daa22
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Sat Jan 11 16:54:22 2020 -0800

    NodalProjector: some bug fixes and some improvements

Src/LinearSolvers/Projections/AMReX_NodalProjector.H
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 84e09da9110e06bbca1b06eaeb7905cb9b660b2f
Merge: 2c61161e0 069fbc974
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Sat Jan 11 16:04:19 2020 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections

commit 069fbc9749f99d7c0feacd664215977443d67ef7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jan 11 14:11:33 2020 -0800

    Rename amrex_compute ... rather than just compute...

Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H

commit 9528e5c59698dd2b8ccc3b688938cc37a18d2ae3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jan 11 14:10:28 2020 -0800

    Add routines to take convective differences -- analogous to the amrex_compute_divergence routine
    but doing convective not conservative differencing

Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H

commit 2c61161e008804fc9eb41f54e5615795e7b21b8f
Merge: fdaa790d4 0bfb8bdcf
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jan 10 14:37:28 2020 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections

commit 914a146a09ff67fc919b54bc4d19a85f74ff411d
Author: kngott <kngott@lbl.gov>
Date:   Fri Jan 10 14:13:33 2020 -0800

    Small changes for compatibility when running CUDA.

Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuUtility.H
Src/Base/AMReX_Random.cpp

commit ef64631b19a8cc0f401380743f62e930a8c65ec5
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Jan 10 14:04:48 2020 -0800

    Avoid std::uninitialized_fill for hip.

Tests/GPU/Locking/main.cpp

commit 0bfb8bdcf4dfd4a9a42ad121b657e0cbac08bed5
Merge: 76866b44c 191d4db72
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jan 10 13:07:23 2020 -0800

    Merge pull request #659 from rporcu/development
    
    Prevent rvalue component assignment for RealVect class

commit 55d15b76668d804f5d1255d786c502c845faea84
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 10 13:06:00 2020 -0800

    fix 'divide real by complex' operator

Src/Base/AMReX_GpuComplex.H

commit ead7bb6672947df56a18cd795562a772badd7779
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 10 12:55:58 2020 -0800

    implement << operator for GpuComplex

Src/Base/AMReX_GpuComplex.H

commit 537c9778428276d354510e096b9f3aa4cb351071
Merge: 138d05211 76866b44c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 10 12:28:51 2020 -0800

    Merge branch 'development' into atmyers/no_thrust

commit 203ec5f6b0b859b94f2ddaa6513784daf096e112
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Jan 9 21:13:16 2020 -0800

    Add mutex to manual MemcpyToSymbol.

Src/Base/AMReX_Random.cpp

commit 191d4db72e4fe64235e44b1e1a3b30b885ca2fd9
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Thu Jan 9 16:09:30 2020 -0800

    Prevent rvalue component assignment for RealVect class

Src/Base/AMReX_RealVect.H

commit fdaa790d4485f2721e5cb6a418edb28381839a35
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jan 9 15:44:57 2020 -0800

    NodalProjector: re-write code and add support for multilevel projection

Src/LinearSolvers/Projections/AMReX_NodalProjector.H
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 76866b44c3f5b919cb36207d2d102e5d7392f58c
Merge: bfb385865 6edea258c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jan 9 15:08:29 2020 -0800

    Merge pull request #658 from rporcu/development
    
    Fix compilation bug for latest functions added in AMReX_Particle.H

commit 6edea258c90c5db1f38df9817c7ba36485e3ea72
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Thu Jan 9 14:56:57 2020 -0800

    Fixed compilation bug for latest functions added i AMReX_Particle.H when
    AMREX_SPACEDIM == 1

Src/Particle/AMReX_Particle.H

commit 988e4eaa582380523cd762992638e1a61bcd0830
Merge: e8836979b bfb385865
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Thu Jan 9 14:55:38 2020 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 138d0521156d01cc881dde48dc4f5570c82ff98b
Merge: 90b43f7ee 0151136fd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 9 13:48:03 2020 -0800

    Merge branch 'development' into atmyers/no_thrust

commit bfb385865516e2f52bc476ae06e1619d5653d558
Merge: a024d1919 0151136fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 9 13:31:11 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a024d191997f1055b1e7d69864cdc6db9dcdd3e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 9 13:31:07 2020 -0800

    MLMG: functions to set constant coefficients

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit dff8c37db64ea47f2bbd8fd5d1bbaaac802cb2d3
Merge: 57a21b5d0 0151136fd
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jan 9 10:35:19 2020 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections

commit 0151136fd0dc6ce3146e1b3ba62b5f4ce193a28d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 9 06:53:24 2020 -0800

    fix some spelling typos

Docs/sphinx_documentation/source/LinearSolvers.rst

commit d99d890150f8db80c86584357637d8afc41b05be
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 9 06:34:03 2020 -0800

    More spelling corrections (thanks ispell!)

Docs/sphinx_documentation/source/GPU.rst

commit 11a9e63392c96b5a3c43a050016c38dcab9c8516
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 9 06:30:00 2020 -0800

    Fix typo

Docs/sphinx_documentation/source/GPU.rst

commit e8836979bc9ef7e02706b08668c8a008ec71bb0a
Merge: 8602c6fda f5e133129
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Wed Jan 8 16:29:59 2020 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8602c6fda9735a84ad8a64924367578fac05c4ab
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Wed Jan 8 15:18:51 2020 -0800

    Revert "Add functions norm and norm_sqr to class RealVect"
    
    This reverts commit 5e7c9996426eaf77cbb5b65aeb85c53caae71730.

Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp

commit e4ca3fd4a8a7cc500d98cab48db6079552ca99bb
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jan 8 15:00:52 2020 -0800

    Add a Fix comment.

Src/Base/AMReX_RealVect.H

commit a26d0821064911d85f8d1eabcdf0bb9a3aafaa7d
Author: Carter Dodd <cdodd@nanohmics.com>
Date:   Wed Jan 8 17:00:07 2020 -0600

    Change cell bilinear to work with odd refinement ratio

Src/AmrCore/AMReX_INTERP_3D.F90

commit 3d8da37480b628c2bd3d73cd655e235778774837
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jan 8 14:27:23 2020 -0800

    Adjusting for HIP. Currently blows up at PODVector.H, line 82 due to std::uninitialized_fill_n.

Tests/GPU/Locking/main.cpp

commit 5e7c9996426eaf77cbb5b65aeb85c53caae71730
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Wed Jan 8 14:09:12 2020 -0800

    Add functions norm and norm_sqr to class RealVect

Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp

commit f5e13312968c279bd4f819dfdf608aa45b7be55b
Merge: bbb294ace c523155db
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jan 8 13:38:42 2020 -0800

    Merge pull request #654 from rporcu/development
    
    Added functionality of extract a RealVect from Particle class

commit 846356ef4a3443777c1771d57ba2f16bb00cfe5e
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jan 8 13:31:35 2020 -0800

    Make sure HIP-nvcc is off for now.

Tools/GNUMake/Make.defs

commit c523155dbf245efd09ad4cbf176b9ddeb7c6043f
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Wed Jan 8 13:24:37 2020 -0800

    Added functionality of extract a RealVect from Particle class

Src/Particle/AMReX_Particle.H

commit 9f3cd5a370b49e2267ef1693d65f1e0055783359
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jan 8 13:23:05 2020 -0800

    std::sqrt and HIP don't mix.

Src/Base/AMReX_RealVect.H

commit 9193e6f5529d942b9f95765da0d627ff0ca7a5ac
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jan 8 13:22:47 2020 -0800

    Adjust for state of HIP Random.

Tutorials/GPU/ParallelReduce/main.cpp

commit 842250ce6db17561d29f6d4b231edcde3e81e7e3
Merge: 76c9647d6 bbb294ace
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jan 8 12:50:59 2020 -0800

    Merge branch 'development' into kngott/hip

commit ebd0020931f922f60d3eb6e9488cc9564c480e61
Merge: 8edd0b40a bbb294ace
Author: cgilet <cgilet@gmail.com>
Date:   Wed Jan 8 11:23:40 2020 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit bbb294ace62ad1ca92ddc9da4e94188cf6c37695
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 7 20:22:36 2020 -0800

    assert -> AMREX_ASSERT, std::min -> amrex::min and std::max -> amrex::max

Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp

commit d208eee2c5f00e61a1b710d199746b737c196203
Merge: 092887062 8e26b786b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jan 7 17:25:41 2020 -0800

    Merge pull request #652 from rporcu/development
    
    Adding AMREX_GPU_HOST_DEVICE to functions and members of class RealVect

commit 8e26b786bd2a3a8bb15ff82cdefdf20ed0dcc04d
Merge: 8ec3f78d9 092887062
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Tue Jan 7 17:11:10 2020 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8ec3f78d914ad2d4769f833daab9e1ce09e7f14d
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Tue Jan 7 17:02:15 2020 -0800

    Added function crossProduct to class RealVect

Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp

commit 2ac2adc03aaaea91188b52976be02133b0380bd2
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Tue Jan 7 16:50:28 2020 -0800

    Adding AMREX_GPU_HOST_DEVICE attribute to functions and members of class RealVect

Src/Base/AMReX_IntVect.H
Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp

commit 09288706217d6535783e8c701feeaf91aacf6e77
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 7 15:39:24 2020 -0800

    add correctness testing for checkpoint / restart in HDF5Benchmark test

Tests/HDF5Benchmark/inputs
Tests/HDF5Benchmark/main.cpp

commit 3ee6b26a7882e9bf566f39277d2b54582511ab98
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 7 10:46:19 2020 -0800

    fix spaces

Src/Particle/AMReX_ParticleTransformation.H

commit e6f1606fb5985d4a76c5360bfb8fec91a9ce5187
Merge: 81ad9683f a043d311d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jan 7 08:25:54 2020 -0800

    Merge pull request #650 from eschnett/patch-2
    
    Convert comment to English

commit a043d311dc557112884d1c33b57942397edab0c4
Author: Erik Schnetter <schnetter@gmail.com>
Date:   Tue Jan 7 10:10:39 2020 -0500

    Convert comment to English

Tools/CMake/AMReX_Defines.cmake

commit 81ad9683faaf735181e0cd943507d398d91cadbc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 6 16:48:47 2020 -0800

    ignore unused return value

Src/Particle/AMReX_ParticleIO.H

commit ac47ee1abab0c6dca2b5890d010353aff31523f1
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Mon Jan 6 15:52:04 2020 -0800

    bug fix missing copy for regular cells

Src/EB/AMReX_EBMultiFabUtil.cpp

commit ba206b9fec0ee47b41cb7b5e75872966bcf84c4f
Merge: f4c6158ad 6b88dd706
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Mon Jan 6 14:18:21 2020 -0800

    Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines

commit 6b88dd706527ad432af52fb0e1970315e143209c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 6 12:34:32 2020 -0800

    docstrings for the particle reduction functions

Src/Particle/AMReX_ParticleReduce.H

commit 43b570f9729bc64b4ecd35f0ccd31875941e435e
Merge: 6e25131f0 b26186db6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jan 6 10:40:27 2020 -0800

    Merge pull request #646 from houjun/development
    
    Add support to write particle data in HDF5 format

commit 6e25131f057a41ebd521f6f08462ad2bfa2566e8
Merge: b4eb21dd4 511879d90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 6 09:45:30 2020 -0800

    Merge branch 'development' into weiqun/dev

commit 511879d90371c2d465d57a21f8d0364d64e39c2b
Merge: 9cf68e868 00179bba0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jan 6 09:26:17 2020 -0800

    Merge pull request #649 from sudormroot/master
    
    The defition of single_level() should be 'void' rather 'int', otherwise compilers will report errors.

commit 9cf68e8687a213bca3351b3d5a93cd3c9225becc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 6 09:17:53 2020 -0800

    fix the pull-request just merged

Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/EB/AMReX_EB2_Level.H
Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit a16b4a53757fce07d1edb66018dcdef6876bfac6
Merge: b6be55026 ff793aba5
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jan 6 08:57:53 2020 -0800

    Merge pull request #639 from rporcu/development
    
    Added begin and end methods to IntVect and RealVect classes

commit 00179bba07dca9f320d80995f5770e7c6c1b4b4d
Author: sudormroot <sudormroot@163.com>
Date:   Sun Jan 5 11:34:47 2020 +0800

    The defition of single_level() should be 'void' rather 'int', otherwise, in some cases, the comiplers will report errors.

OldTutorials/PIC_C/single_level.cpp

commit b6be5502640fd4e7e3b60854ff60d6fc9fdbd6ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 4 19:23:02 2020 -0800

    constexpr void -> void so that it works with C++11

Src/Base/AMReX_Utility.H

commit b26186db61ac87549d62dbead93e11d788161dd5
Author: Houjun Tang <htang4@lbl.gov>
Date:   Fri Jan 3 13:20:34 2020 -0800

    Remove particle write in ascii format

Tests/HDF5Benchmark/main.cpp

commit e7f86d65bd58b3c50b4730d588f2298d93eb8864
Author: Houjun Tang <htang4@lbl.gov>
Date:   Fri Jan 3 13:12:58 2020 -0800

    Add environmental var option to set Lustre stripe parameters

Src/Particle/AMReX_ParticleIO.H

commit 444189954e1387926422184af032dce3c4b0223b
Author: Houjun Tang <htang4@lbl.gov>
Date:   Fri Jan 3 10:47:10 2020 -0800

    Fix an attribute write error with multiple levels

Src/Particle/AMReX_ParticleIO.H

commit d23822256019c3e45ceeaeec0827603912327241
Merge: 5d0b6ce8b 0afe2b6e7
Author: Houjun Tang <htang4@lbl.gov>
Date:   Fri Jan 3 10:20:33 2020 -0800

    Solve conflicts with merge

commit 5d0b6ce8b23dbee5b9eeeeb71bb7fe415b0726c8
Author: Houjun Tang <htang4@lbl.gov>
Date:   Fri Jan 3 10:04:47 2020 -0800

    Add particle data write in HDF5 format

Src/Base/AMReX_PlotFileUtil.cpp
Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_Particles.H
Tests/HDF5Benchmark/main.cpp

commit ff793aba5c451db118bcbd06150116070493c486
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Thu Jan 2 10:49:29 2020 -0800

    Removed comment for variable that is needed in 1D or 2D simulations

Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp

commit b4eb21dd4c4e63a114a119c2ea3c5f76e208224d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 1 21:12:33 2020 -0800

    need to inline TopIndexSpace

Src/EB/AMReX_EB2.H

commit 9f6a51c87d18ba47d5b0ce562056d8f8f81b6c55
Merge: 1dd582017 0afe2b6e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 1 21:07:53 2020 -0800

    Merge branch 'development' into weiqun/dev

commit 0afe2b6e7cfcbafe8db8fbdc4e9e2047707b86c9
Merge: d3de6a9d6 9ec47d3ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 1 08:57:36 2020 -0800

    Merge branch 'weiqun/comm' into development

commit d3de6a9d69e0d4f2bac07469ff155fa0a6688d31
Merge: fd64303ae e45bd82f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 1 08:57:19 2020 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit e45bd82f36b6b5249226707275455a8b09b6cebc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 1 08:46:57 2020 -0800

    update CHANGES

CHANGES

commit 9ec47d3eca334ddfc8bb9fd3840eb367701a9b93
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 1 08:13:53 2020 -0800

    ignore_unuesd: variadic and gpu host device

Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_Utility.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H

commit 1da10a4706271ad10315a2ad83ec0cbe139779c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 31 23:11:54 2019 -0800

    clean up and avoid potential OMP issues

Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit 5b12e4701f214b87b90fc9793ec9e9d473c09b42
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 31 22:56:07 2019 -0800

    fix assertion

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayCommI.H

commit 1a0cfece62d185494f649a1cfa0744687130b386
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 31 22:30:54 2019 -0800

    support up to 128 GB of communication data for FabArray

Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ccse-mpi.H

commit 1a90ec90a8ad797d892cd749d67d58d93ab07529
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 31 21:30:36 2019 -0800

    two new FabArray functions are for USE_MPI only

Src/Base/AMReX_FabArrayCommI.H

commit fd64303aecf2df0cad2be0a6b656b8e44a8f5652
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 31 21:18:14 2019 -0800

    support up to 16 GB of communication data for FabArray

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_FBI.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit 7e0fd8581a46ace7de87852fead9c24357e3768e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 31 16:48:48 2019 -0800

    add amrex::aligned_size

Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp

commit f71cef8258c61aac1b320ee533057d97ee53317a
Merge: 58e8b4d61 ff3264fed
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Dec 31 11:39:45 2019 -0800

    Merge pull request #643 from eschnett/patch-1
    
    Always check MPI buffer size for overflow

commit 1dd582017a5223620f605c5853fc2ad2b008fa8e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 31 11:28:18 2019 -0800

    minor

Src/EB/AMReX_EB2.H

commit ff3264fedcf334bcd8bcdf63cabfd24edb2f603e
Author: Erik Schnetter <schnetter@gmail.com>
Date:   Tue Dec 31 11:45:00 2019 -0500

    Always check MPI buffer size for overflow
    
    Always check MPI buffer size for overflow. This check is very fast compared to the overall communication time.

Src/Base/AMReX_FabArrayCommI.H

commit 58e8b4d61e7cf9b99b190a3d6d0d5499bbbd7544
Merge: 14448043a 30f84f3e2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Dec 30 20:01:51 2019 -0800

    Merge pull request #640 from AMReX-Codes/block_reduce_fix
    
    Handle an edge case where the block size is less than a warp

commit 30f84f3e26d2fc466c96ecc998828ac3266f4944
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 30 11:58:08 2019 -0800

    avoid std::max because in C++11 it doesn't work on GPU and because blockDim.x and warpSize are not the same integer type (one is unsinged whereas the other is signed)

Src/Base/AMReX_GpuReduce.H

commit 14448043a8b453112365f72c1a0383b3eb1ecf95
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Dec 28 03:45:09 2019 -0800

    Use a 1D block/thread layout for most loops

Src/Base/AMReX_GpuDevice.cpp
Tools/F_scripts/write_cuda_headers.py

commit 133b27a6d00e1ad903c4490b37894a76e6cbc465
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Dec 28 00:57:53 2019 -0800

    Select a better block layout for 1D and 2D

Src/Base/AMReX_GpuDevice.cpp

commit bf29d2b0141c9d3ce7c47cb408a1f9b1394eab43
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Dec 27 00:17:34 2019 -0800

    Add GPU pragma option for a device sync

Tools/F_scripts/write_cuda_headers.py

commit 4c77d7acec90e8427e67c17fafa66999cb174a72
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Dec 25 01:27:00 2019 -0800

    Handle an edge case where the block size is less than a warp

Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_fort_mod.F90

commit f4c6158adcd730d17fc58ca2fe1d6a03194db265
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Dec 23 13:14:35 2019 -0800

    Only setVal result components that will be filled.

Src/EB/AMReX_EBMultiFabUtil.cpp

commit 5cd5133b13b66899f633028a9f2d26f607f23316
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Mon Dec 23 11:42:01 2019 -0800

    Fix some warning messages

Src/AmrCore/AMReX_Interp_3D_C.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/EB/AMReX_EB2_Level.H
Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 2d89d44dea03ae182e99d43313296b6e1e55d597
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Sun Dec 22 15:23:47 2019 -0800

    Added begin and end methods to IntVect and RealVect classes

Src/Base/AMReX_IntVect.H
Src/Base/AMReX_RealVect.H

commit b137b42cff06eba95dc933befc1ab3aac2ea8377
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 20 21:06:27 2019 -0800

    Use consistent stencil to move cell-centered data to cell and face centroids.

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit 90b43f7ee60dbc2c088dec91c15bee0cf26c5e73
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 20 11:26:51 2019 -0800

    that is not how complex numbers work

Src/Base/AMReX_GpuComplex.H

commit f3a9410dc912bf709f16b055d8910b2afb636e0e
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Thu Dec 19 15:43:38 2019 -0800

    Revert "WIP fixing interplation"
    
    This reverts commit 81549df93c7a04af1fc61b031695bba139bdb0c0.

Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H

commit 0d62ebfd08139b944071a6538d32d6a804210e6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 19 15:40:48 2019 -0800

    MacProjector: no need for FillBoundary if already on centroid

Src/LinearSolvers/Projections/AMReX_MacProjector.cpp

commit 68ee2a36c798a41f20e9fd4ec64380166f7eab67
Merge: 3cc3f2f85 93c4658b0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 19 15:23:59 2019 -0800

    Merge branch 'development' into atmyers/no_thrust

commit 3cc3f2f8556aa4e8b4c991ee4ecd74e1d2d27cfd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 19 14:55:31 2019 -0800

    fix typo

Src/Base/AMReX_Partition.H

commit 81549df93c7a04af1fc61b031695bba139bdb0c0
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Thu Dec 19 14:30:10 2019 -0800

    WIP fixing interplation

Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H

commit f53fb5e34ef242b296657a3c234c13c91e1d4d62
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 19 13:52:34 2019 -0800

    add GetVecOfArrOfConstPtrs

Src/Base/AMReX_Vector.H

commit 4cc8226018c0e51758a54a8ba062b39d06d8ef77
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 19 13:52:20 2019 -0800

    skip ccmask if already on centroids

Src/EB/AMReX_EBMultiFabUtil.cpp

commit 93c4658b0c100ffff7a1fb81336db530a731fbc7
Merge: 5a6811ae4 b26e9df72
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Dec 19 13:33:18 2019 -0800

    Merge pull request #638 from AMReX-Codes/dw/pmesh
    
    In ParticleToMesh, apply SumBoundary & finalize MultiFab for both GPU and CPU

commit 051923a7ee99cf0836ed3c3c64fa68bcf473caca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 19 13:23:23 2019 -0800

    NodalProjector: simga may not have ghost cells.  No need to call FillBoundary.

Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 4318157a3600ac79946bfd56df04365c557731d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 19 13:21:38 2019 -0800

    EBCellFlag::setCovered: simply assign covered value

Src/EB/AMReX_EBCellFlag.H

commit b26e9df7217498d342bd0712e98fa500793149f8
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Thu Dec 19 13:08:09 2019 -0800

    Move SumBoundary and MultiFab copy & cleanup outside the not-in-launch-region scope.

Src/Particle/AMReX_ParticleMesh.H

commit 5a6811ae41ec46b3c6ddd2fd795fd1019ff84a09
Author: Oscar Antepara <oantepara@lbl.gov>
Date:   Thu Dec 19 13:06:46 2019 -0800

    [Docs] Adding addtional comments on Paraview section

Docs/sphinx_documentation/source/Visualization.rst

commit 21449b7586306fec59f6b030252e375043ac5507
Merge: adfd9f3b7 0717f6206
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 19 12:50:02 2019 -0800

    merging development into atmyers/no_thrust

commit 0717f6206e86eaff776e6506e2e3e0774ca8b8da
Merge: 1735dfa9a 00abe5b34
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 19 12:48:35 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 1735dfa9aa54e06a6e71c898a3f1649933ff71f8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 19 12:48:20 2019 -0800

    a host / device version of swap

Src/Base/AMReX_Algorithm.H
Src/Base/AMReX_PODVector.H
Src/Base/AMReX_Partition.H

commit 32ea5942719735b894fa0558c3757e43a5d13ae3
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Dec 18 18:31:52 2019 -0800

    Fix cc2cent interp stencil in 2D

Src/EB/AMReX_EBMultiFabUtil_2D_C.H

commit adfd9f3b73bea1ac6b4dde43ef5e82f510ba3c58
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 18 15:54:02 2019 -0800

    more code reuse in amrex::Partition and amrex::StablePartition

Src/Base/AMReX_Partition.H

commit 5f15e0f20834cf64922ae04bc1660816ccfac205
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 18 15:07:57 2019 -0800

    fix spaces

Src/Particle/AMReX_ParticleTransformation.H

commit 0ab02eab4c449147b8c12aa2a126c8d1d7510e4c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 18 15:07:46 2019 -0800

    reorder these functions

Src/Base/AMReX_Partition.H

commit 48345f66146622dc8efa117e4b7e80c474066326
Merge: b55f911de 00abe5b34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 18 14:17:08 2019 -0800

    Merge branch 'development' into weiqun/dev

commit 00abe5b3435c584e53aa134a7373d488f63e2f66
Merge: 130b3c2b8 cdb57360c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 18 14:14:32 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b55f911de9368aa432fc76077529ff5ce4bb193a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 18 13:05:17 2019 -0800

    Make FillPatchSingleLevel safe when the destination is the same as source. Change the interface of virtual PhysBCFunctBase::FillBoundary that unfortunately breaks backward compatibility.

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/F_Interfaces/Base/AMReX_FPhysBC.H
Src/F_Interfaces/Base/AMReX_FPhysBC.cpp

commit 8edd0b40a5843f162e794d05049a342740d71815
Author: cgilet <cgilet@gmail.com>
Date:   Wed Dec 18 17:00:36 2019 -0500

    Fix testing for regular cells in compFluxes and compGrad.

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit cb4d4d5f3c95ecc6a4e19dd69f7b5229ff9b73bd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 18 13:35:37 2019 -0800

    ensure that the Partition and ParallelScan Tests still work

Tests/GPU/Partition/main.cpp
Tutorials/GPU/ParallelScan/main.cpp

commit 8288ef114b01ccbd05324f6707948db947b0b7e7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 18 13:35:11 2019 -0800

    move implementation of inclusive_scan and exclusive_scan to get around circular dependency issue

Src/Base/AMReX_GpuContainers.H
Src/Base/AMReX_Scan.H

commit 47f77cb5db3ab3851899fd7c6003d78134c389b6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 18 13:34:23 2019 -0800

    add alternate versions of Parition and StablePartition

Src/Base/AMReX_Partition.H

commit a5e47bd8708a24004339cc09daf805db0ad31acb
Author: cgilet <cgilet@gmail.com>
Date:   Wed Dec 18 16:27:28 2019 -0500

    Add MLEBTensorOp::compFlux at face centroids

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 130b3c2b8c912fa4b9f603f76b09f7911ee585da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 18 09:49:56 2019 -0800

    OrientationIter: ok -> isValid for consistence with MFIter

Src/Base/AMReX_Orientation.H

commit 94d4a81239396cbeb6eb6277c28f74b0ecec49fc
Merge: 89c82ab45 cdb57360c
Author: cgilet <cgilet@gmail.com>
Date:   Wed Dec 18 09:38:10 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 76c9647d6c9d58708a65e2ba8aa7336d60fc2b0f
Merge: 8e76d22ab cdb57360c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Dec 18 04:08:03 2019 -0800

    Merge branch 'development' into kngott/hip

commit c9ad3c03bfb5bdc063e27be0986984202a10458c
Merge: 2c870195f cdb57360c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 17 17:21:31 2019 -0800

    Merge branch 'development' into atmyers/no_thrust

commit 2c870195f84219e57199ec7fac6112565be2e24e
Merge: b9d1a0f97 378fac897
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 17 17:18:41 2019 -0800

    Merge branch 'development' into atmyers/no_thrust

commit b9d1a0f9775bf36b6c3dbb3d07b315fc0de11c53
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 17 17:18:14 2019 -0800

    less confusing implementation of complex int pow

Src/Base/AMReX_GpuComplex.H

commit cdb57360cf7663e5fd77196ae11439498f83fb52
Merge: 378fac897 149997448
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Dec 17 17:17:58 2019 -0800

    Merge pull request #637 from eschnett/development
    
    Avoid compiler warnings

commit 54d02704886c4ae03c22d7a01829759fb6c6db73
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Dec 17 15:26:49 2019 -0800

    Add destComp to EB_interp_CC_to_Centroid

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit 378fac8979817a172a73c83519a2ba02013c8586
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Dec 17 15:10:21 2019 -0800

    CMake: fix problems with PETSc support

Src/CMakeLists.txt
Src/Extern/HYPRE/CMakeLists.txt
Src/Extern/PETSc/CMakeLists.txt
Tools/CMake/AMReX_Options.cmake

commit af1c9406ab4926857ea0f402c82eecd0466e272d
Merge: e37e0672b 29f1fd37a
Author: mic84 <mrosso@lbl.gov>
Date:   Tue Dec 17 15:00:09 2019 -0800

    Merge pull request #636 from petsc/add-petsc
    
    Add support for CMake to handle PETSc

commit fcdb382c2b824c4998d149794b734b6530f5e8a0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 17 14:42:54 2019 -0800

    COMPLEX -> GPUCOMPLEX

Src/Base/AMReX_GpuComplex.H

commit f9abb676e6f90278c5abeee86a18120604b0cc61
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 17 14:21:05 2019 -0800

    add amrex::GpuComplex

Src/Base/AMReX_GpuComplex.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 149997448dddf4ee4e31debe85a298df0b4cf700
Author: Erik Schnetter <schnetter@gmail.com>
Date:   Tue Dec 17 15:57:52 2019 -0500

    Avoid compiler warnings

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleLocator.H
Src/Particle/AMReX_ParticleUtil.H
Src/Particle/AMReX_StructOfArrays.H

commit e13a8054c6b20ceb1a31174463ee3c45ab4869d1
Merge: e03ee8390 e37e0672b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 17 10:58:59 2019 -0800

    Merge branch 'development' into atmyers/no_thrust

commit e37e0672bb6ec39156eff9bbc1c39e05ba0b5592
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Dec 16 22:49:23 2019 -0800

    Move some NVCC options to be included for C source files

Tools/GNUMake/comps/nvcc.mak

commit c2b60f26da030a11f1d2ad9df93fdeb7892a1a63
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Dec 16 22:48:54 2019 -0800

    Include C sources in the CUDA preprocessing

Tools/GNUMake/Make.rules

commit c1bafe5e85ee9536f576c7c6765a22d2c6ddb7c4
Merge: e7ade72e2 0a490f82d
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Mon Dec 16 16:39:57 2019 -0800

    Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines

commit e7ade72e24a222111b15b640316cc1f84ceda74c
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Mon Dec 16 16:39:41 2019 -0800

    CC2Face and CC2FaceCentroid in 3D now

Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit 89c82ab45bebcfc430632d51041c7b9d4e5857fb
Merge: c8af77e99 0a490f82d
Author: cgilet <cgilet@gmail.com>
Date:   Mon Dec 16 19:13:13 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 3897a3f534cc36d957d8ee6e129b62d985646b38
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Mon Dec 16 11:45:13 2019 -0800

    Save more kernel stats to activity record

Src/Base/AMReX_ActivityTraceAsync.H
Src/Base/AMReX_ActivityTraceAsync.cpp

commit 0a490f82d7ed91f1aba44f7a5e82d91906d306fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 16 10:32:16 2019 -0800

    add std::

Src/Base/AMReX_PODVector.H

commit 85ab455d0a3e06d8c9a05dbd6af6a065fe3e261b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 16 10:32:05 2019 -0800

    fix typo

CHANGES

commit c8af77e990cae92e46ffc1c536edecbcc6b2ca9f
Merge: 2998db0c4 4274ca7fd
Author: cgilet <cgilet@gmail.com>
Date:   Mon Dec 16 10:25:59 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 29f1fd37a2d1a363a90a29ef4542b9e60045f518
Author: Barry Smith <bsmith@mcs.anl.gov>
Date:   Sun Dec 15 21:10:58 2019 -0600

    Add support for CMake to handle PETSc
    
    Add missing include files to Src/EB/CMakeLists.txt

Src/CMakeLists.txt
Src/EB/CMakeLists.txt
Src/Extern/PETSc/CMakeLists.txt
Tools/CMake/FindPETSc.cmake

commit 4274ca7fd551a7ca9af7e11e73d261475cf493c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 14 18:27:15 2019 -0800

    FabArray ReduceMin and ReduceMax that can take three FabArrays

Src/Base/AMReX_FabArrayUtility.H

commit 6883a8a74788cf31cee7f627c0163308411095e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 14 18:25:28 2019 -0800

    add FabArray::isAllRegular

Src/Base/AMReX_FabArray.H

commit 38401028ca6c672a495a45ec173a182203251057
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 14 10:05:10 2019 -0800

    only need to fill one ghost cell

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 523078d81dbf3508bc7233f1b5b9e8e9f76f39c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 14 10:04:03 2019 -0800

    new Orientation constructor

Src/Base/AMReX_Orientation.H

commit 3facd4e3972faef06fb0e3fa5147d50225560d2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 14 10:03:24 2019 -0800

    make it safe to construct zero-component Fab

Src/Base/AMReX_BaseFab.H

commit 4393a178724392ae4a018aa7c30797b3403986fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 14 10:02:29 2019 -0800

    add new funcitons to AmrMesh to return vector of Geometry, BoxArray and DistributionMapping on a range of levels

Src/AmrCore/AMReX_AmrMesh.H

commit 1484aacc8a222c08075be1c9e2bd4360fcfc165c
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 13 19:23:12 2019 -0800

    Add scomp/dcomp to functions for face centroid

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H

commit e6efc1f5b4534e0eee842379d9faa0dcb636ee53
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 13 18:51:52 2019 -0800

    Remove grow op on interp function..remnant of where orig code was stolen from

Src/EB/AMReX_EBMultiFabUtil_2D_C.H

commit d2c69d10647901e98dd519f8b028ab96593be2cc
Merge: f620b4311 9dd79f66a
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Fri Dec 13 16:04:00 2019 -0800

    Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines

commit f620b4311054512f1b7f2af24f0bb8b89ce046e7
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Fri Dec 13 16:03:40 2019 -0800

    some cleaning
    note that CC2FaceCentroid is missing in 3D

Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit 646a16fabb07d27b2eb8de72e6b0c7196aab27ad
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Fri Dec 13 15:58:23 2019 -0800

    new design of CC2Centroid to get the correct cells without using a normal
    new routine to interpolate cc to face centroid

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit 14b8c797ba16cac9702ed91493ec977ac39e1299
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Fri Dec 13 11:56:02 2019 -0800

    Added check for RedistributeCPU edge case where particle gets reset to lo boundary, but is not contained in the Box it came from

Src/Particle/AMReX_ParticleContainerI.H

commit c0b505244e3208bf4af4e02d9836f264a7e7ac9e
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Fri Dec 13 11:09:49 2019 -0800

    3Putting 3D version

Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit 2998db0c4ab94c5e18a8e28ea0f03b27d1483f07
Merge: eeaadfe17 9dd79f66a
Author: cgilet <cgilet@gmail.com>
Date:   Fri Dec 13 10:19:05 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 73a226eccdbf86a05ffa69797875664c8801fbed
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Thu Dec 12 15:18:56 2019 -0800

    Some cleaning

Src/EB/AMReX_EBMultiFabUtil.cpp

commit e03ee83909e1e1122feb06c98cfbd3a0fcb6d27f
Merge: dfa7a7834 9dd79f66a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Dec 12 17:37:32 2019 -0500

    Merge branch 'development' into atmyers/no_thrust

commit 9dd79f66adf56bf253ebeb7f3935a5e3eeae5681
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Dec 12 17:37:02 2019 -0500

    fix global parameter shadowing

Src/Particle/AMReX_ParticleBufferMap.cpp

commit 57a21b5d0bdeed9adf6b6a3ff088031f0b26b214
Merge: 2e3b3a308 cc9950f1c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Dec 12 14:30:44 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections

commit dfa7a7834494d1175af532eaca531731bbb2ef52
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Dec 12 16:52:11 2019 -0500

    remove old file from make system, restore some missing ,

Src/Base/AMReX_GpuContainers.H
Src/Base/AMReX_PODVector.H
Src/Base/Make.package

commit cd3b6c97fd5a86e3a2434131a761f2ae5e3375da
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Dec 12 16:40:10 2019 -0500

    removing all thrust calls from amrex

Docs/sphinx_documentation/source/GPU.rst
Src/Base/AMReX_GpuAllocators.H
Src/Base/AMReX_GpuAllocators.cpp
Src/Base/AMReX_GpuContainers.H
Src/Base/AMReX_PODVector.H
Src/Base/CMakeLists.txt

commit 04128e437bcb6c5b4b105cbca8242d48935efb19
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Dec 12 16:31:08 2019 -0500

    fix cpu versions of exclusive and inclusive scan

Src/Base/AMReX_GpuContainers.H

commit c26ae799b35fe6282c0e26ade55a4a3dc6ca958c
Merge: 68c764a86 cc9950f1c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Dec 12 15:40:35 2019 -0500

    Merge branch 'development' into atmyers/scan_compare

commit facfabe423b7f77a3b232829979113a88ffbcd27
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Wed Dec 11 21:05:34 2019 -0800

    cleaning of the 2D routine

Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H

commit 6cc934e5e85c6a0d5ac02ef04b8069d4d398aa39
Merge: c86c20555 cc9950f1c
Author: emotheau <emotheau@lbl.gov>
Date:   Wed Dec 11 20:44:40 2019 -0800

    Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines

commit c86c2055563c5bdbe8465fb38f135ae14c72577f
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Wed Dec 11 20:42:31 2019 -0800

    WIP : create a new routine to interpolate Cell Center values to Centroid

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H

commit cc9950f1c6514451d109f71a5a0c4c126c7c2b63
Merge: c2948a786 60fbfd426
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 11 15:34:30 2019 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit c2948a78628a9bc549f0eb8de018091b56f17d82
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 11 15:33:47 2019 -0800

    Update MAC_Projection_EB tutorial so that when regtest = 1 we don't plot zvel
    (used for regression testing with GPUs)

Tutorials/LinearSolvers/MAC_Projection_EB/inputs_3d
Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp

commit 3b97486eebdcc9788eac70455f6874773271ee26
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Wed Dec 11 14:22:01 2019 -0800

    Cleanup CUPTI GPU timer

Src/Base/AMReX_ActivityTraceAsync.H
Src/Base/AMReX_ActivityTraceAsync.cpp
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp
Src/Base/Make.package
Tests/GPU/CuptiTest/Exec/CUDA/GNUmakefile
Tests/GPU/CuptiTest/Exec/CUDA/myfunc.H
Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp
Tests/GPU/CuptiTest/Exec/CUDA/mykernel.H
Tests/GPU/CuptiTest/Source/main.cpp
Tools/GNUMake/Make.defs

commit 8e76d22abd8c8acbf94cf06cce2792d01796ce04
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Dec 11 14:07:51 2019 -0800

    Clean up hip make system.

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/hip.mak

commit 60fbfd4263d5030e52abc6c7af1e315f2186396e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 11 13:45:06 2019 -0800

    Need to set coverd cells in rhs_cc

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 2ed977fe070c8feda6475a1813e07620f2581bd3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 11 13:27:02 2019 -0800

    Set default maxorder to 3 not 2

Src/LinearSolvers/Projections/AMReX_MacProjector.cpp

commit 382c619b5766ec2c7962da721d5cdf39cc8251d9
Merge: 9bf74235f bfbee79af
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Dec 11 12:55:13 2019 -0800

    Merge branch 'development' into kngott/hip

commit bfbee79af429d55c0b90acf17c5bc25ace50ab13
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Dec 11 15:51:54 2019 -0500

    __CUDA_ARCH__ inside functions instead of defining separate functions (hip-clang error)

Src/Base/AMReX_Random.H
Src/Base/AMReX_Random.cpp

commit 9bf74235f95e2d0419e4b8527efea8e67e64b974
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Dec 11 12:29:46 2019 -0800

    More function marking for hip-clang.

Src/Base/AMReX_BaseFab.H

commit eeaadfe17987c1d9a164b5905a2fe3f8028d1ae1
Merge: 7065a340c e129ae8e4
Author: cgilet <cgilet@gmail.com>
Date:   Wed Dec 11 14:43:32 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 2e3b3a308c8dd4f2ff6434285c479ab28481edc8
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Dec 11 11:14:50 2019 -0800

    NodalProjector: rename m_solver m_mlmg

Src/LinearSolvers/Projections/AMReX_NodalProjector.H
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit bc172f3d29458d2b8ca9b9f375b9b546aaa6fa4c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Dec 11 11:09:40 2019 -0800

    NodalProjector: rename m_matrix m_linop

Src/LinearSolvers/Projections/AMReX_NodalProjector.H
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit e129ae8e421226b31925747a993adb22452db77a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 11 09:59:43 2019 -0800

    fix communicator bug when there is only one multigrid level and the solvability needs to be fixed

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 7065a340c910ca1bda5786b9702430117dda00ba
Merge: 6153c3374 5070a127b
Author: cgilet <cgilet@gmail.com>
Date:   Wed Dec 11 12:22:43 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 5070a127b8b1a56b42951e2cc8f829ec1daf62c3
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Dec 10 17:37:14 2019 -0800

    MacProjector: remove debug statement

Src/LinearSolvers/Projections/AMReX_MacProjector.cpp

commit e61c71fc52d6d678f871ff0d4214e71fdcb16785
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Dec 10 17:36:13 2019 -0800

    Update MAC_Projection_EB test

Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp

commit 4ce674f60e269a7d58037d89c30e5d94998498ad
Merge: 3f5a8f7d9 6f907ebbb
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Dec 10 17:30:23 2019 -0800

    Merge branch 'mr/projections' into development

commit 68c764a86a86e4d1fb2d1d14cc727df7f6330d83
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Dec 10 20:08:59 2019 -0500

    use amrex scan instead of thrust

Src/Base/AMReX_GpuContainers.H

commit 6f907ebbbd1b463be276bc6a9ba844e28cd0ba81
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Dec 10 16:54:41 2019 -0800

    MacProjector: give user access to linear operator and MLMG.
    
    Remove setters which now are superfluous.
    Create MLMG and set options from input file in constructor.

Src/LinearSolvers/Projections/AMReX_MacProjector.H
Src/LinearSolvers/Projections/AMReX_MacProjector.cpp

commit 3f5a8f7d94fc092e3e5cdf0e48145fad2b2b4001
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 10 14:59:28 2019 -0800

    fix incorrect table description in documentation

Docs/sphinx_documentation/source/InputsPlotFiles.rst

commit e6b287860b5aeeef0e86b527b56367fe31689a98
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 10 11:38:01 2019 -0800

    fix a warning

Src/EB/AMReX_EB2_GeometryShop.H

commit bdb717baffec81bc69a4934a64989906920f088e
Author: Oscar Antepara <oantepara@lbl.gov>
Date:   Tue Dec 10 10:22:46 2019 -0800

    Fixing MAC solver options

Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp

commit 28dbe05b35b644eb2c91a11084ce645bc53c225c
Merge: e3a86b0b3 c949c3895
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Dec 9 14:39:52 2019 -0800

    Merge branch 'mr/projections' into development

commit c949c38958ca86c68c5b19e4164f1acd272396e9
Merge: e39567741 f33a41000
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Dec 9 14:39:32 2019 -0800

    Merge branch 'development' into mr/projections

commit e3a86b0b3d1711ba661c77fa45c13ed71744d294
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 9 12:20:44 2019 -0800

    more BL_ -> AMREX_

Src/Base/AMReX_REAL.H
Src/Base/AMReX_fort_mod.F90
Src/Particle/AMReX_Particles.H

commit 1c7b79e02b725ebc4926cde127788f66bd4b4292
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 9 12:16:39 2019 -0800

    more BL_ -> AMREX_

Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_TracerParticles.H

commit e13efe8ac0090424b17575d2e7519b27fc948ba8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 9 12:14:04 2019 -0800

    more BL_ -> AMREX_

Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_ParticleInit.H

commit 4ce1b306a5302d8cd63e64188720618b29765f67
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 9 12:12:45 2019 -0800

    BL_LAZY -> AMREX_LAZY

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit 2f0310dc4e0ae6ebc58cc510ad02942a7c579cfb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 9 12:09:15 2019 -0800

    BL_USE_MPI -> AMREX_USE_MPI

Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleMPIUtil.H
Src/Particle/AMReX_ParticleMPIUtil.cpp

commit 195f9279fedf4b709adc57175f2a34d15cdfff63
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 9 11:56:57 2019 -0800

    rename AMReX_ParIterI.H -> AMReX_ParIter.H

Src/Particle/AMReX_ParIter.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 331839046fc68a544ca20cc7c1e019bdc5ca0ead
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 9 11:55:45 2019 -0800

    move implementation of ParIter

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H

commit 6153c3374ccbf1481aeafe477b39688596e511cf
Merge: 1fe275876 fd90437e6
Author: cgilet <cgilet@gmail.com>
Date:   Mon Dec 9 14:22:06 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit fd90437e6b58e102022edc03dcc4fdf8e6f73bb9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 9 09:41:10 2019 -0800

    add MLMG::getEBFluxes

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 1fe2758766fe08ce7034fae3e9a664e1927f87b8
Merge: a3cd10182 820e0e4ff
Author: cgilet <cgilet@gmail.com>
Date:   Mon Dec 9 11:29:52 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 820e0e4ffbdf6546a91bb20f886812358d95d0f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 9 08:15:11 2019 -0800

    fix 2d EB computeDivergence and computeGradient

Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_2D_C.H

commit a3cd10182024b260cd19aae4f0d6437a2c3c39bd
Merge: afb28f3d9 d7e23ba08
Author: cgilet <cgilet@gmail.com>
Date:   Sat Dec 7 19:23:14 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit d7e23ba089c201004b56228293fe1683da92e599
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Dec 7 10:13:22 2019 -0800

    Specify in suffix if using OpenMP offload

Tools/GNUMake/Make.defs

commit 25f1130e936b91d030b7ce5e898fa890e96bcca6
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Dec 6 18:34:43 2019 -0800

    Nearly fixed. Likely managed isn't appropriately covered.

Src/Base/AMReX_BlockMutex.cpp
Src/Base/AMReX_Random.cpp

commit 92a791ba38c3c8296f35e9c3d0bba1ef167164d1
Merge: 36f26a8d7 cc7db21bc
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Dec 6 18:31:06 2019 -0800

    Merge branch 'development' into kngott/hip

commit 961ca2189da600a80485049ea148cec788315715
Merge: a47703550 9c5e67fd5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Dec 6 17:23:29 2019 -0800

    Merge pull request #632 from AMReX-Codes/twoway_transform
    
    Two-way particle transforms

commit a47703550cc94d28e4464fa682b39432c35dbfe1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 17:14:39 2019 -0800

    further tweaks to locking test

Tests/GPU/Locking/inputs
Tests/GPU/Locking/main.cpp

commit e181cadca8391ab886e6479acfb46bfc4b7a7db4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 17:05:11 2019 -0800

    tweak output of Locking test

Tests/GPU/Locking/main.cpp

commit 9c5e67fd55041cea89227bdb7d77757fc7ce7996
Merge: 6718b8310 a9e75a7db
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 16:59:06 2019 -0800

    Merge branch 'development' into twoway_transform

commit 6718b8310168c83da8564c85391f2ae501b54833
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 16:53:31 2019 -0800

    implement and test two-way filter and transform

Src/Particle/AMReX_ParticleTransformation.H
Tests/Particles/ParticleTransformations/main.cpp

commit f33a41000b988921e7c3569ab3709ba8e9e9a74a
Merge: 8c2f74ea9 bd82c0bd9
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Dec 6 16:27:09 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8c2f74ea95d6162d2fd0c74b3c23ea201de0371f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Dec 6 16:26:59 2019 -0800

    computeGradient(): add support for RZ geometry

Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_2D_C.H

commit a9e75a7dbc241b25c7bf447aa9e68edcc8710c92
Merge: cba0db3bb ea18e035d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 6 16:26:54 2019 -0800

    Merge branch 'development' into weiqun/dev

commit ea18e035de757788ac5e6cc450cacc4903ec9082
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 6 16:24:00 2019 -0800

    fix CXXSTD for nvcc with gcc > 5

Tools/GNUMake/comps/nvcc.mak

commit ec1e8c9c5c0de64058fdd8eb2c525aee8d1d952d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Dec 6 16:21:25 2019 -0800

    computeDivergence(): add support for RZ geometry

Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_2D_C.H

commit bd82c0bd9343b749572da079a1bc2db067eaa293
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 6 16:06:29 2019 -0800

    for nvcc we have to make sure CXXSTD is defined

Tools/GNUMake/comps/nvcc.mak

commit e1aa3c306b0a6eb32f49e1ea4f5b478dabc9dc61
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 15:59:46 2019 -0800

    remove extraneous word from comment

Src/Particle/AMReX_ParticleTransformation.H

commit 5d0f2110ae1a6624c4032cc69d26bd3757732df4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 15:58:01 2019 -0800

    allow the Src and Dst particle tile types to be different for the transform functions

Src/Particle/AMReX_ParticleTransformation.H

commit 489a02f22d45a807137b09958307451845a7e049
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 15:41:45 2019 -0800

    implement and test two-way transforms

Src/Particle/AMReX_ParticleTransformation.H
Src/Particle/AMReX_Particles.H
Tests/Particles/ParticleTransformations/main.cpp

commit cc7db21bcd9bc41d471b857606b451d746758056
Merge: 69f67bf33 b5b9cc90b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Dec 6 15:18:53 2019 -0800

    Merge pull request #631 from AMReX-Codes/lock_reimplement
    
    Lock reimplement

commit 69f67bf33a1c7384c0905a12c184a14130ef5a54
Merge: 4ec5a952e 08530bf64
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Dec 6 15:14:36 2019 -0800

    Merge pull request #630 from ax3l/topic-cxxStdControl
    
    CXXSTD: Project Control of C++ Std

commit b5b9cc90b5300d66306bd9e66744e4f6952756f8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 15:09:50 2019 -0800

    fix order of namespace and #ifdef

Src/Base/AMReX_BlockMutex.cpp

commit 08530bf645a7ecc793e72e2a640e7796ef76b75d
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Dec 5 11:16:06 2019 -0800

    CXXSTD: Project Control of C++ Std
    
    Add a new option, defaulting to C++11, to give projects control over
    the required C++ standard of a project.
    
    This improves the current logic, which does not cleanly fail if a
    compiler does not support e.g. C++14 but instead gave hard-to-read
    error messages such as "hm, dunno what std::make_unique is" :)
    Now the compiler will fail with messages such as:
    "gcc: error: unrecognized command line option ‘-std=c++14’"
    which is better and safes us from re-implementing a ton of logic
    that CMake provides out-of-the-box.

Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/GNUMake/comps/cray.mak
Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/hip.mak
Tools/GNUMake/comps/ibm.mak
Tools/GNUMake/comps/intel.mak
Tools/GNUMake/comps/llvm-flang.mak
Tools/GNUMake/comps/llvm.mak
Tools/GNUMake/comps/nag.mak
Tools/GNUMake/comps/nvcc.mak
Tools/GNUMake/comps/pgi.mak

commit 5b9486a148cae82c4552c0aad295685a5ab2bc26
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 15:04:40 2019 -0800

    put these implementations in namespace amrex

Src/Base/AMReX_BlockMutex.cpp

commit c27de5cb21184d3fe078f8796f9823cecd339e33
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 15:04:21 2019 -0800

    add __threadfence()

Tests/GPU/Locking/main.cpp

commit e7fa758f3d3f3e64c3f4d49aa5aec941a42bfe6e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Dec 6 14:28:00 2019 -0800

    computeDivergence(): fix assertions to work with any AMREX_SPACEDIM

Src/Base/AMReX_MultiFabUtil.cpp

commit 7338a22eab1c9f5610a3017742a1958ef5889ee5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 14:00:15 2019 -0800

    actually add file

Src/Base/AMReX_BlockMutex.cpp

commit 7954bba09f2730a34f736f31d76146f3917c1509
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 13:58:35 2019 -0800

    split up the declaration and definition for BlockMutex

Src/Base/AMReX_BlockMutex.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit d8fcba3a5967c5decff78a88e9775095ec567666
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 13:42:31 2019 -0800

    no need to duplicate this static_assert

Src/Base/AMReX_Random.cpp

commit b6f1d650b4633b5fde8987ea9584b11a4bfabbe6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 13:39:43 2019 -0800

    add block counting to the locking test

Tests/GPU/Locking/main.cpp

commit 36f26a8d7fc501f358387a833e69b2195d75bed2
Merge: a08d0de0d 96879dd69
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Dec 6 13:36:21 2019 -0800

    Merge branch 'development' into kngott/hip

commit 4419aa94e34eb0562570ba179a00876f4edf2cb3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 13:29:58 2019 -0800

    forgot to add new file

Src/Base/AMReX_BlockMutex.H

commit 7dd940245c7b90446b287983890180d145e304ca
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 13:20:31 2019 -0800

    impose a naming convention on the global random state and lock variables

Src/Base/AMReX_Random.cpp

commit 4a570f14d63bb0681bea0857ecb8c4c046e30a4e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 6 13:15:28 2019 -0800

    package the locking together in a BlockMutex class.

Src/Base/AMReX_Random.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tests/GPU/Locking/main.cpp

commit cba0db3bb7b963e82a4e25b41558798cbe67ada9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 6 09:42:27 2019 -0800

    nodal solver on gpu: need to call nodal sync if there are more than one Jacobi sweeps

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 5e660e16e063bc6e497b3fb8add5de7147843ab1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 6 09:36:47 2019 -0800

    tweak nodal solver smoother for gpu

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 4ec5a952ee00e3c1a4f393f163fad66befbc1887
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 5 16:49:41 2019 -0800

    update the section of the documentation about Particles on GPUs

Docs/sphinx_documentation/source/GPU.rst

commit 092eee2cdcabcd9f0a8ebb65b3e26c98c49cbc6f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Dec 5 16:31:40 2019 -0800

    Add documentation performance comment about thrust execution policies.

Docs/sphinx_documentation/source/GPU.rst

commit 959227d1bd9835a06f786687d4b5af667f73d5b2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 5 16:12:13 2019 -0800

    modify this test to execute 100 times in a loop

Tests/GPU/Locking/main.cpp

commit 5711a37969bf2e35801035010a3fec70d1dfda0c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 5 11:11:17 2019 -0800

    move print statement

Tests/GPU/RandomNumberGeneration/main.cpp

commit 8d27e3cb22f2c536ed76174d0d329a25e2a086ed
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 5 11:06:06 2019 -0800

    clean up random number test a little bit

Tests/GPU/RandomNumberGeneration/main.cpp

commit 6736ac30c02f80845975c21ea367f18f33c26464
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 5 10:50:33 2019 -0800

    reimplement lock using 64-bit CAS to simultaneously update the block and the counts.

Src/Base/AMReX_Random.cpp
Tests/GPU/Locking/main.cpp

commit e3956774189309355a322a4829cf6971d3ad9796
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Dec 4 15:13:26 2019 -0800

    MacProjector: streamline handling of solver options

Src/LinearSolvers/Projections/AMReX_MacProjector.H
Src/LinearSolvers/Projections/AMReX_MacProjector.cpp
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit d8cd3dcbb80eadbf76405f484667711b3fb6a8a1
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Dec 4 14:41:05 2019 -0800

    NodalProjector: streamline handling of solver options

Src/LinearSolvers/Projections/AMReX_NodalProjector.H
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit e61f2273ec2bcb5919bf4dd7447ca1a0ba70a720
Merge: f1879e73c 359c10924
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 4 13:09:53 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 359c10924998d5605270b412878644fc77277c7d
Merge: 022775ef7 016edb791
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 4 12:07:25 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 022775ef766499b37c8ee04c14bcadd90a1d34d0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 4 12:07:07 2019 -0800

    change the way this buffer is unpacked to work around potential alignment issues

Src/Particle/AMReX_ParticleContainerI.H

commit f1879e73ca322f3c72a23c359be561c5017ea522
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 4 11:47:01 2019 -0800

    fix template parameter for std::uninitialized_fill

Src/Base/AMReX_PODVector.H

commit 016edb79182f3981597724c563dd6b311ca84f19
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 4 09:51:51 2019 -0800

    missed return type

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H

commit 8acf1d3b97baf4f2dee3fedafae7b0ed153761d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 4 09:47:52 2019 -0800

    linear solver on gpu: change the default grid size for agglomeration and consolidation

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Tests/LinearSolvers/CellEB2/MyTest.H
Tests/LinearSolvers/NodeEB/MyTest.H

commit afb28f3d902ae16e15c922cfe53db314fb694158
Merge: 0c3cfbb4c e86805bee
Author: cgilet <cgilet@gmail.com>
Date:   Wed Dec 4 09:39:32 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit e86805beea3e1d09bc2e93ccb06c7b37028eced3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 3 17:04:15 2019 -0800

    NodeEB test: agglomeration and consolidation parameters

Tests/LinearSolvers/NodeEB/MyTest.cpp

commit 2880de7cb2482709c59a0a674e335e70bdb95f60
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 3 16:54:46 2019 -0800

    mod NodeEB test for scaling test

Tests/LinearSolvers/NodeEB/MyTest.H
Tests/LinearSolvers/NodeEB/MyTest.cpp
Tests/LinearSolvers/NodeEB/main.cpp

commit ed9c740342bff69954e79e050a0c9bf2f04f42db
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 3 16:30:18 2019 -0800

    this method needs to return an iterator

Src/Base/AMReX_PODVector.H

commit 92c737c94bb230e852fb8293c26eb142d7887c91
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 3 16:17:32 2019 -0800

    fix indentation

Src/Base/AMReX_PODVector.H

commit d76e2a71c45e4478bd4d35d9083d69f1fa80d62b
Merge: ab20bff27 aec1ba070
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 3 16:13:28 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ab20bff273cbd1d28b2717f3884d530d80e6eedd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 3 16:13:18 2019 -0800

    handle some shadowing and unused variable warnings

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleTransformation.H
Src/Particle/AMReX_ParticleUtil.H

commit 17de1cea0c18fdc836c69f63ac5adf3b3ff9d0eb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 3 16:12:42 2019 -0800

    handle some edge cases involving inserting into empty PODVectors

Src/Base/AMReX_PODVector.H

commit aec1ba070375a801590ab029eff6fbbbf8871729
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 3 18:16:38 2019 -0500

    CellEB2 test: parameters for agglomeration and consolidation

Tests/LinearSolvers/CellEB2/MyTest.H
Tests/LinearSolvers/CellEB2/MyTest.cpp

commit 3d53df8c07b084418bad586db497c2499b3c0e49
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 3 15:15:58 2019 -0800

    remove unused variable

Src/Particle/AMReX_DenseBins.H

commit 43239eea1ad23cac7e96b491b858ef8b71884ba2
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Dec 3 14:42:42 2019 -0800

    Remove the CPU version of AMREX_GPU_LAUNCH_HOST_DEVICE_LAMBDA_ASYNC. GPU version was previously removed.

Src/Base/AMReX_GpuLaunchMacrosC.H

commit 04f34c95324645378ec1ad0c6c7634bf0edfc584
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 3 13:43:52 2019 -0800

    fix pragma omp

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit a08d0de0d26a1125e1ee8fe3196e77cc4c773bfa
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Dec 3 13:44:05 2019 -0800

    Adjust inputs to allow HeatEquation to run without managed memory.

Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/inputs_3d

commit 96879dd6924d49d3bf38580830cf1a6ac5f8f580
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 3 13:43:52 2019 -0800

    fix pragma omp

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit f4ea453d505f8ae278c67f006b408d5a453871e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 3 13:10:54 2019 -0800

    missed amrex::

Tests/LinearSolvers/CellEB2/main.cpp

commit 8ef4edafd450638a41bdeaa4fb42bb0f672fe08b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 3 13:08:41 2019 -0800

    CellEB2: don't write plotfile if doing scaling test

Tests/LinearSolvers/CellEB2/main.cpp

commit df1b9893928903863c5a2959f7d227c8e6c82908
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 3 11:25:27 2019 -0800

    add some functions to MLMG for querying residuals, number of iterations, etc. after solve() is called.

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit b1858334d1ded409995878aa74067360ab8b393d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 3 08:00:32 2019 -0800

    FArrayBox::initVal: do it on gpu for non-NaN too

Src/Base/AMReX_FArrayBox.cpp

commit 32c796d6dce214a141c407cc9a58b508ff0710c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 21:23:40 2019 -0800

    FArrayBox: use = to initialize snan on gpu

Src/Base/AMReX_FArrayBox.cpp

commit e0114f2ee62e63054f4aad68a6092c68492205c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 21:22:30 2019 -0800

    add init_snan support for float

Src/Base/AMReX_MemPool.cpp

commit d27fe673248e8d44416d67733bb9b33be238cf01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 21:21:19 2019 -0800

    fix for single precision

Src/Base/AMReX_MultiFab.cpp

commit fb5c48a69968e5d578cf773996ee6c28e9f3f57f
Merge: 671c35810 cbf027fdc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 16:03:30 2019 -0800

    Merge branch 'weiqun/dev' into development

commit 671c3581078c2912ce8f301e00c7f8cbab4ffaad
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Dec 2 13:38:02 2019 -0800

    Move OMP offload flags into ibm.mak

Tools/GNUMake/comps/ibm.mak
Tools/GNUMake/sites/Make.olcf

commit cbf027fdcc005b7945aa137c6af4d14a93e66138
Merge: 076e8636d d6236fefb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 12:30:46 2019 -0800

    Merge branch 'development' into weiqun/dev

commit 0c3cfbb4c992b514d1b95a1727c1498b954e617e
Merge: 3807d29e8 8c7b00219
Author: cgilet <cgilet@gmail.com>
Date:   Mon Dec 2 15:12:32 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit d6236fefb76f1ac6b84e4f8fd6c741ac9701f45a
Merge: df66cfa92 8c7b00219
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 12:08:22 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 076e8636d96d96dd85648466d320bd1f709fc0f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 11:52:10 2019 -0800

    CellEB2 test on gpu

Tests/LinearSolvers/CellEB2/Make.package
Tests/LinearSolvers/CellEB2/MyTest.H
Tests/LinearSolvers/CellEB2/MyTest.cpp
Tests/LinearSolvers/CellEB2/MyTest_F.H
Tests/LinearSolvers/CellEB2/MyTest_K.H
Tests/LinearSolvers/CellEB2/mytest_f.F90

commit 8c7b00219eb14639f713ab9b95e48178d93363b5
Author: cgilet <cgilet@gmail.com>
Date:   Mon Dec 2 14:50:53 2019 -0500

    Minor changes in single_level_weighted_redistribute(): add assert, be consistent about not filling ghost cells for div_out

Src/EB/AMReX_EB_utils.cpp

commit 8d31d5656dd6400514e05f1b3c612939f29d1d32
Merge: ba991ed65 df66cfa92
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 11:21:54 2019 -0800

    Merge branch 'development' into weiqun/dev

commit df66cfa92fcb4c0246bccc744d0a8307ee1d4b2a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 10:03:21 2019 -0800

    move some functions used by EBLSCore into its own file

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtilI.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 3807d29e818628187abb7a5cd66d5f5438abf1a3
Author: cgilet <cgilet@gmail.com>
Date:   Mon Dec 2 11:45:09 2019 -0500

    Update single_level_weighted_redistribute()

Src/EB/AMReX_EB_utils.cpp

commit ca5c7f27ed03785c010b068c877678e3b2a1a494
Merge: 9d741714b a367b50a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 08:41:55 2019 -0800

    Merge branch 'master' into development

commit a367b50a1b4c7006fd7d49c52ee38eddf51a2713
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 08:41:05 2019 -0800

    update CHANGES

CHANGES

commit 7ec0e16e461804775fc0fb58c7e43ad1e7bf7101
Merge: 3966a58e8 9d741714b
Author: cgilet <cgilet@gmail.com>
Date:   Mon Dec 2 08:37:05 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 9d741714b7ec5fedca995bfebb33594be899e188
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Nov 30 17:37:08 2019 +0100

    remove amrex submodule, wrong repo

.gitmodules
amrex

commit 3bf5c62eb4e520c169302d29c944fa24e4e0fccc
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Nov 30 17:22:53 2019 +0100

    add amrex

.gitmodules
amrex

commit 0d099047335dff4000b23ababfca8a3c1bb0b36c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Nov 29 13:31:29 2019 -0800

    ParallelScan working, but extremely slow.

Src/Base/AMReX_Scan.H
Tutorials/GPU/ParallelScan/main.cpp

commit 85d04cc4aef7958e5239b2162c45004c674ee103
Merge: 7f7352a48 bbdf4cbf8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 27 21:05:32 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 7f7352a4879cc5b6fb565899fd4d820c52687982
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 27 21:04:47 2019 -0800

    BndryFunc: make RunOnGpu() and hasFabVersion() virtual

Src/Amr/AMReX_StateDescriptor.H

commit 3966a58e8f8e0d743e224debaffe0d04e4cf64fb
Merge: cb6ecf4d3 bbdf4cbf8
Author: cgilet <cgilet@gmail.com>
Date:   Wed Nov 27 21:54:33 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit bbdf4cbf8c2bec0a8afa610cfd3523a5ee60c6fb
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Nov 27 14:29:02 2019 -0800

    add missing header

Src/Base/AMReX_PODVector.H

commit b79af2bbc46cfc7db512381a04e68c750bc6782e
Merge: 284bf23b2 402a18d82
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Nov 27 12:06:57 2019 -0800

    Merge branch 'development' into amrex_mutex

commit cb6ecf4d3832fabec81ab45919987bdfafad5cb0
Merge: cf166df9c 402a18d82
Author: cgilet <cgilet@gmail.com>
Date:   Wed Nov 27 05:28:07 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 284bf23b2531c6b6cfdcf2ab090af193efbdebb7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 26 14:48:25 2019 -0800

    move the position of the __threadfence() to after the random states are updated

Src/Base/AMReX_Random.cpp

commit cfd809eaea06702cfe1f40488b0e0c463534a93b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 26 14:09:24 2019 -0800

    change the way that get_state and free_state are implemented

Src/Base/AMReX_Random.cpp

commit a2270d2abc178f3cc516f2d2ac729e5ceb1fa479
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 26 14:09:07 2019 -0800

    make the Test for random number generation harder to pass

Tests/GPU/RandomNumberGeneration/main.cpp

commit ba991ed659611ab11f97661674f6b05c622905d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 26 13:45:05 2019 -0800

    use BuildMask function

Src/EB/AMReX_EBMultiFabUtil.cpp

commit 23cde1ae45f48f57a6ae7062105ff5aab1476160
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 26 13:38:01 2019 -0800

    fix spaces

Src/Base/AMReX_Random.cpp

commit 402a18d82b7b6ab65a1c674a1689d0eea0d96001
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 26 13:26:21 2019 -0800

    to not break MCNodalLinOP

Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit c2244597d9c7548e6fbdfb784f5bec5d5c86d884
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 26 10:16:41 2019 -0800

    remove duplicated codes

Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 5be2ac0233bb5a7753786b5dcb914dd317e08f77
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 26 09:48:50 2019 -0800

    rework on nodal dirichlet mask

Src/Base/AMReX_FabArray.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 6ce3058684677eeeb6d82cfd1601eb9a45d47b94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 26 09:25:42 2019 -0800

    YAFluxRegister: use the new RecvLayoutMask

Src/Boundary/AMReX_YAFluxRegister.cpp

commit 5a57b6ed9719d6d030abda0e25d23f2ba2f8caf4
Merge: 8460a3415 12cfab736
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 26 08:48:27 2019 -0800

    Merge branch 'development' into weiqun/dev

commit 12cfab7369296acf4af36179c7345f75ba6b8ed7
Merge: 19ba2a8d0 73d2b9401
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Nov 26 08:46:55 2019 -0800

    Merge pull request #628 from AMReX-Codes/statedata_arena
    
    Explicitly specify which Arena StateData uses

commit 19ba2a8d08321c63c6e7fd534f3439d718092854
Merge: 47746185e 9251c9d97
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Nov 26 08:45:52 2019 -0800

    Merge pull request #627 from AMReX-Codes/multifab_swap
    
    Add a MultiFab operation that explicitly swaps dst/src data

commit 9251c9d97a375965d6beccf012fd416aacc0ff6c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Nov 26 00:04:39 2019 -0800

    Fix the ghost cell check

Src/Base/AMReX_MultiFab.cpp

commit 8678ba3d1bcbe0c6fc2d20a8d25aa280cd71415d
Merge: d074714ae 47746185e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Nov 25 23:52:25 2019 -0800

    Merge branch 'development' into multifab_swap

commit d074714ae6aea791ca692522a5f8df7e822fd214
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Nov 25 23:44:51 2019 -0800

    Take a shortcut in MultiFab::Swap() when we can

Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_MultiFab.cpp

commit fb7e38cbdb9e02908e40501f8623647d74376a11
Merge: b34875dc2 0981258a5
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Nov 25 17:55:19 2019 -0800

    Merge branch 'kngott/hip' of https://github.com/AMReX-Codes/amrex into kngott/hip

commit b34875dc252d7226bbc29e6d95029824271bf664
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Nov 25 17:54:58 2019 -0800

    Add the complex MPI support to HIP in Device::Initialize and cleanup Device::Finalize.

Src/Base/AMReX_GpuDevice.cpp

commit 8460a3415916f0f6366e394871534acec2f9afaa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 25 16:30:03 2019 -0800

    nodal solver: reimplement cc mask

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 47746185e3f595f344e63a461e8420a8e6f21ab4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 25 16:02:12 2019 -0800

    BL_ASSERT -> AMREX_ASSERT

Src/Particle/AMReX_LoadBalanceKD.cpp
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParGDB.H
Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_ParticleMPIUtil.cpp
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 06688de331e483f243c952c8ffdbd76b1e73dc39
Merge: 51bc72cca e05ad5ce8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 25 13:06:55 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 51bc72cca2bcd3a3b9e23b221c0636c4f1beb8b0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 25 13:06:46 2019 -0800

    an All-To-All communication pattern for comparison

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit fb398c02b770d4e35d4477f0d9bd79eb2f43b7f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 25 12:20:31 2019 -0800

    MLEBABecLap: build mask using existing function in FabArray

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit e05ad5ce882366bf84f08b6d421b2c75724efd2d
Merge: f564b616a a20981d9b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 25 14:56:41 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f564b616a9979cbe34216c02f03298ce673b365f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 25 14:56:25 2019 -0500

    pp.get -> pp.query

Tests/Particles/Redistribute/main.cpp

commit 9d4771d6eb5178193bafa7db8154a48986509dd2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 25 10:48:29 2019 -0800

    return Arena* instead of const Arena* so that it can be used

Src/Base/AMReX_FabArray.H

commit a20981d9b8e726d5cfcf3f49a88ede1a405c5938
Merge: 703d08002 44ef24b73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 25 10:43:24 2019 -0800

    Merge branch 'weiqun/dev' into development

commit 703d08002c7bf01bd6ff0c73680155dccaac2c97
Merge: 40d92017e adbdbbea7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 25 10:43:19 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 44ef24b7332bf84db4eb5bf52bfd982e27082f61
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 25 10:20:20 2019 -0800

    remove an incorrect assertion

Src/Base/AMReX_FBI.H

commit cf166df9c85034938c76d535a65d9d39f8a63b92
Merge: 7153bbab5 adbdbbea7
Author: cgilet <cgilet@gmail.com>
Date:   Mon Nov 25 13:16:31 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit adbdbbea7b5e003e9c1e3b6416aea57e49796a3c
Author: cgilet <cgilet@gmail.com>
Date:   Mon Nov 25 13:12:11 2019 -0500

    MLNodeLaplacian::compSyncResidualCoarse() - crse_cc_mask only needs 1 ghost cell; fix tests on the mask.

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 7153bbab5b090762807c9882a5c4b4d76e651801
Merge: 7fe7afd06 85c887fd0
Author: cgilet <cgilet@gmail.com>
Date:   Mon Nov 25 09:33:03 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 85c887fd05af26ac5ddc07d1bdf2c8313ac9ff1c
Author: cgilet <cgilet@gmail.com>
Date:   Mon Nov 25 09:30:27 2019 -0500

    MLNodeLaplacian::compSyncResidualCoarse() - crse_cc_mask needs 2 ghost cells.

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 7fe7afd06092d136c4f88a85f804ad93f7f1b8fc
Merge: d4b128271 c31722024
Author: cgilet <cgilet@gmail.com>
Date:   Mon Nov 25 09:08:25 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 73d2b940110dbf983ff4d43c3b3272dc512cf6c6
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Nov 24 14:18:03 2019 -0500

    Explicitly specify which Arena StateData uses

Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp

commit 7c896638f6ba8dca4bf64bafb1e7cb7238ec3c83
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Nov 24 14:14:59 2019 -0500

    Add a MultiFab operation that explicitly swaps dst/src data
    
    Also add this as an option for StateData

Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit 40d92017e9cdea0ebf50373ae8f81ec726777ce9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 23 07:41:02 2019 -0800

    fix new bug in 835565

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit c9e087e7d948cbfca05405a0db3a54c0d3830f7b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 23 07:25:36 2019 -0800

    remove unused variable

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 7a34007f5d7f3a1326a28b175cc10eae2679c006
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 22 19:18:01 2019 -0800

    around gcc bug

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit c31722024951c63a877ff5abf327ff0e38d12546
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 22 17:20:35 2019 -0800

    include lower offset

Src/Particle/AMReX_ParticleLocator.H

commit effb8018b516f95a3244dd4f312127bf7bc317a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 22 16:11:28 2019 -0800

    redo some box intersection stuff in MLMG

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit deae44d187790bdde6cd58c402a45287ca78e04e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 22 15:45:58 2019 -0800

    fix gpu compilation

Src/Boundary/AMReX_YAFluxRegister.cpp

commit 03f1edb987b26983f23d2ba48b11ef47aaea66c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 22 15:36:09 2019 -0800

    reimplement YAFluxRegister part 2

Src/Base/AMReX_MultiFabUtil.cpp
Src/Boundary/AMReX_YAFluxRegister.cpp

commit d0fd8cd7b5c01018a350bc3ca1905d09de34b1a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 22 15:20:39 2019 -0800

    use Reduce::AnyOf in nodal solver

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit b0218a665ae1f413a0a7993c8826ed2b60dcad4f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 22 15:14:14 2019 -0800

    reimplement YAFluxRegister part 1

Src/Boundary/AMReX_YAFluxRegister.cpp

commit c59189f93c9d8ce913458299624981234f9ba048
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 22 15:13:38 2019 -0800

    add Reduce::AnyOf

Src/Base/AMReX_Reduce.H

commit 3b56da9399822ec4d8712e08370ec0f21df8db44
Merge: 14b0943f3 8b91900c6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 22 14:52:40 2019 -0800

    Merge branch 'development' into dense_bins_locator

commit 8b91900c6b15083fd11a0180496809a34cbdb6a9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 22 14:05:46 2019 -0800

    change the function to return a bool instead of Aborting

Src/Base/AMReX_ParmParse.H
Src/Base/AMReX_ParmParse.cpp

commit d8c2be65721b269c0c68c49bfc997c516a1610eb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 22 13:36:45 2019 -0800

    add a function to abort if there are unused ParmParse entries

Src/Base/AMReX_ParmParse.H
Src/Base/AMReX_ParmParse.cpp

commit 14b0943f3bd3487bb021dd926a1025f637f42237
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 22 11:52:20 2019 -0800

    resuse DenseBins in the ParticleLocator

Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_ParticleLocator.H

commit db6fb71b044796e14a8be193d435fa964b509abe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 22 11:07:15 2019 -0800

    around gcc bug

Src/Base/AMReX_iMultiFab.cpp

commit 7696d7a5edba38eb1c7120f2fcf488409568f23e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 22 10:25:15 2019 -0800

    reimplement MultiMask define

Src/Boundary/AMReX_MultiMask.cpp

commit 517ec96b5238252aae266d908103b5ccedb36b91
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 22 10:24:51 2019 -0800

    minor change in Vector to use size_type

Src/Base/AMReX_Vector.H

commit 5133637c13b974137fc12bfb0c869a6cc2725431
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 22 09:41:26 2019 -0800

    don't use amrex:: namespace explicitly here for conciseness.

Src/Particle/AMReX_ParticleMesh.H
Src/Particle/AMReX_ParticleUtil.H

commit d66759dee059ac9c2d654b55b16adf3bfccc14aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 22 09:37:36 2019 -0800

    reimplement owner mask

Src/Base/AMReX_iMultiFab.cpp

commit d4b1282716ff02e0a0f828f7a55043741b672e1e
Merge: 556a6e733 9ce943f14
Author: cgilet <cgilet@gmail.com>
Date:   Fri Nov 22 10:23:57 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 9ce943f14108e599d74e98ad21f51c90c6535844
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 21 16:06:56 2019 -0800

    fix a new typo in launch macro

Src/Base/AMReX_GpuLaunchMacrosG.H

commit 1d9f80fb50aeb4244ae88fa1180e26e17d82a1fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 21 10:21:14 2019 -0800

    nodal solver: sync residual for RAP

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 0dd61542dfddad31c012ec8e5f3f817f10109a97
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 21 09:51:16 2019 -0800

    nodal solver: build grid stencil in case we need it for sync solve.

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit ca4cacb1108095f66cdc4a1fb38b53861736b73d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 21 14:37:02 2019 -0800

    enable these functions only for PC

Src/Base/AMReX_TypeTraits.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleMesh.H
Src/Particle/AMReX_ParticleReduce.H
Src/Particle/AMReX_ParticleUtil.H
Src/Particle/AMReX_Particles.H

commit 60ea2c4abf6aaa48cbc8840caea0dacf8aa8ecb4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 21 13:01:51 2019 -0800

    automatically set USE_PARTICLES=TRUE in Src/Particles/Make.package

Src/Particle/Make.package

commit 0b3ad546116dbbdf44809c4410280ec8be7de0b8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 21 13:01:27 2019 -0800

    add is_particle_iterator and is_particle_container type traits

Src/Base/AMReX_TypeTraits.H

commit 020c29ada3a102c38a076466e37bc197e9621f3a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 21 13:01:02 2019 -0800

    a version of numParticlesOutOfRange that operates only a single tile

Src/Particle/AMReX_ParticleUtil.H

commit 8f45dbed21480e2956779537f760f710e7243980
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 21 13:00:39 2019 -0800

    fix spaces

Src/Particle/AMReX_ParticleContainerI.H

commit 74d85764b83abc15d40b7e06ea1907ca5034980b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 21 13:00:21 2019 -0800

    move getTileIndex to .H file for inline

Src/Particle/AMReX_ParticleUtil.cpp

commit b743901c0ec9742fccdf3d6dba153e48a28731d8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 21 12:59:55 2019 -0800

    add a method allowing users to get a Geom from a ParIter

Src/Particle/AMReX_Particles.H

commit b4105608cd68b52ee47a09a2aa6a4ab6041e979b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 21 12:59:23 2019 -0800

    have the particle iterator store a reference to the parent particle container

Src/Particle/AMReX_ParIterI.H

commit e042dd9121d16ef984c57533d07c2a9377a987f3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 20 17:03:03 2019 -0800

    been doing my briefs wrong for Doxygen...

Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H
Src/Particle/AMReX_ParticleTransformation.H
Src/Particle/AMReX_ParticleUtil.H
Src/Particle/AMReX_Particles.H

commit f09ade54d24468c8618d011a083d68fed7fd9a1d
Merge: 794fd6764 46f8540f5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 20 16:53:15 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 794fd6764ee61f6815a7f01f13541b9b0c2f3529
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 20 16:53:06 2019 -0800

    docstrings for numOutOfRange

Src/Particle/AMReX_ParticleUtil.H

commit 46f8540f58f6a9edd74b62b69b301bad92d537b7
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Nov 20 16:48:15 2019 -0800

    EB redistribution: enable 2D support

Src/EB/AMReX_EB_utils.cpp

commit 556a6e73395781ca23711cb80e0e04e7d9ec5be5
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Nov 20 16:48:15 2019 -0800

    EB redistribution: enable 2D support

Src/EB/AMReX_EB_utils.cpp

commit c208e59906f8dd77a291c57c3249bfb271b3740c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 16:35:44 2019 -0800

    Add CITATION file for AMReX

CITATION

commit 66866e84696ba318e11eecaee2d70a1c6b12f5b1
Merge: c8cd756b9 69544d386
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 20 16:25:55 2019 -0800

    Merge branch 'weiqun/dev' into development

commit 69544d386895ace27698f3b9a1ea3868243ea474
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 20 16:25:40 2019 -0800

    nodal solver sync residual: WIP for RAP

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit c8cd756b95a1bab5a2a5410952e61de4c8486108
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 20 15:55:44 2019 -0800

    remove faulty assertion

Src/Particle/AMReX_DenseBins.H

commit 0981258a533748d3dd2486b8e87a94b07f5cb198
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Nov 20 16:03:34 2019 -0700

    Fix HIP FIX comments

Src/Base/AMReX_Extension.H
Src/Base/AMReX_FBI.H

commit 6e69ab50e5bf404ae58d157a2bb315b6c28d2090
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 20 14:45:54 2019 -0800

    SumBoundary: avoid self copy

Src/Base/AMReX_MultiFab.cpp

commit e9dcabb44a244db6d1fb80a9aa3bffb7aee320fa
Merge: e9171a15b 35ccdcbee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 20 12:52:53 2019 -0800

    Merge branch 'weiqun/dev' into development

commit 35ccdcbee0572d11575e9ecd12d01de1e63d8cea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 20 12:52:21 2019 -0800

    FArrayBox::initVal is back on gpu now

Src/Base/AMReX_FArrayBox.cpp

commit 5a8a07cfbcaf8eb1bd5be24324ced6fa3bea3de8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 20 12:46:56 2019 -0800

    make launch macros more robust

Src/Base/AMReX_GpuLaunchMacrosG.H

commit e9171a15b3dcdda56ca603a34d5071f864409a5b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 20 10:58:29 2019 -0800

    make aborting if not all found an option

Tools/Plotfile/fcompare.cpp

commit a26ae5d5fcbb258b2d324c2f89495b456f3c9efd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 20 10:32:55 2019 -0800

    have fcompare and particle_compare fail if the same variables are not present in the two plotfiles

Tools/Plotfile/fcompare.cpp
Tools/Postprocessing/C_Src/particle_compare.cpp

commit ffacacb1885af4798768289fcfecb7870030332c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 20 10:24:45 2019 -0800

    go back to using lower-case phi for the advection tutorials

Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Tutorials/Amr/Advection_F/Source/plotfile_mod.F90

commit 804cf006a44ed5f5177c89e815abe591d761726b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 20 09:55:09 2019 -0800

    fix function name that has changed

Src/Base/AMReX_FabArray.H

commit 200f7fe053fa4bb490a97c03be7a9d77e754c374
Merge: b1ef82f57 eca997a7a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 20 09:47:36 2019 -0800

    Merge branch 'development' into weiqun/dev

commit b1ef82f5784b073ca1f6dc162a374081c1128165
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 20 09:47:03 2019 -0800

    new makeFineMask that reuses parallel copy meta data

Src/Base/AMReX_FBI.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit eca997a7a9aba57ba58c3ef14b5254b4f34d6d5a
Merge: c300b8b62 3e4b549d1
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Nov 20 08:53:09 2019 -0800

    Merge pull request #584 from shashankNREL/SY/FixSplineIF
    
    Fixes to the spline IF routines

commit 3e4b549d14fb0717acd404d4803d34a7f3e6f990
Author: ShashankNREL <shashank.yellapantula@nrel.gov>
Date:   Wed Nov 20 08:28:11 2019 -0700

    Made changes to solve thomas based on Weiqun suggestions on PR

Src/EB/AMReX_distFcnElement.H
Src/EB/AMReX_distFcnElement.cpp

commit c300b8b627e0953438b2f94f07a7948bbbe397e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 19 16:33:56 2019 -0800

    comment out buggy code

Src/Base/AMReX_FArrayBox.cpp

commit 59d3a7172b4f0e30e934c152caf44776c8fc681f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 19 16:33:56 2019 -0800

    comment out buggy code

Src/Base/AMReX_FArrayBox.cpp

commit 6213a6a1d14e828707e2faad8dfdea78bea9ce7f
Merge: a4a80eea4 17a5e28d8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 19 14:16:09 2019 -0800

    Merge pull request #624 from ax3l/doc-exposeParticleTemplates
    
    Particles: Expose Template Arguments

commit 17a5e28d844d96d55b141191fefd7f9b776139ca
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Tue Nov 19 14:45:34 2019 -0700

    Particles: Expose Template Arguments
    
    In order to code more generically downstream in WarpX,
    let's expose the template arguments that make up a particle
    and particle container as public constexpr.

Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_Particles.H

commit 291c3d02bb77f3698f6f62c1aab88e7018e18be2
Merge: 34bd51eaa 426a9a102
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 19 12:45:10 2019 -0800

    Merge branch 'development' into weiqun/dev

commit a4a80eea4a0d09f11dedfed4e08699f27ae0f145
Merge: 172e9817f 617df7a81
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 12:15:42 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 172e9817f485bcbbf28f3d8f87fad71bd9e78d14
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 12:15:31 2019 -0800

    implement add / copy for particle container in a GPU friendly way

Src/Particle/AMReX_ParticleContainerI.H

commit 309778b59c32b1e8fef0bae7a14f2b58699031a1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 12:15:10 2019 -0800

    add copyParticles form of transformation

Src/Particle/AMReX_ParticleTransformation.H

commit 617df7a81fd6e3c0010b8bacab639b8bbe2b937b
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Nov 19 13:10:26 2019 -0700

    added option in libamrex configure script to specify cuda-arch (#623)
    
    * added option in libamrex configure script to specify cuda-arch
    
    * fixed strip() incompatibility

Tools/libamrex/configure.py

commit f91d915598ac97eb82d379998c42675c4121d9ff
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 11:43:01 2019 -0800

    fix some more spaces

Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_DenseBins.H

commit 426a9a1020ee553f7eae496bea6475f062182bfc
Merge: 2804fe608 f91d91559
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 19 11:41:44 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 40bea036c0b378de45e0366e4aaa9d9a6bc427b1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 11:41:41 2019 -0800

    fix some spaces

Src/Particle/AMReX_ParticleBufferMap.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit 2804fe608216f848a0c419aa5498bb44e45d6523
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 19 11:41:34 2019 -0800

    update assertion

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit 3d286b3a185b33b0260b04bb31d6a7789964b967
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 11:41:08 2019 -0800

    use rvalue references in MeshToParticle, ParticleToMesh

Src/Particle/AMReX_ParticleMesh.H

commit 565b78636c2ae279d3227f592f0b36cf1dfa3fb2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 11:36:51 2019 -0800

    also change the non-Gpu version of these typedefs

Src/Base/AMReX_GpuContainers.H

commit 3f9b95265cb5d05952e595a38824c6389a6100d3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 11:32:27 2019 -0800

    remove CUDA ifdef

Src/Particle/AMReX_ParticleContainerI.H

commit 8e1f943de6c0d0e1043b033468a9259debcd7113
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 11:32:07 2019 -0800

    EnforcePeriodicGPU -> EnforcePeriodic

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 7c08bfdbc2c7666b375860af0d929dbc19a932e3
Merge: 3fea03401 8cf5e3e55
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 11:23:23 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 3fea034012a49f5adf76312a211f0c44c8c65e1c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 11:23:12 2019 -0800

    update the docs re: thrust vectors

Docs/sphinx_documentation/source/GPU.rst

commit 34bd51eaa5f94be9f6342fd85980c53d1cf98a83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 19 11:17:10 2019 -0800

    reimplement gpu version of overlap mask

Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.cpp

commit d33d65f0ca359d6df7024590f311ecbd7a5d1e6f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 11:05:17 2019 -0800

    add some docstrings to the GpuContainers

Src/Base/AMReX_GpuContainers.H

commit 7b466a86a92361d5b3a3f0700175a047e4d79782
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 10:58:22 2019 -0800

    ManagedDeviceVector -> ManagedVector

Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_NeighborList.H
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleLocator.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_StructOfArrays.H
Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp

commit 5b81e97f901fc483134de46b73565f21f0ad22be
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 10:54:59 2019 -0800

    PinnedDeviceVector -> PinnedVector, same for Polymorphic

Src/Base/AMReX_GpuContainers.H
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_Particles.H

commit 8cf5e3e551c0b96465e4cd2477942e36fbc87dc5
Merge: 2329449c3 1f8510edc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 19 10:48:58 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2329449c304eac2ccc1bc82f017d52f9dbe16d8e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 19 10:35:02 2019 -0800

    init signaling nan on gpu in FArrayBox::initVal

Src/Base/AMReX_FArrayBox.cpp

commit 51d58914be6f47c029b406e340db355b912a33b1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 10:32:39 2019 -0800

    remove old thrust test

Tests/Particles/StructOfArrays/CudaManagedAllocator.H
Tests/Particles/StructOfArrays/GNUmakefile
Tests/Particles/StructOfArrays/Make.package
Tests/Particles/StructOfArrays/StructOfArrays.H
Tests/Particles/StructOfArrays/main.cpp

commit 1f8510edc1f548f9f1f3da23329548b13f393ae6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 19 10:29:06 2019 -0800

    fix typo

Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit c0aa96225927e5332ab2b3ee4f1eb16a38007760
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 10:24:09 2019 -0800

    remove unneeded thrust includes

Src/Base/AMReX_Vector.H
Src/Particle/AMReX_NeighborList.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_StructOfArrays.H

commit 35b5788a2ab20a8b47b04b4b642fc3fea8ad6873
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 19 10:24:01 2019 -0800

    fix typo

Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 4682052e4646f2a8c233d8a0903906d61d728a28
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 10:16:54 2019 -0800

    remove unused file / function

Src/Particle/AMReX_Functors.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 7b3ea980af0d2af1fb7be14d447a12ad70a7afa0
Merge: bd188d90e ad70bc1a3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 10:13:42 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit bd188d90e29e6b538b40e2359fdb16d08c044675
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 19 10:13:35 2019 -0800

    reuse copyParticle function in Redistribute

Src/Particle/AMReX_ParticleContainerI.H

commit ad70bc1a373dac10d8360c5ea7d7109f5f83608f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 19 09:44:48 2019 -0800

    rename myArena to arena

Src/Base/AMReX_FabArray.H

commit cd47aead73238c36c72dd3ebecc9b135411ed8b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 19 09:22:05 2019 -0800

    fix a couple issues with tiling and gpu

Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.H
Src/EB/AMReX_MultiCutFab.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 0f04f7571fbbb58598ebfefd1fc408549eee31d2
Merge: 545f19e6f 7c052f50a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 16:42:27 2019 -0800

    Merge branch 'development' into particle_transformation

commit 545f19e6f60d623cc06427a3d5772f23da8b5158
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 16:41:58 2019 -0800

    add some enable_if and decltype for maximum obfuscation

Src/Particle/AMReX_ParticleTransformation.H

commit 7c052f50a12213e47632c37ab91f5c3afa4fe885
Merge: eadec9400 9833b1491
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 18 15:58:39 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit eadec9400d496891c6624ee8853c1b3807f0181e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 18 15:58:29 2019 -0800

    fix corner case for EB tensor solver

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit faaf0492d96f111509f0bf472c83bbeede684a14
Merge: f7b7619a4 9833b1491
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 15:35:51 2019 -0800

    Merge branch 'development' into particle_transformation

commit 9833b14910984e7347471bf893b9a01a4fdac40c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 15:35:25 2019 -0800

    use forwarding references in AMReX_ParticleReduce.H

Src/Particle/AMReX_ParticleReduce.H

commit e9c4690512ee797f6b5ec4329eb4b08fb80dc379
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 18 13:14:25 2019 -0800

    add some LaunchSafeGuards

Src/AmrCore/AMReX_TagBox.cpp

commit f7b7619a4bbdc8e1342fd4c3c60d32f91ef0a4e2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 15:25:36 2019 -0800

    use std::forward

Src/Particle/AMReX_ParticleTransformation.H
Tests/Particles/ParticleTransformations/main.cpp

commit 2db29c377c9bf695dc6381274012b08ec120266d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 14:50:15 2019 -0800

    move all the transformation stuff to a separate file

Src/Particle/AMReX_ParticleTransformation.H
Src/Particle/AMReX_ParticleUtil.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 6f4a7b18a00766f301f06c6efae2e54c55d1edd1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 10:40:31 2019 -0800

    fix spaces

Src/Particle/AMReX_Particles.H

commit 103d46d04ce3b3de0885e8344393aedbcb9924b6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 13:47:10 2019 -0800

    fix and test filterAndTransform

Src/Particle/AMReX_ParticleUtil.H
Tests/Particles/ParticleTransformations/main.cpp

commit 42efed5618bdca62a6587cfb1a00f811ec5b5beb
Merge: fc90f3435 ebdfecc07
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 13:25:53 2019 -0800

    Merge branch 'development' into particle_transformation

commit fc90f3435cb942c246f2157f221462e3952d6219
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 13:25:27 2019 -0800

    make filter tests more strict

Tests/Particles/ParticleTransformations/main.cpp

commit 0aa3d2b5cf720d904b19d742e26a91659fa34c5e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 13:15:49 2019 -0800

    add assertion

Tests/Particles/ParticleTransformations/main.cpp

commit ced10b74d7f397878c2fe0e291f0193db4eba0cc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 13:13:24 2019 -0800

    fix name

Tests/Particles/ParticleTransformations/main.cpp

commit 15fb3b0b254574643abc998f75313882d811e811
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 13:11:52 2019 -0800

    fixes for filter

Src/Particle/AMReX_ParticleUtil.H
Tests/Particles/ParticleTransformations/main.cpp

commit 1f9ccd094ef7d0092f29e639f149d51b0588cefb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 12:52:42 2019 -0800

    some fixes for filter

Src/Particle/AMReX_ParticleUtil.H
Tests/Particles/ParticleTransformations/main.cpp

commit ebdfecc07100dcd2b4e4ff5121850781a9d79c50
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 18 12:08:32 2019 -0800

    add single precision compile test

Tests/SinglePrecision/GNUmakefile
Tests/SinglePrecision/Make.package
Tests/SinglePrecision/main.cpp
Tools/CompileTesting/compiletesting.py

commit e27ae203f37a91ca98bb129bd17f3810ae613b3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 18 11:10:38 2019 -0800

    remove BaseFab RunOn because it doesn't work and there is no nice ways to fix it

Src/Base/AMReX_BaseFab.H

commit 5772132bc7adff6ae31e5303fd06a0c551ed4f5e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 11:07:01 2019 -0800

    some refactoring of the transform test

Tests/Particles/ParticleTransformations/main.cpp

commit cceb8bc8528789c784f5084bdf85d5f6898f92a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 18 10:59:07 2019 -0800

    rm BaseFab::ForEach

Src/Base/AMReX_BaseFab.H
Tests/ThirdPartyLib/foo.cpp

commit 26ffdd176d181a1d281796157c17c2f68c57e3f2
Merge: 2ee205374 199c471ec
Author: cgilet <cgilet@gmail.com>
Date:   Mon Nov 18 13:50:20 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 4082fd24c8c5ef9038bf11410d68fc08580dd50f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 10:41:06 2019 -0800

    Stronger test of transformations

Tests/Particles/ParticleTransformations/main.cpp

commit 54ba9996aeb53e071dec6741d45926123f52e8f0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 10:40:31 2019 -0800

    fix spaces

Src/Particle/AMReX_Particles.H

commit f82ae3af6574beaa5df255e3638855c0dd7ee79a
Merge: 963e315f8 199c471ec
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 18 10:09:26 2019 -0800

    Merge branch 'development' into particle_transformation

commit 199c471ecdf0b6462944e964a8bf6d378ae67616
Merge: d1a5612db 6741c4fef
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Nov 18 08:32:48 2019 -0800

    Merge pull request #621 from ax3l/fix-warningFinal
    
    PhysBCFunct: Final Warning

commit 6741c4fef234f02cf2ae357bc63261e691b8b5db
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Mon Nov 18 00:34:27 2019 -0700

    PhysBCFunct: Final Warning
    
    Warning with Clang:
    ```
    ../amrex/Src/Base/AMReX_PhysBCFunct.H:112:42: warning: class with destructor marked 'final' cannot be inherited from [-Wfinal-dtor-non-final-class]
        virtual ~PhysBCFunctNoOp () override final {}
                                             ^
    ../amrex/Src/Base/AMReX_PhysBCFunct.H:106:7: note: mark 'amrex::PhysBCFunctNoOp' as 'final' to silence this warning
    class PhysBCFunctNoOp
    ```

Src/Base/AMReX_PhysBCFunct.H

commit d1a5612db842d5fe359f1c927b9d7a14e1c2bbfc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 17 18:37:36 2019 -0800

    rm deprecated Fortran files

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.H

commit bffa678da6142242707c8e4c0ce032d3f155fe19
Merge: aef2ba848 9b8c9bda4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 17 17:06:40 2019 -0800

    Merge branch 'development' into weiqun/dev

commit aef2ba8482c9d372c4d9958dd1a50b95e9cb071e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 17 17:04:28 2019 -0800

    nodal solver on gpu: reflux

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/Make.package

commit 5d351fc12a6217fb56c27e2834e0eaf4458b21c2
Merge: 6802ac494 9b8c9bda4
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Nov 15 16:27:29 2019 -0800

    Merge branch 'development' into kngott/hip

commit 9b8c9bda4aad606eb88eccb7efa2fa5a6ff75592
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Nov 15 16:26:13 2019 -0800

    Add access to the Arena used to build a FabArray through a BaseFab::DataAllocator.

Src/Base/AMReX_FabArray.H

commit f015477d515f51e6df0007840e8215d125c83a65
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 15 16:20:15 2019 -0800

    fix warning

Src/Base/AMReX_GpuContainers.H

commit eaeacfc09ffb664be2234db62371493294a37997
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 15 16:20:15 2019 -0800

    fix warning

Src/Base/AMReX_GpuContainers.H

commit af346a31507b3d52b3b6f5368ddd65cc01d16ba6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 15 15:25:57 2019 -0800

    nodal solver on gpu: coarse sync residual

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit c2d0484d369a59670c8b67a503b4d71ac527af70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 15 15:24:11 2019 -0800

    some very important spaces to me

Src/Base/AMReX_Random.H
Src/Base/AMReX_Random.cpp

commit 2898dbae3b8a526590b783c24b5a0a226c841e32
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Nov 15 14:06:19 2019 -0800

    Use Pinned Arena for plotting. Avoids unneeded memory movement.

Src/Base/AMReX_PlotFileUtil.cpp

commit da98b660f0fd911b80571aa2837c944d1158cddd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 15 13:48:49 2019 -0800

    need to include Base in makefile

Tools/Postprocessing/C_Src/GNUmakefile

commit dddbfa083e081c37c40a5be77666c819364cae92
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 15 13:46:33 2019 -0800

    remove debug print

Tools/Postprocessing/C_Src/particle_compare.cpp

commit 0c31231d00d4ee3283d48372ef229bc3a430ee15
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 15 13:45:05 2019 -0800

    fix some typos in fcompare.cpp

Tools/Plotfile/fcompare.cpp

commit 311a08be3c12be880f73ca3683cc49c66134963a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 15 13:44:41 2019 -0800

    make particle_compare respect a relative tolerance

Tools/Postprocessing/C_Src/particle_compare.cpp

commit 4e88756be2589fb75b85733a24c97b070544a8bc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 15 13:14:06 2019 -0800

    sort particle data by id and cpu before comparing

Tools/Postprocessing/C_Src/particle_compare.cpp

commit 6bc284af828f7621a0aa906e03aa3a3a3021e623
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 15 09:33:42 2019 -0800

    fix the number of components

Tutorials/LinearSolvers/NodalPoisson/MyTestPlotfile.cpp

commit 92201d5b002283d2cff1b0133306ecd2b7808304
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 15 09:24:55 2019 -0800

    fix variable names

Tutorials/LinearSolvers/NodalPoisson/MyTestPlotfile.cpp

commit da7daaa8abe563d4fe898796233652b90308884b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 15 08:52:01 2019 -0800

    remove some variables from plotfile for gpu regression test

Tests/LinearSolvers/NodeEB/MyTest.H
Tests/LinearSolvers/NodeEB/MyTest.cpp
Tutorials/LinearSolvers/NodalPoisson/MyTest.H
Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp
Tutorials/LinearSolvers/NodalPoisson/MyTestPlotfile.cpp

commit 6802ac494856033c7815d316d658d7253c47c069
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Nov 14 16:53:36 2019 -0800

    First draft for Pinned copy I/O HeatEquation. Need to store Arena and use same one throughout before it will work.

Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit 963e315f8428e6877b847707c731e2f711e16e46
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 16:38:16 2019 -0800

    AMREX_FOR_1D -> AMREX_HOST_DEVICE_FOR_1D, to respect launch region flag

Src/Particle/AMReX_ParticleUtil.H

commit df4306c313233fe13072558f46ca7299c58cc8f7
Merge: 9b7513829 83a2d3c71
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 14 16:31:11 2019 -0800

    Merge branch 'weiqun/dev' into development

commit dc3da0a8fd7adc622cc5fd3a809532d131dca7e6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 16:31:09 2019 -0800

    make the test abort on error

Tests/Particles/ParticleTransformations/main.cpp

commit 9b75138291d331af62f4dcf8e856d6e1ffbed562
Merge: 2d71d64bc 9eaf3876e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 14 16:31:04 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f5ffd51ba6c4d3cf054edb8265f002b84667d2ee
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 16:29:33 2019 -0800

    use forwarding references for function objects

Src/Particle/AMReX_ParticleUtil.H

commit 3d4a8f82ce4dbeb1e2a60875870a1f374b1668d3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 16:22:37 2019 -0800

    fix comment

Src/Particle/AMReX_ParticleUtil.H

commit 83a2d3c719eee984a9eae6279025329748859aeb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 14 15:54:07 2019 -0800

    fix index type

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 5323bd10ef988730194978e7157102b85150734e
Merge: 7b27ab9e4 9eaf3876e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 15:22:47 2019 -0800

    Merge branch 'development' into particle_transformation

commit 9eaf3876ebfef72c8899756a5db47e9002c4d30a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 15:20:04 2019 -0800

    add an additional debug assert

Src/Particle/AMReX_DenseBins.H

commit dabc585e676fc9da3e8daaff30f21c86a066328f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 15:19:28 2019 -0800

    use Gpu::copy instead of dtod_memcpy, which is a no-op on the CPU

Src/Particle/AMReX_DenseBins.H

commit 8ae492cd8a780d6bcfd1e9ea315b02a91a89c491
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 14 15:17:28 2019 -0800

    fix a warning on calling host function from host device function

Src/Base/AMReX_MultiFabUtil.cpp

commit 0702c0a73e5df3c51241c5669bbcfb4e9175e8c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 14 15:17:05 2019 -0800

    make Array4::operator bool host and device

Src/Base/AMReX_Array4.H

commit 2d71d64bcf37650ba57732c678dfdaf2fac93e5d
Merge: 81bedd553 4654a2f51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 14 15:10:04 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 81bedd55327aec139cf697bd07abe4c312c007fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 14 15:09:37 2019 -0800

    nodal solver on gpu: coarse residual

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 8cd0375fd9c4ba1a15e31db9776c9ab9bd84109e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 14 14:11:42 2019 -0800

    refactor makeFineMask for gpu

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 7b27ab9e40c11081b432b9473797ca2ff7e041c2
Merge: 49dd7cf53 4654a2f51
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 13:54:49 2019 -0800

    Merge branch 'development' into particle_transformation

commit 4654a2f51c4fc6f61c2cfce0da122f0b9283ef89
Merge: dd3bb608a 5fd80b1d4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 13:51:09 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit dd3bb608a30d97b5a5ad4f198950559ac6cfbf04
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 13:51:01 2019 -0800

    need to handle the cpu-only case in these functions

Src/Base/AMReX_GpuContainers.H

commit 49dd7cf53bc5618e54d4ff08a366c2672ba06d9a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 13:45:47 2019 -0800

    initial test for particle transformations

Src/Particle/AMReX_Particles.H
Tests/Particles/ParticleTransformations/GNUmakefile
Tests/Particles/ParticleTransformations/Make.package
Tests/Particles/ParticleTransformations/inputs
Tests/Particles/ParticleTransformations/main.cpp

commit 3e2dfdb8df7762d6be564ec6cf195e9f73741826
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 11:33:00 2019 -0800

    start adding some general particle transformation and filtering routines

Src/Particle/AMReX_ParticleUtil.H

commit 5fd80b1d4b702af2cd9edb53f52aba6467069eee
Merge: b4cb612c2 8e7f439da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 14 11:06:00 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b4cb612c21ba44b12278c29083212c5bfffcba30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 14 11:05:20 2019 -0800

    nodal solver on gpu: coarse contribution to divu

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit e6c2f2fec970924e8458c1ef10beb1b75f374c5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 14 11:04:23 2019 -0800

    add operator bool to Array4

Src/Base/AMReX_Array4.H

commit 8e7f439daaf18fecab63fcfb9181a9dd335402f8
Merge: 41e3b3a1e c9e098c04
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 10:34:25 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 41e3b3a1eb69ea16a4286e4ac3b339830f5b3368
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 10:34:16 2019 -0800

    remove over-zealous assertion

Src/Particle/AMReX_StructOfArrays.H

commit c9e098c04161b3c4046960616f61124b8b3f3482
Merge: f9042b21f fd1a6f393
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Nov 14 10:22:26 2019 -0800

    Merge pull request #619 from AMReX-Codes/amrex_copy
    
    Amrex copy

commit fd1a6f3931f10370903c5801dcdd364376be05ec
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 10:13:48 2019 -0800

    add static_assert for trivial copyability

Src/Base/AMReX_GpuContainers.H

commit 4f9538fdc97a0cb2e2d80b548e4763905a303c6d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 10:03:17 2019 -0800

    fix copy/paste error in docstring

Src/Base/AMReX_GpuContainers.H

commit ed5bdd6fb8a9f16ba2252a2ce91a81926c2a11b9
Merge: 5ba6091e6 f9042b21f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 10:01:44 2019 -0800

    Merge branch 'development' into amrex_copy

commit f9042b21f361ac8b84483503f2c286582ed1c92d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 14 09:59:45 2019 -0800

    the number of bins is actually m_offsets.size()-1

Src/Particle/AMReX_DenseBins.H

commit fa9c0a0505b295b3997b75ebdea441f89ac6c667
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 14 09:24:47 2019 -0800

    nodal solver on gpu: fine contribution to rhs

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 877c7550c0eafdc7a6e1ef5144aaf36a61d054db
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Nov 13 16:10:57 2019 -0800

    qFix AMREX_HIP_OR_CUDA in MemPool init.

Src/Base/AMReX_MemPool.cpp

commit 9978dbbe924ed95c37fe2b13254d6768242f4e91
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Nov 12 23:38:41 2019 -0800

    First MPI HIP adjustments (MPI is WIP -- Pretty much just turned on at this point).

Src/Base/AMReX_FBI.H
Src/Base/AMReX_FabArray.H
Tools/GNUMake/Make.defs

commit adbcbe66fa6b5b0c8765de5ede7cfe8932c22151
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 13 15:11:41 2019 -0800

    fix xsdk

Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_distFcnElement.cpp

commit 1a0aa3a1be60275839ad23e2bfb3ae88108325fa
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 13 14:36:45 2019 -0800

    same for the DenseBins structure

Src/Particle/AMReX_Particles.H

commit f342cf32506ff7a62ddf222db99678bb68e6b6a5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 13 14:35:42 2019 -0800

    need m_ptile_r whether compiling for GPU or not

Src/Particle/AMReX_Particles.H

commit 7510d847594d7640b4d5a362e05fb0b2d9ced3e9
Merge: b1e108950 645254833
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 13 14:27:05 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b1e1089505000596d17c0addca005641479e1c68
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 13 14:26:56 2019 -0800

    don't need this AMREX_USE_CUDA guard

Src/Particle/AMReX_ParticleContainerI.H

commit 02ad00e727c896d9f1889b6bdad5a03f1f61980a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 13 14:26:25 2019 -0800

    add inputs for test that bins particles by cell

Tests/Particles/Redistribute/inputs.rt.cuda.sort

commit 2ee20537459a679aada4606c4fc21a17100a683f
Merge: 4a7b3e28a 2bdf4365c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Nov 13 14:25:16 2019 -0800

    Merge branch 'ebtensor_flux' of https://github.com/AMReX-Codes/amrex into ebtensor_flux

commit 4a7b3e28ae359996ca04a04cc27c243a77adfc9c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Nov 13 14:24:18 2019 -0800

    Fix comp index when calling EB_set_covered in redistribution

Src/EB/AMReX_EB_utils.cpp

commit 6452548339e57052c1b17872aaba263a2b3c834a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Nov 13 14:24:18 2019 -0800

    Fix comp index when calling EB_set_covered in redistribution

Src/EB/AMReX_EB_utils.cpp

commit add72a8c1c8fd383b035fdde7e60b962333bf083
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 13 14:07:09 2019 -0800

    replace runtime_real with runtime_int here

Src/Particle/AMReX_ParticleUtil.H

commit 0abd1e5f73cc1eb0eae2ea4bf9249adb860ff1f1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 13 14:01:09 2019 -0800

    add some docstrings for copyParticle, gather, and scatter

Src/Particle/AMReX_ParticleUtil.H

commit 5ba6091e67694b9fd3a123958f2d253664d78c5c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 13 13:50:46 2019 -0800

    docstrings

Src/Base/AMReX_GpuContainers.H

commit 26e35d967ffb8e1e6f7196000961b5af731b46d3
Merge: 8ddbfbb5b 0014c0f3b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 13 13:31:07 2019 -0800

    Merge branch 'development' into amrex_copy

commit 8ddbfbb5b88cb622693687845cdc825747a97da2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 13 13:29:40 2019 -0800

    fix silly mistake uncovered by this PR

Tests/Particles/Redistribute/main.cpp

commit 0014c0f3b38c71f174035ac6477c7e8d81c80b05
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Nov 13 16:27:57 2019 -0500

    use new swap method of ParticleTile

Src/Particle/AMReX_ParticleContainerI.H

commit 2bdf4365c9dc80f30c61a9b589981e2331d11d6a
Author: cgilet <cgilet@gmail.com>
Date:   Wed Nov 13 16:06:07 2019 -0500

    MLEBTensorOp::compFlux abort if Location!=FaceCenter. Clean up.

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 292956d4060fd287f4ca33819d8b717ffcf95b5d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 13 12:50:13 2019 -0800

    add async versions

Src/Base/AMReX_GpuContainers.H

commit 96e14cc4d3841348cd19ce82e8a5dcbd17ce4f27
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 13 12:48:53 2019 -0800

    replace thrust_copy with amrex_copy

Docs/sphinx_documentation/source/GPU.rst
Src/Base/AMReX_GpuContainers.H
Src/Particle/AMReX_NeighborList.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_ParticleBufferMap.cpp
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_ParticleLocator.H
Tests/Particles/Intersection/main.cpp
Tests/Particles/NeighborParticles/MDParticleContainer.cpp
Tests/Particles/ParticleReduce/main.cpp
Tests/Particles/Redistribute/main.cpp
Tutorials/GPU/NeighborList/MDParticleContainer.cpp

commit e142267ca0b551d14963e5e287d0578a96ebb0f6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 13 10:22:26 2019 -0800

    thrust_copy is in the Gpu:: namespace

Tests/Particles/NeighborParticles/MDParticleContainer.cpp

commit d1b41388a9a857bf8ab1af801cd34cb660fe41f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 13 10:12:17 2019 -0800

    for eb nodal on gpu, do a Jacobi sweep before Gauss Seidel

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 8d083fcd65099663e387948dd662c8173becfcd1
Merge: 869fa0fac d6aa3a3a0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 12 17:24:07 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 869fa0fac0485b874c3f2072844f50994aaf9e35
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 12 17:23:18 2019 -0800

    clean up building this neighbor copy op and add a missing stream sync

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit cd00e125ce440408b62449d844495388f58f32ca
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 12 17:22:38 2019 -0800

    adjust size of counts so we don't have a weird +1

Src/Particle/AMReX_ParticleCommunication.H

commit 9749c7d3cb0e1d0fe8a6fe27b2e5c097191de1a8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 12 17:21:31 2019 -0800

    use 'size' here so these assertions will work when neighbor particles are in play

Src/Particle/AMReX_ParticleTile.H

commit 1ab692d865b4d56ce66580ad5144ca0e939acbfb
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Nov 12 16:56:20 2019 -0800

    More no-GPU fixes.

Src/Base/AMReX_IntVect.H
Src/Base/AMReX_Random.cpp

commit d6aa3a3a05debf5257c5b2ac1d54b621225ddeac
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 12 19:10:08 2019 -0500

    fix typo

Src/Particle/AMReX_ParticleUtil.H

commit c9d9831bf6e7fff10f3b7565fb7977c1c4dfd589
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Nov 12 15:15:50 2019 -0800

    Adjustments for no GPU builds.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuUtility.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MultiFabUtil_nd_C.H
Src/Base/AMReX_Random.cpp

commit f7aa3d44821d513284209a278d8db618ce3e436f
Merge: 873b9569f 1354f8369
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 12 18:09:43 2019 -0500

    fix merge conflict

commit 873b9569fa7ed24e52f1a5f115a41ffc5ac356a2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 12 18:06:58 2019 -0500

    update test

Tests/Particles/Redistribute/main.cpp

commit 361d6593646135dfee87cea509d88a49976490c6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 12 18:06:36 2019 -0500

    go ahead and implement scatter too, why not

Src/Particle/AMReX_ParticleUtil.H

commit 82e725e9932a54261d42a483fd959c3e9c0c9e60
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 12 18:02:07 2019 -0500

    implement gather in terms of a general copyParticle host / device function

Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_ParticleUtil.H

commit 42739fd37259444cbd65e32059a64f6a67d7621f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 12 17:02:26 2019 -0500

    a few missing helper routines for ParticleTile

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_StructOfArrays.H

commit 19f16695d337cd9fab1a69db7a6a522ca9026f41
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 12 16:49:19 2019 -0500

    implement our own gather particles routine, remove calls to the thrust one

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_ParticleUtil.H

commit 1354f83699e4b8c5ec3872dd524078dbced3359f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 12 12:54:53 2019 -0800

    add IntVect n_filled to FabArray to help users to keep track of how many ghost cells have been updated by FillBoundary ParallelCopy

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayCommI.H

commit eb7f6e98443a88259e7a8390c8c94eeb934c6b5c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 12 15:54:43 2019 -0500

    remove unused variables

Src/Particle/AMReX_ParticleContainerI.H

commit 8531b90fbba00dafeb136b29b6d23bac56143d67
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 12 15:48:57 2019 -0500

    reuse m_ptile_r for temp storage

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit ad519247fe0d19d7e0a52122f603ef1e52b265ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 12 12:26:52 2019 -0800

    nodal solver: smooth on gpu and do it twice

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit d6c97ff79435b6316d00d0fcf5f74d93740db626
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 12 10:17:00 2019 -0800

    nodal solver: build stencil on gpu

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 24f4f16d1f6176f8f8976f70140648cab655b54a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 12 09:38:54 2019 -0800

    removed more LaunchSafeGuards from nodal solver

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 262de7ff1db5a5fc8c07b6f2a7b25368cf9538de
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Nov 12 11:06:42 2019 -0800

    Revert to using long through __shfl_down overload.

Src/Base/AMReX_iMultiFab.cpp

commit 39395656f6b8a65d1bfb695dd6cc1d568decbde1
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Nov 12 11:06:16 2019 -0800

    Hipify thrust::cuda::par function.

Src/Base/AMReX_GpuAllocators.H

commit a5ad28c7c7c43d19721444956c3daf5d92fa51b8
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Nov 12 11:05:51 2019 -0800

    Turn <<<>>> into GPU safe macro.

Src/Base/AMReX_FBI.H

commit 1614d0d855474e3c7726d6f7fc649eb2f34103e9
Merge: d0535f0e9 6546855fc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 12 10:01:07 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d0535f0e9bfdb63624be835dd6e907b03c0e545c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 12 10:00:53 2019 -0800

    call should be to the free function, not to a member here

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 14ae49524fc5fa919c45ec8102ff561b1320b56e
Merge: 90d32fd9f 6546855fc
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Nov 11 21:10:52 2019 -0800

    Merge branch 'development' into kngott/hip

commit 6546855fcddf3b9919c9a2b8e3f0a3448bc6b319
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 11 20:44:20 2019 -0800

    fix using namespace Cuda

Src/Base/AMReX_Gpu.H

commit 83444e82b5bbe8525d970dd1faa34a4c7fe544d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 11 20:38:59 2019 -0800

    add array and const_array functions taking starting component to FabArray and BaseFab

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H

commit 90d32fd9f73475dbbc4bc3ba6f90072abb1ce74b
Merge: 1f0c76859 d0b1f05c7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Nov 11 17:57:46 2019 -0800

    Merge branch 'development' into kngott/hip

commit d0b1f05c7827feb1d32f243128491e9e3c51e567
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Nov 11 20:56:22 2019 -0500

    Change Cuda->Gpu in filenames and thrust/container/allocator calls throughout.

Docs/sphinx_documentation/source/GPU.rst
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuAllocators.H
Src/Base/AMReX_GpuAllocators.cpp
Src/Base/AMReX_GpuContainers.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_NeighborList.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_ParticleBufferMap.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_ParticleLocator.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_StructOfArrays.H
Tests/GPU/Locking/main.cpp
Tests/GPU/Partition/main.cpp
Tests/GPU/RandomNumberGeneration/main.cpp
Tests/Particles/NeighborParticles/MDParticleContainer.cpp
Tests/Particles/ParticleReduce/main.cpp
Tests/Particles/Redistribute/main.cpp
Tutorials/GPU/NeighborList/MDParticleContainer.cpp

commit 5304b59edf6f9fd2e3f0a14747a4531f83026646
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Nov 11 20:24:08 2019 -0500

    Convert CudaContainers and CudaAllocators to Gpu.

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaAllocators.cpp
Src/Base/AMReX_CudaContainers.H
Src/Particle/AMReX_ParticleContainerI.H
Tests/GPU/Partition/main.cpp
Tutorials/GPU/ParallelScan/main.cpp

commit 1f0c768594d161920278a6fd0be7bb1bb8431d3c
Merge: 83aad7d15 fd7eebec8
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Nov 11 17:19:20 2019 -0800

    Merge branch 'development' into kngott/hip

commit 8d0d202b121c288b9f0b6e880227fa97385e96c4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 11 19:43:49 2019 -0500

    optionally make this test do an extra particle sort step

Tests/Particles/Redistribute/inputs
Tests/Particles/Redistribute/main.cpp

commit fd7eebec8cea6bcfac770671cf2ccfefa13fb209
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 11 16:37:34 2019 -0800

    add an additional out-of-range check to neighbor list construction

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit feaf146272f1fbf5274c3f3c31644a82054aea32
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 11 16:27:48 2019 -0800

    removed some LaunchSafeGuards in MLNodeLaplacian

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit e6d7f48a40410eeaefde731c87edbe56c367e014
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 11 19:23:18 2019 -0500

    implement Sort in terms of DeviceBins

Src/Particle/AMReX_ParticleContainerI.H

commit 3849ff24f46e28f4a6654d8d86e910a164032202
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 11 19:22:48 2019 -0500

    remove some unused temporaries

Src/Particle/AMReX_Particles.H

commit 302fac0e453ea3cff83ffc08f99adeef6d89f976
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 11 19:22:25 2019 -0500

    thrust_copy -> dtod_memcpy

Src/Particle/AMReX_DenseBins.H

commit 1bb984f7e1505b28d54c310e4a9d44bfbea08626
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 11 19:21:34 2019 -0500

    have this resize run on the device when compiling with GPUs

Src/Base/AMReX_PODVector.H

commit 83aad7d1595dbae681f2fa2568611a0c19d0e641
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Nov 11 16:02:38 2019 -0800

    Couple small HIP things.

Src/Base/AMReX_Random.cpp
Src/Base/AMReX_Scan.H

commit 4abc1a4336364507da63ce29059b1ec9435de2ca
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Nov 11 16:02:05 2019 -0800

    Add long wrapper for shfl_down and label old HIP FIX problems.

Src/Base/AMReX_GpuUtility.H

commit 4ad5db250b6acb034343998310fc9cf0fc81c341
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Nov 11 16:01:27 2019 -0800

    Turn on all reductions and adjust for noexcept.

Tutorials/GPU/ParallelReduce/main.cpp

commit 4257c1119317179cada34e219a41efe466d14ffe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 11 15:45:00 2019 -0800

    forgot ifdef AMREX_USE_GPU

Src/Base/AMReX_FBI.H

commit 0f12b50c983a2c772a733da40b81eac69e86013d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 11 15:09:37 2019 -0800

    FabArray::BuildMask on gpu

Src/Amr/AMReX_Extrapolater.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/Base/AMReX_FBI.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp

commit ca8b5f51ae8a68eb7cd6aa3315e318aac9f9639e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Nov 11 16:39:42 2019 -0500

    Allow code to compile for either old or no-host builds

Src/Base/AMReX_filcc_mod.F90

commit def7c8df405e81fe35ff3d6d38c43649bc891382
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 11 15:33:20 2019 -0500

    begin refactor of SortParticlesByCell

Src/Particle/AMReX_ParticleContainerI.H

commit 9b67a19234ee686109a677b8f65701c09527d26f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 11 15:11:09 2019 -0500

    remove unnecessary thrust::reduce call in NeighborList::build

Src/Particle/AMReX_NeighborList.H

commit bdb04196fc0d140b9e48f9064436fbfd66ad54ec
Merge: c3736efdb d0463208a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 11 14:25:58 2019 -0500

    Merge branch 'runtime_soa' into development

commit c3736efdbabd2cd2623c4c62eb7c88191832e691
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 11 09:12:51 2019 -0800

    Fortran: add a new parallel copy routine that takes array for the number of ghost cells

Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 7759efad45eefcd62e1e08d84bb55de840800fa0
Merge: 0cc07bb72 3b7e7bd6a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Nov 11 08:37:45 2019 -0800

    Merge pull request #617 from AMReX-Codes/update_default_cuda_arch
    
    Update the default CUDA architecture to cc70 (Volta V100)

commit 0cc07bb72ce31345d44588ae759482b7ed302adb
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Nov 10 21:36:03 2019 -0800

    ifdef out CPU boundary fill functions for device-only pragma build

Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp
Src/Base/AMReX_filcc_mod.F90
Src/Base/Make.package

commit 56bd6ee8c2a41bfe76e7bb0e2a5f32077df2593f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Nov 10 21:28:41 2019 -0800

    Define a default value for a new make variable

Tools/GNUMake/Make.defs

commit 864ee51c1fbdd7f2f03ba9c0d04647132351eb3f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Nov 10 21:03:15 2019 -0800

    Add a define if we're using the no-host version

Tools/GNUMake/Make.defs

commit e76f21dd82b201c2e6a765653bce38fe9acedf8f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Nov 10 20:27:02 2019 -0800

    Add option for GPU pragmas to generate only a device version

Tools/F_scripts/gpu_fortran.py
Tools/F_scripts/write_cuda_headers.py
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 1729979c383d82e2bf90924ad5e7de770145734d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Nov 10 19:13:33 2019 -0800

    Implement amrex_fab_filcc without amrex_get_loop_bounds

Src/Base/AMReX_filcc_mod.F90

commit a4844541b6d5dd1125f33dd2c5ca913b7b44e2bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 9 16:50:32 2019 -0800

    add IntVect ghost cells version of some MultiFab functions including Saxpy

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit c46d782a93a93243e5b4f9e4d9cbbc92d5df3ac7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 9 07:25:00 2019 -0800

    Node solver: remove some LaunchSafeGuards

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 3b7e7bd6aacdaa9275b1f04891364b201cef11a2
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Nov 9 10:03:10 2019 -0500

    Update the default CUDA architecture to cc70 (Volta V100)

Tools/GNUMake/Make.defs

commit 23d8121760c7fdc0351c8ad35df0f5f65754c52c
Merge: d038f4814 adc2abd12
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 8 18:41:57 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d038f481493e587ca18b4b8bbf542591b301a4e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 8 18:41:45 2019 -0800

    fix unused variables

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit cf3d5b580180ec69c2b05eae518bd2354f35a6fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 8 16:21:40 2019 -0800

    nodal eb on gpu: 2d intergral

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit d0463208af26554155935bded24d090a925f3389
Merge: 1d15fc974 adc2abd12
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Nov 8 19:17:06 2019 -0500

    Merge branch 'development' into runtime_soa

commit adc2abd1254141795e6fca6d150927ddbfa2b63b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Nov 8 19:16:44 2019 -0500

    remove this execution policy for now

Src/Base/AMReX_CudaContainers.H

commit 1d15fc97493cc4f97ea790b4a117d353df86bada
Merge: 6eb85a13f f65e6c372
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Nov 8 19:05:35 2019 -0500

    Merge branch 'development' into runtime_soa

commit 6eb85a13f6af31a557329d4008edd47da7c3714e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Nov 8 19:05:00 2019 -0500

    add some AMREX_RESTRICT

Src/Particle/AMReX_ParticleTile.H

commit 5b02532a92ef19ac96b4ac317be68da074ad7bb5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Nov 8 18:51:44 2019 -0500

    need to include these changes to ParticleTile as well

Src/Particle/AMReX_ParticleTile.H

commit 17c86a7e6735b391aef59a1143988a9bf7eb1a42
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Nov 8 18:50:48 2019 -0500

    account for optional components in RedistributeGPU

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_Particles.H

commit 700b0d4a6c8d95b9ab01d6a966ae193ef6971350
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 8 15:32:38 2019 -0800

    eb nodal on gpu: rhcc

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 3de668cb03ad3004a506ee7ccc6a4cc8af45a4a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 8 15:02:31 2019 -0800

    fix new bug in eb nodal

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H

commit 266a9b691574bac1f5e30717853d34edad96f467
Author: cgilet <cgilet@gmail.com>
Date:   Fri Nov 8 18:09:12 2019 -0500

    For MLEBTensorOp::compFlux, fix cut cell flux bogus value for 2D

Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H

commit 91fe4c26b86c132a9022950a77d77006d3d4897c
Author: cgilet <cgilet@gmail.com>
Date:   Fri Nov 8 18:05:47 2019 -0500

    Fix MLEBTensorOp::compFlux

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit e3cd43b576135e357c6ba7c603b236a1768897d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 8 14:57:33 2019 -0800

    eb nodal on gpu: mknewu

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 17c537d0856ed5a4e1e168a23640f5b18c5bbe05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 8 13:49:02 2019 -0800

    eb nodal on gpu: divu

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit c20d672b1f743469e713b794d80575f61462119b
Author: Michael Rowan <mrowan137@gmail.com>
Date:   Fri Nov 8 12:30:38 2019 -0800

    Add CUPTI trace feature for GPU kernel timing

Src/Base/AMReX_ActivityTraceAsync.H
Src/Base/AMReX_ActivityTraceAsync.cpp
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp
Src/Base/Make.package
Tests/GPU/CuptiTest/Exec/CUDA/GNUmakefile
Tests/GPU/CuptiTest/Exec/CUDA/Make.package
Tests/GPU/CuptiTest/Exec/CUDA/myfunc.H
Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp
Tests/GPU/CuptiTest/Exec/CUDA/mykernel.H
Tests/GPU/CuptiTest/Make.CUPTI
Tests/GPU/CuptiTest/Source/Make.package
Tests/GPU/CuptiTest/Source/main.cpp
Tools/GNUMake/Make.defs
Tools/GNUMake/comps/nvcc.mak

commit a4beddd9b453702f3699d51293fbdb8fe65a4511
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Nov 8 13:37:59 2019 -0800

    Additional cleanup.

Src/Base/AMReX_GpuLaunchMacrosG.H
Src/Base/AMReX_Random.cpp
Src/Base/AMReX_iMultiFab.cpp

commit 71381ed2735f86c68fb70e322a66fe8877e047ed
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Nov 8 13:37:19 2019 -0800

    Clean up tests.

Tests/GPU/RandomNumberGeneration/GNUmakefile
Tests/GPU/RandomNumberGeneration/main.cpp
Tutorials/GPU/ParallelReduce/main.cpp

commit 44da881124ebf57cc4fb683714398e342a65d557
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Nov 8 13:12:45 2019 -0800

    Remove unneeded ifdef.

Src/Base/AMReX_CudaAllocators.H

commit 457925f1bdccae314ef9e6ea452671a456c18ce8
Merge: 3dd8e07fa f65e6c372
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Nov 8 13:08:42 2019 -0800

    Merge branch 'development' into kngott/hip

commit f65e6c3722840593384a144cee29b452d61ec714
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 8 13:08:54 2019 -0800

    remove unused CudaManagedAllocator

Src/Base/AMReX_CudaAllocators.H

commit 2d5b48b8f5a9e70f5122df068fcc6770275220fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 8 13:08:19 2019 -0800

    eb nodal on gpu: set stencil

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 3dd8e07faf40598abc099ceffb63ad1f06058860
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Nov 8 12:59:36 2019 -0800

    Turn ThrustAllocator on for HIP.

Src/Base/AMReX_CudaAllocators.H

commit 75a83db0f2a6365034eef6f509b3ea980f70bbb9
Merge: 25cd8720e e67e8531c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 8 12:51:23 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 25cd8720e5f84e4bc17788034ad265a8a8e24998
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 8 12:51:09 2019 -0800

    remove unused functors

Src/Particle/AMReX_Functors.H

commit 2764a17d510a7abb0c9257077c232f94119e8fcd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 8 12:47:14 2019 -0800

    be explicit about thrust::device execution policy

Src/Base/AMReX_CudaContainers.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Tutorials/GPU/ParallelReduce/main.cpp

commit c89b4558d74a795a99d03a4a4ce43b560965d0bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 8 11:35:52 2019 -0800

    eb nodal on gpu: set_connection

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit d7eb46ea9cd1e4dfb53e38a5cbb0c1e4605014f8
Merge: 65269c411 e67e8531c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Nov 8 11:33:25 2019 -0800

    Merge branch 'development' into kngott/hip

commit 951fcba866968e50de209312de006e8172b68ae2
Merge: debc51c90 84804b9fe
Author: cgilet <cgilet@gmail.com>
Date:   Fri Nov 8 13:40:08 2019 -0500

    Merge branch 'ebtensor_flux' of https://github.com/AMReX-Codes/amrex into ebtensor_flux

commit debc51c909c09d17a410042f8ede20fa46ba99ef
Merge: 30fdf7aa6 e67e8531c
Author: cgilet <cgilet@gmail.com>
Date:   Fri Nov 8 13:34:27 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit e67e8531ceaedfb9dde05bef9a5c83278046bbe4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 8 09:55:34 2019 -0800

    remove deprecated Fortran functions

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H

commit ec4aadad976d49af023a52a3806e291f53f267fc
Merge: 1967f01c5 4e1e6585e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 8 09:50:00 2019 -0800

    Merge branch 'development' into weiqun/dev

commit 1967f01c50f8e48d878d9e3781e004f6240a3c0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 7 13:48:27 2019 -0800

    mlndlap_stencil_rap on gpu

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit efc1eae6b722bea2a98642787118733725d9744d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 7 13:48:09 2019 -0800

    add Array1D, Array2D and Array3D

Src/Base/AMReX_Array.H

commit 4e1e6585e70fc713cd0143cbd3f5947a85544290
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Nov 7 16:35:17 2019 -0500

    Report numerical CUDA error

Src/Base/AMReX_GpuError.H

commit 28c7b7bd2c33f9b348dd74f44fa82496119820ab
Merge: c67b962e4 9cf789af8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 7 11:56:02 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c67b962e4b526485e818887c4e2ef9851ca65456
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 7 11:55:53 2019 -0800

    const versions of offsetsPtr and permutationPtr

Src/Particle/AMReX_DenseBins.H

commit 84804b9fe69ce20a15059e76569e7d525cde9518
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Nov 7 11:35:15 2019 -0800

    MacProjector: allow to set BCs on a per-level basis

Src/LinearSolvers/Projections/AMReX_MacProjector.H
Src/LinearSolvers/Projections/AMReX_MacProjector.cpp

commit 7a9540c7d83317f98ac8d6981b50d085b6fb1bbe
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Nov 6 15:51:17 2019 -0800

    NodalProjector: fix bug in definition of nodal grids

Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 9cf789af8d7884a8fafe69bc4a32a0528f7e469d
Merge: 3654520c5 0836a3c30
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Nov 7 11:35:21 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 3654520c5a2ae59a65d14e6751b76500daa41fa7
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Nov 7 11:35:15 2019 -0800

    MacProjector: allow to set BCs on a per-level basis

Src/LinearSolvers/Projections/AMReX_MacProjector.H
Src/LinearSolvers/Projections/AMReX_MacProjector.cpp

commit 0836a3c30997b7b01b0627dc75605a9d79f28abd
Merge: d7d52cded 9019a3f46
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Nov 6 16:46:26 2019 -0800

    Merge pull request #614 from AMReX-Codes/dense_bins
    
    Expose "dense bins" data structure so that WarpX can use it to implement binary collisions

commit 9019a3f467d71ec6a1b4e70cbdf9afcdf49a72f0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 6 16:40:33 2019 -0800

    add an extra entry to counts to avoid having +1/-1 below

Src/Particle/AMReX_DenseBins.H

commit 13e077fa6652e1dc3cdda80e0d6d8edffe6c0637
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 6 15:58:42 2019 -0800

    streamSynchronize at the end of DenseBins

Src/Particle/AMReX_DenseBins.H

commit dad8775c253104eea56b46fa2a93498a157835b8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 6 15:57:16 2019 -0800

    use AMREX_D_DECL for 2D

Src/Particle/AMReX_NeighborList.H

commit b6c88342ae4ec8216a94f96e82e509a40d6c5bb0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 6 15:56:12 2019 -0800

    add AMReX_BLProfiler.H

Src/Particle/AMReX_DenseBins.H

commit 643229d353b227a46d7b22ed76a9322401589023
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 6 15:55:12 2019 -0800

    make these types public

Src/Particle/AMReX_DenseBins.H

commit f253c166d5a18b4ec4bfc4a665a658f188ef62cc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 6 15:54:44 2019 -0800

    fix comment

Src/Particle/AMReX_DenseBins.H

commit 3b13a6d504c9dd08e4e8f960a394c03665074edd
Merge: 0c022635f d7d52cded
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 6 15:54:03 2019 -0800

    Merge branch 'development' into dense_bins

commit d7d52cded85ba1c0633da6c239741e85b53571bb
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Nov 6 15:51:17 2019 -0800

    NodalProjector: fix bug in definition of nodal grids

Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit f0a34d5b0335cedfe6d9e72e5438f72243d623b9
Merge: 0ef69cbe4 d7d52cded
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Nov 6 18:49:53 2019 -0500

    Merge branch 'development' into runtime_soa

commit 5de720f3901ca3732558994e84318a75df096c48
Merge: 9d5783807 64e56deba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 6 15:40:08 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9d57838074c1d8eafbcd1b3d5eba59f0eff25bee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 6 15:00:00 2019 -0800

    MLNodeTensorLap tutorial: use cg and increase bottom max iters

Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp
Tutorials/LinearSolvers/NodeTensorLap/MyTest.cpp

commit 65269c4113dbd6533c99afa266e7ea2d4e74d2d5
Merge: 3d130037e 64e56deba
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Nov 6 14:30:12 2019 -0800

    Merge branch 'development' into kngott/hip

commit 3d130037ea0f5c2db9100703cb625e9ba79d791b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Nov 6 14:29:49 2019 -0800

    Add rocprim and rocthrust header-only libraries.

Tools/GNUMake/comps/hip.mak

commit f878f382ae9eb5e7525919c5287f7d457e389be5
Merge: ad77d18a5 618a63e7b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Nov 6 14:29:01 2019 -0800

    Merge branch 'development' into kngott/hip

commit 64e56deba10cf91603108bdbf4c5cf386f217f70
Merge: 536d8c9ad 576c3ea11
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Nov 6 16:16:00 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 536d8c9ad88923d9fee22f46e90c9ed4d9a3951b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Nov 6 16:15:35 2019 -0500

    add missing device synchronize after packing buffer but before copying to pinned memory.

Src/Particle/AMReX_ParticleContainerI.H

commit 576c3ea11ebe184b7f9331bde23e766e815accbb
Merge: 180086142 18cb858b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 6 10:58:35 2019 -0800

    Merge branch 'nodal_tensor_poisson' into development

commit 18cb858b65e70ff3efc3ec6c93f1df30a0417e15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 5 16:14:42 2019 -0800

    MLNodeTensorLaplacian: hypre

Src/Extern/HYPRE/AMReX_HypreNodeLap.H
Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp
Tutorials/LinearSolvers/NodeTensorLap/GNUmakefile
Tutorials/LinearSolvers/NodeTensorLap/MyTest.H
Tutorials/LinearSolvers/NodeTensorLap/MyTest.cpp

commit 30fdf7aa686d34740395c22e10c6a1d8a3278398
Merge: 35c06bf03 180086142
Author: cgilet <cgilet@gmail.com>
Date:   Wed Nov 6 12:03:05 2019 -0500

    Merge remote-tracking branch 'origin/development' into ebtensor_flux

commit 1800861420b66bf933ec3a78f603c07445f576ef
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 5 15:40:45 2019 -0800

    fix oops

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 34bcab5abe9c24ff5631248c00746b655b554453
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 5 15:33:44 2019 -0800

    Need to call normalize on the tilebox not the full box.Z

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 0c022635f82a3704e4f29e5585c0d1b51e2d2856
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 5 15:30:57 2019 -0800

    Revert "start to implement particle locator in terms of DenseBins"
    
    This reverts commit e458866dee5e14b4c8033b50551f86d688c2561c.

Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_ParticleLocator.H

commit 170cf62b8bf8bd1ec0299a9a3adb91c9586557d7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 5 14:59:39 2019 -0800

    make sure we re-calculate the comm_size when enableInverse is toggled

Src/Particle/AMReX_NeighborParticles.H

commit e458866dee5e14b4c8033b50551f86d688c2561c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 5 14:26:11 2019 -0800

    start to implement particle locator in terms of DenseBins

Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_ParticleLocator.H

commit 45e243e2cfed6ee9ad03157034004f7cac3f2fa2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 5 13:49:19 2019 -0800

    expose dense bins data structure so it can be used to implement binary collisions in WarpX

Src/Particle/AMReX_DenseBins.H
Src/Particle/AMReX_NeighborList.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 36a55adb2dc5ab3bb1acbe3205287f44b113966e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 5 13:35:56 2019 -0800

    tutorial for Nodal Tenosr Laplacian solver

Tutorials/LinearSolvers/NodeTensorLap/GNUmakefile
Tutorials/LinearSolvers/NodeTensorLap/Make.package
Tutorials/LinearSolvers/NodeTensorLap/MyTest.H
Tutorials/LinearSolvers/NodeTensorLap/MyTest.cpp
Tutorials/LinearSolvers/NodeTensorLap/MyTestPlotfile.cpp
Tutorials/LinearSolvers/NodeTensorLap/main.cpp

commit e66b3c6eb820e50b3367dc2487299e9b6cd47b48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 5 13:02:49 2019 -0800

    MLNodeTensorLaplacian: 3d

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H

commit 0ef69cbe4459cb2c44f306f3911e2469a871be63
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 5 14:20:28 2019 -0500

    add some runtime components to the redistribute tests

Tests/Particles/Redistribute/inputs.rt.cuda
Tests/Particles/Redistribute/inputs.rt.cuda.mr
Tests/Particles/Redistribute/inputs.rt.cuda.nonperiodic

commit ca6b81f134f79d434bc7158b8a3d28cfb901a2cb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 5 14:13:56 2019 -0500

    also update the type of the snd/rcv buffers in neighbor particles

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit b71d3d07a52cb33520d3a2c163489d3c67371821
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 5 14:03:30 2019 -0500

    restore get/set superparticle, which is used in the reductions

Src/Particle/AMReX_ParticleTile.H

commit e24a99ef74844cf968d53e753b52660ed6a3aadf
Merge: a16f13b50 a0131d234
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Nov 5 10:52:19 2019 -0800

    Merge pull request #613 from dpgrote/fix_xlinker
    
    Mini PR: Fix XLinker option to allow spaces in directory names

commit 2f8c6417f8e45c3f93feaaea32bf58a8597db75c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Nov 5 13:40:45 2019 -0500

    add runtime components setting in the inputs files

Tests/Particles/Redistribute/inputs.rt
Tests/Particles/Redistribute/inputs.rt.cuda
Tests/Particles/Redistribute/inputs.rt.cuda.mr
Tests/Particles/Redistribute/inputs.rt.cuda.nonperiodic

commit 32f2dee4c42ee8c504d52262982b3ec39ce2a5ce
Author: Houjun Tang <htang4@lbl.gov>
Date:   Mon Nov 4 15:55:04 2019 -0800

    Change the HDF5 benchmark to use the new HDF5 write plot file implementation, fix a memory access issue for 1 level data.

Src/Base/AMReX_PlotFileUtil.cpp
Tests/HDF5Benchmark/GNUmakefile
Tests/HDF5Benchmark/Make.package
Tests/HDF5Benchmark/WritePlotfileHDF5.H
Tests/HDF5Benchmark/WritePlotfileHDF5.cpp
Tests/HDF5Benchmark/main.cpp

commit 527f997ccd7582f7d68fe204cd71b5e153b7d8ee
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 4 16:18:29 2019 -0500

    make the runtime comps 0 by default

Tests/Particles/Redistribute/inputs

commit a25a053f35355990bb1050f47f2214e9129fceb2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 4 16:17:40 2019 -0500

    parmparse the runtime components

Tests/Particles/Redistribute/inputs
Tests/Particles/Redistribute/main.cpp

commit 97ab3d810f24d26f1637345b7a6791b226f9502b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 4 16:09:34 2019 -0500

    setup redistribute test to use runtime components

Tests/Particles/Redistribute/main.cpp

commit ee5b013cf8743218a0c7749c9885bacf6a5bd6cf
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 4 16:07:54 2019 -0500

    set up particle tile data with runtime information on the fly

Src/Particle/AMReX_ParticleTile.H

commit d2352564a089eb74ce55ff72129f564d703bc0dd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 4 16:07:28 2019 -0500

    use ptile for temp storage in partition

Src/Particle/AMReX_ParticleContainerI.H

commit ed9189edaffed50f4153b505d7a3ce8c55312cec
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 4 16:05:57 2019 -0500

    also define and return in the local unpack

Src/Particle/AMReX_ParticleCommunication.H

commit 2c8301aa49132242fb5b274ab63704f1a00f32a7
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 4 16:04:31 2019 -0500

    make sure we set up the runtime components in the non-local unpack

Src/Particle/AMReX_ParticleCommunication.H

commit a16f13b50e2192effbed3646b52b9b1437233dc5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 4 12:52:22 2019 -0800

    If we leave in the Gpuable line, the garuda compiler complains (error) when
    DEBUG=TRUE

Src/EB/AMReX_EB2_IF_Polynomial.H

commit 87888a5b972e6aa7bc843cb9329f4aea35673cd8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 4 15:41:00 2019 -0500

    formatting fix

Src/Particle/AMReX_StructOfArrays.H

commit bd1bfe2132cd4cb4327220ac162a02c4fe799aff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 4 11:00:55 2019 -0800

    MLNodeTensorLaplacian: set sigma

Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp

commit 70c545c5bc726f374e41f4498a9808cf0b7393d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 4 10:48:56 2019 -0800

    MLNodeTensorLaplacian: 2d normalize

Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp

commit 98edd9dece2df1c9d0bb00577a10dfc1ea5d5d91
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 4 10:41:08 2019 -0800

    MLNodeTensorLaplacian: 2d Gauss Seidel

Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp

commit bb338a6ac8b51fc39c8e885f2939325c08868356
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 4 10:31:13 2019 -0800

    MLNodeTensorLaplacian: 2d A dot x

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp

commit a0131d234043ae24d2a0faf74a5441b18174d8af
Author: Dave Grote <grote1@llnl.gov>
Date:   Mon Nov 4 10:13:48 2019 -0800

    Fix XLinker option to allow spaces in direector names

Tools/GNUMake/Make.defs

commit 9f0d75505839daf8e83cdb38f14b2ad424a2829d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 4 08:52:55 2019 -0800

    MLNodeTensorLaplacian: move applyBC to MLNodeLinOp

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 27c5bba4373e1b26e4d8cef002037cb81a8c3fb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 1 16:00:42 2019 -0700

    MLNodeTensorLaplacian: WIP

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp
Src/LinearSolvers/MLMG/Make.package

commit 35c06bf0332fb6c64086b9e854ec71f6a1dab4d3
Merge: 1ef6fca59 578198f9a
Author: cgilet <cgilet@gmail.com>
Date:   Mon Nov 4 10:39:17 2019 -0500

    Merge remote-tracking branch 'upstream/development' into TensorFluxes

commit 578198f9a4bbfdea7ec4aadf22a488d95e184b3a
Merge: 49499fb36 cb5eb80e1
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Nov 1 14:08:57 2019 -0700

    Merge pull request #612 from AMReX-Codes/prefixsum-tutorial
    
    In PrefixSum tutorial, update exclusive sum using sorted grid IDs.

commit cb5eb80e1fcf2f5bee1ac03ff27348ecd0dde5e2
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Fri Nov 1 14:00:10 2019 -0700

    In PrefixSum tutorial, update exclusive sum using the previous sorted grid ID. Test with different values in each cell.

Tutorials/Basic/PrefixSum_MultiFab/Parallel-Prefix-Sum.ipynb
Tutorials/Basic/PrefixSum_MultiFab/main.cpp

commit d437f294345099f3878256a49153ae16ec511eea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 21 16:15:42 2019 -0700

    skeleton of MLNodeTensorLaplacian

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp
Src/LinearSolvers/MLMG/Make.package

commit 1f4dd92ee47ff60cf8cb86860040538fb0b93e2b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Nov 1 14:20:51 2019 -0400

    make this member protected

Src/Particle/AMReX_Particles.H

commit f97b5150f01c0903ba80e370282b52c5ebe87820
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Nov 1 13:38:57 2019 -0400

    remove setStream call included by mistake

Src/Particle/AMReX_ParticleCommunication.H

commit 9bf766c8b4401ae250b0579a6719972f4b4fa21a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Nov 1 13:37:42 2019 -0400

    include the runtime components in the initial partition

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 49499fb36839461460e53278a1d299a20d726c30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 1 07:54:09 2019 -0700

    update CHANGES

CHANGES

commit c08fd84d175e732fad855ead63a8a26c62b8b06c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 31 20:30:15 2019 -0700

    AmrCore::regrid: return if the base level is already the max level.

Src/AmrCore/AMReX_AmrCore.cpp

commit 69053281246a1a7a7b8c29865ab3eb02181541f5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 31 19:51:06 2019 -0400

    fix cpu compilation

Src/Particle/AMReX_ParticleTile.H

commit a29b64d78266cf06f973f389405d3d1d249ac4fd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 31 19:43:04 2019 -0400

    make the snd / rcv buffers char

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_Particles.H

commit 6791f57da69f78c5e47126914ecfb81af34e427a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Oct 31 15:37:30 2019 -0700

    NodalProjector: remove unused member variable

Src/LinearSolvers/Projections/AMReX_NodalProjector.H

commit ad77d18a5327b4b4e9e228ebf678c5f6d2776f3d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 31 15:19:23 2019 -0700

    Add libraries. cuRand and hipRand working!

Src/Base/AMReX_Random.cpp

commit a292fbc9fa2228e673c63fabfa50fe4c2ff7d3a0
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 31 15:17:03 2019 -0700

    More noexcepts.

Src/Base/AMReX_BaseFabUtility.H

commit cc0ae5a832e46febbf450963aed9ecd327802e8a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 31 15:16:42 2019 -0700

    Another failed initialization list. Good reproducer option?

Src/Base/AMReX_BaseFab.H

commit 17903fe1ea9208b0064fabc4c7e77751b76ead34
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 31 17:55:45 2019 -0400

    Generalize HIP path names.

Tools/GNUMake/comps/hip.mak

commit 425eaab9f76147489b4b62499d3fdd65f39a53d9
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 31 17:49:33 2019 -0400

    Features needed for HIPrand run on CUDA. Need to test on dogora.

Src/Base/AMReX.cpp
Src/Base/AMReX_Random.cpp
Tests/GPU/RandomNumberGeneration/main.cpp

commit 618a63e7b5632217153cb36e1a41037fb00b9735
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Oct 31 14:14:05 2019 -0700

    NodalProjector: add option to pass LPInfo to constructor

Src/LinearSolvers/Projections/AMReX_NodalProjector.H
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 1418f8ff9bd4715f25620734bfa52207d277944a
Merge: bcab86cfd f3918ed0a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 31 14:55:47 2019 -0400

    Merge branch 'development' into kngott/hip
    
    Conflicts:
            Src/Base/AMReX_BaseFab.H

commit f3918ed0ab51a9b028f881c125be16b2bf59a89a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Oct 30 12:46:51 2019 -0700

    NodalProjector: fix bug introduced with 2D support

Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit b3d16f1e7180f24a460bd45b31d754a842d61910
Merge: db3e5c354 6c398fa50
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Oct 30 10:48:02 2019 -0700

    Merge pull request #607 from AMReX-Codes/mf-prefix-sum
    
    Add MultiFab parallel prefix sum tutorial example.

commit db3e5c3544bcca8550505694997dd0d682fe3cec
Author: MaxThevenet <mthevenet@lbl.gov>
Date:   Wed Oct 30 10:34:39 2019 -0700

    Add one version of FillBoundary (#609)
    
    * FabArray::FillBoundary takes argument nghost, with default loop on comps
    
    * typo

Src/Base/AMReX_FabArray.H

commit c7410205e17b58b6f5143644d44f83d8fd036fb6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 30 09:27:35 2019 -0700

    add EBFArrayBoxFactory::isAllRegular

Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp

commit 1ef6fca59582021ec4a56d301936f9c904d6b6f1
Merge: 322c0eb2d da1008a45
Author: cgilet <cgilet@gmail.com>
Date:   Wed Oct 30 10:32:23 2019 -0400

    Merge remote-tracking branch 'upstream/development' into TensorFluxes

commit da1008a45489268a96fb6258b6f3de90cbe1b93a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 30 02:23:12 2019 -0400

    Set OpenACC stream to be the same as the CUDA stream

Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_acc_mod.F90

commit e225ebd553eb468e0e005024029d90d7ea69631e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 30 02:22:46 2019 -0400

    For OpenACC where CCOMP is not pgc++, still include openacc.h

Tools/GNUMake/comps/pgi.mak

commit f18c7ab911843b0c88f9268b5bda3ca084972516
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 29 20:17:49 2019 -0700

    fix a typo

Src/Base/AMReX_FabArrayUtility.H

commit 4f9fa55cc57fe2dea44dd966845a5f96483309a8
Merge: 304eea13d 076c54c88
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Oct 29 15:22:18 2019 -0700

    Merge pull request #610 from michaeljbrazell/mjb/reducesum_bug
    
    small bug fix for a three MultiFab ReduceSum

commit 304eea13dfca9d9861a41cde3ad8f3bae31553fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 29 15:15:23 2019 -0700

    remove stray #define thanks to Christoph Behrens

Src/Base/AMReX_REAL.H

commit 076c54c88f8558b27f7a0e3aad9948837dcd3f71
Author: michael brazell <michael.brazell@nrel.gov>
Date:   Tue Oct 29 15:11:52 2019 -0700

    small bug fix for a three MultiFab ReduceSum

Src/Base/AMReX_FabArrayUtility.H

commit 0c19db118f07a13837a89f803cdd8993aaceef8e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Oct 29 17:23:19 2019 -0400

    Add peak at OLCF

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.olcf

commit 24b3bfc82c524540c3d06d966c5d33a037929d73
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Oct 28 18:06:00 2019 -0700

    NodalProjector: print diagnostics only if verbosity is enabled

Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 43a2a5fbdbf2d1b1c3544f196a1fdd97133605e5
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Oct 28 18:02:41 2019 -0700

    NodalProjector: replace unique_ptr with standard pointers

Src/LinearSolvers/Projections/AMReX_NodalProjector.H
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 8d32cab030fd0e75679d2325ea245f18ade9ae03
Author: cgilet <cgilet@gmail.com>
Date:   Mon Oct 28 13:24:00 2019 -0400

    Make NodalProjector::define 2D compatable.

Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 3da080f072bdf2c370f4beb4defd2c188a14662c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Oct 28 09:49:21 2019 -0700

    Remove debugging print

Src/AmrCore/AMReX_AmrMesh.cpp

commit 322c0eb2d89f1d08dd62588fbaa8a1c08b76807a
Merge: 83485022b ceceb9a50
Author: cgilet <cgilet@gmail.com>
Date:   Mon Oct 28 09:44:42 2019 -0400

    Merge remote-tracking branch 'upstream/development' into TensorFluxes

commit ceceb9a502b471531169628bcdd284a53dbb6eb0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Oct 27 19:13:21 2019 -0700

    Only include PTX output from PGI if verbose

Tools/GNUMake/comps/pgi.mak

commit d0f236faf3b401512273a1baf4564e79d6220393
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Oct 27 01:12:13 2019 -0700

    Revert "Only define __device__, etc. if using CUDA or HIP"
    
    This reverts commit 6a4ac2da0486642432cb0962e972b6e00ac82ec7.

Src/Base/AMReX_GpuQualifiers.H

commit 6a4ac2da0486642432cb0962e972b6e00ac82ec7
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Oct 27 00:34:55 2019 -0700

    Only define __device__, etc. if using CUDA or HIP

Src/Base/AMReX_GpuQualifiers.H

commit 9b83f379cc4eed9bbde51a303b50b9035c65b517
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 26 07:08:34 2019 -0700

    put NodalProjector into namespace amrex

Src/LinearSolvers/Projections/AMReX_NodalProjector.H
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit 0b31494d14e3cefb02144847dbed8b07cad65d92
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 25 21:22:55 2019 -0700

    In error message, tell people how to get around blocking_factor not power of 2 error.

Src/AmrCore/AMReX_AmrMesh.cpp

commit 83485022b270c0f38eab5f938fbc6c8a3e5ecde3
Merge: 0db095b07 eceb952c2
Author: cgilet <cgilet@gmail.com>
Date:   Fri Oct 25 22:10:28 2019 -0400

    Merge remote-tracking branch 'upstream/development' into TensorFluxes

commit eceb952c25975a301e39d8ec04b578f2fd046570
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 25 18:45:47 2019 -0700

    Add documentation about:
    1) blocking_factor must be power of 2
    2) using n_error_buf to make larger grids.

Docs/sphinx_documentation/source/GridCreation.rst
Docs/sphinx_documentation/source/InputsLoadBalancing.rst

commit c0e7ef80d8c23f402086a42ba7e2520b977e45a9
Merge: 640d5f2ff c93afa00f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 25 18:22:19 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 640d5f2ff9cd81531683c07db46157434c2a632b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 25 18:20:09 2019 -0700

    Enforce in AmrCore (as in Amr) that blocking_factor must be a multiple of 2.

Src/AmrCore/AMReX_AmrMesh.cpp

commit bcab86cfdca1ec4623d8553908de074dc0dc98ae
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 25 16:56:13 2019 -0700

    Go back to managed Vector.

Src/Base/AMReX_CudaContainers.H

commit fed10ea40913b4a1f2a1f5b0e7525a25cc9be8fa
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 25 16:15:38 2019 -0700

    More Random Number Generator Updates

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaContainers.H
Src/Base/AMReX_Random.cpp
Tests/GPU/RandomNumberGeneration/main.cpp

commit 6c398fa5053147d00e6ef780f99cb5934a6ced22
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Fri Oct 25 16:09:04 2019 -0700

    Add MultiFab parallel prefix sum tutorial example.

Tutorials/Basic/PrefixSum_MultiFab/GNUmakefile
Tutorials/Basic/PrefixSum_MultiFab/Make.package
Tutorials/Basic/PrefixSum_MultiFab/Parallel-Prefix-Sum.ipynb
Tutorials/Basic/PrefixSum_MultiFab/README.md
Tutorials/Basic/PrefixSum_MultiFab/inputs
Tutorials/Basic/PrefixSum_MultiFab/main.cpp

commit c93afa00fc5f738a947797f76b10827a571ffcdb
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Oct 25 15:35:39 2019 -0700

    NodalProjector: check grid type of arguments of computeRHS

Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit fe5c740b7e36276eaf44c9b4415f5dcc86b531c1
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 25 14:31:09 2019 -0700

    1st attempt: Random without MemcpyToSymbol

Src/Base/AMReX_Random.cpp

commit 9ed64c6f80c6046b3edd6efbe7d84058c362e523
Merge: 8e3065264 d450ed75b
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Oct 25 13:06:13 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8e30652644b4da0d13a4c46346f6d1b5bbb0d785
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Oct 25 13:06:06 2019 -0700

    NodalProjector: pass arguments to compRHS in correct order

Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit d450ed75b321c1eb5864d9f66cb8fdf3651e9766
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 25 12:40:52 2019 -0700

    add AmrMesh function to return level number given domain box

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit 17d46c51cab330fb509b24e91ad71978343b99d0
Merge: 1a0eccc45 b3e3634b6
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Oct 25 12:36:11 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 1a0eccc45183d3a9ede2ba338f1169e1b5cd75c4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Oct 25 12:36:04 2019 -0700

    NodalProjector: add non-EB version

Src/LinearSolvers/Projections/AMReX_NodalProjector.H
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp

commit b3e3634b6923f4b73fff22aa34f3fb75f06be74f
Merge: 1f29ec3e7 d6c4da885
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Oct 25 12:29:56 2019 -0700

    Merge pull request #606 from houjun/development
    
    Add support to write plotfile in HDF5 format

commit 0db095b075e89782cb1bcb2c5e0f36218c6b1e4b
Author: cgilet <cgilet@gmail.com>
Date:   Fri Oct 25 14:57:45 2019 -0400

    WIP - add EBTensorOp::compFlux() with restriction that cut cell fluxes are not set to a bogus value

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 389d3bc747ed08f5b77c4a7c037c9952ab7e0a29
Merge: cfa446f16 3166d72cd
Author: cgilet <cgilet@gmail.com>
Date:   Fri Oct 25 14:45:36 2019 -0400

    Merge branch 'TensorFluxes' of https://github.com/cgilet/amrex into TensorFluxes

commit 3166d72cda824f3e71c92c1960a3bd45a8036be2
Merge: bbc4f7a9c 1f29ec3e7
Author: cgilet <cgilet@gmail.com>
Date:   Fri Oct 25 14:42:00 2019 -0400

    Merge remote-tracking branch 'upstream/development' into TensorFluxes

commit d6c4da88594762386a9dec1b146ed864887760a6
Author: Houjun Tang <htang4@lbl.gov>
Date:   Fri Oct 25 09:40:29 2019 -0700

    Add support to write plotfile in HDF5 format

Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_PlotFileUtil.cpp

commit 1f29ec3e72ad70e8419ad313deb9aee89e18f83f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 24 22:30:00 2019 -0700

    Add NodalProjector class to amrex/Src/LinearSolvers/Projections

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/Projections/AMReX_NodalProjector.H
Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp
Src/LinearSolvers/Projections/Make.package

commit 947a8184ba9bc2940b622f9ef6ec617b1dc31886
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 24 17:18:19 2019 -0700

    Simplify the abort fix.

Src/Base/AMReX_Machine.cpp

commit f35c6dcbecb5ed4a00abd30b7a49822fc40d79cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 24 12:24:53 2019 -0700

    Reduce* for FabArray can now take lambda working on Array4.  bug fix and optimization in the new EB functions added to MulitFab. tidy.

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_REAL.H

commit 11bc438ee0d020f4bc192ee85d63a301ca7d6df4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 24 11:00:45 2019 -0700

    add AMREX_REAL_MIN, AMREX_REAL_MAX and AMREX_REAL_LOWEST for convenice.

Src/Base/AMReX_REAL.H

commit cd6766f5e19d3d8cd1cfe8eb0792903b4ab4466d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 23 15:54:19 2019 -0700

    rm AMREX_PRAGMA_SIMD for reduce loops

Src/Base/AMReX_Reduce.H

commit 7ad5295c98efb6129696c3fcf7c3005f0db1a95d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 23 15:53:02 2019 -0700

    make launch functions macros safe with empty boxes

Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuLaunchMacrosG.H
Src/Base/AMReX_GpuRange.H

commit 1225ca4501ae6661450f6d025fa907a1fd9f987e
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Oct 24 04:44:39 2019 -0700

    make sure dummy_mf gets updated

Src/Particle/AMReX_ParticleContainerI.H

commit 1c78b9e29505e3b0a7de9ef667f3ce6ecd883e95
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 23 16:45:47 2019 -0700

    Fix make system and get rpath working.

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/hip.mak

commit 34730233cc485025db069b569a133290843f6522
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 23 16:45:02 2019 -0700

    More NOEXCEPTs

Src/Base/AMReX_GpuLaunch.H

commit 0afd4913bec953469430da049f16e76a3ea1e059
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 23 16:44:50 2019 -0700

    Get rid of memcpy_to_symbol.

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_Random.cpp

commit c9e8e93580b00e53c1e1e44ce9c327787bb1d025
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 23 16:44:26 2019 -0700

    AMREX_NOEXCEPT and additional initialization lists.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Extension.H

commit 08dabb4520ec581b8ce8ad0f6c3433243505c8a0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 23 19:19:23 2019 -0400

    nghsot -> nghost

Src/Base/AMReX_FabArray.H

commit b83c2ba6a3475d33771dd6e2a8d7f63205e72ec5
Merge: 4b6ed005c 3f5686191
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 23 18:17:17 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4b6ed005cbb5e4f82e7ae57effda1699efceda79
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 23 18:16:42 2019 -0400

    add missing Gpu::Device::synchronize() to InitFromBinaryFile

Src/Particle/AMReX_ParticleInit.H

commit 3f5686191a34292eb54dd4d01acd078f094d02d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 23 14:47:09 2019 -0700

    remove FabView from BaseFab

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFabUtility.H
Src/Boundary/AMReX_Mask.H
Src/EB/AMReX_EB2_GeometryShop.H
Tests/Vectorization/kc.H
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H

commit 0112718e1335cbd9d62b57c6f63b36fceb2d37fe
Merge: 2720d6166 78141f059
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 23 16:13:44 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2720d616673fcef38a8e32429e053df27f706b49
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 23 16:13:23 2019 -0400

    when deciding if a particle stays or not, we must also consider the case that particles have been added to the correct grids, not NOT on the correct procs

Src/Particle/AMReX_ParticleBufferMap.H
Src/Particle/AMReX_ParticleBufferMap.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit 78141f05958a4da13cf4c2b8a37f2fdd1701ab5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 23 12:24:30 2019 -0700

    fix some warnings

Src/Base/AMReX_GpuLaunch.H
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tests/LinearSolvers/EBTensor/MyTest.cpp
Tests/LinearSolvers/EBTensor/MyTest_K.H

commit fba7ef82b36ccb9f23d11c554fe89173425b2174
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 23 11:19:46 2019 -0700

    rm unused file

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H
Src/LinearSolvers/MLMG/Make.package

commit 699d0ad4b2d5e9f5cfe8acd9a51067a028cea70d
Merge: a21a523ff f84a3d070
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Oct 23 12:09:09 2019 -0700

    Merge pull request #604 from kcdodd/development
    
    Change MPI_Frotran to MPI_Fortran

commit f84a3d0703e03e4f1b3871cac747fff2dcf2d1a2
Author: Carter Dodd <cdodd@nanohmics.com>
Date:   Wed Oct 23 13:44:03 2019 -0500

    Change MPI_Frotran to MPI_Fortran

Src/F_Interfaces/CMakeLists.txt

commit d9f6d38f83e6117d2732be24f069945c13a048bc
Merge: 3185f92a0 a21a523ff
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 23 11:43:35 2019 -0700

    Merge branch 'development' into kngott/hip

commit a21a523ffe01852445d53a130b2996f8d2abf9da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 23 11:01:26 2019 -0700

    Replace AMREX_IS_D_LAMBDA with armex::IsDeviceLambda. This will fix a template parameter deduction issue.

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_TypeTraits.H

commit aa5a26b0835c89432b5189baa54b8e062b822e86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 23 10:23:23 2019 -0700

    missed a return

Src/Base/AMReX_FabArrayUtility.H

commit 787bbca0b38d8243ace4f7e5f7f3f1c2c7a976fd
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 23 07:18:56 2019 -0700

    Avoid race conditions in reduction code called multiple times
    
    cuda-memcheck --tool racecheck reported race conditions in this code
    if we called the block reduction multiple times in a kernel, since some
    warps in the first reduction could be reading from shared memory at the
    same time as other warps in the second reduction were writing to it. By
    inserting a syncthreads prior to the first write to shared memory, we
    avoid this (at some performance cost for the cases where we only call
    the reduction once in a kernel).

Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_fort_mod.F90

commit cfa446f16f480ae896eacfeefc68a41d84b6218b
Merge: bb7c600ad 14af20e6e
Author: cgilet <cgilet@gmail.com>
Date:   Wed Oct 23 09:48:50 2019 -0400

    Merge remote-tracking branch 'upstream/development' into TensorFluxes

commit 3185f92a09f2e5eda84344f84ca885077a7f3326
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 22 15:31:42 2019 -0700

    Label std::abort() HIP FIX.

Src/Base/AMReX_Machine.cpp

commit 931b56945f602c0561b2d9b2233e322ee9b98391
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 22 15:30:37 2019 -0700

    Saving before noexcept attempt.

Src/Base/AMReX_GpuQualifiers.H
Tools/GNUMake/Make.defs
Tools/GNUMake/comps/hip.mak

commit 14af20e6e2d581168dd0ac3633cc2b8c7f75285b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Oct 22 12:32:31 2019 -0400

    Reorder to work around XL compiler bug

Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 27e948b3857e197c7286e994562dc479415624f3
Merge: 7efd37fe1 11ba3b2f0
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 22 09:17:45 2019 -0700

    Merge branch 'development' into kngott/hip

commit 11ba3b2f03b5984d59e96190252e6dec8f932893
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 22 12:14:43 2019 -0400

    Temporary fix for std::abort in HIP. This allows AMReX to compile with HIP on Summit.

Src/Base/AMReX_Machine.cpp

commit fb0e97e05671be9bbc97d383b54a0c29112d6247
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 22 12:14:06 2019 -0400

    Fix HIP error messages in cudaGraphs.

Src/Base/AMReX_CudaGraph.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuError.H
Src/Base/AMReX_GpuQualifiers.H
Tools/GNUMake/Make.defs

commit 6d9b602b95eb7bea13ef4403bf9b285f3b46a2d7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 22 12:10:59 2019 -0400

    Update HIP calls.

Src/Base/AMReX_Arena.cpp

commit 91231d76804febc09430c84a3d32da8c84193757
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 21 18:14:31 2019 -0700

    Fix redistribute so it doesn't assume we start at component 0.

Src/EB/AMReX_EB_utils.cpp

commit 650c786783d4dc6f35a2915b218c37c84e2a0c44
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 21 17:29:40 2019 -0700

    Fix compilation of AMReX_EB_utils.cpp in 2D.

Src/EB/AMReX_EB_utils.H
Src/EB/AMReX_EB_utils.cpp

commit 8a684e0e778dbcea17bade2ec2b90cede32c856d
Merge: 676372b6b 444110075
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 21 16:18:29 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 676372b6b87c257da5612110eba592ea1a253841
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 21 16:18:16 2019 -0700

    Oops -- accidentally committed the un-weighted version.

Src/EB/AMReX_EB_utils.cpp

commit 4441100757ca8c4ad73e78e2ab39b9ab580e8f4f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 21 16:17:06 2019 -0700

    BaseFab::linComb missed default template parameter

Src/Base/AMReX_BaseFab.H

commit f6bf1ed8dd9f0f08a7fd6df675ab960472327a9b
Merge: 4707fe9c0 90cc50bf5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 21 15:43:20 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 4707fe9c0d6c045e855196326e120526a7735c00
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 21 15:43:02 2019 -0700

    Move single-level redistribution code from incflo to amrex/Src/EB.

Src/EB/AMReX_EB_utils.H
Src/EB/AMReX_EB_utils.cpp

commit 7efd37fe14407bd7f0158eddd61a344f0dcb5e92
Merge: d9e066238 90cc50bf5
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 21 12:09:25 2019 -0700

    qMerge branch 'development' into kngott/hip

commit d9e06623821b6f62516635fedfa7ad9c2483fe47
Merge: 7395fe32d 7910f2c0d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 21 12:08:50 2019 -0700

    Merge branch 'development' into kngott/hip

commit 90cc50bf5ddaf09913399afb08a0e8a0dc6f3589
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 21 10:01:55 2019 -0700

    InterpBndryData: make sure index is within bound for 2d refratio=4 case

Src/Boundary/AMReX_InterpBndryData_2D_K.H

commit bb7c600ad0ef478b94987107c4d5f270676da0dd
Merge: cd2e17c69 aa7d9ab55
Author: cgilet <cgilet@gmail.com>
Date:   Mon Oct 21 10:59:48 2019 -0400

    Merge remote-tracking branch 'upstream/development' into TensorFluxes

commit cd2e17c69b98554c28202c061696174608e3edf6
Merge: c50605a08 b8062c23f
Author: cgilet <cgilet@gmail.com>
Date:   Mon Oct 21 10:56:53 2019 -0400

    Merge branch 'development' into TensorFluxes

commit aa7d9ab55e6c22ae763473a3f3f55e63d72a74de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 20 18:31:08 2019 -0700

    add std::

Src/AmrCore/AMReX_Cluster.cpp
Src/Base/AMReX_RealBox.H
Tools/C_util/Statistics/ComputeAmrDataStat.cpp

commit 1809d8e4b01465fc772bd1bacb1bab89c2a4220f
Merge: 1561d1bef 897c23cf4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 20 17:17:23 2019 -0700

    Merge branch 'fix_tensor_corner' into development

commit 897c23cf481fde33c475c7ce6d1f099c82b69019
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 20 15:38:11 2019 -0700

    Merge branch 'development' into fix_tensor_corner

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_Derive.H
Src/Amr/AMReX_Derive.cpp
Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_Array.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_ParmParse.cpp
Src/EB/AMReX_EB2_2D_C.cpp
Src/EB/AMReX_EB2_3D_C.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_Particles.H
Tutorials/Basic/HelloWorld_C/main.cpp

commit 1561d1bef30b61efb67cf0e117bc55d8fd368d51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 20 15:24:55 2019 -0700

    make set_eb_data gpu host device function

Src/EB/AMReX_EB2_2D_C.cpp
Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EB2_C.H

commit 72b3b3c49df895bd9c88b0fe5908e4e1831c1051
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 20 15:13:47 2019 -0700

    MLMG tensor: cleanup

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit d3d340418751e4104718721e10a92afeb4a225e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 20 14:19:49 2019 -0700

    MLMG: fill corners for 3d tensor

Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit e52b6ac455a67d25b301a16fe43a0647df9f86d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 20 12:09:56 2019 -0700

    MLMG: fill edges for 3d tensor

Src/Boundary/AMReX_InterpBndryData_1D_K.H
Src/Boundary/AMReX_InterpBndryData_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit f5b6c6684e54a1524822d670a5a54b0c74ee6783
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Oct 19 19:49:30 2019 -0700

    We had "abs" rather than "std::abs" in two lines in one of the RAP interpolation routines --
    turns out that plain abs turns 5.1 into 5 and 0.51 into 0 ... not what was intended!

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H

commit 5d87b172c806f67f00bb33da7262c2a6b65579a8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Oct 19 15:18:14 2019 -0700

    When we set cells to covered because vfrac < small_volfrac, we must
    also make sure that any originally Regular cells touching them get
    relabeled to SingleValued and their EB-related data must be set correctly.

Src/EB/AMReX_EB2_2D_C.cpp
Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EB2_C.H

commit 72d868566cf69ddc681336f3d6166b0759147d0f
Merge: 88c271ccb e7f3bc7a2
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Fri Oct 18 15:24:31 2019 -0700

    Merge pull request #600 from AMReX-Codes/feature_nd_Pele
    
    Feature nd pele/IAMR

commit 4ac343d99ecfc7b9edd04efba7b3667b9c2677f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 18 14:37:29 2019 -0700

    WIP: MLMGBndry/InterpBndry in 2d fills corners too

Src/Amr/AMReX_AmrLevel.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_InterpBndryData_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H

commit 88c271ccbbe8cf7d2cba4930b57162579682d015
Merge: 7910f2c0d da3d8a7a7
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Oct 18 10:11:46 2019 -0700

    Merge pull request #601 from AMReX-Codes/abort_on_unused_inputs
    
    Abort on unused inputs

commit da3d8a7a7c0d1a26f3d6ce96642d2b1abd4ccb21
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 18 09:51:12 2019 -0700

    Add option to abort at the end of the run if unused variables are in the ParmParse table, instead of exiting cleanly.

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_ParmParse.cpp

commit e7f3bc7a2234c2626045276ac18c22be56dd0820
Merge: 8afad8778 7910f2c0d
Author: Lucas Esclapez <lesclapez@lbl.gov>
Date:   Thu Oct 17 18:49:04 2019 -0700

    Merge branch 'development' into feature_nd_Pele

commit 8afad8778e06905620b48837fdf7387136a7a57b
Author: Lucas Esclapez <lesclapez@lbl.gov>
Date:   Thu Oct 17 18:47:46 2019 -0700

    [Feature_nd_Pele] Missing change for 3D bc function in some amr level derive
    call.

Src/Amr/AMReX_AmrLevel.cpp

commit 7910f2c0d91599637e288a9df7a72bc34a8e3711
Merge: 6084bfdf5 cf0e26e47
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 17 16:24:59 2019 -0700

    Merge branch 'weiqun/dev' into development

commit 6084bfdf5534ea6299f0f91cb56c801eb9d66100
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 17 15:38:29 2019 -0700

    fix typo

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 67d827661ce297f0add206f2ef1767c8df3376c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 17 15:33:51 2019 -0700

    tensor 2d: test for true corner

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H

commit aee576ce33a91ee0170ec4f6282679d697fdf8d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 17 14:16:39 2019 -0700

    use amrex::coarsen for int coarsening

Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H

commit 0d7695c7797317c7a7946e787f51271787816b38
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 17 14:03:42 2019 -0700

    replace hardwired numbers with enum

Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H

commit ab49a459eba522753ef8d00615c34ca56a6c37ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 17 13:52:44 2019 -0700

    add new file to gnu make and cmake systems

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/Make.package

commit aadb6b06c7d1c2563c93232eeacd5b22bae2bc14
Merge: 4c13f8451 db48d4a2a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 17 12:36:57 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4c13f84516fe403d99767beff9c9d1ffe3ce8350
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 17 12:36:34 2019 -0700

    fix typo

Src/Particle/AMReX_Particles.H

commit 9cc63d98accb1a123c0ee330151f21713d3412b9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 17 12:35:02 2019 -0700

    ba -> BoxArray

Src/Particle/AMReX_Particles.H

commit 6ed6abac847c77ab8d73edc85ee444f120f31897
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 17 12:34:29 2019 -0700

    fix typo

Src/Particle/AMReX_Particles.H

commit 386361c0c5a6cfa901eba2d4edab05f1d6ca76a0
Merge: dc847f5c9 b662a3537
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 17 12:20:27 2019 -0700

    Merge branch 'development' into pr-598

commit db48d4a2a233525c920b2888c9055d215555d16c
Merge: b662a3537 c0772b10c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Oct 17 12:16:44 2019 -0700

    Merge pull request #599 from lucafedeli88/enable_range_based_loops_for_GpuArray
    
    added begin() and end() to GpuArray

commit cf0e26e47dcd1c967aa273ce9d27a84915f6f140
Merge: c95915afc b662a3537
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 17 12:15:51 2019 -0700

    Merge branch 'development' into weiqun/dev

commit b662a35372753507aa91ed5145852b82a60cbef1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 17 12:15:30 2019 -0700

    fix some makefiles for the MacProjector change

GNUmakefile.in
Tutorials/EB/MacProj/GNUmakefile
Tutorials/LinearSolvers/MAC_Projection_EB/GNUmakefile

commit c95915afcdc9bf942d93d05e11e62c7ef9d10d84
Merge: 31c12f445 bf9de17e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 17 11:25:08 2019 -0700

    Merge branch 'development' into weiqun/dev

commit 31c12f445a4c628be38453d1fcc090767ba55e3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 16 14:47:25 2019 -0700

    add RunOn to more BaseFab functions

Src/Base/AMReX_BaseFab.H

commit bf9de17e399625b99c0b42fe4dfdd9943dd697e2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 17 10:06:57 2019 -0700

    Move MacProjector* out of LinearSolvers/MLMG into LinearSolvers/Projections.

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/Make.package
Src/LinearSolvers/Projections/AMReX_MacProjector.H
Src/LinearSolvers/Projections/AMReX_MacProjector.cpp
Src/LinearSolvers/Projections/Make.package

commit c0772b10cf74fca5166e522c1a1d8a81cd65b4a4
Author: Luca Fedeli <luca.fedeli@cea.fr>
Date:   Thu Oct 17 10:06:06 2019 +0200

    added begin() and end() to GpuArray

Src/Base/AMReX_Array.H

commit dc847f5c977396fe340f95bf54ebfcdc261f5bc9
Author: cgilet <cgilet@gmail.com>
Date:   Thu Oct 17 00:27:59 2019 -0400

    Add updated mltensor_fill_corners().

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit 98c52f8fb69699c15daf5bcfff44883b72b8c820
Merge: 5fa313e45 9690689fa
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 16 16:23:32 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5fa313e453baa76f08f60268f82cafa0e73f9d28
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 16 16:23:23 2019 -0700

    fix compilation of electrostatic pic tutorial

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H

commit 9690689fa4532a67c26792c1c4d512150846e6eb
Merge: 086630371 57996077a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 16 14:18:24 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 086630371c606429a2f8d9dbfe0068397ec86e3d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 16 14:18:03 2019 -0400

    fix intersection test

Tests/Particles/Intersection/main.cpp

commit c50605a08e5d4ab0e1d9219bc1ff091c2fa20f52
Merge: bbc4f7a9c afcd33c5c
Author: cgilet <cgilet@gmail.com>
Date:   Wed Oct 16 13:29:25 2019 -0400

    Merge remote-tracking branch 'origin/mltensor_corner_fill_fix' into TensorFluxes

commit afcd33c5c9b12a5d77a3ef38d6b8f7f740ead614
Author: cgilet <cgilet@gmail.com>
Date:   Wed Oct 16 13:11:10 2019 -0400

    More clean up.

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H

commit d00e12dadb33cf71bf298b5c2e48ee3a41bcf838
Author: cgilet <cgilet@gmail.com>
Date:   Wed Oct 16 12:58:37 2019 -0400

    Clean up.

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H

commit 67e73856f94a38f64007abad335223041f98593b
Author: cgilet <cgilet@gmail.com>
Date:   Wed Oct 16 11:37:29 2019 -0400

    Add missing colon. Remove debugging

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 2641dbffd358ccbf0397901d5ce893474135a594
Merge: 327e78007 57996077a
Author: cgilet <cgilet@gmail.com>
Date:   Wed Oct 16 10:28:55 2019 -0400

    Merge remote-tracking branch 'upstream/development' into mltensor_corner_fill_fix

commit 57996077ac4bbb3a92ecd9f55aba904bcb8337cd
Merge: a67269b23 8ed96c134
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Oct 15 16:07:41 2019 -0700

    Merge pull request #595 from AMReX-Codes/doc_Paraview
    
    [Docs] Update Paraview section with new implementations of Paraview 5.7.

commit a67269b2320d5f15e99a5484c852f7868405a832
Merge: 0e3326b74 239ad64e8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 15 14:41:44 2019 -0700

    Merge pull request #594 from AMReX-Codes/jmsexton/particle
    
    host_device enforcePeriodic matching cpu version, fab setVal -> multifab setVal

commit 0e3326b744d62cfccdab29421ff6e54004c6fe67
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Oct 15 14:18:43 2019 -0700

    Fix grammar

Src/Base/AMReX_GpuDevice.cpp

commit 8ed96c1341ecef220290ff43cffd203936cdca70
Author: Lucas Esclapez <lesclapez@lbl.gov>
Date:   Tue Oct 15 12:33:07 2019 -0700

    [Docs] Update Paraview section with new implementations of Paraview 5.7.

Docs/sphinx_documentation/source/Visualization.rst

commit 0868f803c6899b654a1d62c8f56609fd72f90344
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 15 09:41:59 2019 -0700

    use abspath for rpath

Tools/GNUMake/Make.defs

commit 32af3a7fcc0504c2a6bdd8c8ffe00eeeef55f4b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 15 09:30:33 2019 -0700

    add -L when USE_RPATH

Tools/GNUMake/Make.defs

commit 9d6279e524fe8dd8d697da529d03f33e7b894662
Merge: e7e4c2035 d87808595
Author: Lucas Esclapez <lesclapez@lbl.gov>
Date:   Mon Oct 14 17:52:40 2019 -0700

    Merge branch 'development' into feature_nd_Pele

commit d87808595694873f23e06b5c8eba9105b22c7c1c
Merge: 3406baeab 2aa0af167
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Oct 14 16:03:59 2019 -0700

    Merge pull request #592 from DUGKS/dugks-dev
    
    add mathematical boundary types : HOEXTRAPLI

commit 3406baeab81829224af2eea4117ebc5911b70469
Merge: b52b03c3b cba673a69
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Oct 14 15:39:58 2019 -0700

    Merge pull request #593 from AMReX-Codes/convergence_tool
    
    Convergence tool

commit b52b03c3bf3b23f5cba7fb622965e702f289ae11
Merge: 048060feb 8056fe61a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Oct 14 15:33:11 2019 -0700

    Merge pull request #590 from ax3l/topic-rpathSupport
    
    Linker: Use RPath

commit 8056fe61af8dc3c9cae558e7b1f022f26bfa7b8f
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Oct 10 11:13:55 2019 -0400

    USE_RPATH: Do not yet enable by default
    
    Let's test this for a period of time on volunteering downstream
    projects (WarpX, Castro, ...?).

Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/GNUMake/Make.defs

commit 048060febe0f2377032ee7debc23d3153f3f9d1e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 14 14:53:16 2019 -0700

    More Reduce functions can now take a device lambda.

Src/Base/AMReX_FabArrayUtility.H
Tutorials/GPU/EBCNS/Source/CNS.cpp

commit 7395fe32dcb13fe1a6b8cc9ad95409731af658ea
Merge: 0c39c4431 cfa6d098e
Author: Kevin N Gott <kngott@DOE-7072661.dhcp.lbnl.us>
Date:   Mon Oct 14 11:54:07 2019 -0700

    Merge branch 'development' into kngott/hip

commit cfa6d098e713bb3c0cd343de7a3f0e4a0cf0293c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 14 11:26:08 2019 -0700

    ReduceMin can now take a device lambda.  However if the lambda is a device lambda and the launch region is off, a runtime error will occur.

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_TypeTraits.H
Tutorials/GPU/CNS/Source/CNS.cpp

commit 338e6569ff4903dec324207f4bc911141d802cca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 14 09:26:28 2019 -0700

    print out the total number of gpus used only if nvcc >= 10

Src/Base/AMReX_GpuDevice.cpp

commit b425b67d490179c6ef759f9727b581d342ff9e22
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Oct 14 10:52:47 2019 -0700

    docstrings for the Particle IO routines

Src/Particle/AMReX_Particles.H

commit 69e057c6bd05ae60faa560a730cc8c8f88d63f85
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Oct 14 10:27:52 2019 -0700

    docstring formatting changes

Src/Particle/AMReX_Particles.H

commit e3c2e5758f0fb7aa080398c7570477d701d359f0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Oct 14 10:09:43 2019 -0700

    more docstrings for ParticleContainer

Src/Particle/AMReX_Particles.H

commit 544f9db9b4a3f6e50a81f134e1425ca69d3f8981
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Oct 14 09:52:42 2019 -0700

    remove unused function

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 2d83e26d81dedb4639ce81ec7b360d11433ac7a4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Oct 14 09:51:59 2019 -0700

    add some docstrings to the ParticleContainer constructors / define methods

Src/Particle/AMReX_Particles.H

commit fbae0870c68718fb3c0aec316fe5f969acb41bae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 12 16:20:11 2019 -0700

    add RunOn to BaseFab functions

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_MultiFabUtil.cpp
Tutorials/Basic/HelloWorld_C/main.cpp

commit cba673a69fa6f060e5a1b371320a8048fc7b2221
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 12 13:13:39 2019 -0400

    make the output more readable, disable latex by default

Tools/C_util/Convergence/RichardsonConvergenceTest.cpp

commit a95e783d1412fa9724a80816e7c8a23f69447e60
Merge: 76f34eee4 f9205c16d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 12 12:27:27 2019 -0400

    Merge branch 'development' into convergence_tool

commit 2aa0af167febd918e3d591ae6608bcbc45c5c353
Author: DUGKS <yzr.aero@outlook.com>
Date:   Sat Oct 12 21:17:39 2019 +0800

    add HOEXTRAPCC boundary type

Src/Base/AMReX_BC_TYPES.H
Src/Base/AMReX_FilCC_1D_C.H
Src/Base/AMReX_FilCC_2D_C.H
Src/Base/AMReX_FilCC_3D_C.H
Src/Base/AMReX_bc_types.fi
Src/Base/AMReX_bc_types_mod.F90
Src/Base/AMReX_filcc_mod.F90

commit 7345753f592a73e5b475ae015e15651e63ae4c3e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Oct 11 16:09:01 2019 -0700

    Fix args order in call to MultiFab constructor when computing EB-norm0

Src/Base/AMReX_MultiFab.cpp

commit 2c083fd630e86c58dce0e4eeb9c946486ed9180d
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Oct 11 13:15:00 2019 -0700

    expand the particle reduction tests

Tests/Particles/ParticleReduce/main.cpp

commit bcb621303830f2e39ef4796e3902b3831cdcf6e3
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Oct 11 13:14:43 2019 -0700

    update the particle reduction functions to work with SoA data

Src/Particle/AMReX_ParticleReduce.H

commit 4fb0e3f7831b7bbf21dba0d9a6a9a3cc3e0e40f6
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Oct 11 13:14:19 2019 -0700

    do some bounds checking for the particle components if DEBUG=TRUE

Src/Particle/AMReX_Particle.H

commit fa8c932e77b67d5d4b78a649a9eae9ea8fe1da4a
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Oct 11 13:14:01 2019 -0700

    fix some order of initialization issues

Src/Particle/AMReX_ParticleLocator.H

commit 239ad64e8c73d95b5fcea6fc00fecbe96df533fd
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Fri Oct 11 13:33:22 2019 -0400

    Make one setVal a multifab setVal, make enforcePeriodic match cpu version to fix losing particles in single precision

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleUtil.H

commit 327e780078a056743a5120950646d2e07f74e889
Author: cgilet <cgilet@gmail.com>
Date:   Fri Oct 11 13:23:28 2019 -0400

    give accurate error message

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit b6231668cf9a5a23c68f89bccbf294630cfec36d
Author: cgilet <cgilet@gmail.com>
Date:   Fri Oct 11 12:11:16 2019 -0400

    Fix applyBCTensor: Must take StateMode into account.

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 8e26d6a6d64e7f5d12416455988dfa880334ec0a
Merge: 7785e7e77 ee47967c3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Oct 11 08:51:00 2019 -0700

    Merge pull request #589 from eschnett/development
    
    Avoid compiler warnings

commit 99f5c9a0590b0622b75c464d9465693bb8479e93
Merge: 207d4a98c 7785e7e77
Author: cgilet <cgilet@gmail.com>
Date:   Fri Oct 11 10:23:23 2019 -0400

    Merge remote-tracking branch 'upstream/development' into mltensor_corner_fill_fix

commit 7785e7e77ef24ed09342e7ed689be521c7ba8833
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 11 07:07:09 2019 -0400

    Clean up CudaGraphs and Tests. Only preferred method remains.

Src/Base/AMReX_CudaGraph.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp
Tests/GPU/CudaGraphs/CrazyGraphs/GNUmakefile
Tests/GPU/CudaGraphs/CrazyGraphs/main.cpp
Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d
Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp
Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp
Tests/GPU/CudaGraphs/Readme.txt

commit f91e3ed71cc80ebbf0a5562869d39e782dba3710
Author: DUGKS <yzr.aero@outlook.com>
Date:   Fri Oct 11 16:23:59 2019 +0800

    add mathematical boundary types : HOEXTRAPLI

Src/Base/AMReX_BC_TYPES.H
Src/Base/AMReX_FilCC_1D_C.H
Src/Base/AMReX_FilCC_2D_C.H
Src/Base/AMReX_FilCC_3D_C.H
Src/Base/AMReX_bc_types_mod.F90
Src/Base/AMReX_filcc_mod.F90

commit 1ff6d684d59d2da3844021dd6f49c51cc2ca6a17
Merge: cf7bb47e6 838561d07
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Oct 11 00:31:27 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cf7bb47e642ece3d2833723b4510e80a2eab135b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Oct 11 00:24:38 2019 -0400

    calculate the early exit properly for local=false

Src/Particle/AMReX_ParticleCommunication.cpp

commit 0fb914ee1c9ec3282d1ea2f98986c4205dbfd967
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Oct 11 00:23:40 2019 -0400

    make sure the local option gets passed through correctly

Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleContainerI.H

commit 0c39c443176125eb62d94acbb27eebfdccf30def
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 10 13:24:34 2019 -0400

    Turn Random back on in ParallelReduce tests.

Tutorials/GPU/ParallelReduce/main.cpp

commit e4aab89e9f834170430e79502c365840c2be83d2
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 10 13:22:48 2019 -0400

    Mark {{ Initialization lists for now.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_PlotFileDataImpl.H

commit 3478d66a2bbc21c390cad2188db8f09a7b04958b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 10 11:33:35 2019 -0400

    Fix and use the memcpy_to_symbol wrapper.

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_Random.cpp

commit f3591f47f4ee29ebda8c4d1fcca296b8afbaa8d6
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 10 10:44:35 2019 -0400

    Strip managed variable out of Random for HIP compatibility.

Src/Base/AMReX_Random.cpp

commit 6601c6263903c031a8b0b27bb06da87329a384a7
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Oct 10 10:03:43 2019 -0400

    Linker: Use RPath
    
    Although AMReX does not come with much dependencies besides runtimes,
    the build system allows to add various libraries for downstream
    application dependencies.
    
    In the case of WarpX, we link auxiliary libraries for I/O among
    others. When linking against shared libraries, these dependent
    libraries (think: `.so`|`.dylib`|`.dll` files) must be present
    and accessible at runtime again. Usually, one sets their paths in
    `export LD_LIBRARY_PATH` hints which is both cumbersome for users
    as well as bad for file-systems which will be heavily loaded with
    meta-data operations while searching for the corresponding
    dependencies, especially at scale.
    
    Luckily, all modern Unix systems support RPath hints, which embed
    the location of a dependent shared library at link time into the
    generated binary.
      https://en.wikipedia.org/wiki/Rpath
    We now enable this feature by default. The linker flag is
    implemented in a generic way that works with the most common
    compilers:
    - clang :heavy_check_mark:
    - gcc :heavy_check_mark:
    - nvcc :heavy_check_mark:
    - icc :heavy_check_mark:
    - pgcc :heavy_check_mark:
    - xlC :heavy_check_mark:
    - crayc++ "classic" :heavy_multiplication_x:
    - crayc++ 9.0+ "LLVM": :heavy_check_mark:
    
    In case there are any regressions or the intentional wish to
    not use RPaths, users can just set `USE_RPATH=FALSE` as `make`
    option.

Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/GNUMake/Make.defs

commit 838561d07a1052d2d8d7de93d0f37eb2ae737a2f
Merge: 40f110b36 5172271fe
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Oct 9 14:47:25 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 40f110b3611795681f521245d81643ba67b87f49
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Oct 9 14:46:02 2019 -0700

    get the NeighborList particle tutorial running again.  instead of crashing right away, it now crashes after 15 time steps for unknown reason

Tutorials/Particles/NeighborList/GNUmakefile
Tutorials/Particles/NeighborList/inputs
Tutorials/Particles/NeighborList/inputs.mr
Tutorials/Particles/NeighborList/main.cpp

commit 5172271fe17ea01274f5871f26335e7b9a216977
Author: cgilet <cgilet@gmail.com>
Date:   Wed Oct 9 16:51:02 2019 -0400

    Minor fix in EB_computeDivergence: Only assert on 3rd dimension if AMREX_SPACEDIM==3

Src/EB/AMReX_EBMultiFabUtil.cpp

commit 207d4a98c0746ca6e9e8f2e30ccda6fd522ce3a3
Author: cgilet <cgilet@gmail.com>
Date:   Wed Oct 9 16:17:49 2019 -0400

    Update MLEBTensor::applyBCTensor

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit d54f4bfb5b49b59207cbe431d0a821bf797b3dd9
Author: cgilet <cgilet@gmail.com>
Date:   Wed Oct 9 16:15:32 2019 -0400

    Force inline

Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H

commit 8bb4601c3eb2f936d05f359882cff0a780e7f798
Merge: 6268af922 42f7964e0
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 9 14:26:58 2019 -0400

    Merge branch 'development' into kngott/hip

commit 6268af922c9d2f3d00f97f43488230a65c93d62d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 9 10:38:15 2019 -0700

    Wrap libraries and includes for HIP.

Tests/GPU/RandomNumberGeneration/GNUmakefile

commit 442af0f3fc2c081a2b041984465d2b7109c57662
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 9 10:35:08 2019 -0700

    First draft of HIP for random. Need to fix memcpytoSymbol wrapper and make gpu_nstates non-managed.

Src/Base/AMReX_Random.H
Src/Base/AMReX_Random.cpp

commit b506ebf241482cf12b69ecc3e7942670d07e42a0
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 9 10:33:49 2019 -0700

    memcpytoSymbol wrapper. [WIP] Doesn't seem to be working in Random.cpp

Src/Base/AMReX_GpuDevice.H

commit 7c3fdfc370ad78f078a5d879105a826b394ec08f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 9 10:32:59 2019 -0700

    Initialize Random after Arenas to allow Arena use in Random Initiatlize.

Src/Base/AMReX.cpp

commit 33281c34d1239c6d962dab16efd8b171c8d2fe71
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 9 10:31:52 2019 -0700

    Add HIPrand librarys and includes to the GNUmakefile for RandomNumberGenerator.

Tests/GPU/RandomNumberGeneration/GNUmakefile

commit bf476542fa048506a36db85515591caa402693b1
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 9 10:27:57 2019 -0700

    Is this library needed?

Src/Base/AMReX_GpuUtility.H

commit 27919c362fa724ff5220ae3d23341161160ee1d6
Author: cgilet <cgilet@gmail.com>
Date:   Wed Oct 9 12:28:44 2019 -0400

    Bug fix for case BCMode::Homogeneous

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit e916a48420bcffe6f33741a6d9d3bb4d4255631a
Merge: dfd00f033 42f7964e0
Author: cgilet <cgilet@gmail.com>
Date:   Wed Oct 9 11:31:43 2019 -0400

    Merge remote-tracking branch 'upstream/development' into mltensor_corner_fill_fix

commit dfd00f033b1f10b197ed149ef31e9ecbacf3a0f0
Author: cgilet <cgilet@gmail.com>
Date:   Wed Oct 9 11:31:23 2019 -0400

    WIP - MLMG not converging. Corner/edge cells fill appears reasonable

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit 42f7964e040a2f8e7edfef5dbe384539b844142a
Merge: 12c228e90 5cdb3461f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 9 06:48:13 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 12c228e90254231d0d754c500b6bb741513aa976
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 9 06:47:49 2019 -0700

    allow thrust::complex in PODVector, even though it doesn't strictly meet the requirements of std::is_trivially_copyable

Src/Base/AMReX_PODVector.H

commit 9555c24d360bfda5615466e75ce37598441fa477
Merge: df2d572cd 5cdb3461f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 8 17:38:03 2019 -0700

    Merge branch 'development' into kngott/hip

commit 5cdb3461feed09530720cd03536e422b2067161b
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Oct 8 15:58:05 2019 -0700

    CMake: add AMReX_Random.H and AMReX_Random.cpp to CMakeLists

Src/Base/CMakeLists.txt

commit 2631250d436da31a56fbd00c20e09628f3f4cfa0
Merge: 213f34516 a1b7a9f88
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 8 16:40:50 2019 -0400

    Merge branch 'kngott/random' into development

commit a1b7a9f881ff1833efddfa7ce29bfb174debbc69
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 8 16:40:01 2019 -0400

    Fixing Random libraries.

Src/Base/AMReX_Random.H
Src/Base/AMReX_Utility.H

commit c80035112676ab23727d765681da97d566f0d667
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 8 12:35:28 2019 -0700

    Move Random functionality to separate file.

Src/Base/AMReX.cpp
Src/Base/AMReX_Random.H
Src/Base/AMReX_Random.cpp
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Src/Base/Make.package

commit df2d572cde6c1a4f2aa5e6e4060155ee5aea0937
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 8 12:05:54 2019 -0700

    1st version of HIP HeatEquation. No output.

Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/myfunc.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/mykernel.H

commit 2eca21b79844c813400052b1bfb5911467c5b762
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 8 12:04:47 2019 -0700

    Setup testing of ParallelReduce tutorial.

Tutorials/GPU/ParallelReduce/GNUmakefile
Tutorials/GPU/ParallelReduce/main.cpp

commit 0d46d02d4afe0e23dafabb1772e9f3f17d104fe3
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 8 12:03:39 2019 -0700

    Updated makefiles for testing.

Tutorials/Basic/HelloWorld_C/GNUmakefile
Tutorials/GPU/Launch/GNUmakefile

commit 4b173b830b707964233f8a79dfb972c47b129ede
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 8 11:59:47 2019 -0700

    HelloWorld Work around for HIP shuffle intrinsics.

Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_iMultiFab.cpp

commit 213f3451658b3982ebfa888e8ec23e117a104de1
Merge: a3754a39f aefa1644a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 8 10:28:12 2019 -0700

    Merge branch 'development' into atmyers/vector_memory_usage

commit aefa1644ae399e651a42f512fe520a7147095e87
Merge: cad3614cf 58c293670
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 8 10:27:41 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cad3614cfe956cc3458229b3ccf10f4931e192c5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 8 10:27:24 2019 -0700

    fix ParticleMesh test

Tests/Particles/ParticleMesh/main.cpp

commit a3754a39feeba9a741e0dd49e10929ac3c7a3d07
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 8 12:57:00 2019 -0400

    offload 'assign' in PODVector

Src/Base/AMReX_PODVector.H

commit b2918e2e698664e5654a9dfb81fcc46759055e0a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 8 12:31:01 2019 -0400

    templated implementation of == and != for the Allocators

Src/Base/AMReX_CudaAllocators.H

commit ccd57a89551460dd0be2ca15e7290d7bb9b25611
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 8 08:39:53 2019 -0700

    fix cpu compilation

Src/Base/AMReX_CudaContainers.H

commit ee47967c3773fdc4ea8a26dc63fbc32af083b681
Author: Erik Schnetter <schnetter@gmail.com>
Date:   Tue Oct 8 11:31:58 2019 -0400

    Avoid compiler warnings
    
    Avoid warnings about signed/unsigned comparisons and about unused variables.

Src/Base/AMReX_FBI.H
Src/Base/AMReX_FabArrayCommI.H

commit 81707603e6008ca83c20cc2a5556e4742f02885d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 8 08:26:12 2019 -0700

    some refactoring and simplication of the gpu allocators

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaContainers.H

commit 58c293670d728b2547dbc69e15b13a3796102202
Merge: d91052fc3 605b65eb3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Oct 8 08:08:01 2019 -0700

    Merge pull request #588 from ax3l/fix-printfWarnings
    
    GCC 7.4.0 Warnings in Prints

commit d91052fc38ab7cb529245f52342310ba319a6174
Merge: 17b84c095 964666d92
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Oct 8 08:07:10 2019 -0700

    Merge pull request #586 from AMReX-Codes/bugfix-install
    
    add a missing D in the Make.package file for MLNodeLap

commit 70a641d27b621f98a279eb6caf101e819535c661
Merge: ac59fe275 17b84c095
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 8 07:00:04 2019 -0700

    merging development into amrex/vector_memory_usage

commit 17b84c095e380469455a3c43d4e8415cb8a8958f
Merge: 60ea95ce6 382d6ce6b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 8 06:40:31 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 60ea95ce6674304211bbf38d33363948f8a5ae71
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 8 06:40:08 2019 -0700

    iterate over map directly when early exiting from RedistributeGPU

Src/Particle/AMReX_ParticleContainerI.H

commit 605b65eb33909239f4b00c93711a121b7d17bb29
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Tue Oct 8 09:24:01 2019 -0400

    GCC 7.4.0 Warnings in Prints
    
    Fix warnings of the type
    ```
    In file included from /usr/include/stdio.h:862,
                     from /usr/include/c++/8/cstdio:42,
                     from ../amrex/Src/Base/AMReX_ParallelDescriptor.cpp:2:
    /usr/include/x86_64-linux-gnu/bits/stdio2.h:64:35: note: ‘__builtin___snprintf_chk’ output between 105 and 617 bytes into a destination of size 512
       return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
              ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
            __bos (__s), __fmt, __va_arg_pack ());
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    ../amrex/Src/Base/AMReX_ParallelDescriptor.cpp: In function ‘void amrex::ParallelDescriptor::Barrier(const string&)’:
    ../amrex/Src/Base/AMReX_ParallelDescriptor.cpp:198:23: warning: ‘%s’ directive output may be truncated writing up to 512 bytes into a region of size 383 [-Wformat-truncation=]
          snprintf(buf, N, "AMReX MPI Error: File %s, line %d, %s: %s",
                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    ```
    when compiling with WarpX.

Src/Base/AMReX_ParallelDescriptor.cpp

commit 964666d92dcf606e817eb4888c9ce20524198c2e
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Mon Oct 7 15:30:05 2019 -0600

    add a missing D in the Make.package file

Src/LinearSolvers/MLMG/Make.package

commit 382d6ce6bfea2186cd4c1d11024d17900aec094c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Oct 5 15:07:36 2019 -0700

    The point of passing in "loc" is to use it!  Replace "MLMG::Location::FaceCenter"
    by loc in call to get Fluxes.

Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp

commit 4c2c93062c787416ec6686ad640231b67c2c9052
Merge: 6b60f2aa5 1d422cb24
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Oct 5 14:56:42 2019 -0700

    Merge pull request #585 from AMReX-Codes/max_gpu_streams
    
    Reduce number of CUDA streams to 4

commit 1d422cb24ed4d306d6fd2a1ec5adb9a7cc6b73cb
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Oct 5 16:27:47 2019 -0400

    Reduce number of CUDA streams to 4

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_MFIter.cpp

commit 6b60f2aa54ac12daf48bedcd3d297ab4db10d2cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 4 20:23:31 2019 -0700

    for gpu regression tests, avoid saving errors in plotfiles

Tests/LinearSolvers/CellEB2/MyTest.cpp
Tests/LinearSolvers/EBTensor/MyTestPlotfile.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/MyTestPlotfile.cpp

commit 6970468f530a61fb31f053f2d63894382f741e92
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 4 17:58:22 2019 -0700

    add inputs for Nodal Poisson regression test

Tutorials/Basic/HelloWorld_C/main.cpp
Tutorials/LinearSolvers/NodalPoisson/inputs-rt

commit 0e0a04c3482c0520a814775997b9f2bf1d337fba
Author: cgilet <cgilet@gmail.com>
Date:   Fri Oct 4 16:50:28 2019 -0400

    WIP - bug fix in mltensor_fill_edges(). some clean-up

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H

commit 33e2c60c6b2bd5deba524b3052ac473aea53a358
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Fri Oct 4 13:26:43 2019 -0700

    update EB/MacProj tutorial to match last version of AMReX

Tutorials/EB/MacProj/main.cpp

commit 58b510ae290ea34c5e02d6f65fa01c0b1dee69a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 4 13:17:17 2019 -0700

    add a new function for removing duplicates using hash

Src/Base/AMReX_Vector.H

commit 5f0b2fc8cf8a0090d484b495772808963ade5090
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 4 12:54:14 2019 -0700

    Add fortran to hip builds. Straight copy from llvm using gfortran.

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/hip.mak

commit 0d0d9d4ce923c0a898a3923ee2c079c542ac982c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 4 12:53:47 2019 -0700

    shfl note.

Src/Base/AMReX_GpuReduce.H

commit b8062c23fe3b07299c669dd80777beda0ac27f28
Merge: c4a56aa02 b5d4fa0b1
Author: cgilet <cgilet@gmail.com>
Date:   Fri Oct 4 15:05:06 2019 -0400

    Merge remote-tracking branch 'upstream/development' into development

commit 8bf0b146d98a220988fadfda6f9444fdbea9398d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 3 13:21:35 2019 -0700

    Cleanup.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Geometry.H

commit b5d4fa0b1991a0ec2757d142d5c427d12b236be7
Merge: 8bb904a80 a9c393f0c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 3 12:19:02 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8bb904a80d42c551f546d6d0fee905e207e33c41
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 3 12:18:54 2019 -0700

    fix corner case bug in ParticleCopyPlan::build

Src/Particle/AMReX_ParticleCommunication.H

commit e24875addb9ccc3940a2858d16a70376c36eabc0
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 3 11:50:28 2019 -0700

    Callback on HIP.

Src/Base/AMReX_GpuAsyncArray.H
Src/Base/AMReX_GpuAsyncArray.cpp
Src/Base/AMReX_GpuElixir.cpp

commit 58fd40e73fd31dd4f0f69d315f7f7bd51fb9ef92
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 2 17:45:02 2019 -0700

    Covert to AMREX_HIP_TO_CUDA.

Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_MultiFabUtil_nd_C.H

commit bd9d27667a113677192c07b0ca06c95c879ab63e
Merge: 6c373053e a9c393f0c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 2 16:36:07 2019 -0700

    Merge branch 'development' into kngott/hip

commit 6c373053e7aba3835407e158f132fd39dcaa3cef
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 2 16:34:59 2019 -0700

    Add label to update Random to HIP.

Src/Base/AMReX_Utility.cpp

commit 1178281d2c0c2f6ff4230f2172d47637484733cf
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 2 15:56:32 2019 -0700

    Label FabView HIP changes.

Src/Base/AMReX_BaseFab.H

commit 6e231f96400a192f4b6ca7a79167ea23215aef89
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 2 15:55:05 2019 -0700

    Add labels to HIP FIX comments.

Src/Base/AMReX.cpp
Src/Base/AMReX_Array4.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_GpuAsyncArray.H
Src/Base/AMReX_GpuElixir.cpp
Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_Utility.cpp

commit 5bd0eb17196b4413b9fbe0b1c741bdc03551df8d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 2 15:54:19 2019 -0700

    std function wrappings for HIP.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MultiFabUtil_nd_C.H

commit 2fd4a8e5745377ec07f25ade462f7f14ef1e2a66
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 2 15:52:18 2019 -0700

    Add iMultiFab destructor for HIP.

Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp

commit f44ce46a5c628bb0eb0a98ee78fa2267262166f8
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 2 15:51:10 2019 -0700

    __all_sync and __any_sync for HIP

Src/Base/AMReX_FBI.H

commit 19b74aa1522f615eea7c287fdf36e3bc0a1e0cfa
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 2 15:22:25 2019 -0700

    Add a CPU CArena option for HIP.

Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_MemPool.cpp

commit a9c393f0c12150412f3d141d47b66d91ae551923
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 2 14:00:13 2019 -0700

    readBoxArray: make the special flag optional

Src/Base/AMReX_BoxArray.H

commit 74a575af8d54c724a48533f7b9e6f4ea27601d53
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 2 16:51:59 2019 -0400

    add another specialization for placementNew that explicitly does nothing for arithmetic types

Src/Base/AMReX_BaseFab.H

commit ab2a34edaf62b95e264ef416c41e388a6d4c5226
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 2 13:11:10 2019 -0700

    make gnu make NVCC_HOST_COMP more robust

Tools/GNUMake/Make.defs

commit e7e4c20354846c6db141349130a64a9672fc256d
Author: Lucas Esclapez <lesclapez@lbl.gov>
Date:   Wed Oct 2 11:59:01 2019 -0700

    [feature_nd_Pele] Add a 3D version of bc in Derive for dim. agnostic
    codes.

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_Derive.H
Src/Amr/AMReX_Derive.cpp

commit 1e4702a19ba60adbe8fae823866e7a303b28da4b
Author: shashankNREL <shashank.yellapantula@nrel.gov>
Date:   Fri Sep 6 10:18:07 2019 -0600

    Fixes to the spline IF routines

Src/EB/AMReX_distFcnElement.H
Src/EB/AMReX_distFcnElement.cpp
Tutorials/EB/GeometryGeneration/main.cpp

commit d59c4b01f0c879af99bf7a08e783fe1efa4f2b29
Merge: 8af435766 159461a47
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 2 07:17:54 2019 -0700

    Merge branch 'development' into mr/multicomp-div

commit 90ee8c6ffa90a17f297c14d7e46e6a36da9c6c38
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 17:07:48 2019 -0700

    manual memset. alloc doesn't seem to be working.

Src/Base/AMReX_MemPool.cpp

commit 38a95751797c5ce73b2b68528733d6b9748dd965
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 17:07:22 2019 -0700

    FabView Constructor wrappers for DEBUG and USE_HIP=FALSE.

Src/Base/AMReX_BaseFab.H

commit a6867be24b8e516721c13c14e6fc2ff0190b3a5c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 16:30:15 2019 -0700

    HIP doesn't like memset? HelloWorld is running with HIP.

Src/Base/AMReX_MemPool.cpp

commit c4a7c8791d5c3dadd266c32916428ebf5f123617
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 16:20:50 2019 -0700

    Remove the C++14 flag.

Tools/GNUMake/comps/hip.mak

commit fed441acaae7f0ae2ed83bdc18b5c794a81e272a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:40:51 2019 -0700

    Comment out virtual destructor. Conflict with LLVM 'key function'?

Src/Base/AMReX_iMultiFab.H

commit 01bc7276af77ccb5529d5358e83e16fcc38b8ae7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:40:12 2019 -0700

    Comment out std distribution functions.

Src/Base/AMReX_Utility.cpp

commit 71353837735b499bb61d5600f50d84b8aa50b237
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:39:46 2019 -0700

    More launch macros.

Src/Base/AMReX_Reduce.H

commit 6544a7700375a98a5f641aa1ee3189ebebcec761
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:39:34 2019 -0700

    std::floor to floor.

Src/Base/AMReX_MultiFabUtil_nd_C.H

commit acca5523457b921148fa7f671a450853ba0dcd15
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:39:23 2019 -0700

    std::abs to abs.

Src/Base/AMReX_IntVect.H

commit dab8b5b82dbbfa2a69dcd8845aa51de750783559
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:39:07 2019 -0700

    Comment out _shfl_down_sync.

Src/Base/AMReX_GpuReduce.H

commit 999866bbfc2f00a64b0966fcb22e6b91c9a706e1
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:38:39 2019 -0700

    Comment out callback functions.

Src/Base/AMReX_GpuAsyncArray.H
Src/Base/AMReX_GpuAsyncArray.cpp
Src/Base/AMReX_GpuElixir.cpp

commit e4955b69e83e9b3df4c71df754b51dae6e6c4965
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:38:14 2019 -0700

    Comment out _any_sync and _all_sync.

Src/Base/AMReX_FBI.H

commit 91ab0cef38c7b85e6ac20621d891e4018011c456
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:37:53 2019 -0700

    Getting around failing initalization lists.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_Geometry.H

commit 9e544faa38e29a9043a1e302154cc657ecac3af6
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:37:12 2019 -0700

    Comment out printf on device.

Src/Base/AMReX.cpp
Src/Base/AMReX_Array4.H

commit b4a332f0a7190eaa084deaf4920d1b26110b1475
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:36:48 2019 -0700

    Launch Macro. Switch between (<<< >>>) and hipLaunchKernelGGL.

Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuLaunchMacrosG.H

commit ce8e8f5ca0501fd61374ea596d281ff345931fd4
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:34:54 2019 -0700

    hipHostAlloc -> hipHostMalloc & hipFreeHost -> hipHostFree

Src/Base/AMReX_Arena.cpp

commit caee68dc7e6001197058fb0a0858ae0778915828
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:22:47 2019 -0700

    DEBUG=FALSE and NO_FORT build.

Tutorials/Basic/HelloWorld_C/GNUmakefile

commit 446197fbfec24c8c9ed5323fc140f1ab6a210610
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 1 15:22:15 2019 -0700

    lineinfo unknown and start tracking down -std=c++11 flags.

Tools/GNUMake/comps/hip.mak

commit 159461a47f0be4054b2022baa01e2a84b5a00558
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 1 15:18:05 2019 -0700

    update success string

Tests/Particles/ParticleReduce/main.cpp

commit 5b1ebf3582a1c8fbe7c65268062fc34eaacd941b
Merge: 908b639ec 9c00149ca
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 1 15:14:03 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 908b639ecf497e928c7b8030414184f4a99e0e10
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 1 15:13:54 2019 -0700

    rewrite particle reductions in the new style

Src/Particle/AMReX_ParticleReduce.H

commit 5ec826cdf45d10b3f95fbd83f48e9acae4c9c590
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 1 15:13:31 2019 -0700

    update ParticleReduce test

Tests/Particles/ParticleReduce/main.cpp

commit 9c00149ca01b5a027058ac570f14790c461c63ee
Merge: 1990d7c02 f4cbb17e9
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 1 14:45:07 2019 -0700

    Merge pull request #583 from AMReX-Codes/single_precision_random
    
    Single precision random

commit f4cbb17e9c5070d42e4e414932a20bea31954acf
Merge: e4e7c3fc7 1990d7c02
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 1 14:24:08 2019 -0700

    Merge branch 'development' into single_precision_random

commit e4e7c3fc7007b4582ff5abd91c5802fdac430df5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 1 14:19:32 2019 -0700

    Real -> amrex::Real

Src/Base/AMReX_Utility.cpp

commit 3435f967f01a1c39870a6a793735dcb9910b684e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 1 14:15:41 2019 -0700

    Random and RandomNormal for single and double precision

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit 1990d7c027d53d6141695999345858c8f5432bce
Merge: 3db90209c 317bd6ea6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 1 13:57:48 2019 -0700

    Merge pull request #581 from ax3l/fix-tracerNarrowingFloat
    
    Tracer Particles: Fix Narrow Warnings

commit 317bd6ea6ffec96a1a4ff7f34dfa821e2794af5a
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Tue Oct 1 13:48:04 2019 -0700

    Tracer Particles: Narrow Warnings
    
    Mitigate some narrowing warnings in tracer particles when compiling
    in single precision:
    ```
    Src/Particle/AMReX_TracerParticle_mod_K.H:86:27:
      warning: narrowing conversion of
      ‘(1.0e+0 - ((double)xint))’ from ‘double’ to
      ‘amrex::Real {aka float}’ inside { } [-Wnarrowing]
    ```

Src/Particle/AMReX_TracerParticle_mod_K.H

commit 8af4357663e3b8917cfe5d3642bf76821ff3b835
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Oct 1 12:25:14 2019 -0700

    Make EB_computeDivergence components-aware

Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.H
Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit dbb5fd73a5a01e8d4e1d68157ea4166eb5c5a44d
Merge: 89b55703e 3db90209c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Oct 1 10:43:19 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/mf-eb-methods

commit 3db90209c6df3e343f03881116263d7790cd6708
Merge: b7c1e4fc6 d97ba204a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 1 06:48:43 2019 -0700

    Merge branch 'weiqun/dev' into development

commit b7c1e4fc6d38ee9340331ce30a24dd84f79b9ee2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 1 06:47:12 2019 -0700

    update CHANGES

CHANGES

commit 5bca4b65e00c6b4763136f3794a91eef823dd18d
Merge: 346882f3a ccefb4dfc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 1 06:31:17 2019 -0700

    Merge branch 'development'

commit d97ba204a2df9f50337784da01ff84cb1c6304a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 30 19:58:28 2019 -0700

    gpu nodal rap: restriction

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit ccefb4dfcca14933b0a463d8df54e2f9e24ef2c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 30 20:07:45 2019 -0700

    fix dangling pointer

Src/Base/AMReX.cpp

commit 679e091c6e7971fc8176a128c79a1c40d0e63d49
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Sep 30 18:06:37 2019 -0700

    Add flag for enabling ptxas verbosity

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/nvcc.mak

commit 968d074df7620485ff3f78adad0dfb73a8f3afba
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Sep 30 18:06:09 2019 -0700

    Do not use device_prop.uuid for CUDA < 10

Src/Base/AMReX_GpuDevice.cpp

commit cfb2817033240c42a1c25fc2dddf4ad9177e3a0e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Sep 30 16:39:46 2019 -0700

    Add Device method for returning GPU model name

Src/Base/AMReX_GpuDevice.H

commit bb56d80bc85b1a436449ff80f3499498ebf1ccfa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 30 12:51:34 2019 -0700

    gpu nodal rap: interpadd

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 45d6080a4b004de4449915a5db161af5d95fe7d1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Sep 30 12:32:43 2019 -0700

    tweak these prints as well

Tests/Particles/NeighborParticles/MDParticleContainer.cpp

commit 7f9ba81b98affaff8ffb96dfb4c84f03d6e6f4d0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Sep 30 12:29:54 2019 -0700

    tweak this test to diff a plain txt file

Tests/Particles/NeighborParticles/MDParticleContainer.cpp
Tests/Particles/NeighborParticles/main.cpp

commit 603da943db0b94ddb4e02d8f0dab455322b7c9f6
Merge: e010cde46 c6ed9686a
Author: cgilet <cgilet@gmail.com>
Date:   Mon Sep 30 14:15:46 2019 -0400

    Merge remote-tracking branch 'upstream/development' into mltensor_corner_fill_fix
    
     Conflicts:
            Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
            Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit bdce7ca29924ec4ac1dbb16ce47d1532a18b9d18
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Sep 30 11:05:37 2019 -0700

    add more inputs scripts to the redistribute test for regression testing

Tests/Particles/Redistribute/inputs.rt.cuda
Tests/Particles/Redistribute/inputs.rt.cuda.mr
Tests/Particles/Redistribute/inputs.rt.cuda.nonperiodic

commit e010cde461a44c3e1bf241d30555ea01ca4cb799
Author: cgilet <cgilet@gmail.com>
Date:   Mon Sep 30 12:04:34 2019 -0400

    Updates for 3D.

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit 1fa9cb09e6a681d37c9e3ff8b22df98b9bc21ddf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 29 21:37:49 2019 -0700

    gpu nodal: jacobi stencil version

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 3d2dd8911f861e4c12415a01dd44fca75367b9e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 29 21:27:38 2019 -0700

    gpu nodal: gauss seidel stencil version

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 7ad21d9284af2b335bfe1b6a8ad41e9ab4ebf8e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 29 21:07:21 2019 -0700

    gpu nodal: normalize stencil version

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 5022ad28c4d8831fd912b5c67cd8267b1dded990
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 29 20:47:05 2019 -0700

    gpu nodal: A dot x stencil version

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit e2ac5e6b63dbcef081a5d4c23cc2e3e9666a34a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 29 20:29:01 2019 -0700

    nodal gpu: set stencil

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit e7233b0b2a52825bf8b1df76ecf9cfbb8f224aa1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 29 17:02:20 2019 -0700

    gpu nodal: fill bc for nodal phi

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp

commit 4dca4be57a17e555f5079ffaa6fda8300fd3e3a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 29 15:56:33 2019 -0700

    gpu nodal: fix bug

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 0f556e08f1adc8f04fee7f26c782bb085fed5bba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 29 15:24:39 2019 -0700

    2d compiles

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H

commit ac425b02dd167ae298b92730b013f1573b6eb035
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 29 15:04:37 2019 -0700

    gpu nodal: fill bc for sigma

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp

commit dd7213c381cdb9cc31ebdbe8783b3dd3ddb422d4
Merge: 5a2ecbe3c 7c6663bf7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 29 07:24:20 2019 -0700

    Merge branch 'development' into weiqun/dev

commit c6ed9686a12c188f0fb0dc962b73fab719a40634
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Sep 28 17:26:10 2019 -0700

    Update MAC projector documentation to reflect that, when USE_EB=TRUE,
    we must now specify whether the incoming (and outgoing) face velocities are
    defined on face centers or centroids

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 2383c180dc82388b25d2db3c2c2ad85e8df57352
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Sep 28 17:21:13 2019 -0700

    Create interface in the absence of EB that does not require the specification of FaceCenter vs FaceCentroid.

Src/LinearSolvers/MLMG/AMReX_MacProjector.H

commit 813ec8248fcd2fc4ff246d927c9f3bef9f25f5c1
Merge: 08c620df0 fd4a60fec
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Sep 28 17:12:03 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 08c620df0718ceac3353ef51b0a2de243dae4c35
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Sep 28 17:11:11 2019 -0700

    We must now specify whether the MAC projection is being given normal velocities at face centers
    or at face centroids.

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MacProjector.H
Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp
Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp

commit fd4a60fec3f572d492c013abc53f0409b840cfd2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 28 12:58:30 2019 -0700

    fix the inputs for gpu regression test

Tutorials/GPU/CNS/Exec/RT/inputs-rt

commit 6c497073d9338f039d3805d7056ef198eef009c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 28 12:45:23 2019 -0700

    add inputs for gpu regression tests

Tutorials/GPU/CNS/Exec/RT/inputs-rt
Tutorials/GPU/CNS/Exec/Sod/inputs-rt

commit 78f5603d53a36bc605271cda7b03ba9cca87dd9b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 27 22:51:18 2019 -0700

    add garuda

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.ccse

commit a45432f5656a26b81ce06f20f7c3bca5c99eca5a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 27 17:01:08 2019 -0700

    BaseFab host device.

Src/Base/AMReX_BaseFab.H

commit b0caab9be65256e85f7069d20224442688e87161
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 27 16:40:18 2019 -0700

    __host__ __device__ on declarations and functions test.

Src/Base/AMReX_IntVect.H

commit d3479e03aca9929a434255dcb4dd2a804902ea2d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 27 16:36:06 2019 -0700

    Corresponding HIP makefile for the build system.

Tutorials/Basic/HelloWorld_C/GNUmakefile

commit 1abfab0afd784f00d59dbab6c6758a1a98524f08
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 27 16:35:35 2019 -0700

    Add hip library. Why is this needed? It's in AMReX_Gpu.H

Src/Base/AMReX_GpuQualifiers.H

commit 7e9d63c434b2440b3e61f3b886139ee8f3e6220b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 27 16:35:06 2019 -0700

    Quick first hack-y build system update for HIP.

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/hip.mak

commit 7c6663bf78479a7bcee95052c652d27bbb307201
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Sep 27 12:32:23 2019 -0700

    CMake: fix typo

Src/Extern/Conduit/CMakeLists.txt

commit 4ce8cd8bd8b4a640f54f011315849b03223e57ac
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Sep 27 09:44:22 2019 -0700

    Count number of GPUs used in total

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp

commit 5a428d2b057fe5f7ace811fbe95125131bd23bc0
Merge: e37deefd3 4b6fd5c4a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Sep 26 17:11:36 2019 -0700

    Merge pull request #578 from ax3l/topic-userLiteralForParticleReal
    
    C++ User Literal for amrex::ParticleReal (_prt)

commit 4b6fd5c4afdc1a8852a498de1bd91b2fe2c0ba17
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Sep 26 17:05:40 2019 -0700

    Typo & Doxygen

Src/Base/AMReX_REAL.H

commit 39dd95d103d7391a7146cd809a2dce877e2d0306
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Sep 26 16:33:08 2019 -0700

    C++ User Literal for amrex::ParticleReal (_prt)
    
    Same as the literal for `amrex::Real`.

Src/Base/AMReX_REAL.H

commit e37deefd3808ed3bf673c1cbe06aa03210d2b167
Merge: 773aa759d 9465815d7
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Sep 26 16:17:04 2019 -0700

    Merge pull request #577 from ax3l/topic-userLiteralForReal
    
    C++ User Literal for amrex::Real (_rt)

commit 9465815d7dc0420731801ef6173b7ea87b7d330d
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Sep 26 15:30:57 2019 -0700

    Use new Real literal in code base

Src/Amr/AMReX_Amr.cpp
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Src/Base/AMReX_FArrayBox.cpp
Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_ParticleContainerI.H

commit 47a3c40d53d47e84ddc224d48c7f4e8b651a0ab3
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Thu Sep 26 15:32:16 2019 -0700

    C++ User Literal for amrex::Real (_rt)
    
    This adds a user literal for `amrex::Real`. This is a C++11
    feature and allows to type constants properly instead of relying
    on implicit conversation.
    
    A typical fallacy is the following user code:
    ```C++
    auto const mypi = 3.14;
    Real const sphere_volume = 4/3 * mypi * pow(r,3);
    ```
    
    The first term `4/3` makes the whole expression an `int` until
    the result is casted to `amrex::Real`. Urgh!
    
    We can do better, with `amrex::Real(4)/::amrex:Real(3)` but who
    wants to write such verbose code, right? So C++11 user literals
    to the rescue!
    ```C++
    auto const mypi = 3.14_rt; // that's a real, too!
    Real const sphere_volume 4_rt / 3_rt * mypi * pow(r,3);
    ```

Src/Base/AMReX_REAL.H

commit 773aa759d5eb46afdae00219261c75c8028fa9e0
Merge: a8fa098c7 0a1623d07
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Sep 26 17:55:41 2019 -0400

    Merge branch 'development' into multilevel_gpu_redistribute

commit 0a1623d077fe752e6d168077e50c347ebd14a220
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 26 14:51:14 2019 -0700

    add int8_t support in typecheck

Tools/typechecker/typechecker.py

commit 70b03eb5215e1cbe1a9b29c1630f1f9f9e69f62b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 26 14:49:29 2019 -0700

    add amrex::Long

Src/Base/AMReX_BLFort.H
Src/Base/AMReX_INT.H
Src/Base/AMReX_IntVect.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit a8fa098c742befef3f088a886700bd445389e289
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Sep 26 17:46:34 2019 -0400

    handle case that people have added particles on grids that aren't owned by the proc in question

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit f9205c16dde74b9cac4307050be8bfdc0b6f7553
Merge: 366cef4a8 70894ced0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Sep 26 13:37:50 2019 -0700

    Merge pull request #576 from AMReX-Codes/single_precision
    
    various fixes for single precision and particle real

commit 70894ced00e6e8fe9ca48b12fcf89becb4224288
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 26 13:30:13 2019 -0700

    various fixes for single precision and particle real

Src/Base/AMReX_REAL.H
Src/Base/AMReX_VectorIO.H
Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H
Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_Particle_mod_K.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_StructOfArrays.H
Src/Particle/AMReX_TracerParticle_mod_K.H

commit d4217e695f5fa969c51db2c02f3953d834c0bde9
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Sep 26 15:37:05 2019 -0400

    remove m_need_handshake, which isn't used any more

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 818cc4cb15dee256db901062860528fb3050505e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Sep 26 15:36:50 2019 -0400

    update neighbor_copy_op with level information

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 12dc799cdb6b3f5cf9dbda5c699c4559698be631
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Sep 26 15:11:26 2019 -0400

    also remove the redistribute mask from enforce periodic

Src/Particle/AMReX_ParticleContainerI.H

commit ab3fa5e6a9aa3d32adbc4db79818fd0b209d8cb2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Sep 26 14:38:01 2019 -0400

    don't need mask in RedistributeGPU any more

Src/Particle/AMReX_ParticleContainerI.H

commit 5a2ecbe3ca0fe394caa4f2b5e5974eba7c3268fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 25 21:23:37 2019 -0700

    gpu nodal: interpadd

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit f0e701856f48053141871543859a527a90c3e99a
Merge: 3a8e6660c 366cef4a8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 25 17:50:57 2019 -0700

    Merge branch 'development' into multilevel_gpu_redistribute

commit 3a8e6660c02c118477496efd99973c71ae1bf952
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 25 17:29:02 2019 -0700

    skip invalid particles in numOutOfRange

Src/Particle/AMReX_ParticleUtil.H

commit 366cef4a8c3af171b43fc4256ee7f3758f2b2dc1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 25 17:25:52 2019 -0700

    fix formatting?

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit 2c90e756a15494960ffb950c140e8305d8ecf62b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 25 16:54:15 2019 -0700

    Add comments about AMReX on Windows (per Weiqun)

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit 842c4f1b02767ff68b4259da6eae453bdaf6d5e6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 25 15:00:19 2019 -0700

    update test for 1 and 2D

Tests/Particles/Redistribute/main.cpp

commit a9bdb4ee6b109767e0ff46c444eab5c49238c6db
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 25 14:35:20 2019 -0700

    add methods for changing the geometry object of particle locator

Src/Particle/AMReX_ParticleLocator.H

commit d8bd500c35b13cdab329674aa75815c4d345c7ac
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 25 14:34:25 2019 -0700

    need to set lev_max here

Src/Particle/AMReX_ParticleContainerI.H

commit 070c75d4eaa0b1ab8f18fc306c74d1bdfc616581
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 25 13:21:47 2019 -0700

    need to clamp these quantities in 2D

Src/Particle/AMReX_ParticleLocator.H

commit 3f4d348366c649928fa0937c0402de7d1af5d2a8
Merge: 7e7b66aab d54cbc5bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 25 12:37:01 2019 -0700

    Merge branch 'development' into weiqun/dev

commit d54cbc5bb7a25dcc51335019ce8d5b37ca8809ea
Merge: cde68b826 5939f8dc2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 25 09:14:57 2019 -0700

    Merge pull request #574 from awehrfritz/UNSW
    
    Tools/GNUMake - Add Australian machines

commit cde68b826e18e4f8d50b331afa63f290430e1648
Merge: cb416f0a1 f3cd2ebd6
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 25 08:07:28 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit cb416f0a1acbe2bf154c4f426624553bf75b2970
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 25 08:07:09 2019 -0700

    note about subset -> levels in VisIt

Docs/sphinx_documentation/source/Visualization.rst

commit f3cd2ebd658dfa8612eadd6a206e7a13648cc79a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 24 18:02:57 2019 -0700

    slight clean-up of tensor solve section

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 7e7b66aab4049477309cef48218924a4943a9b4a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 24 16:57:12 2019 -0700

    gpu nodal: restriction

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 02a2563eb04ddf6610edbcdf9e67f941d54e86a6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 24 16:38:19 2019 -0700

    Add code snippet for calling the tensor solve explicitly

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 5920bc2c4c67d69e550ef26eaa8156802963fbab
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 24 16:26:29 2019 -0700

    update tensor stencil

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 4046734b740b549af593e9e7db30b6162dbc4455
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Sep 24 19:22:29 2019 -0400

    fix new bug in ParticleBufferMap

Src/Particle/AMReX_ParticleBufferMap.cpp

commit 00e5ca8f014ff6ccc1c2a09fb2205e31ba3258b8
Merge: 69f49f55f 576183c00
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 24 15:37:19 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 69f49f55feb0b70d1227ce64d8264aed4eb88a31
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 24 15:35:48 2019 -0700

    Update formulat in tensor solve documentation

Docs/sphinx_documentation/source/LinearSolvers.rst

commit c496e2cbafe4697c75a0a398678d9f9bcc15f351
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Sep 24 18:23:35 2019 -0400

    fix assertion

Src/Particle/AMReX_ParticleCommunication.H

commit f95f0da5909d8906607d023ee152e173e5ae260a
Merge: 411a3f53d 576183c00
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 24 14:51:04 2019 -0700

    Merge branch 'development' into multilevel_gpu_redistribute

commit 576183c00d937f93b57d5eac83f6c64a475afbbe
Merge: 086ca71d8 48172595b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 24 14:50:22 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 086ca71d8a70351e5c9b74a1161e67f9448dfdec
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 24 14:50:02 2019 -0700

    make the return type of this function template match the function body

Src/Base/AMReX_Tuple.H

commit 411a3f53d33478559957590766b1ecc7d14dcee8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 24 14:49:26 2019 -0700

    don't need to use std::forward here any more

Src/Particle/AMReX_ParticleLocator.H

commit cde37bdaa1798d4d11177613ca495b6a3fe1a9c3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 24 14:44:52 2019 -0700

    need temporaries for the lev

Src/Particle/AMReX_Particles.H

commit d621ca869a70731ee091ba837ffb7c17fa6ff0ce
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 24 14:39:01 2019 -0700

    missed a factor of the level offset in building the buffer map

Src/Particle/AMReX_ParticleBufferMap.cpp

commit 636a530b458c61d11360e749178dec9cbf36f8b8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 24 12:28:47 2019 -0700

    use tuple in the grid assignor

Src/Particle/AMReX_ParticleLocator.H

commit 861181e8c72032d9e2278fef6e69fb25b25ff4ec
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 24 12:28:22 2019 -0700

    computing dst lev

Src/Particle/AMReX_ParticleContainerI.H

commit 5a0f18050bb73d381c9a23ac5b5b79faef4fffbe
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 24 12:27:56 2019 -0700

    lev -> dst_lev

Src/Particle/AMReX_ParticleCommunication.H

commit 3b8ae464dc8167c1d94167aeb06d90e079de8167
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 24 10:39:32 2019 -0700

    more flexible construction for AmrParticleLocator

Src/Particle/AMReX_ParticleLocator.H

commit 2880164f6759eafb823077d128caa4e33e6815b2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 24 10:27:26 2019 -0700

    another form of () for the particle locator

Src/Particle/AMReX_ParticleLocator.H

commit 4453c565dee6852589186b115a4e9a6afa29907a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 24 10:26:49 2019 -0700

    move this call to outside the loop over levels

Src/Particle/AMReX_ParticleContainerI.H

commit 48172595b3b1d20e6b828678b05bbe77ddbdd618
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 24 09:49:31 2019 -0700

    EB Tensor solver: enforce periodic boundary

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 77188fab8e931006e591790d21e4385f6032f8c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 23 21:28:00 2019 -0700

    Tensor solver: enforce periodic boundary

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 8315dd8251ae7265da8b5217439f6bb1c44a64df
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Sep 23 20:32:53 2019 -0400

    move the loop over levels to inside the particle locator

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleLocator.H

commit 8bbc18b3e1753e631dc8b9592eacb15d34371863
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 23 16:58:24 2019 -0700

    update tensor stuff

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 89b55703e08898573ea5984c1bddd60da72a7f84
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Sep 23 16:56:53 2019 -0700

    MultiFab: add EB-aware implementation of norm0, max and min

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit aa013f8e6fde9679fe76081d77d4d1039ca52112
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Sep 23 19:56:48 2019 -0400

    fix some (new) bugs in the particle locator

Src/Particle/AMReX_ParticleLocator.H

commit 046794674ace1336cd5e84aad3e3cafa748e779e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 23 16:50:51 2019 -0700

    Fix math

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 6f0fe63c6d711571c9b93a48b9ac174905e684e5
Merge: e7ec1ac10 072eb00a1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 23 16:27:37 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit e7ec1ac102ba64ea8f9dbf9fe23469a0c01130b5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 23 16:27:05 2019 -0700

    intro to tensor solve

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 072eb00a11611fa093fe6280a297d8f265994789
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 23 16:20:29 2019 -0700

    fix tensor solver's domain bc corners

Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit bbc4f7a9cae8aa2fe4f82d294cafb362348f79f9
Author: cgilet <cgilet@gmail.com>
Date:   Mon Sep 23 12:23:35 2019 -0400

    A little clean-up

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit 25dcf56b675960d51dcec6238cb14f2839de124a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 23 08:44:02 2019 -0700

    Fix 1 --> ncomp in AssignDensity; we were a bit mix-n-match before.

Src/AmrCore/AMReX_AmrParticles.H

commit 89c5cd28dc8e2008555227920c432ec0c9a0e5ba
Merge: c3a3422a9 6cea2c32b
Author: cgilet <cgilet@gmail.com>
Date:   Mon Sep 23 09:41:18 2019 -0400

    Merge remote-tracking branch 'upstream/development' into TensorFluxes

commit 6cea2c32bdb3145d12c8b8ffb0909d171e5c60da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 22 18:09:40 2019 -0700

    avoid gcc bug

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H

commit 1bcaf5e915d52f16e510aa2826733b74b06a5ce6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 22 17:36:38 2019 -0700

    gpu nodal: gauss seidel

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 386899b30f721fdb0df3c5910515e7fb5e139f9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 22 17:00:01 2019 -0700

    gpu nodal: jacobi

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit f413b255a11953919edd63e94d18b4e41db8d96a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 22 16:25:04 2019 -0700

    gpu nodal: normalize

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 82007b85ba2a0fe5c8574c15993d84170e8538ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 22 13:45:44 2019 -0700

    fix 1d

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H

commit d973f3f8a8877f0ac5f5c4367f4d759895a822a4
Merge: 84d3f615a 3959dbc87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 22 12:56:14 2019 -0700

    Merge branch 'development' into weiqun/dev

commit 84d3f615a376985636d3c76940978f25349848d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 22 12:55:06 2019 -0700

    gpu nodal: adotx aa version

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 815fcbc82dbefa19979f461d3d5d4c3afc954d44
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 22 12:34:23 2019 -0700

    gpu nodal: adotx ha version

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit d74b8a6e5102a210bf881300172e3d80fbe23915
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 22 10:26:58 2019 -0700

    nodal gpu: average down sigma

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 3959dbc87e4d32956f3917d04a7311b7c300fc67
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 21 21:08:57 2019 -0700

    fix nodal mc test

Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp

commit 60196629596146d8d99358f07ceafaa969ee3a12
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 21 19:56:51 2019 -0700

    gpu nodal: dot mask

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit f5ba7c11694f17884f1357f8638321622579188d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 21 19:12:08 2019 -0700

    gpu nodal: res mask

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit be58649c603820df87ac236c3a52832952ec9c0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 21 19:05:32 2019 -0700

    gpu nodal: dirichlet mask

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 7d47fce43cac1130386fe11c7516d0747e7693d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 21 17:55:50 2019 -0700

    gpu nodal: nodal mask

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 05b4b562107e272952becc2f6651bd32c51737d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 21 16:58:45 2019 -0700

    gpu nodal: fix sign

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H

commit a0256388cb16a9f2c035810d465da5e562d5ede6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 21 09:19:32 2019 -0700

    gpu nodal: pass the correct mask to divu

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit b86eaa57fce73827f27d2008d221ec897ee87f88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 21 09:19:32 2019 -0700

    gpu nodal: fix bug in the new Neumann BC

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H

commit 49f4f517d23d53b0259d2620f09a9d69b73b7933
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 21 08:13:20 2019 -0700

    gpu nodal: mknewu

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 784dbf994f9643ed2642faac51b028429a36a8ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 21 07:43:24 2019 -0700

    gpu nodal: rhcc

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 25e2368d80edcf14af795d7c6b1903943f7bbda1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 20 22:22:57 2019 -0700

    gpu nodal: divu

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 08d60c2f00fc74a8b84d1482c7b2fa7380c8910b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 20 21:36:54 2019 -0700

    gpu nodal: impose neumann bc

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 1510fcf86c2de2c791c4ce9cc56ae18d6c3339e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 20 18:50:00 2019 -0700

    add AMREX_HOST_DEVICE_PARALLEL_FOR_?D

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchMacrosC.H
Src/Base/AMReX_GpuLaunchMacrosG.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_iMultiFab.cpp
Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_FabSet.cpp
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_MultiMask.cpp
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/EB/AMReX_EB2_Level.cpp
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit bb259585c9d0194e8b5448ce15764a8a4b051620
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 20 16:55:38 2019 -0700

    gpu nodal: ported some anyd functions

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_ND_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/Make.package

commit 08183e99f118a491f8e55bc809a806397dfd7fe2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 20 19:52:02 2019 -0400

    update Redistribute test for multiple levels

Tests/Particles/Redistribute/inputs
Tests/Particles/Redistribute/inputs.rt
Tests/Particles/Redistribute/main.cpp

commit 8aaf9b415ac6e5a068bc96add28b8354c1bd813a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 20 19:51:36 2019 -0400

    fix error in level offset calculation in ParticleBufferMap

Src/Particle/AMReX_ParticleBufferMap.cpp

commit b7f081b396d243d3919d2bc3269f7bdde1c88afb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 20 16:24:20 2019 -0700

    add some empty files in preparation for rewriting nodal solver kernels

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_ND_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/Make.package

commit b113f15627f8bf4a864bd5d1df61c04fe2d8e075
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 20 19:14:47 2019 -0400

    particle locator seems to be accounting for multiple levels correctly

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleLocator.H
Src/Particle/AMReX_Particles.H

commit d5898231901e1399b57a8fa62ad4b1422aa8f777
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 20 16:12:55 2019 -0700

    add a missing if(Gpu::notInLaunchRegion())

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit e3492a2130cf139a646844645c312c490cbde5e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 20 15:52:34 2019 -0700

    MLMG: nodal interp on gpu

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_F.H
Src/LinearSolvers/MLMG/AMReX_MLMG_K.H
Src/LinearSolvers/MLMG/Make.package

commit e8441c494f158af4acdadf23feb8c8cb5b471d94
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 20 18:35:01 2019 -0400

    Amr version of ParticleLocator

Src/Particle/AMReX_ParticleLocator.H

commit 0fdd50d5d8a964331239d4880302726e7886ba0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 20 14:37:55 2019 -0700

    MLMG: eb_cc_interp on gpu

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H

commit 14828da6b11e94eed1c4ad52bb3579e9986b9758
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 20 16:52:08 2019 -0400

    do loop over levels throughout particle communication code

Src/Particle/AMReX_ParticleCommunication.H

commit 56e9301833cbe72cb6da052c26bdf28755883165
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 20 16:30:31 2019 -0400

    add loop over levels to pack and build

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_Particles.H

commit 974ec17c64c68dece11dd839f2ea773acf8a6afa
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 20 16:30:05 2019 -0400

    methods for computing the neighbor procs on the fly, without as mask

Src/Particle/AMReX_ParticleUtil.H
Src/Particle/AMReX_ParticleUtil.cpp

commit c9304aa0adc2881a439f4dfa7426ec9245740979
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 20 16:29:17 2019 -0400

    a few more methods for particle buffer map

Src/Particle/AMReX_ParticleBufferMap.H

commit 1aedb81fe3fd7888641f170ce90c1d057fcd4ddb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 20 12:53:31 2019 -0700

    add regression test inputs for EBTensor

Tests/LinearSolvers/EBTensor/inputs.rt.3d

commit c3a3422a9da9d5255b135e954a4fe81520c6b8a4
Merge: 32efff60c 76c1d7759
Author: cgilet <cgilet@gmail.com>
Date:   Fri Sep 20 15:35:37 2019 -0400

    Merge remote-tracking branch 'upstream/development' into TensorFluxes

commit c4a56aa028ee8ef3d757b011abce2398d2907bc7
Merge: e86d462a6 76c1d7759
Author: cgilet <cgilet@gmail.com>
Date:   Fri Sep 20 15:34:50 2019 -0400

    Merge remote-tracking branch 'upstream/development' into development

commit e86d462a6b2b55c87ee82dd40ab3bfe86fbec5e0
Merge: f07671bcc 251c59b1d
Author: cgilet <cgilet@gmail.com>
Date:   Fri Sep 20 15:27:58 2019 -0400

    Merge remote-tracking branch 'upstream/development' into development

commit 32efff60ce0334c1c0df3c094776460017c180e2
Merge: fbc90e19a 251c59b1d
Author: cgilet <cgilet@gmail.com>
Date:   Fri Sep 20 15:26:03 2019 -0400

    Merge remote-tracking branch 'upstream/development' into TensorFluxes

commit fbc90e19ab069f90fe6faf095b54c8364a9622ad
Merge: c19740dd6 9efd66178
Author: cgilet <cgilet@gmail.com>
Date:   Fri Sep 20 15:10:09 2019 -0400

    Merge branch 'TensorFluxes' of https://github.com/cgilet/amrex into TensorFluxes
    
     Conflicts:
            Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit c19740dd6b859f175735831f4293bd15a07daba4
Author: cgilet <cgilet@gmail.com>
Date:   Fri Sep 20 14:10:31 2019 -0400

    WIP - 2D now compiles
    
    2D not tested further. Cut cell fluxes not yet defined correctly.
    Set to bogus val to know if they're being used.
    3D not done yet.

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H

commit 76c1d77595e20b41ff2eef3f7b3602110dc2338c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 20 09:47:02 2019 -0700

    rm Gpu::LaunchSafeGuard from MLEBTensorOp::apply

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit 68cd9150ebf7c42103b68ee72ab1a5cec567b53d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 19 17:16:17 2019 -0700

    fix habec

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90

commit 6495db56c6d1edd8564299f0934ac31db26a1d67
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 19 15:48:10 2019 -0700

    MLEBABecLap::interpolation on gpu and rm deprecated files

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_K.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H
Src/LinearSolvers/MLMG/Make.package

commit 4aef19ffe81df1ac413820eabbc461c06d514f8e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Sep 19 18:54:06 2019 -0400

    generalize the ParticleCopyOp for multi-level

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit 346882f3ae96ac8f71dd8d7862b2452199bf01ad
Merge: 2d905c33b b4f79407f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 19 13:35:40 2019 -0700

    Merge branch 'master' of github.com:AMReX-Codes/amrex

commit 43b8d7fe6908094faeb68e040f867b120534ce1e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 19 13:27:09 2019 -0700

    MLEBABecLap::normalize on gpu

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H

commit 25b9f0919a6fbde0ea45f3c4fd051c1a134df502
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Sep 19 14:55:24 2019 -0400

    extending the particle buffer map to work with multiple levels

Src/Particle/AMReX_ParticleBufferMap.H
Src/Particle/AMReX_ParticleBufferMap.cpp
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit 13f49232e1eac955a1df4079db75a6f75ec73b95
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 19 09:48:13 2019 -0700

    clean up

Src/Base/AMReX.cpp
Src/Base/AMReX_FabArray.H

commit 5939f8dc221b7aa775afc9d0298d153a2bd8a396
Author: Armin Wehrfritz <armin.wehrfritz@unsw.edu.au>
Date:   Thu Sep 19 03:47:11 2019 +1000

    Tools/GNUMake - Add Australian machines

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.nci
Tools/GNUMake/sites/Make.pawsey

commit 7a45a5040af6add69be3192155b4575f8c324a74
Merge: f746e2833 89cece487
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 18 18:31:16 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f746e28336a65e8cbb7b8e8cdb937a4a44af6bc2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 18 18:28:37 2019 -0700

    cleanup

Src/Base/AMReX_GpuLaunchFunctsG.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H

commit 89cece4872369dfde6565195924d3dd643879946
Author: Stefan Vater <svater@users.noreply.github.com>
Date:   Thu Sep 19 03:28:14 2019 +0200

    some modifications for the Nodal poisson tutorial program (#563)
    
    * - fixed exact solution for 2d
    - added plotting routine
    
    * added averaging from nodal to cell values for plotting

Tutorials/LinearSolvers/NodalPoisson/Make.package
Tutorials/LinearSolvers/NodalPoisson/MyTest.H
Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp
Tutorials/LinearSolvers/NodalPoisson/MyTestPlotfile.cpp
Tutorials/LinearSolvers/NodalPoisson/main.cpp

commit 89566964a9efe3da62bc7bb5df2d40dfa2efd7f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 18 15:32:02 2019 -0700

    MLEBABecLap::compGrad on gpu

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H

commit 2329b4e11004690d26acb9942709891c2b505e77
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 18 12:51:56 2019 -0700

    MLEBABecLap::FFlux on gpu

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 7042203361fe74efb0efb3f2adb6b319e753772c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 17 17:24:58 2019 -0700

    cleanup

Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H

commit 554a5b25b58076d306c25bfcdd3844d772ac0854
Merge: a42467b44 4da4fe3d0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 17 15:28:56 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a42467b4482721cbe588aec95833473b8cbc28c1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 17 15:28:39 2019 -0700

    remove incorrect assertion(s)

Src/Particle/AMReX_NeighborParticlesCPUImpl.H

commit 4da4fe3d03a821e3d1432df812c61751cb5f53f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 17 15:26:38 2019 -0700

    manually write out the loops so that gcc 8 does not crash

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H

commit f88e9a6a8f87084bbdf29582ff26ea078109dbe6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 17 15:06:24 2019 -0700

    fix new bug: have to rebuild array4 because fab has been shifted

Src/Boundary/AMReX_MultiMask.cpp

commit 46f955b5233f6e89d849fbe0316509dc33dfaafd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 17 14:55:00 2019 -0700

    fix typo

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H

commit 1af1e8bfc077ebbc3289324df5fd78b2abe9ac08
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 17 13:42:11 2019 -0700

    fix a new bug I merged into development this morning. The original beta has only one component.

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 8234f20a4b91f4f75e9175d920778f34e64da2b9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 17 12:27:02 2019 -0700

    Update nodal projection code snippet

Docs/sphinx_documentation/source/LinearSolvers.rst

commit a11de4851a9a804f164fae5b14c2144d3f62be8a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 17 11:46:16 2019 -0700

    Update formatting slightly and README.

Tutorials/LinearSolvers/MAC_Projection_EB/README
Tutorials/LinearSolvers/Nodal_Projection_EB/README
Tutorials/LinearSolvers/Nodal_Projection_EB/main.cpp

commit 739c3d6d68f0d4a4537e8e8be8591f57dce1c2ba
Merge: 4f7e53aa8 87d4b8290
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 17 11:40:11 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4f7e53aa875297241fa83aa3d1e95ef5ecbb2b84
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 17 11:39:53 2019 -0700

    fix Nodal_Project_EB tutorial

Tutorials/LinearSolvers/Nodal_Projection_EB/main.cpp

commit 87d4b829056b2ce82a74b2042a663125b0eb44c5
Merge: 724ea5efb b1575042d
Author: asalmgren <asalmgren@lbl.gov>
Date:   Tue Sep 17 11:11:49 2019 -0700

    Merge pull request #569 from AMReX-Codes/fi_lincomb_fix
    
    Fix indexing in fortran interface for MultiFab::LinComb

commit b1575042dfc28a8e8388cbb0299c09dd01a9add9
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date:   Tue Sep 17 11:06:04 2019 -0700

    Decrement source component for multifab 2 in amrex_multifab_lincomb for the Fortran interface.

Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit f436dcb0b0fbabda05b130f604bb6a9ef7f9bfba
Merge: 724ea5efb 134547c30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 17 11:02:28 2019 -0700

    Merge branch 'weiqun/dev' into development

commit 724ea5efb70ea29c63ead0336a57e61af3a35e8d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 17 10:37:40 2019 -0700

    Update documentation about tutorials.

Docs/sphinx_documentation/source/LinearSolvers.rst
Docs/sphinx_tutorials/source/LinearSolvers_Tutorial.rst

commit 3f682a0cc4364b5936e07b4b59f12e5f1476eb7c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 17 10:08:12 2019 -0700

    Add example of nodal projection with EB analogous to the example in
    MAC_Projection_EB.  Current commit does not compile.

Tutorials/LinearSolvers/Nodal_Projection_EB/GNUmakefile
Tutorials/LinearSolvers/Nodal_Projection_EB/Make.package
Tutorials/LinearSolvers/Nodal_Projection_EB/README
Tutorials/LinearSolvers/Nodal_Projection_EB/inputs_3d
Tutorials/LinearSolvers/Nodal_Projection_EB/main.cpp

commit 9d2784bdb6c4f0d24a69660d91b9d9937c25b603
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 17 08:11:32 2019 -0700

    Simplify the EB MAC projection tutorial so it just sets nine obstacles
    rather than reading in the IDs from the inputs

Tutorials/LinearSolvers/MAC_Projection_EB/README
Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp

commit 7468387650aa78663e52e171254b3e6f6c95f478
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Sep 16 19:22:40 2019 -0400

    slight optimization(s)

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit ab21a5714209f1d41476c065774fb868cadae912
Merge: 3fbb1bff1 0a831349e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Sep 16 14:32:35 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 3fbb1bff10e5be33c8dcb6e08871485e84ffbfc3
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Sep 16 14:32:22 2019 -0700

    Update doc on nodal projection

Docs/sphinx_documentation/source/LinearSolvers.rst

commit ec9e0b574df10396ed6f40838276ac984e2c56a6
Author: cgilet <cgilet@gmail.com>
Date:   Mon Sep 16 16:37:59 2019 -0400

    WIP - make sure coarse-fine boundary corner cells get filled for AllPeriodic case.
    fix const qualifier in relation to m_bndry_sol in applyBCTensor.
    
    2D seems to work
    3D not finished yet

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit 0a831349e03e6065589d7131e41213eaeed31772
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 16 12:21:40 2019 -0700

    small update to docs

Docs/sphinx_documentation/source/AmrLevel_Chapter.rst

commit f6f35a89e1362de34a2398e77f0632e71724837c
Author: cgilet <cgilet@gmail.com>
Date:   Mon Sep 16 15:10:58 2019 -0400

    WIP - Add MLEBTensorOp::compFluxes(). Needs testing.

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 134547c30311c5dbcfbcb88da9b488676686e279
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 15 13:09:22 2019 -0700

    WIP: MLEBABecLap: gsrb on gpu

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H

commit ea806a44f01c8b9fc34948f96795e443bd28032f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 15 15:26:35 2019 -0700

    EB nodal solver: average cell-centered rhs to node

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 8572bcde16be61775c8cfd48798c3a7f8c26f53c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Sep 15 07:03:34 2019 -0700

    update documentation re bc's for linear solvers

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H

commit 2f2a270e461ec182e5c8cdb2e6a7e0884cea0684
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Sep 15 07:03:18 2019 -0700

    Add more detail re bc's for linear solvers

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 1b754697a9b4e39ec684ec7faae0686e7d51a6bb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Sep 14 19:15:30 2019 -0700

    Update to section on Linear Solvers: Boundary Conditions

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 58a1cc07b63ee66bcb0a863f34110989deef7f79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 14 16:47:22 2019 -0700

    MLEBABecLap: adotx on gpu

Src/Base/AMReX_Array4.H
Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H
Src/LinearSolvers/MLMG/Make.package

commit 64e4fac347463871fe0a267234a2ae683645b61d
Merge: 10f77a210 1b1d6c934
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Sat Sep 14 16:53:01 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 10f77a210aff7d79bf20a6a2b573713dc74fc340
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Sat Sep 14 16:52:48 2019 -0700

    CMake: add missing include statement

Tools/CMake/AMReXTargetHelpers.cmake

commit 1b1d6c934c441110b5a3350f4f081d85c7fba874
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Sep 14 16:43:12 2019 -0700

    Update the solver bc stuff and the MacProjection section.

Docs/sphinx_documentation/source/LinearSolvers.rst

commit b8a35448acb73edcc055f1ec66fbce535caf59ef
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Sep 14 15:31:18 2019 -0700

    Update section about boundary conditions for linear solvers

Docs/sphinx_documentation/source/LinearSolvers.rst

commit d21523b562071d1c244f05fa58e4789aae01c7ed
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 13 20:15:49 2019 -0700

    fix typos

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 705078d1572b854b6dd0777fe2e3b94b81b007ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 13 18:30:41 2019 -0700

    more gpu support in MLEBABecLap

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 00aa7bd9ef17f22a1bbc31fdde566c4951ff9a95
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 13 17:44:37 2019 -0700

    update FlowerIF

Tests/LinearSolvers/CellEB/MyEB.H
Tests/LinearSolvers/CellEB2/MyEB.H
Tests/LinearSolvers/EBConvergenceTest/MyEB.H
Tests/LinearSolvers/EBflux_grad/MyEB.H

commit 251c59b1d99cf2a895d71d36f6bd23f27e523e74
Merge: 8a8e7d994 9b64ea375
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Sep 13 17:40:12 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8a8e7d9948a6c167b9554d3070b24ac3914db5ec
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Sep 13 17:39:58 2019 -0700

    Doc: add snippet for nodal projection

Docs/sphinx_documentation/source/LinearSolvers.rst

commit af9b08897e842e1626eaab028f02d7e1bb51f8ce
Merge: 78ecbff7d 9b64ea375
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 13 11:58:59 2019 -0700

    Merge branch 'development' into weiqun/dev

commit 9b64ea375586d032b65ff64f8d1d8ab3b7bb5208
Merge: ad1e3fe1b fc72b7d4c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Sep 13 11:16:23 2019 -0700

    Merge pull request #560 from bcfriesen/bcf/cce9
    
    Tools: update compiler flags for Cray compiler v9

commit 4a3ecd6d7b1155d41147ffd3f18c47890682ddad
Merge: 5d757ec97 ad1e3fe1b
Author: cgilet <cgilet@gmail.com>
Date:   Fri Sep 13 10:41:01 2019 -0400

    Merge remote-tracking branch 'upstream/development' into TensorFluxes

commit 3676d6ab94e20d9b4506f72955c5dc0c573f896f
Author: cgilet <cgilet@gmail.com>
Date:   Fri Sep 13 10:28:02 2019 -0400

    WIP - 2D appears to work for MLTensorOp
    
    not fully tested yet

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H

commit ad1e3fe1bcb9dc04d8efde837dc0db75f268d530
Merge: 93a3d048b ceb2251bb
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Sep 12 16:41:29 2019 -0700

    Merge branch 'mr/cmake' into development

commit ceb2251bba23af7de3d2cc5f8254e9bdb614dd7b
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Sep 12 16:07:02 2019 -0700

    Revert "CMake: improve handling of arguments passed to makebuildinfo.py"
    
    This reverts commit ca09eddd5d5e2f82c6f84641ed1101b47a27ec30.

Tools/CMake/AMReXBuildInfo.cmake

commit ca09eddd5d5e2f82c6f84641ed1101b47a27ec30
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Sep 12 14:42:51 2019 -0700

    CMake: improve handling of arguments passed to makebuildinfo.py

Tools/CMake/AMReXBuildInfo.cmake

commit 92a1cce9032baa046cf37a9f12a7bd09d7dfcd42
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Sep 12 13:34:27 2019 -0700

    CMake: add quotes to arguments when invoking build info script

Tools/CMake/AMReXBuildInfo.cmake

commit 93a3d048b051601b32b49d191f7f9dc564aaf1dd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 12 12:50:52 2019 -0700

    Add first text about nodal approximate projection.

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 154679833f37b007c440da4cd87d089dab92cfef
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 12 11:34:31 2019 -0700

    Update to reflect we can't do level solves with this functionality yet.

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 404567294e8e4122795d844133447c42da9af022
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Sep 12 10:55:07 2019 -0700

    CMake: use verbatim mode to issue command to makebuildinfo python script

Tools/CMake/AMReXBuildInfo.cmake

commit 06320a01d5c8a8663579b00b0e2575c31d9629ed
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 12 02:57:18 2019 -0700

    add inhomog Neumann as boundary type

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 78ecbff7d3add7861ecb50b981e716b71edc1065
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 11 16:54:28 2019 -0700

    prepare some linear solver tests for gpu

Tests/LinearSolvers/CellEB/MyTest.H
Tests/LinearSolvers/CellEB/MyTest.cpp
Tests/LinearSolvers/EBflux_grad/MyTest.H
Tests/LinearSolvers/EBflux_grad/MyTest.cpp
Tests/LinearSolvers/NodeEB/MyTest.H
Tests/LinearSolvers/NodeEB/MyTest.cpp

commit ec945bdaeaa231decde6ff7f1ba278e6388d5598
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 11 15:34:28 2019 -0700

    gpu for Mask

Src/Boundary/AMReX_MultiMask.cpp

commit ad668b8d7acafc8570304a6c8d31ff28f3806822
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 11 15:12:50 2019 -0700

    add inhomogNeumann to opeartor<< and minor clean up

Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_LO_BCTYPES.cpp

commit c9923e9be3e1592ea8ebe76c89a40db572db1dbd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 11 15:12:24 2019 -0700

    minor changes to get NodalPoisson test compile with cuda

Tutorials/LinearSolvers/NodalPoisson/MyTest.H
Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp

commit e16a4b9d5703e17b64ab963597e9ab1d14661ee7
Merge: 71f8baa3a 603b3624f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Sep 11 17:57:47 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 71f8baa3a928e047e193dc908c0938cec9df7c74
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Sep 11 17:48:30 2019 -0400

    always get the list of neighbor ranks from the redistribute mask

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_Particles.H

commit 6bf8f68ce7d9efff4748f37ab9c30c9990721299
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Sep 11 17:47:53 2019 -0400

    these memcopies need to be synchronous

Src/Particle/AMReX_ParticleContainerI.H

commit 603b3624ffcda70b73a1dfebfb03e87ae2cc2cf1
Merge: 2a7d2e537 7b77f05e5
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 11 14:32:53 2019 -0700

    Merge pull request #561 from ax3l/topic-constCorrectness
    
    FabConv: Little Const-Correctness Params

commit 2a7d2e537af6bbe03113cf578663d46428b167c2
Merge: 9a0c93ced 811ac1534
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 11 14:31:14 2019 -0700

    Merge pull request #562 from ax3l/doc-mpiCUDA
    
    Docs: Intro (+MPI/CUDA)

commit 811ac1534e5c68da72f0616ed033267d2aef93ab
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Sep 11 14:21:23 2019 -0700

    Docs: Intro (+MPI/CUDA)
    
    Update the introduction in the docs:
    AMReX also supports MPI/CUDA these days :)

Docs/sphinx_documentation/source/Introduction.rst

commit 7b77f05e54dacd5f7e341f6c509892b77a4f5897
Author: Axel Huebl <axel.huebl@plasma.ninja>
Date:   Wed Sep 11 14:15:13 2019 -0700

    Little Const-Correctness Params
    
    Just two little places found when compiling WarpX with
    clang tidy and:
    https://clang.llvm.org/extra/clang-tidy/checks/readability-non-const-parameter.html

Src/Base/AMReX_FabConv.cpp

commit fc72b7d4c3aafd708a493edc19ebd094023a7b42
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Sep 11 10:48:47 2019 -0700

    Tools: update compiler flags for Cray compiler v9
    
    In CCE 9, Cray overhauled their C/C++ compilers and moved to clang/LLVM, so the
    flags for C/C++ compilers are totally different than in previous versions of
    CCE. Confusingly, the Fortran compiler was *not* changed significantly in CCE
    9, so its flags are the same as before. As a result, we need some more complex
    logic to get the right flags for the right version of CCE.

Tools/GNUMake/comps/cray.mak

commit 9a0c93cedb61828ae635796723674c9766506442
Author: cgilet <cgilet@gmail.com>
Date:   Wed Sep 11 13:43:10 2019 -0400

    Fix typo, n-> icomp

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit bbb3575d31ce6b3e1c29e6361c9280ccf8000000
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 11 10:22:16 2019 -0700

    need to update the multi-component version of setDomainBC

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit b4f5caa8d028bc273892a39004dcfb10cba61da4
Author: Candace Gilet <cgilet@users.noreply.github.com>
Date:   Wed Sep 11 12:18:41 2019 -0400

    Make sure Vector bounds check catches negative indices. (#559)
    
    * Make sure Vector bounds check catches negative indices.
    
    * Cleaner way to check Vector bounds

Src/Base/AMReX_Vector.H

commit f07671bccbf91bc83e83a3a2d0f63a8a10b4f704
Merge: 82d9bb7c8 1db1b179f
Author: cgilet <cgilet@gmail.com>
Date:   Wed Sep 11 12:15:19 2019 -0400

    Merge remote-tracking branch 'upstream/development' into development

commit 82d9bb7c82aca2a0e623a5b65bd624518b843851
Author: cgilet <cgilet@gmail.com>
Date:   Wed Sep 11 12:14:36 2019 -0400

    Cleaner way to check Vector bounds

Src/Base/AMReX_Vector.H

commit 1db1b179f9129efb383c417dbbf79f04069f1752
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 10 21:04:39 2019 -0700

    inhomogeneous Neummann in curvilinear coordinates

Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit a2a31c2a0dbda45f46a90fcb29ef7c80662019e3
Author: cgilet <cgilet@gmail.com>
Date:   Tue Sep 10 20:55:03 2019 -0400

    Make sure Vector bounds check catches negative indices.

Src/Base/AMReX_Vector.H

commit adfb00b8c430761514350c8f4aa03c9dc569c069
Merge: c0fd94d09 431f5ad1c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Sep 10 16:31:18 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c0fd94d0941b7f7a66cbd5084b2fcd1dea864742
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Sep 10 16:30:37 2019 -0400

    need to add a Barrier at the start of communicateParticles

Src/Particle/AMReX_ParticleCommunication.H

commit 431f5ad1c31d0a100f527c8fe07b6d61d8bba91e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 10 10:33:12 2019 -0700

    minor optimization

Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H

commit d1a3eb16769e26ca0c4ef600486d20aba824f9b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 10 09:56:54 2019 -0700

    fix test problem boundary

Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H

commit f599e85af1e33ac7c9731416db92a77efbeea8ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 9 22:15:45 2019 -0700

    MLMG: inhomogeneous Neumann

Src/Boundary/AMReX_LO_BCTYPES.H
Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/MyTestPlotfile.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H
Tutorials/LinearSolvers/ABecLaplacian_C/inputs-inhomNeumann

commit 6ea36dd251f0ff346ef364138c96fa4bafc1a37e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 8 16:12:05 2019 -0700

    fix order of initialization

Src/Particle/AMReX_ParticleLocator.H

commit 7c89abac3b2245ff8856b9bd8b80f576c3264bb1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 8 14:38:27 2019 -0700

    fix some bugs in BaseFab

Src/Base/AMReX_BaseFab.H

commit 3c9f647938caa1ac4d5535f47d04352db8150984
Merge: 12825e658 9746b6a06
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 7 18:28:41 2019 -0700

    Merge branch 'weiqun/dev' into development

commit 9746b6a06d88bc5524a2143f2fbd4853c8e5040a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 7 21:25:13 2019 -0400

    fix type

Src/Base/AMReX_GpuReduce.H

commit 3d1c9a51e023a2054dc37ca5cf31e88eefccfb09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 7 18:14:32 2019 -0700

    fix new bug

Src/Base/AMReX_GpuReduce.H

commit 195a2e3797463aba63c39ab6220edbe639647b36
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 7 18:03:18 2019 -0700

    minor

Src/Base/AMReX_Reduce.H

commit 22992d0fc02dee1349d5062526dc283d7217772d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 7 16:14:42 2019 -0700

    optimization of iMultiFab::sum

Src/Base/AMReX_iMultiFab.cpp

commit e09715044c21bc5030e6e65cb4a6feb11bb2167c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 7 15:56:16 2019 -0700

    reimplement FabArray Reduce

Src/Base/AMReX_FabArrayUtility.H

commit e5816d9eaf47d9cbf9f4e6b21f63922ecbc98b5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 7 15:55:34 2019 -0700

    add ReduceOpLogicalAnd and Or

Src/Base/AMReX_Reduce.H

commit 0003da79d74e6c4cecb76dddb2a7d04b9e1538d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 7 14:53:00 2019 -0700

    add deviceReduceLogicalAnd and Or

Src/Base/AMReX_Functional.H
Src/Base/AMReX_GpuReduce.H

commit 12825e658fdaf12a61a9b9a47fc20962ba580c2b
Merge: 7017e21e9 14c29ab92
Author: asalmgren <asalmgren@lbl.gov>
Date:   Sat Sep 7 13:08:12 2019 -0700

    Merge pull request #558 from cgilet/development
    
    Development

commit 7017e21e9addc3486d93105ba3d2af68b968f4d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 7 12:22:36 2019 -0700

    ReduceOps now takes lambda on Box

Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_Reduce.H
Src/Base/AMReX_Utility.H
Tutorials/GPU/ParallelReduce/main.cpp

commit dc7b72e372550e01f111b439b14e5284762d90a6
Merge: 3a1afb7be 5c0c14bdc
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Sep 6 16:44:55 2019 -0700

    Merge branch 'mr/cmake' into development

commit 5c0c14bdcbdd8daf22042453cb8bfc60183b4adb
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Sep 6 16:41:45 2019 -0700

    CMake: improve build summary printout

Src/CMakeLists.txt
Tools/CMake/AMReX_Config.cmake

commit 4f279e5975195ecf77f4a0061fa9ad95cdb366e0
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Sep 6 15:19:24 2019 -0700

    CMake: add comments to document new modules

Tools/CMake/AMReXBuildInfo.cmake
Tools/CMake/AMReXTargetHelpers.cmake

commit 1ada310f6909ebebe14ace16516ee8751b248d36
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Sep 6 14:39:21 2019 -0700

    CMake: add GIT info in BuildInfo

Tools/CMake/AMReXBuildInfo.cmake

commit 3a1afb7be0e22b306870c521b4020ce2f9ff6c47
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 6 12:41:41 2019 -0700

    move -> forward because we have recently changed the parameters from r-value to forwarding reference

Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_GpuLaunchFunctsG.H

commit c95776aa0c31d95f432ca9adce2e5fb633e14728
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Sep 6 11:30:05 2019 -0700

    CMake: make OpenMP imported targets GLOBAL

Tools/CMake/AMReX_Config.cmake

commit b629b1135cc806f447cbbdcfb6a4146acfd266c1
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Sep 6 11:20:17 2019 -0700

    CMake: make imported targets GLOBAL

Src/Base/CMakeLists.txt
Src/Extern/Conduit/CMakeLists.txt
Src/F_Interfaces/CMakeLists.txt
Tools/CMake/FindHYPRE.cmake
Tools/CMake/FindSUNDIALS.cmake

commit da30684a6d2dc79a008cb4d3f86f1778f80ab41d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 6 09:47:27 2019 -0700

    added PETSc to linear solver doc

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 14c29ab92a0e78c67c39a8fb4eaa2021a59c7ab8
Author: cgilet <cgilet@gmail.com>
Date:   Fri Sep 6 11:21:53 2019 -0400

    update MACProjector documentation and tutorial

Docs/sphinx_documentation/source/LinearSolvers.rst
Docs/sphinx_tutorials/source/LinearSolvers_Tutorial.rst

commit aa1bf886d64c7f038211557d120e75b2aa78c916
Author: cgilet <cgilet@gmail.com>
Date:   Fri Sep 6 11:09:26 2019 -0400

    Update so commented examples will work if uncommented.

Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp

commit 0e73f21c8f074ee8025984a2e1e0a118aa41a387
Author: cgilet <cgilet@gmail.com>
Date:   Fri Sep 6 11:02:44 2019 -0400

    Update comments to reflect what code actually does

Tutorials/LinearSolvers/MAC_Projection_EB/inputs_3d

commit 008d037ed5ebc4ea9e8e8322f6e18f6b69d217a2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 6 02:08:38 2019 -0700

    Add comment that Dirichlet bc's are assumed to be homogeneous

Docs/sphinx_documentation/source/LinearSolvers.rst

commit bf646f521bd953e9072ce0514bc8269b6913d523
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 6 02:04:44 2019 -0700

    Merge the description of non-zero S with the rest of the text.

Docs/sphinx_documentation/source/LinearSolvers.rst

commit e0aeea779499807c5f61c67f470628909ba88335
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Sep 5 18:32:11 2019 -0700

    CMake: handle amrex path when generating build info

Tools/CMake/AMReXBuildInfo.cmake

commit 8a6d5bb7793540982664a5215d5754068cbbd794
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Sep 5 18:27:39 2019 -0700

    CMake: make get_target_prop_recursive() more robust

Tools/CMake/AMReXTargetHelpers.cmake

commit cc59803e110dbd0711567a6ad9c2dbc5a0b32080
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Sep 5 16:08:56 2019 -0700

    CMake: fix typo

Tools/CMake/AMReXBuildInfo.cmake

commit 7aba0f9d281bf422717cd54a5f00ed3f67e8d9e4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Sep 5 16:07:46 2019 -0700

    CMake: make BuildInfo module more robust

Tools/CMake/AMReXBuildInfo.cmake

commit 20bebfc52f7271aa219a710454369884059a7138
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Sep 5 15:49:12 2019 -0700

    note on how to specific non-zero divergence for MAC projection tutorial

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 1a654edab85ac8359ce737b87257f4e9e7cb5d0a
Merge: 78e55950d 011bcacbf
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 15:26:46 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 78e55950d20495f0e8f8710a595f80f6368f3eb5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 15:10:48 2019 -0700

    Fix typo

Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst

commit 011bcacbf754356f3a420c9079e3d0a5093ba768
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 5 15:03:23 2019 -0700

    latest AMReX regression test script

Tools/RegressionTesting/AMReX-tests.ini

commit bbd5330b88e3806ca21ddf21afa044df63d2865d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 14:52:38 2019 -0700

    hypre --> External Solvers (still needs petsc info)

Docs/sphinx_documentation/source/LinearSolvers.rst

commit a442c46cda17bccfb27bf5a884b64303b1719058
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 14:49:55 2019 -0700

    Swap B <--> beta in linear solver notation

Docs/sphinx_documentation/source/LinearSolvers.rst
Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst

commit 78738496d4600b7988567d45102b6c2a930902cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 5 14:35:56 2019 -0700

    minor change and make it work for C++11

Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp

commit db01dbe8d490729c6c8604ebc6aac1aa4bf21aa6
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Sep 5 13:37:44 2019 -0700

    updated mac projection tutorial documentation + comments

Docs/sphinx_documentation/source/LinearSolvers.rst
Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp

commit f3fa7be8f06a86a4f2a8811342ecd8ddddfeadcf
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Sep 5 10:36:20 2019 -0700

    CMake: update some modules to reflect new changes

Tools/CMake/AMReXTypecheck.cmake
Tools/CMake/AMReX_Config.cmake

commit b4f79407f07989fc4a63317c5e69715277af0e86
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 06:39:21 2019 -0700

    Update docs

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 7236800c920b661dafd47fdee46c601a60728fae
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 06:32:42 2019 -0700

    Update MACProjector documentation and tutorial.

Docs/sphinx_documentation/source/LinearSolvers.rst
Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp

commit 54db3a97d86cd5b87ccb9618c3b6bf003cc131db
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 04:10:00 2019 -0700

    Fix formatting

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 7e3b7651fe49529ef4b7aa851e469661d432416e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 04:10:00 2019 -0700

    Fix formatting

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 04b6967657355481b593f8cc16cd4ad49b18f67f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 03:55:26 2019 -0700

    Update with code snippet for MAC Projection.

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 3772272cd221dae3b15d8668235031dfea80d218
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 03:55:26 2019 -0700

    Update with code snippet for MAC Projection.

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 404cd3f46b54a27c233a786eeebf47ead319ee7c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 03:23:30 2019 -0700

    change default

Tutorials/LinearSolvers/MAC_Projection_EB/Backtrace.0
Tutorials/LinearSolvers/MAC_Projection_EB/GNUmakefile

commit a6cf6104f24d78b793fdcb3c22507bf0758e91f3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 03:22:27 2019 -0700

    Oops -- didn't want to commit the plotfile

Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Header
Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Level_0/Cell_D_00000.REMOVED.git-id
Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Level_0/Cell_H

commit 2752fabf1b9354d9363bf4fa42ac422b2c457a1e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 03:21:37 2019 -0700

    Add new tutorial demonstrating MACProjection with EB obstacles.

Tutorials/LinearSolvers/MAC_Projection_EB/Backtrace.0
Tutorials/LinearSolvers/MAC_Projection_EB/GNUmakefile
Tutorials/LinearSolvers/MAC_Projection_EB/Make.package
Tutorials/LinearSolvers/MAC_Projection_EB/README
Tutorials/LinearSolvers/MAC_Projection_EB/inputs_3d
Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp
Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Header
Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Level_0/Cell_D_00000.REMOVED.git-id
Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Level_0/Cell_H

commit 3f43eb2d8ce294d6fcfb1f7f34105b7bd50f7999
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 02:13:40 2019 -0700

    Update linear solver section of documentation

Docs/sphinx_documentation/source/LinearSolvers.rst
Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst

commit a9b5ac54059109bd96eebf608c8b00c2fda6d07f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 5 02:13:40 2019 -0700

    Update linear solver section of documentation

Docs/sphinx_documentation/source/LinearSolvers.rst
Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst

commit 08500484ac27cbc40eed92d458c6493e193f6150
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Sep 4 17:51:18 2019 -0700

    CMake: change paradigm to include build info into app code.
    
    * Create a dedicated CMake module
    * Let application code to drive the inclusion of build info into
      consuming target.

Src/CMakeLists.txt
Tools/CMake/AMReXBuildInfo.cmake

commit a39926c9dfbb44da0de621c1471599900b9a8ec2
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Sep 4 17:49:53 2019 -0700

    CMake: add a module to collect helpers to handle targets

Tools/CMake/AMReXTargetHelpers.cmake

commit 6bc7af4fb202adef92193df793fa1f6222d5c99e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Sep 4 17:38:24 2019 -0700

    CMake: improve GENEX handling.
    
    * Group genex-related macros/functions in a dedicated module file
    * evaluate_genex: add support for NOT operation
    * evaluate_genex: improve handling of COMPILE_LANGUAGE genex

Tools/CMake/AMReXGenexHelpers.cmake
Tools/CMake/AMReX_Utils.cmake

commit 71699c5bfee86e48c1f6a0ff33dd9c12f0d4adf5
Merge: 138b1a3cf 9cbb98ad2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Sep 4 19:02:55 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 138b1a3cfceeab4e185a22671a37e9264140d4ef
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Sep 4 19:02:33 2019 -0400

    optimization - reduce number of messages sent in communicateParticles

Src/Particle/AMReX_ParticleCommunication.cpp

commit 5d757ec976cc9d71fd2494536d638bcb88c92f1a
Merge: 8e5f6dbe6 9cbb98ad2
Author: cgilet <cgilet@gmail.com>
Date:   Wed Sep 4 16:49:24 2019 -0400

    Merge remote-tracking branch 'upstream/development' into TensorFluxes

commit 9cbb98ad29d657ae8aa7ac6f3e567ff8ebde5b98
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 4 13:03:56 2019 -0700

    a fix for the local + CPU + single precision particles

Src/Particle/AMReX_ParticleContainerI.H

commit 5b76d34eab080a20c34f13c53af6697748c369b4
Merge: 17929af07 4f7b4a43d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 4 10:59:22 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 17929af0709fe005f90de1ea81366490afd64206
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 4 10:59:11 2019 -0700

    convert image to png (docs) (travis)

Docs/sphinx_documentation/source/LinearSolvers.rst
Docs/sphinx_documentation/source/LinearSolvers/refluxfreecoarsefine.png

commit 053d18b01f8a755b3184a347ebdbab5ab5d97789
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 4 10:51:19 2019 -0700

    (travis) remove this package

.travis.yml

commit 4f7b4a43deebb015ee7d44436e3baf6a3dbf9fa8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 4 10:21:14 2019 -0700

    fcompare: option to set a relative tolerance

Tools/Plotfile/fcompare.cpp

commit 4a5deef8003d6cc1b50c6cd20c8e92ac4f5fe566
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 3 17:01:32 2019 -0700

    add svg package to travis build

.travis.yml

commit 9229d21d926e4cf2d5c6f04bca373fad93d7f290
Merge: c56f8af2a 3c5529e9c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 3 16:50:24 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c56f8af2ae8c26f11477dfb403251badf464fca4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 3 16:50:09 2019 -0700

    seems that we need travis_wait again

.travis.yml

commit 3c5529e9cdcaa0369e0e9a96bd1f065b818562c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 3 16:25:53 2019 -0700

    remove noexcept so that Intel 18 is happy

Src/EB/AMReX_EBCellFlag.H

commit 2d905c33b2b5e678222b8b7db90af2e8b98c25f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 3 16:25:53 2019 -0700

    remove noexcept so that Intel 18 is happy

Src/EB/AMReX_EBCellFlag.H

commit 2663b515bdbf9f6009f262e82ccf21cfe26172a8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 3 16:24:30 2019 -0700

    move assignment and constructor for ParticleContainer

Src/Particle/AMReX_Particles.H

commit d1915ec18412141becf8a1f1c93e4e215bf1061e
Merge: cba6b99ca 08e8856e6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Sep 3 18:39:25 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cba6b99caee19a559584a92999301015ae99f566
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Sep 3 18:38:50 2019 -0400

    need to reset the m_need_handshake flag when calling fillNeighbors

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit db496c41d1b1f7ab62b8bce31407a1624c0d4fbf
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Sep 3 15:29:06 2019 -0700

    Add missing include guards.
    
    CMake: do no process installed headers with name ending in "*I.H"
    since they are meant to always be included by host headers which
    are properly processed after installation.

Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_ParticleInit.H
Tools/CMake/modify_installed_headers.cmake

commit 08e8856e6b6f24336a044b6a08d449d737f7705a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 3 13:12:22 2019 -0700

    MultiComponent tutorial: call Finalize()

Tutorials/LinearSolvers/MultiComponent/main.cpp

commit beccdce9df0ce4aff04674f243eb4b0447246e3f
Merge: efc8c2eea 4810b679f
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 3 12:09:45 2019 -0700

    Merge pull request #556 from AMReX-Codes/mcmlmg-test
    
    Mcmlmg test

commit 4810b679fe82d1b5fbd65e37b1b0078cdad69313
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Sep 3 12:21:53 2019 -0600

    added sphinx documentation

Docs/sphinx_documentation/source/LinearSolvers.rst
Docs/sphinx_documentation/source/LinearSolvers/refluxfreecoarsefine.pdf
Docs/sphinx_documentation/source/LinearSolvers/refluxfreecoarsefine.svg
Docs/sphinx_tutorials/source/LinearSolvers_Tutorial.rst

commit efc8c2eea13397c9e5af854af7bd091d9c79e631
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 3 10:26:32 2019 -0700

    add missing parameter to inputs.rt

Tests/Particles/Redistribute/inputs.rt

commit 5e5953426fa1e620e344eebda36f19c65c348c48
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 3 10:25:00 2019 -0700

    change test name

Tests/Particles/Intersection/main.cpp

commit ac507c8f89ef340afcc850e04651099a6d6b5eda
Merge: 4179e74be 841b39215
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 3 10:24:17 2019 -0700

    Merge branch 'global_redistribute_gpu' into development

commit 016898f4e017c8045b2ad3cff08130d21d80ec4f
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Sep 3 11:17:16 2019 -0600

    added documentation to tutorial

Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.H
Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp
Tutorials/LinearSolvers/MultiComponent/inputs
Tutorials/LinearSolvers/MultiComponent/main.cpp

commit 4179e74be5f865dea412787ae120aa1f4f8c254e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 3 09:07:09 2019 -0700

    update CHANGES

CHANGES

commit 5de4d3a2487c3d261adb760aa2c6068c74d6e844
Merge: 68d0036bb 32a5f97b3
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Sep 3 09:47:15 2019 -0600

    Merge branch 'development' into mcmlmg-test

commit 68d0036bb9fce5af504207ddb5b68defe610dde5
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Sep 3 09:46:40 2019 -0600

    moved to tutorials

Tutorials/LinearSolvers/MultiComponent/GNUmakefile
Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.H
Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp
Tutorials/LinearSolvers/MultiComponent/Make.package
Tutorials/LinearSolvers/MultiComponent/inputs
Tutorials/LinearSolvers/MultiComponent/main.cpp

commit 32a5f97b31c5fe04caf925f50f2dbfabfb535458
Author: Jean Sexton <jmsexton@lbl.gov>
Date:   Sat Aug 31 14:22:15 2019 -0400

    Fix typo

Src/Particle/AMReX_NeighborParticlesI.H

commit 59c01ff2a4e78df937ec14731e032dee12964b25
Merge: 0c28d4ae5 c1729131b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 30 16:56:31 2019 -0700

    Merge branch 'weiqun/dev' into development

commit c1729131b8fa27b020d1bf7b8b6e98f68d1cd7d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 30 16:43:36 2019 -0700

    add explicit host dtors so that host device versions are not generated

Src/EB/AMReX_EB2_IF_Complement.H
Src/EB/AMReX_EB2_IF_Difference.H
Src/EB/AMReX_EB2_IF_Extrusion.H
Src/EB/AMReX_EB2_IF_Intersection.H
Src/EB/AMReX_EB2_IF_Lathe.H
Src/EB/AMReX_EB2_IF_Rotation.H
Src/EB/AMReX_EB2_IF_Translation.H
Src/EB/AMReX_EB2_IF_Union.H

commit 3f0c1f375bfd23b5442d34d78c8f8fc53fbd1a2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 30 13:29:48 2019 -0700

    PolynomialIF on GPU

Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuMemory.H
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EB2_IF_Intersection.H
Src/EB/AMReX_EB2_IF_Polynomial.H
Src/EB/AMReX_EB2_IF_Translation.H
Src/EB/AMReX_EB2_IF_Union.H

commit 841b392159ce95e803bcf8347be792288a4f2ed2
Merge: 952ddecdc 709261bf9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 30 13:47:22 2019 -0700

    Merge branch 'global_redistribute_gpu' of github.com:AMReX-Codes/amrex into global_redistribute_gpu

commit 952ddecdc7ebdf4fa6926bc0ba0b7a8e4c1d32ed
Merge: ed272f30f 0c28d4ae5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 30 13:47:03 2019 -0700

    Merge branch 'development' into global_redistribute_gpu

commit 0c28d4ae5fe50b228ce10dbabaac1a359e3bc2d1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 30 13:45:37 2019 -0700

    fix typos

Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleContainerI.H

commit 241dbb88e0c0dab69fb6d6f51f19965c16156364
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 30 13:44:22 2019 -0700

    call base fab setVal instead of fab array one in threaded region (avoids race condition)

Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleContainerI.H

commit 709261bf93827dab0afb3f0809384d07bfadf056
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 30 15:20:32 2019 -0400

    fix typo in test

Tests/Particles/Redistribute/main.cpp

commit 9606c8cd72339346a9df6ecd1a4ece30878f1ca1
Merge: 941ea6f49 19d52da90
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 30 15:08:56 2019 -0400

    Merge branch 'development' into global_redistribute_gpu

commit 19d52da90959d833abf4c15f008bff32b25d03dd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 30 11:27:14 2019 -0700

    use an ifdef for MPI in these particle comm routines

Src/Particle/AMReX_ParticleCommunication.cpp

commit 1a3f65100ed48f518c264bdaf88eb27fbdd8ea7a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 30 11:08:55 2019 -0700

    workaround for gcc 8.2 bug

Src/Particle/AMReX_ParticleLocator.H

commit 941ea6f49640843c2f428424dd688d687af0ad0b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 29 21:17:19 2019 -0400

    some more error checking

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleLocator.H

commit 3e6e41469c7ddb9c95eaf553eeae5ecf6b52703d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 29 21:15:02 2019 -0400

    set this size so it can be used in error checking

Src/Particle/AMReX_ParticleTile.H

commit bce8ae8073485aebed33d9f99c0d6e6e594b8778
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 29 17:51:46 2019 -0700

    rm deprecated functions

Src/Base/AMReX_MultiFabUtil_1D_C.H
Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H

commit ed272f30fc88fdcfedec0b71a8a73856cbfa087c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Aug 29 17:35:51 2019 -0700

    make sure we rebuild the particle locator even if not local

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleLocator.H

commit fdafac6ce0cea7a79090664296ca6faed79bd18d
Merge: 9b3512a64 6b4b8dda2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 29 17:34:16 2019 -0700

    Merge branch 'development' into weiqun/dev

commit 6b4b8dda2cc65d8abe78296a71f819d8d0d4c040
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 29 19:47:35 2019 -0400

    fix particle locator for 2D

Src/Particle/AMReX_ParticleLocator.H

commit 5b42f4ed282bcc017579a2085fef6901cd0f1611
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 29 19:48:55 2019 -0400

    fix dmap in test

Tests/Particles/Redistribute/main.cpp

commit effee01844a74590ca74cece44f39c2752280821
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 29 19:48:31 2019 -0400

    update Intersection test for multiple levels

Tests/Particles/Intersection/inputs
Tests/Particles/Intersection/main.cpp

commit 13028965d20144a4f8e50ca4707fbccba3e53068
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 29 19:47:35 2019 -0400

    fix particle locator for 2D

Src/Particle/AMReX_ParticleLocator.H

commit 4fefe62968f6fbb4e191c0e8e8beee694a1e7e37
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 29 19:47:11 2019 -0400

    add timer

Src/Particle/AMReX_ParticleBufferMap.cpp

commit 9b3512a64a51a8ddd7f6f83f6270f3efaf491450
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 29 16:25:29 2019 -0700

    should not include old header

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit edb0d51af6f8d4ab381ffe2dc04c23e8cfcce9ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 29 16:17:28 2019 -0700

    rm deprecated Fortran files

Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_3d.F90
Src/EB/AMReX_EBMultiFabUtil_F.H
Src/EB/CMakeLists.txt
Src/EB/Make.package

commit a54a2b1a6ec2d2155322b72e20567280fa1aaac2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 29 16:03:48 2019 -0700

    EBMultiFabUtil on GPU

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFabUtil_1D_C.H
Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit 6a422fae1c09ed26eeb91d4b15ab7b2c0bb804ad
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 29 15:54:12 2019 -0400

    add test for global gpu redistribute

Tests/Particles/Redistribute/inputs
Tests/Particles/Redistribute/main.cpp

commit b89f02a3fcdbd2ba658743497048b6a84816b06b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 29 15:53:46 2019 -0400

    allow non-local redistribute to be dispatched to the GPU

Src/Particle/AMReX_ParticleContainerI.H

commit 668e753641d9dff0388792cfeefe022ceb3b5ba8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 29 15:26:41 2019 -0400

    implement non-local mpi communication pattern for gpu redistribute

Src/Particle/AMReX_ParticleCommunication.cpp

commit 1db0a894dc6f289fdaf31d0cbd7585e594cf58e3
Merge: 8e42f03a7 ed60ddbf5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 29 14:39:33 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ed60ddbf5c59cd580d23b1e1438a7c29d2af7d42
Merge: 6a8450425 fd4b944b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 29 10:33:16 2019 -0700

    Merge branch 'weiqun/dev' into development

commit 6a8450425ddf02c2ba4f219a53d55e29598357a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 29 10:33:10 2019 -0700

    add an assertion

Src/Base/AMReX_FabArray.H

commit fd4b944b12cbf1ec3fb893e2e3d26d62881435f1
Merge: 9b39b9a19 1a21a0aec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 29 10:07:23 2019 -0700

    Merge branch 'development' into weiqun/dev

commit 9b39b9a19e8be135c00e912539e4a29f4106fc59
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 29 10:06:59 2019 -0700

    tidy

Src/AmrCore/AMReX_Interpolater.cpp
Src/Base/AMReX_GpuLaunch.H
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EBInterpolater.cpp

commit 1a21a0aecce23e8b593138ee67bc4fd988dc0d19
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 29 09:09:15 2019 -0700

    fix knapsack when nmax is very small

Src/Base/AMReX_DistributionMapping.cpp

commit 0c80f47cfb37ecb20dc4c8e36ad9394cca845891
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 29 04:42:45 2019 -0700

    EBFluxRegister: rm Fortran

Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_1d.F90
Src/EB/AMReX_EBFluxRegister_2D_C.H
Src/EB/AMReX_EBFluxRegister_2d.F90
Src/EB/AMReX_EBFluxRegister_3D_C.H
Src/EB/AMReX_EBFluxRegister_3d.F90
Src/EB/AMReX_EBFluxRegister_F.H
Src/EB/CMakeLists.txt
Src/EB/Make.package

commit e78b43df62ce3870dd9b255c571532c7e41096c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 28 22:09:38 2019 -0700

    avoid name conflicts

Src/Base/AMReX_GpuLaunchMacrosG.H

commit b2d1baae7723e6f9df4b4f98786eaa296d693401
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 28 21:58:06 2019 -0700

    EBFluxRegister: rereflux

Src/Base/AMReX_GpuLaunchMacrosG.H
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_2D_C.H
Src/EB/AMReX_EBFluxRegister_3D_C.H

commit e2a62d8646b14f1f48b41b55061363895b73d0e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 28 18:05:17 2019 -0700

    EBFluxRegister: fine add dm

Src/EB/AMReX_EBFluxRegister.H
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_2D_C.H
Src/EB/AMReX_EBFluxRegister_3D_C.H
Src/EB/AMReX_EBFluxRegister_nd.F90

commit e6434bc851a35b1a49eb57ad15e6c85ad2d1b616
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 28 17:05:00 2019 -0700

    EBFluxRegister fine_add: rm a temporary array

Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_2D_C.H
Src/EB/AMReX_EBFluxRegister_3D_C.H

commit 8e42f03a7244e8c8e9a09ca8f10e98cd0200c0f3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 28 19:53:22 2019 -0400

    some more code reuse

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleUtil.H

commit 2eeac2a3ea157afb0825a5f5a97eed9ad1b15b98
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 28 19:47:00 2019 -0400

    some code reuse

Src/Particle/AMReX_ParticleUtil.H

commit 6e61fe0fbfb30f65f115a23b89c65dc51f1c935d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 28 19:37:12 2019 -0400

    fix cpu compile

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleLocator.H

commit 81ef27d0b246ccc3012e0ea76f00191ec15d63d0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 28 19:18:24 2019 -0400

    use the new non-local distributor in the gpu redistribute

Src/Particle/AMReX_ParticleContainerI.H

commit 55bf3deaf076e7ff4c1611ca2096839aaef8cc93
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 28 16:15:52 2019 -0700

    EBFluxRegister: fineadd

Src/Base/AMReX_Array4.H
Src/Base/AMReX_GpuLaunch.H
Src/EB/AMReX_EBFluxRegister.H
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_2D_C.H
Src/EB/AMReX_EBFluxRegister_3D_C.H

commit 4a4069255cc745785ae45acd9d4b947e8b7fc27f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 28 18:06:56 2019 -0400

    a particle locator to the ParticleContainer class

Src/Particle/AMReX_Particles.H

commit 34e0b7c24e8da15f047cbd9e0a41101908149474
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 28 18:06:28 2019 -0400

    a get particle cell function

Src/Particle/AMReX_ParticleUtil.H

commit b56b964b7e1b98b31d667e5a9ae0168604d6eda6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 28 17:29:47 2019 -0400

    test for the GPU boxarray intersection class

Tests/Particles/Intersection/GNUmakefile
Tests/Particles/Intersection/Make.package
Tests/Particles/Intersection/inputs
Tests/Particles/Intersection/main.cpp
Tests/Particles/Intersection/script.sh

commit 2a20abfbbd6217c0429b7c9cdd0100b6f50ba9ba
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 28 17:28:00 2019 -0400

    add class for locating particles on the gpu with no assumption of locality

Src/Particle/AMReX_ParticleLocator.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 9aaa81afd68f4e8a02ba768a4616f13613c9e419
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 28 17:27:23 2019 -0400

    add early exit for size 0 messages

Src/Particle/AMReX_ParticleCommunication.cpp

commit 5dcde5172ab116057f9b35e821addd51f7013d4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 28 08:31:34 2019 -0700

    EBFluxRegister: crseadd

Src/Boundary/AMReX_YAFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_2D_C.H
Src/EB/AMReX_EBFluxRegister_3D_C.H
Src/EB/AMReX_EBFluxRegister_C.H
Src/EB/CMakeLists.txt
Src/EB/Make.package

commit 98f36e58fb83ca6ac0ce306cadb7c61947cc3292
Merge: 2d92aef2b 9e13c3db4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 27 21:04:49 2019 -0700

    Merge branch 'weiqun/dev' into development

commit 9e13c3db4679fc3ee62e21246b6f9ef69f771576
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 27 20:26:27 2019 -0700

    prefer const_array() to implicit conversion of the result of array()

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/GPU.rst
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_Interpolater.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Boundary/AMReX_FabSet.H
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_EB2_MultiGFab.cpp
Src/EB/AMReX_EBAmrUtil.cpp
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/F_Interfaces/Octree/AMReX_octree_fi.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 3e523ca0f18264670991cb5bd1e4e73ba9008ee1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 27 17:26:29 2019 -0700

    make sure no race condition in LaunchSafeGuard even in omp parallel region

Docs/sphinx_documentation/source/Basics.rst
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_Interpolater.cpp
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EBInterpolater.cpp

commit 37e44b49e3626c828b12662810f1f5469e5cdd38
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 27 15:49:19 2019 -0700

    GPU: EBInterpolater

Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBInterp_F.H
Src/EB/AMReX_EBInterpolater.cpp
Src/EB/AMReX_ebinterp_1d.F90
Src/EB/AMReX_ebinterp_2d.F90
Src/EB/AMReX_ebinterp_3d.F90
Src/EB/CMakeLists.txt
Src/EB/Make.package

commit e1772106cd142460e86b26b4055100e5f8c0a4d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 27 15:07:50 2019 -0700

    EBCellFlag: rm region

Src/EB/AMReX_EB2_Level.cpp
Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBCellFlag.cpp
Src/EB/AMReX_EBFArrayBox.cpp

commit d2c208b25422708975d15ec52a11c3d559ec4ee0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 27 14:10:23 2019 -0700

    add MultiCutFab::const_array

Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp

commit 3f5c3313301db744b11f50df666d46b612d1781e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 27 13:39:02 2019 -0700

    EB2_Level: more gpu

Src/EB/AMReX_EB2_Level.cpp

commit 2d92aef2b629592953be22859c391a205d1b0b15
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 27 13:28:46 2019 -0700

    rewrite the buffer_size calculation to be more idiomatic

Src/Particle/AMReX_ParticleContainerI.H

commit 1c2a4ca949978bc5c982b7b32c4ca817d289bc71
Merge: 8bcd76342 2909827f1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 27 13:15:23 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8bcd76342967ce02ae5af2a4ddf1432b24c4dbd3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 27 13:15:14 2019 -0700

    tweak particle mesh test

Tests/Particles/ParticleMesh/main.cpp

commit 72842755a6650a6548271e881bcf312e1748f4b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 27 13:13:18 2019 -0700

    minor

Src/EB/AMReX_EB2_Level.cpp

commit 96998b2cab7863dd82888b61d22f63cd1d10e48e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 27 12:52:56 2019 -0700

    fix a bug

Src/EB/AMReX_EB2_IF_Box.H

commit 24fd63ad3401e36fd225497770dd8a1ea3651d89
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 27 12:42:23 2019 -0700

    EB: rm deprecated parameter

Src/EB/AMReX_EB2.H
Src/EB/AMReX_EB2.cpp

commit 41a93bd71dc61f0c1058ac68aa6c88a849bb72f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 27 12:32:38 2019 -0700

    GeometryShop: getBoxType on gpu

Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_EB2_Level.cpp

commit 2909827f16e6684325cf9543d4c46c6f85338068
Merge: d4359e238 d4fb03f29
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Aug 27 15:29:58 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d4359e2381fd54999f93fb2613d991e4b9f4a2f0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Aug 27 15:29:42 2019 -0400

    don't use int for total number of particles in this test

Tests/Particles/Redistribute/main.cpp

commit d4fb03f2976c62d2e97c7f436457b7a98e577b57
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 27 12:28:36 2019 -0700

    tweak test

Tests/Particles/ParticleMesh/main.cpp
Tools/RegressionTesting/AMReX-tests.ini

commit 54ba44cffe33d47637d9735c36610a1382b95049
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 27 12:19:54 2019 -0700

    add an automated test for particle-mesh operations

Tools/RegressionTesting/AMReX-tests.ini

commit af8b36de1b0478877c952b359cbd509b420b4de6
Merge: 9a1312fc2 ca05839a4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 27 11:36:10 2019 -0700

    Merge branch 'mpi_datatype' into development

commit 9a1312fc25acb8c827909440325a3343c5452f8e
Merge: 9fbab69c7 95cf27676
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Aug 27 13:53:58 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9fbab69c7cdc3e7c98095e4690f72dff30685297
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Aug 27 13:53:37 2019 -0400

    early exit from these MPI routines when we only have 1 process

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit 95cf276760fdbde48e406576968b5d81eec60b01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 27 10:42:30 2019 -0700

    Option to use default stream in MFIter

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 0797f8900d9639b5dec7b25217b7c913564a753e
Merge: 1d4b4d235 85d740674
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 26 20:55:52 2019 -0700

    Merge branch 'weiqun/dev' into development

commit 85d7406743d537562659f57fb0958f448405fd1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 26 20:55:26 2019 -0700

    fix new bug in eb_set_covered_nodes

Src/EB/AMReX_EBMultiFabUtil_3D_C.H

commit ca05839a4ca63155f6365600d0233410528dc933
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Aug 26 18:10:47 2019 -0700

    use an mpi data type other than char to up the limit on the number of particles that can be communicated (cpu-only)

Src/Particle/AMReX_ParticleContainerI.H

commit d09598b94417bd0164e582d718b7c3dab4c3ee7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 26 16:11:18 2019 -0700

    EBCellFlag: fix new OMP issue

Src/EB/AMReX_EBCellFlag.cpp

commit 2ffabefbe703694e8276fbf4243772d315564737
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Aug 26 15:33:42 2019 -0700

    add a MPI data type for unsigned long long

Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ccse-mpi.H

commit 6f24f0cd8dd4738fdfdf0ff32fc0e18a05405ced
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 26 13:44:14 2019 -0700

    EB: fix a new 2d bug

Src/EB/AMReX_EB2_2D_C.H
Src/EB/AMReX_EB2_Level.cpp

commit 64e04d72d7f0e41a058c546edeccdc7f05e9bebd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 26 13:24:32 2019 -0700

    EBCellFlagFab: getType on GPU

Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuControl.cpp
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Src/EB/AMReX_EB2_Level.cpp
Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBCellFlag.cpp
Src/EB/AMReX_EBCellFlag_F.H
Src/EB/AMReX_distFcnElement.cpp
Src/EB/AMReX_ebcellflag_mod.F90
Src/EB/CMakeLists.txt
Src/EB/Make.package

commit 5c52537cdaee7201378147eaf607c6660c2a9a8e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 25 21:23:23 2019 -0700

    wip

Src/EB/AMReX_EB2_Level.cpp
Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBFArrayBox.cpp

commit 1d4b4d2357433cdf93a408e24350aefc09f58ea8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 25 20:41:52 2019 -0700

    distFcnElement: pass x by reference

Src/EB/AMReX_distFcnElement.H
Src/EB/AMReX_distFcnElement.cpp

commit 5372993ea3063e3fac6c127630496c49bd4c9310
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 25 20:38:25 2019 -0700

    GPU: compute integrals

Src/EB/AMReX_algoim.cpp

commit 3e1ce784000fa59c7f81a8cd33857f8ad5b5f25c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 25 19:13:18 2019 -0700

    GPU: eb_set_covered

Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_3D_C.H
Src/EB/AMReX_EBMultiFabUtil_3d.F90
Src/EB/AMReX_EBMultiFabUtil_F.H

commit 0c00090fb0ceb61c889f9b2383b11f28d9c62877
Merge: c0ed5b5b2 f7e07743a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 25 15:40:12 2019 -0700

    Merge branch 'weiqun/dev' into development

commit f7e07743adec11e13d81bc5d5b1115440bc081a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 25 15:35:53 2019 -0700

    EB 3d: For uncovered cell, set self-connection

Src/EB/AMReX_EB2_3D_C.H

commit 544f9def38d5f8dcf9ba5cca64dfda86d105845d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 25 08:52:24 2019 -0700

    EB GPU: fix bugs in the new coarsen_from_fine function

Src/EB/AMReX_EB2_3D_C.H

commit f38bea2ae3a65e142bebda32356fe70461f4f0cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 24 22:11:36 2019 -0700

    GPU: build_cellflags_from_ap

Src/EB/AMReX_EB2_2D_C.H
Src/EB/AMReX_EB2_3D_C.H
Src/EB/AMReX_EB2_F.H
Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_EB2_Level.cpp
Src/EB/AMReX_eb2_2d.F90
Src/EB/AMReX_eb2_3d.F90
Src/EB/CMakeLists.txt
Src/EB/Make.package

commit 19077b0554afdda4e65022cbb9e9246640b6ca67
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 24 18:07:53 2019 -0700

    switch to use C++ coarsen_from_fine

Src/EB/AMReX_EB2_F.H
Src/EB/AMReX_EB2_Level.cpp
Src/EB/AMReX_eb2_2d.F90
Src/EB/AMReX_eb2_3d.F90

commit 2994307de5b4d55204ba734adfaacbf53fc531b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 24 17:06:15 2019 -0700

    GPU: coarsen from fine

Src/EB/AMReX_EB2_2D_C.H
Src/EB/AMReX_EB2_3D_C.H
Src/EB/AMReX_EB2_Level.cpp

commit c0ed5b5b205a7efab1266a4ab91068eee012a539
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 23 17:49:36 2019 -0700

    tweak test

Tests/Particles/Redistribute/inputs.rt
Tests/Particles/Redistribute/main.cpp
Tools/RegressionTesting/AMReX-tests.ini

commit 88c639e0a40dcbde361552f41e8b8e4e52cdc144
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 23 17:30:51 2019 -0700

    turn off CUDA by default

Tests/Particles/Redistribute/GNUmakefile

commit 67064de677e5d8188f8e3bc7f937ae0ea09d29fc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 23 17:30:25 2019 -0700

    config entry for redistribute test

Tools/RegressionTesting/AMReX-tests.ini

commit cd00cd0ada50665248c11ec791dc56503a4e34f6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 23 17:29:59 2019 -0700

    configure this as a self-test

Tests/Particles/Redistribute/main.cpp

commit ff72c353f4d462869d8f3d595c8bcb653dea9293
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 23 17:29:46 2019 -0700

    regtest inputs for Redistribute

Tests/Particles/Redistribute/inputs.rt

commit e2ea5e2d7884001d26b6b85b4edb9af93c7d49f9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 23 17:04:52 2019 -0700

    enable omp in numParticlesOutOfRange

Src/Particle/AMReX_ParticleUtil.H

commit 615079f975817a412ae5b8a6e4eeeb16816ef373
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 23 17:04:29 2019 -0700

    combine two forms of OK()

Src/Particle/AMReX_ParticleContainerI.H

commit 3c0d78ff1c5eb5141a96e7da32d91a1c66b35f1b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 23 19:50:19 2019 -0400

    tweak RedistributeTest inputs and script

Tests/Particles/Redistribute/inputs
Tests/Particles/Redistribute/script.sh

commit cc7697f2c5e73683c1a00a9d819b3840cd166aaa
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 23 19:45:40 2019 -0400

    reimplement OKGPU in terms of numParticlesOutOfRange

Src/Particle/AMReX_ParticleContainerI.H

commit 5a2741baabab0d541e4c4f1423640709c4aa337d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 23 19:45:12 2019 -0400

    add overload for numParticlesOutOfRange that lets you set the levels

Src/Particle/AMReX_ParticleUtil.H

commit 44508f93c8d54283da5d2cfb06b166e0dae9fbde
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 23 17:24:08 2019 -0400

    small world bug (gpu, newish) - need to apply periodic boundary conditions to particles that cross a periodic domain BUT stay on the same grid

Src/Particle/AMReX_ParticleContainerI.H

commit 48902a815926fa4915930a9b14ce12ce5b5e197a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 23 13:53:03 2019 -0400

    function to validate that the particles are in range of the local redistribute function

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleUtil.H

commit 8e5f6dbe6e787614e361b136a04d1ab6924d42cd
Merge: 75e1effbc 0ca353f7c
Author: cgilet <cgilet@gmail.com>
Date:   Fri Aug 23 10:55:24 2019 -0400

    Merge remote-tracking branch 'upstream/development' into TensorFluxes

commit accccec58dbe5661b4a2311b88796a36fdde2448
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 22 11:58:14 2019 -0700

    switch to use C++ check_mvmc

Src/EB/AMReX_EB2_2D_C.H
Src/EB/AMReX_EB2_3D_C.H
Src/EB/AMReX_EB2_F.H
Src/EB/AMReX_EB2_Level.cpp
Src/EB/AMReX_eb2_2d.F90
Src/EB/AMReX_eb2_3d.F90

commit 0ca353f7c78ec22ce4655eebcc9b9889b9f0f2a4
Merge: 1b2827c67 99c49340a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 22 09:33:52 2019 -0700

    Merge branch 'weiqun/dev' into development

commit 99c49340a2c4fe1178526764be41a7439d601332
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 22 09:32:12 2019 -0700

    add Gpu::synchronize after fabs are allocated in case kernesl are launched to do placement new

Src/Base/AMReX_FabArray.H

commit 56811204f341b1351a2f24c4bccc28a328a5be62
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 21 15:31:23 2019 -0700

    wip

Src/Base/AMReX_FabArray.H
Src/EB/AMReX_EB2_2D_C.H
Src/EB/AMReX_EB2_3D_C.H
Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_EB2_Level.cpp
Src/EB/AMReX_EBMultiFabUtil.cpp

commit 1b2827c67624e0115f8ecd0d22e0cf828a49c925
Author: kngott <kngott@lbl.gov>
Date:   Wed Aug 21 14:19:54 2019 -0700

    Add number of streams to MFIter Info options.

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 5a70c78493376b1e0f58fe8201745dfc3a20fa90
Author: kngott <kngott@lbl.gov>
Date:   Wed Aug 21 14:15:36 2019 -0700

    Make numGpuStreams available when USE_GPU=FALSE.

Src/Base/AMReX_GpuDevice.H

commit 3e42848f9f9f04a6cc9f8663ad01bf790b2534bc
Merge: ab6d76a69 dd45b69b0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 21 12:48:17 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ab6d76a69a86458dbd5e6688996f30597900829d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 21 12:48:06 2019 -0700

    add a couple of convenience functions to ParIter

Src/Particle/AMReX_Particles.H

commit dd45b69b06142d3ca874a899ff6be241367960ce
Author: kngott <kngott@lbl.gov>
Date:   Wed Aug 21 12:30:19 2019 -0700

    Update CoriGPU example run script.

Tutorials/GPU/run.corigpu

commit b0547ae90a21f69e55172ac1b61d7aad0bae580f
Merge: 38f941c1f f62675f54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 21 06:15:44 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f62675f54c147cf3861819b7861baa0a19247386
Author: kngott <kngott@lbl.gov>
Date:   Tue Aug 20 18:35:39 2019 -0700

    Thread multiple test and results on linear solver.

Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/inputs.test
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-1.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-16.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-2.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-32.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-4.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-64.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-8.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-1.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-16.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-2.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-32.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-4.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-64.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-8.sh
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/main.diff
Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/results.org

commit ae6af3b0923b4ee6726becd57d9d20d33fa2d96b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 20 17:30:19 2019 -0700

    always do handshake in fillNeighbors

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 38f941c1f68c167e67c07be294e4ef2e3ae7e535
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 20 15:39:27 2019 -0700

    ParallelFor taking multiple Boxes and lambdas

Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Tools/CompileTesting/compiletesting.py

commit 2ff96e509c1fbf3aab57d630fe9aefdd617044da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 20 14:02:53 2019 -0700

    EB integral: add integral of x*y*z

Src/EB/AMReX_algoim.H
Src/EB/AMReX_algoim.cpp
Src/EB/AMReX_algoim_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 95342996354fbdfe21c5025cd308e5a8c2a058b8
Merge: e08783249 db4d88120
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Aug 20 13:21:42 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit e08783249cf15cf52a0761b78820cabf0dd089f0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Aug 20 13:21:15 2019 -0400

    only need to call doHandShake after regrid, not every Redistribute

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit db4d8812065d138044b1cea07bda87f52f250673
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 19 17:06:25 2019 -0700

    comments on pinned arena. simplify an Array4 ctor.

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_Array4.H

commit b299b41d021058344740fbf127064352feb2eaba
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Aug 19 17:05:42 2019 -0700

    2D bugfix

Src/Particle/AMReX_ParticleContainerI.H

commit 6123abdbe82dd2a80f8f4e2c87af1ba93c005aef
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Aug 19 16:37:24 2019 -0700

    move all the particle IO routines into a separate file

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleIO.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit cd6a7a6d8f880633c4765c2eb426e67342c2ccfc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 19 13:04:45 2019 -0700

    HostDevice::Atomic::Add that does OMP atomic for host code

Src/Base/AMReX_GpuUtility.H

commit 093fbdcaa53e0eb945c496b6fbda396fc305c974
Merge: c6b8da79d 6a09bb617
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun Aug 18 18:12:02 2019 -0700

    Merge pull request #550 from AMReX-Codes/convergence_cleanup
    
    Convergence cleanup

commit 6a09bb617042162ca52d052628723e2b6f31b58b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Aug 18 19:51:51 2019 -0400

    remove unused files + fix 1-d compilation

Src/Extern/ProfParser/AMReX_AVGDOWN_1D.F
Tools/C_util/Convergence/AVGDOWN_1D.F
Tools/C_util/Convergence/AVGDOWN_2D.F
Tools/C_util/Convergence/AVGDOWN_3D.F
Tools/C_util/Convergence/AVGDOWN_F.H
Tools/C_util/Convergence/Add.cpp
Tools/C_util/Convergence/DiffFab.cpp
Tools/C_util/Convergence/DiffSameDomainRefined.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/GNUmakefile.temp
Tools/C_util/Convergence/Make.package.SAVE
Tools/C_util/Convergence/Make.package.temp

commit 76f34eee415f28daf017470816cc1bf0ca234878
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Aug 18 19:41:14 2019 -0400

    some work on making a no-Latex version

Tools/C_util/Convergence/AVGDOWN_1D.F
Tools/C_util/Convergence/AVGDOWN_2D.F
Tools/C_util/Convergence/AVGDOWN_3D.F
Tools/C_util/Convergence/RichardsonConvergenceTest.cpp

commit c6b8da79dd38b0e525dd67370a6131b1c3b22180
Merge: 654336784 1fa9a90c4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 16 11:44:28 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6543367843f51b097d50058d0afd446ffb4ef7a2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 16 11:44:17 2019 -0700

    a test for the multilevel redistribute mask

Tests/Particles/AssignMultiLevelDensity/main.cpp
Tests/Particles/ParticleReduce/main.cpp

commit 1fa9a90c42a02acb510b3c82d992e7ceb64826f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 16 11:32:11 2019 -0700

    option to add extra flags from command line

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/nvcc.mak

commit 8bddef09a1f5ead66398a4d6e51c06bd2aebd51f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Aug 16 13:42:17 2019 -0400

    Thread Multiple time

Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/results.org

commit 466d2afdf16c185bf244299d9ba1490875d10e4a
Merge: 9235f2c27 a5f555ab4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 16 09:59:05 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9235f2c279a9cf7cb39e23f5f94b54a09e8aeb2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 16 09:58:49 2019 -0700

    add new constructors for alias Fab to avoid implicit conversion

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp

commit a5f555ab4e355af1d3052fda2cbbb737ad11d7d6
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Aug 15 20:08:31 2019 -0400

    Make all scaling tests gcc.

Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-16.sh
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-32.sh
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-8.sh

commit d2fab1bca2b9ceecb61483a59925797686eecd6e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Aug 15 11:43:06 2019 -0700

    add test for particle reduce

Src/Particle/AMReX_ParticleReduce.H
Tests/Particles/ParticleReduce/GNUmakefile
Tests/Particles/ParticleReduce/Make.package
Tests/Particles/ParticleReduce/inputs
Tests/Particles/ParticleReduce/main.cpp
Tests/Particles/Redistribute/main.cpp

commit e98696a4ea40c045fe8578df0f311d1d4e1db1b8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Aug 15 11:04:19 2019 -0700

    also use the ParIter in AMReX_ParticleReduce.H

Src/Particle/AMReX_ParticleReduce.H

commit 267499cc8e3013655186be306a1791775427d606
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Aug 15 10:50:22 2019 -0700

    make code shorter using ParIter

Src/Particle/AMReX_ParticleMesh.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit 184ec762af808d29190d176dd0988311581418f2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Aug 15 10:34:14 2019 -0700

    fix some things in MeshToParticle

Src/Particle/AMReX_ParticleMesh.H
Tests/Particles/ParticleMesh/main.cpp

commit 9e1bb58a7488425cc258c4058c22f0582230b4b9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Aug 15 09:59:07 2019 -0700

    implement lambda MeshToParticle

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleMesh.H
Tests/Particles/ParticleMesh/main.cpp

commit e22b559ce8f40d6b2b1fccfba39d29761e08986d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 15 07:07:25 2019 -0700

    fix compFlux for 1d

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit f75737aec148488007d0b7eaf0f6c2cc4ed6048b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 14 19:11:22 2019 -0700

    periodicShift MultiFab

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 31c995eca78e11b099b493c776ee5607d8e21ed8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 14 16:41:33 2019 -0700

    fix off-by-one error

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 90092d180fb4233e9bebcd3520efeae67d85ccce
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 14 16:36:54 2019 -0700

    add timer

Src/Particle/AMReX_ParticleMesh.H

commit 47c4c0544c4b67c0ede831ba8436bf37bc8aa83c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 14 16:30:30 2019 -0700

    this pointer should not be unique

Src/Particle/AMReX_ParticleMesh.H

commit 99c0cbaba4a03ac65bad7ea27b2c9bc2757f3013
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 14 16:30:12 2019 -0700

    tweak inputs

Tests/Particles/ParticleMesh/inputs

commit c55d27a7e6919ca2ee9ecfe0e680b1e7f2c4f01d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 14 16:18:35 2019 -0700

    add particle mesh lambda test

Tests/Particles/ParticleMesh/GNUmakefile
Tests/Particles/ParticleMesh/Make.package
Tests/Particles/ParticleMesh/inputs
Tests/Particles/ParticleMesh/main.cpp

commit b1f61e1895075199d984593df2afcc471b7614a2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 14 13:58:56 2019 -0700

    implementing a general particle-to-mesh function with lambdas

Src/Particle/AMReX_ParticleMesh.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 07bc03f5991057c494fa22413ad47302c48c9a16
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 14 13:55:05 2019 -0700

    And, Or -> LogicalAnd, LogicalOr

Src/Particle/AMReX_ParticleReduce.H

commit c1c962dab209142b9bc7c867c2026da0b934227f
Merge: 11fea0772 6ae4a428d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 14 13:46:20 2019 -0700

    Fixing merge conflict

commit 6ae4a428daef681de7a35e89f89c475718c75f5d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 14 13:41:34 2019 -0700

    need to reset m_nrcvs when doing early exit

Src/Particle/AMReX_ParticleCommunication.cpp

commit 34391250c1e65465e1868a2b13cb530b811754b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 14 13:26:59 2019 -0700

    forgot a new file

Src/Boundary/AMReX_LO_BCTYPES.cpp

commit b9ecb0f40cc5e372d9e28aa81f44ee0ce78a1891
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 14 13:05:09 2019 -0700

    operator<< for LinOpBCType

Src/Boundary/AMReX_LO_BCTYPES.H
Src/Boundary/CMakeLists.txt
Src/Boundary/Make.package

commit 449b589b183ff681dd2436bf9066bb2ff1ef1198
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 14 12:52:29 2019 -0700

    MLMG: coarsen geometry correctly without using any system defaults in case special geometry is passed in

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit b4cc6a25d865602eb4a316c31a222bfdd259be7d
Merge: fdf9d55a2 89e1fcefe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 14 12:06:50 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit fdf9d55a278a6d756a9c0216188628228e3d5da8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 14 12:06:25 2019 -0700

    Atomic::And -> Atomic::LogicalAnd, Atomic::Or -> Atomic::LogicalOr

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_GpuUtility.H
Src/Particle/AMReX_ParticleUtil.H

commit 11fea077235cf715f1fd9f3ac418ab6a331c31c1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 14 10:58:44 2019 -0700

    move the particle reduction functions into their own file.

Src/Particle/AMReX_ParticleReduce.H
Src/Particle/AMReX_ParticleUtil.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 89e1fcefed84b32d2f3807083a3cbe12e8c9c74c
Merge: f99c2d29f 240f922f7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 14 10:37:47 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f99c2d29f2a03782f66d64ed9310a8fd2ee03de5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 14 10:37:25 2019 -0700

    add additional overloads for particle reduction operations

Src/Particle/AMReX_ParticleUtil.H

commit 240f922f752861bb5d01120d810a1f206a0b6ecd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 14 10:35:32 2019 -0700

    Move DataServicesTest0 from OldTutorials into Tests

Tests/DataServicesTest0/DataServicesTest0.cpp
Tests/DataServicesTest0/GNUmakefile

commit 5593825a36f7784beacd58572b9abbe65930f7c1
Merge: 0e81dff10 befa8b29b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 14 10:23:37 2019 -0700

    Merge branch 'development' into redistribute_opt

commit befa8b29bcd85c3ea2b0dfb39573c8ce17552965
Merge: a84b43f1b ce5a9c51a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 14 09:55:27 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a84b43f1b638e4454abe9a9f38135fb04ef99788
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 14 09:54:30 2019 -0700

    makeFineMask: add optional arguments specifying coarse and fine flag values

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit ce5a9c51aae0f0415d285ceb7e549e1cb9864e3d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Aug 14 09:49:55 2019 -0700

    CMake: remove C_CellMG

Src/LinearSolvers/CMakeLists.txt

commit f0fb80ad394d50a125b78f656802d68d2747cb96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 14 09:04:33 2019 -0700

    rename for consistence

Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_Reduce.H

commit d936961fa5dc66608b6b4e720c5e9cade845d8b6
Merge: 20d758c89 9d1a667b4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Aug 14 08:46:34 2019 -0700

    Merge pull request #547 from cgilet/development
    
    Development

commit 9d1a667b4d8b5bf9423ce2552e92e697612b8fee
Author: cgilet <cgilet@gmail.com>
Date:   Wed Aug 14 10:38:00 2019 -0400

    Clean up MLTensorOp::compFluxes().
    
    Remove unnecessary variable. Fix comments.

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 20d758c89e55a7c6b0c5b85f42a6839a0786682e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 14 07:23:21 2019 -0700

    rm C_CellMG from many makefile because MLMG no longer uses files in C_CellMG

GNUmakefile.in
Tests/LinearSolvers/CellEB/GNUmakefile
Tests/LinearSolvers/CellEB2/GNUmakefile
Tests/LinearSolvers/ComparisonTest/COEF_1D.F
Tests/LinearSolvers/ComparisonTest/COEF_3D.F
Tests/LinearSolvers/ComparisonTest/COEF_F.H
Tests/LinearSolvers/ComparisonTest/COMP_NORM_1d.f90
Tests/LinearSolvers/ComparisonTest/COMP_NORM_3d.f90
Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H
Tests/LinearSolvers/ComparisonTest/GNUmakefile
Tests/LinearSolvers/ComparisonTest/Make.package
Tests/LinearSolvers/ComparisonTest/compute_norm.cpp
Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord2
Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord3
Tests/LinearSolvers/ComparisonTest/inputs-rt-Neu
Tests/LinearSolvers/ComparisonTest/inputs.3d
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp
Tests/LinearSolvers/ComparisonTest/writePlotFile.H
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp
Tests/LinearSolvers/EBConvergenceTest/GNUmakefile
Tests/LinearSolvers/EBTensor/GNUmakefile
Tests/LinearSolvers/EBflux_grad/GNUmakefile
Tests/LinearSolvers/MLMG/GNUmakefile
Tests/LinearSolvers/NodeEB/GNUmakefile
Tools/CompileTesting/compiletesting.py
Tutorials/Basic/HeatEquation_EX3_C/Exec/GNUmakefile
Tutorials/EB/MacProj/GNUmakefile
Tutorials/EB/Poisson/GNUmakefile
Tutorials/ForkJoin/MLMG/GNUmakefile
Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile
Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile
Tutorials/LinearSolvers/NodalPoisson/GNUmakefile
Tutorials/SDC/MISDC_ADR_2d/Exec/GNUmakefile

commit 0207252bf54aed79d5c819ffc4948d65299f8872
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 14 06:38:11 2019 -0700

    remove old regression tests

Tools/RegressionTesting/AMReX-tests.ini

commit d47532b86e8ebf98a12653209bd6af967cd17f4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 14 06:32:23 2019 -0700

    fix 2d EB

Src/EB/AMReX_EBFluxRegister_2d.F90

commit 96922c0cd86226bfc5eb64e0497a3ad44ee959bc
Merge: d22835e70 d40b43e8b
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Aug 14 01:47:27 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d22835e7029a8e0fc30e46d1cc52737c3ad78e55
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Aug 14 01:47:14 2019 -0700

    update the make system of AmrTask tutorials

Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.omp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.pthreads
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.upcxx
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/Make.Adv.upcxx
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/Backtrace.0
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/CMakeLists.txt
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/Make.Adv
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Make.package
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Prob.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/probin
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Make.package
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probin
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/README
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Adv_F.H
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.H
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/LevelBldAdv.cpp
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Make.package
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/Make.package
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/slope_2d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/Make.package
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/slope_3d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/Make.package
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/tagging_params.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/main.cpp
Tutorials/AmrTask/MiniApps/HeatEquation/GNUmakefile
Tutorials/AmrTask/MiniApps/HeatEquation/Make.package
Tutorials/AmrTask/MiniApps/HeatEquation/advance.cpp
Tutorials/AmrTask/MiniApps/HeatEquation/advance_2d.f90
Tutorials/AmrTask/MiniApps/HeatEquation/advance_3d.f90
Tutorials/AmrTask/MiniApps/HeatEquation/init_phi_2d.f90
Tutorials/AmrTask/MiniApps/HeatEquation/init_phi_3d.f90
Tutorials/AmrTask/MiniApps/HeatEquation/inputs_2d
Tutorials/AmrTask/MiniApps/HeatEquation/inputs_3d
Tutorials/AmrTask/MiniApps/HeatEquation/main.cpp
Tutorials/AmrTask/MiniApps/HeatEquation/myfunc.H
Tutorials/AmrTask/MiniApps/HeatEquation/myfunc_F.H
Tutorials/AmrTask/MiniApps/HeatEquation/physbc.cpp
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/GNUmakefile
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/LiDryer.c
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/Make.package
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC.H
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC.cpp
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC_F.H
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC_advance.cpp
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC_init.cpp
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC_io.cpp
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/chemistry_module.f90
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/derivative_stencil.f90
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/init_data.f90
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/inputs_SMC
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/kernels.f90
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/main.cpp
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/make_plot.f90
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/transport_properties.f90
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/variables.f90
Tutorials/AmrTask/UnitTests/001_TokenRing.C
Tutorials/AmrTask/UnitTests/002_Jacobi_StaticGraph.C
Tutorials/AmrTask/UnitTests/003_Jacobi_DynamicGraph.C
Tutorials/AmrTask/UnitTests/Makefile

commit d40b43e8be91fab038bdf068ac7f904e98b5d5d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 13 21:31:24 2019 -0700

    make some changes for xSDK

Src/EB/AMReX_WriteEBSurface.H
Src/EB/AMReX_WriteEBSurface.cpp
Src/EB/AMReX_WriteEB_F.H
Src/EB/AMReX_eb_to_pvd.F90

commit 92f761d926f26eb580b13eb76ba4f51c70970af2
Merge: 7c08f66fe 05f0ee606
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 13 21:15:07 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 05f0ee606e8c84abf8927cd516a838088e2a227d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 13 17:18:42 2019 -0700

    Remove old multigrid tutorial

OldTutorials/MultiGrid_C/CMakeLists.txt
OldTutorials/MultiGrid_C/COEF_2D.F90
OldTutorials/MultiGrid_C/COEF_3D.F90
OldTutorials/MultiGrid_C/COEF_F.H
OldTutorials/MultiGrid_C/GNUmakefile
OldTutorials/MultiGrid_C/Make.package
OldTutorials/MultiGrid_C/README
OldTutorials/MultiGrid_C/RHS_2D.F90
OldTutorials/MultiGrid_C/RHS_3D.F90
OldTutorials/MultiGrid_C/RHS_F.H
OldTutorials/MultiGrid_C/inputs
OldTutorials/MultiGrid_C/inputs-rt-c-neu
OldTutorials/MultiGrid_C/inputs-rt-c-ord2
OldTutorials/MultiGrid_C/inputs-rt-c-ord3
OldTutorials/MultiGrid_C/main.cpp
OldTutorials/MultiGrid_C/writePlotFile.H
OldTutorials/MultiGrid_C/writePlotFile.cpp
OldTutorials/README_C

commit e5db7530909a510defcf29d086c0d49e2a7adc6d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 13 17:17:03 2019 -0700

    Add new tutorial

OldTutorials/libamrex_C/MyAmr.H
OldTutorials/libamrex_C/MyAmr.cpp
OldTutorials/libamrex_C/main.cpp
OldTutorials/libamrex_C/myf.f90
Tutorials/Basic/Build_with_libamrex/GNUmakefile
Tutorials/Basic/Build_with_libamrex/MyParams.H
Tutorials/Basic/Build_with_libamrex/main.cpp
Tutorials/Basic/Build_with_libamrex/my_func.f90
Tutorials/Basic/Build_with_libamrex/test_parameters.cpp

commit 4401eeceaae6494a19094064558802f79808b7f4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 13 17:16:49 2019 -0700

    Add new tutorial

Docs/sphinx_tutorials/source/Basic_Tutorial.rst

commit 0e81dff10ff2e7ebcefe7a2a677c872bdd8e7833
Merge: dd7906262 077321cea
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 13 16:48:26 2019 -0700

    Merge branch 'development' into redistribute_opt

commit dd790626261182249ff2abb660112b157c320518
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 13 16:47:30 2019 -0700

    handle non-gpu aware mpi in a better in the particle communication routines

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit a5205b72a1f2ad2b54a67547aa07137c7ed7067e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 13 16:05:35 2019 -0700

    restore use_gpu_aware_mpi flag to false by default

Tests/Particles/Redistribute/inputs

commit d990668f1f5d93e723286d769219d4c058a85f44
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 13 15:39:07 2019 -0700

    fix indentation

Src/Particle/AMReX_TracerParticle_mod_K.H

commit 077321cea6f8055486cab2dd22664e5b8c58152d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 13 13:47:19 2019 -0700

    Move the EB writing files into Src/EB instead of Tutorials and/or mfix code.

Src/EB/AMReX_WriteEBSurface.H
Src/EB/AMReX_WriteEBSurface.cpp
Src/EB/AMReX_WriteEB_F.H
Src/EB/AMReX_eb_to_pvd.F90
Src/EB/CMakeLists.txt
Src/EB/Make.package
Src/Extern/ProfParser/AMReX_AVGDOWN_1D.F
Tutorials/EB/Donut/Src/EB_F.H
Tutorials/EB/Donut/Src/Make.package
Tutorials/EB/Donut/Src/main.cpp

commit 5be5217a11ee49b4ef12d1dd5841df4477392398
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 13 13:22:50 2019 -0700

    Fix comments only in interpolation routines

Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/AmrCore/AMReX_Interpolater.cpp
Src/EB/AMReX_WriteEBSurface.cpp
Src/EB/CMakeLists.txt
Src/EB/Make.package

commit cd4ff66fa15a02537546364a131d6e4348d68ef8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 13 12:39:17 2019 -0700

    1) remove Racetrack -- that was committed by accident
    2) move Src/AmrTask/tutorials to Tutorials/AmrTask

Src/EB/AMReX_EB2_IF_Racetrack.H
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.omp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.pthreads
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.upcxx.pthreads
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/Make.package
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/Prob.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/inputs
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/probin
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/Make.package
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/Prob.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/inputs
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/probdata.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/probin
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/README
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv.H
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv.cpp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/AdvBld.cpp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv_F.H
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv_advance.cpp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv_dt.cpp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv_io.cpp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Adv_setup.cpp
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Make.package
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_2d/Adv_2d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_2d/Make.package
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_2d/compute_flux_2d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_2d/slope_2d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_3d/Adv_3d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_3d/Make.package
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_3d/compute_flux_3d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_3d/slope_3d.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Adv_nd.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Make.package
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Tagging_nd.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_nd/tagging_params.f90
Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/main.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.omp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.pthreads
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/Make.Adv.upcxx.pthreads
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/Prob.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/inputs
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/probin
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/Prob.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/inputs
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/probdata.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/probin
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/README
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv.H
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/AdvBld.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv_F.H
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv_dt.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv_io.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Adv_setup.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_2d/Adv_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_2d/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_2d/compute_flux_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_2d/slope_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_3d/Adv_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_3d/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_3d/compute_flux_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_3d/slope_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_nd/Adv_nd.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_nd/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_nd/Tagging_nd.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/Src_nd/tagging_params.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Source/main.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/Backtrace.0
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/Prob.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/inputs
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/probin
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/GNUmakefile
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/Prob.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/inputs
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/probdata.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/probin
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/README
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv.H
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/AdvBld.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv_F.H
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv_advance.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv_dt.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv_io.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Adv_setup.cpp
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/Adv_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/compute_flux_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/slope_2d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/Adv_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/compute_flux_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/slope_3d.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Adv_nd.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Make.package
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Tagging_nd.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/tagging_params.f90
Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/main.cpp
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/CMakeLists.txt
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/Make.Adv
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Make.package
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Prob.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/probin
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Make.package
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probin
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/README
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Adv_F.H
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.H
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/LevelBldAdv.cpp
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Make.package
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/Make.package
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/slope_2d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/Make.package
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/slope_3d.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/Make.package
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/tagging_params.f90
Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/main.cpp
Tutorials/AmrTask/MiniApps/HeatEquation/GNUmakefile
Tutorials/AmrTask/MiniApps/HeatEquation/Make.package
Tutorials/AmrTask/MiniApps/HeatEquation/advance.cpp
Tutorials/AmrTask/MiniApps/HeatEquation/advance_2d.f90
Tutorials/AmrTask/MiniApps/HeatEquation/advance_3d.f90
Tutorials/AmrTask/MiniApps/HeatEquation/init_phi_2d.f90
Tutorials/AmrTask/MiniApps/HeatEquation/init_phi_3d.f90
Tutorials/AmrTask/MiniApps/HeatEquation/inputs_2d
Tutorials/AmrTask/MiniApps/HeatEquation/inputs_3d
Tutorials/AmrTask/MiniApps/HeatEquation/main.cpp
Tutorials/AmrTask/MiniApps/HeatEquation/myfunc.H
Tutorials/AmrTask/MiniApps/HeatEquation/myfunc_F.H
Tutorials/AmrTask/MiniApps/HeatEquation/physbc.cpp
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/GNUmakefile
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/LiDryer.c
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/Make.package
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC.H
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC.cpp
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC_F.H
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC_advance.cpp
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC_init.cpp
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC_io.cpp
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/chemistry_module.f90
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/derivative_stencil.f90
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/init_data.f90
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/inputs_SMC
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/kernels.f90
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/main.cpp
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/make_plot.f90
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/transport_properties.f90
Tutorials/AmrTask/MiniApps/SMC_fixed_dt/variables.f90
Tutorials/AmrTask/UnitTests/001_TokenRing.C
Tutorials/AmrTask/UnitTests/002_Jacobi_StaticGraph.C
Tutorials/AmrTask/UnitTests/003_Jacobi_DynamicGraph.C
Tutorials/AmrTask/UnitTests/Makefile

commit 7c08f66fe12eb97fdbaae1bbc1954ab9fe3dd1d2
Merge: 0152499cf edc55d6d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 13 12:32:00 2019 -0700

    Merge branch 'newcomm' into development

commit 0152499cf4e35d591e7375b4cb35a68e9ba13736
Merge: 259e7cde9 a537ea19e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 13 12:31:49 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9c78c3d9a3c0b323e60122307e8f817895c1c45e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 13 12:30:05 2019 -0700

    1) get rid of "dble" in Src code
    2) get rid of hard-wired single- or double-precision constants (use,e.g one/half/zero instead)

Src/AmrCore/AMReX_INTERP_1D.F90
Src/EB/AMReX_EB2_IF_Racetrack.H
Src/EB/AMReX_EBFluxRegister_2d.F90
Src/EB/AMReX_EBFluxRegister_3d.F90
Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_3d.F90
Src/EB/AMReX_EB_Tagging.F90
Src/EB/AMReX_EB_geometry.F90
Src/EB/AMReX_EB_levelset_F.F90
Src/EB/AMReX_compute_normals.F90

commit edc55d6d20448a60d1fe5d163c88df09053c317f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 13 11:10:01 2019 -0700

    revert accidental changes

Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp

commit a537ea19ee7ffb3494df21f68c5e995317c8ba9f
Merge: 907c0ad03 21e818fd4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 13 10:48:10 2019 -0700

    Merge pull request #548 from rhouim/development
    
    Development

commit 131994686086fb2796272a6ccd2f0e55f779e027
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 13 10:26:12 2019 -0700

    clean up the vector version of FillBoundary

Src/Base/AMReX_FabArrayCommI.H

commit 5ae2e79636a43331cb67a2e6b49104698e7d5a0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 13 12:26:54 2019 -0400

    add the latest linear solver scaling test result

Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/results.org

commit 8345b1ffad622f9a98508a962647b72d4f852979
Merge: 0ee95e7f9 259e7cde9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 13 00:12:53 2019 -0400

    Merge branch 'newcomm' of github.com:AMReX-Codes/amrex into newcomm

commit 0ee95e7f975e7f3d980c801bdb27fdb0619aa0b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 13 00:12:27 2019 -0400

    add linear solver scaling test stuff

Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/inputs.test
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/main.diff
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/results.org
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-1.sh
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-1024.sh
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-128.sh
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-16.sh
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-2.sh
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-2048.sh
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-256.sh
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-32.sh
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-4.sh
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-512.sh
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-64.sh
Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-8.sh

commit 0ad4378246a7147536bee9b1f4adb944b7e5e685
Merge: fe9e2074e 907c0ad03
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 12 20:25:42 2019 -0400

    Merge branch 'development' into redistribute_opt

commit fe9e2074e866cddaf96ffd0926fefd5a2472196a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 12 20:25:32 2019 -0400

    powers of 6 for summit

Tests/Particles/Redistribute/inputs
Tests/Particles/Redistribute/script.sh

commit 510d9a71b85f902faac2d6bfe83317e24c9d7571
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 12 20:24:56 2019 -0400

    remove commented out code

Src/Particle/AMReX_ParticleContainerI.H

commit e7c7b676caa94902cf5c592a3594395d64712ffe
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 12 20:00:52 2019 -0400

    fix Redistribute test to be more sensitive to soa errors

Tests/Particles/Redistribute/main.cpp

commit 2abb0af7170212d8097c8a8eb973956074a5ff8e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 12 20:00:20 2019 -0400

    fix new bug

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 907c0ad039c2c7769dfdb3d7cf2997d4f2a03651
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 12 19:46:35 2019 -0400

    remove un-needed synchronization points

Src/Base/AMReX_Utility.cpp

commit 762982a91a37fe35f797905357a65651077ea7ff
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 12 19:45:56 2019 -0400

    use volatile in this test

Tests/GPU/Locking/main.cpp

commit 259e7cde9ff2d8caa50e45bef39a758f0e9b49a3
Merge: 1e515dc08 e45396c2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 12 16:09:06 2019 -0700

    Merge branch 'development' into newcomm

commit 21e818fd419bce977c43b10cd07d8dcd3e397e0b
Author: Ryan Houim <rhouim@mics.mae.ufl.edu>
Date:   Mon Aug 12 17:41:04 2019 -0400

    Fixed some bugs with the interpolation routines.

Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90

commit 1e515dc08fe12c307595755069ea08db553e707c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 12 12:58:59 2019 -0700

    fuse kernels in ParallelCopy

Src/Base/AMReX_FBI.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_PCI.H

commit 878ab66268cb17a33e32982bf182eb892d53c02a
Author: Ryan Houim <rhouim@mics.mae.ufl.edu>
Date:   Mon Aug 12 15:52:36 2019 -0400

    This commit fixes a strange issue with AMReX cell bilinear interp.
    
    We setup a 1D simulation (planar flame) on a 2D grid.  After some time steps there would be significant transverse velocities (which should be zero) that affected the flame.  This only occured with the Intel compiler with DEBUG=False and with the cell_bilinear interpolation.  Compiling with GNU orIntel with DEBUG=True did not produce this behavior.  Rearranging the interpolation procedure to the method typically done by students when interpolating tables by hand seems to work fine where the data is first interpolated long x-lines, then the x-line interpolated data is interpolated in the y-direction, and finally the y-interpolated data is interpolated in the z-direction to give the final value.

Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90

commit c09e25930811f8351733594974a8e724730ba700
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 12 11:01:58 2019 -0700

    reorganize ParallelCopy's local copy

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_PCI.H

commit 6478a525d60e2730e3cbc66fb1c83cfcf6f1c3d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 12 10:34:05 2019 -0700

    fix new bugs

Src/Base/AMReX_FBI.H
Src/Base/AMReX_FabArrayCommI.H

commit a7dad87f43f84aea1ac9fd1d325e99456c348895
Author: cgilet <cgilet@gmail.com>
Date:   Mon Aug 12 12:48:21 2019 -0400

    Add MLTensorOp::compFluxes()

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit a23c327cc5e74abb619678db87c1c483e399c3a4
Author: cgilet <cgilet@gmail.com>
Date:   Mon Aug 12 12:45:39 2019 -0400

    Fix typo in error message

Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H

commit 75e1effbccbcf72e2e666cd557e7c757341f7b26
Author: cgilet <cgilet@gmail.com>
Date:   Mon Aug 12 11:18:47 2019 -0400

    In MLCellLinOp::compFlux(), make sure temporary flux is sized to hold all components.

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit bc4d9777a3f912b6f4cff07e403dc13f3d4c044a
Author: cgilet <cgilet@gmail.com>
Date:   Fri Aug 9 16:14:58 2019 -0400

    WIP Add MLTensorOp::getFluxes(). Compiles, but no further testing.

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit c7e0bd0894aab679be042bae8d4c86f14c10307a
Author: cgilet <cgilet@gmail.com>
Date:   Fri Aug 9 16:13:14 2019 -0400

    Fix typo in error message

Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H

commit 81a28e7190948288c3c64e9f1187003853466313
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 11 22:04:15 2019 -0700

    fix index for maskfabs

Src/Base/AMReX_FBI.H

commit 1c803c5461477bb431d75cfde3a359d9150860ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 11 21:11:13 2019 -0700

    tidy

Src/Base/AMReX_FBI.H
Src/Base/AMReX_FabArrayCommI.H

commit 9aa3c8bfd1e8c773e5a6406cbbe6542cc4f191ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 11 23:26:38 2019 -0400

    minor

Src/Base/AMReX_FBI.H
Src/Base/AMReX_FabArray.H

commit a2a2fd97252ce6fc8f5bedf3605365eb47e4f0c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 11 18:59:47 2019 -0700

    fuse gpu kernels in fillboundary and reorganization

Src/Base/AMReX_FBI.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_PCI.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 54718eba6bee6dce4e82a8a05ff411191fb99d18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 10 20:15:15 2019 -0700

    remove deprecated PreAllocatable and isCopyOMPSafe

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit 5cb1b27391ab5afdced145a7cdc2da785f735630
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 10 18:10:35 2019 -0700

    fix omp for StreamIter

Src/Base/AMReX_GpuUtility.cpp

commit 1a885fc54c9edf5bb716b0b15afb5d5b3381f8fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 10 17:56:12 2019 -0700

    fuse local copy part of parallel copy

Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_TypeTraits.H
Src/EB/AMReX_EBCellFlag.H

commit 22197ba45e7e095fc9ec0d1df8a6b0ca07579c98
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 10 11:29:15 2019 -0700

    generalize fab_to_fab function and operator interfaces

Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_TypeTraits.H
Src/EB/AMReX_EBCellFlag.H

commit e45396c2e38294e7ef3aa77c4247bf90508ab1a9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 10 06:53:44 2019 -0700

    Replace 1.e-14 by "small" and 1.e-15 by "tiny" to be consistent with 2d

Src/EB/AMReX_EB2_3D_C.cpp

commit 6d86900a76692edd0d271c212a352f64488849ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 9 22:01:52 2019 -0700

    amrex::HasAtomicAdd

Src/Base/AMReX_TypeTraits.H

commit 42f76ae585b39a5dcaf02eb18d02e821a260b1b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 9 21:51:46 2019 -0700

    amrex::IsCopyAtomicSafe

Src/Base/AMReX_TypeTraits.H
Src/EB/AMReX_EBCellFlag.H

commit ce137f0865ea612a5e97719fc1ecc228a7958837
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 9 21:08:28 2019 -0700

    fix compilation for cuda < 10

Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_GpuDevice.cpp

commit 08072fbb439dbfa10799b674882ee19939cb0a2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 9 19:23:03 2019 -0700

    add eb2.small_volfrac

Src/EB/AMReX_EB2_2D_C.cpp
Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EB2_C.H
Src/EB/AMReX_EB2_Level.H

commit 54ce2700fb88d2ac0e74dff8fb66010700b26376
Merge: 8e95ff523 f8f2426fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 9 17:14:52 2019 -0700

    Merge branch 'kngott/cudaGraphs' into weiqun/fuse

commit 8e95ff523167901c057850ab990e17f3a3414737
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 9 17:05:32 2019 -0700

    fused local copy

Src/Base/AMReX_FabArrayCommI.H

commit 36526b4f2d759f23be22e661a97d976fee50799a
Merge: bbbb5f88a 729f9bc67
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 9 13:44:47 2019 -0700

    Merge pull request #544 from ChrisDeGrendele/rng2
    
    RNGs are now assigned a block instead of a thread + a test problem to test locking

commit 69c1514d90aa85ee84720b1c317d3f9da3530b4c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 9 16:43:15 2019 -0400

    fix debug build error

Src/Particle/AMReX_ParticleCommunication.cpp

commit 729f9bc676dce0f3813885ae8e7fd1250c64636d
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Fri Aug 9 13:31:30 2019 -0700

    Added threadfence to ensure global memory write is complete

Src/Base/AMReX_Utility.cpp
Tests/GPU/Locking/main.cpp

commit 9efd66178131f0f7840307783431a52bbad650b3
Author: cgilet <cgilet@gmail.com>
Date:   Fri Aug 9 16:14:58 2019 -0400

    WIP Add MLTensorOp::getFluxes(). Compiles, but no further testing.

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit fc680f466e69d033d652cdc307dc2b2079842c67
Author: cgilet <cgilet@gmail.com>
Date:   Fri Aug 9 16:13:14 2019 -0400

    Fix typo in error message

Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H

commit 36c7d5de2874c23eeede2a2d96a74ced1757f1c7
Merge: ed74d53a0 bbbb5f88a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 9 14:45:28 2019 -0400

    Merge branch 'development' into redistribute_opt

commit ed74d53a09e1301f638eca823d1acbfa91729a00
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 9 14:35:59 2019 -0400

    replace redistribute with the new version

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleUtil.H
Tests/Particles/Redistribute/main.cpp

commit 6c7fc8ee1b8bf953e0314db9ec21cf12a73f9070
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 9 14:08:12 2019 -0400

    some AMREX_RESTRICT

Src/Particle/AMReX_ParticleTile.H

commit 2e8ce3de4fffd93b146f0aabfa175c0f9638920e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 9 14:05:22 2019 -0400

    remove print

Src/Particle/AMReX_ParticleContainerI.H

commit 6bb799f613fafc0e4082728b67bf0d2bbae1ea94
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 9 14:04:06 2019 -0400

    assert that the soa / aos data is correct

Tests/Particles/Redistribute/main.cpp

commit 2f1ec1cae88ebcd3c081d94c24a64c1f9a3632d2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 9 13:35:27 2019 -0400

    update inputs

Tests/Particles/Redistribute/inputs

commit b7a343c6f99b11d24578d464412170dc25804475
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 9 13:35:02 2019 -0400

    add some soa data to the test

Tests/Particles/Redistribute/main.cpp

commit 366e063b200fa5d00f4f15a92d93494016280e98
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 9 13:34:39 2019 -0400

    handling soa data

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_Particles.H

commit bbbb5f88a21913c30c23ac5c2eac4224ed67ba75
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 9 06:27:39 2019 -0700

    update to VisIt caveat

Docs/sphinx_documentation/source/Visualization.rst

commit e36fe4520088e35511a795ffe7411972aa40550f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 8 20:08:19 2019 -0700

    fix bug in fixing small EB cell faces

Src/EB/AMReX_EB2_3D_C.cpp

commit f8f2426fb3d5a1c7873f060a9a9f158e54655d0e
Merge: 6a937e97e f23dfe57a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Aug 8 19:18:29 2019 -0400

    Merge branch 'development' into kngott/cudaGraphs
    
    Conflicts:
            Src/Base/AMReX_GpuDevice.cpp

commit f23dfe57a8700dfc1b0be1f5102577dd78154277
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 8 11:09:14 2019 -0700

    Add comments about how VisIt reads "Cycle" from plotfile names

Docs/sphinx_documentation/source/Visualization.rst

commit 4c901fcbe8d158c5de13fcc690cd593833e8d51e
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Thu Aug 8 10:43:49 2019 -0700

    Modify test problem to actually test

Tests/GPU/Locking/main.cpp

commit cd263a5c377460504cdc41073c33a1b7d27e3030
Merge: 351cbaf64 876bde340
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 8 13:09:59 2019 -0400

    Merge branch 'development' into redistribute_opt

commit 6a937e97e715a5cc8963d4b4e03e5a57175f3b5f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Aug 7 20:35:59 2019 -0400

    Move graph building inside (N_recv > 0) check.

Src/Base/AMReX_FabArrayCommI.H

commit 876bde340261076fe0d068ab86b1561bcf6e2ab8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 7 17:11:12 2019 -0700

    change GpuTuple::operator= to match std

Src/Base/AMReX_Tuple.H

commit 94549baea05f48fa855d800913a35c70d13eaab9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 7 16:56:54 2019 -0700

    ForwardAsTuple

Src/Base/AMReX_Tuple.H

commit 351cbaf64fe9e70de7d908ef0cae25c7dff5c9a3
Merge: 4a81697d9 ffe45566f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 7 19:49:50 2019 -0400

    Merge branch 'development' into redistribute_opt

commit ffe45566f511784db478625d6dc0c6a0d0098a81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 7 16:48:56 2019 -0700

    missed a move

Src/Base/AMReX_Tuple.H

commit 4a81697d9cba3d39acc9aba07deff66d57818f26
Merge: 7a5078b2b f9cfdf555
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 7 19:44:34 2019 -0400

    Merge branch 'development' into redistribute_opt

commit 7a5078b2bb92af6adf86ff8561b6cbee8b8f445a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 7 19:44:03 2019 -0400

    use gpu-aware mpi in this test

Tests/Particles/Redistribute/inputs

commit 953a7ba4cd6b0ce4412d4377a5389720ba1104a9
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 7 19:43:39 2019 -0400

    use the ParticleTileData in pack/unpack

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit f9cfdf5550cfc5582845de125a1b11c55c086875
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 7 16:43:02 2019 -0700

    GpuTuple: Tie and operator=

Src/Base/AMReX_Tuple.H

commit 7aed05f22402f281b174194a3ab0fa64a60193f9
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Tue Aug 6 12:31:24 2019 -0700

    RNGs are now assigned a block instead of a thread
    
    Other random function as well
    
    Safer locking mechanism by thread block for older GPUs
    
    Now test problem actually uses locking

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Tests/GPU/Locking/GNUmakefile
Tests/GPU/Locking/Make.package
Tests/GPU/Locking/main.cpp

commit e0cd2b7a90e187436244423854208e01211e1455
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 7 15:51:23 2019 -0400

    method for accessing all particle data on the GPU (whether AoS or SoA)

Src/Particle/AMReX_ParticleTile.H

commit e5b39837ae266e78d182dfe05bb4f9043440075c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 7 15:50:37 2019 -0400

    respect the use_gpu_aware_mpi flag

Src/Particle/AMReX_Particles.H

commit 2af026eb173b14d708fe6c654027cc6a91d3cea8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 7 12:39:51 2019 -0700

    GpuTuple: allow conversion

Src/Base/AMReX_Tuple.H

commit 09e1f852344ec95e9338550ac7893b579bb712f3
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Aug 7 13:49:41 2019 -0400

    Fix GraphInit test.

Tests/GPU/CudaGraphs/GraphInitTest/main.cpp

commit 6a92c2b78ad03b6aebd99798fa90c1c817ed2545
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 7 09:46:35 2019 -0700

    Apply

Src/Base/AMReX_Tuple.H

commit 7d81e4f48895b74fd5d9160e19ab885bfc320e37
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Aug 7 12:27:44 2019 -0400

    Add working InitGraph.

Src/Base/AMReX_GpuDevice.cpp

commit 532313acdd41f339f721be49e52a2dd543982293
Merge: 071712bc2 225f3b520
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Aug 6 23:58:04 2019 -0400

    Merge branch 'development' into redistribute_opt

commit 071712bc2e95140f2ab4a2fe2b74b2d0ee93f14d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Aug 6 23:51:01 2019 -0400

    allow overlapping communication / computation when building the mpi copy plan

Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit 225f3b5205a8089dc705730649f57ec5ed529787
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 6 19:51:19 2019 -0700

    TupleCat

Src/Base/AMReX_Tuple.H

commit dd1beaff2733a29e5a5905c604417d8fc9228bb7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Aug 6 20:13:06 2019 -0400

    Simplified init function.

Tests/GPU/CudaGraphs/GraphInitTest/main.cpp

commit def6e293f4d4007ed49fd9b71c192901e6105cff
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Aug 6 19:16:57 2019 -0400

    Minimized graph init.

Tests/GPU/CudaGraphs/GraphInitTest/main.cpp

commit 2652fc4615b747953c7f225613d580f6b674dae7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Aug 6 17:38:32 2019 -0400

    Working version of graph init: events.

Tests/GPU/CudaGraphs/GraphInitTest/main.cpp

commit a7e1d8a033754a016c4eb24f8d186558624eae16
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Aug 6 15:13:48 2019 -0600

    fixed the problem! it was that the boundary conditions were not getting set properly

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp
Tests/LinearSolvers/MultiComponent/main.cpp

commit 3cb282fcd31649087952abfdeba213a7c7821a86
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Aug 6 14:00:33 2019 -0700

    review lock-free sync points in the MPI backend

Src/AmrTask/rts_impls/mpi/Perilla.cpp

commit fa1f252e9a456ddf65eacb1ed66c9144f61cfead
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Aug 6 13:06:58 2019 -0600

    added makefile

Tests/LinearSolvers/MultiComponent/GNUmakefile

commit 5f269004a854a763a9d8e82350e7ecc1fb364f26
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Aug 6 09:51:52 2019 -0600

    updated BC update

Tests/LinearSolvers/MultiComponent/main.cpp

commit c841f6c642f92fd890b6e2608bb2f058c8b3091a
Merge: 31d3a96b2 5753344c8
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Aug 6 09:42:45 2019 -0600

    Merge branch 'development' into mcmlmg-test

commit 31d3a96b2e3f7262e2c89eb1ef828f089261cf90
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Aug 6 09:42:11 2019 -0600

    Generally working but bottom solver still failing

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp
Tests/LinearSolvers/MultiComponent/inputs
Tests/LinearSolvers/MultiComponent/main.cpp

commit 958aecb023a4dbe205a64ea3dfae511acbf3f597
Merge: b16306860 5753344c8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 5 23:31:46 2019 -0400

    Merge branch 'development' into redistribute_opt

commit b1630686009ae9456f47d933b109d8c2e41a44b5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Aug 5 23:30:51 2019 -0400

    use amrex::Scan instead of thrust::partition in the particle redistribute

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 5753344c82170dc274fbf7b8ee64767ad40b68f9
Merge: a28493088 1d02043ab
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Aug 5 11:49:14 2019 -0700

    Merge pull request #539 from rporcu/rporcu
    
    Roberto Porcu

commit 1d02043abc2bd36a9ffe90bd4c969fc740ee84ed
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Mon Aug 5 11:14:31 2019 -0700

    Remove Warnings for getFluxes method which is only partially overwritten in MLCellABecLap and MLNodeLaplacian classes

Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H

commit a2d16061c2db0ef4ff8f4b85d0c5f39fcebbb248
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Mon Aug 5 11:01:27 2019 -0700

    Add missing header files

Src/Particle/AMReX_Particle.H

commit 783411b143cabb55cae6b6b51de404bfee3feb36
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Mon Aug 5 11:00:52 2019 -0700

    Add getter of Gpu shared memory size in Device properties

Src/Base/AMReX_GpuDevice.H

commit d7bab483e3e288bbc5dfc560cd1d1e5bebdca610
Author: Roberto Porcu <robertoporcu@lbl.gov>
Date:   Mon Aug 5 10:59:29 2019 -0700

    Add dataPtr() and size() methods to struct Array4

Src/Base/AMReX_Array4.H

commit a284930885879f652fd493d321ea5bc4a2c7354a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 3 20:25:53 2019 -0700

    ignore command line argument after --

Docs/sphinx_documentation/source/Basics.rst
Src/Base/AMReX.cpp

commit bdf3c72f61a6f0410f62caaa8c4ca1d46ff1d66b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 3 18:46:24 2019 -0700

    put omp pragma inside ifdef

Src/Base/AMReX_GpuReduce.H

commit 329ded74a9714dd5b99ef495fabdf78680893b1c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 3 16:08:28 2019 -0700

    re-try formatting

Docs/sphinx_documentation/source/Basics.rst

commit 7e376ebfd0f03c7a55e7671506604b65e5f04830
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 3 15:52:44 2019 -0700

    Fix formatting

Docs/sphinx_documentation/source/Basics.rst

commit 85362b1643a519e15a45ca1579efb902a496824c
Merge: 230debd2e 046d484e9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 3 15:38:00 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 230debd2e077d9340075125b1ff9ea89b3c3d001
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 3 15:18:46 2019 -0700

    Add section about setting argc=2 so amrex doesn't try to read past the inputs file name
    on the command line

Docs/sphinx_documentation/source/Basics.rst

commit 6c3e7cebaec75cf55a5446f339820c682aa5145d
Merge: 1abd2425e 046d484e9
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Aug 3 17:21:44 2019 -0400

    Merge branch 'development' into redistribute_opt

commit 046d484e9a657d786c5d1c4a83ae9afbf9823990
Merge: 1a844b04a df17dd684
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Aug 3 17:20:19 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 1a844b04a149fa80a4c98f2f3b2bc752217264e8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Aug 3 17:20:08 2019 -0400

    GPU version of Random_int

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit df17dd6844ee159df39cdfa7206d942d09a77f07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 3 10:23:16 2019 -0700

    amrex::StablePartition

Src/Base/AMReX_Partition.H
Tests/GPU/Partition/main.cpp

commit 0a25f4ef418ad54bd8ed6147a16f1fce2336435f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 3 09:27:49 2019 -0700

    partition: return number of trues

Src/Base/AMReX_Partition.H
Src/Base/AMReX_Scan.H
Tests/GPU/Partition/main.cpp

commit 331539d7746831995adb933be60390ab1d059c22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 2 21:22:32 2019 -0700

    update Partition test

Tests/GPU/Partition/main.cpp

commit 688bee6d81d4d72ad9e8fbf8d0c0784e3e70014a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 2 21:19:36 2019 -0700

    amrex::Partition

Src/Base/AMReX_Partition.H
Src/Base/AMReX_Scan.H

commit 32f2d5033d3542838c4ddbaf893c6df27e3edb20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 2 19:18:08 2019 -0700

    generailize scan to take functions

Src/Base/AMReX_Partition.H
Src/Base/AMReX_Scan.H

commit e9f5b4676b12e6bf7e6f38cda481059c7e45d488
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 2 18:57:33 2019 -0700

    fix some typos

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_Partition.H

commit af9935fb8d0b5308b67d60ddb20603023ef327f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 2 18:50:03 2019 -0700

    #ifdef put gpu scan code

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_Partition.H
Src/Base/AMReX_Scan.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 9724998ce624e390989ff4d12b4d4e1450f418e7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Aug 2 20:15:04 2019 -0400

    Current Graph Init test.

Tests/GPU/CudaGraphs/GraphInitTest/inputs_3d
Tests/GPU/CudaGraphs/GraphInitTest/main.cpp

commit 6a24b8dea297f3055c1f3f859ff40c51591eb6ed
Merge: f6cb577f0 c5ad3d5a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 2 16:17:54 2019 -0700

    Merge branch 'weiqun/reduce' into development

commit f6cb577f02f221760ec416735ada522d3551a203
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 2 18:52:07 2019 -0400

    an indepedent test of the particle partition

Tests/GPU/Partition/GNUmakefile
Tests/GPU/Partition/Make.package
Tests/GPU/Partition/inputs
Tests/GPU/Partition/main.cpp

commit c5ad3d5a46ae15f3f5dcd49375c2d2a713085b3f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 2 13:59:40 2019 -0700

    scan: use volatile

Src/Base/AMReX_Scan.H

commit 1abd2425e526c1fcbdf70e5baa7d6e3cffd28bad
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 2 16:55:45 2019 -0400

    thrust::device_vector -> Gpu::DeviceVector

Src/Particle/AMReX_ParticleContainerI.H

commit e8d008bbd1fc12f3b687d4471e4998dd59ebc8f8
Merge: d929f3897 22c2f61c0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 2 16:31:42 2019 -0400

    Merge branch 'development' into redistribute_opt

commit d929f3897dc31a5cd64726a4bb200e0c82c48312
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 2 16:30:50 2019 -0400

    use point-to-point communication to determine the number of bytes to rcv when the communication pattern is local

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit d1e8bfa6106107a2ec0cdf708b0a59dd83cac5e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 2 10:20:23 2019 -0700

    scan: use __threadfence for reliability

Src/Base/AMReX_Scan.H

commit 585caf1a15654265f3454192c95d51783de6e75f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 1 22:52:49 2019 -0400

    scan: avoid asyncarray and devicescalar

Src/Base/AMReX_Scan.H

commit 22c2f61c0054815e17500797a0cf67a8db159516
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 1 18:18:09 2019 -0700

    "gird" --> "grid"

Tutorials/EB/Donut/Src/eb_to_pvf.F90

commit 8a2cfdc96de4cb8d3aaecbe95e0b52c6f90c5e5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 1 20:49:57 2019 -0400

    scan test: add synchronize just in case

Tutorials/GPU/ParallelScan/main.cpp

commit 9c755e2134b43dbc4ad7214923cfaa12f8dfb29a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 1 18:09:32 2019 -0400

    scan: optimization

Src/Base/AMReX_Scan.H

commit e2cdad01cbfc0ea1cddb64a73afcc989e12e98b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 1 14:35:43 2019 -0400

    scan: tweak # of chunks

Src/Base/AMReX_Scan.H

commit f0f219631d6d9b87cc32a2066ffefd30b38cfd22
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Aug 1 14:21:08 2019 -0400

    use non-blocking sends in the communicateParticles and ParticleCopyPlan::buildMPI routines

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit f4df94a485268c67d4a34cdfe9720ee55c751535
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 1 11:04:46 2019 -0700

    scan: parallel lookback

Src/Base/AMReX_Scan.H

commit 38567bd4e90f60da8d1b196c9b0083e3fa02dc5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 1 08:59:24 2019 -0700

    update CHANGES

CHANGES

commit 26c7610ab2409e6bc9901875b691c424cd5ea53c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 31 21:37:43 2019 -0700

    scan: memory fence optimization

Src/Base/AMReX_Scan.H
Tutorials/GPU/ParallelScan/main.cpp

commit e29b6fc20267a888491377619c97ee1a823161d2
Merge: 88eff5e61 ab82b1607
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 31 20:55:44 2019 -0400

    Merge branch 'development' into redistribute_opt

commit afe4c9cedd181053093d8567bae66ac5fa79b331
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 31 20:52:19 2019 -0400

    scan: tweak the number of chunks

Src/Base/AMReX_Scan.H
Tutorials/GPU/ParallelScan/main.cpp

commit 88eff5e613d796f16acb420e4bbf4f5ad36ad44d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 31 20:13:03 2019 -0400

    fix typo affecting debug mode

Src/Particle/AMReX_ParticleCommunication.H

commit ab82b1607657f17e3e020b72b7c1393359291fa8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 31 17:06:17 2019 -0700

    fix omp in tracer particles

Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit 3ef91646f9923e7635ee729a3d53275932a7cdda
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 31 17:04:26 2019 -0700

    add ParallelScan test

Tutorials/GPU/ParallelScan/GNUmakefile
Tutorials/GPU/ParallelScan/Make.package
Tutorials/GPU/ParallelScan/main.cpp

commit 99376182044997220707f20fa571c8b14c00795d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 31 16:38:01 2019 -0700

    first version of scan

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Scan.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit d06af3cf4257b6fb6976510ec3d181ee6d56748e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 31 16:53:22 2019 -0700

    continue should be return here

Src/Particle/AMReX_TracerParticles.cpp

commit e92e70abeb8df157c57ea0cac0aaf4df246905bb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 31 16:38:40 2019 -0700

    a little bit of reorganization

Src/Particle/AMReX_TracerParticles.cpp

commit f7fb25f9bf1e644d67015be083ce898700e37ab8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 31 14:44:21 2019 -0700

    fix mac advection for tracer particles

Src/Particle/AMReX_TracerParticle_mod_K.H

commit e6c58d8d68716809a1bf74715aa5a9caf2db29ba
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 31 17:26:40 2019 -0400

    overlap communication with computation in Redistribute

Src/Particle/AMReX_ParticleContainerI.H

commit ce022323a806c62f7918d03b79594b5bd4c52c84
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 31 16:14:34 2019 -0400

    split up start and finish in the MPI communicateParticles so it can be overlapped

Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleBufferMap.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit def25a9c0d43c4d35e21f306b91496aa41e409a2
Merge: 653963060 c312d3dd1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jul 31 13:07:02 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 65396306062dd34884e6bd4b3b67ed770d5f2943
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jul 31 13:02:31 2019 -0700

    Fix bug in mac_interpolate used in advection of tracer particles.

Src/Particle/AMReX_TracerParticle_mod_K.H

commit 1d5ffd609dd02f44baff8600dae6ae6fd9f0e033
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 31 15:17:48 2019 -0400

    fix resize error

Src/Particle/AMReX_ParticleCommunication.cpp

commit e904e93cbfff7d4181e8213c48c047db743e271d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 31 15:06:53 2019 -0400

    remove commented out code

Src/Particle/AMReX_ParticleCommunication.H

commit 10c4b72877e3167a18b32c23f35a43fac833a541
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 31 15:05:26 2019 -0400

    remove redundant all-to-all in communicateParticles

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit 3b03d04bef5f601ada7feba31bd6773ca6ec8694
Merge: 2e8eaaea9 c312d3dd1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 31 11:39:57 2019 -0700

    Merge branch 'development' into weiqun/reduce

commit c312d3dd1b20a654cf49d19dc18193759ce0797b
Author: Donald E. Willcox <dwillcox@users.noreply.github.com>
Date:   Tue Jul 30 21:04:45 2019 -0700

    Fix case-sensitive bug in gpu_fortran.py preprocessor script. (#522)

Tools/F_scripts/gpu_fortran.py

commit 46c35ca2822b7e30c47425ab3c7b3b9a818a433d
Merge: 4e64649a1 ab4829c71
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jul 30 17:10:43 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4e64649a190920d10921c6ab549534a1b6c334d8
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jul 30 17:10:38 2019 -0700

    Add tool to generate turbulence files from plotfiles

Tools/Postprocessing/C_Src/GNUmakefile
Tools/Postprocessing/C_Src/PlotfileToTurb.cpp
Tools/Postprocessing/C_Src/PlotfileToTurb_nd.f90

commit 115ba6267047c8237bc78d14e59fa5991bd7895b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 30 20:09:27 2019 -0400

    missed a couple

Src/Particle/AMReX_ParticleCommunication.cpp

commit fe5f48873a9006354f2c79ff1e650caeae1ab4c0
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jul 30 20:09:15 2019 -0400

    Basic init test running. Need to add graphs to it.

Tests/GPU/CudaGraphs/GraphInitTest/main.cpp

commit 964be86a385a2cf884450eb0642dc3c604b0db90
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 30 20:00:26 2019 -0400

    fix CPU compilation

Src/Particle/AMReX_ParticleCommunication.H

commit b5aa1f2af2b3a6c9756766f06fb876af62aee3b6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 30 19:55:18 2019 -0400

    add timer around the partition

Src/Particle/AMReX_ParticleContainerI.H

commit 70545eef4e928c2576d300f707fb775cfc6fbe6d
Merge: b90ac56a7 ab4829c71
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 30 19:25:20 2019 -0400

    Merge branch 'development' into redistribute_opt

commit b90ac56a7d8ad002e5e77568b9fb78028fe5a3ed
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 30 19:24:37 2019 -0400

    perform an initial partition to keep the size of the redistribute copy operation down

Src/Particle/AMReX_ParticleContainerI.H

commit 6389d767740ab9c42b464b77e7ce4948e96fb27b
Merge: af92d8721 ab4829c71
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jul 30 18:58:21 2019 -0400

    Merge branch 'development' into kngott/cudaGraphs

commit ab4829c71d8f33f1c6eca87d8e674ed73631787b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jul 30 18:56:28 2019 -0400

    Set initial stream after device setup to the default stream.

Src/Base/AMReX_GpuDevice.cpp

commit cf0bdc4216020d8833a389313e76d353a74b03a9
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Jul 30 12:28:09 2019 -0700

    fix a small error in the AMFIter

Src/AmrTask/rts_impls/runtime_common/RGIter.cpp
Src/AmrTask/rts_impls/runtime_common/WorkerThread.H
Src/AmrTask/rts_impls/runtime_common/WorkerThread.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv_advance.cpp

commit 2e8eaaea93bb5e6646aeb435fa0a1f1cd4756773
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 30 11:57:51 2019 -0700

    reduce tutorial: use long for sum of iMultiFab for consistence with iMultiFab::sum function

Tutorials/GPU/ParallelReduce/main.cpp

commit 50d1b453c97da23463067b8bfa88a0590d5c0c3c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 30 11:50:25 2019 -0700

    fix type in reduce

Src/Base/AMReX_GpuReduce.H

commit af92d8721ffe55be93cf623c54b72aebb0a93735
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jul 30 14:50:17 2019 -0400

    Start of GraphInitTest.

Tests/GPU/CudaGraphs/GraphInitTest/GNUmakefile
Tests/GPU/CudaGraphs/GraphInitTest/Make.package
Tests/GPU/CudaGraphs/GraphInitTest/inputs_3d
Tests/GPU/CudaGraphs/GraphInitTest/main.cpp

commit f75b096b497bcf784b6faa3f5d9e7db521124067
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 30 11:18:11 2019 -0700

    finish simplification of reduce interface

Src/Base/AMReX_Reduce.H
Src/Base/AMReX_Tuple.H
Tutorials/GPU/ParallelReduce/main.cpp

commit 8708a7060bca492fdd032cc388d8d888f153cb5f
Merge: b08fdf902 b5cb86b26
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jul 30 13:51:18 2019 -0400

    Merge branch 'development' into kngott/cudaGraphs

commit b5cb86b265bfce903f5cf1838385ecc83c6e0d1e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 30 10:18:19 2019 -0700

    id_rsa_travis -> deploy_key

build_and_deploy.sh

commit 01dc3e2a78600d02cdf0e027af72d4b6079d52b1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 30 13:17:55 2019 -0400

    don't actually need to clear the copy op and plan here

Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleContainerI.H

commit 458804755f33a4d5b4f4f8c65751b7e97f08dc33
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 30 13:14:40 2019 -0400

    parmparse nsteps in redistribute test

Tests/Particles/Redistribute/inputs
Tests/Particles/Redistribute/main.cpp

commit e668e7d5aee5735c19a19dc03f4fab31519698cc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 30 10:07:10 2019 -0700

    update deploy key used by Travis CI

build_and_deploy.sh
deploy_key.enc
id_rsa_travis.enc

commit f7cfdbd3491da93b4fd14a99eea22e0af9d1efaf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 30 07:20:28 2019 -0700

    simplify the interface for reduce

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_Reduce.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tutorials/GPU/ParallelReduce/main.cpp

commit 80202711a5f5f5729e7a41d2cc3854d63b34dc0e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 29 17:09:21 2019 -0700

    more 1D compilation errors

Src/Particle/AMReX_TracerParticle_mod_K.H

commit c47046e3b2727ae65938e505f913ff7c9d78dbb3
Merge: d76fbe0b3 ae05bd9e1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 29 17:07:06 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d76fbe0b34e33ef6b600e09d57448d4df3cbccbd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 29 17:06:53 2019 -0700

    fix 1D tracer particles

Src/Particle/AMReX_TracerParticle_mod_K.H

commit 274c1eb4e96e9ccc2cc8946df1763809f2768d9a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 29 15:59:34 2019 -0400

    keep around the redistribute copy plan and op so it doesn't need to do any reallocation

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 9f796c1b8f1a9cc87ee533b8c1b14f4148f994ed
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 29 15:53:14 2019 -0400

    avoid pushing back onto device vector in particle communication

Src/Particle/AMReX_ParticleCommunication.cpp

commit ae05bd9e1fe9138cf49bb203c4b6e36f60adb35e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 29 12:44:15 2019 -0700

    two *.H files were missing from Make.package

Src/Particle/Make.package

commit 1bb462984e5f87f3033e005ea6d511680f591e5b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 29 15:25:18 2019 -0400

    fix routine name in profile region

Src/Particle/AMReX_ParticleCommunication.H

commit fdd03aafa488ac7154fd3f6a030b6aa3940c71fb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 29 15:04:01 2019 -0400

    move early exit

Src/Particle/AMReX_ParticleContainerI.H

commit 467a446c82bf6847777bc30508fb18a370102739
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 29 15:03:21 2019 -0400

    actually used the parmparsed values of move_dir and do_random

Tests/Particles/Redistribute/inputs
Tests/Particles/Redistribute/main.cpp

commit f91036ac5255b4da55c52181627a25aa82fd738c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 29 14:27:16 2019 -0400

    change repo in submission script

Tests/Particles/NeighborParticles/script.sh
Tests/Particles/Redistribute/script.sh

commit f5eea1453a29360c0c587873de6d63349b01de1a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 29 14:26:59 2019 -0400

    add random move option for redistribute test

Tests/Particles/Redistribute/main.cpp

commit f2cc07c1db936224e0eb7d4d17bef2af9b89edb0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 29 14:06:52 2019 -0400

    update script

Tests/Particles/NeighborParticles/script.sh

commit c992577cf0fde3cce1399889e886c06d29e26cc8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 29 14:06:13 2019 -0400

    properly handle particles that leave the domain in non-periodic directions.

Src/Particle/AMReX_ParticleCommunication.H

commit bc5c3461753d676f985cd60343aaafdbdd64359f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 29 13:58:54 2019 -0400

    fix typo in script

Tests/Particles/Redistribute/script.sh

commit 2966f1efd118e0fe520f68de3f9b36b6b567273c
Merge: 61c0e7e15 3fd33a22b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 29 13:38:14 2019 -0400

    Merge branch 'development' into redistribute_opt

commit c47b0eb46ab2a548444f7f89199df190e7999152
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 28 19:28:19 2019 -0400

    Reduce::Min, Reduce::Max and Reduce::MinMax

Src/Base/AMReX_Functional.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Tutorials/GPU/ParallelReduce/main.cpp

commit 93d136ec5350ed46f1c64ba30fcab23c5c832af8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 28 15:12:22 2019 -0400

    ParallelForReduce -> FabReduce and VecReduce. add Reduce::Sum

Src/Base/AMReX_Functional.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuReduce.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tutorials/GPU/ParallelReduce/main.cpp

commit 3fd33a22b9feb93a9aad1bd06c11fc99526d6189
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Jul 28 10:27:33 2019 -0700

    Remove setMaxCoarseningLevel since it wasn't working anyway

Src/LinearSolvers/MLMG/AMReX_MacProjector.H

commit ca26d772abf344d6fb9ace16ed6a201c4712342c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Jul 28 10:14:13 2019 -0700

    Add a new MacProjector constructor that takes an lp_info so that we can pass
    m_max_coarsening_level in

Src/LinearSolvers/MLMG/AMReX_MacProjector.H
Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp

commit 4c4b042ec147fdb27f1cc68744ab825a6542f304
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 27 12:39:44 2019 -0400

    ParallelForReduce: more overloads

Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuMemory.H
Src/Base/AMReX_GpuReduce.H
Tutorials/GPU/ParallelReduce/main.cpp

commit 80073a4358fc85dd4ac191bcc2b5429005b0e315
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 27 11:03:58 2019 -0400

    ParallelForReduce

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuReduce.H
Tests/GPU/ParallelReduce/main.cpp
Tutorials/GPU/ParallelReduce/GNUmakefile
Tutorials/GPU/ParallelReduce/Make.package
Tutorials/GPU/ParallelReduce/main.cpp

commit 0d7325fb817146a5098a1357b635980d7b643485
Merge: 5b7dfb5c9 627a429f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 27 00:03:17 2019 -0400

    Merge branch 'development' into weiqun/reduce

commit 61c0e7e1546c47f9cea673e2bc215f3886865e38
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 17:57:56 2019 -0400

    checking particle redistribute test

Tests/Particles/Redistribute/GNUmakefile
Tests/Particles/Redistribute/Make.package
Tests/Particles/Redistribute/inputs
Tests/Particles/Redistribute/main.cpp
Tests/Particles/Redistribute/script.sh

commit cfb0447e281eff877297abf7a51c2144288d17eb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 17:38:41 2019 -0400

    forgot to put *

Src/Particle/AMReX_ParticleContainerI.H

commit e911bd4a2eb90bf754031028b5fd49e0a0d7ca83
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 17:32:34 2019 -0400

    implement unpack policies so that the same communication routines can handle both redistribute and neighbor unpacking patterns

Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleContainerI.H

commit 07b6e67fb102fe1de4bb588ad9a04e7abbf8e5c1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 16:11:40 2019 -0400

    do the same for communicateParticles

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleCommunication.H

commit 5b7dfb5c9bf1c2f4a19158adf62f1641f8a8825e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 26 12:35:42 2019 -0700

    reducesum using __shfl_down_sync

Src/Base/AMReX_GpuReduce.H
Tests/GPU/ParallelReduce/GNUmakefile
Tests/GPU/ParallelReduce/Make.package
Tests/GPU/ParallelReduce/main.cpp

commit 6048e8d360e25dc2a3718ae28e0674b072bd5688
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 15:28:16 2019 -0400

    move pack and unpack buffers out of neighbor particle container so they can be reused.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit 1d4e8e8a060dfd8a696cb93d93d831f75b56d643
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Jul 26 13:06:32 2019 -0600

    works with multilevel and multigrid, but bottom solve is still failing

Tests/LinearSolvers/MultiComponent/inputs

commit ccbe827ffa07aedf545b326c1cfb65ab682f4a12
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Jul 26 13:03:37 2019 -0600

    variable inputs working, but bottom solver is still failing for mglev>0

Tests/LinearSolvers/MultiComponent/MCNodalLinOp.H
Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp
Tests/LinearSolvers/MultiComponent/inputs
Tests/LinearSolvers/MultiComponent/main.cpp

commit e744e141eecd6921ad65dc9377d7f8262da39151
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 14:48:44 2019 -0400

    remove extra clearNeighbors calls

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit dfd69e7053f399e7cff10d8e8deb62500914b3df
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 14:42:42 2019 -0400

    also build the parallel portion of the copy plan

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit 509aab86e4f58e090ccc54910d0c549939f70ae5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 14:29:28 2019 -0400

    build method for ParticleCopyPlan

Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp
Src/Particle/AMReX_Particles.H

commit cd14b40b95b47dc523d1add5e27f724f0cb5da29
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 14:01:52 2019 -0400

    seperate the op and the plan

Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit 627a429f34d0ae91ff2284e71f33462dfae89ec4
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Jul 26 13:49:46 2019 -0400

    if (Gpu::notInLaunchRegion())

Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.cpp

commit 55bf0535b93d2ba4197b76d146be05f49044e9b8
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Jul 26 12:41:03 2019 -0400

    OwnerMask -> GPU.

Src/Base/AMReX_iMultiFab.cpp

commit 39a4905c7d4af5fddecd9a08f0d2d16aca65541f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 13:45:55 2019 -0400

    create structs for particle copy ops and plans

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleCommunication.H
Src/Particle/AMReX_ParticleCommunication.cpp

commit 847775accce0719dd4fdd125f429acd576e1d2be
Merge: edef7f121 abaf6cae4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 13:09:37 2019 -0400

    Merge branch 'development' into redistribute_opt

commit abaf6cae41c62820116f528171172059ffe22e2b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 13:09:09 2019 -0400

    add an explanatory comment about the default number of cuda random states.

Src/Base/AMReX_Utility.cpp

commit 02158a53931fba8f712745cce24ccea77e619ca5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 13:07:42 2019 -0400

    make it so that users no longer need to call InitRandomSeedOnDevice explicitly

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Tests/GPU/RandomNumberGeneration/main.cpp

commit edef7f1214d062194d0155f530e6d8aeaaa027e8
Merge: d8acb0b48 4b66a19f0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 12:54:30 2019 -0400

    Merge branch 'development' into redistribute_opt

commit 4b66a19f0ecae3a7a75331dc23ae2f09d6bd8acc
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 12:52:49 2019 -0400

    use std namespace for floor, don't use line continuation symbols

Src/Particle/AMReX_TracerParticle_mod_K.H

commit d8acb0b48304c80f5f0e93b686f9a50581b640a3
Merge: c232b0d08 6ca05c162
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 12:47:25 2019 -0400

    Merge branch 'development' into redistribute_opt

commit 6ca05c162914678bc52a5e7582ddb9606e8fd11f
Merge: cf954e5c3 0bfcbaeec
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 09:42:25 2019 -0700

    Merge pull request #534 from ChrisDeGrendele/tracerparticles_2
    
    This adds gpu support to tracer particles

commit cf954e5c37b308828e66bb746f10c83135cf45d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 26 12:21:47 2019 -0400

    value_type -> Real

Src/Base/AMReX_VisMF.cpp

commit 0bfcbaeecebfe9f4b2af2247ee90941b87224896
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Fri Jul 26 02:01:44 2019 -0400

    Fixed segfault error

Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit a5f0e4da1c5e87a9537501f75b039450cd66f23b
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Thu Jul 25 22:34:21 2019 -0700

    commit the changes

Src/Particle/AMReX_TracerParticles.cpp
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit 40ee9785d6b0e211cf3933084e17e5aeb3450264
Merge: d2442fa9b ae1f992c2
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Thu Jul 25 22:24:47 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into tracerparticles_2

commit d2442fa9b57831d9925386cc7f1b78cc76d932e1
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Thu Jul 25 22:10:38 2019 -0700

    fixed off by 1 index error again

Src/Particle/AMReX_TracerParticle_mod_K.H

commit 0756a5ba736948d1d7aa398c10cec0bf7a3ef632
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Thu Jul 25 22:07:35 2019 -0700

    tracer

Src/Particle/AMReX_TracerParticle_mod_K.H

commit c232b0d0893e79a6f8bdbf733e0eae8381be39be
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 26 00:01:23 2019 -0400

    more work on refactoring the particle communication code

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 19a391d613115ab54c7a6e71c914ce6bb2080d51
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 22:46:09 2019 -0400

    remove some unused variables

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit f64e2cdb94b52df3d6f6a42063cefc34aca837c0
Merge: 589f976be ae1f992c2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 22:36:14 2019 -0400

    Merge branch 'development' into redistribute_opt

commit ae1f992c22a84dfb7927acd8788435fabe86d6f1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 22:31:45 2019 -0400

    make sure these variables are initialized

Src/Base/AMReX_Utility.cpp

commit 8b8e7dd4da5f6bba4bac5489ccb553867a454efd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 20:50:18 2019 -0400

    remove sync I just added

Src/Base/AMReX_Utility.cpp

commit feaa261f1ce9ce7f5f6f11542741a71320ae9cfd
Merge: 33061f019 46026bf13
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 20:41:04 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 33061f01999a48c2bd806726458c5c8626b1c9ca
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 20:40:40 2019 -0400

    turn on TINY_PROFILE by default

Tests/GPU/RandomNumberGeneration/GNUmakefile

commit 46026bf1399174ebcb3b99751c31f157f2675e6b
Merge: 8be85ba2a d10808444
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 25 17:31:40 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8be85ba2a688792409623c7b8a6a05c5fc155890
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 25 17:31:01 2019 -0700

    when there are callbacks in MFIter, use two streams only

Src/Base/AMReX_GpuAsyncArray.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuElixir.cpp
Src/Base/AMReX_MFIter.cpp

commit d108084444bc76cd7e4641aaeebdd48951839a21
Author: kngott <kngott@lbl.gov>
Date:   Thu Jul 25 17:19:35 2019 -0700

    OverlapMask on the GPU.

Src/Base/AMReX_MultiFab.cpp

commit 20cbb7918fe81c73c7e76fd4696dfb15e7512b26
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 20:15:09 2019 -0400

    Should call device synchronize after initializing the random seeds

Src/Base/AMReX_Utility.cpp

commit 84bac46d82daf34a603c67da32aa7b92b7c9e97a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 20:03:59 2019 -0400

    parmparse nstates and ndraw in the random number generation test

Tests/GPU/RandomNumberGeneration/main.cpp

commit fefbecacf3451023eb7c339ea65adbc9190800b4
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Jul 25 17:25:51 2019 -0600

    wip - currently works but bottom solve is failing

Tests/LinearSolvers/MultiComponent/MCNodalLinOp.H
Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp
Tests/LinearSolvers/MultiComponent/inputs
Tests/LinearSolvers/MultiComponent/main.cpp

commit 92426d391fb364dc36d7158ea23b7c07a19dcffd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 18:51:48 2019 -0400

    don't need separate variables for host and device size of the state array

Src/Base/AMReX_Utility.cpp

commit f6878072146abb91622743a696be9579ea0e899b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 18:46:07 2019 -0400

    remove unused function

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit b6144c1a856935bbbf4fb44d965311417ecffaea
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 18:45:39 2019 -0400

    some renaming

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit 104941ce0790458165d431f8adc18c1ae9c1bdeb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 17:58:36 2019 -0400

    some reorganization

Src/Base/AMReX_Utility.cpp

commit 48d8e73ab6d888cb1da5ea308c359131050447d7
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 17:51:36 2019 -0400

    also use the locks in amrex::RandomNormal

Src/Base/AMReX_Utility.cpp

commit 9b37e151c0f4c6564fdec3c61ac333b5521f9698
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 17:50:31 2019 -0400

    update random number gpu test

Tests/GPU/RandomNumberGeneration/main.cpp

commit fb743125b2c57909e045ac35cc53988aea603304
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 17:50:10 2019 -0400

    also add a free_state function to release the lock

Src/Base/AMReX_Utility.cpp

commit 97deb3d982dc045de45ac8679c3e00500f39d5eb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 17:40:21 2019 -0400

    use same nstates variable to keep track of both the random states and the lock array

Src/Base/AMReX_Utility.cpp

commit b176a9b0295f25af43493427edaa249f98218b30
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 17:39:20 2019 -0400

    fix index bug in amrex::Random

Src/Base/AMReX_Utility.cpp

commit 4f997b2b3d21d43ec3e7afec6af63ce6c510d721
Merge: b92641b6d d5f5e0d49
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 25 14:37:57 2019 -0700

    Merge pull request #532 from ChrisDeGrendele/gpu_rng
    
    Random number generation on gpus

commit 5e4d505143599bc146512b129bee7bcca3322f0c
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Jul 25 15:33:37 2019 -0600

    re-committed with spurious files removed

Tests/LinearSolvers/MultiComponent/MCNodalLinOp.H
Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp
Tests/LinearSolvers/MultiComponent/Make.package
Tests/LinearSolvers/MultiComponent/inputs
Tests/LinearSolvers/MultiComponent/main.cpp

commit b92641b6d62a0103090be0c1ab375e24c7cd9dc5
Author: kngott <kngott@lbl.gov>
Date:   Wed Jul 24 14:19:09 2019 -0700

    Remove hanging variable.

Src/Base/AMReX_Utility.cpp

commit bd15b5b613f9fe73b52b952160c780805fbd8852
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Jul 25 10:04:16 2019 -0700

    change add command in build_and_deploy.sh

build_and_deploy.sh

commit e7e497568ad404a47cbff86b003bb04304eb0839
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 25 09:18:52 2019 -0700

    fix c++ std flag when pgi is used as nvcc host compiler

Tools/GNUMake/comps/nvcc.mak
Tools/GNUMake/comps/pgi.mak

commit 2b9dcff39ab02780eb4acb86ca5432bdb2b88242
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 24 18:23:03 2019 -0700

    fix id_rsa_travis path

build_and_deploy.sh

commit d5f5e0d4918f86250153e46e4a3d631f3fedd0cf
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 17:26:56 2019 -0700

    get_state should only be declared if we're using gpus

Src/Base/AMReX_Utility.cpp

commit 5e64ad21cce30f49c291b3d1fa6160af36c6a316
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 24 17:09:37 2019 -0700

    move doc to AMReX-Codes.github.io

build_and_deploy.sh

commit b3edd79f132dfa2ee1ee7362c0833d4f7f5349be
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 17:01:04 2019 -0700

    fixed whitespaces

Src/Base/AMReX_Utility.cpp

commit 4272c1561aba4dd6e5d7940dc23f57a2ef6cb39c
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 16:58:28 2019 -0700

    fixed

Src/Base/AMReX_GpuUtility.cpp

commit 9a3e547ba272783a20dae4b44fcab94ee0df86d8
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 16:48:41 2019 -0700

    Forgot };

Src/Base/AMReX_Utility.cpp
Tests/GPU/RandomNumberGeneration/main.cpp

commit 487846a6915ad01fe424ee32ffe9ded5e07d75db
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 16:42:15 2019 -0700

    Tracer Particle GPU support

Src/Base/AMReX_Utility.cpp
Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_Particle_mod_K.H
Tests/GPU/RandomNumberGeneration/GNUmakefile
Tests/GPU/RandomNumberGeneration/launc_gpu.sh
Tests/GPU/RandomNumberGeneration/main.cpp
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile

commit 1c6f79eec6b419a1ef30dec9ae8b9d3ff87e3da9
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 16:28:59 2019 -0700

    Random Number Generation on GPUs

Src/Base/AMReX_GpuUtility.cpp
Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_Particle_mod_K.H
Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp
Tests/GPU/RandomNumberGeneration/GNUmakefile
Tests/GPU/RandomNumberGeneration/launc_gpu.sh
Tests/GPU/RandomNumberGeneration/main.cpp
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit ff91d72b795de73129c27ba12e4974466208498a
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 15:55:20 2019 -0700

    one last thing

Src/Base/AMReX_GpuUtility.H

commit ac80f65870dafb78463457aae2089ce421772ce7
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 15:51:41 2019 -0700

    removed more files

Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Backtrace.0
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/Backtrace.0
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/viz.py

commit a9ab86ccf182afb110bcdc04a50985f76623a7c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 24 15:47:46 2019 -0700

    trigger travis

LICENSE

commit b0713f29ce919b74b7df7e70073d62dd53447934
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 15:47:25 2019 -0700

    Removed old func decleration

Src/Base/AMReX_Utility.H

commit 062d0bfcb04da34088914dbf38ef42b5714c19d3
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 15:44:22 2019 -0700

    removed more unnecessary commits

Src/Particle/#AMReX_TracerParticles.cpp#
Src/Particle/out.txt
Tests/GPU/Particles/Redistribute/Backtrace.0
Tests/GPU/RandomNumberGeneration/out.txt.REMOVED.git-id
Tutorials/GPU/NeighborList/#MDParticleContainer.cpp#

commit 4b857626a1706e60fdca133b8e6693276c6de288
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 15:40:17 2019 -0700

    Deleted accidental pushes

Src/Base/#AMReX_FArrayBox.H#
Src/Base/#AMReX_FArrayBox.cpp#
Src/Base/#AMReX_GpuUtility.cpp#
Src/Particle/#AMReX_TracerParticles.cpp#
Src/Particle/AMReX_TracerParticles.cpp
Src/Particle/out.txt
Tests/GPU/Particles/Redistribute/Backtrace.0
Tests/GPU/RandomNumberGeneration/GNUmakefile
Tests/GPU/RandomNumberGeneration/launc_gpu.sh
Tests/GPU/RandomNumberGeneration/main.cpp
Tests/GPU/RandomNumberGeneration/out.txt.REMOVED.git-id
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Header
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Level_0/Cell_D_00000.REMOVED.git-id
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Level_0/Cell_H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Header
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Level_0/Cell_D_00000.REMOVED.git-id
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Level_0/Cell_H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Header
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Level_0/Cell_D_00000.REMOVED.git-id
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Level_0/Cell_H
Tutorials/GPU/NeighborList/#MDParticleContainer.cpp#
Tutorials/Particles/NeighborList/Backtrace.0.0

commit 3ccab6c251411e9e2a1680fc2c4c6692626bcda4
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 15:33:02 2019 -0700

    Merged back into Random() funct

Src/Base/AMReX_Utility.cpp

commit 70bf151be40210a3e0e8840ddcb7274b29c3474c
Merge: b36efca32 d12f632ee
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 15:22:36 2019 -0700

    synced with no devicevector version

commit 589f976befb551cdfa7aeafd32c328504cedf060
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 24 17:54:15 2019 -0400

    just do construction of the map on the CPU

Src/Particle/AMReX_ParticleBufferMap.H
Src/Particle/AMReX_ParticleBufferMap.cpp

commit 78e25e62096f5f44f823dddef41d39be2e168ede
Merge: e10e02ee5 d12f632ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 24 14:46:27 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b36efca325aec4dd1bb059f74050cd16d89f7ed8
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jul 24 14:36:25 2019 -0700

    GPU random number generation

Src/Base/AMReX_Utility.cpp

commit d12f632ee38cf8434f3ec0cc9fa7fc3570de7246
Author: jmsexton03 <jmsexton@lbl.gov>
Date:   Wed Jul 24 14:13:37 2019 -0700

    Update run.summit w/1 resource set per GPU comment

Tutorials/GPU/run.summit

commit 0c3303e6ea5d58fcc6aa47784219b65b8c4ca41e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 24 16:49:50 2019 -0400

    forgot to add these files

Src/Particle/AMReX_ParticleBufferMap.H
Src/Particle/AMReX_ParticleBufferMap.cpp

commit a2601327fbb228e91e9ebcd88a7e42f08aa6f738
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 24 16:49:18 2019 -0400

    some tweaks to the ParticleBufferMap class

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Tests/Particles/NeighborParticles/script.sh

commit 0c2f3fa94b423031262db8fec65624f38508beb0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 24 15:22:24 2019 -0400

    reorganize some of the recent changes to the neighbor particle code

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit cc3ac385c34404fcaed3d978b414ef6080ab733d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 24 13:57:21 2019 -0400

    remove commented code

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit f40b3d76d511b8bdd1b1232b1be92586ce4ab923
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 24 13:56:53 2019 -0400

    some cleanup in BuildRedistributeMask

Src/Particle/AMReX_ParticleContainerI.H

commit e334d63cfbc03436a2237235416c7c9232bee53a
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Jul 24 11:16:20 2019 -0600

    implementing nodal multicomponent mlmg test

Tests/LinearSolvers/MultiComponent/Make.package
Tests/LinearSolvers/MultiComponent/inputs
Tests/LinearSolvers/MultiComponent/main.cpp

commit 915745d6cf21b17b361e986fb45e42351a5dde65
Author: kngott <kngott@lbl.gov>
Date:   Tue Jul 23 16:57:39 2019 -0700

    MultiFab functions test.

Tests/GPU/ScratchPad/GNUmakefile
Tests/GPU/ScratchPad/inputs_3d
Tests/GPU/ScratchPad/main.cpp

commit eaa9c05bf70db0f7bfca47835f667efba5902f09
Author: kngott <kngott@lbl.gov>
Date:   Tue Jul 23 16:57:06 2019 -0700

    Self-dot and updated MultiFab::norm2 function.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit d1aa84f93b0220fff36ae9d6679cccaea8dd693d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 19:41:37 2019 -0400

    remove this unit test, as it has been rolled into the other one

Tutorials/GPU/NeighborParticlesUnitTest/CMakeLists.txt
Tutorials/GPU/NeighborParticlesUnitTest/CheckPair.H
Tutorials/GPU/NeighborParticlesUnitTest/Constants.H
Tutorials/GPU/NeighborParticlesUnitTest/GNUmakefile
Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.H
Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.cpp
Tutorials/GPU/NeighborParticlesUnitTest/Make.package
Tutorials/GPU/NeighborParticlesUnitTest/README.md
Tutorials/GPU/NeighborParticlesUnitTest/inputs
Tutorials/GPU/NeighborParticlesUnitTest/main.cpp
Tutorials/GPU/NeighborParticlesUnitTest/script.sh

commit 1840541e0deb27039dbcdb373d3977e2ad0ff7e1
Merge: 23c6a180b d0f607e88
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 19:37:37 2019 -0400

    Merge branch 'development' into mfix_hackathon

commit d0f607e88f5f30def91d358882f5f65541c642d9
Merge: 2352c6302 859eb6ffc
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 19:36:54 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2352c6302c3968b2f5761f7df2acb86d3906d201
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 19:36:42 2019 -0400

    remove use of thrust vector as global variable

Src/Base/AMReX_Utility.cpp

commit 23c6a180b47d3f24f1526075bd46ad809e8a641d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 18:43:39 2019 -0400

    move test to Tests

Tests/Particles/NeighborParticles/CMakeLists.txt
Tests/Particles/NeighborParticles/CheckPair.H
Tests/Particles/NeighborParticles/Constants.H
Tests/Particles/NeighborParticles/GNUmakefile
Tests/Particles/NeighborParticles/MDParticleContainer.H
Tests/Particles/NeighborParticles/MDParticleContainer.cpp
Tests/Particles/NeighborParticles/Make.package
Tests/Particles/NeighborParticles/README.md
Tests/Particles/NeighborParticles/inputs
Tests/Particles/NeighborParticles/main.cpp
Tests/Particles/NeighborParticles/script.sh

commit e0405fad2b9a08832f11edd080c221e57cc8091d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 18:41:02 2019 -0400

    consolidate and reorganize test

Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H
Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp
Tutorials/GPU/NeighborListUnitTest/inputs
Tutorials/GPU/NeighborListUnitTest/main.cpp
Tutorials/GPU/NeighborListUnitTest/script.sh

commit 39717e44261a6231ae8fcaf6087048482e3a414c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 18:14:08 2019 -0400

    use the wrapped version of exclusive_scan

Src/Base/AMReX_CudaContainers.H
Src/Particle/AMReX_NeighborList.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Tutorials/GPU/NeighborParticlesUnitTest/script.sh

commit 6d17024fdbc65162e6710404cf111215394e5a38
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 18:11:15 2019 -0400

    modify print statements in test

Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp
Tutorials/GPU/NeighborListUnitTest/main.cpp

commit 45bc81f1af301de472b0a2df76955182798b0565
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 17:35:07 2019 -0400

    compute num_copies in a cleaner way

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 0e9f709bbb9f1750db1fb1973930c7ca93ca65b3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 17:14:54 2019 -0400

    std::cout -> amrex::Print()

Tutorials/GPU/NeighborListUnitTest/main.cpp

commit 14fcb8d8c3aed51dee5848ff331ad81236c2953f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 17:14:18 2019 -0400

    fix rcv buffer offset calculation

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit f7e851b3bfee7e6650d9b1ac1b7c1fe2d0c84b23
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 16:32:12 2019 -0400

    remove some now unused functions

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit af9ef562b21f87749ed5e62f216a43768c5dff19
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 16:15:55 2019 -0400

    fix timer name

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 13e37ae058d2c8a9adb78097889c047882118df0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 16:15:34 2019 -0400

    this doesn't need to be a member

Src/Particle/AMReX_NeighborParticles.H

commit 31cb3ca14db3de30356471c209e763e452acc6e0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 16:07:09 2019 -0400

    put this operator in the amrex namespace so amrex::Print() can find it

Tutorials/GPU/NeighborListUnitTest/main.cpp

commit 5cf139eb7bee03bb8390edf4ea0a5a9fef03bc6d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 15:38:46 2019 -0400

    fix mpi neighbor particle test

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 808ba1f747681e7d49cf4d87d0e1dad9e2e8a89b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 13:50:29 2019 -0400

    modify some prints

Tutorials/GPU/NeighborListUnitTest/main.cpp

commit e3202f1dbc0ae441311e178d6fde0def28da9b9a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 13:49:52 2019 -0400

    some work towards fixing the MPI portion of updateNeighbors... almost right now.

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit a705898c8c62528e9042be48cae3ac87c13bde44
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 13:23:18 2019 -0400

    templated overload of << for pair

Tutorials/GPU/NeighborListUnitTest/main.cpp

commit 08c988e301fd0bada0dbfcc416ab27424d449364
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 23 13:22:58 2019 -0400

    modify test to compare both min and max of the inter-particle spacing

Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H
Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp

commit dde9e1aac8f2b0c649887babddf47b2839086a1c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 22 20:20:08 2019 -0400

    some work on debugging parallel

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit e10e02ee55f12a447b2275d2e074b43febf6248c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 22 15:23:53 2019 -0700

    fix the fix that tried to remove hardwired warp size

Src/Base/AMReX_FabArrayUtility.H

commit 859eb6ffceb13b4c2cc12ba6beb9493571039fb8
Merge: 197237e1d c8ba1d76e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 22 11:20:13 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 197237e1da0c3d0dd0e2259aac5c19ddbfb32999
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 22 11:19:55 2019 -0700

    add compiler generated move for AmrMesh and AmrCore

Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrMesh.H

commit c8ba1d76e81faa171240aa6fe964da707deb422e
Merge: 232e0ae7d 1da27415a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jul 22 09:45:52 2019 -0700

    Merge pull request #527 from Alpine-DAV/task/2019_07_blueprint_updates
    
    bugfixes for conduit blueprint support

commit b64c1b73e986ccf03ebb01e96ddf3785887a18a6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Jul 21 16:07:07 2019 -0700

    Fix spelling so 'git grep' searches will find the right thing

Src/Particle/AMReX_ParticleContainerI.H

commit 232e0ae7d99e444c2b35248baf80811ddb8c6888
Merge: 9e24752ba 6614b20ab
Author: mic84 <mrosso@lbl.gov>
Date:   Fri Jul 19 18:28:39 2019 -0700

    Merge pull request #526 from rupertnash/development
    
    CMake install step: make header modification more cross-platform

commit 9e24752ba5124c0cd0fdb333dd48626325b116a4
Merge: d78cd92f0 07679922a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 19 16:22:21 2019 -0700

    Merge branch 'hackathon' into development

commit 79c526b1a18bd913e98027f6800355ba82b9e788
Merge: bdd0c8ec8 9446d4139
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 19 14:45:37 2019 -0400

    Merge branch 'mfix_hackathon' of github.com:AMReX-Codes/amrex into mfix_hackathon

commit bdd0c8ec8826490ec663e426778b3395fb304026
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 19 14:45:06 2019 -0400

    need to change where we are setting the number of neighbors from the remotes

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 1da27415ab0ec9135e38e3c63a7e93076a988ac1
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Fri Jul 19 10:11:31 2019 -0700

    clarify comment

Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp

commit 07679922a86d4ab0c5df370afdb9c2464b519b47
Merge: aeb0059e3 0c0b033cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 19 09:19:54 2019 -0700

    Merge branch 'weiqun/hackathon' into hackathon

commit aeb0059e3a91a80058bf2b106fdee77c70750510
Merge: 7d1d31ed3 e8c9afeaa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 19 09:18:59 2019 -0700

    Merge branch 'hackathon' of github.com:AMReX-Codes/amrex into hackathon

commit 7d1d31ed3665381deae2c2e9451f2ae4cfd33de8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 19 06:23:21 2019 -0700

    libamrex: move AMReX_Config.H inside include guard

Tools/GNUMake/Make.rules

commit 6614b20ab8eb39a9c031658ad3c2a25b9d9e0fdb
Author: Rupert Nash <r.nash@epcc.ed.ac.uk>
Date:   Fri Jul 19 14:26:19 2019 +0100

    insert include AMReX_Config.H within include guard

Tools/CMake/modify_installed_headers.cmake

commit 73ab017b410e628587fe6d89b3d74e3e58bc9624
Author: Rupert Nash <r.nash@epcc.ed.ac.uk>
Date:   Fri Jul 19 13:17:57 2019 +0100

    make header modification use cmake to be more cross-platform

Tools/CMake/modify_installed_headers.cmake

commit 19c01e9bb8cd8844c06bdb28611fb1b78bbcaf20
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 19 03:41:19 2019 -0400

    some towards fixing the mpi

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 4df2382d0d22fb76df19d1855e896eebdb5f626d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 18 19:41:52 2019 -0400

    exchange the total number of rcv bytes

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 3fc1981e2a23a08396161b602893e3bc1cb0e2cc
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 18 19:08:15 2019 -0400

    fix proc_box_offsets

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 2bf381b70b3dd7147f680b6c1ac02a1fc9f4d380
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 18 18:41:37 2019 -0400

    taking out a print statement

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 29f650fd1f6daad25d2f1001864b8efb3b894735
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 18 18:38:44 2019 -0400

    computing proc ids and offsets

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 6d7f264dcdd6b652774fe243e737b0a7b1c641bd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 18 17:53:19 2019 -0400

    pack particles into the send buffer such that all the boxes bound for the same proc id are together

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 9d6195416542bcb90cdc1e7b3fe7c2a792478937
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 18 17:25:54 2019 -0400

    don't need to do any communication to figure out which procs sent what boxes to me

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 02510d342e077bf1e69c90624b0d05f618f14ba6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 18 16:46:18 2019 -0400

    a test getBoxRcvCounts function

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 9446d413967fd8ceab2f9bc0c35e743a5a0f2e11
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Thu Jul 18 09:54:55 2019 -0400

    Fix printing so that we only print off the processor that owns grid 0

Tutorials/GPU/NeighborListUnitTest/main.cpp

commit 0b7911edd34bec37f899038276ef55adc67de476
Merge: 3b44c3fc7 b7005481e
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Thu Jul 18 09:45:15 2019 -0400

    Merge branch 'mfix_hackathon' of https://github.com/amrex-codes/amrex into mfix_hackathon
    
    Conflicts:
            Tutorials/GPU/NeighborList/main.cpp

commit 3b44c3fc7199ff8540a1b9cd01e454f4f06efe6d
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Thu Jul 18 09:34:42 2019 -0400

    Slight clean-up of main

Tutorials/GPU/NeighborList/main.cpp

commit b7005481e8bc9cd77f9ac87284df3bafb2a2cffb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 18 00:05:12 2019 -0400

    also look at particle positions in the neighbor list test

Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H
Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp
Tutorials/GPU/NeighborListUnitTest/main.cpp

commit 485da8fce65f49df64bd3f716c946f7528ce6bbe
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 23:31:02 2019 -0400

    change some printing behavior

Tutorials/GPU/NeighborList/MDParticleContainer.cpp
Tutorials/GPU/NeighborList/inputs
Tutorials/GPU/NeighborList/main.cpp

commit 9bffc48ef18149b09afc47938be6c97e8f1d1b38
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 23:21:05 2019 -0400

    add a final call to redistribute

Tutorials/GPU/NeighborList/main.cpp

commit 5eb842f205f07210d8853e4491732c7c0cf10bba
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 23:12:38 2019 -0400

    don't print min dist unless requested

Tutorials/GPU/NeighborList/main.cpp

commit 785bf3aee1d20bb7c6d432d4469d11cb6151dbe4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 23:10:31 2019 -0400

    don't print the neighbor list unless requested

Tutorials/GPU/NeighborList/main.cpp

commit e8c9afeaa55f8d92c6b4b058f4e4cfd40a653b37
Author: kngott <kngott@lbl.gov>
Date:   Wed Jul 17 17:40:13 2019 -0700

    Fix summit script flags for CUDA aware MPI.

Tutorials/GPU/run.summit

commit 71aa55e15e031c74c683578896d035b6c27b8259
Merge: 88e7d6d82 386316a19
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 19:31:45 2019 -0400

    merging.

commit 88e7d6d829dfab05638c7fff7795fc726183e48d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 19:26:25 2019 -0400

    modify inputs for neighbor list test

Tutorials/GPU/NeighborListUnitTest/inputs

commit cfa7f01190358c79f0e9ef6a09c723b401f3ea09
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 19:24:30 2019 -0400

    missed a box offset

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 386316a1975998f7efc8898d8f472a61fde9b9b8
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Wed Jul 17 19:16:13 2019 -0400

    This has the CPU version of the checkParticles() version -- it gives the "correct"
    answer with 1 MPI process but not with 2 MPI processes.

Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp

commit 016c227e5f1ff8cc603bd9a45882042f66c4e2fd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 18:44:57 2019 -0400

    src -> dst

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 8e1248ab3964690acfdda6f7ffd68872d6bae3b9
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 18:29:11 2019 -0400

    implement update and Fill in terms of the new halo functions

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 383f42fdf2c8af74850fcd256d9ea4f8a2650119
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Wed Jul 17 18:19:08 2019 -0400

    We need to explicitly call the sychronize before printing

Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp

commit 1e34d2491abb8ad747e882b13808890340671453
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Wed Jul 17 18:16:07 2019 -0400

    Don't try to access "mine" when it's not actually set

Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp

commit 01ed6c451ea5464f48be0c5f60de7662ff7fc135
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Wed Jul 17 18:12:41 2019 -0400

    Actually lets use num_ppc = 1

Tutorials/GPU/NeighborListUnitTest/inputs

commit 5b7e43e25f8ba4b7e7406c4178f8318c44c9a4ba
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Wed Jul 17 18:12:08 2019 -0400

    This is the inputs for this test

Tutorials/GPU/NeighborListUnitTest/inputs

commit 32fdf9d64799fc187a7749d8c4f1a8bca659c428
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Wed Jul 17 18:10:53 2019 -0400

    Change the print statements to work in parallel

Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp

commit 9b9a7a4935badfda570aa11c2de798a0a03d7f7b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 17 15:08:26 2019 -0700

    add optional shared memory to ParallelFor

Src/Base/AMReX.cpp
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_GpuLaunchFunctsG.H

commit fa3ca1809b7101c5b587069fbd9209ea227c735d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 17:15:21 2019 -0400

    remove commented out code

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 5850e5d5d93923ab7551aa1c70cc51c5bba1c22b
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Wed Jul 17 17:03:18 2019 -0400

    This does all the testing on CPU even when the neighbor list is built on GPU.

Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.cpp
Tutorials/GPU/NeighborParticlesUnitTest/inputs
Tutorials/GPU/NeighborParticlesUnitTest/main.cpp

commit 9e6db163057d4baf998ef915703278b5d4ac52b0
Merge: a6ae2f9b6 9477744c5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 16:58:19 2019 -0400

    Merge branch 'mfix_hackathon' of github.com:AMReX-Codes/amrex into mfix_hackathon

commit a6ae2f9b6814cd3d8a611b5f469b9d005acfbcfa
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 16:56:48 2019 -0400

    apply periodic when packing the buffer

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit d9676a13a449a4015f165102571cfd7308b8f273
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 16:43:41 2019 -0400

    compute the dst indices correctly

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 87667c5376faa0d4338d0008e8b1f7c3bda286ee
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 16:14:09 2019 -0400

    don't reset the counters inside the mfiter loop to sort the snd buffer by destination only

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 2c1c5730a0883c077196cf4a688afae4a9e23e45
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 15:43:58 2019 -0400

    implement pack and unpack

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 9477744c5ac0f4675131f740ba490e31a560c8c2
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Wed Jul 17 15:00:45 2019 -0400

    New unit test for testing BuildNeighborList which creates particle-neighbor lists

Tutorials/GPU/NeighborParticlesUnitTest/CMakeLists.txt
Tutorials/GPU/NeighborParticlesUnitTest/CheckPair.H
Tutorials/GPU/NeighborParticlesUnitTest/Constants.H
Tutorials/GPU/NeighborParticlesUnitTest/GNUmakefile
Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.H
Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.cpp
Tutorials/GPU/NeighborParticlesUnitTest/Make.package
Tutorials/GPU/NeighborParticlesUnitTest/README.md
Tutorials/GPU/NeighborParticlesUnitTest/inputs
Tutorials/GPU/NeighborParticlesUnitTest/main.cpp
Tutorials/GPU/NeighborParticlesUnitTest/script.sh

commit 932fe23eecec65f070a5747bb94a78c3fac3e682
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 15:00:45 2019 -0400

    resize the snd_buffer to the appropriate size

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 19a0b0ed02f5479de4425fc7515f12e98eaef877
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Wed Jul 17 11:45:38 2019 -0700

    fix export of blueprint files for mult-domain, fix wrapping of multiple fields, add cycle info

Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp

commit 1916c22ca09ab274579d393ad7bebf01458a18c4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 14:34:37 2019 -0400

    handle periodicity; compute box counts and offsets

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 9a0221ac14aff30471aaecfac89475d5b0eef4b5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 14:10:54 2019 -0400

    seperate out computing the halo particles and computing the copy plan

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit d78cd92f07f4649d72e6f52726448333d2c06ce9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jul 17 10:56:44 2019 -0700

    Add option to change _device suffix for GPU pragma

Tools/F_scripts/write_cuda_headers.py
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 4f96c55d54f20c94b1b86fd73697830fdc712379
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jul 17 10:01:13 2019 -0700

    Add pragma gpu option to disable host version

Tools/F_scripts/write_cuda_headers.py

commit 538516fedb6d31e87dc89b853497beb6bac2c155
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jul 16 23:15:02 2019 -0700

    Allow PGI -gopt to be disabled

Tools/GNUMake/comps/pgi.mak

commit d118719c6105c3aa6edcf1560608534b412cf12a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 17 01:09:24 2019 -0400

    some work towards reimplementing neighbor particle communication

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit f9886599367e36f0631fb7ad233cb7540d4e9988
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Tue Jul 16 20:43:48 2019 -0400

    New unit test for FillNeighbors and UpdateNeighbors

Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H
Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp
Tutorials/GPU/NeighborListUnitTest/README.md
Tutorials/GPU/NeighborListUnitTest/main.cpp

commit b2a4a785abbf720c7a8dd200af9ac3c36be5257b
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Tue Jul 16 19:14:11 2019 -0400

    add inputs

Tutorials/GPU/NeighborListUnitTest/inputs

commit c19c1d299b12e71f76f82848f41aa83d9ed31e8f
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Tue Jul 16 19:13:55 2019 -0400

    Starting point for new unit test

Tutorials/GPU/NeighborListUnitTest/CMakeLists.txt
Tutorials/GPU/NeighborListUnitTest/CheckPair.H
Tutorials/GPU/NeighborListUnitTest/Constants.H
Tutorials/GPU/NeighborListUnitTest/GNUmakefile
Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H
Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp
Tutorials/GPU/NeighborListUnitTest/Make.package
Tutorials/GPU/NeighborListUnitTest/main.cpp
Tutorials/GPU/NeighborListUnitTest/script.sh

commit 786fc90640c1296b5706918ba50b4b540fffddb4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jul 16 14:52:44 2019 -0700

    Add attributes(host) attributes(device) macro

Tools/GNUMake/Make.defs

commit a2985282547946c04f283059e3851badfe43f247
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Tue Jul 16 16:45:15 2019 -0400

    Add run-time option to control whether we compute and print the minimum distance
    between particles

Tutorials/GPU/NeighborList/inputs
Tutorials/GPU/NeighborList/main.cpp

commit 5146e6000f14460ff40d1fa4f9c1a2da2a8ed052
Merge: 0a93f84d6 adee7bfc3
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Tue Jul 16 15:39:57 2019 -0400

    Merge branch 'mfix_hackathon' of https://github.com/amrex-codes/amrex into mfix_hackathon
    
    Conflicts:
            Tutorials/GPU/NeighborList/main.cpp

commit 0a93f84d61cf8eb16cd85c2443020dc89d68e2c8
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Tue Jul 16 15:38:24 2019 -0400

    Update this GPU neighborlist tutorial to make it closer to the MFiX-Exa
    conditions (2.5 particle diameters per grid cell, for example)

Tutorials/GPU/NeighborList/Constants.H
Tutorials/GPU/NeighborList/MDParticleContainer.H
Tutorials/GPU/NeighborList/MDParticleContainer.cpp
Tutorials/GPU/NeighborList/README.md
Tutorials/GPU/NeighborList/inputs
Tutorials/GPU/NeighborList/main.cpp

commit 13b74f310ba57155ca4232e7e006ddd918b31c9e
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jul 16 11:40:32 2019 -0700

    need to skip ebfacets that coincide with cell boundaries when looking for eb-facet edges

Src/EB/AMReX_EB_geometry.F90

commit adee7bfc36aee81fd874f40e5dcc319cebfc8a0c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 16 14:14:42 2019 -0400

    remove extra set acceleration to 0.0

Tutorials/GPU/NeighborList/MDParticleContainer.cpp

commit ab0138277d631809acd913676fd56980e5ec2439
Merge: 39552f356 9b053eae7
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 16 13:56:40 2019 -0400

    Merge branch 'mfix_hackathon' of github.com:AMReX-Codes/amrex into mfix_hackathon

commit 39552f356b1e40dea2b6f189eac9d6152581338d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 16 13:55:53 2019 -0400

    add some more sanity checking

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 9b053eae7663180981a6f2bc667dcb5add786fb8
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jul 16 13:46:17 2019 -0400

    Make dt an input parameter and set it to a reasonable default value

Tutorials/GPU/NeighborList/main.cpp

commit 58cd5c3ef3ffdcb4eb318ae91d17bd10a32ede2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 16 10:04:35 2019 -0700

    return -1 as mask if particle id is negative

Src/Particle/AMReX_Functors.H
Src/Particle/AMReX_ParticleContainerI.H

commit 370ec1588ebf24c3a24936acd6cb5eec30dd42ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 16 06:58:25 2019 -0700

    add a new version of RealBox::contains

Src/Base/AMReX_RealBox.H

commit d238ef120f5c070be6eea1add0493457d426c5c2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 16 04:05:14 2019 -0400

    tweak inputs

Tutorials/GPU/NeighborList/inputs

commit 03dad45b6ad1e8984bb35532ab7973d7d5fc3133
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 16 04:05:01 2019 -0400

    print out an error metric

Tutorials/GPU/NeighborList/main.cpp

commit ae7588123b75fc877a2d7a4213de8df2eaba9e00
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 16 04:04:29 2019 -0400

    function to print out the min distance between particles over the whole simulation

Tutorials/GPU/NeighborList/MDParticleContainer.H
Tutorials/GPU/NeighborList/MDParticleContainer.cpp

commit 066138910044c6ff4ca9041af556941b0ad4e20f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 16 04:03:58 2019 -0400

    tweak CheckPair

Tutorials/GPU/NeighborList/CheckPair.H

commit 7132148a28752f76791dd58e858333e33ae44681
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 16 03:06:53 2019 -0400

    fix typo

Tutorials/GPU/NeighborList/main.cpp

commit c2c41c540efd703cf61a45d8537f74d180a5f607
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 16 03:04:04 2019 -0400

    parmparse rebuild int and num_ppc

Tutorials/GPU/NeighborList/inputs
Tutorials/GPU/NeighborList/main.cpp

commit a48ebe553c49af9fd273cd950b86103efda2bf3d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 15 20:59:25 2019 -0400

    need to clear the neighbors before we re-generate the halo information

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit f54514166c4e5dc97fddbad0d74d5efe17e192f6
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jul 15 17:22:13 2019 -0700

    CMake: always link to Threads

Src/Base/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in

commit eba7f955061fab67c41b981ee01301142f479fff
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 15 17:47:29 2019 -0400

    only count real particles

Src/Particle/AMReX_ParticleContainerI.H

commit 13a17a585292be5e3b0736d5e0e3f62fa7f670fa
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 15 17:28:55 2019 -0400

    don't include neighbor particles in ascii files

Src/Particle/AMReX_ParticleContainerI.H

commit a6d2a742ad5fdd47d3bb37fa5a61588abd760081
Merge: 5f4d2b389 243a3c6ca
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Mon Jul 15 15:05:25 2019 -0400

    Merge branch 'mfix_hackathon' of https://github.com/amrex-codes/amrex into mfix_hackathon

commit 5f4d2b389e6ef8298bd113c6474b7325ab8464f4
Author: Ann Almgren <asalmgren@login1.ascent.olcf.ornl.gov>
Date:   Mon Jul 15 15:04:19 2019 -0400

    Add flag to allow nvprof to work on ascent.

Tutorials/GPU/NeighborList/script.sh

commit 243a3c6cab645ee1a7e5742a31a78b98ed67a5a0
Merge: 32a2aaf4a 19e29493e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 15 14:50:48 2019 -0400

    Merge branch 'mfix_hackathon' of github.com:AMReX-Codes/amrex into mfix_hackathon

commit 19e29493e6348e6853f1bec710aaabcbde2feb2e
Author: Oscar Luis Antepara Zambrano <oantepar@login1.ascent.olcf.ornl.gov>
Date:   Mon Jul 15 14:49:23 2019 -0400

    Increasing the number of particles by 8 per cell

Tutorials/GPU/NeighborList/main.cpp

commit 4e7ccb1bdb320ab695fbc4dfbe459c821dcb26d1
Author: Oscar Luis Antepara Zambrano <oantepar@login1.ascent.olcf.ornl.gov>
Date:   Mon Jul 15 14:43:58 2019 -0400

    adding a print statement for number of particles generated

Tutorials/GPU/NeighborList/MDParticleContainer.cpp

commit 32a2aaf4a12accc3498585776b5ae97d770f8e80
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 15 14:38:56 2019 -0400

    rebuild the neighbor list every 25 time steps

Tutorials/GPU/NeighborList/main.cpp

commit df8cd54cd1c759a70b7d9dc70134594c78afcbfe
Author: Oscar Luis Antepara Zambrano <oantepar@login1.ascent.olcf.ornl.gov>
Date:   Mon Jul 15 14:30:30 2019 -0400

    adding a print statement for number of particles generated

Tutorials/GPU/NeighborList/MDParticleContainer.cpp

commit e70516e242b243a94124548bb11895505829eda4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 15 12:17:43 2019 -0400

    adding a run script for the hackathon

Tutorials/GPU/NeighborList/script.sh

commit 0c0b033cf9a643fe46b25d4f2866ae224e8b978a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 15 09:00:36 2019 -0700

    check for nullptr after malloc

Src/Base/AMReX_Arena.cpp

commit bb8717ca509171aab238ff2c4a78f446a67c77c0
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jul 14 22:40:17 2019 -0700

    ooops... forgot this

Src/EB/AMReX_EB_levelset_F.F90

commit 2ba32709ff6512e441dcf23d9af772043d881467
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jul 14 22:34:10 2019 -0700

    fix off-by-epsilon error when filling level-set

Src/EB/AMReX_EB_geometry.F90
Src/EB/AMReX_EB_levelset_F.F90

commit 106298c8779289554cc515490b42df8db3cc104e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 14 12:53:18 2019 -0700

    replace usleep with std::this_thread::sleep_for

Src/Base/AMReX_VisMF.cpp

commit 162b38449b4415c865b6b346f593444db218e2cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 14 07:07:32 2019 -0700

    get around Cray

Src/Particle/AMReX_ParticleContainerI.H

commit e1d345f957b63f95036fc8e3dcecd634bcb3de1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 13 22:41:47 2019 -0700

    fix for Cray

Src/F_Interfaces/Base/AMReX_fab_mod.F90

commit acd2980959a7333476020293233e6085100603d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 13 21:47:21 2019 -0700

    fix a number of warnings

Src/EB/AMReX_EB2_IF_Cylinder.H
Src/EB/AMReX_EB2_IF_Scale.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 7ed1a9fc3e46493fa5dcbef2e7a78fd18013d95b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 13 21:16:43 2019 -0700

    remove old fortran amrex_eb2_build_cells

Src/EB/AMReX_EB2_F.H
Src/EB/AMReX_eb2_3d.F90

commit 45e1900aadb3815ba391de8894e166d1099bf25e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 13 21:14:49 2019 -0700

    wrong move

Src/EB/AMReX_EB_LSCoreBase.cpp

commit 56edcd3dfd9bc07da900abbef13e662fdccd91df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 13 20:34:13 2019 -0700

    fix bug in a new IOProcessor function

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_VisMF.cpp

commit 2b738f916ad72783d96b21bd2d034c9148ba1f8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 13 20:29:00 2019 -0700

    clean up

Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunchFunctsC.H

commit b5f83484f54b514d6fb157694820e75bee4e9340
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 13 19:44:45 2019 -0700

    add a default constructor to DataDeleter

Src/Base/AMReX_BaseFab.H

commit 0c1494e8e38c7a3a6baf235753ff89967adfcf21
Merge: 5becd01bb 07347b918
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 13 18:11:12 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5becd01bb2503a4e62d2e819293a313b17eb21a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 13 18:10:50 2019 -0700

    minor. std::async already creates a temporary in its internal buffer, so it's safe to use const&

Src/Base/AMReX_VisMF.cpp

commit 07347b918d85ecffb05a71c7d3dc3bd5c3a5ad7c
Merge: 147989685 43d7f2974
Author: atmyers <atmyers2@gmail.com>
Date:   Sat Jul 13 17:12:21 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 147989685819bc32fb85780becdd1f88fc802c8f
Author: atmyers <atmyers2@gmail.com>
Date:   Sat Jul 13 17:12:09 2019 -0700

    add remaining reduction operations (logical and and logical or)

Src/Particle/AMReX_ParticleUtil.H

commit 43d7f29740f89d54a3b5ab9e06f5c6a52bc3e55c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 13 13:45:16 2019 -0700

    WriteAsync: tweak sleep time

Src/Base/AMReX_VisMF.cpp
Tests/VELOC/multifab/main.cpp

commit 7928f0ad5fc19f04925196c0ea565017e34fdca8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 13 10:28:14 2019 -0700

    collect WriteAsyn status

Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp
Tests/VELOC/multifab/main.cpp

commit cf23bba6b455853b06a020493b08962929093e30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 12 21:01:22 2019 -0700

    make sure AMREX_CXX_* is properly included

Src/Base/AMReX_TypeTraits.H

commit 2d050a22e8a6942e1de41284d5baf0f6ace286f7
Merge: 5c84569d6 c3e1f4a1e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jul 12 19:17:32 2019 -0700

    Merge pull request #518 from eschnett/development
    
    Avoid warning about (safely) uninitialized variable

commit c3e1f4a1e0171c7715bd01bcec76e76ed045d70b
Author: Erik Schnetter <schnetter@gmail.com>
Date:   Fri Jul 12 21:34:19 2019 -0400

    Avoid warning about (safely) uninitialized variable

Src/Base/AMReX_FabArrayCommI.H

commit 5c84569d61b5b09c29fdbb1e4ba27ecf910f799e
Merge: ce92ad203 5a81038f6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 12 17:05:21 2019 -0700

    Merge branch 'development' into particle_reductions

commit ce92ad2038d82031b2cef0ad02ae38bdfdee73ad
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 12 17:02:10 2019 -0700

    fix copy/paste errors

Src/Particle/AMReX_ParticleUtil.H

commit f4333764982aa0131e9d906e88ae374ac5041693
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 12 16:57:26 2019 -0700

    fix typo

Src/Particle/AMReX_ParticleUtil.H

commit 995ca68ad4cd9a4d847168e0604d0de96e2c6f91
Merge: c7c584478 37a894deb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 12 19:32:50 2019 -0400

    Merge branch 'particle_reductions' of github.com:AMReX-Codes/amrex into particle_reductions

commit 37a894debc921d16ef5cac1dcb3f162bae181192
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 12 16:33:37 2019 -0700

    use decltype instead of extra template parameter

Src/Particle/AMReX_ParticleUtil.H

commit c7c584478e2a96e60f51f8052306a0998f8bf629
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 12 19:32:29 2019 -0400

    fix typos

Src/Particle/AMReX_ParticleUtil.H

commit a472e4a65f8d94ae870dbc0b084ad80bbf1ceeb5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 12 16:08:00 2019 -0700

    simplifing

Src/Particle/AMReX_ParticleUtil.H

commit 05dfe296bddb445f2b22a7db6c9545d21d0c6c08
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 12 16:03:35 2019 -0700

    also template on the lambda return type

Src/Particle/AMReX_ParticleUtil.H

commit e66431f8aa48286d370431750edf5c972f042c9b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 12 15:29:50 2019 -0700

    add ReduceRealMax and ReduceRealMin functions as well.

Src/Particle/AMReX_ParticleUtil.H

commit 5a81038f625033708c2b3686f612a890e6f4b4b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 12 18:28:10 2019 -0400

    fix for IBM compiler on summit that still use a very old gcc

Src/Base/AMReX_Extension.H
Src/Base/AMReX_TypeTraits.H

commit 4a0bdbc0f4cb92ff1b607aad21a66be966883245
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 12 14:45:55 2019 -0700

    add a ReduceRealSum for particle data

Src/Particle/AMReX_ParticleUtil.H

commit 18ae19a33f986c3a414ce26da318e744ea0c45a4
Merge: f9447aedd c99378b6b
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 12 14:34:04 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit f9447aeddb1f09543ac3ade8061f0f63458dbac2
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 12 14:33:42 2019 -0700

    CMake: add pthreads to dependency list for non-MPI builds

Src/Base/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in

commit c99378b6b3d5716d018942e81f7b3acee510d5d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 12 14:30:06 2019 -0700

    add -pthread to llvm

Tools/GNUMake/comps/llvm.mak

commit 811cdc7bf94b324cd74a6738334ea396c34d7499
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 12 14:21:21 2019 -0700

    add -pthread to intel

Tools/GNUMake/comps/intel.mak

commit d2a387c86d1d5acfc38b6c144773590d48eb5b07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 12 14:06:06 2019 -0700

    pass -pthread to g++

Tools/GNUMake/comps/gnu.mak

commit 2570f97d56c7e58903c2ad6981433707d2bad0f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 12 13:18:11 2019 -0700

    more aggressive inline with AMREX_FORCE_INLINE

Docs/sphinx_documentation/source/GPU.rst
Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/Base/AMReX_Algorithm.H
Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_GpuRange.H
Src/Base/AMReX_GpuReduce.H
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H
Src/Boundary/AMReX_InterpBndryData_1D_K.H
Src/Boundary/AMReX_InterpBndryData_2D_K.H
Src/Boundary/AMReX_InterpBndryData_3D_K.H
Src/Boundary/AMReX_LOUtil_K.H
Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_YAFluxRegister_1D_K.H
Src/Boundary/AMReX_YAFluxRegister_2D_K.H
Src/Boundary/AMReX_YAFluxRegister_3D_K.H
Src/EB/AMReX_EB2_2D_C.H
Src/EB/AMReX_EB2_3D_C.H
Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_algoim_K.H
Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLALap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLALap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLALap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H
Src/Particle/AMReX_Particle_mod_K.H
Tests/GPU/CudaGraphs/GraphBoundary/Prob.H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Tagging.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/mykernel.H
Tutorials/GPU/Launch/MyKernel.H
Tutorials/GPU/NeighborList/CheckPair.H
Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H

commit be58fefaa54d61ac206f358c6a326fc580ad0bd2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 12 09:43:31 2019 -0700

    modify the veloc test

Tests/VELOC/multifab/main.cpp

commit a4a4beee762433dafc5da5f2562441b3852f1de1
Merge: 1d2c2a70a d64794988
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 12 09:23:45 2019 -0700

    Merge branch 'development' into weiqun/asynco

commit d6479498828a3b3bed0e0b044559e69d4c2a256d
Merge: 3d9d8505a 731313767
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 12 09:22:12 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 731313767a0286850cfaf4f841e469b9accf00a6
Author: Stefan Vater <svater@users.noreply.github.com>
Date:   Fri Jul 12 16:43:06 2019 +0200

    Doc update (#515)
    
    Doc update from @svater

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/BuildingAMReX.rst
Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst
Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_documentation/source/LinearSolvers.rst
Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst

commit a19b7c5564c0dffb0f1df9945e6bf6e1cdc576d0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 11 20:19:01 2019 -0700

    also wrap thrust::exclusive_scan, providing CPU implementation

Src/Base/AMReX_CudaContainers.H

commit 1d2c2a70aa4cc2091fa41265be7c12891de4a06e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 11 19:34:33 2019 -0700

    make the veloc test more general

Tests/VELOC/multifab/GNUmakefile
Tests/VELOC/multifab/main.cpp

commit 8822f00bbe24066bc48a17087ee8d197ab5adf3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 11 19:10:03 2019 -0700

    fix another bug in WriteAsync

Src/Base/AMReX_VisMF.cpp

commit 2d467ce395cc9f97f597c0ffa153034d32634b95
Merge: a0a3519a5 0ba3c26c0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 11 17:28:17 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ef84e7887c849a1ae61677526f44f22f242defc2
Merge: ff97fa401 2d467ce39
Author: Christopher DeGrendele <ChrisDeGrendele>
Date:   Thu Jul 11 17:27:57 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 59d942e8f1f966c6e88df81f488b6d0b64ef3af5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 11 17:27:03 2019 -0700

    fix index

Src/Base/AMReX_VisMF.cpp

commit a0a3519a5c4bb529d365bd427d891cf6188666d1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 11 17:26:44 2019 -0700

    fix box_threads_and_blocks for AMREX_SPACEDIM < 3

Src/Base/AMReX_GpuDevice.cpp

commit ff97fa40129e578148eb6929fa6eab44d033a9fe
Merge: 29d2d4861 0ba3c26c0
Author: Christopher DeGrendele <ChrisDeGrendele>
Date:   Thu Jul 11 17:04:39 2019 -0700

    merge with upstream

commit 1126d925565725bdb0d8a5c65cb93b16151f9021
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 11 16:54:24 2019 -0700

    VisMF::WriteAsync for multi cpus

Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp
Tests/VELOC/multifab/main.cpp

commit 29d2d4861e0ad289bcf68760629308c492c856d6
Author: Christopher DeGrendele <ChrisDeGrendele>
Date:   Thu Jul 11 16:42:45 2019 -0700

    commented out

Src/Base/AMReX_Utility.cpp

commit 131c5fa91baa429e918519fa4b2e9833d736340c
Author: Christopher DeGrendele <ChrisDeGrendele>
Date:   Thu Jul 11 16:11:23 2019 -0700

    temp

Src/Base/#AMReX_GpuUtility.cpp#
Src/Base/AMReX_GpuUtility.H
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Tests/GPU/RandomNumberGeneration/GNUmakefile
Tests/GPU/RandomNumberGeneration/launc_gpu.sh
Tests/GPU/RandomNumberGeneration/main.cpp
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Header
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Level_0/Cell_D_00000.REMOVED.git-id
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Level_0/Cell_H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Header
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Level_0/Cell_D_00000.REMOVED.git-id
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Level_0/Cell_H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Header
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Level_0/Cell_D_00000.REMOVED.git-id
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Level_0/Cell_H

commit 0ba3c26c029aa363cfa8ffdecd7f9c3d088782f4
Merge: 6d8cf4f26 c82865310
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 11 15:07:23 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 6d8cf4f26747fc4f6a9953532a839f2ec7e66891
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 11 15:07:14 2019 -0700

    fix formatting

Src/Particle/AMReX_TracerParticles.cpp

commit c82865310f40d43bd784d6f0a6265af9bc7bcd62
Author: kngott <kngott@lbl.gov>
Date:   Thu Jul 11 14:37:44 2019 -0700

    Fix typo.

Tutorials/GPU/run.summit

commit d5da22490d3137d7559ceea77f5a8054b29d8f51
Merge: 5bb99f977 c82680df9
Author: Christopher DeGrendele <ChrisDeGrendele>
Date:   Thu Jul 11 14:33:15 2019 -0700

    Merge branch 'development' of https://github.com/ChrisDeGrendele/amrex into development

commit c82680df99189f8ca77b4f446904a746d993536f
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date:   Thu Jul 11 17:32:34 2019 -0400

    CIC grid error - I pushed this earlier but I guess it didn't actually push

Src/Particle/AMReX_TracerParticle_mod_K.H

commit 959653566eb85771be58ce86ed5931dece337cb0
Merge: f6c2ab5cc 8827bc3b9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 11 14:30:03 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f6c2ab5cc6c51dbc467993d3fdab70b456b22b69
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 11 14:29:48 2019 -0700

    a wrapper around thrust::inclusive_scan for portability between GPU and CPU codes

Src/Base/AMReX_CudaContainers.H
Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp

commit 8827bc3b9668a311f0a510ee557d07041b6ca57c
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Thu Jul 11 14:15:52 2019 -0700

    Add nvprof profiler flags to run.summit script

Tutorials/GPU/run.summit

commit 31334d8f25ef96a6688a37093928e23dd42c4cb0
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date:   Thu Jul 11 17:04:19 2019 -0400

    deleted unnecessary file

Src/Particle/#AMReX_TracerParticles.H#

commit 131939d38b54aec45bbb271fbab61cbffdfa9d4c
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date:   Thu Jul 11 17:03:55 2019 -0400

    Didn't mean to change this file

Src/Particle/#AMReX_TracerParticles.H#
Src/Particle/AMReX_ParticleContainerI.H

commit 5b2a91a4cc15af3bc5e12b352bedda0643ec14ba
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 11 11:53:41 2019 -0700

    remove the 'unsigned short int' version of the atomicCAS wrapper, which we don't need and is only available in 10.1

Src/Base/AMReX_GpuUtility.H

commit cb06fc26260ff04e5e772cc22b48f6b9a33b537d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 11 11:37:37 2019 -0700

    finished VisMF::WriteAsync for single cpu

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_Utility.H
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp

commit 6789d309463574fc3d0bdd489d8418c7f8309426
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 11 11:36:26 2019 -0700

    use memcpy to avoid potential alignment issue

Src/Base/AMReX_FabConv.H
Src/Base/AMReX_FabConv.cpp

commit 5bb99f97714b8cbeb2f1f9eee651b2e72af0fd95
Merge: 5827e0c17 21f159ddf
Author: Christopher DeGrendele <ChrisDeGrendele>
Date:   Thu Jul 11 10:05:56 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit b08fdf902a8e444f9e6d63010bbd63044db4915f
Merge: 77d5b1e6a 21f159ddf
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jul 10 22:09:52 2019 -0400

    Merge branch 'development' into kngott/cudaGraphs

commit 21f159ddf90f809aeaa0e66e18c5c2480c131632
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 10 17:07:58 2019 -0700

    fix indentation

Src/Base/AMReX_GpuUtility.H

commit e65bdba45f7260421ab840ddd466c101275fd008
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 10 17:03:48 2019 -0700

    add wrappers around Cuda's atomicCAS

Src/Base/AMReX_GpuUtility.H

commit 3d9d8505a67786138b8c434701cd325e01e8a5ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 10 13:18:10 2019 -0700

    use mlock on memory in The_Pinned_Arena when USE_CUDA=FALSE

Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_DArena.H
Src/Base/AMReX_DArena.cpp
Src/Base/AMReX_EArena.H
Src/Base/AMReX_EArena.cpp

commit 68800a804ec6004b8b011198557f90f1a3f80fc8
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Wed Jul 10 13:07:30 2019 -0700

    Remove --pretty-print from AMReX_BLBackTrace.cpp since this gives an error on cori-gpu

Src/Base/AMReX_BLBackTrace.cpp

commit 7e14f7843ded496755aba2fd9813a54026ac237b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 10 10:49:01 2019 -0700

    add optional communicator argument to some VisMF functions

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp

commit 8d012014ece7a20224b27a1b52dd15253f381a2a
Merge: 6df597a38 eab70c9ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 9 14:16:57 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6df597a38cd21228ddee1903b84629010e08aed9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 9 14:16:47 2019 -0700

    use pinned memory

Tests/VELOC/multifab/main.cpp

commit eab70c9ef0a86bb7e1a5773daf2f51da211dd936
Merge: f88f85f45 8cd6bac61
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 9 13:25:15 2019 -0700

    Merge pull request #512 from KiranEiden/keiden/amrex
    
    Fix issues RealBox equality check

commit f88f85f45e45bbfd838b2393a8fe258fc3594419
Merge: 3e7595874 3e7238b07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 9 13:17:50 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 3e75958749508293a53c74a8109c366fd7dad47f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 9 13:17:09 2019 -0700

    add BaseFab::release

Src/Base/AMReX_BaseFab.H
Tests/VELOC/multifab/GNUmakefile
Tests/VELOC/multifab/inputs
Tests/VELOC/multifab/main.cpp

commit 8cd6bac61017143a5d3969aa1418343dd33c4360
Author: Kiran Eiden <keiden@eidensystems.com>
Date:   Tue Jul 9 13:09:55 2019 -0700

    Switched to <= for RealBox equality check

Src/Base/AMReX_RealBox.cpp

commit 01ed464f7eee27d77f3dd0b28e8b68a30d73f7ff
Author: Kiran Eiden <keiden@eidensystems.com>
Date:   Tue Jul 9 12:34:38 2019 -0700

    Revert to doing exact comparison by default
    
    Using machine epsilon to do inexact comparison is a bit confusing - it's
    probably better to have the user supply their own value if they want
    a tolerance.

Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp

commit 51a8b84c0d04c7dda02831538204cb70b2cd9559
Author: Kiran Eiden <keiden@eidensystems.com>
Date:   Tue Jul 9 11:54:23 2019 -0700

    Switch to using machine epsilon

Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp

commit 3e7238b07e03c1153307311dc3cc7785f9361f06
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 9 11:43:17 2019 -0700

    make the default eps for contains be the roundoff error for Real

Src/Base/AMReX_RealBox.H

commit 14147fa3e0d4281a062a74b5f6b1c2710c7efab5
Merge: 084781521 ac062bf45
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 9 11:33:59 2019 -0700

    Merge pull request #511 from KiranEiden/development
    
    Added function for checking RealBox equality

commit ac062bf45fcdcda3fa81db4d0468b7b9fc17cea6
Author: Kiran Eiden <keiden@eidensystems.com>
Date:   Tue Jul 9 11:21:39 2019 -0700

    Added exclamation point to comment for consistency

Src/Base/AMReX_RealBox.H

commit 3653841cdf2a144ae65c89705144cb74c6321405
Author: Kiran Eiden <keiden@eidensystems.com>
Date:   Tue Jul 9 11:16:28 2019 -0700

    Added function for checking RealBox equality
    
    Added the AlmostEqual function to the amrex namespace, which checks
    that the domains represented by two real boxes are the same within a
    tolerance.

Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp

commit 0847815211ceeedd80f1e860bd3c158ce9aa9a0d
Merge: ef6a8be24 66334cb07
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jul 9 09:35:49 2019 -0700

    Merge pull request #510 from AMReX-Codes/checkinput
    
    Enforce AMR validity checks on max_level

commit 0cd8d6e653df34d257b10fcff3acccd8d691c31b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 9 09:24:10 2019 -0700

    VeloC test: write and read MultiFab

Tests/VELOC/multifab/GNUmakefile
Tests/VELOC/multifab/Make.package
Tests/VELOC/multifab/Readme
Tests/VELOC/multifab/inputs
Tests/VELOC/multifab/main.cpp
Tests/VELOC/multifab/veloc.cfg

commit dacc1c421d270ed2f0df6141890cc65f7bece0b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 9 08:58:17 2019 -0700

    add DistributionMappin::readFrom and writeOn

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit d16534ebb41e3daf3e4f86e28fa542e7d9f8422e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 9 06:47:59 2019 -0700

    dtoh_memcpy and htod_memcpy for MultiFabs

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MultiFabUtil.H

commit 66334cb079eff0c371473b30d2e69413de801157
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 8 19:27:50 2019 -0700

    Enforce AMR validity checks on max_level
    
    The inputs validity check on the AMR quantities was not checking on max_level.
    So, e.g., if you had amr.max_level=0 then you could do things which would not
    make sense, like have amr.blocking_factor be larger than amr.max_grid_size.

Src/Amr/AMReX_Amr.cpp

commit 33b0ea1139e02697c92a116f0a19b2a806e073ae
Merge: ada159824 ef6a8be24
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 8 16:33:46 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ef6a8be2437d8e2c7941eced9cc54d28792a306c
Author: Michele Rosso <mrosso@login1.ascent.olcf.ornl.gov>
Date:   Mon Jul 8 18:53:21 2019 -0400

    CMake: make public the OpenMP flags passed to CUDA host compiler

Tools/CMake/AMReX_Config.cmake

commit ada159824a46539cd8513704de5e6566c7f9a23e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 8 11:27:47 2019 -0700

    use PhysBCFunctNoOp in amrex

Tutorials/Particles/ElectrostaticPIC/main.cpp

commit 7c53f0131f22031fdbe6ffd835df85f4ba2b7a78
Merge: 25073e2bb a7dbede01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 8 10:44:57 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 25073e2bb49620eadbdf1d6a4b1d48d4606c1783
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 8 10:44:47 2019 -0700

    add a comment

Src/EB/AMReX_EBCellFlag.H

commit a7dbede0144b0e522377f1875c91782ebf3abd97
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 8 00:28:15 2019 -0700

    Only write initial checkpoint if checkpoints are requested

Src/Amr/AMReX_Amr.cpp

commit 1ccad8ac0c95380046c41b14296ef7260d583715
Merge: 9a4fd73c5 e41149eec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 7 17:06:49 2019 -0700

    Merge branch 'weiqun/dev' into development

commit e41149eec8a3796d013aaf37e2e9e7041f7ddc37
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 7 16:49:31 2019 -0700

    fix new index typo due to typo

Src/EB/AMReX_EB2_3D_C.cpp

commit 2a576387faf4cd0260220d0efe5fb59ce4ab1454
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 7 15:45:45 2019 -0700

    build 3d eb cells on gpu

Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EB2_C.H
Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_EBCellFlag.H

commit 07b4ee757400bf2a63087449b4b1c8e01f49e4d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 6 22:31:26 2019 -0700

    WIP: build 3d eb cells on gpu

Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EB2_C.H
Src/EB/AMReX_EB2_Level.H

commit 9a4fd73c5148ca8ca9146fd725a9b5c4c8930ea7
Merge: 844fdcbe9 b0f1479b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 6 19:22:55 2019 -0700

    Merge branch 'weiqun/dev' into development

commit b0f1479b904ac8a2afde53f8571c0710eddfbbab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 6 17:16:53 2019 -0700

    3d EB: build faces on gpu

Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EB2_C.H
Src/EB/AMReX_EB2_F.H
Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_eb2_3d.F90

commit 844fdcbe9e768cde7b24c3e60764c6bb68546fd1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 6 08:10:59 2019 -0700

    assuming -lgomp only works gcc

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/nvcc.mak

commit 829ca05e630c932a6474a7c5d82b7bd5b9cdc87e
Merge: 49fb948dd 063d3df4b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 6 07:59:48 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 063d3df4b99f19a783b8c1d60a1f85f316d9745d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 5 15:51:43 2019 -0700

    CMake: fix bug in config file

Tools/CMake/AMReXConfig.cmake.in

commit b00040b057bf789f4905420b040b3abee100b057
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 5 14:30:33 2019 -0700

    CMake: manually pass OpenMP flag to CUDA host compiler

Tools/CMake/AMReX_Config.cmake

commit e657cdec0b96d5406865e5f0596aa4053fd3f558
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 5 12:46:56 2019 -0700

    CMake: use C++ bindings for MPI in addition to C bindings.
    
    This fixes bugs with certain MPI implementations still using
    C++ bindings.

Src/Base/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in

commit 49fb948dd595949f9363d6403969303ec6079833
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 5 12:10:35 2019 -0700

    2d EB: build_cells on gpu

Src/EB/AMReX_EB2_2D_C.cpp
Src/EB/AMReX_EB2_C.H
Src/EB/AMReX_EB2_F.H
Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_eb2_2d.F90

commit d67e5473d107e2f705bf5125f43cb7258bdd96c7
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 5 10:54:04 2019 -0700

    CMake: allow builds with both CUDA and OMP

Tools/CMake/AMReX_Options.cmake

commit 4619a738a3a71ff40c86d5e9066f7977ae1b4fb4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jul 5 13:43:36 2019 -0400

    remove restriction that OMP and CUDA/HIP can't be enabled at the same time.

Tools/GNUMake/Make.defs

commit 7f8f9bb79494afe477acc46b1057960ee2036417
Merge: f3f57faf9 fdc40e3a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 5 10:41:57 2019 -0700

    Merge branch 'development' into weiqun/dev

commit fdc40e3a923c12f5e87c62cbf25535e8048d0a41
Merge: 768cfebe4 2a425f243
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 5 10:40:44 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f3f57faf97815585e90098557e2eb5fba584a067
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 5 10:40:34 2019 -0700

    EB: build_faces on gpu

Src/EB/AMReX_EB2_2D_C.cpp
Src/EB/AMReX_eb2_2d.F90

commit 2a425f2438c227a43757248529bb61f5d1ebe718
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 5 10:33:47 2019 -0700

    use value semantics instead of pointers for rhoarr

Src/Particle/AMReX_ParticleContainerI.H

commit d26a384296606160c545e20e9be4abeefe7a7790
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 5 10:14:31 2019 -0700

    initialize rhoarr pointer to nullptr

Src/Particle/AMReX_ParticleContainerI.H

commit 283f94cf94ff070b7f8972129b61a40a8d47c324
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 5 10:04:25 2019 -0700

    update AssignCellDensitySingleLevel to handle the case where OMP and CUDA are on, but we are not in a launch region

Src/Particle/AMReX_ParticleContainerI.H

commit 44e9e434dedb56db7de5a56c77bb64dbfb7901b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 5 08:10:10 2019 -0700

    WIP: 2d compiles

Src/EB/AMReX_EB2_C.H
Src/EB/AMReX_EB2_Level.H

commit 2a23fdea1b06755b1f8f9348da00d270681d31db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 5 07:55:31 2019 -0700

    add LoopOnCpu to get rid of nvcc warnings

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_Loop.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/EB/AMReX_EB2_GeometryShop.H

commit 02702ff93c93d39232e6d0a5800faf17a0c26ece
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 5 06:28:53 2019 -0700

    WIP: EB2::build_faces on gpu

Src/Base/AMReX_Box.H
Src/EB/AMReX_EB2_2D_C.cpp
Src/EB/AMReX_EB2_3D_C.cpp
Src/EB/AMReX_EB2_C.H
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EB2_Level.H
Src/EB/CMakeLists.txt
Src/EB/Make.package

commit 06463cb673e2def560fd5ec366664b10207db333
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 4 19:01:20 2019 -0700

    pass bottom_reltol and bottom_abstol through the MacProjector

Src/LinearSolvers/MLMG/AMReX_MacProjector.H
Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp

commit 768cfebe4a554e8eb07bdde71fddf5e7d7c10b1e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 4 13:22:05 2019 -0700

    EB: get intercepts on gpu if we can

Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EB2_Level.H

commit b6357ebf3d9f29d306daf274bd368c0ac2040dfb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 3 20:35:03 2019 -0700

    old versions of eu-addr2line do not support pretty-print

Src/Base/AMReX_BLBackTrace.cpp

commit 3388f80b9b9d7629e7ed764feade2e288e1ce132
Merge: a64322906 9688c2462
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 3 18:42:35 2019 -0700

    Merge branch 'development' into weiqun/dev

commit a6432290623e83ebdfb61d3f1ad69316fc27f52f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 3 18:30:34 2019 -0700

    around a possible gcc bug

Src/Base/AMReX_BLBackTrace.cpp

commit 9688c2462e97dacbeaeb378c88230582d6f32d7b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jul 3 17:11:47 2019 -0700

    Need to only touch inverse_tags if enable_Inverse() is true

Src/Particle/AMReX_NeighborParticlesCPUImpl.H

commit 5cb23803a6671072aa5b579d5ddf6468dfce0c42
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 3 16:23:44 2019 -0700

    Fix problem where the size of inverse_tags wasn't getting reset to 0 properly

Src/Particle/AMReX_NeighborParticlesCPUImpl.H

commit d33e8ab9488892e730d39069fffa6b88a60ac721
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 3 15:23:32 2019 -0700

    fix typo

Src/Base/AMReX_BLBackTrace.cpp

commit f1b0dc3126ee8f64907ae0e68beb8668113b1cfb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 3 15:17:24 2019 -0700

    use eu-addr2line if present

Src/Base/AMReX_BLBackTrace.cpp

commit dba1e7a1bd8846e578ebd9fea099456112a4bb69
Merge: cb5168234 57852530e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jul 3 14:58:27 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit cb516823443ac99e62b9388b7378bf45df7aea89
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jul 3 14:58:16 2019 -0700

    default enable_inverse to false

Src/Particle/AMReX_NeighborParticlesI.H

commit 57852530e2181926d91e6ca61ee0961d7aa3dffe
Merge: 3b9c4e5b8 0daa9725d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 3 17:17:26 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 3b9c4e5b8125c593bb73b0cb0dc9bc7ebf995c1a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jul 3 17:17:05 2019 -0400

    workaround for compiler bug in gcc < 4.9

Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.cpp
Src/Particle/AMReX_Particle.H

commit 0daa9725d843b0274e4ef634792542ab646f5ba2
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jul 3 14:13:41 2019 -0700

    CMake: add -fimplicit-none to Fortran flags preset

Tools/CMake/AMReXFlagsTargets.cmake

commit 12838b811ca76ff5a464d3ed7c8da23f7979be65
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 3 12:35:44 2019 -0700

    GNU make: load Make.local-pre if present

Tools/GNUMake/Make.defs

commit 365d5faac4d00201c72cfd36a850d09596702044
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 3 10:26:41 2019 -0700

    fix warning for clang

Src/Base/AMReX_TypeTraits.H

commit 9e626237a71caeaa44af8fc550c78dbf217fcb08
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 3 13:14:07 2019 -0400

    workaround gcc 4

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_TypeTraits.H

commit 9e970bbd081f64803d54b1ef98e2e6092ecc2697
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 3 09:40:38 2019 -0700

    add EXPORT_DYNAMIC to llvm-flag.mak

Tools/GNUMake/comps/llvm-flang.mak

commit 0e4c2fd67c82d9383356cc4e5a23d559c9d9872b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 3 09:26:00 2019 -0700

    Backtrace on mac: llvm is supported

Src/Base/AMReX_BLBackTrace.cpp
Tools/GNUMake/Make.defs
Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/llvm.mak

commit c3227249d416391387e6c5bc93333ff8600a5353
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 3 07:22:03 2019 -0700

    move dynamic load flags to gnu.mak

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/gnu.mak

commit 33815bacd7acd7cd5c35ea92bfddb6cf40d1c961
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 3 07:02:33 2019 -0700

    turn dynamic load by default for Darwin+gcc

Tools/GNUMake/Make.defs

commit 7e11843d448d738e1accabfbd6c309d9d3e50a9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 3 06:41:39 2019 -0700

    use atos for backtrace on mac

Src/Base/AMReX_BLBackTrace.cpp

commit e6755c205dd753e678ac819f523d5443dc614439
Merge: 256a73917 0544a7f6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 2 20:47:45 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 256a73917bf20854e2822083c2321754c49ebb63
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 2 20:47:28 2019 -0700

    If available, print the tiny profiler stack when backtracing

Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp

commit 0544a7f6a26eafd1b6b126264eb9e30de79443ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 2 19:10:19 2019 -0700

    set handler for SIGFPE

Src/Base/AMReX.cpp

commit b27f10392a658a3be285dfd524bbfd18b08e2987
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 2 18:49:42 2019 -0700

    For backtrace, do not omit frame pointer

Src/Base/AMReX_BLBackTrace.cpp
Tools/GNUMake/comps/gnu.mak

commit 3c5ec487fa177081e372f18eec35c711ca8b5eaf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 2 18:23:53 2019 -0700

    backtrace on Mac

Src/Base/AMReX_BLBackTrace.cpp
Tools/GNUMake/Make.defs
Tools/GNUMake/comps/gnu.mak

commit 8ec490d359a54cda4a3586255bc4925680b86018
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 2 15:43:30 2019 -0700

    enable floating pointer exception and backtrace for Mac

Src/Base/AMReX.cpp
Src/Base/AMReX_BLBackTrace.H
Src/Base/AMReX_BLBackTrace.cpp

commit 4cace2d0cc89617daee331021ffd892926a51cdd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 1 21:20:34 2019 -0700

    fix 2d problem in my last commit

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H

commit 88b156506be8ba6cc6d29f84a122938d3fe579b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 1 20:43:14 2019 -0700

    Linear Solver: option to set non-zero domain bc locations

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp

commit 9fc854d5c20dfd06ede71235043bc8a04b57177d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 1 19:07:45 2019 -0700

    fix parse_bt.py

Tools/Backtrace/parse_bt.py

commit 9d2c3af7ebb75582854a58caae5bc38ef435bdd8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 1 18:50:37 2019 -0700

    addr2line: skip libc.so because it causes troubles

Src/Base/AMReX_BLBackTrace.cpp
Tools/Backtrace/parse_bt.py

commit 754903a6d9f01066936cc204a98ca5d70cd0e6c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 1 18:33:05 2019 -0700

    try to use the address in () for addr2line if we can

Src/Base/AMReX_BLBackTrace.cpp

commit 60c962c721b74e791986c01de6b8999a3619d3f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 1 18:16:16 2019 -0700

    Revert "backtrace: use the address returned by backtrace, not the one extraced from bactrace_symbols"
    
    This reverts commit a5794ef4a68f11d45a05e1fe20290afee42f4b0a.

Src/Base/AMReX_BLBackTrace.cpp
Tools/Backtrace/parse_bt.py

commit a5794ef4a68f11d45a05e1fe20290afee42f4b0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 1 16:04:19 2019 -0700

    backtrace: use the address returned by backtrace, not the one extraced from bactrace_symbols

Src/Base/AMReX_BLBackTrace.cpp
Tools/Backtrace/parse_bt.py

commit f90a295750dafdcb1d99879d3ffcdfac2c626870
Merge: 648b18fac 6fe1d9f67
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 1 09:16:01 2019 -0700

    Merge branch 'weiqun/dev' into development

commit 648b18facb8dd665c828a1fe9c59afc213c90262
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 1 09:13:27 2019 -0700

    update CHANGES

CHANGES

commit 6fe1d9f6714fa5315d62bee8a3fd89ec121e5deb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 29 13:30:24 2019 -0700

    fix warnings

Src/Base/AMReX_PhysBCFunct.H
Src/EB/AMReX_EBFluxRegister_2d.F90
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_algoim.cpp
Src/EB/AMReX_algoim_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit c9f296356b4ea22422f6d1ab0240eb49cf8844c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 29 11:47:57 2019 -0700

    option to turn off Wshadow because there are so many in thrust.  fix some warnings

Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_EArena.cpp
Src/Base/AMReX_Lazy.cpp
Src/Base/AMReX_Machine.cpp
Tools/GNUMake/comps/gnu.mak
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/EBCNS/Source/CNS.cpp

commit cb962dc7c74c9c004a70554fa4f5467608780f4f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 29 11:05:06 2019 -0700

    provide default constructor to EBCellFlag because nvcc cannot generate default device version

Src/EB/AMReX_EBCellFlag.H

commit 9a9dc9c4586948d01838a618cfe646f25a45e66d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 29 07:17:10 2019 -0700

    put amrex::min and amrex::max in new file AMReX_Algorithm.H. add max_lbound and min_ubound functions

Src/Base/AMReX_Algorithm.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_Utility.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/EB/AMReX_EB2_2D_C.H
Src/EB/AMReX_EB2_3D_C.H

commit 5827e0c1785f1bac79a528e9c0296a4bf253ed18
Author: Christopher DeGrendele <chrisdeg@cori03.nersc.gov>
Date:   Fri Jun 28 14:48:40 2019 -0700

    fixed the same indice error from before on CIC grids

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 4b5531659800a79c48aaad8833f9c96c26a34bf1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 28 10:32:02 2019 -0700

    clean up

Src/Base/AMReX_BaseFab.H
Src/Particle/AMReX_ParticleContainerI.H

commit 5f3f1a83fe82907e31fc0650e6c418f2994b1ad7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 27 21:50:27 2019 -0700

    for non-trivially_default_contructible types, do placement new on gpu to avoid touching memory on cpu.  This will help BaseFab<std::complex<T>> and BaseFab<EBCellFlagFab>.

Src/Base/AMReX_BaseFab.H

commit c50d3b00ab8dfb7d884d1149bbdacd4cd76ed06e
Merge: e7c05438b 49f3c405e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 27 16:05:32 2019 -0700

    Merge branch 'mr/cmake' into development

commit 49f3c405e5ae0f356f1802d2a56f52683e5c7977
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 27 16:05:06 2019 -0700

    CMake: add module to perform typecheck.

Tools/CMake/AMReXTypecheck.cmake

commit 12295594ab5c9d7938606bedda5c3ca2538a542c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 27 14:15:53 2019 -0700

    update documentation and launch tutorial

Docs/sphinx_documentation/source/AmrCore.rst
Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_documentation/source/LoadBalancing.rst
Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst

commit 92cf67a242523995843a68dbbe27a74fe0ab7827
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 27 13:22:25 2019 -0700

    use amrex::Loop

Tutorials/GPU/Launch/MyKernel.H
Tutorials/GPU/Launch/main.cpp

commit e7c05438bc0c3a8a405b57d9249ba57f7562b9d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 27 12:43:17 2019 -0700

    add amrex::Loop and amrex::LoopConcurrent

Src/Base/AMReX_Box.H

commit a7bc34a9797e9c43cd96df6143901897bd88e91c
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date:   Thu Jun 27 15:29:32 2019 -0400

    Mac routine is now dimension agnostic. This is ready for testing

Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit f4d93081d017ed8edd2c5e65009fe1bdfbeb1083
Merge: c781aad03 5f72fe0e0
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 27 11:39:38 2019 -0700

    Merge branch 'development' into mr/cmake

commit c781aad03e649338061da0376fb078db1c9857b4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 27 11:14:12 2019 -0700

    CMake: clean up

Tools/CMake/AMReX_Utils.cmake

commit 5f72fe0e0ce209acad0f7b38be664c0259537649
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 27 08:11:27 2019 -0700

    Fix typo

Src/EB/CMakeLists.txt

commit 0c355b89df69e4cc07884d2e7eaccef9317d4617
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 27 07:49:55 2019 -0700

    fix index bug

Src/EB/AMReX_EBMultiFabUtil.cpp

commit ec29247c4bdac6728186d0857cb993f51949b118
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 27 07:47:43 2019 -0700

    fix index bug

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 8cbdec34974579d011ca936d669c9b10ffc54aa1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 27 07:04:16 2019 -0700

    fix cmake

Src/EB/CMakeLists.txt
Src/EB/Make.package

commit 8d41be6b388131e43f1d1450563511b1ea5b1ba7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 26 20:45:34 2019 -0700

    remove deprecated Fortran routine

Src/EB/AMReX_eb2_3d.F90

commit 4d211ed3bead6eea6f501f142d4bc1ef7c2edd35
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 26 20:13:45 2019 -0700

    EB: build types on gpu

Src/EB/AMReX_EB2_2D_C.H
Src/EB/AMReX_EB2_3D_C.H
Src/EB/AMReX_EB2_C.H
Src/EB/AMReX_EB2_F.H
Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_EB2_MultiGFab.cpp
Src/EB/AMReX_eb2_2d.F90
Src/EB/AMReX_eb2_3d.F90
Src/EB/CMakeLists.txt
Src/EB/Make.package

commit 2b76bff200e75d737b24e347c2511e426ba52594
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 26 15:54:44 2019 -0700

    EB: fill leveset on gpu

Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_EB_levelset.H

commit 663d92367de1bc30428e3a62085df98698f74885
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 26 16:56:06 2019 -0700

    CMake: update evaluate_genex

Tools/CMake/AMReX_Utils.cmake

commit 0c8a510ea278d9823b43aa8202823e3a317b1738
Merge: b8b961e41 7165274ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 26 13:42:34 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 7165274efcdf5681a1e87d0f93e8bdb4002e22f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 26 13:40:27 2019 -0700

    make sure we don't dereference nullptr

Src/Base/AMReX_FabArray.H

commit 38bd36a1a1eba6204be8eda17a29e35877122ece
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date:   Wed Jun 26 16:12:12 2019 -0400

    Fixed a bug and deleted unnecessary lines

Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 1127512d0ba40282ff691d553ab01f4613d4c1ea
Author: kngott <kngott@lbl.gov>
Date:   Wed Jun 26 13:08:41 2019 -0700

    Fix labels in launch test.

Tests/GPU/FusedLaunches/main.cpp

commit b8b961e4124540b22e58fd9f9ab73efc4211a8c4
Merge: 852b2ed3b f6a798af2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 26 12:24:32 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 852b2ed3b440600b59f13cc9393f8f90baccf990
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 26 12:18:24 2019 -0700

    gpu: set covered cells and faces

Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2D_C.H
Src/EB/AMReX_EBMultiFabUtil_3D_C.H
Src/EB/AMReX_EBMultiFabUtil_C.H
Src/EB/AMReX_EBMultiFabUtil_F.H
Src/EB/AMReX_EBMultiFabUtil_nd.F90
Src/EB/CMakeLists.txt
Src/EB/Make.package
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit f6a798af2f4ff6c9fdc2d5f68734b2af66672eed
Author: kngott <kngott@lbl.gov>
Date:   Wed Jun 26 11:49:40 2019 -0700

    Updated launch tester.

Tests/GPU/FusedLaunches/main.cpp

commit 9796f26e46aeb46033197500cbb3d23da69fa818
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date:   Wed Jun 26 12:19:38 2019 -0400

    removed unwanted files

Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/Backtrace.0

commit 9b84068c0d3cc07e43a329bb42e2b8e2a19e8809
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 26 09:05:11 2019 -0700

    gpu: EBAmrUtil

Src/EB/AMReX_EBAmrUtil.cpp
Src/EB/AMReX_EBAmrUtil_F.H
Src/EB/AMReX_EBAmrUtil_nd.F90
Src/EB/CMakeLists.txt
Src/EB/Make.package

commit 87dfe837414ee20aa28e0bc749421a160b7f0576
Merge: 375861d8c 29bf4c9d1
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 25 19:47:07 2019 -0700

    Merge branch 'development' into kngott/fused

commit 29bf4c9d12ca6c80370487a69f8c21e58ca0619c
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 25 19:46:48 2019 -0700

    Adjust make system for Brian's new modules.

Tools/GNUMake/sites/Make.nersc

commit ea72119ce758e38a97ec98665adbcdbe22195281
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 25 17:13:08 2019 -0700

    Fix nodal solver owner mask.  This will break regression tests.

Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit e5b9f9be4fce571076469a3bcb712296eef0cf52
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 25 16:07:01 2019 -0700

    fix an off-by-one index error

Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 2b389a4e6df5952eb0476afe3e84d036cdd1fe94
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 25 16:04:59 2019 -0700

    change this variable name to keep yt happy

Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit 131af99347f4959902946d0e82da2e3751e5c1ee
Merge: f08b0d145 1afd7c079
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 25 15:43:29 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f08b0d145578fb7742f743119a2581233419754b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 25 15:43:19 2019 -0700

    BoxList: make sure block size is not zero

Src/Base/AMReX_BoxList.cpp

commit 1afd7c0794a413bd32b7600a0e7da8d8b27b45ae
Merge: ec0d2c1e7 5fcdcfe52
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jun 25 15:33:45 2019 -0700

    Merge pull request #508 from OscarAntepara/oscar
    
    Adding bottomSolver_maxIter and solver_maxIter to the MacProjector

commit 5fcdcfe523195ceb8f89125a89c0afbc8d117e15
Author: Oscar Antepara <oantepara@lbl.gov>
Date:   Tue Jun 25 15:03:29 2019 -0700

    Adding bottomSolver_maxIter and solver_maxIter to the MacProjector

Src/LinearSolvers/MLMG/AMReX_MacProjector.H
Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp

commit ec0d2c1e77fab8094d8cb1f469d2f1244efdc71d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 25 14:20:10 2019 -0700

    Typechecker: add support for _Bool type

Tools/typechecker/typechecker.py

commit 3695191ad7408dea8d5cb3b96be4c7178800ea95
Merge: 6c7513e63 504daae2c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 25 13:41:46 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 6c7513e6323db3b3da8923815e2bc1f61db407eb
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 25 13:41:38 2019 -0700

    Fix bug in doc that prevents latexpdf to compile

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit e82c4fe0dbe7493f7e07345d71333fce07875c86
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date:   Tue Jun 25 16:06:10 2019 -0400

    f

Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00014
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Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00019
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Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00019
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Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00003
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Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00019
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Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_0/phi_D_00019
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Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00120/Level_2/phi_D_00019
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Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_H

commit bc64f66353e5659f946ba3d1dabcb6f4f6872f1a
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date:   Tue Jun 25 15:27:59 2019 -0400

    Removed plotfile

Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Header
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_0/Cell_D_00000
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_0/Cell_H
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_1/Cell_D_00000
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_1/Cell_H
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_2/Cell_D_00000
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_2/Cell_H
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Header
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_0/DATA_00000
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_0/Particle_H
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_1/DATA_00000
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_1/Particle_H
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_2/DATA_00000
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_2/Particle_H

commit bbc2d03221254831d5e396fdca5b6904605531a7
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date:   Tue Jun 25 15:27:12 2019 -0400

    Reorganized

Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Backtrace.0
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Header
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Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00001
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Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00010/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00020/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00030/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00040/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00050/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00060/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00070/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00080/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00090/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00100/Level_2/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Header
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_0/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_1/phi_H
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00000
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00001
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00002
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00003
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00004
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00005
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00006
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00007
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00008
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00110/Level_2/phi_D_00017
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Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00009
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00010
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00011
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00012
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00013
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00014
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00015
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00016
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00017
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00018
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_D_00019
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_H
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/Backtrace.0
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Header
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_0/Cell_D_00000
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_0/Cell_H
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_1/Cell_D_00000
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_1/Cell_H
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_2/Cell_D_00000
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_2/Cell_H
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Header
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_0/DATA_00000
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_0/Particle_H
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_1/DATA_00000
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_1/Particle_H
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_2/DATA_00000
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_2/Particle_H
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/viz.py
Tutorials/Particles/NeighborList/Backtrace.0.0

commit 504daae2cb9d410d05bd19460aaef75bbcae4cde
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 25 12:03:46 2019 -0700

    fix jump to case label error

Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp

commit 1eb0d65e79c34bdeb8654bac397d7afef7254448
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 25 10:57:17 2019 -0700

    add noexcept to some functions

Src/Base/AMReX_PlotFileDataImpl.H
Src/Base/AMReX_PlotFileDataImpl.cpp
Src/Base/AMReX_PlotFileUtil.H

commit 0aaa8e91e11a879b0dd3ca1726e4d7ad3aec0995
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 25 09:19:11 2019 -0700

    add amrex_set_finest_level to amrex_amrcore_module

Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90

commit 52f81640c37272e536983d808d3f23cd83019447
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 25 04:16:42 2019 -0700

    Add more RegionTags to AmrLevel

Src/Amr/AMReX_AmrLevel.cpp

commit 375861d8cadfdcf9f53779297b5980c56ba9967e
Merge: 7aca5e105 9265fcc73
Author: kngott <kngott@lbl.gov>
Date:   Mon Jun 24 15:46:26 2019 -0700

    Merge branch 'development' into kngott/fused

commit 9265fcc7363581ceeeb4deeada998b80327c705e
Merge: bcb7a6086 45a9f4e9d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jun 24 14:43:13 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit bcb7a608604eb198b38a5018944574aa2accace7
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jun 24 14:43:01 2019 -0700

    CMake: fix bug in OpenMP support

Tools/CMake/AMReX_Config.cmake

commit 45a9f4e9dbcb73e4639c99e1340362bff13af028
Merge: 1410499cb dd39829f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 24 12:52:11 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a9811bc9e1a1c1df5ce781b4ce936f77f19cb2c4
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date:   Mon Jun 24 13:21:26 2019 -0400

    CIC routine is now dimension agnostic, MAC routine has a bug

Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 1410499cb5bfb81cac5617e506ee3217722acf17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 24 08:24:42 2019 -0700

    YAFluxRegister: no need to test fab ptr

Src/Boundary/AMReX_YAFluxRegister.cpp

commit dd39829f329a21997513a85a676f2a438b727a2a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 24 08:14:01 2019 -0700

    Add statedata region tags

Src/Amr/AMReX_AmrLevel.cpp

commit e19e3d6abe753fdbb67070c37b6baedeef45d7ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 24 07:02:20 2019 -0700

    need to BaseFab's DataAllocator ctors host and device

Src/Base/AMReX_BaseFab.H

commit 2e33fdc274d27207360d088a80b6941c485a0494
Merge: 91f1db2b2 590d26130
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 23 17:43:21 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 91f1db2b28f3ac074de2583d8385dbef00e296a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 23 17:43:10 2019 -0700

    make sure FabArray<FAB> works for non-BaseFab FAB

Src/Base/AMReX_FabArray.H

commit 590d2613028554d420cb2fc144b8a5644432e9da
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sun Jun 23 19:57:05 2019 -0400

    better to apply periodic shift for the remotes on the CPU, since they are to be copied off anyway

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 1af7c643c4f6064b2f4052e5425951808a1be403
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 23 16:53:06 2019 -0700

    minIndex and maxIndex for iMultiFab

Src/Base/AMReX_iMultiFab.cpp

commit 91714378256a24c6dc8e386d35c9ed361aceabdd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sun Jun 23 19:19:38 2019 -0400

    copy directly to pinned memory; use std::memcpy instead of cudaMemcpy

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit ece4af197db2bcfca4ee482a8b0e7beb2e6c60a1
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 23 09:22:41 2019 -0700

    Add StateData tag to MFs

Src/Amr/AMReX_StateData.cpp

commit 82feafd878298aafc90c1ae89f323b74dd128b23
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 23 09:06:20 2019 -0700

    fix for C++11

Src/Base/AMReX_BaseFab.H

commit d2bca5ed416d08e07d1024c97e09d25e1de9582c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 23 07:31:30 2019 -0700

    add MultiFab::queryMemUsage

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 77d74e3e70d64e5318dde870507f8bd1806b7410
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 23 07:12:18 2019 -0700

    add tags to MultiFab/FabArray and use them to track memory usage

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 071557b77ceca7c4ffc98b7331a0050b0d6f32fb
Merge: fc9e8f81a 93ac54bf4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 22 22:38:30 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit fc9e8f81a2bc72bcdf67649fb418551560e1a9d1
Merge: 2d0e22516 0bbb6bf2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 22 22:38:12 2019 -0700

    Merge branch 'mlmg-2d' into development

commit 93ac54bf4a8f2cb1f195c5526fef74a8e054d9b6
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 22 21:41:01 2019 -0700

    Add option to perform asynchronous MF prefetch

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_MFIter.H

commit f0feb384b25d567f69fb177c14471619a87311ad
Merge: 6b6ab38f6 2d0e22516
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Jun 22 23:25:31 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6b6ab38f64e4a27f2e0c53ec04c67daf9ce2c476
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Jun 22 23:24:49 2019 -0400

    use std::memcpy instead of cudaMemcpy for host-to-host transfers

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 2d0e2251643d93b8bdd7b827b7951e1bb4126ca4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 22 18:35:41 2019 -0700

    use arena in FabArray

Src/Base/AMReX_FabArray.H

commit fcead2beec1a4d67471937265610292db85e8121
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 22 17:56:46 2019 -0700

    --no-edit

Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabFactory.H
Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IArrayBox.cpp
Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_Mask.cpp
Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBCellFlag.cpp
Src/EB/AMReX_EBFArrayBox.H
Src/EB/AMReX_EBFArrayBox.cpp
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_MultiCutFab.H

commit 191a4179f329553aed51a0a88e375d01f424f36d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Jun 22 21:10:56 2019 -0400

    also get rid of the transform when packing the MPI buffers

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 293d646ea78d9593fc244497172aef4acba13ee3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Jun 22 20:26:44 2019 -0400

    avoid the thrust::transform call, which is also blocking

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 859450e0c12d1fdb4f730979adf6537023437494
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Jun 22 19:23:38 2019 -0400

    use an async copy here instead of thrust::copy, which is blocking

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit d42cb88d85c9fb12ab96e2526a90b6fc7a9dd81a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 21 17:53:29 2019 -0700

    BaseFab: remove allocator template paramter. instead make allocator base of BaseFab

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_TypeTraits.H

commit c16d19c808e09c6eb73dde93a59764b3acbfa4ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 21 17:09:33 2019 -0700

    BaseFab no longer needs BaseFabData as base

Src/Base/AMReX_BaseFab.H

commit 6bf7f89e744746c60b2851ca1e894905ae47a964
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 21 16:13:44 2019 -0700

    remove asyncfab

Src/Base/AMReX.cpp
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuAsyncFab.H
Src/Base/AMReX_GpuAsyncFab.cpp
Src/Base/AMReX_GpuAsyncFabImpl.H
Src/Base/AMReX_GpuAsyncFabImpl.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit c44df3e619ecc10792e57b621e968592d1207fae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 21 16:11:02 2019 -0700

    update license information

Docs/sphinx_documentation/source/index.rst
Docs/sphinx_tutorials/source/index.rst

commit c62e4c96437e1244713b348a3fd29469807d69b2
Merge: 2aa10bab7 910e17989
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jun 21 15:32:35 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit abf33debda9ccbfdd9b15e70d9b19b6d45ca4127
Merge: cf742655b 910e17989
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jun 21 10:32:05 2019 -0700

    Merge branch 'development' into mr/cmake

commit 910e17989a9a3059465a056946c7229b6dcd7136
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 20 17:11:35 2019 -0700

    remove fab device ptr

Docs/sphinx_documentation/source/BuildingAMReX.rst
Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_FabAllocator.H
Src/Base/AMReX_FabAllocator.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_FabFactory.H
Src/Base/AMReX_GpuAsyncFabImpl.H
Src/Base/AMReX_GpuAsyncFabImpl.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_VisMF.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/Boundary/AMReX_FabSet.H
Src/Boundary/AMReX_InterpBndryData.cpp
Src/EB/AMReX_EB2_MultiGFab.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp
Src/F_Interfaces/Octree/AMReX_octree_fi.cpp
Tests/GPU/AsyncFab/GNUmakefile
Tests/GPU/AsyncFab/Make.package
Tests/GPU/AsyncFab/main.cpp
Tests/GPU/libamrex_CUDA/main.cpp
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/GNUMake/Make.defs

commit 2aa10bab76349453fb7c94b5ca92687feb058865
Merge: 6f0adc081 45de01f7a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jun 20 17:52:07 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 45de01f7aa25793893d9bbc18c950fa35abe2157
Merge: 8e7cc93d0 50721056c
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 20 13:56:41 2019 -0700

    Merge pull request #505 from esclapez/dev_CleanDiffSameDomainRefined
    
    Clean the screen output of DiffSameDomainRefined.

commit 8e7cc93d0cd555737f5cb60c541a3970c618915d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 20 13:55:41 2019 -0700

    Revert "change names in tutorial documentation and update license information"
    
    This reverts commit 66a1e8a55997a8396a3c5d6904c9e3837c75cea4.

Docs/sphinx_documentation/source/index.rst
Docs/sphinx_tutorials/source/conf.py
Docs/sphinx_tutorials/source/index.rst
build_and_deploy.sh

commit 50721056ca127e432a3f33c819015daab1701d51
Author: Lucas Esclapez <lesclapez@lbl.gov>
Date:   Thu Jun 20 13:31:57 2019 -0700

    Missing \n from previous commit ...

Tools/C_util/Convergence/DiffSameDomainRefined.cpp

commit 491033a3fdd70db70612334bf380fd875a8f5cbd
Author: Lucas Esclapez <lesclapez@lbl.gov>
Date:   Thu Jun 20 13:20:40 2019 -0700

    Clean the screen output of DiffSameDomainRefined.

Tools/C_util/Convergence/DiffSameDomainRefined.cpp

commit ebe558b3be32321b30f35c9b39e3d5731aeebcd8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 20 11:12:22 2019 -0700

    add amrex_set_boxarray, distromap and geometry to amrex_core_module

Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90

commit 6f0adc081b3dd99e54e30fdde41b33ebc3d96225
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jun 20 13:14:26 2019 -0400

    add early exit for EnforcePeriodicGPU at the end of RedistributeGPU

Src/Particle/AMReX_ParticleContainerI.H

commit 0d008b645172b7806c0ab97886cf9a1487809b2e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jun 19 20:43:41 2019 -0400

    change some HostToHost to HostToDevice

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit e88163d0fe5699f9261c8a93a9afbd6962008727
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jun 19 20:29:08 2019 -0400

    some optimizations for FillNeighborsGPU

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 58cd50a62a24a5f850fe0955d7d99b74c5c48a19
Merge: 19b3157b1 c76e60eaa
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date:   Wed Jun 19 18:56:04 2019 -0400

    Merge branch 'development' of git://github.com/AMReX-Codes/amrex into development

commit 19b3157b1af742abe37522517d677b88e440c431
Author: Chris DeGrendele <christopher.degrendele@stonybrook.edu>
Date:   Wed Jun 19 15:03:15 2019 -0700

    added umac interpolate function

Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit c76e60eaaba1433e30e9047139dcc63121071f03
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 19 13:45:29 2019 -0700

    documentation: minor fix

Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_documentation/source/InputsLoadBalancing.rst

commit d05898a8ba29bdba3b139775d233a4d9cf07ad98
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 19 13:31:58 2019 -0700

    documentation: kernel launch

Docs/sphinx_documentation/source/GPU.rst

commit 73640ad27db7941dec79f3b226f515532e2c707b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 19 13:24:39 2019 -0700

    documentation: kernel launch

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/GPU.rst

commit 9066abae218e6326f9df65c7ab18b69f00a6a5ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 19 10:14:27 2019 -0700

    documentation: AsyncArray and Elixir

Docs/sphinx_documentation/source/GPU.rst

commit 8a7927bdc6cbc3137864c881b66f03c95290c53a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 18 16:18:02 2019 -0700

    AMREX_OMP_OFFLOAD -> AMREX_USE_OMP_OFFLOAD.  Remove AsyncFab from documentation

Docs/sphinx_documentation/source/GPU.rst
Tools/GNUMake/Make.defs
Tutorials/GPU/Launch/MyKernel_F.F90
Tutorials/GPU/Launch/MyKernel_F.H
Tutorials/GPU/Launch/main.cpp

commit dd2c955f46da7e2b73b9c98c7421a823719c4df4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 18 14:59:26 2019 -0700

    documentation: update boundary

Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_documentation/source/GPU_Chapter.rst

commit 2fc15e15294d563324ad53215382359ef0c73f51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 18 14:55:51 2019 -0700

    documentation: update boundary

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/LinearSolvers.rst

commit 1481c0a45d171be170f11c4d75b4bf4b81b3b7ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 18 14:37:08 2019 -0700

    documentation: update kernel section

Docs/sphinx_documentation/source/Basics.rst

commit beb3194d8f3163b2d7b050bfc4d44e8aedc27d6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 18 14:03:10 2019 -0700

    documentation: update tiling section to use C++

Docs/sphinx_documentation/source/Basics.rst

commit e993ec3b5af2f3d0af666dc4b7465631f1537371
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 18 13:23:12 2019 -0700

    add Array4::nComp and update documentation for Dim3 and Array4

Docs/sphinx_documentation/source/Basics.rst
Src/Base/AMReX_Array4.H

commit b02380381a0d43a284d1e39d5046c727ebea89be
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jun 19 13:00:52 2019 -0700

    add some more verbosity to the build_and_deploy script to make it easier to debug

build_and_deploy.sh

commit 79479d07fc4ae392e01fac9a89c9cef955a47084
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jun 19 14:27:11 2019 -0400

    need to use different names for these derived type components

Tutorials/Particles/NeighborList/neighbor_list_3d.f90

commit 7aca5e105eaa5c85f0abc5f3d0bfb7558ed93680
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 18 16:36:02 2019 -0700

    Update for hip changes.

Tests/GPU/FusedLaunches/main.cpp

commit 6d761c749c978a2507c3389d1ca2f4a05858a569
Merge: 118244e70 aae3f7582
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 18 16:33:09 2019 -0700

    Merge branch 'development' into kngott/fused

commit ef3389bb2b357e70fdd00579e5f9dec65533e211
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 18 16:02:17 2019 -0700

    remove unused variable

Src/Particle/AMReX_TracerParticles.cpp

commit 617aac1272c15adb670536ba474b5d1db9192c70
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 18 15:55:26 2019 -0700

    use different approach in interp_2

Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 9cec506dd15185bf86c7c1ef4c1d0ca86476e6bc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 18 15:34:13 2019 -0700

    add a debugging print

Src/Particle/AMReX_TracerParticles.cpp

commit fb7b7899fd4a8e81166fdc53149f5d2b61744ba9
Author: Christopher DeGrendele <chrisdeg@cori06.nersc.gov>
Date:   Tue Jun 18 15:30:21 2019 -0700

    s

Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit cf742655b84c1fa9344366c25f623af6afc86ed5
Merge: b73a83d08 aae3f7582
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 18 14:45:38 2019 -0700

    Merge branch 'development' into mr/cmake

commit aae3f75822080736f456f270ed9eb06f78f989cd
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 18 14:36:23 2019 -0700

    CMake: turn off tutorials by default

CMakeLists.txt
Docs/sphinx_documentation/source/BuildingAMReX.rst

commit 2d4a7aba08ff6cabdb86bbb7c88f3d2cc5caeb40
Merge: e19e10705 dd60dc605
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 18 14:34:51 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit e19e107059b4616dd022793d52fa6c11ac985e62
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 18 14:34:45 2019 -0700

    CMake: allow user to build and install plotfile tools. Fixes issue #501

CMakeLists.txt
Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/Plotfile/CMakeLists.txt

commit 77d5b1e6a93a51d0b82d0c949984f9eb602aae94
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 18 13:55:24 2019 -0700

    Add timer regions to GraphBoundary test.

Tests/GPU/CudaGraphs/GraphBoundary/main.cpp

commit 49a087a17ce4f2bed50cb63e6f72f26b3a1053d1
Merge: 34ed0239a dd60dc605
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 18 13:53:37 2019 -0700

    Merge branch 'development' into kngott/cudaGraphs

commit dd60dc605e37834306a18f0a7436b162634ba082
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 18 13:53:03 2019 -0700

    Fix include guards.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H

commit e0c2f717286b8a75fc94d3f3a18459fc92f580b3
Author: Christopher DeGrendele <chrisdeg@cori07.nersc.gov>
Date:   Tue Jun 18 13:34:07 2019 -0700

    revert back to no idx

Src/Particle/#AMReX_TracerParticles.cpp#
Src/Particle/.#AMReX_TracerParticles.cpp
Src/Particle/AMReX_TracerParticle_mod_K.H

commit e5fcaadfcacb8d8808103bccb63874627b5f07a7
Author: Christopher DeGrendele <chrisdeg@cori07.nersc.gov>
Date:   Tue Jun 18 13:25:52 2019 -0700

    cpu

Src/Particle/#AMReX_TracerParticles.cpp#
Src/Particle/.#AMReX_TracerParticles.cpp
Src/Particle/AMReX_TracerParticle_mod_K.H

commit 185218af2c60720e952ea338e5267b0930415394
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 18 13:18:50 2019 -0700

    Turn off OpenMP if GPU.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 0d53195165d22cc46bdf90dce24b0e7cdffed62c
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 18 12:51:08 2019 -0700

    Update BCs and Patch calls for GPUs.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/Kernels_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Make.package
Tutorials/GPU/Advection_AmrCore/Source/bc_fill.H
Tutorials/GPU/Advection_AmrCore/Source/bc_fill_nd.F90

commit 4d65b9ff195f40aa16da4fb0dcd090cc47334947
Author: kngott <kngott@lbl.gov>
Date:   Mon Jun 17 20:31:25 2019 -0700

    Add GPU tagging.

Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/Kernels_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src_nd/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90
Tutorials/GPU/Advection_AmrCore/Source/Tagging.H

commit 033e103adc7bf405577329bddd57516dfa9ddb39
Author: Christopher DeGrendele <chrisdeg@cori07.nersc.gov>
Date:   Tue Jun 18 11:39:33 2019 -0700

    This now compiles on CPUs

Src/Particle/AMReX_TracerParticle_mod_K.H

commit 80e5d068c2ce362ec5d86bf10938d2107075a887
Author: Christopher DeGrendele <chrisdeg@cori07.nersc.gov>
Date:   Tue Jun 18 11:29:13 2019 -0700

    function parameters

Src/Particle/#AMReX_ParGDB.H#
Src/Particle/#AMReX_ParticleContainerI.H#
Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 7f9c319b51f31ccb0a589c5e8a81fad61093c7e8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 18 10:53:36 2019 -0700

    Remove unused variable

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit 08cc2209ec2f17f4f36420c6e3c5a8f530377834
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 18 10:51:48 2019 -0700

    change function signature of the interp function

Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 9d456183b8d36200e0035ba792ff3a5caf0da09a
Merge: 66a1e8a55 2e720cce9
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jun 18 10:48:42 2019 -0700

    Merge pull request #504 from KiranEiden/keiden/amrex
    
    Fixed typo in print_backtrace_info

commit 2e720cce925e3771d2fb6548e68b256e873f9c2f
Author: Kiran Eiden <keiden@eidensystems.com>
Date:   Tue Jun 18 10:40:46 2019 -0700

    Fixed typo in print_backtrace_info

Src/Base/AMReX_BLBackTrace.cpp

commit be500b06b7fd38d62a47f47fc1b88450aa29028f
Author: Christopher DeGrendele <chrisdeg@cori05.nersc.gov>
Date:   Tue Jun 18 10:33:59 2019 -0700

    push

Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 66a1e8a55997a8396a3c5d6904c9e3837c75cea4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 18 10:03:19 2019 -0700

    change names in tutorial documentation and update license information

Docs/sphinx_documentation/source/index.rst
Docs/sphinx_tutorials/source/conf.py
Docs/sphinx_tutorials/source/index.rst
build_and_deploy.sh

commit e3a542f6d14aba1d56a4c222f59ea25fba389103
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 18 09:16:38 2019 -0700

    point to parse_bt.py in backtrace message

Src/Base/AMReX_BLBackTrace.cpp
Tools/Backtrace/parse_bt.py

commit 7edf2a9c96db0c3b28653c9951cd5bad9d710520
Merge: 10c8682a4 318dc951c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jun 18 08:48:46 2019 -0700

    Merge pull request #503 from AMReX-Codes/mz
    
    increase precision of output

commit 318dc951c8d8b28d6c4771d781ea4c3d5bb44a2c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 18 11:38:51 2019 -0400

    increase precision of output so we can use the results for
    mapping for problem inits to roundoff

Tools/Plotfile/fextract.cpp

commit 3a61bad82c9396d4610aeadb60fd717986a975fd
Author: Christopher DeGrendele <chrisdeg@cori07.nersc.gov>
Date:   Tue Jun 18 08:04:46 2019 -0700

    testing

Src/Particle/AMReX_TracerParticle_mod_K.H

commit 10c8682a46336dff7c658ad81a0edd07e331ef7d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 17 20:43:27 2019 -0700

    fix typecheck. It doesn't like __attribute__

Src/Base/AMReX_Extension.H
Tools/GNUMake/Make.rules

commit 217167b0e1a5ded4e647644bc9ecdb9f0475e9b3
Merge: bb35be534 49b5191d1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 17 20:21:21 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit bb35be534646a2499e7b8e689ccc07795ff9f42f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 17 20:21:02 2019 -0700

    a better check for OpenMP < 3.1

Src/Particle/AMReX_Particle.H

commit 49b5191d19c9cba066961a1e725acd7a220504c3
Merge: 8dc4071ef abb991019
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 17 20:14:35 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 8dc4071ef0d15d8fe6e9c3a7fa0bc943a5bc8820
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 17 20:11:07 2019 -0700

    Need to test on apz(i,j,k+1) not apz(i,j,k) when testing the hi-side terms

Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 34ed0239a6047ea25b9dbf04f5e50397f0970e5b
Author: kngott <kngott@lbl.gov>
Date:   Mon Jun 17 18:04:30 2019 -0700

    Fix header.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H

commit abb99101967db07ca31d0e7736298171a5f44df2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 17 16:13:48 2019 -0700

    fix omp race condition

Src/Base/AMReX_BoxArray.cpp

commit cb93b55c21e83ed6243b4a29df22f3520731871f
Author: Christopher DeGrendele <chrisdeg@cori06.nersc.gov>
Date:   Mon Jun 17 15:06:06 2019 -0700

    Trial 2

Src/Base/#AMReX_FArrayBox.H#
Src/Base/#AMReX_FArrayBox.cpp#
Src/Particle/#AMReX_ParGDB.H#
Src/Particle/#AMReX_TracerParticles.cpp#
Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 1c99b1338b37747d8fb2c2e96344ac9587b90f2b
Merge: d7c8c3c8a 46c05b129
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 17 09:21:23 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d7c8c3c8a2af379658980e882a95887639f680a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 16 18:22:28 2019 -0700

    add MacProjector::setBottomVerbose function

Src/LinearSolvers/MLMG/AMReX_MacProjector.H

commit 46c05b129f2a72bf81856045877236942d2da1fa
Merge: b4bd2202f 340a85f9e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sun Jun 16 17:31:31 2019 -0700

    Merge branch 'development' into sum_neighbors

commit 340a85f9e8bf0cc3659bddd831f2a772f7a856a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 15 17:13:26 2019 -0700

    make sure it works with OMP < 3.1

Src/Base/AMReX_MultiFab.cpp

commit b4bd2202f3e2619701a4e22ded926bbad5cddb24
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Jun 15 16:31:48 2019 -0700

    add test integer comp to neighbor list tutorial

Tutorials/Particles/NeighborList/NeighborListParticleContainer.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborList/inputs
Tutorials/Particles/NeighborList/main.cpp
Tutorials/Particles/NeighborList/neighbor_list_2d.f90
Tutorials/Particles/NeighborList/neighbor_list_3d.f90

commit 0ed5d0d1a446cb7a13f00b7ede92d0b62e3754d9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Jun 15 16:31:24 2019 -0700

    add sumNeighbors for int comps too

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleContainerI.H

commit 445ebec3cab3c6089f13d5a597196e64c20e585a
Merge: 3c30a8133 5c01ebd8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 15 16:25:12 2019 -0700

    Merge branch 'hip' into development

commit af21c228afdfc70a52cf9eab963cd6a9dce786b1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Jun 15 16:16:47 2019 -0700

    more descriptive variable name

Src/Particle/AMReX_NeighborParticlesCPUImpl.H

commit f502f972c3d483876c0ca8947cc80e687f90f751
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Jun 15 16:15:00 2019 -0700

    fix bug in sumNeighbors

Src/Particle/AMReX_NeighborParticlesCPUImpl.H

commit f9915fb34569985fa6dbfbfcf041fc012841fb62
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Jun 15 15:29:17 2019 -0700

    unpack the communicated data

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_ParticleContainerI.H

commit aefe1bcb382be2c27f56cc0bb9a269fd8fa8fd2b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Jun 15 15:28:46 2019 -0700

    ignore this unused

Src/Base/AMReX_FabArrayCommI.H

commit 36735775a198067099025fb46a7de0512d86a0c5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Jun 15 14:38:21 2019 -0700

    minor formatting changes

Src/Particle/AMReX_NeighborParticles.H

commit 96ceaf4a076077b52559374407a061007f8b4353
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Jun 15 14:35:55 2019 -0700

    implementing MPI portion of sumNeighbors

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_ParticleContainerI.H

commit 3c30a8133218def80b2945228dd51fa072edf91f
Merge: 19d1a66ba 4e769bfc5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 15 14:12:20 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 0cbcb8e46488cc83064c11d5c229322f0cda0a32
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Jun 15 13:59:13 2019 -0700

    implement local form of sumNeighbors

Src/Particle/AMReX_NeighborParticlesCPUImpl.H

commit a8f852b57f62995518b177d1945ebefe6343dc48
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Jun 15 13:32:10 2019 -0700

    adding a level to the InverseCopyTag

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 282c7ec7343aaebe993e152f8adec7d035fb0ba7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Jun 15 13:24:08 2019 -0700

    starting to work on implementing the sumNeighbors MPI exchange

Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 5c01ebd8d640e6bf556f78297427c2775c19830e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 15 13:04:55 2019 -0700

    fix typo in interp 2d

Src/AmrCore/AMReX_Interp_2D_C.H

commit 631c60077c5338b443acd85005d72bd59d1ec4fe
Merge: 2d98120f3 d32ff0b75
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 15 12:50:41 2019 -0700

    Merge branch 'hip' of github.com:AMReX-Codes/amrex into hip

commit 2d98120f387b902f5653a71917bcd240fde27e39
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 15 11:49:30 2019 -0700

    add lbound, ubound and length for Array4. remove fabPtr and AsyncFab from Interpolater

Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/Base/AMReX_Array4.H

commit 4e769bfc531247a4dc5ecd16f36ad4b623ef304a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Jun 15 00:16:00 2019 -0400

    fix off-by-one error

Src/Particle/AMReX_ParticleContainerI.H

commit d32ff0b759a39d854163ab71557efaba35452cc5
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Jun 14 20:26:52 2019 -0700

    getting rid of some fabPtr in the particle classes

Src/Particle/AMReX_Functors.H
Src/Particle/AMReX_ParticleContainerI.H

commit 2c8edd8137553383491acfb8c35800d0f73b05e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 14 18:43:57 2019 -0700

    use Array4 in neighbor particles

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit d9011fc25bcb7c63f753301cc544260fbe35b7ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 14 18:43:06 2019 -0700

    fix commit 69791966a864e27

Src/Amr/AMReX_AmrLevel.cpp

commit 7a4194de7852d93f69f7097754cfbf8219450830
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 14 18:16:51 2019 -0700

    put Array4 and Dim3 into their own files so that we can have Array4::operator() taking IntVect

Src/Base/AMReX_Array.H
Src/Base/AMReX_Array4.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_Dim3.H
Src/Base/AMReX_GpuUtility.H
Src/Base/AMReX_IntVect.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 7ae5228c5af6bb39ecec887f87dda70b3a4d89c8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 17:25:54 2019 -0700

    fix compilation error in sumNeighbors

Src/Particle/AMReX_NeighborParticlesCPUImpl.H

commit a30bce88c891858009b7ab76a854fd1e1f59f181
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 17:23:57 2019 -0700

    fix comments

Src/Particle/AMReX_NeighborParticles.H

commit 12b126e87598f951c8a10ae05284f37f89e797e7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 17:22:55 2019 -0700

    output operator for InverseCopyTag

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H

commit 5b829d456cccf535b492e8dfb3ade1f74535a6fc
Merge: 41014e267 16d211031
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 17:16:33 2019 -0700

    Merge branch 'development' into sum_neighbors

commit 41014e267219cd9f5e948bba81b3d4babcb41f75
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 17:14:55 2019 -0700

    use getter for enableInverse

Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 302d2c748912468b08bd83e5941835574e7fe692
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 17:12:33 2019 -0700

    make enable_inverse static

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 508ce00c47ff9e0398a7e4fb840244421b956096
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 17:11:31 2019 -0700

    getters / setters for enable inverse

Src/Particle/AMReX_NeighborParticles.H

commit 1862718af2b9a4618c33afa9de926e8d8d9e76a5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 17:10:04 2019 -0700

    abort if calling sumNeighbors without enable_inverse

Src/Particle/AMReX_NeighborParticlesCPUImpl.H

commit 8457f4595ef398df7598c2ab885537bb22bf9354
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 17:08:51 2019 -0700

    remove Redistribute-based implementation of sumNeighbors

Src/Particle/AMReX_NeighborParticlesCPUImpl.H

commit c705af94069dcbdb8972f5be56f4e67100b7e1a3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 17:08:13 2019 -0700

    wrap the inverse neighbor particle stuff in a boolean flag

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 2b6296201ac384173e461cbb4d01c4b1cfd9e500
Author: Christopher DeGrendele <chrisdeg@cori09.nersc.gov>
Date:   Fri Jun 14 16:04:55 2019 -0700

    not yet working gpu code

Src/Particle/#AMReX_ParticleContainerI.H#
Src/Particle/#AMReX_TracerParticles.cpp#
Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_Particle_mod_K.H
Src/Particle/AMReX_TracerParticle_mod_K.H
Src/Particle/AMReX_TracerParticles.cpp

commit 7c22bf1fa59e7133c6c69374e82253097b0b8326
Merge: 69791966a 19d1a66ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 14 16:04:44 2019 -0700

    Merge branch 'development' into hip

commit 69791966a864e2703f3e51bda0a58c4cfef050b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 14 16:03:59 2019 -0700

    update Amr/ to avoid fabPtr

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AuxBoundaryData.H
Src/Amr/AMReX_Extrapolater.cpp
Src/AmrCore/AMReX_AmrParticles.H
Src/AmrCore/AMReX_FillPatchUtil.cpp

commit 7baa200d89f28e4662d5a9fa6ee28a9e90ae67f2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 12:53:05 2019 -0700

    keep track of information needed to reverse the neighbor particle communication.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 66df989ccbe05afa8fbab2c19decf86174df85e2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 11:10:38 2019 -0700

    calling sumNeighbors in the main evolve loop

Tutorials/Particles/NeighborList/main.cpp

commit 85ed015a98d583e202a430b2d15fd338c253738d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 11:10:14 2019 -0700

    add a test comp to the neighbor particle tutorial

Tutorials/Particles/NeighborList/NeighborListParticleContainer.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborList/neighbor_list_2d.f90
Tutorials/Particles/NeighborList/neighbor_list_3d.f90

commit 1a469a0a50a75aeafa9824152a13447a2b1946ac
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 11:08:57 2019 -0700

    add Redistribute-based implementation of sumNeighbors

Src/Particle/AMReX_NeighborParticlesCPUImpl.H

commit 082c57c5767636fe7346f59c365a0bd7a14c1acc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 11:08:28 2019 -0700

    add dispatch for CPU implementation of sumNeighbors

Src/Particle/AMReX_NeighborParticlesI.H

commit 7461573e8e84289b0a643eada9d835c9ec235077
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 11:07:48 2019 -0700

    initialize a tmp PC from a known ParGDB

Src/Particle/AMReX_Particles.H

commit d59eea3586b67cf8193e361661ff8ed5407f55bd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 14 11:07:18 2019 -0700

    adding a sum neighbors method for the NeighborPC

Src/Particle/AMReX_NeighborParticles.H

commit 16d2110317f7899edae1da752724a89fe2457fac
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Fri Jun 14 10:06:10 2019 -0700

    Add GPU debugging section, make ReduceSum include function prototype in documentation

Docs/sphinx_documentation/source/GPU.rst

commit 19d1a66ba37070e7203c47e11ed9a384ba73a792
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 14 09:31:53 2019 -0700

    MLMG: fab Ptr to Array4

Src/Boundary/AMReX_MultiMask.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit f2dbaef853bf0d1135d91e6cd4f73c2a8b9583dc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jun 14 09:32:48 2019 -0700

    Remove mfix-specific text

Docs/sphinx_documentation/source/InputsProblemDefinition.rst

commit 534bd6bafddbe1954a5dc29dc5fc03f83b3a7323
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 14 09:23:28 2019 -0700

    Mask: add constructors taking Array4

Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_MultiMask.cpp
Src/Boundary/AMReX_YAFluxRegister.cpp

commit 7d966002680cc049fb4d4914e10c5502c383e74b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jun 14 09:21:18 2019 -0700

    Add default load balancing strategy

Docs/sphinx_documentation/source/LoadBalancing.rst

commit 58c58bd963eb333ecb9e2a2a004708bf5e43e3ac
Merge: 3765e3113 ac849b567
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 14 08:56:23 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ac849b567f6bb488257bf0a83ba8611291c4b375
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Thu Jun 13 16:03:02 2019 -0700

    Add Run-time Inputs chapter based off amrex-specific portions of MFIX-Exa documentation

Docs/sphinx_documentation/source/InputsCheckpoint.rst
Docs/sphinx_documentation/source/InputsLoadBalancing.rst
Docs/sphinx_documentation/source/InputsPlotFiles.rst
Docs/sphinx_documentation/source/InputsProblemDefinition.rst
Docs/sphinx_documentation/source/InputsTimeStepping.rst
Docs/sphinx_documentation/source/Inputs_Chapter.rst
Docs/sphinx_documentation/source/index.rst

commit fa5ffb15b54dd1b4db86a5f15b3edbfedef60dc0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 13 15:11:48 2019 -0700

    remove outdated limitations from the GPU section

Docs/sphinx_documentation/source/GPU.rst

commit 650dd3ac16f95a97bfc68d4921c19640d5b16005
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 13 15:06:59 2019 -0700

    fix a formatting problem

Docs/sphinx_documentation/source/Particle.rst

commit e0f6ed6eff91778c35ec2c446abacd558d6b71a3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 13 15:03:15 2019 -0700

    note the prefix for the amrex.use_gpu_aware_mpi flag

Docs/sphinx_documentation/source/GPU.rst

commit dd87d9f6e0d4016ebfbc23764d80f0bdca17e2b3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 13 14:47:35 2019 -0700

    add some documentation about inputs parameters relevant for the behavior of amrex particles, including IO and GPU performance

Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_documentation/source/Particle.rst

commit 3765e31135350ff91888b1b7ce816733d8278c22
Merge: 025ff90cc 6439e5e40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 13 14:30:55 2019 -0700

    Merge branch 'hip' into development

commit 6439e5e40a3220ba40cac9d46077ac8f3b75a6e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 13 14:02:13 2019 -0700

    PhysBCFunct: pass host fab to m_f

Src/Base/AMReX_PhysBCFunct.H

commit 025ff90ccf7b5bb19c51e2dfca89f7567a0ea9e9
Merge: 0fb0d2b02 0e3d17676
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 13 13:43:28 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 0e9659c3b6055ca42e4e44f46eecf67c2a189557
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 13 13:39:41 2019 -0700

    update amrex_avg_down*

Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_Perilla.cpp
Src/Base/AMReX_MultiFabUtil_nd_C.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Tests/Slice/main.cpp
Tests/SliceWithInterp/main.cpp

commit 6638056d02c06bcb4c334896e298c5326a7ba2d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 13 13:27:19 2019 -0700

    add noexcept

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_IArrayBox.H
Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBCellFlag.cpp

commit 0fb0d2b0269f6d5e7c3ccfbf4e95425abd6e99a1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 13 12:55:32 2019 -0700

    remove these now unimplemented functions - they are in the Gpu:: namespace directly now

Src/Base/AMReX_GpuDevice.H

commit 0e3d17676096eaa0d45340d2930c7615f219d303
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 13 12:55:21 2019 -0700

    use explicit device-to-host copies here rather than relying on page faults

Src/Particle/AMReX_ParticleContainerI.H

commit b73a83d082a71e54a0eb6432061a5135b6042b53
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 13 12:25:12 2019 -0700

    CMake: update documentation.

Docs/sphinx_documentation/source/GPU.rst

commit f04990d73bd0268a9a1911c81799ec8b7d8b86f1
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 13 12:14:01 2019 -0700

    CMake: improve CUDA support.
    
    * Set C++ and CUDA required standard via CMake compile features
    * Force CUDA setup in application codes if ENABLE_CUDA=on

Src/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_SetupCUDA.cmake
Tutorials/GPU/NeighborList/CMakeLists.txt

commit 5cc30dbfd7d4f9b7ebbc7159257869f81e42c279
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 13 11:33:54 2019 -0700

    fab to array4 in a number of MultiFabUtil functions

Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.H
Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H
Src/Base/AMReX_MultiFabUtil_Perilla.cpp
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/F_Interfaces/Octree/AMReX_octree_fi.cpp

commit 38a093af5a735abe82abdfee4cd83e107ad2f51c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 13 09:38:53 2019 -0700

    remove fabPtr from avg_cc_to_fc

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.H
Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H
Src/Base/AMReX_Utility.H
Tutorials/EB/Poisson/Poisson.cpp

commit 0bbb6bf2e9bc637b529729e6066a310b3c389f49
Merge: 6949d7f1b c52a1512a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 12 17:35:26 2019 -0700

    Merge branch 'development' into mlmg-2d

commit c52a1512a3d422551ad41baf1bdedf44f06a85de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 12 17:22:43 2019 -0700

    Add IndexType to FArrayBox contructed from Array4 to avoid assertion failure

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_IArrayBox.H

commit f8a3aef2a7aba7f6657e23b7dc8d76ac154c3dfd
Merge: 2be8f52b8 09030e1a0
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 12 16:01:53 2019 -0700

    Merge branch 'development' into mr/cmake

commit 6949d7f1b29fb2d89dde3c8449ca191effc3d94a
Merge: d7a6a222c 45864247f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 12 14:17:46 2019 -0700

    Merge branch 'development' into mlmg-2d

commit d7a6a222c5b6bf3ae38b32799bc9f033ebd6e093
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 11 21:15:37 2019 -0700

    reimplement the treatment of metric terms in MLMG

Src/LinearSolvers/MLMG/AMReX_MLALap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLALap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H

commit 09030e1a05faa0a05ced7fd182080bab4037be1f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 12 11:08:21 2019 -0700

    CMake: fix var_NOT-FOUND bug

Tools/CMake/AMReX_Config.cmake

commit 5cc62c3d0b2c3ae54711ad5bc8a2a6ec66eb935f
Merge: b3e1c3e3c 45864247f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 12 13:30:37 2019 -0400

    Merge branch 'development' into kngott/cudaGraphs

commit 45864247fd836da4ab53cddec00e48c91285425e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 11 20:37:53 2019 -0700

    fix enable_if

Src/Particle/AMReX_Particles.H

commit e5394eb36466e9c831a3ebf9b2c517337f46c9bc
Merge: 8aa918da7 f78799166
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 11 18:55:08 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8aa918da775c3aa775578ffd0622a9f2ca3d4805
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 11 18:54:22 2019 -0700

    CMake: add nvToolsExt library to link line

Tools/CMake/AMReX_Config.cmake

commit 4d9c108d67ca87e8d8c96808b2953cc04dfbf553
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 11 18:41:37 2019 -0700

    CMake: fix CUDA tutorials

Tutorials/GPU/Launch/CMakeLists.txt
Tutorials/GPU/NeighborList/CMakeLists.txt

commit ff1b785deb405d1c6b6ef9a30b3349547c968918
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 11 18:30:05 2019 -0700

    CMake: fix incorrect required Fortran flag for PGI compiler

Tools/CMake/AMReXFlagsTargets.cmake

commit f7879916611afef6f72c94560da149f39094a044
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jun 11 20:57:08 2019 -0400

    std::enable_if_t is C++14, using another approach

Src/Particle/AMReX_Particles.H

commit b3e1c3e3c49178da6ee173cc7062ea8dc3e3da2a
Merge: fccff75ef 5a13bb9f0
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jun 11 20:27:01 2019 -0400

    Merge branch 'development' into kngott/cudaGraphs

commit fccff75efbd11d1d4d374f1c1895126e093a368f
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 11 17:22:41 2019 -0700

    Strictly define regions in test.

Tests/GPU/CudaGraphs/GraphBoundary/main.cpp

commit 2e74ec473bbef46d895a5b133638e06dee41ed8d
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 11 17:09:14 2019 -0700

    Move copyFromBuffer graph creation to try to get some additional overlap with MPI.

Src/Base/AMReX_FabArrayCommI.H

commit 5a13bb9f03ffee3295379beb0c0eeb8ab5e48033
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 11 16:56:28 2019 -0700

    CMake: enforce C++14 standard

Tools/CMake/AMReX_Config.cmake

commit cb2ea241c5c2b26cd113f6bd676e80b8355e98a3
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 11 16:19:21 2019 -0700

    Change FillBoundary graphs to include memcpy.

Src/Base/AMReX_FabArrayCommI.H

commit 5fd2e9d62b399476e0503343bd61b6c6234e4eec
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 11 15:51:54 2019 -0700

    Add speedup calc to FillBoundary test.

Tests/GPU/CudaGraphs/GraphBoundary/main.cpp

commit f99ad2d4d5a8bac0c72284748a2eab30faf89b4b
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 11 14:45:26 2019 -0700

    Add check to memcpy if not added to the graph.

Src/Base/AMReX_CudaGraph.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp

commit 2be8f52b878a147f30240b6a491dfeb31d81e4f8
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 11 15:03:33 2019 -0700

    CMake: document latest changes

Docs/sphinx_documentation/source/BuildingAMReX.rst
Docs/sphinx_documentation/source/GPU.rst

commit 07d5c72d756bfabba94e79904c0ce530a56d0f57
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 11 15:03:11 2019 -0700

    CMake: use a component-centric approch in exported config file

Tools/CMake/AMReXConfig.cmake.in

commit da6e3ca2b36b0164bb08c0e1f0966a8657475256
Merge: cc2022b93 7406a57ee
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jun 11 13:41:31 2019 -0700

    Merge pull request #497 from mattbement/master
    
    add an option to enable PIC to the configuration script

commit cc2022b9363221baa99b97c429cc39f06a4ae302
Merge: 5ff599167 825a16ad4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 11 13:29:17 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5ff599167366da305ff2599bba934475a326254b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 11 13:29:02 2019 -0700

    prevent implicit conversion of 'const char *' to 'bool' from selecting this function overload

Src/Particle/AMReX_Particles.H

commit 825a16ad47d44fca24baabc96524656ef90b4ca3
Merge: c644395e2 71d93fdc0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 11 12:51:13 2019 -0700

    Merge branch 'hip' into development

commit c644395e2ce2fad3052eaa430259df0805e215cf
Merge: 313a8ed2f 210c71dda
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 11 12:51:01 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 1924fd9d429a7c31f23080ae4e2f89584e740bae
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 11 12:23:39 2019 -0700

    De-sync FB local copy graph.

Src/Base/AMReX_FabArrayCommI.H

commit 71d93fdc03fba5920e8413ca8719d4effe69026d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 11 12:22:51 2019 -0700

    fix make file for linking with mpif90

Tools/GNUMake/sites/Make.unknown

commit fc62aecb01c117104c3e7d415e9eb569865ccf5a
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 11 12:15:46 2019 -0700

    Change CudaGraph execute to use Gpu::Device function.

Src/Base/AMReX_CudaGraph.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp

commit 51ee1d18c98ea7efb9476ccace88017177a5659b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 11 11:20:59 2019 -0700

    use omp atomic capture instead of critical

Src/Base/AMReX_MultiFab.cpp

commit 8d51c4768fbc2d033f0572a65ae108a63e2a5c9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 11 10:15:34 2019 -0700

    MultiFabUtil: use Array4

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.H
Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit cd65b11cc0158db4355f81beef05c18a4eeaa7f6
Merge: 88e02bb39 210c71dda
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 11 10:41:37 2019 -0700

    Merge branch 'development' into mr/cmake

commit 6622a3e891c2ba15d3a37814bb1f53362140bb45
Merge: 62e5904c5 210c71dda
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 11 10:32:13 2019 -0700

    Merge branch 'development' into kngott/cudaGraphs

commit 77cb031db47b9f12def1d3e59b92568e697d3fc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 11 10:10:23 2019 -0700

    fix for non-MPI

Src/Base/AMReX_ccse-mpi.H

commit a6c17fed76e6903da3276efe37cbe7168e976e4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 11 09:45:18 2019 -0700

    add Gpu::Atomic::Exch and reimplement MultiFab::minIndex and maxIndex

Src/Base/AMReX_GpuUtility.H
Src/Base/AMReX_MultiFab.cpp

commit 62e5904c5d286e1f5cd061b16ac298e4c9bca790
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 11 01:13:30 2019 -0700

    Implement and test graph building with cudaEvents.

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp

commit 127eeb8328b1a0e6dc31728966e9ef8dba4c511c
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 11 01:09:36 2019 -0700

    Properly order graphs to hide FB build.

Tests/GPU/CudaGraphs/GraphBoundary/main.cpp

commit 483d5eddf385e4709d139bffe05bdf8b6de8c99e
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 11 01:05:41 2019 -0700

    Add additional graph building options to setVal graph test.

Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp

commit 9d3f9d1a1ebed97b15177617db12d0486fc0a7e8
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 11 01:02:22 2019 -0700

    Turn off synchs in all graph creation loops in FillBoundary.

Src/Base/AMReX_FabArrayCommI.H

commit 5a32de13af5c7c7a461283306238ab6a5ced4627
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 11 00:51:22 2019 -0700

    Add StreamItInfo and option to turn off syncing.

Src/Base/AMReX_GpuUtility.H
Src/Base/AMReX_GpuUtility.cpp

commit d972ece09f7455096d7a61330703e8165c67c86a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 10 18:37:37 2019 -0700

    reimplement minIndex

Src/Base/AMReX_MultiFab.cpp

commit 210c71dda5a21435805f32e4ea016a84bf273120
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jun 10 16:32:22 2019 -0700

    Modify macro for consistency

Src/Base/AMReX_Gpu.H

commit 7406a57eea75b15e613aaf92b237385a67c3ed3e
Author: Matt Bement <bement@lanl.gov>
Date:   Mon Jun 10 14:49:22 2019 -0600

    add an option to enable position independent code to the configuration script

Tools/libamrex/configure.py

commit bccd41b81667fcae817e3a32d0cdd2a00ca0ebb0
Author: kngott <kngott@lbl.gov>
Date:   Mon Jun 10 13:38:54 2019 -0700

    Add optional flag to make graphExecution asynchronous.

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp

commit 313a8ed2faa07def0243d904aff39ebcc75585b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 10 13:23:54 2019 -0700

    add MultiFab::norminf

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit 1c7576fc206df1b8fcd7ed356d2c43d785318ca2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 10 13:22:43 2019 -0700

    Box constructor for extracting Box from Array4

Src/Base/AMReX_Box.H

commit 5db0f45d7dff60599991abd2feeaedd5c28dad55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 10 13:20:31 2019 -0700

    remove const so that comiler generates operator= for BndryFuncArray

Src/Base/AMReX_PhysBCFunct.H

commit acdff3e9f3999e1d74332894264eef6b6ef9498c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 10 13:09:13 2019 -0700

    fix DEBUG build

Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_IArrayBox.H

commit d8a26f72c74279032481deb94f80f46946c55a00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 10 10:55:18 2019 -0700

    add comment on initVal

Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_IArrayBox.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit 36e4c4dd0dd7a62462106cbda076cb5a00bacb4e
Merge: 343f3f653 67dd208f6
Author: kngott <kngott@lbl.gov>
Date:   Sun Jun 9 23:25:52 2019 -0700

    Merge branch 'development' into kngott/cudaGraphs

commit 4b54eb6373deda6af97567a7203c4ca5128c35be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 9 18:50:34 2019 -0700

    update FArrayBox

Src/Base/AMReX_FArrayBox.H

commit 0be8699e3ecd797f45b2a1970436796ae29affba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 9 18:18:40 2019 -0700

    update reduce for amd device

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuReduce.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 5415ea9bdf6e17c5c2abb260b74869d4e48b2b7a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 9 17:20:25 2019 -0700

    avoid fabPtr in FabArrayUtility

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayUtility.H

commit 1a03289d8daca897221961ff9b95a4572c3d6d06
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 9 15:57:05 2019 -0700

    update Tutorials

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/EBCNS/Source/CNS_advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.cpp
Tutorials/GPU/Launch/MyKernel_F.F90
Tutorials/GPU/Launch/MyKernel_F.H
Tutorials/GPU/Launch/main.cpp

commit d84114f6e0eed6e45737ba1b28bd964b58db6af8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 9 10:48:16 2019 -0700

    add a new field int ncomp to Array4.  add new constructor to fabs so that we can make fab from Array4 on device

Src/Base/AMReX_Array.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaGraph.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_IArrayBox.H
Tutorials/GPU/Launch/main.cpp

commit 67dd208f648ae431895adf93d83ea0787b0e8d9c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 8 21:04:56 2019 -0700

    remove AsyncFab from StateData::FillBoundary

Src/Amr/AMReX_StateData.cpp

commit 2913e1d0a4f6fefa5f53113d54fc91a18adaed39
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 8 18:38:12 2019 -0700

    update boundary fill functions to take Array4 instead of FArrayBox

Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_FilCC_1D_C.H
Src/Base/AMReX_FilCC_2D_C.H
Src/Base/AMReX_FilCC_3D_C.H
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp
Tutorials/GPU/CNS/Source/CNS_bcfill.cpp
Tutorials/GPU/EBCNS/Source/CNS_bcfill.cpp

commit 63d8b3f876765339732dfdfd2cc2250163408e31
Merge: 324ce2342 4956dcca1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 8 10:47:17 2019 -0700

    Merge branch 'development' into hip

commit 4956dcca1f9cd6710273a532dfa1f263a07e9642
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 8 10:46:42 2019 -0700

    Fix the Poisson solver issue with dirichlet EB in periodic domain.  It was mistakenly treated as singlular.

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Tutorials/EB/Poisson/main.cpp

commit 324ce234212d8e4cb31655873ac7111ba9489c3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 8 10:23:04 2019 -0700

    update FillDomainBoundary for gpu

Src/Base/AMReX_BCUtil.H
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_PhysBCFunct.H

commit 89be080c4cc50fef19091b1899297f2794bd3dc3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 7 23:10:13 2019 -0700

    allow z-direction cylinder in 2d

Src/EB/AMReX_EB2.cpp
Src/EB/AMReX_EB2_IF_Cylinder.H
Tutorials/EB/Poisson/main.cpp

commit 0bafa80ba19945d490c8f7ac9c75be98c1173e53
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 7 17:51:20 2019 -0700

    BL_BACKTRACING -> AMREX_BACKTRACING

Docs/Notes/Readme.backtrace
Src/Base/AMReX_BLBackTrace.H
Src/Base/AMReX_BLBackTrace.cpp
Tools/GNUMake/Make.defs

commit 9742528bed6b92d0d27de9c8a8e4a8a361044f98
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 7 17:44:40 2019 -0700

    BL_TESTING -> AMREX_TESTING

Tools/GNUMake/Make.defs
Tutorials/EB/CNS/Source/CNS_io.cpp
Tutorials/GPU/EBCNS/Source/CNS_io.cpp

commit 758c3458490eb28d4d25c0ceffe8adcb9d35ebf8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 7 17:39:33 2019 -0700

    BL_TINY_PROFILING -> AMREX_TINY_PROFILING

Src/Base/AMReX_BLProfiler.H
Tools/GNUMake/Make.defs

commit bbfe45aaa255e6908c229bf60aa012bf0aa2e748
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 7 17:35:30 2019 -0700

    BL_MEM_PROFILING -> AMREX_MEM_PROFILING

Src/Amr/AMReX_Amr.cpp
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Src/Base/AMReX.cpp
Src/Base/AMReX_BArena.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_MultiFab.cpp
Src/EB/AMReX_EB_LSCoreBase.cpp
Tools/GNUMake/Make.defs
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 88d5b94de0e9b8e5387728553716ff4c59b2aefe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 7 17:25:44 2019 -0700

    make BArena use malloc and free directly, which is supposed to be for CPU memory

Src/Base/AMReX_BArena.H
Src/Base/AMReX_BArena.cpp

commit d5319abf13a0863cf12184afc3d21c07af558d8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 7 16:01:25 2019 -0700

    update __CUDA_ARCH__

Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_Array.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Extension.H
Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuQualifiers.H

commit 548477b0c40d0df4bbed21ccd8563f918085bf74
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 7 15:46:00 2019 -0700

    hip: update Arena

Src/Base/AMReX_Arena.cpp

commit 88e02bb39df4cfe8b61aa8c65f6a589c9e416281
Merge: dee0e9b97 4d001942d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jun 7 15:07:36 2019 -0700

    Merge branch 'development' into mr/cmake

commit 4d001942dd0bc99b4af5ab4360a5924492807623
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jun 7 15:07:12 2019 -0700

    CMake: add option to enable pinned memory

Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake

commit 9e535915359b4f9d34b8084552eac157f251a58c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jun 7 14:42:02 2019 -0700

    Revert "add AMREX_USE_GPU if ENABLE_CUDA"
    
    This reverts commit df9808bb32daa487c5c63d93a6b47a4f95497c40.
    AMREX_USE_GPU was already passed to the compiler for CUDA builds.

Tools/CMake/AMReX_Defines.cmake

commit 6ee029145a49768178800ef29e8601d736fba5b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 7 14:35:19 2019 -0700

    add -DAMREX_FAB_IS_MANAGED

Src/Base/AMReX_FabAllocator.cpp
Tools/GNUMake/Make.defs

commit d9e2d5533a8b35835b6235d16cbb5499c484641e
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Jun 7 12:53:54 2019 -0700

    change the order of these loops to be cache-friendly

Src/Particle/AMReX_Particle_mod_K.H

commit 46607d6bdfe50f822842ca17be9e670ddc8e780a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 7 12:12:56 2019 -0700

    No need to use the legacy hipThreadIdx_* etc.

Src/Base/AMReX_CudaReduce.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuLaunchMacrosG.H
Src/Base/AMReX_GpuRange.H

commit c1891211faa5bcd07a37320332f765490fe686a3
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Jun 7 10:37:29 2019 -0700

    std::min/max -> amrex::min/max

Src/Particle/AMReX_Particle_mod_K.H

commit 34eb0c5d67b1c4217bf69092dad3970b0a3b13af
Merge: 3dd7af396 2b4297e2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 7 07:47:13 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2b4297e2e95be8fe049272ee75b1fecaff8a0c67
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 6 19:17:08 2019 -0700

    fix 1d nodal

Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90

commit 3dd7af396123bb0bd5db49c75f9a5318c02d2fe4
Merge: a1a02ce80 60d6c21d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 6 19:05:16 2019 -0700

    Merge branch 'development' into hip

commit 60d6c21d062c8754985bbd36346f7c02d1f6aab5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 6 17:19:48 2019 -0700

    simplify EB/Poisson tutorial

Tutorials/EB/Poisson/Make.package
Tutorials/EB/Poisson/Poisson.cpp
Tutorials/EB/Poisson/Poisson_F.H
Tutorials/EB/Poisson/main.cpp
Tutorials/EB/Poisson/poisson.F90

commit a1a02ce8092877be2a4037f357e2594dd4eeb429
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 6 14:34:46 2019 -0700

    fix leading underscore

Src/AmrCore/AMReX_AmrParticles.H
Src/Base/AMReX_BLFort.H
Src/Base/AMReX_MultiFabUtil_Perilla.H
Src/EB/AMReX_EB_LSCore_F.H
Src/Extern/ProfParser/AMReX_AVGDOWN_F.H
Src/Extern/amrdata/AMReX_AmrData.H
Src/Extern/amrdata/AMReX_AmrvisConstants.H
Src/Extern/amrdata/AMReX_DataServices.H

commit e191c6ac05a787d9aaaef63cb9af56b0e744e4d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 6 14:14:06 2019 -0700

    update launch macros and functions for hip

Src/Base/AMReX_CudaGraph.H
Src/Base/AMReX_CudaReduce.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunch.cpp
Src/Base/AMReX_GpuLaunchFunctsC.H
Src/Base/AMReX_GpuLaunchFunctsG.H
Src/Base/AMReX_GpuLaunchMacrosC.H
Src/Base/AMReX_GpuLaunchMacrosG.H
Src/Base/AMReX_GpuRange.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp
Tests/GPU/Test/main.cpp

commit fba880ff02f2d05f2a118d04099c8f3e779db1b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 6 13:18:39 2019 -0700

    reorganize launch macros and functions

Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuLaunch.cpp
Src/Base/AMReX_GpuLaunchMacrosC.H
Src/Base/AMReX_GpuLaunchMacrosG.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 23857740b2a6eb857fc26c90200b7d0c26058cb6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 6 12:19:19 2019 -0700

    update Range for hip

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuRange.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit e0fcbdbf6d519380e7fa3d108d84ff9108cbd2a5
Merge: e0e025828 ef6084e1b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jun 6 12:09:28 2019 -0700

    Merge pull request #495 from AMReX-Codes/mlcgfix
    
    fixed an error in the sxay function definition

commit ef6084e1b11bdfcc407260400c74893f5390446f
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Jun 6 12:46:49 2019 -0600

    fixed an error in the sxay function definition

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit a17b0ffd86fc66ad8d7d001c7c887dbc39a86359
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 6 11:19:07 2019 -0700

    hip: CudaMemory -> GpuMemory

Src/Base/AMReX_Box.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuMemory.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 01bdfa4e4342209e7684cb1fee3edcf155026c68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 6 10:28:46 2019 -0700

    update Elixir for hip

Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuElixir.H
Src/Base/AMReX_GpuElixir.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 4085a3101a059d813f0e2ff06f1a08663ff04ac0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 6 09:25:17 2019 -0700

    remove unused variable

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit e0e025828c3b8dc39f07855482f17012d7ebc241
Merge: 58ac0b987 614cc47f6
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jun 6 09:19:43 2019 -0700

    Merge pull request #489 from AMReX-Codes/nodeghostcells-pr
    
    Merge nodeghostcells into development

commit 614cc47f698ee0e7adc59ab648ba24b6a6a9b0e1
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Jun 5 16:03:38 2019 -0600

    changed ncomp in fine_mask to 1

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit d3838ce6bc6d06f8a6bbae058aea4e29a25b6edc
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Jun 5 15:54:10 2019 -0600

    addressed weiqun's comments

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_F.H

commit 1e62c8a14e2966ba19ae17b34df9ad843f40ce85
Merge: e5cac5b88 58ac0b987
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Jun 5 14:44:48 2019 -0600

    Merge branch 'development' into nodeghostcells-pr

commit 58ac0b98774a961d1977e074c052325431991120
Merge: 475a58732 e645f917d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 4 22:04:06 2019 -0700

    Merge branch 'hip' into development

commit 475a58732c25149a6316aa872f630cb28b3b9a71
Merge: 04faaca15 c825490f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 4 22:03:55 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit dee0e9b971361d7ad38b7f2342135104d61c9f03
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 4 18:11:02 2019 -0700

    CMake: add doc regarding exported targets

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit 343f3f6530b2c382dc3e9bfe494f149e26f50bd4
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 4 16:22:29 2019 -0700

    Add pinned std::vector allocator and Vector.

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaContainers.H

commit c825490f941dace5d18858654a4521c5cd08dbd3
Merge: c4c111456 606aed47e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jun 4 16:09:04 2019 -0700

    Merge pull request #494 from AMReX-Codes/init_redist_gpu
    
    Init redist gpu

commit 8658a786190a61b94f6e20b01d3483ead9c254d0
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 4 13:52:42 2019 -0700

    Updating graph tests for hip.

Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp
Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit 8204d86a0a7373ae9900446222da6187cbf91394
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 4 13:45:41 2019 -0700

    Adjust for hip merge.

Src/Base/AMReX_CudaGraph.H
Src/Base/AMReX_GpuDevice.cpp
Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp

commit 0907cf8fdab2b456ef5ea4066c2d55ba1f1fb454
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 4 13:21:28 2019 -0700

    Fix merge on GpuDevice

Src/Base/AMReX_GpuDevice.cpp

commit 6a7306828e088694896fbc9a8c9bc68f53bd467b
Merge: e68a37d3c e645f917d
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 4 13:15:30 2019 -0700

    Merge branch 'hip' into kngott/cudaGraphs

commit e68a37d3cf2d87155d033a8730a45132e1f44b83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 17:06:06 2019 -0700

    add AMREX_USE_GPU if ENABLE_CUDA

Tools/CMake/AMReX_Defines.cmake

commit 512f51f9ab5650d43b490eb3a9908b383208df3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 15:23:48 2019 -0700

    add runtime boolean parameter `amrex.fpe_abort_on_out_of_gpu_memory`
    to address Issue #485.

Src/Base/AMReX_Arena.cpp

commit dd3cc8e993ac40c11e83ff2207fd97457389c687
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Fri May 31 10:57:41 2019 -0700

    blueprint support: allow mpi tasks without mesh data

Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp

commit 53a706c0b8b93b1c21c1eb44c0b8d4c4fe600b9d
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Thu May 30 10:18:08 2019 -0600

    use BL_SINGLE_PRECISION_PARTICLES to select particle data type

Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H

commit 4f486dcc7d42f08c679b8c3c08248cee2f12ce84
Author: kngott <kngott@lbl.gov>
Date:   Tue Jun 4 11:23:06 2019 -0700

    [WIP]: currently breaks FB, working version in development -> test putting memcpy into cudaGraph.

Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaGraph.H
Tests/GPU/CudaGraphs/GraphWithMemcpy/GNUmakefile
Tests/GPU/CudaGraphs/GraphWithMemcpy/Make.package
Tests/GPU/CudaGraphs/GraphWithMemcpy/inputs_3d
Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp
Tests/GPU/CudaGraphs/GraphWithMemcpy/run.corigpu

commit e645f917dd88b591835fac01c9f32b497858e7a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 4 09:59:28 2019 -0700

    fix the use of numCudaStreams

Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp

commit bce3ad68608b402964f71b5576222885f93acd06
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 4 09:48:39 2019 -0700

    fix merge

Src/Base/AMReX_Arena.cpp

commit fcdef8cad5adef0ab91ceda24b7ec0da59d6f5d1
Merge: 6c4474412 04faaca15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 4 09:46:25 2019 -0700

    Merge branch 'development' into hip

commit 04faaca157d9f5311c07aa8fc7aa741a876a2754
Merge: 34cc6be5b c4c111456
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 4 09:38:58 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c4c11145640bbb50510b61dcf21814a0f7d74385
Merge: d90dcdfaf fceb7e626
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jun 4 09:36:27 2019 -0700

    Merge pull request #476 from AMReX-Codes/kngott/cudaGraphs
    
    [WIP] Adding CUDA graph support to FillBoundary

commit 606aed47eec35dbef069e154ebd43a17314eb635
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Tue Jun 4 09:30:31 2019 -0700

    Updated RedistributeMPI to use HostVector if AMREX_USE_CUDA=TRUE, fixed fortran indexing bug in particle test

Src/Particle/AMReX_ParticleContainerI.H
Tests/GPU/Particles/Redistribute/test_3d.F90

commit 317c0b001a96323a6472dd9703416e47befad499
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Thu May 23 05:40:48 2019 -0700

    Added HostVector to thrust::copy version of RedistributeMPI for the RedistributeCPU version

Src/Particle/AMReX_ParticleContainerI.H

commit 34cc6be5b055d43e42266278ab01ef7cd059983d
Merge: d90dcdfaf fceb7e626
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 17:23:35 2019 -0700

    Merge branch 'kngott/cudaGraphs' into development

commit 6c4474412a32cc5cae7bf32509d67545174da4bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 17:16:42 2019 -0700

    fix AMREX_HIP_OR_CUDA macro

Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp

commit d90dcdfaffb286ae9f17cb5fae4a372419252345
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 17:06:06 2019 -0700

    add AMREX_USE_GPU if ENABLE_CUDA

Tools/CMake/AMReX_Defines.cmake

commit df9808bb32daa487c5c63d93a6b47a4f95497c40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 17:06:06 2019 -0700

    add AMREX_USE_GPU if ENABLE_CUDA

Tools/CMake/AMReX_Defines.cmake

commit 4c7e477193d7cbccd092dd3ca82a8ef7ec84446e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 16:49:54 2019 -0700

    rename some Cuda* files to Gpu*

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaElixir.cpp
Src/Base/AMReX_CudaGraph.H
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuAsyncArray.H
Src/Base/AMReX_GpuAsyncFab.H
Src/Base/AMReX_GpuAsyncFab.cpp
Src/Base/AMReX_GpuAsyncFabImpl.H
Src/Base/AMReX_GpuAsyncFabImpl.cpp
Src/Base/AMReX_GpuDevice.H
Src/Base/AMReX_GpuDevice.cpp
Src/Base/AMReX_GpuUtility.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tools/F_scripts/write_cuda_headers.py

commit a87000ae21a18ee0d11c7e43c095a191178e2c94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 16:33:30 2019 -0700

    fix merge

Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaGraph.H

commit b3360971ea7c8a24e4ec9043fb76291ceb6b1c1e
Merge: 1ca21e17a fceb7e626
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 16:25:45 2019 -0700

    Merge branch 'kngott/cudaGraphs' into hip

commit 00c4f657b93ce94c729396f286fbd4102606720c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 15:23:48 2019 -0700

    add runtime boolean parameter `amrex.fpe_abort_on_out_of_gpu_memory`
    to address Issue #485.

Src/Base/AMReX_Arena.cpp

commit fceb7e6264878fbf7ec3c80b1e72b27a6ee758b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 12:59:06 2019 -0700

    make cuda graph opt-in

Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuControl.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 2e08dc482af397d7f44d55af76c467cbaca735fc
Merge: 91dbbd21d b372630d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 12:51:18 2019 -0700

    Merge branch 'development' into kngott/cudaGraphs

commit 91dbbd21d29aa5bcc98355d089cb7f8e6659d241
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 12:39:53 2019 -0700

    allow empty tags

Src/Base/AMReX_FabArrayCommI.H

commit 47e2cfcb27f8cff7472e308d9b429a7d4d679be7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 09:49:36 2019 -0700

    check __cplusplus instead gcc version. add constexpr

Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaGraph.H

commit 68ed0414fe43737e4e4273d9b9c9e71d12835f69
Merge: b372630d2 3e44dd633
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jun 3 09:20:59 2019 -0700

    Merge pull request #491 from Alpine-DAV/task/2019_05_blueprint_updates
    
    conduit blueprint integration updates

commit b372630d20d4f02db18f00ed9a123ca49c9bc970
Merge: f3a1a1b21 24a24023c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 07:49:02 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f3a1a1b2128fa7964935caa2fe18c0ab7f044778
Merge: f536ee205 ef3c8a97d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 3 07:47:35 2019 -0700

    Merge branch 'master' into development

commit f536ee20544c383133c14c46a7f688d4c58d735f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 2 09:16:51 2019 -0700

    fix merge

Src/AmrCore/AMReX_FluxReg_3D_C.H

commit 8b512382acafe7540cc549e57d59509424ddc5d9
Merge: 288df8082 4b5e6781e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 2 09:15:20 2019 -0700

    Merge branch 'weiqun/dev' into development

commit 24a24023c03769728b1e8034fefb699ae143d25b
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Jun 1 16:55:31 2019 -0700

    fix a memory deallocation bug

Src/Amr/AMReX_Amr.cpp

commit f819cdb9fb0f77fc460486e62c8483b8c5626e6d
Merge: c8216a869 69237b982
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Jun 1 15:44:05 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c8216a8699b8dcb91fd4e045001c980be603d938
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Jun 1 15:43:41 2019 -0700

    upcxx backend that survived a few production tests

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AsyncFillPatch.cpp
Src/AmrTask/rts_impls/mpi/Makefile
Src/AmrTask/rts_impls/mpi/PackageQueue.H
Src/AmrTask/rts_impls/mpi/PackageQueue.cpp
Src/AmrTask/rts_impls/mpi/Perilla.cpp
Src/AmrTask/rts_impls/mpi/PerillaConfig.H
Src/AmrTask/rts_impls/mpi/PerillaRts.H
Src/AmrTask/rts_impls/mpi/PerillaRts.cpp
Src/AmrTask/rts_impls/runtime_common/Perilla_common.cpp
Src/AmrTask/rts_impls/runtime_common/RGIter.cpp
Src/AmrTask/rts_impls/runtime_common/RegionGraph.H
Src/AmrTask/rts_impls/runtime_common/RegionGraph.cpp
Src/AmrTask/rts_impls/runtime_common/RegionQueue.H
Src/AmrTask/rts_impls/runtime_common/RegionQueue.cpp
Src/AmrTask/rts_impls/upcxx/Makefile
Src/AmrTask/rts_impls/upcxx/PackageQueue.H
Src/AmrTask/rts_impls/upcxx/PackageQueue.cpp
Src/AmrTask/rts_impls/upcxx/Perilla.H
Src/AmrTask/rts_impls/upcxx/Perilla.cpp
Src/AmrTask/rts_impls/upcxx/PerillaConfig.H
Src/AmrTask/rts_impls/upcxx/PerillaRts.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi.omp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_advance.cpp
Tools/GNUMake/Make.upcxx

commit 4b5e6781ebb234c1c443184d3c3995c69fe955a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 1 09:01:28 2019 -0700

    fix calls to interp and protect

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AsyncFillPatch.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp
Src/AmrTask/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_GpuControl.H
Src/EB/AMReX_EBInterpolater.H
Src/EB/AMReX_EBInterpolater.cpp

commit fd76d044f1217e276360798aaa4d894828ee7d2b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 1 08:15:07 2019 -0700

    add RunOn parameter to virtual Interpolater::interp

Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_Interpolater.cpp

commit 288df80820feb337e1764d6023983f2c46dc5d7b
Merge: 15f299ab3 b48912444
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 1 07:56:22 2019 -0700

    Merge branch 'weiqun/dev' into development

commit b489124447a5bbb6b9a5c0ebc06fc7fa0cd833d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 31 22:13:30 2019 -0700

    Add RunOn parameter to FluxRegister::FineAdd

Src/AmrCore/AMReX_FluxReg_1D_C.H
Src/AmrCore/AMReX_FluxReg_2D_C.H
Src/AmrCore/AMReX_FluxReg_3D_C.H
Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp

commit 15f299ab3091426d568edd36670c59fbdc71d187
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 31 22:13:30 2019 -0700

    Add RunOn parameter to FluxRegister::FineAdd

Src/AmrCore/AMReX_FluxReg_1D_C.H
Src/AmrCore/AMReX_FluxReg_2D_C.H
Src/AmrCore/AMReX_FluxReg_3D_C.H
Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp

commit 5d4ca8053cb653427e5a12625eb01a9071ddd5cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 31 15:36:00 2019 -0700

    add RunOn parameter to some YAFluxRegister functions and fix MLMG

Src/Base/AMReX_GpuControl.H
Src/Boundary/AMReX_YAFluxRegister.H
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/Boundary/AMReX_YAFluxRegister_1D_K.H
Src/Boundary/AMReX_YAFluxRegister_2D_K.H
Src/Boundary/AMReX_YAFluxRegister_3D_K.H
Src/EB/AMReX_EBFluxRegister.H
Src/EB/AMReX_EBFluxRegister.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp

commit d7a47b2c48c88fb063cdc35becb858b34b6b915b
Merge: ca721a542 929a6e691
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 31 13:53:08 2019 -0700

    Merge branch 'weiqun/attribute_weak' into development

commit ca721a542a998447477ee8c9383f2b9ff2757519
Merge: 69237b982 b1f2ff4c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 31 13:52:22 2019 -0700

    Merge branch 'weiqun/amrex' into development

commit ef3c8a97ded20c78b4f7178e6f41e4d82d432538
Merge: b33a70551 899631ce1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 31 13:50:55 2019 -0700

    Merge branch 'development'

commit 69237b982bd98db6d9e932d4417344bbcb2ff731
Merge: 899631ce1 1313eaca4
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri May 31 12:31:28 2019 -0700

    Merge pull request #492 from burlen/development
    
    fix some issues w SENSEI tutorials

commit 1313eaca4ee5b32da0ec8f5ee87d0e595c162377
Author: Burlen Loring <bloring@lbl.gov>
Date:   Fri May 31 12:06:56 2019 -0700

    clean up SENSEI AmrLevel tutorial
    
    Build & run with sensei by default and fix path to source code

Tutorials/SENSEI/Advection_AmrLevel/Exec/Make.Adv
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs

commit 20101167a580326a6bb0cfa360b6766db1eb6008
Author: Burlen Loring <bloring@lbl.gov>
Date:   Fri May 31 12:01:44 2019 -0700

    clean up SENSEI AmrCore tutorial
    
    Build & run with sensei by default and fix path to source code

Tutorials/SENSEI/Advection_AmrCore/Exec/Make.Adv
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/inputs

commit 2dabf2810d66cf4c69a3cdcbab884a1fc9d9185e
Author: Burlen Loring <bloring@lbl.gov>
Date:   Fri May 31 10:58:34 2019 -0700

    remove UniformVelocity from SENSEI AmrLevel tutorial
    
    Using SENSEI with amrex::Amr class is already covered in the
    SingleVortex tutorial.

Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/Make.package
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/inputs
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/probin

commit 899631ce1843b30fd0c77e184302e7bdf246b0ee
Author: kngott <kngott@lbl.gov>
Date:   Fri May 31 11:20:23 2019 -0700

    Fix check for mvapich vs. openmpi on CoriGPU.

Tools/GNUMake/sites/Make.nersc

commit c735da03b1f5cc68d741e443fd7027b06f70f8ca
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 31 11:01:23 2019 -0700

    test on particle_lvl_offset here, instead of dxi and pdxi

Src/Particle/AMReX_ParticleContainerI.H

commit 453f84d3e30e2fc77e75d1f8bf69745123a2da61
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 31 10:59:23 2019 -0700

    remove unused variables

Src/Particle/AMReX_ParticleContainerI.H

commit 3e44dd633413fb22dd91d4d1d3f0f0365c793aa0
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Fri May 31 10:57:41 2019 -0700

    blueprint support: allow mpi tasks without mesh data

Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp

commit be8e9b0937113824ad433581490dcb8d68900342
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 31 10:39:02 2019 -0700

    make this runtime assertion into a compile-time one

Src/Particle/AMReX_ParticleContainerI.H

commit b33a70551be30a41b05455f6c48f1ed6c3a05ecf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 31 08:04:29 2019 -0700

    update CHANGES

CHANGES

commit 1ca21e17aac6d0789666f7d23d471684e0a18a10
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 30 15:51:08 2019 -0700

    rename some Cuda* files to Gpu*

Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuAsyncArray.H
Src/Base/AMReX_GpuAsyncArray.cpp
Src/Base/AMReX_GpuUtility.H
Src/Base/AMReX_GpuUtility.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 1aad2d2c8d0b0ed5364f9170087dd86d945164e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 30 15:40:20 2019 -0700

    add AMREX_DEVICE_COMPILE macro and update CudaUtility for hip

Src/Base/AMReX_CudaAsyncFab.H
Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_CudaUtility.cpp
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_GpuControl.H
Src/Particle/AMReX_NeighborList.H

commit 81898b81371cb2c4a29cd8629b9c2512010a77e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 30 14:00:04 2019 -0700

    hip: update AsyncFab

Src/Base/AMReX_CudaAsyncFab.H
Src/Base/AMReX_CudaAsyncFab.cpp
Src/Base/AMReX_CudaAsyncFabImpl.H
Src/Base/AMReX_CudaAsyncFabImpl.cpp

commit a7efc0ed9dde2f7e8a22eb4bc124eb4b6173b360
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 30 13:31:23 2019 -0700

    hip: update BaseFab and allow __managed__ when cuda is backend

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_GpuQualifiers.H

commit bd6a81b4c44366184e8ade48f592eb28617da438
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 30 12:38:38 2019 -0700

    move some functions and classes to namespace amrex::Gpu. update Gpu::AsyncArray

Docs/sphinx_documentation/source/GPU.rst
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaAsyncArray.H
Src/Base/AMReX_CudaAsyncArray.cpp
Src/Base/AMReX_CudaAsyncFab.cpp
Src/Base/AMReX_CudaAsyncFabImpl.cpp
Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaElixir.cpp
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaUtility.cpp
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_MFIter.cpp
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Tests/GPU/Test/main.cpp
Tests/GPU/TestB/main.cpp
Tests/GPU/TestC/main.cpp
Tools/F_scripts/write_cuda_headers.py
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.cpp

commit fc0c5b5528bcbea53bd344335ea022ff8bfdd740
Merge: 97d59bb77 978cc240e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 30 15:17:13 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 97d59bb77c1870291c48b1e1408bf617932996b1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 30 15:16:49 2019 -0400

    need to call define on the particle tile when restarting and runtime soa components are in play

Src/Particle/AMReX_ParticleContainerI.H

commit e5cac5b881322fa304dfc464d600f7bc6abfa41f
Merge: bd5877962 978cc240e
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu May 30 11:44:27 2019 -0600

    Merge branch 'development' into nodeghostcells-pr

commit 1da833e9053c94a7be52ac50c9bff0de4a24833b
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Thu May 30 10:18:08 2019 -0600

    use BL_SINGLE_PRECISION_PARTICLES to select particle data type

Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H

commit a7fd7070eb7e556eb47c7f38f80ffe52e2fb799c
Author: kngott <kngott@lbl.gov>
Date:   Thu May 30 00:42:14 2019 -0700

    Seperate stopGraphRecording and setGraph.

Src/Base/AMReX_FabArrayCommI.H

commit 9d2bb614b0de8ae1d8a6ed835d9fe6bf3439ab6c
Author: kngott <kngott@lbl.gov>
Date:   Thu May 30 00:07:24 2019 -0700

    Change startRecord and stopRecord locations to work properly with Iter method.

Src/Base/AMReX_FabArrayCommI.H

commit b6121ada6f2ec09ccd5b70d8a43c7645e22700cc
Author: kngott <kngott@lbl.gov>
Date:   Wed May 29 23:20:16 2019 -0700

    Fix initialization list for CopyMemory.

Src/Base/AMReX_CudaGraph.H

commit 8dbcb505ca5c0c88e6ad3b045db51aa4ec924682
Author: kngott <kngott@lbl.gov>
Date:   Wed May 29 22:34:47 2019 -0700

    Add instantiate error check to debug mode.

Src/Base/AMReX_CudaDevice.cpp

commit eb37cc7f52ebdac3d033c80d4d39cb03d738fd62
Author: kngott <kngott@lbl.gov>
Date:   Wed May 29 22:32:37 2019 -0700

    DEBUG -> AMREX_DEBUG

Src/Base/AMReX_MFIter.cpp

commit ef112b4324d45ccfac8d1cca16a48a6db6f7c260
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 29 17:25:14 2019 -0700

    fix for cuda

Src/Base/AMReX_CudaDevice.H

commit 72bb15410611d3f6d28f2954dc7911a1a1cba669
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 29 17:22:16 2019 -0700

    add AMREX_HIP_OR_CUDA macro

Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_GpuControl.H

commit a305732e7c953e81687a50edb6894aac715781cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 29 16:51:44 2019 -0700

    hip: Device::Finalize()

Src/Base/AMReX_CudaDevice.cpp

commit 21a98e477ad0456919480412fb2640cfd42b3130
Merge: d89f895f0 978cc240e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 29 16:30:45 2019 -0700

    Merge branch 'development' into hip

commit bd58779627d9e1cdd288d45ee42f954d824a5b3d
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed May 29 17:28:42 2019 -0600

    added additional residual correction

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit b592e65a3414528209c9a1c0744fa6970531166f
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed May 29 17:27:05 2019 -0600

    implemented compatibility enum in mlmg - running unit tests

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 978cc240e1cb7272168ff66857dacc17bfd5567f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 29 16:14:38 2019 -0700

    MLNodeLaplacian: make normalization threshold a parameter and set the default to 1.e-10

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 52e0d0fbfd971b3f129c3506d4103df8162c770d
Merge: 577181c35 a4c45709e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 29 14:51:24 2019 -0700

    Merge branch 'algoim' into development

commit 577181c3588d069a2a9b546738a63feb4751c9d7
Merge: 534887c06 3b056f043
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 29 14:49:32 2019 -0700

    Merge branch 'algoim' into development

commit 534887c0610995b2e3957b5d2866c552f9760fb2
Merge: 8009e4e29 343159425
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 29 14:49:21 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d89f895f0e98a89b334827c662211644ad3a9efb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 07:10:29 2019 -0700

    hip: device and streams

Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaAsyncArray.H
Src/Base/AMReX_CudaAsyncFab.cpp
Src/Base/AMReX_CudaAsyncFabImpl.cpp
Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaElixir.cpp
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaUtility.cpp
Src/Base/AMReX_FabArrayUtility.H
Tools/F_scripts/write_cuda_headers.py

commit 3431594253b7683bc817f168de7712a31eb730ed
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 29 11:26:55 2019 -0700

    fix a couple of bugs in the dx != particle_dx version of deposit_cic

Src/Particle/AMReX_Particle_mod_K.H

commit 60a17fc8930cdceed04d7cc3a2f80f91b2f4dda1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 29 11:26:33 2019 -0700

    remove unused variables

Src/Particle/AMReX_ParticleContainerI.H

commit 427d989e2bb5f2197aba6bbf325d4d7997c5ca1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 29 10:50:56 2019 -0700

    executeGraph can be const

Src/Base/AMReX_CudaGraph.H
Src/Base/AMReX_FabArrayCommI.H

commit 3e205fca3cfb20273c8c3e793359d9deb083700e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 29 10:24:31 2019 -0700

    Real --> value_type

Src/Base/AMReX_FabArrayCommI.H

commit 118244e7016b795c3992da329ac53b1431b3fba3
Author: kngott <kngott@lbl.gov>
Date:   Tue May 28 17:25:59 2019 -0700

    Reorganize into a function-based test to allow easy reading and easy scale testing of different launch strategies.

Tests/GPU/FusedLaunches/main.cpp

commit b28efcd8cc0050fe1587d9cf95a2809750659e28
Author: kngott <kngott@lbl.gov>
Date:   Tue May 28 16:41:10 2019 -0700

    Store cudaStream as cudaStream_t.

Src/Base/AMReX_CudaDevice.cpp

commit 1819b8d5f13aedef7a63aed899e1655b7436c4fb
Merge: 211884633 e70fdbb63
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 28 15:49:19 2019 -0700

    Merge branch 'development' into pic_c++

commit a4c45709eab6cd4130d080ca289f8fa727f9c5c5
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue May 28 15:28:54 2019 -0700

    CMake: get rid of Algoim and Blitz (finally)

Src/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_InstallExternalLibs.cmake
Tools/CMake/AMReX_Options.cmake

commit 21188463386b342f5f7941811efcd6e0c1014d08
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 28 15:01:47 2019 -0700

    fix AMREX_SPACEDIM

Src/Particle/AMReX_Particle_mod_K.H

commit 11425edaafeabf94489aa2bfe90438c368c113af
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 28 15:01:26 2019 -0700

    correct function signature for amrex_interpolate_cic

Src/Particle/AMReX_ParticleContainerI.H

commit e70fdbb63067db3aee698ee5800de094e87fd3df
Merge: e6ddfdd80 8031759e0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue May 28 14:33:26 2019 -0700

    Merge pull request #486 from burlen/development
    
    fix SENSEI_INSITU build

commit 0d6ce3d5c42ed5f8ece1b2b3c2d91bc464e60478
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 28 14:22:04 2019 -0700

    implement these functions for AMREX_SPACEDIM != 3

Src/Particle/AMReX_Particle_mod_K.H

commit efb00a760abb89d05d6fa69b0c7ea2193bfb20eb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 28 14:21:47 2019 -0700

    Fix this test for AMREX_SPACEDIM != 3

Tests/Particles/AssignDensity/main.cpp

commit 474d62c5cfeeaeddf35c577749bfa7a487313810
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 28 14:02:00 2019 -0700

    add explicit GraphSafeGuard

Src/Base/AMReX_GpuControl.H

commit 8031759e02726945298f093a85de01cf2ddfd89b
Author: SENSEI SC18 VM <sensei@sensei-insitu.org>
Date:   Tue May 28 14:01:33 2019 -0700

    fix SENSEI_INSITU build

Tools/GNUMake/Make.defs

commit a108ccf37750b2b3affe3236c23cb218b3e42ee9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 28 13:58:42 2019 -0700

    tidy

Src/Base/AMReX_FabArrayCommI.H

commit 0b7ad307666c950d7c97ad5d4ff09db463e77aba
Merge: cabd6fd36 8009e4e29
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 28 13:53:34 2019 -0700

    Merge branch 'development' into kngott/cudaGraphs

commit cabd6fd362d7330b84a8756ecf9b0837b5098306
Merge: 525e9bf65 3f51a6e96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 28 13:42:02 2019 -0700

    Merge branch 'kngott/cudaGraphs' of github.com:AMReX-Codes/amrex into kngott/cudaGraphs

commit 83c3e75eebcaab074db4615de173d6b1ba66ed24
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 28 13:25:03 2019 -0700

    remove the OMP Deposition helper - this is done in BaseFab now

Src/Particle/AMReX_OMPDepositionHelper_nd.F90
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit df66628d0096af0a9fbc70e71b9f69a2cb2b0519
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 28 13:19:15 2019 -0700

    hardwired 1 -> ncomp

Src/Particle/AMReX_ParticleContainerI.H

commit f2211d1d6b637c92291c122e2c089c27b0b143de
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 28 13:05:30 2019 -0700

    remove now unused Fortran routines

Src/Particle/AMReX_Particle_mod_1d.F90
Src/Particle/AMReX_Particle_mod_2d.F90
Src/Particle/AMReX_Particle_mod_3d.F90
Src/Particle/AMReX_Particles_F.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 7c6adf6b7ab7d2826f5337d6dc8858d9459b4153
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 28 12:45:27 2019 -0700

    implement and use C++ versions of the particle deposition routines

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particle_mod_K.H
Src/Particle/AMReX_Particles.H

commit accf4622abe226f3b8a2e67587f76407db31382d
Merge: 981e2f1ea e6ddfdd80
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 28 10:19:49 2019 -0700

    Merge branch 'development' into pic_c++

commit 3b056f043f4a47dca21ec570bcab2b8d86642541
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 28 09:37:04 2019 -0700

    update node eb solver test

Tests/LinearSolvers/NodeEB/MyTest.cpp

commit 269e3cb2859c22a1be7973388a53e2999c4a9791
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 28 09:21:40 2019 -0700

    remove Src/Extern/Algoim and update documentation

Docs/sphinx_documentation/source/BuildingAMReX.rst
Src/Extern/Algoim/AMReX_algoim_integrals.H
Src/Extern/Algoim/AMReX_algoim_integrals.cpp
Src/Extern/Algoim/CMakeLists.txt
Src/Extern/Algoim/Make.package
Tests/Algoim/GNUmakefile
Tests/LinearSolvers/NodeEB/GNUmakefile
Tools/GNUMake/Make.defs
Tools/GNUMake/packages/Make.algoim

commit 8009e4e29661a3ad2894ff2b4d0990dc37316003
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 22:07:27 2019 -0700

    turn on omp for computing integrals using algoim

Src/EB/AMReX_algoim.cpp

commit 52ca58c3470c9b7d5f8e2ea3f9eab85f76647eea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 22:05:14 2019 -0700

    switch to new algoim in 3d nodal solver

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit e6ddfdd801b86e14af4b57f71050227b4fa39537
Merge: cd36da0fd 745c9e465
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 19:07:43 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cd36da0fd3eb4f9984dea3efd8c7c0982c0e5f88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 18:58:42 2019 -0700

    algoim: make it gpu ready

Src/EB/AMReX_algoim.cpp
Src/EB/AMReX_algoim_K.H

commit e115fb5356ad30a65623e6d66403abce67b48842
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 18:06:35 2019 -0700

    algoim: add gpu qualifier, constexpr and inline

Src/EB/AMReX_algoim_K.H
Tests/Algoim/main.cpp

commit d1d7fc7627b8eaf137fab36e5a709b92741239cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 17:53:45 2019 -0700

    algoim: replace std::bitset with our own bitwise operation

Src/EB/AMReX_algoim_K.H

commit 610ecd43c9d3d718bcf2896f3701df0dc7c8a54b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 17:19:16 2019 -0700

    algoim: use gpu friendly containers

Src/EB/AMReX_algoim_K.H

commit 5a45ebbb994394a56f2fea657868c54441921e1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 16:51:57 2019 -0700

    algoim: simplify BoundingBox

Src/EB/AMReX_algoim_K.H

commit d036829bfe713dba8613e22e73f44bd3ef6ff89b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 16:38:44 2019 -0700

    algoim: simplify Interval

Src/EB/AMReX_algoim_K.H

commit 2feb605023885c9d52829e38b3d46889d16d9071
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 16:33:07 2019 -0700

    algoim: use array instead of vector because the number of roots is at most 2

Src/EB/AMReX_algoim_K.H

commit dfdf5236e9b96cc427cf493eb72b9a98bdf7ea95
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 16:21:12 2019 -0700

    alogim: use fixed size array instead of vector because we know the maximal size it can get to.

Src/EB/AMReX_algoim_K.H

commit f68bf2214e3f559a5b57c9ee6ae5fdfdd82bcd2f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 12:37:41 2019 -0700

    set precision in algoim test

Tests/Algoim/main.cpp

commit c9d017a92cad98767255293c020a5cceeb9d01b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 12:07:19 2019 -0700

    test algoim performance

Tests/Algoim/main.cpp

commit b38e1e04078f7c55c773a3487bee7cff6c48024c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 11:36:45 2019 -0700

    update cmake to include algoim

Src/EB/AMReX_algoim.cpp
Src/EB/CMakeLists.txt
Src/EB/Make.package

commit 75096365fcabf6524a7240d865a01d0bd211e29c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 11:03:01 2019 -0700

    add algoim test

Src/EB/AMReX_algoim_K.H
Tests/Algoim/GNUmakefile
Tests/Algoim/Make.package
Tests/Algoim/main.cpp

commit 745c9e4653b2f7bf62ac7af685bffbcb9b5c7c57
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon May 27 10:56:51 2019 -0700

    add missing AMREX_D_TERM macros to fix SPACEDIM != 3

Src/Particle/AMReX_ParIterI.H

commit 0bf18c475a15bb25c9734c036f288935ec274ec9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 27 07:50:57 2019 -0700

    copy algoim to Src/EB and remove its dependency on blitz

Src/EB/AMReX_algoim.H
Src/EB/AMReX_algoim.cpp
Src/EB/AMReX_algoim_K.H
Src/EB/Make.package

commit 981e2f1ea29976ba61c25f0c82f31a15ec2d4a47
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 24 14:18:51 2019 -0700

    start C++ implementations of amrex pic routines

Src/Particle/AMReX_Particle_mod_K.H

commit 72e2dac3b6e1cbfc9449090457bc5ea53b413854
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri May 24 14:16:13 2019 -0700

    Doc typo.

Docs/sphinx_documentation/source/GPU.rst

commit 25a07c957b7d018c6cd42b5c3ac840656354ad35
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 24 13:43:21 2019 -0700

    add missing stream sync

Src/Particle/AMReX_ParIterI.H

commit 8bc1cb1005e400630aa0a618dede48bb4971e544
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 24 13:19:33 2019 -0700

    amrex_build_nl also doesn't exist any more

Src/Particle/AMReX_Particles_F.H

commit a108a25e78bd7a44b2a7dbee93ced00d615cde91
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 24 13:18:53 2019 -0700

    remove now un-used Fortran routines from the particle code

Src/Particle/AMReX_Particle_mod_1d.F90
Src/Particle/AMReX_Particle_mod_2d.F90
Src/Particle/AMReX_Particle_mod_3d.F90
Src/Particle/AMReX_Particles_F.H

commit 4eaa4dd0716a113e5fd53d5629860d548e093c0f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 24 13:18:32 2019 -0700

    don't need these functors any more

Src/Particle/AMReX_Functors.H

commit 079575170d3c531f325735f278d989d28a20e1a4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 24 13:18:07 2019 -0700

    switch to C++ in get/set particle position

Src/Particle/AMReX_ParIterI.H

commit e3840f9732d67dd744eb9c59b0fa8dd00a9d6b95
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 23 17:07:27 2019 -0700

    AMREX_CUDA_MAX_THREADS -> AMREX_GPU_MAX_THREADS

Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_fort_mod.F90
Tools/CMake/AMReX_Defines.cmake
Tools/GNUMake/Make.defs

commit 0b6d91ee3079344d5f1a6359b4250abd00323b1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 23 17:02:29 2019 -0700

    hip: error checking

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_CudaAsyncFab.cpp
Src/Base/AMReX_CudaAsyncFabImpl.cpp
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaElixir.cpp
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuError.H

commit f1429079d50b27f0770753a8c17dd89fac0bb0e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 23 15:25:39 2019 -0700

    hip: inLaunchRegion

Src/Base/AMReX_CudaAsyncArray.H
Src/Base/AMReX_CudaAsyncFab.cpp
Src/Base/AMReX_CudaAsyncFabImpl.cpp
Src/Base/AMReX_CudaContainers.H
Src/Base/AMReX_CudaElixir.cpp
Src/Base/AMReX_CudaMemory.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuControl.cpp

commit 68db8f708636d29b441b532efc0d5cd6355383b9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 23 15:13:45 2019 -0700

    fix a few more warnings

Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_AmrParticles.H
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90

commit 3f51a6e960e462e4fe92c7cde27a6fe532920910
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu May 23 17:51:14 2019 -0400

    Adjustments for older GNU versions.

Src/Base/AMReX_CudaGraph.H

commit 0df1e6b3b9d23443bec287741e57eeaba7eb5f1b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu May 23 17:50:15 2019 -0400

    Add check for cuda version due to API change.

Src/Base/AMReX_CudaDevice.cpp

commit 4b390f5b687de00db5063a42e9236d0e6f5160b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 23 14:47:30 2019 -0700

    make: add HIP_PLATFORM

Src/Base/AMReX_GpuQualifiers.H
Tools/GNUMake/Make.defs
Tools/GNUMake/comps/hip.mak

commit ee1537750c1c033f1fb83d909893c013a480bab3
Merge: 5843e73fe 16ac0c078
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu May 23 16:59:44 2019 -0400

    Merge branch 'development' into kngott/cudaGraphs

commit 319cecd5a42a03e60b42bed78052037e71fef453
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 23 13:56:11 2019 -0700

    fixing some more parameter shadowing / unused variable warnings

Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_filcc_mod.F90
Src/Boundary/AMReX_BndryRegister.cpp
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 16ac0c07867b8a75637896a10f43f41e9682e4ea
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 23 13:21:32 2019 -0700

    fix some parameter shadowing warnings

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H

commit b8739674a808c11de6ad4c72a4f506a085971389
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 23 13:06:43 2019 -0700

    start hip with nvcc as backend

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/hip.mak

commit de2596e3dd3082f65bb18806f9a25917bdb93fca
Merge: bfea077f5 eb7155121
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 23 14:24:14 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit bfea077f53304a55e1a493ccc0779f97010b636f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 23 14:23:37 2019 -0400

    correct this size of these vectors to account for possibly runtime-added components

Src/Particle/AMReX_ParticleContainerI.H

commit 175f4792bbf8184030d6f9b5e8bdb5a3ff05b666
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 23 14:03:26 2019 -0400

    add assertion to catch problems earlier

Src/Particle/AMReX_ParticleContainerI.H

commit 3fe970489f97233ac4b8c8d765ab0a643d6d52f8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 23 13:58:54 2019 -0400

    fix size of comp_name and boolean write arrays

Src/Particle/AMReX_ParticleContainerI.H

commit eb7155121e5c60ece6bbcbacd717feea879dd6a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 23 10:48:22 2019 -0700

    Tensor solver: fix periodic bc

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit d3f7e55e2e43a0435ede13123d199c00427a51d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 22 16:15:03 2019 -0700

    remove explicit from ErrorFunc and ErrorFunc2 because codes rely on implicit conversion

Src/AmrCore/AMReX_ErrorList.H

commit 5943432cf2f7c3274b83a80866914bef00c6e0a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 22 16:10:21 2019 -0700

    MLNodeLap: tweak normalization parameter to reduce the number of bicg iterations

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 2d8c923ecbe4fc2a336fd7845f4982e99c2f4921
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 22 16:07:56 2019 -0700

    Allow implicit conversion from int to BoundCond.

Src/Boundary/AMReX_BoundCond.H

commit fe80097cb63522ec8958ff1beda8ddcfe350fdf5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 22 15:24:50 2019 -0700

    fix a bunch of warnings by cppcheck mostly on explicit ctor

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AuxBoundaryData.cpp
Src/AmrCore/AMReX_AmrParGDB.H
Src/AmrCore/AMReX_Cluster.H
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_ErrorList.H
Src/AmrCore/AMReX_Interpolater.H
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BoxIterator.H
Src/Base/AMReX_CudaAsyncArray.H
Src/Base/AMReX_CudaAsyncFab.H
Src/Base/AMReX_CudaMemory.H
Src/Base/AMReX_CudaRange.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_Print.H
Src/Base/AMReX_RealVect.H
Src/Base/AMReX_TinyProfiler.H
Src/Boundary/AMReX_BoundCond.H
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBInterpolater.H
Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp

commit 37d9ebb3267274f5af67c0482282744e655235ef
Author: kngott <kngott@lbl.gov>
Date:   Wed May 22 14:49:40 2019 -0700

    Updated fused Test.

Tests/GPU/FusedLaunches/main.cpp

commit 3de50d9bcf72dc358b8a08adfdae632456f97af4
Author: kngott <kngott@lbl.gov>
Date:   Wed May 22 14:49:30 2019 -0700

    Function to get num streams from Device.

Src/Base/AMReX_CudaDevice.H

commit 599cdb8dda46c336ba10ffd9749c0f42f74261a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 22 14:20:38 2019 -0700

    initialize values so that static analysis tools don't complain

Src/AmrCore/AMReX_AmrCore.cpp

commit dce3a0eb00904e9ca764715f73caa69e21b81e9b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 22 13:51:43 2019 -0700

    fix out of bound error for 1d

Src/Base/AMReX_Geometry.cpp

commit 63d37bfba6597e3487f16e65c1331ac67c1ced64
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 22 14:42:09 2019 -0400

    update nvml path on summit

Tools/GNUMake/sites/Make.olcf

commit b1f2ff4c44dcd6585a9382868ba9ec894a765b8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 21 19:20:37 2019 -0700

    FPinfo: pass the correct Geometry

Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_Geometry.H
Src/EB/AMReX_EB2.H
Src/EB/AMReX_EB2_IndexSpaceI.H

commit 1bccc04eb73175976b838bbde720b2b71adb8c66
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 21 16:44:04 2019 -0700

    Geometry: functions to reset the default

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp

commit 7a0738eacf23fdf4cd8b35136d5acc0a9fe22428
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 21 16:33:47 2019 -0700

    Geometry default ctor: copy from AMReX stack if we can

Src/Base/AMReX.H
Src/Base/AMReX_Geometry.cpp

commit 739520def4bbc459791fdfb3fcf943176cc49913
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 21 16:08:00 2019 -0700

    fix periodicity flags after Amr restart

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp

commit e7a7734850757f2d8ed71498bcf63b3fa986b19c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 21 13:44:50 2019 -0700

    add periodic to Geometry I/O

Src/Base/AMReX_Geometry.cpp

commit 26e12516bfe661ee68cf59314e3b96e2b15b38e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 21 13:43:59 2019 -0700

    add IntVector ctor taking Array as argument

Src/Base/AMReX_IntVect.H

commit 12da1ac4b9eb366be289d15d0d29967a090b41c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 21 13:43:28 2019 -0700

    tidy

Src/Base/AMReX_CoordSys.cpp

commit ee5e7bfcff8a998e31f388fea9562f6a78b3ed89
Author: kngott <kngott@lbl.gov>
Date:   Tue May 21 12:38:18 2019 -0700

    Fused Launches Test, first draft.

Tests/GPU/FusedLaunches/GNUmakefile
Tests/GPU/FusedLaunches/Make.package
Tests/GPU/FusedLaunches/inputs_3d
Tests/GPU/FusedLaunches/main.cpp
Tests/GPU/FusedLaunches/run.corigpu

commit 02c15dc1ba8f92b4d05256abfbfada9f5d8af1d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 21 09:03:52 2019 -0700

    fix a typo in documentation

Docs/sphinx_documentation/source/Basics.rst

commit c0079c513234e20c7b22f61d915e35b438ec241b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 20 16:47:56 2019 -0700

    DefaultGeometry: use the one at the top of AMReX stack.

Src/Base/AMReX_Geometry.H

commit 3d681c08792d3130095c413684cb2e1bf455081c
Merge: ba1943af8 ab6281555
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 20 16:17:21 2019 -0700

    Merge branch 'development' into weiqun/amrex

commit ab62815554b32e969ca3cf0fbb12592319fcb027
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 20 16:16:32 2019 -0700

    added DefaultGeometry function

Src/Base/AMReX_Geometry.H

commit ba1943af8b6cd0d7e8d22a337f480638ca5dd7c5
Merge: 36c664a20 6565e29f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 20 15:53:40 2019 -0700

    Merge branch 'development' into weiqun/amrex

commit 6565e29f1488b3b2dda2e220f96b259cbeee26fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 20 15:40:57 2019 -0700

    MLEBABecLap: fix index bug

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 36c664a202e9cb0aca3fc8fc8000f0c315c1d385
Merge: 4e1ed235c da7e7b8c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 20 15:26:51 2019 -0700

    Merge branch 'development' into weiqun/amrex

commit da7e7b8c9bc0efe108511d04cad2b2c128e994e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 20 13:30:58 2019 -0700

    added some geometry functions to help migration

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp
Src/Base/AMReX_Geometry.H

commit 4e1ed235cc85817bd42f7f04e1d70a02ecabfd70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 20 12:16:35 2019 -0700

    fix an old tutorial

OldTutorials/DataServicesTest0/DataServicesTest0.cpp

commit 9d68de498c403ebab36cc9c4005417076f48737d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 20 11:26:53 2019 -0700

    Geometry: fix tests and tutorials

Docs/sphinx_documentation/source/Basics.rst
Tests/LinearSolvers/CellEB/MyTest.cpp
Tests/LinearSolvers/CellEB2/MyTest.cpp
Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp
Tests/LinearSolvers/EBflux_grad/MyTest.cpp
Tests/LinearSolvers/NodeEB/MyTest.cpp
Tools/C_util/WritePlotFile.cpp
Tutorials/GPU/EBCNS/Source/CNS_init_eb2.cpp
Tutorials/GPU/EBCNS/Source/CNS_io.cpp
Tutorials/SENSEI/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit 5843e73fee89ac1595ed14314781f78af4354c96
Author: kngott <kngott@lbl.gov>
Date:   Mon May 20 11:08:42 2019 -0700

    Clean up copy with graphs test.

Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit b2ad8c68045b9f6510f8051adcb9ade640b4a6c6
Merge: f73135f74 0a08d83f7
Author: mic84 <mrosso@lbl.gov>
Date:   Mon May 20 10:59:36 2019 -0700

    Merge pull request #474 from maikel/feature/CMake/require_MPI_C_not_CXX
    
    [CMake] Require only C bindings to MPI

commit 3789156b2c4206cf9ed2c4976734295e56c05203
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 20 10:36:34 2019 -0700

    remove apple crap

Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/._Exec
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/._README
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/._Source
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/._Make.Adv
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/._SingleVortex
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/._UniformVelocity
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._face_velocity_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._inputs
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._probin
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._inputs
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._probdata.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._probin
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv.H
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._AdvBld.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv_F.H
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv_advance.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv_dt.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv_io.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv_setup.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Src_2d
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Src_3d
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Src_nd
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._main.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_2d/._Adv_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_2d/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_2d/._compute_flux_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_2d/._slope_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/._Adv_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/._compute_flux_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/._slope_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._Adv_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._Tagging_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._tagging_params.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/._Exec
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/._README
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/._Source
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/._Make.Adv
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/._SingleVortex
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/._UniformVelocity
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._face_velocity_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._probin
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._probdata.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._probin
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._AdvBld.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_F.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_advance.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_dt.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_io.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_setup.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Src_2d
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Src_3d
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Src_nd
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._main.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._Adv_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._compute_flux_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._slope_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._Adv_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._compute_flux_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._slope_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._Adv_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._Tagging_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._tagging_params.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/._Exec
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/._README
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/._Source
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/._Make.Adv
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/._SingleVortex
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/._UniformVelocity
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._face_velocity_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._probin
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._probdata.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._probin
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._AdvBld.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv_F.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv_advance.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv_dt.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv_io.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv_setup.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Src_2d
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Src_3d
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Src_nd
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._main.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/._Adv_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/._compute_flux_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/._slope_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._Adv_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._compute_flux_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._slope_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._Adv_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._Tagging_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._tagging_params.f90
Src/AmrTask/tutorials/MiniApps/HeatEquation/.DS_Store

commit c18d28b527a057953c61eb15975e4e6acdb28535
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 20 10:33:05 2019 -0700

    Geometry: update AmrTask

Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv_io.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_io.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_io.cpp
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Src/AmrTask/tutorials/MiniApps/HeatEquation/physbc.cpp

commit ec0fa51b4e110a9e4ec3e151a8dd2cb3df513550
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 20 10:22:10 2019 -0700

    Geometry: update EB

Src/EB/AMReX_EB2_Level.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_init_eb2.cpp
Tutorials/EB/CNS/Source/CNS_io.cpp
Tutorials/EB/CNS/Source/CNS_setup.cpp

commit f73135f7443e5c0da2f24dc4a8c57dcfb1dd4857
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 20 09:55:07 2019 -0700

    MLEBTensorOp: forgot to set scalars

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit 14a17354c64fcd7f1f8990fa03dd2d8674d54db4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 19 21:43:27 2019 -0700

    Geometry: update Particle

Src/Particle/AMReX_ParticleContainerI.H

commit 2b8ddb67d961d52ede9d1cd563b8769e49143baf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 19 21:33:43 2019 -0700

    Geometry: update Amr

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit 2aa60332fbc4817ee9c7aca33ea581050aa1cbdd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 19 18:59:59 2019 -0700

    Geometry: put the first Geometry object to the top of AMReX stack and use arguments passed in whenever available.  AmrMesh: repsect constructor parameters when building Geometry

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp
Src/Base/AMReX_Geometry.cpp

commit ac79021b80cabded2fca11043999345e3e6763b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 19 17:16:45 2019 -0700

    Geometry::define: fix comparison

Src/Base/AMReX_Geometry.cpp

commit 5eb6f851bcfeef0fe219484bb73d35298cd1aed1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 19 14:34:40 2019 -0700

    add scalars to Tensor solver

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit 8f78df8f979e4857c43fb38d426203b57486971b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 19 13:59:24 2019 -0700

    Geometry: update AmrCore

Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/Base/AMReX_Geometry.H

commit 01081da0482f8e8f802477fe7f1201e541382438
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 19 12:13:55 2019 -0700

    Geometry: update linear solver

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit cf23b20c0d5601cdca2d069439c719971e006687
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 19 11:41:10 2019 -0700

    fix comments in inputs

Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs_2d
Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs_3d
Tutorials/Basic/HeatEquation_EX3_C/Exec/inputs_2d
Tutorials/Basic/HeatEquation_EX3_C/Exec/inputs_3d

commit e0edc4378a31f9d7f3ca09017549a441339aa2eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 19 11:34:06 2019 -0700

    Geometry: update F_Interfaces

Src/F_Interfaces/Base/AMReX_geometry_fi.cpp
Src/F_Interfaces/Octree/AMReX_octree_fi.cpp

commit f94cb4563a3701481e05febc1b50a30970b63d57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 19 10:27:21 2019 -0700

    removed static data from Geometry and updated Base

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PlotFileUtil.cpp

commit b808fad3cc215667a5175826f9ca0388bbc1a928
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 18 15:27:51 2019 -0700

    WIP

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp

commit 51b2c6a287d9e6ca316d1af55e51fdd9b3658775
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 18 14:36:38 2019 -0700

    AMReX stack

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp

commit b377f1b187575b31aa79617ab39a7c01e3976b49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 18 09:25:36 2019 -0700

    EB2::IndexSpace: make sure it's safe to push pointers that are already owned by the stack.

Src/EB/AMReX_EB2.H
Src/EB/AMReX_EB2.cpp

commit d18ee0c635c775b67abd57e7fc65ee61a8c06c43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 17 16:57:17 2019 -0700

    MLMG: if the solution multifab has ghost cells, set them to zero, otherwise uninitialized values might get used.

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 3c308ce0fa21afd85b80e653199bb9487bc5c22c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 17 14:50:36 2019 -0700

    Nodal Poisson tutorial: multi-level

Src/Base/AMReX_PhysBCFunct.H
Tutorials/LinearSolvers/NodalPoisson/Make.package
Tutorials/LinearSolvers/NodalPoisson/MyTest.H
Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp
Tutorials/LinearSolvers/NodalPoisson/MyTest_F.H
Tutorials/LinearSolvers/NodalPoisson/init_prob.F90

commit a71415bbf9a3f13ab4643f8f7c2c58ee51ef3000
Author: kngott <kngott@lbl.gov>
Date:   Fri May 17 14:12:35 2019 -0700

    Small fix.

Src/Base/AMReX_CudaDevice.cpp

commit 9d006b6b531f6d423a49ad972655cc99b62da8e5
Author: kngott <kngott@lbl.gov>
Date:   Fri May 17 14:10:03 2019 -0700

    Update BuildingGraphs for easier reading.

Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp

commit 29e546d0a42f183224bf9ac16c67a1d2c514114b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri May 17 09:50:22 2019 -0700

    (more) cleanup only; make macros more readable/distinguishable from each other

Src/Base/AMReX_ArrayLim.H

commit 250e0653b3cb4bf5848f06baf7ee0f3c23fad1d6
Merge: b8cac2bff ca5bcfabe
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri May 17 09:48:39 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit b8cac2bff9e12bb8cfb3284e5ee354d9af2b39f2
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri May 17 09:48:15 2019 -0700

    cleanup only; make macros more readable/distinguishable from each other

Src/Base/AMReX_ArrayLim.H

commit ca5bcfabef01039e93bff8c985da05261d05fa49
Merge: e15561a02 163d44b08
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 16 21:03:05 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit e15561a0236cd10cf2fe468da9c475271b85e71d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 16 20:47:53 2019 -0400

    remove debug print

Src/Particle/AMReX_ParIterI.H

commit 4ccf376f20186fdbdac5d4af3edc93ab916e00d4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 16 20:34:16 2019 -0400

    bug fix for set particle position, which wasn't properly copying the particles ids

Src/Particle/AMReX_Functors.H
Src/Particle/AMReX_ParIterI.H

commit 1198c9b3a444722ff750ed0cf2ee0cab6e8801ec
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 16 20:33:06 2019 -0400

    format fix

Src/Particle/AMReX_ParticleTile.H

commit d3ffa9166b0dc92935437b366a132b6ec7db29f6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 16 20:32:51 2019 -0400

    format fix

Src/Particle/AMReX_StructOfArrays.H

commit 163d44b08f64673b6c3b96c63175428d0c11aaa5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 16 17:17:11 2019 -0700

    EBTensor test: convergence test results

Tests/LinearSolvers/EBTensor/results.org

commit 8991789213f8c43cce328a0ff5a92a1e4cc14d86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 16 16:42:29 2019 -0700

    MLEBTensor: fix bug

Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 912ed5d8c72eaf87f1080c4ca49cb74d5305a521
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 16 14:58:22 2019 -0700

    EBTensorOp: fix bug

Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit a3f4c71c4bcfc4cde9be9bf61053b1176fce6172
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 16 14:55:24 2019 -0700

    EBTensor test

Src/EB/AMReX_EBFabFactory.H
Tests/LinearSolvers/EBTensor/GNUmakefile
Tests/LinearSolvers/EBTensor/Make.package
Tests/LinearSolvers/EBTensor/MyTest.H
Tests/LinearSolvers/EBTensor/MyTest.cpp
Tests/LinearSolvers/EBTensor/MyTestPlotfile.cpp
Tests/LinearSolvers/EBTensor/MyTest_K.H
Tests/LinearSolvers/EBTensor/inputs
Tests/LinearSolvers/EBTensor/main.cpp

commit 525e9bf651fe634161f924b18487c26cdf573625
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 16 16:42:29 2019 -0700

    MLEBTensor: fix bug

Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 003436a9f5a7ceadd16ca116b542a470d482bc9b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 16 14:58:22 2019 -0700

    EBTensorOp: fix bug

Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit bb6b5e9c45892458571c0a527f5773f453ca0b00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 16 14:55:24 2019 -0700

    EBTensor test

Src/EB/AMReX_EBFabFactory.H
Tests/LinearSolvers/EBTensor/GNUmakefile
Tests/LinearSolvers/EBTensor/Make.package
Tests/LinearSolvers/EBTensor/MyTest.H
Tests/LinearSolvers/EBTensor/MyTest.cpp
Tests/LinearSolvers/EBTensor/MyTestPlotfile.cpp
Tests/LinearSolvers/EBTensor/MyTest_K.H
Tests/LinearSolvers/EBTensor/inputs
Tests/LinearSolvers/EBTensor/main.cpp

commit 9c636cf2d9c3985357dd13b73b83115fec17bfcd
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu May 16 13:05:06 2019 -0600

    fixes error where solution only converges in mlmg with verbosity >= 0 - need a better solution

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 5c4964ee4619f440e0784b8a526b8e4b4e0383d5
Author: kngott <kngott@lbl.gov>
Date:   Wed May 15 23:49:14 2019 -0700

    Additional graph fixing.

Src/Base/AMReX_CudaDevice.cpp

commit 159168c32518f09ddc0c5f4c6ffde97e21d3df30
Author: kngott <kngott@lbl.gov>
Date:   Wed May 15 20:51:25 2019 -0700

    Add cudaGraph and cudaGraphExec destroy calls.

Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaGraph.H

commit 8674d16021d7788e79d5386824a71d61546dc3ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 15 14:59:37 2019 -0700

    rm setGraphRegion call from linear solver tutorial

Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp

commit 828f0a76f8c623bce7d6d21476825c248f188851
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 15 14:59:11 2019 -0700

    add GraphSafeGuard

Src/Base/AMReX_GpuControl.H

commit f440ead98c4038bf48e1bb1f8e8d556b3e703208
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 15 14:51:44 2019 -0700

    add AMReX_CudaGraph.H to cmake

Src/Base/CMakeLists.txt

commit df1826963afc3ff693864fbe217f1822f5de30f1
Merge: c91ee3745 8fe800d00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 15 14:48:04 2019 -0700

    Merge branch 'development' into kngott/cudaGraphs

commit 8fe800d00c4117d49a1f89b60a34470ff611417e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 15 11:04:45 2019 -0700

    MLEBTensor: fix bug

Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 3efe7f91cd1d5419e662b0c37a6a28f4fc19a2c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 14 16:33:23 2019 -0700

    EB_average_down_boundaries: fix for multi-component

Src/EB/AMReX_EBMultiFabUtil.cpp

commit c91ee3745111a77264d12b79c285332212d88340
Author: kngott <kngott@lbl.gov>
Date:   Tue May 14 15:33:18 2019 -0700

    Tweak to be more consistent with non-graphed code.

Src/Base/AMReX_FabArrayCommI.H

commit 8ef9b58d79a8243e37fce147d052505e03281b4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 14 13:35:49 2019 -0700

    MLEBTensor: fix sign

Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 4d888e79341d4741bcdcf65ae3ad3d99c620a13e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 14 12:45:55 2019 -0700

    Tensor solver: finish the coarsening of bulk viscosity

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 4d8e0ed9ff18a81a3c8209b164cf9860c7820f93
Author: atmyers <atmyers2@gmail.com>
Date:   Mon May 13 17:02:12 2019 -0700

    Make OK and Redistribute respect the launch region flag.

Src/Particle/AMReX_ParticleContainerI.H

commit f14a00c9e40e5ea61fdaa62ebf93e3a168a7d037
Author: kngott <kngott@lbl.gov>
Date:   Mon May 13 15:26:39 2019 -0700

    Fix GraphBoundary test error check to include user-specified number of components and ghost cells.

Tests/GPU/CudaGraphs/GraphBoundary/main.cpp

commit 82ec2e7987cbdfbb74be7914c40fab1dc6ad2784
Author: kngott <kngott@lbl.gov>
Date:   Mon May 13 15:26:03 2019 -0700

    Cleanup in Building test.

Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp

commit bbb1768ef679e2a3e0ece2e05d740490793e1b9c
Merge: 5c4ef4f13 e954997b5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon May 13 15:45:29 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5c4ef4f13d129e829695c06213fbf6ab1730f76f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon May 13 15:45:14 2019 -0400

    these define calls are needed when using the runtime soa capability on the GPU

Src/Particle/AMReX_ParticleContainerI.H

commit e954997b5c7768eac063f5f6b175653793d43706
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 13 12:03:31 2019 -0700

    Noal RAP: don't renormalize if the diagonal component is too small compared to the global maximum

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit a4c7ab982efb6ac3f85965df383634d3f1b9a907
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 13 09:56:23 2019 -0700

    MLEBTensorOp: fix EB flux

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 761869bce01b4eb4b29c9c200d1419f401cecfda
Merge: d31b3fa85 d50bb8520
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon May 13 09:55:01 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit d31b3fa85fb375883b6d32b33c3f2eccc4dc4908
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon May 13 09:54:32 2019 -0700

    Set USE_MPI = FALSE in GNUMakefile since this version of diffmultifab
    only works in serial

Tools/C_util/DiffMultiFab/GNUmakefile

commit d50bb85205d633f2338e2f3fee59832416375a3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 13 09:20:08 2019 -0700

    Edison is gone

Src/Base/AMReX_Machine.cpp
Tests/HDF5Benchmark/GNUmakefile
Tests/Slice/GNUmakefile
Tools/CMake/AMReX_Machines.cmake
Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.nersc

commit 5d47e2be23105075c2314bd29e8cce48d43c85ad
Merge: 9dbeb3804 26bd9bb8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 12 12:45:51 2019 -0700

    Merge branch 'master' into development

commit 26bd9bb8cfa50057b00644313406def720e0ddf6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 12 12:45:23 2019 -0700

    add citation to README.md

README.md

commit 9dbeb38046895f9da8c2077cf3c28f3c5e48a3e4
Merge: 349338589 9814f9204
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 12 10:47:41 2019 -0700

    Merge branch 'master' into development

commit 9814f92043cc6960b4b072d63698e6f678c04b48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 12 10:40:19 2019 -0700

    add JOSS status badge

README.md

commit b8ed63a64da40dc9562d7bdb4ca84d7680b583d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 12 08:37:51 2019 -0700

    fix IAMR DOI

paper/paper.bib

commit 1aca4ebd695c3158bccb16f7673019710f8ef88a
Merge: f9cc19632 d0aa7c819
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun May 12 07:54:25 2019 -0700

    Merge pull request #481 from kyleniemeyer/patch-4
    
    Update paper.bib

commit d0aa7c819ceb1d4864b239839b6358d4feccc130
Author: Kyle Niemeyer <kyle.niemeyer@gmail.com>
Date:   Sun May 12 00:41:03 2019 -0700

    Update paper.bib

paper/paper.bib

commit f9cc19632ae12087cddc8269e6b283ac17a3aeb0
Merge: ed18c1f0d 16a24db43
Author: asalmgren <asalmgren@lbl.gov>
Date:   Sat May 11 20:59:53 2019 -0700

    Merge pull request #480 from kyleniemeyer/patch-3
    
    Update paper.bib

commit ed18c1f0dadc44b13a30350ee1b442c33ad5279c
Merge: 92a53bda9 070eaba1b
Author: asalmgren <asalmgren@lbl.gov>
Date:   Sat May 11 20:55:25 2019 -0700

    Merge pull request #479 from kyleniemeyer/patch-2
    
    Fixes case of multiple references in paper

commit 16a24db433dc41e869c23da03ef4c12cd001683a
Author: Kyle Niemeyer <kyle.niemeyer@gmail.com>
Date:   Sat May 11 20:51:33 2019 -0700

    Update paper.bib

paper/paper.bib

commit 070eaba1b430149802cecc084f541da96ef7094f
Author: Kyle Niemeyer <kyle.niemeyer@gmail.com>
Date:   Sat May 11 20:43:01 2019 -0700

    Fixes case of multiple references in paper

paper/paper.md

commit 92a53bda9c1c236520e8ef60d1ea7883c98014b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 11 19:15:22 2019 -0700

    paper: minor changes

paper/paper.md

commit 178a691a54cd08506c4a531bcdd61e61769c8c6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 11 18:52:48 2019 -0700

    spell out JCP

paper/paper.bib

commit 1b9e09bbc7f2cb5e67c01b7ffdd118cf731be6d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 11 18:48:51 2019 -0700

    Fix paper.bib

paper/paper.bib
paper/paper.md

commit 38ba904d77fe9e2186f2cba9013f060e0b71f8a5
Merge: f8e92b80f 39a198738
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 11 18:41:59 2019 -0700

    Merge branch 'master' of github.com:AMReX-Codes/amrex

commit f8e92b80f56e867261ba4666e5e38654330ec4ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 11 18:41:48 2019 -0700

    Fix paper.bib

paper/paper.bib

commit 39a19873838dcbdbfbca185ab44220fb91a72ef9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 11 17:37:22 2019 -0700

    Update with many references.

paper/paper.bib
paper/paper.md

commit 34933858958b331337cd953c0cb2d25838a406c9
Merge: 078f85d89 ed11b5e0e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 11 17:37:33 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 078f85d89a38ac85bbed612f57655d279ba8532d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 11 17:37:22 2019 -0700

    Update with many references.

paper/paper.bib
paper/paper.md

commit ed11b5e0e19cb56fd5f333ec34012807dc120cda
Merge: e8d58f802 8c51b8af0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 11 17:24:16 2019 -0700

    Merge branch 'weiqun/mlmg' into development

commit 8c51b8af02a730a2ec17c353d16080acf37efa87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 11 17:19:16 2019 -0700

    MLEBTensor: calling cross terms

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 11c17318144bd0f883ccce11dcdb2839327eee24
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 11 16:46:38 2019 -0700

    MLEBTensor: 2d cross terms

Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 65ccd1eafaf575e42b302bc3495d41896639f252
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 11 15:31:23 2019 -0700

    MLEBTensor: 3d cross terms

Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit a8a5eb8e8c62d45751d6162f3c853b3574cb14f0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 10 17:12:49 2019 -0700

    Add references for SUNDIALS, hypre, PETSc and xSDK.

paper/paper.bib
paper/paper.md

commit b36a8428fb88d554871c16b49c63a9e574445773
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 10 16:28:34 2019 -0700

    Add city and country to the author affiliations.

paper/paper.md

commit e8d58f802faf26220345727bf278af9fb08d3e99
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 10 17:12:49 2019 -0700

    Add references for SUNDIALS, hypre, PETSc and xSDK.

paper/paper.bib
paper/paper.md

commit f4118f5be894e1f745ae5c2740fcecdf0ee451d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 10 17:08:48 2019 -0700

    WIP: MLEBTensorOp

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit af7cab1765a8c69ee3c1039b93d4ab0fff7d2f9e
Merge: 58d4c08d3 451066888
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 10 16:28:52 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 58d4c08d37fa56bcfadc1ee4354ca093c70e2b0f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 10 16:28:34 2019 -0700

    Add city and country to the author affiliations.

paper/paper.md

commit c20f084f6e1a66ff3ee737019947529d2b34cd07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 10 15:39:01 2019 -0700

    MLEBTensor: fill the corners of regular fabs too

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit 1fa7ad1388ebc366db1d87b61048868434ea6d36
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 10 13:55:45 2019 -0700

    MLEBTensor: save fluxes in MultiFab so that we don't have to have 2 ghost cells

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit 7cf9062ef32dd596ba9268d9cb95eac026219339
Merge: 13da3a462 4f03be844
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 10 14:15:40 2019 -0700

    Merge pull request #478 from kyleniemeyer/patch-1
    
    Typographic edits in paper

commit 4f03be844d30dd254fddeb2ab5d3079b1829cba6
Author: Kyle Niemeyer <kyle.niemeyer@gmail.com>
Date:   Fri May 10 14:13:34 2019 -0700

    Typographic edits in paper

paper/paper.md

commit ac59fe275f0a4859b7fcd2087d53a6bd9761cbcc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 10 12:14:49 2019 -0700

    size should be capacity here

Src/Base/AMReX_PODVector.H

commit 451066888fc0e4139437b7698119678bad9f59cc
Merge: 21d8a427f b6a7b719c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 10 11:18:37 2019 -0700

    Merge branch 'weiqun/mlmg' into development

commit b6a7b719cbd29e8e3de752b31ad0e053e27fff0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 10 10:55:43 2019 -0700

    MLEBABecLap: fix typo

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H

commit e4c5386e3fc3b018da8cbf0d3b5685c9fb8213cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 10 09:42:08 2019 -0700

    MLEBABecLap: fix new bug in mask

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H

commit 376f57d6cf922344e833312944e70cb2ab6bf122
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 10 09:01:26 2019 -0700

    WIP: MLEBTensor

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H

commit 60e3a2a111b5036674314aa0b1082baeb8eeec0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 9 18:38:19 2019 -0700

    MLEBTensor: cross term fluxes

Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBCellFlag.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 89c62f87f1e7e2f77135711e118525aeda8754ba
Author: kngott <kngott@lbl.gov>
Date:   Thu May 9 17:24:06 2019 -0700

    Readme for CudaGraph tests.

Tests/GPU/CudaGraphs/Readme.txt

commit 8184c385360b3062c1c2a3e802fdc0e37979e944
Author: kngott <kngott@lbl.gov>
Date:   Thu May 9 17:15:53 2019 -0700

    Clean up older, redundant graph tests.

Tests/GPU/CudaGraphs/ArrayReuse/GNUmakefile
Tests/GPU/CudaGraphs/ArrayReuse/Make.package
Tests/GPU/CudaGraphs/ArrayReuse/inputs_3d
Tests/GPU/CudaGraphs/ArrayReuse/main.cpp
Tests/GPU/CudaGraphs/ArrayReuse/run.corigpu
Tests/GPU/CudaGraphs/GraphCopy/GNUmakefile
Tests/GPU/CudaGraphs/GraphCopy/Make.package
Tests/GPU/CudaGraphs/GraphCopy/inputs_3d
Tests/GPU/CudaGraphs/GraphCopy/main.cpp
Tests/GPU/CudaGraphs/GraphCopy/run.corigpu
Tests/GPU/CudaGraphs/GraphIterReuseCopy/GNUmakefile
Tests/GPU/CudaGraphs/GraphIterReuseCopy/Make.package
Tests/GPU/CudaGraphs/GraphIterReuseCopy/inputs_3d
Tests/GPU/CudaGraphs/GraphIterReuseCopy/main.cpp
Tests/GPU/CudaGraphs/GraphIterReuseCopy/run.corigpu

commit 54f15cd2db930ffd4d1bdc627f1025f90b68ce51
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 9 16:08:24 2019 -0700

    also use the PODVector on CPU code (for now, to test it)

Src/Base/AMReX_CudaContainers.H

commit c14c9b16e470557490d9bcde38dc7518b9eaf946
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 9 15:15:26 2019 -0700

    MLEBABecLap: prepare it for tensor solve

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90
Src/LinearSolvers/MLMG/Make.package

commit 21d8a427f73c680846f89a8cbc1a82a17c4b9de2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 9 14:55:38 2019 -0700

    correct the number of comps when writing particle data to plt files

Src/Particle/AMReX_ParticleContainerI.H

commit 67784e0c1aadea9942459c9fd0f5e98a1f92261e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 9 12:45:57 2019 -0700

    MLEBABecLap: switch to new gsrb with multi-component b coefficient

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 0e76d0280b95cb4f54ce2f4e4e89c27185b5076a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 9 11:19:57 2019 -0700

    simplification

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp

commit b15b1d2a8da7b0b997f8e483b471ff2b8a7e2d3c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 9 10:47:36 2019 -0700

    WIP: MLEBTensorOp

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 7dcd6e1e65ad294f549977c92cf8752d9443286c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 9 09:03:28 2019 -0700

    make some functions public for cuda

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H

commit b4893f43a39d88aa1f685c32ea3d74c3d4c66857
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 18:34:58 2019 -0700

    MLEBABecLap: fix new bug introduced when removing HO EB

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit c1a85dc5a2f28a5c4c95e845f216115cb1fee70b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed May 8 19:43:20 2019 -0400

    mark these functions as noexcept, since we don't catch those ever

Src/Base/AMReX_PODVector.H

commit e4a58ce8d4c8c558848db44b27f595edef9730aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 16:39:48 2019 -0700

    MLEBTensorOp: add eb kappa

Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H

commit 3c8c4516ff05b5c43b41131054d22ec8c834b5a0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed May 8 19:25:52 2019 -0400

    split this constructor for PODVector into two

Src/Base/AMReX_PODVector.H

commit b7be90fa07d3adff0a72a52654e73c8c418725da
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed May 8 19:20:56 2019 -0400

    don't need thrust::raw_pointer_cast anymore

Src/Particle/AMReX_ParticleContainerI.H

commit f2ed00545be6be1b94197db8bb782ae70deef8e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 15:48:07 2019 -0700

    MLEBABecLap 2D: remove blend beta

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit 025cde7d1893fe83b264c7fb0228813d32c1f949
Merge: f7a796f4b 37c3faf70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 15:39:29 2019 -0700

    Merge branch 'development' into weiqun/mlmg

commit 37c3faf70c7c03c84462c5d1470d7ae2ae472b43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 15:38:23 2019 -0700

    add a missing header

Src/Base/AMReX_ParmParse.H

commit f7a796f4bfdc5595db5017e04618e9c5d8b17545
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 15:00:24 2019 -0700

    MLEBABecLap: update for multi-component

Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_F.H
Src/EB/AMReX_EBMultiFabUtil_nd.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90

commit 39c836c57e814030b0e68c499af7793d0623190b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed May 8 18:08:38 2019 -0400

    copying the grid start and stop indices using thrust_copy instead of the copy constructor

Src/Particle/AMReX_ParticleContainerI.H

commit e93dab73c74cbc6b4b305bac3521d7ec89cb6c31
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed May 8 16:32:16 2019 -0400

    Fix run.summit script. -N = email, not number of nodes.

Tutorials/GPU/run.summit

commit 25528e43bb3d53adcaf3a8348a7a9b77dbb9f5c5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed May 8 16:27:59 2019 -0400

    remove debug print statement

Src/Base/AMReX_PODVector.H

commit f66ed9c3d3b487dd697a72d0c8c2bbb059c72be9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 13:04:40 2019 -0700

    MLEBABecLap: remove HO EB

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit fcb52dd3726dcf3ebe8ac567bb93a10dc71acb84
Author: kngott <kngott@lbl.gov>
Date:   Wed May 8 12:47:05 2019 -0700

    Proper CUDA Callback calls for CUDA 9 & CUDA 10, Part 2.

Src/Base/AMReX_CudaAsyncFab.cpp

commit f9bf8841668e4a4256cff480a60dee15e8d8b725
Author: kngott <kngott@lbl.gov>
Date:   Wed May 8 12:41:55 2019 -0700

    Proper CUDA Callback calls for CUDA 9 & CUDA 10.

Src/Base/AMReX_CudaAsyncFab.cpp

commit 84f3abce80345f0f2020427055d0ef64d1c8aeb4
Author: kngott <kngott@lbl.gov>
Date:   Wed May 8 12:20:28 2019 -0700

    Hide max_cuda_streams function when USE_CUDA=FALSE.

Src/Base/AMReX_CudaDevice.H

commit 618ef094876af9d8755937226ec248bf5b22f728
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 12:01:47 2019 -0700

    MLTensor: limit kappa to mg level 0

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 5518eff068513bbc71be2a8af35e5dfd0fbaa67a
Merge: 9783b79d7 fa43d9a79
Author: kngott <kngott@lbl.gov>
Date:   Wed May 8 11:49:01 2019 -0700

    Merge branch 'development' into kngott/cudaGraphs

commit 2071003f8a4792fc40c5b738da969277b6dbde03
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 09:41:22 2019 -0700

    MLTensor: move as much as possible into the laplacian

Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit 9783b79d7d861e6c866094969b0b5cd79a3a082f
Author: kngott <kngott@lbl.gov>
Date:   Wed May 8 11:47:25 2019 -0700

    Clean up.

Src/Base/AMReX_FabArrayCommI.H

commit 13da3a4627acdf7a8671b2ed377e145628f32f04
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 8 11:43:08 2019 -0700

    Oops -- forgot to actually remove the text

LICENSE

commit fa43d9a7997ca3bbd1af94ac164d942e7ad59d01
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 8 11:43:08 2019 -0700

    Oops -- forgot to actually remove the text

LICENSE

commit e069976b36c585bb4e8f1045fa72d0a3d5562d7f
Author: kngott <kngott@lbl.gov>
Date:   Wed May 8 11:42:23 2019 -0700

    Fix indentation in FillBoundary w/ Graphs.

Src/Base/AMReX_FabArrayCommI.H

commit fc619fdce1f0553333b71ae848d35ff2f84a0c61
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 8 11:40:17 2019 -0700

    Update license.txt -> LICENSE and replace modified BSD by standard 3-clause BSD.

LICENSE
README.md

commit 18f452ae4f256e7d37f44f59a00ebd0c8fed0a3d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 8 11:40:17 2019 -0700

    Update license.txt -> LICENSE and replace modified BSD by standard 3-clause BSD.

LICENSE
README.md

commit 6e574f9a2afb86ab45714912b9b9f334cb205b56
Merge: f7586cd9e 66d8a46bd
Author: kngott <kngott@lbl.gov>
Date:   Wed May 8 11:35:01 2019 -0700

    Merge branch 'development' into kngott/cudaGraphs

commit f7586cd9ec324429c84b7f2c6d03860907be28b0
Author: kngott <kngott@lbl.gov>
Date:   Wed May 8 11:34:18 2019 -0700

    Add number of ghost cells and components to test inputs.

Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d

commit 8ce293ad8a4c6b78f77c60d4011a8238b4b55967
Author: kngott <kngott@lbl.gov>
Date:   Wed May 8 11:32:55 2019 -0700

    Add runtime flag to turn on/off graphs to LinearSolver Tutorial.

Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp

commit 91199880018afb6f281ba1ad383608e2810f5461
Author: kngott <kngott@lbl.gov>
Date:   Wed May 8 11:31:56 2019 -0700

    Rename re-used timer.

Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp

commit 18bb26fd9817c257cda18e2e7c70b51ba9307f03
Author: kngott <kngott@lbl.gov>
Date:   Wed May 8 11:31:22 2019 -0700

    Clean up FillBoundary graph test.

Tests/GPU/CudaGraphs/GraphBoundary/main.cpp

commit 2cf8523fa64cfd341c3d7b6923bb1005afd5eb02
Merge: 9545d80be 66d8a46bd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed May 8 13:53:47 2019 -0400

    Merge branch 'development' into atmyers/vector_memory_usage

commit 42073726f446ac8dd0743f4b3c04d607da891767
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 7 22:12:38 2019 -0700

    MLTensor: apply the cross terms at all levels

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit e48a89f893c3d6457e70910161f03eb50c3fdd0b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 7 19:34:45 2019 -0700

    WIP: MLEBTensorOp

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp

commit 66d8a46bde5baf7ac3e410fd560d6705fc38668c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 7 18:06:28 2019 -0700

    Add notes about being able to install amrex using spack.

Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst
Docs/sphinx_documentation/source/GettingStarted.rst

commit 95b428ac6bbf51334c1f94d0c4fe0f8215482c00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 7 16:09:28 2019 -0700

    MLEBTensorOp: stubs

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLEBTensor_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/Make.package

commit af07eb7a5be433e4e44a2cb46848ca5d64ca938f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 7 15:54:36 2019 -0700

    MLTensor: bc at corners

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit 9047db69c7f4b4cd9808fd4c251dbb2f620ad1e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 6 16:07:47 2019 -0700

    MLMG: when using EB, the coarest domain size is now >= 4.

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit fb079185c4f07af9b98948afc3e24acceb842105
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 6 14:46:07 2019 -0700

    MLTensor: simplification

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 31757085d71708d94b978fbda0aae3b0e67d57d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 6 14:10:43 2019 -0700

    MLTensor: include all cross terms

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit a6f69d55d37d1f2da2c3bad91f1932005da8f44c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun May 5 15:57:15 2019 -0700

    fix typos

Docs/sphinx_documentation/source/GridCreation.rst
Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst

commit 1dfef654a951a6a9fe82d59fd36ccaaf56cdac8e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun May 5 15:42:35 2019 -0700

    more on gridding

Docs/sphinx_documentation/source/GridCreation.rst
Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst

commit 7251c87a4d94f89bc934d7a6b8690ea272aed50b
Merge: fab14b6c0 bc89383e9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun May 5 15:08:11 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit fab14b6c0a29dbb63e7401f97a8116b46b8f5574
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun May 5 15:07:59 2019 -0700

    update to gridding stuff

Docs/sphinx_documentation/source/DualGrid.rst
Docs/sphinx_documentation/source/GridCreation.rst
Docs/sphinx_documentation/source/LoadBalancing.rst
Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst

commit bc89383e99e36f873bfeb984f847b8456c972cc2
Merge: e2b9b5d69 c992ae224
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 5 13:53:12 2019 -0700

    Merge branch 'weiqun/mlmg' into development

commit c992ae2241d0eba9666cd441f91899568ab48673
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 5 13:52:57 2019 -0700

    comments about the tensor solver

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H

commit e2b9b5d6978f5110f88ca7cbb12ab3275f23d412
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun May 5 12:56:26 2019 -0700

    fix formatting

Docs/sphinx_documentation/source/LoadBalancing.rst

commit da28ba423c088f52f34231f861678a3b34fb1b66
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun May 5 12:39:17 2019 -0700

    Add short text about load balancing

Docs/sphinx_documentation/source/DualGrid.rst
Docs/sphinx_documentation/source/LoadBalancing.rst
Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst

commit e9afc6f7e62bb7b6d4db17bd3f83823d649b30f9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 20:16:07 2019 -0700

    Remove gridding from AmrCore now that it lives in its own section.

Docs/sphinx_documentation/source/AmrCore.rst

commit b6d1e4fa4b0e9c6c1958b1c1d28954a4c8df7f05
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 20:10:06 2019 -0700

    fix typo

Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst

commit 1a128f70b5e702f8251beea610224ed051dd28be
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 20:02:35 2019 -0700

    Add text about dual gridding.

Docs/sphinx_documentation/source/DualGrid.rst
Docs/sphinx_documentation/source/GridCreation.rst
Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst

commit ee13c67359f375d36e9166f88a4719675b86eea3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 19:48:31 2019 -0700

    More clarification

Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst

commit 284f84250c89ace2e0085459e5b7f0d256c216ea
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 19:27:58 2019 -0700

    fix typo

Docs/sphinx_documentation/source/ManagingGridHierarchy.rst

commit 080490b983e63a210b9bb806d97d365781183c93
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 19:26:46 2019 -0700

    more fixes for grid creation

Docs/sphinx_documentation/source/ManagingGridHierarchy.rst

commit 9d7870ed20cfe5c181bb32b97e3e7ab3bbe35c0b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 19:21:39 2019 -0700

    more grid creation update

Docs/sphinx_documentation/source/ManagingGridHierarchy.rst

commit f964bd8469d66ea9d8c9d0240773057608e8b294
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 19:03:44 2019 -0700

    More detail

Docs/sphinx_documentation/source/ManagingGridHierarchy.rst

commit 1427d5404b4b6c47c2fa5c89d897f8d5ef4ecf3c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 18:31:12 2019 -0700

    Add refine_grid_layout

Docs/sphinx_documentation/source/ManagingGridHierarchy.rst

commit 366c966f7bc4708a3f28659657af5fed2eedf120
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 18:16:08 2019 -0700

    Fix oops re cpp use

Docs/sphinx_documentation/source/ManagingGridHierarchy.rst

commit 843d168baad6175b21d4a5d65acfc3b8b00ec2fc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 18:14:15 2019 -0700

    More update on grid creation

Docs/sphinx_documentation/source/ManagingGridHierarchy.rst

commit 2ec6dfac0074fbcb06e5485adeb95e6a12e66a7b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 17:57:54 2019 -0700

    More detail re grid creation

Docs/sphinx_documentation/source/ManagingGridHierarchy.rst

commit 168eee4d320dcbc5875a71c7c0014635ca4868b6
Merge: 44647b983 cbd29aa71
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 11:20:02 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 44647b983e815a025168286eaab60440c1a12530
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 4 11:19:43 2019 -0700

    Fix the headings for managing  grid hierarchy

Docs/sphinx_documentation/source/ManagingGridHierarchy.rst

commit e9f91a3962321e5d9df9f9e175f8deb58130ec53
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 4 09:04:31 2019 -0700

    MLTensor: override apply instead of solutionResidual

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H

commit 23398439c98d18aafbbeef106343b2c48f0688e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 3 21:48:06 2019 -0700

    MLTensor: hide setScalars

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit cbd29aa715007223b1bd49d05bf931d4df835e30
Merge: 137f45cf0 421af5572
Author: asalmgren <asalmgren@lbl.gov>
Date:   Fri May 3 18:21:47 2019 -0700

    Merge pull request #475 from AMReX-Codes/docs-libamrex
    
    Expand section on building libamrex

commit 421af557231f1526b1e12dee12f750d10ed6c8e4
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date:   Fri May 3 18:04:42 2019 -0700

    Expand section on building libamrex with details about how to set C++ flags and linker flags for the application code.

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit 137f45cf070536b8d8725b7936dc4ce27bd265b1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 3 17:57:58 2019 -0700

    Add Chapter intro for ManagingGridHierarchy

Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst

commit aae549bd2e87dee875161dc97d8154295d8b0e31
Author: kngott <kngott@lbl.gov>
Date:   Fri May 3 17:28:20 2019 -0700

    ifdefs to protect CUDA 10 features. Needs testing on Summit.

Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayCommI.H

commit 749a2c8f7053f8f8e934d52cf269f8de730057e7
Merge: 8b04d1ad8 1249b1ca6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 3 17:00:50 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 8b04d1ad88f3ef74dd70964159f1e8864ab77249
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 3 17:00:35 2019 -0700

    add separate section on managing the grid hierarchy

Docs/sphinx_documentation/source/ManagingGridHierarchy.rst
Docs/sphinx_documentation/source/index.rst

commit 4e4f1e519a6ca959a991913033e955dbe7fccbd3
Author: kngott <kngott@lbl.gov>
Date:   Fri May 3 16:00:31 2019 -0700

    Update FillBoundary to switchable graph recording methods.

Src/Base/AMReX_FabArrayCommI.H

commit 3f8424de740c4a2530c0646b010d88a178f7fe31
Author: kngott <kngott@lbl.gov>
Date:   Fri May 3 15:59:08 2019 -0700

    Add flag to switch graph recording methods and single start and stop function to choose.

Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp

commit 7cc4c4e0b93dbf96d97362efe87b7fc8e2452b1a
Author: kngott <kngott@lbl.gov>
Date:   Fri May 3 15:57:29 2019 -0700

    Reorganize and cleanup output.

Tests/GPU/CudaGraphs/GraphBoundary/main.cpp

commit d7a382a2e5385cdeb103d522ea8fd808abd60a60
Author: kngott <kngott@lbl.gov>
Date:   Fri May 3 15:56:12 2019 -0700

    Whitespace cleanup.

Src/Base/AMReX_GpuControl.H

commit 1249b1ca6889665df3c3d30ccce71b8fb10f3b09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 3 15:27:09 2019 -0700

    Fix bndry for hypre and petsc

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 9545d80beec5ecbc12aab92c44bd0265110a7cec
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri May 3 17:53:49 2019 -0400

    fix move assignment operator

Src/Base/AMReX_PODVector.H

commit 539eb05f9054f303e5a9755cb47f46fd47ee1e4c
Merge: aa6741c65 34092a5d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 3 14:43:12 2019 -0700

    Merge branch 'weiqun/mlmg' into development

commit 34092a5d8493aa28d6581f76cb2d69af2c643d43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 3 14:42:47 2019 -0700

    MLTensor: add extra terms to residual

Src/Base/AMReX_MultiFabUtil_1D_C.H
Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H
Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensor_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLTensor_K.H
Src/LinearSolvers/MLMG/Make.package

commit 871c06875d32c1b19781ca400cb75bfb58cacc6b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri May 3 17:37:05 2019 -0400

    implement erase, assign, insert

Src/Base/AMReX_PODVector.H

commit 517afa944afbf8431c9a132f63597fe5543dcf01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 3 12:59:25 2019 -0700

    add computeGradient

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.H
Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 9dadef8b8cd5cf93a6e0564e1271e83353f42b32
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri May 3 13:55:06 2019 -0400

    can implement these Vector using simple typedefs now

Src/Base/AMReX_CudaContainers.H

commit e2d3be1bd48dd7cbc6075d9dea183bf3b4dfaecb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri May 3 13:54:20 2019 -0400

    don't need this allocator to inherit from the thrust one

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_PODVector.H

commit 5406c08584d21c0de44ced27cad77819ccecb140
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 3 10:53:21 2019 -0700

    MLTensorOp: prepareForSolve

Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit e02130b32ec3f03406beb2116393ba1e33cc0a08
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri May 3 13:52:49 2019 -0400

    use the wrapped version of Gpu::HostVector here

Src/Particle/AMReX_ParticleContainerI.H

commit 522c58748ef88fac1dc86011bf118e2a8969c2c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 3 09:55:51 2019 -0700

    MLEBABecLap: update for multi-component

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit aa6741c65786da1bcaa51d3a21f8f9ce50b07f21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 3 07:15:37 2019 -0700

    Fix FillPatch for EB

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_FabArrayBase.H

commit 0a08d83f7d451956ad8e9c6b942ca23165c64a9d
Author: Maikel Nadolski <maikel.nadolski@gmail.com>
Date:   Fri May 3 10:49:21 2019 +0200

    Link against the C version of MPI

Src/Base/CMakeLists.txt

commit afac4e3890987efbe731cfbf7933585952bcaeac
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu May 2 19:19:36 2019 -0700

    Fix WritePlotFile to allow few levels in output that in orig, based on length of mf data passed in

Tools/C_util/WritePlotFile.cpp

commit bdaef55a55aff0cd36a9aa28ed529ffc55ff04e4
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu May 2 18:50:57 2019 -0700

    Update isoToVTK.py to be python3-compliant

Tools/EBSurfaceTools/isoToVTK.py

commit 1d818c3f893601c0cc26eab5f38d26a97fd7dc3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 2 16:53:22 2019 -0700

    MLCellLinOp: update for multi-component

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit 718f36ba7411bb803934e12ac1b4e217921adb22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 2 16:38:54 2019 -0700

    MLABecLap: update for multi-component

Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp

commit 0043eb360cf6824053307d2f263356b4e8d4f264
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu May 2 19:00:38 2019 -0400

    a vector implementation where we control the growth and reallocation strategy

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaContainers.H
Src/Base/AMReX_PODVector.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 40c62cc4d0d8ba60a5ff74fe7427380af6314260
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 2 15:30:18 2019 -0700

    MLMG: fine mask only needs to have 1 component.  BaseFab::norinfmask now assumes the mask has only 1 component.

Src/Base/AMReX_BaseFab.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 41a38aba1b3cd47d98f52361fdd7ce272611823c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 2 13:51:48 2019 -0700

    new version of contains_inf with IntVect argument for ghost cells

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit d312ff08d3a2e9b44094cb69de2c66378ce4bafa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 2 13:46:21 2019 -0700

    new version of SumBoundary with argument for number of ghost cells

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit dbf8aef2be063695b6ffe037578485718a6d3690
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 2 12:09:38 2019 -0700

    Remove duplicated code in FillPatch

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit a9a0347f1661a72e727e42e370e45697d3c3f619
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 2 10:04:35 2019 -0700

    MLMG nodal rap: change the number of ghost cells to 1 at the bottom

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 948cb60fccc5f7bd84cfd91d3fb83224e0ba5b7f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 2 13:21:50 2019 -0700

    change the assert about the particle type to be even stronger

Src/Particle/AMReX_ParticleContainerI.H

commit 7fae8b4c18fde89fafe84acc45fe6070846fdb96
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 2 13:14:19 2019 -0700

    let the constructor for the Particle struct be compiler-defined

Src/Particle/AMReX_Particle.H

commit 278f7aa4776243cd538f888f87d61620b26a27b2
Merge: c39648484 867bd8f56
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 2 10:04:21 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c39648484de3976b3cd7e80ea166ff5336d894b5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 2 10:03:58 2019 -0700

    The pointer incrementing logic here was wrong due to the possibility of structure padding.

Src/Particle/AMReX_NeighborParticlesCPUImpl.H

commit c98d66c8248ebef820820793fcfec6c9192f1d05
Author: Maikel Nadolski <maikel.nadolski@gmail.com>
Date:   Thu May 2 17:58:33 2019 +0200

    Do not require CXX libraries for MPI which are deprecated.

CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in

commit 867bd8f566743cc9eda4aedb877db22f16da8c9c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 1 20:47:18 2019 -0700

    fix symmetry issue of nodal rap stencil in 2D

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit 8c225f8dc6a65747d6b89778ce444ff52113e72b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 1 19:13:18 2019 -0700

    fix symmetry issue of nodal rap stencil

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 805ff0f714c5bdae16c671ef5fb9a2288c86759c
Merge: 9b7b0a746 aa0b4e4af
Author: kngott <kngott@lbl.gov>
Date:   Wed May 1 12:22:25 2019 -0700

    Merge branch 'development' into kngott/cudaGraphs

commit 9b7b0a746992aba08fcb2f9b6d4ab5ac75809953
Author: kngott <kngott@lbl.gov>
Date:   Wed May 1 12:21:36 2019 -0700

    Output adjustment.

Tests/GPU/CudaGraphs/GraphBoundary/main.cpp

commit aa0b4e4afea1a26ff59a2c9bb5625939b239bec0
Merge: f0fe60c36 01bd97c5e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 1 10:10:46 2019 -0700

    Merge pull request #471 from AMReX-Codes/particle_realdescriptor_fix
    
    bug fixes for particles when BL_FLOAT is used.

commit f0fe60c36e1f7e6315e4109687b68289dccbe0ec
Merge: adcf40035 a8e4bfa66
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 1 10:07:28 2019 -0700

    Merge pull request #472 from maikel/feature/FillPatch_IndexSpace
    
    EB: Add an additional overload for FillPatchTwoLevels.

commit 641f9dc883e08a1b44be052cbae5f4f72c561f3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 1 09:11:55 2019 -0700

    MLMG: remove assertion to maintain backward compatibility

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 3c2641aef1dec1f8124061a91f846557d13a3395
Merge: ffe5eff88 adcf40035
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 1 09:06:01 2019 -0700

    Merge branch 'development' into weiqun/mlmg

commit adcf400351198159f6c1cbc618c912ecf033f170
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 1 09:04:52 2019 -0700

    update CHANGES

CHANGES

commit c76bcf6349919f15306b9e7148511ddb8cf17c1e
Merge: 2b96cafc6 cad29442c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 1 08:44:20 2019 -0700

    Merge branch 'development'

commit cad29442cfd4c692e23a477dbb25a00e8b46baaf
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Apr 30 17:29:35 2019 -0700

    factor upcxx backend code

Src/AmrTask/rts_impls/mpi/Make.package
Src/AmrTask/rts_impls/mpi/Perilla.cpp
Src/AmrTask/rts_impls/mpi/perilla.mak
Src/AmrTask/rts_impls/runtime_common/Make.package
Src/AmrTask/rts_impls/runtime_common/Perilla_common.cpp
Src/AmrTask/rts_impls/runtime_common/RGIter.cpp
Src/AmrTask/rts_impls/runtime_common/RegionGraph.H
Src/AmrTask/rts_impls/runtime_common/RegionGraph.cpp
Src/AmrTask/rts_impls/runtime_common/WorkerThread.H
Src/AmrTask/rts_impls/runtime_common/WorkerThread.cpp
Src/AmrTask/rts_impls/runtime_common/perilla.mak
Src/AmrTask/rts_impls/upcxx/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/upcxx/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/upcxx/Barrier.H
Src/AmrTask/rts_impls/upcxx/Barrier.cpp
Src/AmrTask/rts_impls/upcxx/LocalConnection.H
Src/AmrTask/rts_impls/upcxx/Make.package
Src/AmrTask/rts_impls/upcxx/Perilla.cpp
Src/AmrTask/rts_impls/upcxx/PerillaConfig.H
Src/AmrTask/rts_impls/upcxx/PerillaRts.H
Src/AmrTask/rts_impls/upcxx/PerillaRts.cpp
Src/AmrTask/rts_impls/upcxx/Perilla_common.cpp
Src/AmrTask/rts_impls/upcxx/RGIter.H
Src/AmrTask/rts_impls/upcxx/RGIter.cpp
Src/AmrTask/rts_impls/upcxx/RegionQueue.H
Src/AmrTask/rts_impls/upcxx/RegionQueue.cpp
Src/AmrTask/rts_impls/upcxx/RemoteConnection.H
Src/AmrTask/rts_impls/upcxx/WorkerThread.H
Src/AmrTask/rts_impls/upcxx/WorkerThread.cpp
Src/AmrTask/rts_impls/upcxx/mylock.h
Src/AmrTask/rts_impls/upcxx/perilla.mak

commit ffe5eff882978dfc6c2ceae6b85af31636bf25cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 30 17:04:10 2019 -0700

    MLMGBndry: multi-component

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp

commit eecd1c27bc75fe3d95743dca312d13940d75c433
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 30 16:45:12 2019 -0700

    MLMG: multi-component BndryCondLoc

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H

commit 2a7d7a29c9647882bba387ea628c06f40d501c71
Author: kngott <kngott@lbl.gov>
Date:   Tue Apr 30 16:19:01 2019 -0700

    FillBoundary MPI graphed and tested on one node. CopyTo, Local & CopyFrom all graphed.

Src/Base/AMReX_FabArrayCommI.H

commit 01bd97c5e57c037dd3cdb3a89aac56082be1f7fd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 30 15:50:57 2019 -0700

    make sure the format and order is consistent for each of the real conversion functions

Src/Base/AMReX_FabConv.cpp

commit c37b030a9240baffc722b5f1bb3a289c0376c14e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 30 15:26:03 2019 -0700

    float -> double

Src/Base/AMReX_FPC.cpp

commit 671d64ca7d75f5908a39ab64fa4df2cc4f0b1775
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 30 15:06:31 2019 -0700

    make domain bc vector so that each component could have its own bc type

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H

commit f7002c1e3553ae6c9ea630b28811c362d8cf7789
Author: kngott <kngott@lbl.gov>
Date:   Tue Apr 30 14:57:41 2019 -0700

    Get rid of StreamIter loops where not needed.

Src/Base/AMReX_FabArrayCommI.H

commit 7bdd2860272c5a2da86d0e05880de3cc942a830d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 30 14:40:43 2019 -0700

    MLTensorOp: derive from MLABecLaplacian

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp

commit 4f1cb78034770a43946008dfc72db2c0684e2042
Author: kngott <kngott@lbl.gov>
Date:   Tue Apr 30 14:38:16 2019 -0700

    SendToBuffer Graphed

Src/Base/AMReX_FabArrayCommI.H

commit e55a71ef7dc2f6b8760906487bf8061109bcafc4
Author: kngott <kngott@lbl.gov>
Date:   Tue Apr 30 14:36:33 2019 -0700

    Better run script.

Tests/GPU/CudaGraphs/GraphBoundary/run.corigpu

commit d0ca7303d25952ea65d119c39aa3220de03d4bb1
Author: kngott <kngott@lbl.gov>
Date:   Tue Apr 30 14:36:16 2019 -0700

    Small tweaks.

Tests/GPU/CudaGraphs/GraphBoundary/main.cpp

commit 58cbc7b9b421b5203253a1c44748d99ab17bce1b
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Apr 30 13:26:13 2019 -0700

    delete duplicated codes

Src/AmrTask/rts_impls/mpi/RegionGraph.H
Src/AmrTask/rts_impls/mpi/RegionGraph.cpp

commit 354b0363e3d6f351aff26fa7b71714ba7a6596dd
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Apr 30 13:24:12 2019 -0700

    delete duplicated codes

Src/AmrTask/rts_impls/mpi/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/mpi/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/mpi/Barrier.H
Src/AmrTask/rts_impls/mpi/Barrier.cpp
Src/AmrTask/rts_impls/mpi/LocalConnection.H
Src/AmrTask/rts_impls/mpi/RGIter.H
Src/AmrTask/rts_impls/mpi/RGIter.cpp
Src/AmrTask/rts_impls/mpi/RegionQueue.H
Src/AmrTask/rts_impls/mpi/RegionQueue.cpp
Src/AmrTask/rts_impls/mpi/RemoteConnection.H
Src/AmrTask/rts_impls/mpi/WorkerThread.H
Src/AmrTask/rts_impls/mpi/WorkerThread.cpp
Src/AmrTask/rts_impls/mpi/mylock.h

commit b4025c682b7b12b333e67c01d355eb01de13fde2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 30 10:23:43 2019 -0700

    Start tensor solver

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H
Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp
Src/LinearSolvers/MLMG/Make.package

commit a8e4bfa6606a0840317e46964f69cef07e1af9fa
Author: Maikel Nadolski <maikel.nadolski@gmail.com>
Date:   Tue Apr 30 09:50:47 2019 +0200

    Allows to create FPInfo objects with an associated EB2::IndexSpace.
    
    For enabled EB these changes allow to choose the EB2::IndexSpace which
    will be used for the interpolation regions in FillPatchTwoLevels.
    
    This commit also makes it possible to use FillPatchTwoLevels without any
    EB2::IndexSpace built at a prior stage. In this case it will do the same
    communication logic as if AMReX would not be built with enabled EB.

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/EB/AMReX_EB2.H
Src/EB/AMReX_EB2.cpp

commit 498593ddd7adc2d52bd379484c194512c7d82f95
Merge: 405feb15c 11beeb82b
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Apr 29 21:52:39 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 405feb15c6a6412798b79128e1141b65e11b9fe0
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Apr 29 21:51:29 2019 -0700

    factor codes in omp and pthreads backends

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/AmrTask/rts_impls/mpi/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/mpi/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/mpi/Barrier.H
Src/AmrTask/rts_impls/mpi/Barrier.cpp
Src/AmrTask/rts_impls/mpi/LocalConnection.H
Src/AmrTask/rts_impls/mpi/Make.package
Src/AmrTask/rts_impls/mpi/Makefile
Src/AmrTask/rts_impls/mpi/PackageQueue.H
Src/AmrTask/rts_impls/mpi/PackageQueue.cpp
Src/AmrTask/rts_impls/mpi/Perilla.H
Src/AmrTask/rts_impls/mpi/Perilla.cpp
Src/AmrTask/rts_impls/mpi/PerillaConfig.H
Src/AmrTask/rts_impls/mpi/PerillaRts.H
Src/AmrTask/rts_impls/mpi/PerillaRts.cpp
Src/AmrTask/rts_impls/mpi/RGIter.H
Src/AmrTask/rts_impls/mpi/RGIter.cpp
Src/AmrTask/rts_impls/mpi/RegionGraph.H
Src/AmrTask/rts_impls/mpi/RegionGraph.cpp
Src/AmrTask/rts_impls/mpi/RegionQueue.H
Src/AmrTask/rts_impls/mpi/RegionQueue.cpp
Src/AmrTask/rts_impls/mpi/RemoteConnection.H
Src/AmrTask/rts_impls/mpi/WorkerThread.H
Src/AmrTask/rts_impls/mpi/WorkerThread.cpp
Src/AmrTask/rts_impls/mpi/mylock.h
Src/AmrTask/rts_impls/mpi/perilla.mak
Src/AmrTask/rts_impls/mpi_pthreads/Make.package
Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/runtime_common/Barrier.H
Src/AmrTask/rts_impls/runtime_common/Barrier.cpp
Src/AmrTask/rts_impls/runtime_common/LocalConnection.H
Src/AmrTask/rts_impls/runtime_common/Make.package
Src/AmrTask/rts_impls/runtime_common/PerillaMemCheck.H
Src/AmrTask/rts_impls/runtime_common/PerillaMemCheck.cpp
Src/AmrTask/rts_impls/runtime_common/RGIter.H
Src/AmrTask/rts_impls/runtime_common/RGIter.cpp
Src/AmrTask/rts_impls/runtime_common/RegionQueue.H
Src/AmrTask/rts_impls/runtime_common/RegionQueue.cpp
Src/AmrTask/rts_impls/runtime_common/RemoteConnection.H
Src/AmrTask/rts_impls/runtime_common/WorkerThread.H
Src/AmrTask/rts_impls/runtime_common/WorkerThread.cpp
Src/AmrTask/rts_impls/runtime_common/mylock.h
Src/AmrTask/rts_impls/runtime_common/perilla.mak
Src/AmrTask/rts_impls/upcxx/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/upcxx/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/upcxx/Barrier.H
Src/AmrTask/rts_impls/upcxx/Barrier.cpp
Src/AmrTask/rts_impls/upcxx/LocalConnection.H
Src/AmrTask/rts_impls/upcxx/Make.package
Src/AmrTask/rts_impls/upcxx/Makefile
Src/AmrTask/rts_impls/upcxx/PackageQueue.H
Src/AmrTask/rts_impls/upcxx/PackageQueue.cpp
Src/AmrTask/rts_impls/upcxx/Perilla.H
Src/AmrTask/rts_impls/upcxx/Perilla.cpp
Src/AmrTask/rts_impls/upcxx/PerillaConfig.H
Src/AmrTask/rts_impls/upcxx/PerillaRts.H
Src/AmrTask/rts_impls/upcxx/PerillaRts.cpp
Src/AmrTask/rts_impls/upcxx/Perilla_common.cpp
Src/AmrTask/rts_impls/upcxx/RGIter.H
Src/AmrTask/rts_impls/upcxx/RGIter.cpp
Src/AmrTask/rts_impls/upcxx/RegionGraph.H
Src/AmrTask/rts_impls/upcxx/RegionGraph.cpp
Src/AmrTask/rts_impls/upcxx/RegionQueue.H
Src/AmrTask/rts_impls/upcxx/RegionQueue.cpp
Src/AmrTask/rts_impls/upcxx/RemoteConnection.H
Src/AmrTask/rts_impls/upcxx/WorkerThread.H
Src/AmrTask/rts_impls/upcxx/WorkerThread.cpp
Src/AmrTask/rts_impls/upcxx/mylock.h
Src/AmrTask/rts_impls/upcxx/perilla.mak

commit 11beeb82bd1d04f05d6aba88efca19f2df5b5f88
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Apr 29 21:23:53 2019 -0700

    eb level's `fillLevelSet` needs to be public

Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_EB_levelset.H

commit 6db482adf6115be422d34ff4e3d317ac71dac9a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 29 16:55:32 2019 -0700

    minor changes for format and consistence

Src/AmrCore/AMReX_AmrMesh.cpp

commit 0cac7a83148d573f6fadccf9e399776736216378
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 29 16:44:49 2019 -0700

    MLEBABecLap: loop fusion

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit e9563d164000ba3eb2f251f9710ac3c3249cc525
Author: kngott <kngott@lbl.gov>
Date:   Mon Apr 29 16:10:38 2019 -0700

    CUDA Graphs API works for non-lambdas. Test later for lambdas?

Tests/GPU/CudaGraphs/CrazyGraphs/main.cpp

commit feff050bd24f6568be508692121c0b30709ef866
Author: Maikel Nadolski <maikel.nadolski@gmail.com>
Date:   Tue Apr 30 00:06:21 2019 +0200

    EB: Add an additional overload for FillPatchTwoLevels.
    
     * This adds an EB2::IndexSpace paramter to FillPatchTwoLevels.
       That way one can specify the exact EB2::IndexSpace for the
       interpolation region.
     * Add a defaulted FabFactory parameter to the constructor of FPInfo.

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 16de912ecabc31b9550059005e54fdca511fd3a3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 29 11:01:33 2019 -0700

    bug fixes for particles when BL_FLOAT is used.

Src/Base/AMReX_FPC.H
Src/Base/AMReX_FPC.cpp
Src/Base/AMReX_FabConv.cpp
Src/Particle/AMReX_Particles.H

commit 3abb14a69f71c5ee6b406394137ad33b71c9b6ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 29 08:58:24 2019 -0700

    Fix NodeEB test

Tests/LinearSolvers/NodeEB/MyTest.cpp

commit 5cc33860d3cc1e50022a416d0b54a80f74caa1a4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Apr 28 21:32:18 2019 -0700

    Add parameter for dynamic shared memory

Tools/F_scripts/write_cuda_headers.py

commit a49ca7c2a51c671e7256048c0ead47ebff11db6c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Apr 28 17:04:14 2019 -0700

    Use different format for passing box to pragma

Tools/F_scripts/write_cuda_headers.py

commit 31511eee6312dcc2eb56c5cb08926156aa1e94d7
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Apr 28 15:57:19 2019 -0700

    Allow the GPU pragma to accept information about the box

Tools/F_scripts/write_cuda_headers.py

commit 88f7768ba043a328b392ea53e2a1176c306822fa
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Apr 28 15:57:01 2019 -0700

    Add version of grid stride calculation that uses box information

Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp

commit 8802ac6f661c409b5cf9def5f150eebfe5b8b503
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Apr 28 15:56:26 2019 -0700

    Add functions for shared memory reductions

Src/Base/AMReX_fort_mod.F90

commit b1b6e009a1c49a0a4438afc0ce0d605d674ea3b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 27 11:04:54 2019 -0700

    Change the default bottom solver to bicgcg for nodal RAP

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H

commit 4e98a228f8aa588d530479f70eb460c06e0577fb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Apr 27 09:06:34 2019 -0700

    Pass the mg_cg_verbose flag through the MacProjector

Src/LinearSolvers/MLMG/AMReX_MacProjector.H
Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp

commit ae61eb954876668d8c2fa4766808e5b68c3160a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 26 22:51:29 2019 -0700

    MLMG bottom solver: add new types cgbicg and bicgcg.  They will start with cg or bicg.  If fails, it will switch to the other.  If the alternative succeeds, the switch becomes permanent.

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit a49cfcf7d8cfec03de65d26ac0aec0fff88fc516
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 26 22:03:29 2019 -0700

    Fix omp bug in nodal solver with RAP

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit f15ee11afff2093ee2ada37493436053f4caa879
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 26 19:28:57 2019 -0700

    Remove use_hypre parameter from MLNodeLaplacian ctor

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 70d617fa0054c8178adb9e951adc329550304200
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 26 20:38:58 2019 -0400

    CMake: fix incorrect path

Src/CMakeLists.txt

commit f96cb4119c444067491834b4dcc177474a5f56a4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 26 20:32:00 2019 -0400

    CMake: fix printing of CUDA options

Tools/CMake/AMReX_SetupCUDA.cmake

commit 57d324d9d25e6774037870868c5beb953a1441db
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 26 17:08:13 2019 -0700

    Fix the indexes.

Src/Base/AMReX_FabArrayCommI.H

commit 36052abce4049bd58a15531fa40c6af2a5bed6aa
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 26 17:07:24 2019 -0700

    Free before allocing if resize a sized CudaGraph.

Src/Base/AMReX_CudaGraph.H

commit 5817608a37aa7884eede6fa23b64de5daad6f46d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 26 16:41:50 2019 -0700

    CMake: move CUDA-specific options to AMReX_SetupCUDA.cmake

Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_SetupCUDA.cmake

commit ba2538a32433b7e8162d8a501874c7d69b2bef95
Merge: 699592071 20a27e108
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 26 16:37:10 2019 -0700

    Merge branch 'development' into mr/cmake

commit ee9e95d3c84507fb24edb8f666c1084bd98ea258
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 26 15:34:03 2019 -0700

    Default run test case without nvprof.

Tests/GPU/CudaGraphs/GraphBoundary/run.corigpu

commit d5a2801027ba204cb6e50cecdc5b6d58030d3b71
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 26 15:33:31 2019 -0700

    Working test case comparing CPU, GPU and CudaGraph versions of FillBoundary.

Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d
Tests/GPU/CudaGraphs/GraphBoundary/main.cpp

commit a1a955b3b249fe29f6a484c40ecedd5fee4eb20e
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 26 15:32:29 2019 -0700

    First working version of FillBoundary using Graphs with MPI = 1.

Src/Base/AMReX_FabArrayCommI.H

commit fe0a2e88e97daa5a7f0780da265a32bf8999bdea
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 26 15:32:00 2019 -0700

    Change FB initialization to resize CudaGraphs.

Src/Base/AMReX_FabArrayBase.cpp

commit 9a560de6319c09c347c43098ee7541c9f90371ee
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 26 15:31:26 2019 -0700

    Clean up CudaGraph and allow resizing.

Src/Base/AMReX_CudaGraph.H

commit a11344e510a89c4a852411b49196f264deb1301b
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 26 15:07:43 2019 -0700

    Smarter GraphRegion checks and CPU version of functions.

Src/Base/AMReX_GpuControl.H

commit 20a27e10855e01044d07e1fdebbcea27ff2fed92
Merge: 1cf1b9f44 a07a2338d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 26 14:27:58 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 1cf1b9f441a79706a6efe7f489c9fa38084e9369
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 26 14:27:48 2019 -0700

    methods for defining the number of runtime real and integer components in the particle container

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 685c0eaf2fa6b6168e351c3b754dd0108bfc0903
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 26 14:24:13 2019 -0700

    update struct-of-arrays test to include runtime-added components

Tests/Particles/main.cpp

commit a07a2338df106d0cd377aa81decf9576ce96d4f3
Merge: 10cc51429 cb66da428
Author: mic84 <mrosso@lbl.gov>
Date:   Fri Apr 26 13:38:35 2019 -0700

    Merge pull request #467 from mwm126/patch-5
    
    Change FindPythonInterp (deprecated) to FindPython

commit 445b21b0e45f4d68e4e2d59ca0b05d8f051c93ea
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 26 13:03:18 2019 -0700

    including the runtime added comps in the ParticleContainer functions

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit cb66da42852da45a053b9acb6b829912cec83f48
Author: Mark Meredith <mwm126@gmail.com>
Date:   Fri Apr 26 15:54:31 2019 -0400

    Change FindPythonInterp (deprecated) to FindPython
    
    Since CMake 3.12, FindPython is the preferred way of detecting Python.
    Also run makebuildinfo_C.py with the detected Python version (instead of assuming env python)

Src/CMakeLists.txt

commit 6716ad84e69de088a386ff54d2603d8670b5bb5c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 26 12:24:57 2019 -0700

    functions for adding runtime real and int components

Src/Particle/AMReX_Particles.H

commit 2c4c0e2db290b23442287577168122fcc370bb8c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 26 12:21:25 2019 -0700

    Have the particle container keep track of how many runtime comps it has

Src/Particle/AMReX_Particles.H

commit 923bfb00197bbc3e0e546a96d64b6c680c1dec1e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 26 11:48:15 2019 -0700

    adding runtime soa components to StructOfArrays

Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_StructOfArrays.H

commit 10cc514296e634359690a308bd7f92e8ae34c323
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 26 11:34:48 2019 -0700

    Further summit script adjustment.

Tutorials/GPU/run.summit

commit 699592071f1fa08e9313ef9e209f07881f21c426
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 26 10:32:30 2019 -0700

    CMake: fix scope of Particle compile definitions

Src/Particle/CMakeLists.txt

commit b45a4191159365b14ee0d40dffa84ab6e94db307
Merge: ab1a090ee 04d8db7eb
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 26 10:28:02 2019 -0700

    Merge pull request #466 from maikel/feature/FabUtils_ngrow_IntVect
    
    Add more support for non-uniform grow vectors to MultiFab and FabArrayUtility

commit e0ec5c9ed7bfc232d658d63df03d83b19274f06a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 26 10:02:17 2019 -0700

    CMake: completely include AMReX_buildInfo.H into build tree.

Src/CMakeLists.txt
Tools/CMake/AMReXInstallHelpers.cmake

commit ab1a090ee2c87df8662e098d1338558e29190f62
Merge: 174fc9cb4 725da0f80
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 26 09:55:28 2019 -0700

    Merge pull request #465 from maikel/feature/Improve_Move_Assignment
    
    Improve move assignment operators for BoxArray and DistributionMapping

commit 174fc9cb416c69f77ff5905461f07a8b9221f42f
Merge: af4ece1fb ce6434991
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 26 09:19:10 2019 -0700

    Merge pull request #464 from rhouim/development
    
    Added a trilinear interpolation option for 3D on cpu.  This can be us…

commit 04d8db7ebba404631db36509f488a05a4e39f0f5
Author: Maikel Nadolski <maikel.nadolski@gmail.com>
Date:   Fri Apr 26 13:19:29 2019 +0200

    Add more support for non-uniform grow vectors to MultiFab and FabArrayUtility.

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit 725da0f80b8dd55c4c734e6774283d31fcb1df49
Author: Maikel Nadolski <maikel.nadolski@gmail.com>
Date:   Fri Apr 26 11:27:21 2019 +0200

    Use rule of six to improve constructors of BoxArray and DistributionMapping

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit af4ece1fbef6265b124a0c998c5bac49f8e9d8bd
Merge: 92846c516 e89e3c277
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Apr 25 21:58:15 2019 -0700

    Merge pull request #463 from maikel/feature/AmrMesh_refrat
    
    Improve AmrCore and AmrMesh constructors.

commit 92846c516c265d4102188bb64004c37c6f60fa82
Merge: cf568821d 476e659da
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Apr 25 19:57:47 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cf568821d3ade13bfed3840a43e6658fa91ea04b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Apr 25 19:57:30 2019 -0400

    also apply the shift to the remote neighbors (gpu neighbor particles)

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 476e659dad93e9901dffa3caa1c84eca6c03ad3c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 25 16:36:08 2019 -0700

    Remove debug lines

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 23fb2549a6c482cdfc9eeafb896ad8783b1b4de3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 25 16:33:48 2019 -0700

    Nodal 2d solver: save some codes in comments

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit f1985849761ffb58c2edab9bfe5333f544be4ab4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Apr 25 18:51:51 2019 -0400

    keep track of periodicity (gpu neighbor particles)

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit a994adb68758aea5fba871129f9996d05d2fd343
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Apr 25 18:51:09 2019 -0400

    nested struct for keeping track of neighbor tasks to perform

Src/Particle/AMReX_NeighborParticles.H

commit 43e138ad496545c42e5e1af0f7a0ca4e19bad8c3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Apr 25 18:50:39 2019 -0400

    functor for shifting neighbor particles periodically so that naive distance calculation will return the shortest distance

Src/Particle/AMReX_Functors.H

commit 6de9f597cf3ddc463f2d1a6884d27e6b63388b02
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 25 15:27:55 2019 -0700

    CMake: add options to enable/disable tutorials

CMakeLists.txt

commit 6e03e33f31d95f00add682c1c2f5c07120c9caef
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 25 15:18:53 2019 -0700

    CMake: change location of configuration files

Src/CMakeLists.txt
Tools/CMake/AMReXInstallHelpers.cmake

commit 9da635bf0bba3909f4d93abed85cfb536e0a557a
Merge: a81b9c743 b66f1cd11
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Apr 25 15:46:20 2019 -0600

    Merge branch 'development' into nodeghostcells

commit e1cdab269aa11647a76446cd9761d544b97e4638
Merge: 18eb7664a b66f1cd11
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 25 14:02:13 2019 -0700

    Merge branch 'development' into weiqun/mlmg

commit 18eb7664a05386f36105f502f56b8b4bdbc27c7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 25 14:01:19 2019 -0700

    Nodal RAP: fix R

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit b66f1cd11bc0f6b25d143e9eb470fe0ac735c7e3
Author: kngott <kngott@lbl.gov>
Date:   Thu Apr 25 12:41:28 2019 -0700

    Update script for shared nodes. Will be important to get resources as more users are added to the system.

Tutorials/GPU/run.corigpu

commit a66aedff421737bf085218b5e2d7f07166a184ff
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Apr 25 13:48:46 2019 -0400

    store information about the periodic shift in the grid map (gpu neighbor particles)

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit b4d74c99117d31fcb7c9e783929bbe6de573f28e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Apr 25 07:12:57 2019 -0700

    Revert "When we run the "bottom solver" at mglev = 0, we want to go ahead and"
    
    This reverts commit 43ecb9cecaa700ff77ce900e80180cbf34eba379.

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 43ecb9cecaa700ff77ce900e80180cbf34eba379
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 24 17:34:37 2019 -0700

    When we run the "bottom solver" at mglev = 0, we want to go ahead and
    solve to completion, so we set the "bottom solver tolerance" to the
    tolerance specified in the solve call, rather than 1e-4.

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit ce643499192be29fabdcde6e5091e835b850e38b
Author: rhouim <rhouim@ufl.edu>
Date:   Wed Apr 24 19:36:03 2019 -0400

    Added a trilinear interpolation option for 3D on cpu.  This can be used by using cell_bilinear_interp in the FillPatch routines.  This was tested with the Advection_AmrCore tutorial and it behaved as expected.

Src/AmrCore/AMReX_INTERP_3D.F90
Src/AmrCore/AMReX_Interpolater.cpp

commit cc3708a0461936ba957cd4ddac66526f1447b26a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 24 16:32:56 2019 -0700

    Change from cell-by-cell testing on volfrac to testing on flag

Src/Extern/Algoim/AMReX_algoim_integrals.cpp

commit 140761ec309f9145d674303b0bf020767878a65e
Merge: cb06bb30a af5e91619
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 24 14:11:30 2019 -0700

    Merge branch 'development' into weiqun/mlmg

commit 9dcbc68ceac9b70446bf9fcfe6c5eba436b02946
Author: kngott <kngott@lbl.gov>
Date:   Wed Apr 24 14:09:36 2019 -0700

    WIP: Starting conversion of 1 Rank FillBoundary.

Src/Base/AMReX_FabArrayCommI.H

commit 3f209ae6f1072aa0236a96fc4b00bbe284eabf35
Author: kngott <kngott@lbl.gov>
Date:   Wed Apr 24 14:09:16 2019 -0700

    Add graphs to FB object

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 80a418cb3211e37da3dc83538905ee21cdfc99e6
Author: kngott <kngott@lbl.gov>
Date:   Wed Apr 24 14:08:40 2019 -0700

    Add AMReX_CudaGraph.H to AMReX_Gpu.H and add bool declaring if graph is ready.

Src/Base/AMReX_CudaGraph.H
Src/Base/AMReX_Gpu.H

commit c76155835f746753124e7ffa2c9322b651e86533
Author: kngott <kngott@lbl.gov>
Date:   Wed Apr 24 14:07:09 2019 -0700

    Label auto const's as Arrayk4's for clarity.

Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit cb06bb30a57c032ca2277bdc02d53b1bfb7d4455
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 24 13:54:44 2019 -0700

    WIP: first pass of RAP coarsening

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit af5e91619bbf46ed67aa48499a928c2c21fa7ca4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Apr 24 11:33:49 2019 -0700

    Change '#if AMREX_USE_GPU' to '#ifdef AMREX_USE_GPU'

Src/Base/AMReX_FabArray.H

commit 3e4e7653663d3e9f1d0b7227c99f92be219481a7
Merge: f8a4694eb 7844b4fd7
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Apr 24 10:47:15 2019 -0700

    Merge branch 'development' into mr/cmake

commit 7844b4fd7d4c846f994a311b0956f7b92da4987b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 24 10:32:07 2019 -0700

    Revert "Don't set regular stencils when volfrac < 1e-12 -- go ahead and"
    
    This reverts commit fd5dade48cf3fb52cbd2b3076946b3cd382760ef.

Src/Extern/Algoim/AMReX_algoim_integrals.cpp

commit fd5dade48cf3fb52cbd2b3076946b3cd382760ef
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 24 09:29:53 2019 -0700

    Don't set regular stencils when volfrac < 1e-12 -- go ahead and
    compute the integrals.

Src/Extern/Algoim/AMReX_algoim_integrals.cpp

commit e89e3c277cc7b5ad8ac58fd81814d77e68801c12
Author: Maikel Nadolski <maikel.nadolski@gmail.com>
Date:   Wed Apr 24 09:47:04 2019 +0200

    Use std::move to avoid allocations.

Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_AmrMesh.cpp

commit b7ff3247713c4e84cd3eddb3e4d2df25cf66a970
Author: Maikel Nadolski <maikel.nadolski@gmail.com>
Date:   Wed Apr 24 09:32:08 2019 +0200

    Improve AmrCore and AmrMesh constructors.
    
    Change the refinement ratio paramter of AmrMesh's constructor from
    std::vector<int> to amrex::Vector<IntVect> to be more consistent with
    non-uniform refinement ratios.
    
    Add a refrat parameter to AmrCore's constructor. Before this change
    AmrMesh's refinment parameter was never set to this custom value.

Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit 530db41797eae40d36066e1904aad2c095dc55bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 23 16:54:49 2019 -0700

    WIP: RAP stencil: add A matrix

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 948755d2d2053d2760ea541ad3f0aac2b20956df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 23 16:19:19 2019 -0700

    WIP: RAP stencil: P

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 7ebd60f966413e8caa274fc7752738950704af07
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 23 16:12:48 2019 -0700

    formatting fix

Docs/sphinx_documentation/source/Testing.rst

commit 8ae2c9ca5b910aecf599c9885a137ffd6b12d8c3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 23 16:11:54 2019 -0700

    remove redundant statement (test runner docs)

Docs/sphinx_documentation/source/Testing.rst

commit cfee094f71d84d87f3add3eb0a9e8c3024870b6d
Merge: 9cf51ea96 1bbc83cf7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 23 16:09:12 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9cf51ea96226d3be3c1b59f1660ef1d20b2325a6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 23 16:09:00 2019 -0700

    fix typo

Docs/sphinx_documentation/source/Testing.rst

commit c8ab96844e4c2e7b4419c2f2d4d822cddd6dd873
Author: kngott <kngott@lbl.gov>
Date:   Tue Apr 23 16:07:41 2019 -0700

    Store void* in CopyMemory instead of Array4

Src/Base/AMReX_CudaGraph.H
Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit d79237b25db8bee69225c1ca5a55d881fe669a90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 23 15:17:06 2019 -0700

    WIP: RAP stencil: interp_from

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 5c29d1da3d631d3b47f38f080e6ceb53754216c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 23 15:01:19 2019 -0700

    WIP: RAP stencil

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 53a168f76c028cee178f9cf022e4a24735535887
Author: kngott <kngott@lbl.gov>
Date:   Mon Apr 22 19:49:12 2019 -0700

    Move to Arenas.

Src/Base/AMReX_CudaGraph.H
Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit ee850e27baec9a8c80aba6dea14a4dec6f9af98e
Author: kngott <kngott@lbl.gov>
Date:   Mon Apr 22 17:22:59 2019 -0700

    Move AMReX_CudaGraph to Src/Base.

Src/Base/AMReX_CudaGraph.H
Src/Base/Make.package
Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit 94a81cc4970584addbd78d5f2d76c84c0556b936
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 23 13:16:32 2019 -0700

    use Array4<void> in cuda graph

Src/Base/AMReX_Array.H
Tests/GPU/CudaGraphs/GraphReuseCopy/AMReX_CudaGraph.H
Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit f8a4694eb76c8b87574f153a8effb5f25a2743d7
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Apr 23 11:52:16 2019 -0700

    CMake: get interface properties rather than private properties for Flags targets

Tools/CMake/AMReX_Config.cmake

commit 1bbc83cf7c5cde64e225d39f8c12cb0e1e79f278
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 23 11:24:57 2019 -0700

    minor

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 022bcad68bf4fbeee44abd53b869bed9a7eb17be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 23 11:19:41 2019 -0700

    No need to call FillBoundary on integrals because we compute them in ghost cells.

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit a95848df1d4653be65d17ba908b673ddd7b41eaf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 23 10:57:38 2019 -0700

    Use Array4 in computing integrals using algoim

Src/Extern/Algoim/AMReX_algoim_integrals.H
Src/Extern/Algoim/AMReX_algoim_integrals.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit fd09d1d57bc889bbf1051bf88ec5871d981d4378
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 23 10:23:18 2019 -0700

    Add Make.algoim. USE_ALGOIM -> AMREX_USE_ALGOIM. For hypre and petsc, both _DIR and _HOME are allowed.

Src/Extern/Algoim/CMakeLists.txt
Src/Extern/Algoim/Make.package
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tests/LinearSolvers/NodeEB/GNUmakefile
Tools/GNUMake/Make.defs
Tools/GNUMake/packages/Make.algoim
Tools/GNUMake/packages/Make.hypre
Tools/GNUMake/packages/Make.petsc

commit 75ba20ea4bea9761ee9082fedfb3bf5186aa0f0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 23 08:59:51 2019 -0700

    FabArray: m_host_fabs_v is gone.

Src/Base/AMReX_FabArray.H

commit c15ec2907dfe9f0294f98ef6baa17e681ba44e6f
Author: kngott <kngott@lbl.gov>
Date:   Mon Apr 22 17:07:38 2019 -0700

    Remove un-needed MemCpy from CudaGraph.

Tests/GPU/CudaGraphs/GraphReuseCopy/AMReX_CudaGraph.H

commit 1e0c4d44f763198d8e4d4138d972daac7981a85e
Author: kngott <kngott@lbl.gov>
Date:   Mon Apr 22 17:01:40 2019 -0700

    Update test for improved CudaGraph object.

Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit 900276a9faf29b717f0100b82080f39097c7242e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 22 17:00:07 2019 -0700

    adding some pages to the documentation about the regression testing

Docs/sphinx_documentation/source/Regression_Testing_Chapter.rst
Docs/sphinx_documentation/source/Testing.rst
Docs/sphinx_documentation/source/index.rst

commit ee31daee833669f83d4ce8a1c0f22d962a6de959
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 22 15:51:49 2019 -0700

    adding a sample .ini for running the amrex regression tests locally

Tools/RegressionTesting/AMReX-tests.ini

commit 7dc7789542c003bc3e9be5a454475928d1a743a8
Merge: 1d660a810 4f095bf31
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 22 15:41:27 2019 -0700

    Merge branch 'development' into weiqun/mfdtor

commit a8e0b2d89eda7eff40b80bf97f0d2d1d8bc9d6c9
Merge: b88767d1e 4f095bf31
Author: kngott <kngott@lbl.gov>
Date:   Mon Apr 22 15:30:39 2019 -0700

    Merge branch 'development' into kngott/cudaGraphs

commit 4f095bf3124d2b9b9ac13bd82305fb0f2b7da9f0
Author: kngott <kngott@lbl.gov>
Date:   Mon Apr 22 15:27:10 2019 -0700

    Make Array4 Variables non-const.

Src/Base/AMReX_Array.H

commit b88767d1e6a28d896ce36dba5e1cb21d2c416662
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 22 15:11:05 2019 -0700

    Tidy cuda graph classes

Tests/GPU/CudaGraphs/GraphReuseCopy/AMReX_CudaGraph.H

commit ce9f2a02cd4739d200db6d06103ede0eb94b5799
Merge: 087982fa9 b68fadfc1
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 22 13:46:47 2019 -0700

    Merge branch 'development' into mr/cmake

commit b68fadfc1071c3e615d7ed65fe641a5910c17f96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 22 12:58:22 2019 -0700

    Add prerequisites for building AMReX.  This addresses comment #1 in Issue #458.

Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst

commit 84e222fad80f77577e84877dcb0cafa4ab3eadf4
Author: kngott <kngott@lbl.gov>
Date:   Mon Apr 22 12:41:21 2019 -0700

    Separate CudaGraph object.

Tests/GPU/CudaGraphs/GraphReuseCopy/AMReX_CudaGraph.H
Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit 0f783533b8feffd3e68682816ce443289d83a58f
Merge: 10f9372bc 87ca50e70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 22 12:27:23 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 10f9372bc2e64ae211577242b3e5e73f6790cc84
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 22 12:27:16 2019 -0700

    Update compilestesing.py for python 3

Tools/CompileTesting/compiletesting.py

commit 2b96cafc674ac07b2e32fbc3847f529db7976daa
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Apr 22 10:31:22 2019 -0700

    Add John to core contributor list.

README.md

commit 87ca50e7025d0191cc49e0e94e68b73d38bf25fa
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Apr 22 10:31:22 2019 -0700

    Add John to core contributor list.

README.md

commit a4ca75cdcb4d21ec208ff2534f7ea0be34507561
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Apr 22 06:48:04 2019 -0700

    Fix oops in how we read in n_error_buf now that it is locally an IntVect

Src/AmrCore/AMReX_AmrMesh.cpp

commit 0268c8326c600e5baa73c5f28e4061b4a2dce476
Author: kngott <kngott@lbl.gov>
Date:   Mon Apr 22 00:31:16 2019 -0700

    First draft of working Graph object.

Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit 18b8159006c03f2355681ac46c3a8e08b112d3ac
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 21 13:18:53 2019 -0700

    Add more detail about using GitHub issues.

README.md

commit b213ee796cd1b57f2de08b47f96b53e58e8ad65a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 21 13:09:36 2019 -0700

    Add list of current "core developers" to AMReX README

README.md

commit 8183041a3d4461e9680dc3d0e38d5a697eec0d8d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 21 13:18:53 2019 -0700

    Add more detail about using GitHub issues.

README.md

commit 46146292dde1961146071fa66a230de050d42220
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 21 13:09:36 2019 -0700

    Add list of current "core developers" to AMReX README

README.md

commit f0dff6e75ff66c8a03c5de8b4b4aa3b0adaf2877
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 20 20:19:58 2019 -0700

    Add optional argument for direction to AmrMesh::nErrorBuf function.  Add IntVect version, nErrorBufVect.  add optional argument for direction to FabArrayBase::nGrow

Src/AmrCore/AMReX_AmrMesh.H
Src/Base/AMReX_FabArrayBase.H

commit 1d660a810b89d5c4f26390b1df58d6e0a411cac4
Merge: 9f23f314c 515df37b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 20 18:37:00 2019 -0700

    Merge branch 'development' into weiqun/mfdtor

commit 515df37b2b3735a51fb4671e227d695d32071d2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 20 18:03:42 2019 -0700

    add a new BoxArray::growcoarsen function that takes IntVect as ngrow parameter and use it in TagBoxArray

Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit 11891071c7c736cba4270bf2023e8d57f3c8c46e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 20 17:59:58 2019 -0700

    return IntVect from TagBoxArray::borderSize

Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_IntVect.H

commit 9f23f314cb6cd2c0bdb4a05c52480776c91f0a00
Merge: df47ebb5e 3ce3ab881
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 20 17:47:53 2019 -0700

    Merge branch 'development' into weiqun/mfdtor

commit df47ebb5e4bad4e4869d0bf13f7f95b02aac1ce8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 20 17:47:04 2019 -0700

    TagBoxArray: host ptr is the owner now

Src/AmrCore/AMReX_TagBox.cpp

commit 3ce3ab881f9764403baa17420cce613be7dc5f7e
Merge: df61a42c9 cf9775d57
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Apr 20 17:02:45 2019 -0700

    Merge pull request #461 from chaw0023/HypreDeclaration
    
    Add missing declaration for hypre_int

commit cf9775d57b4084e24f8c2892df6fac258b1e2364
Author: Saurabh Chawdhary <saurabh.chawdhary@gmail.com>
Date:   Sat Apr 20 17:57:45 2019 -0500

    Add missing declaration for hypre_int

Src/Extern/PETSc/AMReX_PETSc.cpp

commit df61a42c97e01f73f9c135ff109c1be36798a8af
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Apr 20 15:56:28 2019 -0700

    Makes n_error_buf in AmrMesh class an IntVect rather than an int.
    Note that AmrCore-based codes can use this option by setting n_error_buf_x, n_error_buf_y, n_error_buf_z
    rather than setting simply n_error_buf in the inputs file, but setting n_error_buf will still work.
    AmrLevel-based applications are only able to use the int functionality since they don't currently have
    an errorEst routine that takes an IntVect.
    AmrCore-based apps may need to change based on this change; AmrLevel-based codes should not have to.

Src/Amr/AMReX_Amr.cpp
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp

commit cad287871f6d6202fc550dac1db4d2cceb4d2577
Merge: 2f5779244 7f819b191
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 20 12:01:13 2019 -0700

    Merge branch 'development' into weiqun/mfdtor

commit 7f819b19119505faac2a050d577ddde3d921ca02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 20 12:00:36 2019 -0700

    avoid fortran keyword

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90

commit 3f2a8fec28d401d56946b04a878ebd0a479c1d85
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 20 11:51:54 2019 -0700

    shorten names

Tests/Slice/GNUmakefile
Tests/Slice/Make.package
Tests/Slice/inputs
Tests/Slice/main.H
Tests/Slice/main.cpp
Tests/SliceWithInterp/inputs
Tests/SliceWithInterp/main.cpp

commit 2f57792441ead08764fb6939634970344d88b345
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 20 09:13:06 2019 -0700

    Update the new fabDevicePtrAtLocalIdx and fabHostPtrAtLocalIdx functions because m_host_fabs_v has been removed

Src/Base/AMReX_FabArray.H

commit 9dd2aee2caedc63a30526fda7f0a33635fc2b3aa
Merge: c71309755 264d4bf77
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 20 08:53:09 2019 -0700

    Merge branch 'development' into weiqun/mfdtor

commit 264d4bf77bd9ea8c42d78198de080f9c55726c2a
Merge: 6d834eef1 a6fdc77b1
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 19 20:22:37 2019 -0700

    Merge pull request #459 from chaw0023/PetscSolveLS
    
    Petsc bottom solver in F_interface; update GNUmakefile

commit 6d834eef18f07230d87a769597881fc95fdb239f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 19 20:09:27 2019 -0700

    add inputs.hypre and inputs.petsc to ABecLaplacian_C tutorial

Tutorials/LinearSolvers/ABecLaplacian_C/inputs.hypre
Tutorials/LinearSolvers/ABecLaplacian_C/inputs.petsc

commit c5ab471a585bcbe9e69e86bf2123ba307ecfa841
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 19 19:49:39 2019 -0700

    PETSc: remove dependency on HYPRE

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/PETSc/AMReX_PETSc.H
Src/Extern/PETSc/AMReX_PETSc.cpp
Src/Extern/PETSc/AMReX_PETSc_fort_mod.F90
Src/Extern/PETSc/Make.package

commit 087982fa99390df771f2a56581656464abfbf856
Merge: ad0e2bd55 e031ae679
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 19 17:35:40 2019 -0700

    Merge branch 'development' into mr/cmake

commit ad0e2bd55653fae52948ff38f982510013ebdf3d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 19 17:34:59 2019 -0700

    CMake: clean up

Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/TestManager.cmake
Tools/CMake/select_gpu_arch.cmake

commit c3085b6a1aac3ecb0641c0f8ef4e5dbf31cd51c1
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 19 17:31:38 2019 -0700

    CMake: fix bug in CUDA flags due to recent changes

Tools/CMake/AMReX_Config.cmake

commit 299f345cdb656d018767a84e673f9681022013bc
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 19 17:17:01 2019 -0700

    CMake: treat C++ and Fortran flags in a target-oriented fashion
    
    * Define INTERFACE targets for C++ and Fortran flags.
    * Export those targets so that app codes can use them.

Src/CMakeLists.txt
Tools/CMake/AMReXFlagsTargets.cmake
Tools/CMake/AMReXInstallHelpers.cmake
Tools/CMake/AMReX_Compilers.cmake

commit a6fdc77b17a19ae4be6b0082e7d144e082d2782c
Author: Saurabh Chawdhary <saurabh.chawdhary@gmail.com>
Date:   Fri Apr 19 18:25:25 2019 -0500

    Add Particle fortran interface directory to Pdir

GNUmakefile.in

commit ae58f6dd2a0734577251b0ac20070ffd631f14f2
Author: Saurabh Chawdhary <saurabh.chawdhary@gmail.com>
Date:   Fri Apr 19 18:02:07 2019 -0500

    Add option for using petsc as bottom solver

Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90

commit b6dd1be8707f46a0f23f5d097e785c9697bf15f7
Author: Saurabh Chawdhary <saurabh.chawdhary@gmail.com>
Date:   Fri Apr 19 18:11:31 2019 -0500

    Add option --enable-petsc to use PETSc as bottom solver

GNUmakefile.in
Tools/libamrex/configure.py

commit e031ae6797943d4752678dc02f96fa00ec7802a8
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 19 15:52:48 2019 -0700

    run.summit update #4.

Tutorials/GPU/run.summit

commit c9e2251e32c3735e60a571721a32cfd882f6ca8c
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 19 15:40:21 2019 -0700

    run.summit update #3.

Tutorials/GPU/run.summit

commit a528bf6cafe4e470d03daa6814c5c67f2065e4be
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 19 14:03:30 2019 -0700

    More Summit and CoriGPU script updates.

Tutorials/GPU/run.corigpu
Tutorials/GPU/run.summit

commit 3f1e2423abc85065f19e58b078319384369782d6
Merge: ac36e5165 ecdbbcbfc
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Apr 19 16:37:52 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ac36e51651e8dc880d87fe31f1a827a00a8025d6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Apr 19 16:37:40 2019 -0400

    remove misleading timer from NeigborList::build

Src/Particle/AMReX_NeighborList.H

commit e10716e63398bc55836ee45e03e9f2ddc8ff9efe
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Apr 19 16:37:07 2019 -0400

    change AMREX_ALWAYS_ASSERT to AMREX_ASSERT here

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit ecdbbcbfc158e18fb4d3c8fe06dd6ee02f03d846
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 19 12:41:50 2019 -0700

    Add Summit and jsrun specs to sample run script.

Tutorials/GPU/run.summit

commit dafdea5b1628c6893a8cda2c3f3ad1141e36df12
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 19 12:36:05 2019 -0700

    amrex::Tuple is now an alias to std::tuple

Src/Base/AMReX_Tuple.H

commit 0baf0cdc439d33a10318945ca062c3169bf1ccd6
Merge: aaadc34db 60b7687a6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 19 11:23:49 2019 -0700

    Merge pull request #440 from RevathiJambunathan/SliceGenerationForDiagnostics_RJ
    
    Slice generation for diagnostics rj

commit aaadc34db48146f3cffb2ee89c7f70625b019240
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 19 10:59:44 2019 -0700

    AmrMesh: relax the assumption that the base level domain has even number of cells in each direction

Src/AmrCore/AMReX_AmrMesh.cpp

commit 73e381e9f4443e9144d273ba75f3ee5e9dbcfa3f
Merge: 06a58e9bd c81211585
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 19 10:36:09 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 06a58e9bde1cdba6298cacd783569aec3129c893
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 19 10:35:56 2019 -0700

    minor tutorial notes

Docs/sphinx_documentation/source/EB.rst
Docs/sphinx_tutorials/source/EB_Tutorial.rst

commit 67058fb0ee21fe224803feb39c3e979e1692574f
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 19 10:14:40 2019 -0700

    Graphs using Graph Class. WIP.

Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit c81211585e5473fdb954d0c29dbf26a52e89e107
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 19 09:32:20 2019 -0700

    octree average down leaves: fix component index

Src/F_Interfaces/Octree/AMReX_octree_mod.F90

commit 343ff3d2f6214a93c8f6f46b295277b9d1718f88
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 19 09:13:01 2019 -0700

    EB/Poisson tutoral (enclosed sphere at zero potential with a point charge in the interior); fixed convergence issue - for now must specify Dirichlet domain boundary conditions, even if the fluid doesn't touch the domain boundary (AMReX was thinking the problem was singular)

Tutorials/EB/Poisson/inputs
Tutorials/EB/Poisson/main.cpp

commit 576b755c48d700ba1a5d6f49da7998d946efc448
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 19 08:34:42 2019 -0700

    init_data function

Tutorials/EB/Poisson/Make.package
Tutorials/EB/Poisson/Poisson.H
Tutorials/EB/Poisson/Poisson.cpp
Tutorials/EB/Poisson/Poisson_F.H
Tutorials/EB/Poisson/main.cpp
Tutorials/EB/Poisson/poisson.F90

commit 60b7687a6ac6c5ecfd7b02eb597059f8dc943ef7
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Thu Apr 18 23:20:28 2019 -0700

    Modified the diagnostic slice generation to inherent the index type of the underlying data. The code reads in lo and hi of the slice, and coarsening ratio. If the input for coarsening ratio is not an exponent of 2, then within the code, the ratio is modified to the nearest exponent of 2. The slice is generated in three steps. First, using the input lo and hi, the slice is generated with geom.CellSize() equal to the computational domain. Note that, in this test case, only one level of refinement is assumed. Next, if a 2D slice is extracted at a location where the data points are not available, then values are interpolated on the slice from the nearest points. Finally, if the coarsening ratio in any direction is > 1, then the data from the refine slice is averaged and stored on the coarsened slice ensuring that the box array sizes for both, refined and coarse slice are equal. I have assumed nghost > 0, since for interpolation, we need values from the ghost cells. The initial values for the baseline slice is such that the 0th,1st, and 2nd component correspond to x-pos y-pos, and z-pos, respectively.

Tests/CreateSliceForDiagnosticsWithInterpolation_adjusttocoarsenIfrequired/inputs
Tests/CreateSliceForDiagnosticsWithInterpolation_adjusttocoarsenIfrequired/main.cpp

commit c8f7df4e52135a95e174c5c07bf7746b26f216ee
Merge: a4011bcac 1f04f65b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 18 21:40:38 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a4011bcac9b6512e7f5776cd16754c2d3e8821f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 18 21:40:03 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

Src/Particle/AMReX_NeighborList.H
Src/Particle/AMReX_ParticleContainerI.H
Tutorials/EB/MacProj/GNUmakefile
Tutorials/EB/MacProj/Make.package
Tutorials/EB/MacProj/initEB.H
Tutorials/EB/MacProj/initEB.cpp
Tutorials/EB/MacProj/main.cpp
Tutorials/EB/Poisson/GNUmakefile
Tutorials/EB/Poisson/Make.package
Tutorials/EB/Poisson/inputs
Tutorials/EB/Poisson/main.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile.libamrex
Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp

commit 9afd6457542e4475a6055aa23d71df2d398281a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 18 21:36:25 2019 -0700

    octree average_down: support for components and volume weighted

Src/F_Interfaces/Octree/AMReX_octree_fi.cpp
Src/F_Interfaces/Octree/AMReX_octree_mod.F90

commit 000aa22131d4e36389835d516a191e9583ed3452
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 18 21:04:16 2019 -0700

    fix bug in octree leaf index array

Src/F_Interfaces/Octree/AMReX_octree_fi.cpp

commit 157d59cf4123a8e83999ec53712e3032f29f6517
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 18 20:44:56 2019 -0700

    average down octree leaves

Src/F_Interfaces/Octree/AMReX_octree_fi.cpp
Src/F_Interfaces/Octree/AMReX_octree_mod.F90

commit 0f5429e6e3b7181b3d1bb01d07908fa9666d1a49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 18 20:44:06 2019 -0700

    add FabArray member functions for getting fab ptr given local index

Src/Base/AMReX_FabArray.H

commit 1f04f65b973e61be03ba1d1c06d3d2daf03db084
Merge: e0c5cfc7e 902f0c642
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 18 17:45:13 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit e0c5cfc7e2930bbf1c47c47a1d779ca0707e85d0
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 18 17:44:27 2019 -0700

    EB Poisson solver example.  Needs a little tweaking still as the MG isn't converging well yet.

Tutorials/EB/Poisson/GNUmakefile
Tutorials/EB/Poisson/Make.package
Tutorials/EB/Poisson/inputs
Tutorials/EB/Poisson/main.cpp

commit 902f0c642015edb6e82419cfc1cb1af7ad1b0643
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Apr 18 19:58:32 2019 -0400

    instruct thrust to use pooled memory for it's internal reduce operation in build neighbor list gpu

Src/Particle/AMReX_NeighborList.H

commit 0688ac20d2b3b03d7d99052f2ec2200013210ad5
Merge: eb9c07acb 63baf3cb4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Apr 18 19:10:23 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit eb9c07acb9c4580f644cad692effaf06e05fa30b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Apr 18 19:09:34 2019 -0400

    cache temporary variables in GPU NeighborList::build to save memory and avoid expensive cudaMalloc/cudaFree calls

Src/Particle/AMReX_NeighborList.H

commit 63baf3cb4dfde4cd3c4c5b61b0e160cfb4df2e47
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 18 12:34:13 2019 -0700

    update PIC tutorial makefile

Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile.libamrex

commit 7695e8f07a0de9f2c969861f31c8f8e0909c4f6c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 18 11:13:44 2019 -0700

    dual grid particle restart - still need to skip if the header doesn't exist

Src/Particle/AMReX_ParticleContainerI.H

commit 21e6f94a6bc0c870de91c44e7d99bf590b74091f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 18 10:59:40 2019 -0700

    fix typo

Src/Particle/AMReX_ParticleContainerI.H

commit 0380809fca54c17a4e9a39a31379e7e75003811d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 18 10:58:17 2019 -0700

    in the particle restart, open the data file in binary mode. text mode is not sure to work for all implementations

Src/Particle/AMReX_ParticleContainerI.H

commit d026c805655394d466c9f375c67ccea584a337a9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 18 10:57:08 2019 -0700

    fix logic in the dual grid restart to handle the case where not all levels have particles

Src/Particle/AMReX_ParticleContainerI.H

commit d24e9c81c4c53ee9e0764bdf3830ce372f9e2efc
Merge: b972db4b9 b498ec9ae
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 18 10:52:13 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b498ec9aebcf81cdd810e5e464345ca88d5defe1
Merge: a7bcbbd8c 7a7bc18e1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Apr 18 13:50:23 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b972db4b97e6212da1e97ae6405eeda7bb1ed5df
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 18 10:50:18 2019 -0700

    fix whitespace errors in Makefile

Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile.libamrex

commit a7bcbbd8cd382e53a47be0c83c137d1a0acdd34a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Apr 18 13:49:59 2019 -0400

    add missing file

Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp

commit 7a7bc18e1743a38657fd1fd463dbce83230e55d2
Merge: dc78bd0f2 7f010c9b2
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 18 09:42:38 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit dc78bd0f2535c75466db58c0d8ad29ea1abce9f1
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 18 09:42:26 2019 -0700

    cleanup, comment tutorial

Tutorials/EB/MacProj/GNUmakefile
Tutorials/EB/MacProj/Make.package
Tutorials/EB/MacProj/initEB.H
Tutorials/EB/MacProj/initEB.cpp
Tutorials/EB/MacProj/main.cpp

commit d652fdce8487f67ebda190df557b4907031143ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 18 09:14:54 2019 -0700

    octree: add BoxArray and DistributionMapping for leaf nodes only

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.H
Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H
Src/F_Interfaces/Octree/AMReX_octree_fi.cpp

commit 7f010c9b2675d6b56c2c01cfeaf3750181f7a0ac
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 17 19:42:21 2019 -0400

    move GNUmakefile.libamrex to the proper location

Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile.libamrex

commit bc18fc80c66615c71edcdd619600c4153d289b9a
Merge: f66a97a3f d0853a069
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 17 19:41:35 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f66a97a3febe8c0e1e4a434ae991d13ba15e02f6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 17 19:41:11 2019 -0400

    Adding a makefile, courtesy of Chris Daley and Weiqun, for building the PIC tutorial using a shared amrex library

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile.libamrex

commit 2a4360606ad71ca0706ac9c95c085df497ae23b8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 17 19:40:28 2019 -0400

    add a few more options to the configure.py script for libamrex

Tools/libamrex/configure.py

commit d0853a0692c6fc16a832bc5a6300dc8a34c85a5a
Merge: 29db67e01 e17dc4c90
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 17 15:37:15 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit e17dc4c90644e804818a1809f0e5fb6b128e66d1
Merge: 2136fbeb4 31b75c447
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 17 18:36:44 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 29db67e01c56ff2ebaec5fc7b2e5dba4beb417e8
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 17 15:36:31 2019 -0700

    this tutorial now uses a mac projection to compute flow around a sphere given an initial velocity field of (1,0,0).  There is also now a plotfile output that outputs the initial and final velocity and divergence

Tutorials/EB/MacProj/main.cpp

commit 2136fbeb4dafeaeba0500a748240a33410527084
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 17 18:36:11 2019 -0400

    use the share, gpu-enabled initialization routines for all the different versions of the EM PIC Tutorial

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/EMParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Source/Make.package

commit 242d0026cc63ac610956193557befbff59c7fca4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 17 18:34:57 2019 -0400

    update repo name in job submission script

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/script.sh

commit 8a1c44ac27ecc8f967ced89981ed4b2a256c8d06
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 17 18:14:05 2019 -0400

    some tweaks and bug fixes to init particles

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp

commit afe615c7766b6fbd042dac7e2b797ff06d176dad
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 17 18:06:36 2019 -0400

    minor formatting change

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90

commit 61e8f44517bf96e718d637d8b786b55114f41904
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 17 18:02:15 2019 -0400

    correct CUDA version of gather_fields routine (EMPIC Tutorial)

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H

commit c5bba7492809b528974569f0abb224c349a2bfd5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 17 15:00:39 2019 -0400

    update python utility to look for the correct number of digits in the output

Tools/Py_util/amrex_particles_to_vtp/amrex_binary_particles_to_vtp.py

commit c71309755086051f2c0e4703ad6d29bb51945315
Merge: a24e0a889 fd0fd9ca0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 17 11:01:20 2019 -0700

    Merge branch 'development' into weiqun/mfdtor

commit a24e0a8897cdffe04c07c17ed288a62600f28e7a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 17 11:01:11 2019 -0700

    no need to build device fabs for the temporary multifab in overridesync

Src/Base/AMReX_FabArrayUtility.H

commit a8a2399e4e87ff537cd27c22bda43337b6e472cd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 17 13:44:32 2019 -0400

    EM PIC Tutorial fix - need to convert this box so that it has the same type as jx (in check_langmuir_solution)

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp

commit 7d10a8722bfb2210bc0a9ea578139f9b3e0c39c4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Apr 17 13:43:03 2019 -0400

    mark these functions __host__ __device__ so they can also be run on the host for debugging

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H

commit 31b75c44745cff48ef2480e3f099447275a3d08b
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Apr 17 10:07:51 2019 -0700

    CMake: add path to typechecker in export config file

Tools/CMake/AMReXConfig.cmake.in

commit fd0fd9ca0ca71f1201c3139ede50616a12ab6660
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 17 07:47:47 2019 -0700

    fix particle restart when finestLevel() goes down

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit b0ca1ea577e13a9a11db7ebbb7bfdf013f31318b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 16 21:58:04 2019 -0700

    fix a bug in tutorial

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 132c15e405fbff99b7a60393b4421c7dd465cdc4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 16 19:04:17 2019 -0700

    fix alias FabArray

Src/Base/AMReX_FabArray.H

commit 18bed7f4d3815922049d4d495e848565f64c8538
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 16 17:03:04 2019 -0700

    fix data ptr consistence check

Src/Base/AMReX_FabArray.H

commit 6cf022043079664e194be7b4dc02087ae7504fae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 16 16:56:53 2019 -0700

    skip delete for nullptr

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabFactory.H

commit df60503107a62d0f6a9b474a7d5b83dc58097f34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 16 14:43:33 2019 -0700

    Option to not create device fabs

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.cpp

commit 56ccba9bea51bbd83e3f3926cd958dffa69981eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 16 14:25:23 2019 -0700

    remove unused function

Src/Base/AMReX_FabFactory.H

commit 41a5b51119f7a12a2db2cf747cee9295c8c20174
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 16 14:19:52 2019 -0700

    make sure setFab only takes host fab. remove some deprecated functions in CoordSys

Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_VisMF.cpp
Src/EB/AMReX_EB2_MultiGFab.cpp
Src/EB/AMReX_MultiCutFab.cpp

commit ae7025a55912cb1ac6c68cd867bd28c9eacc2a72
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Apr 16 14:00:53 2019 -0700

    support on demand mode where an MFIter loop can be easily transformed into the async form

Src/Amr/AMReX_Amr.cpp
Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp
Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp
Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/pthreads_common/RGIter.H
Src/AmrTask/rts_impls/pthreads_common/RGIter.cpp
Src/AmrTask/rts_impls/pthreads_common/WorkerThread.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/._Exec
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/._README
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/._Source
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/._Make.Adv
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/._SingleVortex
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/._UniformVelocity
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.omp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.pthreads
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.upcxx.pthreads
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._face_velocity_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._inputs
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/._probin
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/face_velocity_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/inputs
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/probin
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._inputs
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._probdata.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/._probin
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/inputs
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/probdata.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/probin
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/README
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv.H
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._AdvBld.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv_F.H
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv_advance.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv_dt.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv_io.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Adv_setup.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Src_2d
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Src_3d
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._Src_nd
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/._main.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv.H
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/AdvBld.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv_F.H
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv_advance.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv_dt.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv_io.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv_setup.cpp
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_2d/._Adv_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_2d/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_2d/._compute_flux_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_2d/._slope_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_2d/Adv_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_2d/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_2d/compute_flux_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_2d/slope_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/._Adv_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/._compute_flux_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/._slope_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/Adv_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/compute_flux_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/slope_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._Adv_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._Tagging_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._tagging_params.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Adv_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Tagging_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/tagging_params.f90
Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/main.cpp
Src/Base/AMReX_MultiFabUtil_Perilla.cpp

commit e2d4a9845c44bc679e11febe0e3bd2ebaf3de2a8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Apr 16 15:11:16 2019 -0400

    formatting change

Src/Particle/AMReX_Particles.H

commit d62b1750678de777162520d49ae3cce5b12fe3a1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Apr 16 15:10:44 2019 -0400

    offloading init particles in the CUDA version of the EM PIC Tutorial

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp

commit c5d83f538cf291d8bdfb3dc11bb348e17555c010
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Apr 16 15:09:44 2019 -0400

    add functions to StructOfArrays that return a GPU-accessible holder for the data pointers.

Src/Particle/AMReX_StructOfArrays.H

commit 54b34bfe9b3f9e4b77ead0a3ca04855b2e1e3bbe
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Apr 16 15:02:25 2019 -0400

    implement GPU version of RandomNormal

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit 8bab9adee54ab39471fa74c08a9e0eb5104ab3cc
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Apr 16 15:01:45 2019 -0400

    automatically deallocate the random number arrays in amrex::Finalize

Src/Base/AMReX.cpp
Tests/GPU/RandomNumberGeneration/main.cpp

commit b98061daef33d5cfe685347c91c38923d8713214
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 16 10:30:13 2019 -0700

    remove deprecated ctors

Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IArrayBox.cpp
Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_Mask.cpp
Src/EB/AMReX_EBFArrayBox.H
Src/EB/AMReX_EBFArrayBox.cpp

commit 26481ab33b3a527ffb992c31144fb3b2e4db8e73
Merge: 39c1804c4 d666cc265
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 16 10:04:01 2019 -0700

    Merge branch 'development' into weiqun/mfdtor

commit 39c1804c4b2c9c43fa1dc52a2aa30f3082064454
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 16 10:02:18 2019 -0700

    FabArray: make host fab the main owner and device fab an alias.  This will allow for not creating device fabs at all

Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabFactory.H
Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_Mask.cpp
Src/EB/AMReX_EBFArrayBox.H
Src/EB/AMReX_EBFArrayBox.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_MultiCutFab.H

commit d666cc265f6ae49236f7f7f3f57988b5c4ed559e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 16 12:59:30 2019 -0400

    manually inline static constexpr member for device functions

Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBCellFlag.cpp

commit a51601e7428cf885be441028eb3f3bdac5efc5be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 16 12:08:40 2019 -0400

    std::max --> amrex::max in device function

Src/EB/AMReX_EB2_IF_Cylinder.H

commit 38f1e53f473538a2211a992900677cc1834943d0
Author: kngott <kngott@lbl.gov>
Date:   Tue Apr 16 08:25:52 2019 -0700

    FAB* and Array4 versions both available. Array4 expected due to future unified memory flags.

Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit 69cab283c296b83f86ea5fbb9d368857e5fef518
Merge: 106a5682a 6fe10378c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 15 15:32:17 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 106a5682a986d8492362b40a5512d8098f27715a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 15 15:32:08 2019 -0700

    update the neighbor particle documentation to account for the fact that the neighbors are Vector<ParticleType>, not Vector<char> now.

Docs/sphinx_documentation/source/Particle.rst

commit 6fe10378c3daf196fa0bbce21a042575895cd82f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Apr 15 12:25:28 2019 -0400

    Add option to output fextract in scientific notation

Tools/Plotfile/fextract.cpp

commit c2c93c1ed71fb091517000ae922a8d0740b5557c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 12 19:41:09 2019 -0700

    put dx_eb computation in a function and use it to fix hypre

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 4e32b05d136d65b9fb6e47daa470cba7d728517e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 12 19:21:22 2019 -0700

    fix the formular for dx_eb

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 5ac082ec85256c8ce3108f01c8e7e3e08b3034f3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Apr 12 18:37:20 2019 -0700

    oops - missed one declaration -- compiles now

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit 03b810e9052c13b77c40fa9b7a7bc075a29a4141
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Apr 12 18:29:20 2019 -0700

    Update the stencil used for dphi/dn at EB walls when using Dirichlet bcs.

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 55516b137e96510de8e82cd23efc3996ca7fec6a
Merge: c8f91df1f e682d934f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 12 17:14:12 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit c8f91df1f4fc08c780c9ba07f583fff01fcdcca4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 12 17:14:06 2019 -0700

    CMake: update documentation

Docs/sphinx_documentation/source/BuildingAMReX.rst
Docs/sphinx_documentation/source/GPU.rst

commit e682d934f184e45769f32eac22e51d7bb6528c7f
Merge: cc1d00925 a8b0fe1a4
Author: mic84 <mrosso@lbl.gov>
Date:   Fri Apr 12 16:01:29 2019 -0700

    Merge pull request #451 from mwm126/patch-2
    
    Use "  sed -i''  " for BSD sed on Mac

commit a8b0fe1a4a4c3ae11541f33cefe2d5f80c186a85
Merge: d91fc4b62 cc1d00925
Author: mic84 <mrosso@lbl.gov>
Date:   Fri Apr 12 16:01:17 2019 -0700

    Merge branch 'development' into patch-2

commit 8e4dbc1e0dcffc25b6edb369cb6cedff6295172b
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 12 15:41:08 2019 -0700

    1 Graph per Iter methodology added.

Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Tests/GPU/CudaGraphs/GraphIterReuseCopy/GNUmakefile
Tests/GPU/CudaGraphs/GraphIterReuseCopy/Make.package
Tests/GPU/CudaGraphs/GraphIterReuseCopy/inputs_3d
Tests/GPU/CudaGraphs/GraphIterReuseCopy/main.cpp
Tests/GPU/CudaGraphs/GraphIterReuseCopy/run.corigpu

commit d91fc4b621747539df981ca7a69841bc2b3b3abb
Author: Mark Meredith <mwm126@gmail.com>
Date:   Fri Apr 12 18:26:29 2019 -0400

    Use "  sed -i''  " for BSD sed on Mac

Tools/CMake/AMReX_InstallExternalLibs.cmake

commit dcea92f0c8e9bb8bc50a4d85c572d957b44cc406
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 12 14:44:42 2019 -0700

    Separate Instantiate Function.

Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp

commit e56ece2bab84cb55b890a41976bb89868f8dc2af
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 12 14:34:55 2019 -0700

    Change name of Graph functions to prepare for adding multiple capture methods.

Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Tests/GPU/CudaGraphs/ArrayReuse/main.cpp
Tests/GPU/CudaGraphs/GraphCopy/main.cpp
Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit 0aead5a7bde2728f32060b4e4e4671a3148c5bd3
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 12 14:15:33 2019 -0700

    Add proper free

Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit 99abc261b3de4614bd7c71a2f4118e123e3bd59d
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 12 14:11:45 2019 -0700

    Graph Reuse using Device Memory.

Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit 81155d60e26ea2c3a2887cf7d608ffd7922c2253
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 12 13:39:06 2019 -0700

    FAB lambda variation.

Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit f4477f5a62cafbf8910c3a8481b5449cedbd0a51
Author: kngott <kngott@lbl.gov>
Date:   Fri Apr 12 13:28:10 2019 -0700

    Array4 and FAB* methods for reusing graph on different MultiFabs.

Tests/GPU/CudaGraphs/ArrayReuse/GNUmakefile
Tests/GPU/CudaGraphs/ArrayReuse/Make.package
Tests/GPU/CudaGraphs/ArrayReuse/inputs_3d
Tests/GPU/CudaGraphs/ArrayReuse/main.cpp
Tests/GPU/CudaGraphs/ArrayReuse/run.corigpu
Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp

commit fe6d5e5415f53d3929ecfffa3791beb0be6fa839
Author: kngott <kngott@lbl.gov>
Date:   Thu Apr 11 15:22:44 2019 -0700

    Missed a noexcept.

Src/Base/AMReX_CudaDevice.H

commit 01dc07957e0d1fca9bbae251f5bc52ff5674109b
Author: kngott <kngott@lbl.gov>
Date:   Thu Apr 11 15:22:25 2019 -0700

    Update callback for Cuda 10.

Src/Base/AMReX_CudaAsyncFab.cpp

commit 7a46b9d116e726e469800e41b08e548fc4482cf7
Author: kngott <kngott@lbl.gov>
Date:   Thu Apr 11 15:22:04 2019 -0700

    Sync Array fully with development.

Src/Base/AMReX_Array.H

commit 27556858aa87f6b79a0404ed80cdb62b56716089
Author: kngott <kngott@lbl.gov>
Date:   Thu Apr 11 14:40:59 2019 -0700

    Corrected CommI.H

Src/Base/AMReX_FabArrayCommI.H

commit fcd183527be08b3f30a854ffd83bc5064cef76a3
Merge: 2e6504d8e cc1d00925
Author: kngott <kngott@lbl.gov>
Date:   Thu Apr 11 13:55:51 2019 -0700

    Merge branch 'development' into kngott/cudaGraphs

commit cc1d009253e647b033aa6b6fe7d09fc668ac2ee0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 11 12:16:28 2019 -0700

    make: when USE_CUDA, make sure comm and space are always defined before substition of compiler flags

Tools/GNUMake/Make.defs

commit cdb8de6fc5641c6abf2b37e31d05ad90bb8ed5fc
Merge: c82d3e236 cd1133e22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 11 12:07:37 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c82d3e23601e22619749f44e52b9c047bcf29030
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 11 12:07:19 2019 -0700

    hide errors in calling mpic++ -link_info

Tools/GNUMake/sites/Make.nersc

commit cd1133e229c0a221b765c1be3823622e44cde414
Merge: e1ee32790 188bb5962
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 11 11:07:14 2019 -0700

    Merge pull request #450 from AMReX-Codes/init_from_random_restart_gpu_friendly
    
    copy particles from host to device in one batch, 3 more funtions

commit e1ee32790acca2cbe5bd33796876d72c05ea2d27
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 11 10:36:55 2019 -0700

    option to fix -pthread for nvcc

Tools/GNUMake/Make.defs

commit 1ac221a422de0076ec3e7ddbbc43c6c587177b45
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 11 07:52:06 2019 -0700

    fix sign and unsigned comparison in 1d

Src/Base/AMReX_CudaDevice.cpp

commit af6e0ce44e51a9f44cf4d2ac53c163f1429fa53e
Merge: 7ec432c09 00d24855f
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Apr 10 22:13:10 2019 -0700

    Merge pull request #448 from AMReX-Codes/pgi-opt-fix
    
    Define PGI_OPT for any choice of AMREX_CCOMP and AMREX_FCOMP in pgi.mak

commit 7ec432c09171fdf75e6e8bd12ca8aebdf297704e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 10 21:54:33 2019 -0700

    have to remove Werror=cross-execution-space-call because of cori

Tools/GNUMake/comps/nvcc.mak

commit 0b4d19efb18adb782047d7e4295e847784051f99
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 10 21:20:35 2019 -0700

    simplify USE_HYPRE

Tests/LinearSolvers/CellEB/GNUmakefile
Tests/LinearSolvers/CellEB2/GNUmakefile
Tests/LinearSolvers/EBConvergenceTest/GNUmakefile
Tests/LinearSolvers/EBflux_grad/GNUmakefile
Tests/LinearSolvers/MLMG/GNUmakefile
Tests/LinearSolvers/NodeEB/GNUmakefile
Tools/GNUMake/packages/Make.ascent
Tools/GNUMake/packages/Make.hypre
Tools/GNUMake/packages/Make.petsc
Tutorials/EB/MacProj/GNUmakefile
Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile
Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile

commit 6fba7be9ce58b69f19038875db4082b7fd86d49e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 10 20:40:38 2019 -0700

    if -> ifdef for consistence

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AsyncFillPatch.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp
Src/Base/AMReX_CudaUtility.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_Machine.cpp
Src/Base/AMReX_TypeTraits.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tests/C_BaseLib/tMF.cpp
Tutorials/EB/CNS/Source/CNS_io.cpp
Tutorials/GPU/CNS/Source/CNS_bcfill.cpp
Tutorials/GPU/EBCNS/Source/CNS_bcfill.cpp
Tutorials/GPU/EBCNS/Source/CNS_io.cpp

commit 00d24855f2a5d2f7adf825d3b07f888256c3a887
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date:   Wed Apr 10 20:16:05 2019 -0700

    Define PGI_OPT even if AMREX_CCOMP is not pgi in case AMREX_FCOMP is pgi.

Tools/GNUMake/comps/pgi.mak

commit 188bb5962cbbe18435854ac2489244159c7f5dbc
Author: Jean Sexton <jmsexton@lbl.gov>
Date:   Wed Apr 10 21:48:39 2019 -0400

    copy particles from host to device in one batch in InitRandom, InitNRandomPerCell, and Restart

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H

commit a81b9c743246e8f4681c2a045003bef2a5a79e9e
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Apr 10 17:55:03 2019 -0600

    added bottom abs tolerance

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 56c9fa7d71c6d9f3f82dd62972fa0899376d2705
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 10 16:47:46 2019 -0700

    remove .mod files in clean

Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile.libamrex

commit 6f7257c0e9d797f78247b1a5e8351c47675e5591
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 10 16:33:52 2019 -0700

    libamrex: add lib/pkgconfig/amrex.pc

GNUmakefile.in
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/cray.mak
Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/ibm.mak
Tools/GNUMake/comps/intel.mak
Tools/GNUMake/comps/llvm-flang.mak
Tools/GNUMake/comps/llvm.mak
Tools/GNUMake/comps/nag.mak
Tools/GNUMake/comps/nec.mak
Tools/GNUMake/comps/pgi.mak
Tools/libamrex/configure.py
Tools/libamrex/mkpkgconfig.py
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile.libamrex

commit 317c978f4411dfa1679fe720539208b2d197f641
Merge: 047eddf02 bd684825c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 10 11:35:52 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 047eddf02ccfd740ff666e3c3c6480c499e9e023
Merge: b91808a31 0bbc0ee00
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 10 11:35:39 2019 -0700

    Merge branch 'init_from_binary_gpu_friendly' into development

commit 0bbc0ee0027ab3e48c655fd99ea555cf3389f2fe
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 10 11:34:48 2019 -0700

    add sync after InitFromBinary

Src/Particle/AMReX_ParticleInit.H

commit bd684825c8788c5252da9ed52183116447919eeb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 10 10:16:45 2019 -0700

    configure: implement the allow_different_compiler option.  Add an example makefile to heat equation OpenACC tutorial

GNUmakefile.in
Tools/libamrex/mkconfig.py
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile.libamrex

commit 2e6504d8e0b76eeaec521d94a84ac6cfba8a1048
Merge: 0a18cff34 4aaf0d8fc
Author: kngott <kngott@lbl.gov>
Date:   Tue Apr 9 17:14:43 2019 -0700

    Merge branch 'development' into kngott/cudaGraphs

commit 4aaf0d8fccb306e518c2a4912d448350ec3ebb1a
Merge: b91808a31 486539e78
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Apr 9 17:03:06 2019 -0700

    Merge pull request #446 from ghweber/master
    
    Add missing include for Conduit/Make.package and missing linker optio…

commit b91808a31ec14db121aae6a0acbd56f7a52c3194
Merge: 6c8913512 216b49abd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 16:30:44 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 216b49abd7a285d3baca9a95439c7f03bd0bfda3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 9 15:58:07 2019 -0700

    make Array4 is_trivially_copyable

Src/Base/AMReX_Array.H

commit 6c8913512590390f057dae6337dac1931ef34968
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 15:35:53 2019 -0700

    add some overloads for backwards compatability

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit d2127d26bfe85f828b7803d68e7100e4666428e2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 13:37:50 2019 -0700

    fix typo in assert statement

Src/Particle/AMReX_ParticleContainerI.H

commit 026ecf1f448b375bd42a8247594f886db70ae266
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 12:45:20 2019 -0700

    fix logic error

Src/Particle/AMReX_ParticleContainerI.H

commit 0710727f2aa7de451dd503824738e493edf0ce34
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 12:33:17 2019 -0700

    update Checkpoint call in AssignDensity test

Tests/Particles/AssignDensity/main.cpp

commit d476de410447b1021ad2656b844f1c46d352e3c8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 12:32:59 2019 -0700

    update Header to reflect new num comps

Src/Particle/AMReX_ParticleContainerI.H

commit 71626307db3755f57379bd1a1ed5f84d4360cd5a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Apr 9 12:16:37 2019 -0700

    CMake: improve SUNDIALS support

Src/Extern/SUNDIALS4/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/FindSUNDIALS.cmake

commit 497c3f06b5afb43e525518fbf658424380d3a991
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 11:52:42 2019 -0700

    nuke is_checkpoint

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 235f264243599e5dd542984fd86843212580c6f3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 11:29:42 2019 -0700

    also add all those versions of WritePlotFile

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 91f0a4d1f2ced9e651e35fe8cfc7973581ad45aa
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 11:17:33 2019 -0700

    more formatting changes

Src/Particle/AMReX_ParticleContainerI.H

commit 0e63af22785ecd1e9a8dd3297ee6822180590236
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 11:15:48 2019 -0700

    update ReadParticles to account for these changes

Src/Particle/AMReX_ParticleContainerI.H

commit 44b01d46e28b6e782f9688ddbc8b356261048e55
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 10:57:28 2019 -0700

    update ReadParticles Function

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 76311680f60c907b60fd40c9bc05b747fb066ce0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 10:54:42 2019 -0700

    formatting changes

Src/Particle/AMReX_ParticleContainerI.H

commit b97fce2e8a1e3866e8f717a8bff7e4c49ee764aa
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 10:52:42 2019 -0700

    add a new Restart function, implement the specific one in terms of the general

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 0d81f5dd4b6e135bd5c40fd2632df8042e550d6d
Merge: 4ffa510fa 5074d83ff
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Apr 9 10:52:02 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 4ffa510faf8e6088095bd03cfb77365ef76d8063
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Apr 9 10:50:31 2019 -0700

    CMake: improve HYPRE support
    
    * Add HYPRE detection to AMREX config file
    * Add minimum required version for HYPRE

Src/Extern/HYPRE/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/FindHYPRE.cmake

commit ef27155c4aa1bd50eabf300eaad37fb021cc431c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 10:48:53 2019 -0700

    modify the WriteParticles method to only write out the requested components

Src/Particle/AMReX_ParticleContainerI.H

commit c3224ec83e9fd7f5a26da9d11da5f8b29f135b33
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 10:35:19 2019 -0700

    more formatting changes.

Src/Particle/AMReX_Particles.H

commit 98fc8fd7f2decd01741c63ca99c0fbaf686f8c3e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 10:31:36 2019 -0700

    implement the special Checkpoint functions in terms of the most general one.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit ff5ce628a3134d96e9aeea573814c403e33af67a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 10:15:24 2019 -0700

    add overloaded versions of Checkpoint that allow for toggling IO on/off for specific particle components.

Src/Particle/AMReX_Particles.H

commit 91461b7970ee0c8cf0b150d94beb3bc5887bef07
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 10:05:40 2019 -0700

    formatting changes

Src/Particle/AMReX_ParticleContainerI.H

commit 8addd98619c6a532083a731b35f9f78fc5277ffd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 9 09:57:10 2019 -0700

    copy particles from host to device in one batch

Src/Particle/AMReX_ParticleInit.H

commit 5074d83ff08ac85ef53b9cc0be8968b2ccbaeafa
Merge: 09154aa57 4ebb075fc
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Apr 8 21:35:23 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 486539e7843293be3d96b6bf65620513139c82f0
Author: Gunther H. Weber <GHWeber@lbl.gov>
Date:   Mon Apr 8 18:35:17 2019 -0700

    Move include for conduit packages from Make.defs to Make.conduit

Tools/GNUMake/Make.defs
Tools/GNUMake/packages/Make.conduit

commit 09154aa5771c5a7426072e8c34a84e0485897833
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Apr 8 21:35:04 2019 -0400

    gpu neighbor list bug fix

Src/Particle/AMReX_NeighborList.H

commit ac9aeaab2879b7512131d2da8a871f6eefd201d4
Author: Gunther H. Weber <GHWeber@lbl.gov>
Date:   Mon Apr 8 17:35:08 2019 -0700

    Add missing include for Conduit/Make.package and missing linker options for Conduit/Ascent

Tools/GNUMake/Make.defs
Tools/GNUMake/packages/Make.ascent
Tools/GNUMake/packages/Make.conduit

commit 4ebb075fc99ccfd3202801ce234b127cc3d6109c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 8 17:20:48 2019 -0700

    CMake: add HYPRE support

Src/CMakeLists.txt
Src/Extern/HYPRE/CMakeLists.txt
Tools/CMake/AMReX_Options.cmake
Tools/CMake/FindHYPRE.cmake
Tutorials/CMakeLists.txt
Tutorials/LinearSolvers/ABecLaplacian_C/CMakeLists.txt

commit 0531972cb843b6a93843a9b5c90be8fd4538d28a
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Mon Apr 8 12:31:08 2019 -0700

    slicevalues are assigned based on the nearest grid point. Modified initialization of the multifabs such that the values represent the exact x,y,z location in the computational domain to assist with verification of the values assigned to the slice grid points.

Tests/CreateSliceForDiagnostics/inputs
Tests/CreateSliceForDiagnostics/main.cpp

commit c5e7ab3c9731228fd55913c575115175c4b6ec4d
Merge: 8d4405e00 af2bcc45b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 6 08:16:32 2019 -0700

    Merge branch 'development' into weiqun/hypre-node

commit 8d4405e00621779bf1b7e6061d2edd005113cd34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 6 08:12:39 2019 -0700

    HypreNodeLap: 2d

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 26d2f6c2a098e82396770443e52357a27f87f4c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 5 21:37:15 2019 -0700

    HypreNodeLap: switch to use RAP

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 426464793958ef85434f500a88ba1e2825c9ef0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 5 21:25:35 2019 -0700

    HypreNodeLap: set use_hypre only once

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tests/LinearSolvers/NodeEB/MyTest.cpp

commit 4c4aa0f85885d867123f81f7fea2fd21e59b1bf5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 5 16:37:54 2019 -0700

    HypreNodeLap: fix id

Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit af2bcc45b4ab467623e998b0a0e8c7093311bf42
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 5 16:36:05 2019 -0700

    CMake: add back option I deleted by mistake

Tools/CMake/AMReX_Options.cmake

commit 280fa93f7ee91cc48a6d66b3fcb2cc339cfe2aaf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 5 13:25:26 2019 -0700

    reorganize OverrideSync so that it can be used on any FabArray, not just MultiFab

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp

commit 6f4f4adc619c4ba741987b0062f1e44b1c761611
Merge: faf9c1de6 795d67029
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Fri Apr 5 13:24:08 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into SliceGenerationForDiagnostics_RJ

commit 795d67029280b79a52a1fa3694f0bc574bfecd73
Merge: 9fa218b39 12cb3fc57
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 5 11:54:59 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 9fa218b395a80119337264b40f05d9cdb2198fc6
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 5 11:54:47 2019 -0700

    CMake: change how AMReX CUDA settings are passed to app codes

Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_SetupCUDA.cmake

commit 12cb3fc5790061ecf5150f67de24c766a58679b6
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Apr 4 20:32:02 2019 -0700

    Put main code in local scope to avoid seg fault bug.

Tools/Postprocessing/C_Src/HorizontalAvg.cpp
Tools/Postprocessing/C_Src/IntegrateComp.cpp
Tools/Postprocessing/C_Src/MultiFabToMatLab.cpp
Tools/Postprocessing/C_Src/PlotfileToMatLab.cpp
Tools/Postprocessing/C_Src/PtwisePltTransform.cpp

commit 9b289bb5a2a74c415789c1e38596e38758b5d867
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 4 17:08:55 2019 -0700

    CMake: streamline CUDA setup

Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_SetupCUDA.cmake

commit 82b9cc5dd931e0c45d81aaaa13cd163e2b89651f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 4 16:33:26 2019 -0700

    HypreNodelap: implement loadVectors and getSolution

Src/Extern/HYPRE/AMReX_HypreNodeLap.H
Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp

commit 1ef26bcb6316197fe0f46dda3ba59d3dc8155346
Merge: 0b1860fd0 ef538d173
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 4 16:24:44 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit ef538d173898a6fe3b814fc955b97232c27fad19
Merge: ab6f075bf f34071192
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Apr 4 19:23:41 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ab6f075bf15388b26d3a22c298446e422f51634c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Apr 4 19:23:22 2019 -0400

    need to make a local copy of the particle struct pointer to pass into kernels when building the neighbor list

Src/Particle/AMReX_NeighborList.H

commit f3407119296913781c3e7447af91c2f70aafbc55
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Apr 4 16:06:35 2019 -0700

    Change the default box_min_width for EB in the multigrid solves -- when AMREX_USE_EB
    make the min width 4 instead of 2

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H

commit 5f784d3b66452b17d3b3ac27d33135ef453f6507
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 4 14:53:44 2019 -0700

    HypreNodeLap: placeholder for loadVectors and getSolution

Src/Extern/HYPRE/AMReX_HypreNodeLap.H
Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 3724b80a470de4fedaa727f3a898c37bb5ef49ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 4 14:40:17 2019 -0700

    HypreNodeLap: setup amg solver

Src/Extern/HYPRE/AMReX_HypreNodeLap.H
Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 0b1860fd0b8a46e8fa84e0b7ec45667faaba485b
Merge: d9294e811 a5e8b3912
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 4 14:39:04 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit a5e8b3912bc670cf94c9f0ac527809d755727fc2
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 4 14:26:44 2019 -0700

    CMake: allow 1D builds. Fixes Issue 400

Docs/sphinx_documentation/source/BuildingAMReX.rst
Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt

commit 3d1b9f54505083c32c361d02d0e8320f32fe6d7b
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 4 13:58:17 2019 -0700

    CMake: fix MPI search in config file

Tools/CMake/AMReXConfig.cmake.in

commit f7065c755ccc9c95159885a61587981a717d68da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 4 09:05:46 2019 -0700

    MLNodeLaplacian: fill IJ matrix for non-EB

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit faf9c1de6ec6d195e60744faa103285286af5e87
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Thu Apr 4 13:29:47 2019 -0700

     modified main.cpp to generate error messages if cell size of slice is not an integer multiple of computational domain's cell size. Additional error messages include ensuring that the max_grid_size of box arrays are integer multiples of the coarsening ratio.

Tests/CreateSliceForDiagnostics/inputs
Tests/CreateSliceForDiagnostics/main.cpp

commit b79ca70b454cd95f98d88151aa39522eaedf25c9
Merge: fc2d48fc3 2b9f858c2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Apr 4 12:26:59 2019 -0700

    Merge pull request #442 from jrood-nrel/fix_fcompare3D_intel
    
    Fix fcompare3D for the Intel compiler

commit fc2d48fc394a9265174bd64c6978141bd25cdb13
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 4 12:25:22 2019 -0700

    EB: remove small cells with volume fraction less than 1.e-14

Src/EB/AMReX_eb2_2d.F90
Src/EB/AMReX_eb2_3d.F90

commit d9294e8115c5cd4886c738df14c5eee0a76813eb
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 4 10:09:13 2019 -0700

    CMake: remove obsolete check

Tools/CMake/AMReX_SetupCUDA.cmake

commit 2b9f858c2a6c1fe7835b08a256e24d587a7b563a
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Wed Apr 3 19:37:48 2019 -0600

    Fixing line continuation in AMReX_FABUTIL_3D.F so that the Intel compiler can compile this file.

Src/Extern/amrdata/AMReX_FABUTIL_3D.F

commit c327b9cbd4e9ad122eb6478c5f8a1b9d7e8d0a68
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Apr 3 18:01:04 2019 -0700

    corrected modification of max grid slice such that IntVect coarseslice can be an integer multiple for any dimension.

Tests/CreateSliceForDiagnostics/main.cpp

commit 85c722da1739dcbe130a72fdaed35b7e43eb9578
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Apr 3 17:38:07 2019 -0700

     modified max_grid_size for slice box array to enable slice generation such that the coarse IntVect can be any integer multiple of the baseline slice and not limited to a multiple of two.

Tests/CreateSliceForDiagnostics/main.cpp

commit 0077d6b0d52cfb9db072be2face4fc9f4b881060
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 3 16:41:29 2019 -0700

    HypreNodeLap: ask MLNodeLaplacian to fill IJ matrix

Src/Extern/HYPRE/AMReX_HypreNodeLap.H
Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 6a934bd6a5e9d6bf5ef855c1c2eeca1c2b9df09c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 3 15:45:33 2019 -0700

    HyperNodeLap: set up node id

Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreNodeLap.H
Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tests/LinearSolvers/NodeEB/MyTest.cpp

commit 0a18cff34e0d962307e60507cc4f876f9ea6e48d
Author: kngott <kngott@lbl.gov>
Date:   Wed Apr 3 14:59:06 2019 -0700

    First draft of reusing copy graph on a different MultiFab.

Tests/GPU/CudaGraphs/GraphReuseCopy/GNUmakefile
Tests/GPU/CudaGraphs/GraphReuseCopy/Make.package
Tests/GPU/CudaGraphs/GraphReuseCopy/inputs_3d
Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp
Tests/GPU/CudaGraphs/GraphReuseCopy/run.corigpu

commit a3c33d2ccf862a8bafa911b5c1c90ee36798d145
Author: kngott <kngott@lbl.gov>
Date:   Wed Apr 3 14:55:59 2019 -0700

    Adjust Array4 to allow needed access for CudaGraphs. Hopefully, a better way can be found later.

Src/Base/AMReX_Array.H

commit 08b185da9ac28c7b2d46741ddfea4b20000cd284
Author: kngott <kngott@lbl.gov>
Date:   Wed Apr 3 14:54:13 2019 -0700

    Adjust GraphRecordingStop to return the graph instead of take by reference. Also comment out graph log output for now.

Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp

commit adaa02fba55e728607a34db623aab52462c299fc
Author: kngott <kngott@lbl.gov>
Date:   Wed Apr 3 14:52:05 2019 -0700

    Turn off FillBoundary preliminary graphing. Need to test more, leave complete marker locations for now.

Src/Base/AMReX_FabArrayCommI.H

commit b526a676d69eb21cf834fdcf2d684a041da7ab69
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 3 12:28:20 2019 -0700

    start HypreNodeLap

Src/Extern/HYPRE/AMReX_HypreNodeLap.H
Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp
Src/Extern/HYPRE/Make.package
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tests/LinearSolvers/NodeEB/MyTest.cpp

commit 2503f4ef37bbafbcf3e37bdc79a816b14f0501fe
Merge: 35f125a66 6d4fd7bc8
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Apr 3 12:17:06 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into SliceGenerationForDiagnostics_RJ

commit 35f125a66afa119c2d6f206a1ec91c37d9d41c0c
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Apr 3 12:16:47 2019 -0700

    Adding test case to generate slice for diagnostics

Tests/CreateSliceForDiagnostics/GNUmakefile
Tests/CreateSliceForDiagnostics/Make.package
Tests/CreateSliceForDiagnostics/inputs
Tests/CreateSliceForDiagnostics/main.H
Tests/CreateSliceForDiagnostics/main.cpp

commit 6d4fd7bc8b4057f9b8272481f2999d3b8576eb0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 3 09:49:50 2019 -0700

    fix memory issue related to using AsyncFab in non-launch region

Src/Base/AMReX_CudaAsyncFabImpl.cpp

commit a4ee51d60c29c286daed1052c7de5e6da4288340
Merge: 77f514db1 2e2c19364
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 2 17:04:16 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 77f514db1050722643a5d13d58311dcf3e5a868b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 2 17:04:05 2019 -0700

    make it clear where LIBRARIES can be modified in make system

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit 2e2c1936447fdb7496b62674b837421782f052ac
Merge: 739f30ffd 205ec28e4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Apr 2 15:44:12 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 739f30ffd5ce74c20d2d40d7a9c712ba87e0f9ad
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Apr 2 15:43:23 2019 -0700

    Allow VisMF::Read to read an empty MultiFab without an error if and only if
    we pass in a flag (allow_empty_mf) that explicitly says its ok -- the default
    is still that it's not ok

Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp

commit 205ec28e4b00737f935f353f412c89d0bdd9534d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 2 15:40:50 2019 -0700

    write a debug chekcpoint file for MLNodeLaplaian

Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_Utility.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit f6d1352c0c97889b5c558a7fc6a7483aa90d9f2f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 2 13:24:20 2019 -0700

    fix a bug in 2d eb

Src/EB/AMReX_eb2_2d.F90

commit 74aeb23b40ecbb85c71ac4efc37ffc42b190db72
Merge: 6872995e7 be96d9c33
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 2 13:28:46 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6872995e71a2376755e36bb5bbc0b7446c47afb5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 2 13:24:20 2019 -0700

    fix a bug in 2d eb

Src/EB/AMReX_eb2_2d.F90

commit be96d9c33c71a771041e88599c123a645de7530b
Merge: 8e4a6729d b9496c998
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Apr 2 12:26:47 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8e4a6729d1e7a9bc4b09fb87a0fa00bdfbec555a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Apr 2 12:26:42 2019 -0700

    CMake: find OpenMP dependency in AMReX export file

Tools/CMake/AMReXConfig.cmake.in

commit b9496c998370ff814f85965f8a7d88eae8b5fe51
Merge: b7d5e7aba 45a40a4e5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Apr 2 14:22:56 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b7d5e7abaa605902d938c4cc905324f0df185c79
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Apr 2 14:22:42 2019 -0400

    need to fill the index sequence before using it...

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 45a40a4e5142ed82d58dde36470a6a6fae87521a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Apr 2 11:21:07 2019 -0700

    CMake: add missing define for Algoim

Src/Extern/Algoim/CMakeLists.txt

commit 6fcd9d69daa3ec069e0fda86ac6b9dce021f738f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 2 10:18:16 2019 -0700

    change the interface of Interpolater::interp.  Note that this is a virtual function, so it will break derived classes!

Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/EB/AMReX_EBInterpolater.H
Src/EB/AMReX_EBInterpolater.cpp

commit 517f6df31db90b5ef5ad64a9b02a115e7e676c18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 2 10:13:15 2019 -0700

    fix default path to amrex

Tools/Plotfile/GNUmakefile

commit 9565e8d6365d668eb6c6a773812f0fd7fd03e39e
Merge: 916c943bf e8bf23961
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 2 10:10:44 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 916c943bfe27afb635595bdb40bf4071b522bbf7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 2 10:10:22 2019 -0700

    remove C_Src/fcompare and fextract to avoid confusion

Tools/Postprocessing/C_Src/GNUmakefile
Tools/Postprocessing/C_Src/fcompare.cpp
Tools/Postprocessing/C_Src/fextract.cpp

commit e8bf23961ecec4e04d6e4f67dad0b95e1d93305d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Apr 1 20:50:17 2019 -0400

    bail if cuda 9.2 used with USE_EB=TRUE

Tools/GNUMake/comps/nvcc.mak

commit cd50eb9c7636768a15334e3f01ad3c1463ebd708
Merge: 4ddd58c67 9bdf6484b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Apr 1 20:20:41 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9bdf6484b428d6791aa5266f1f1b66f15654d788
Merge: 659a80a3a 79c2fc7d3
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 1 17:22:50 2019 -0700

    Merge branch 'mr/cmake' into development

commit 79c2fc7d3241020c5dda1d0073b97a5a514a2058
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 1 17:22:30 2019 -0700

    CMake: bump up CMake minimum required version

CMakeLists.txt

commit 4ddd58c6728fda4c1fbe23d77554f527c5aed4f1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 28 10:38:22 2019 -0700

    mark EBCellFlag functions __host__ __device__

Src/EB/AMReX_EBCellFlag.H

commit baf4463b66f9b4fa544b7bf45699ae6b26fd2804
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Mar 28 19:37:13 2019 -0400

    early exit for when neighbors don't need to be filled.

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 743bb306e78dc3a49907d13be47fb8d2977af7e3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Apr 1 20:18:23 2019 -0400

    workaround for Thrust bug in Cuda 9.1

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 7f49eee73aa0337d41e0f3d950ff6854d8e26918
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 1 18:55:10 2019 -0400

    Update doc

Docs/sphinx_documentation/source/Fortran.rst

commit 16c99d836df84c28024df6e2a077e7d123c80ee8
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 1 18:54:27 2019 -0400

    CMake: return with error message if CUDA 9.2 is used whit ENABLE_EB=ON

Tools/CMake/AMReX_SetupCUDA.cmake

commit 659a80a3ab8e1818c3dc9e60fad4822d37e07236
Merge: 3936c7377 9c6ffaeed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 1 13:47:56 2019 -0700

    Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu

commit 3936c73772808a45ce28c4484d9c1b3076898ce8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 1 13:47:45 2019 -0700

    Reduce: replace AsyncArray with DeviceScalar

Src/Base/AMReX_FabArrayUtility.H

commit 9c6ffaeed008d33a32cc9c94e66677c5587d0ad0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 1 13:44:59 2019 -0700

    fix UnionIF and IntersectionIF

Src/EB/AMReX_EB2_IF_Intersection.H
Src/EB/AMReX_EB2_IF_Union.H

commit 0cf191ae684cd09050206075854a7eb6671fcf12
Merge: 8e2a33ff1 83e253432
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 1 13:16:54 2019 -0700

    Merge branch 'development' into weiqun/gpu

commit 8adf716290037c1efefba3eb854de14bbff33717
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 1 11:18:10 2019 -0700

    Fix #ifdef inconsistency

Src/Base/AMReX_filcc_mod.F90

commit 83e2534328e8215356391ec20fca06ef00347a59
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 1 11:18:10 2019 -0700

    Fix #ifdef inconsistency

Src/Base/AMReX_filcc_mod.F90

commit 8e2a33ff140fa9256105f953a7368a9b0a8817d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 1 13:01:15 2019 -0700

    UnionIF: fix typo

Src/EB/AMReX_EB2_IF_Union.H

commit fd1575c217461a4238177aeb138a2f0ffcd7a8c0
Merge: 6200d3088 b8434d3ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 1 12:33:32 2019 -0700

    Merge branch 'development' into weiqun/gpu

commit 99c95a68b4896f726f477a6bd7a738fc5d638462
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 1 14:51:40 2019 -0400

    Replace some #if with #ifdef

Src/Base/AMReX_CudaMemory.H
Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_FabArray.H
Src/Particle/AMReX_ParIterI.H

commit f33234c7fb76f555a7af8166df50eefbea5ccf29
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 1 11:18:10 2019 -0700

    Fix #ifdef inconsistency

Src/Base/AMReX_filcc_mod.F90

commit 2b1698e16d03418201771f2d67f2b0945cfd57ec
Merge: 75e42783e b8434d3ae
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 1 10:46:54 2019 -0700

    Merge branch 'development' into mr/cmake

commit b8434d3ae5903779eef079a6c318d4b12dd908bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 1 09:07:43 2019 -0700

    update changes

CHANGES

commit f34f31ab260173497a837fcf3cee74b614c7b9e6
Merge: 51b262002 2a61fdfc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 1 08:58:28 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2a61fdfc7a9642d76e5e7f4fe2f1b4ef09475563
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Mar 30 12:08:22 2019 -0700

    Initialize xlcuf

Src/Base/AMReX_CudaDevice.cpp

commit 7d92a8a11f16e01391d1aa2d3947194af1346b76
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Mar 30 12:08:00 2019 -0700

    Fix make syntax

Tools/GNUMake/Make.rules

commit 0121543012dde3d71fc8499f4c378fa6334ac43e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Mar 30 11:29:29 2019 -0700

    Generalize register capping to support xlf

Tools/GNUMake/Make.rules

commit 90051adc5cbd574b50268a5de85ebdd3fcc79129
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Mar 30 11:29:17 2019 -0700

    Target the specific GPU arch for xlf

Tools/GNUMake/comps/ibm.mak

commit e10d278823fc93023b4277b4201067dcd60457cb
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Mar 30 10:31:40 2019 -0700

    Disallow unrestricted private statements in the Fortran GPU script

Tools/F_scripts/gpu_fortran.py

commit c8c35da70504fb1e9942e68de8f6c12a9364fd02
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Mar 30 10:31:18 2019 -0700

    Explicitly write out the device version of amrex_filccn

Src/Base/AMReX_filcc_mod.F90

commit 51b262002a1c460421bf38336e1854e7372c4603
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 29 16:17:33 2019 -0700

    User's Guide: parallel descriptor

Docs/sphinx_documentation/source/Basics.rst

commit 75e42783e82f3463b5f79ba48943388864ea281c
Merge: db062be90 c797c1cc8
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Mar 29 15:39:20 2019 -0700

    Merge branch 'development' into mr/cmake

commit db062be905b298196b14b7b0ed49d00624394514
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Mar 29 15:18:59 2019 -0700

    CMake: start moving config and dependecies in the subdir where they are needed

Src/Base/CMakeLists.txt
Src/CMakeLists.txt
Src/Extern/Algoim/CMakeLists.txt
Src/Extern/Conduit/CMakeLists.txt
Src/F_Interfaces/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_SetupThirdPartyLibs.cmake

commit 6200d30881b46abe9ebe3045bab5e6d51ff8f9bf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 29 13:25:41 2019 -0700

    constexpr amrex::SpaceDim

Src/Base/AMReX_SPACE.H

commit c797c1cc88f8a5508f1a60194ec567bc3a5f1a47
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 29 13:13:40 2019 -0700

    User's Guide: verbosity and make system

Docs/sphinx_documentation/source/BuildingAMReX.rst
Docs/sphinx_documentation/source/GettingStarted.rst

commit 10dd6c0457e2c3387840db4f0a6ee1367211364a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 29 11:07:31 2019 -0700

    make it easy to use python3

Docs/sphinx_documentation/Makefile

commit a1afcb23f1fa37982cbb23bdb9cb5038541e00b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 29 08:31:52 2019 -0700

    nvcc: error on calling host function from host device function

Tools/GNUMake/comps/nvcc.mak

commit 7231333cab133c4d5e430b564d6943a8658bc237
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Mar 28 21:52:27 2019 -0700

    Only cap registers if needed

Tools/GNUMake/Make.rules

commit a1f0000694b6cb5411cf4352da8573784faf58fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 28 17:28:42 2019 -0700

    gpu: Intersection and Union IF

Src/EB/AMReX_EB2_IF_Intersection.H
Src/EB/AMReX_EB2_IF_Union.H

commit 930035a6158ab49f0e486ec159ea8e86b6255be0
Merge: 2eaed24d1 46d2bbfb8
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Mar 28 17:11:35 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2eaed24d199213be88d3451dc26ef096fc38b641
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Mar 28 17:11:18 2019 -0700

    OpenMP backend for asyncMFIter

Src/Amr/AMReX_Amr.cpp
Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/mpi_omp/Barrier.cpp
Src/AmrTask/rts_impls/mpi_omp/LocalConnection.H
Src/AmrTask/rts_impls/mpi_omp/Make.package
Src/AmrTask/rts_impls/mpi_omp/PackageQueue.H
Src/AmrTask/rts_impls/mpi_omp/PackageQueue.cpp
Src/AmrTask/rts_impls/mpi_omp/Perilla.H
Src/AmrTask/rts_impls/mpi_omp/Perilla.cpp
Src/AmrTask/rts_impls/mpi_omp/PerillaConfig.H
Src/AmrTask/rts_impls/mpi_omp/PerillaRts.H
Src/AmrTask/rts_impls/mpi_omp/PerillaRts.cpp
Src/AmrTask/rts_impls/mpi_omp/RGIter.H
Src/AmrTask/rts_impls/mpi_omp/RGIter.cpp
Src/AmrTask/rts_impls/mpi_omp/RegionGraph.H
Src/AmrTask/rts_impls/mpi_omp/RegionGraph.cpp
Src/AmrTask/rts_impls/mpi_omp/RegionQueue.H
Src/AmrTask/rts_impls/mpi_omp/RegionQueue.cpp
Src/AmrTask/rts_impls/mpi_omp/RemoteConnection.H
Src/AmrTask/rts_impls/mpi_omp/WorkerThread.H
Src/AmrTask/rts_impls/mpi_omp/WorkerThread.cpp
Src/AmrTask/rts_impls/mpi_omp/perilla.mak
Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.H
Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp
Src/AmrTask/rts_impls/pthreads_common/RGIter.H
Src/AmrTask/rts_impls/pthreads_common/RGIter.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi.omp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/GNUmakefile
Src/Base/AMReX_MemPool.cpp

commit 46d2bbfb8fbb4353109efc2f7db84cea03cb07eb
Merge: d6b74f4b9 7269b933c
Author: mic84 <mrosso@lbl.gov>
Date:   Thu Mar 28 17:04:33 2019 -0700

    Merge pull request #436 from balos1/development
    
    add SUNDIALS 4 support

commit f018af3ca5b4110d330efd9b425b6cfa1fdaa606
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 28 19:10:48 2019 -0400

    add __host__ __device__ to amrex::get for GpuTuple

Src/Base/AMReX_Tuple.H

commit 5370377fdb6330e79d5eebe3e2a55e70520525f8
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Mar 28 15:37:50 2019 -0700

    CMake: use add_subdirectory to include sub-folders into top-level CMakeLists.
    
    This change is made possible by CMake 3.13+. By doing so we can get rid of
    include(), use a more target-centric approach, and have a better localization
    of dependencies detail.

Src/Amr/CMakeLists.txt
Src/AmrCore/CMakeLists.txt
Src/Base/CMakeLists.txt
Src/Boundary/CMakeLists.txt
Src/CMakeLists.txt
Src/EB/CMakeLists.txt
Src/Extern/Algoim/CMakeLists.txt
Src/Extern/Conduit/CMakeLists.txt
Src/Extern/ProfParser/CMakeLists.txt
Src/Extern/SENSEI/CMakeLists.txt
Src/Extern/SUNDIALS3/CMakeLists.txt
Src/Extern/amrdata/CMakeLists.txt
Src/F_Interfaces/CMakeLists.txt
Src/LinearSolvers/CMakeLists.txt
Src/Particle/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake

commit 96a556e6994bab663d7e80314a86cfaeace17d4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 28 14:17:24 2019 -0700

    Tuple: add constexpr

Src/Base/AMReX_Tuple.H

commit e7e5f0229f203731e5e2a35e3276cf0ab3391a78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 28 13:52:45 2019 -0700

    add makeTuple

Src/Base/AMReX_Tuple.H

commit 8ee93abd9431b1c4b6391816acd479b11dbcb950
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 28 13:33:35 2019 -0700

    use amrex::Tuple in UnionIF and IntersectionIF

Src/Base/AMReX_Tuple.H
Src/EB/AMReX_EB2_IF_Intersection.H
Src/EB/AMReX_EB2_IF_Union.H

commit 13dc9e1a696ca7b9bc3d6934d2518fef22207fb3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 28 10:36:50 2019 -0700

    first pass of Tuple

Src/Base/AMReX_IndexSequence.H
Src/Base/AMReX_Tuple.H

commit d6b74f4b9f380592d0ba9b5e10edbdbf867eef2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 28 12:02:25 2019 -0700

    fix for clang, thanks to Jon Rood

Src/Amr/AMReX_StateDescriptor.H

commit c2119f326e3d5c3624f324ff9ab0ebe73ddc0477
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 28 10:40:33 2019 -0700

    Revert "mark these functions AMREX_GPU_HOST_DEVICE so they can be used in device code"
    
    This reverts commit 40ddf688e40caa3f9253092c57b96957dbe49545.

Src/EB/AMReX_EBCellFlag.H

commit f9c756aa4c51d7b6c61a729d2a6855397e6a106d
Merge: 40ddf688e 2b10462df
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Mar 27 19:56:39 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 40ddf688e40caa3f9253092c57b96957dbe49545
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Mar 27 19:56:20 2019 -0400

    mark these functions AMREX_GPU_HOST_DEVICE so they can be used in device code

Src/EB/AMReX_EBCellFlag.H

commit 7269b933cc68488775c9b34c71ff5b0abacb6dd0
Author: Balos, Cody Joe <balos1@llnl.gov>
Date:   Wed Mar 27 16:13:15 2019 -0700

    remove unused file from SUNDIALS4

Src/Extern/SUNDIALS4/farkode_butcher_mod.f90
Src/Extern/SUNDIALS4/fsunlinsol_dense.f90
Src/Extern/SUNDIALS4/fsunnonlinsol_mod.f90

commit 94ec419d8e770c0acee952692aab13ae42c20068
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Mar 27 16:02:24 2019 -0700

    CMake: clean-up output for algoim

Tools/CMake/AMReX_InstallExternalLibs.cmake

commit 2b10462dfd98cadd359f1969307497790bed42ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 27 15:25:48 2019 -0700

    removed the use of Tuple and old hypre interface

OldTutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H
OldTutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp
OldTutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F
OldTutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H
OldTutorials/MultiGrid_C/HypreABecLap/Make.package
Src/Boundary/AMReX_BndryData.H
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H
Tests/LinearSolvers/C_CellMG/main.cpp
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_3D.F
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_F.H
Tests/LinearSolvers/ComparisonTest/HypreABecLap/Make.package

commit cadef8b78c5fc6d64a15dd27b380485c40c074c0
Merge: 42d37cbe7 df82fc28d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 27 15:03:00 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 89d746a1f86fa59bae1381b2344f72f6b12b33e6
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Mar 27 14:52:50 2019 -0700

    CMake: use configuration header to propagate definitions to application codes.
    
    * Generate and install AMReX_Config.H
    * Make defines (except Fortran ones) just a build requirement, i.e. not an
      install requirement
    * Modify installed headers to include AMReX_Config.H
    * Group install code into a single CMake modulex

Src/CMakeLists.txt
Tools/CMake/AMReXInstallHelpers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Utils.cmake
Tools/CMake/modify_installed_headers.cmake

commit df82fc28dc0eff40fab7704ecebfb3ffdeee249f
Merge: ebb265836 7cf248727
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 27 14:10:48 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 42d37cbe7174822acd31df1c3c86f977f5bd0536
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 27 14:01:41 2019 -0700

    gpu: more on EB IF classes

Src/EB/AMReX_EB2_IF.H
Src/EB/AMReX_EB2_IF_Ellipsoid.H
Src/EB/AMReX_EB2_IF_Extrusion.H
Src/EB/AMReX_EB2_IF_Intersection.H
Src/EB/AMReX_EB2_IF_Lathe.H
Src/EB/AMReX_EB2_IF_Plane.H
Src/EB/AMReX_EB2_IF_Rotation.H
Src/EB/AMReX_EB2_IF_Scale.H
Src/EB/AMReX_EB2_IF_Sphere.H
Src/EB/AMReX_EB2_IF_Torus.H
Src/EB/AMReX_EB2_IF_Translation.H

commit ebb265836d03830a3757b37242da626a1361aed7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 27 13:59:44 2019 -0700

    dudn --> dphidn for consistency

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 8deeb0dd28f34586080d8aabc42673a8e509d428
Author: kngott <kngott@lbl.gov>
Date:   Wed Mar 27 13:24:12 2019 -0700

    Comments to make reading graph method a little easier.

Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp

commit e4a06c6c8c848734b67a81a9faafc607b5d66ed0
Author: kngott <kngott@lbl.gov>
Date:   Wed Mar 27 13:23:37 2019 -0700

    Label commented out section.

Tests/GPU/CudaGraphs/GraphCopy/main.cpp

commit a98f2bde98f8b230fe06359e2ec98ba238dfb00e
Author: kngott <kngott@lbl.gov>
Date:   Wed Mar 27 13:04:13 2019 -0700

    Add initial run to get clean timings and adjust timer names.

Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp

commit d4c82ace86a0a4d5e26746a541921fb97d8b29f0
Author: kngott <kngott@lbl.gov>
Date:   Wed Mar 27 12:49:13 2019 -0700

    Implement the work as a function at the top to easily test Graphs on different MFIter loops.

Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp

commit 7cf2487273e7bf913890f0f05d83e9736837b46a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 27 12:07:07 2019 -0700

    gpu: eb DifferenceIF

Src/EB/AMReX_EB2_IF_Difference.H

commit ea982aa99665401acf2d7ca1ebd77b59c8232438
Author: kngott <kngott@lbl.gov>
Date:   Wed Mar 27 11:42:02 2019 -0700

    Adjust graph timers.

Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp

commit 51d30cea1b52879a9f0aaf7e247f8148dafb8a18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 27 11:11:10 2019 -0700

    use defaulted ctors

Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EB2_IF_Box.H
Src/EB/AMReX_EB2_IF_Complement.H
Src/EB/AMReX_EB2_IF_Cylinder.H

commit 62fc189220df15b09b2f2ee3104779f034ef1b15
Merge: e9aff909f b8a5f16c3
Author: Balos, Cody Joe <balos1@llnl.gov>
Date:   Wed Mar 27 11:03:51 2019 -0700

    Merge branch 'development' of https://github.com/amrex-codes/amrex into development

commit e9aff909fa4d1083fe7819fb02ab6f7e9d2f1310
Author: Balos, Cody Joe <balos1@llnl.gov>
Date:   Wed Mar 27 11:00:56 2019 -0700

    add SUNDIALS 4 support
    
    cmake: support sundials 4 instead of 3
    gnumake: support sundials 3 by default or optionally sundials 4

Src/CMakeLists.txt
Src/Extern/SUNDIALS4/CMakeLists.txt
Src/Extern/SUNDIALS4/Make.package
Src/Extern/SUNDIALS4/arkode_interface.f90
Src/Extern/SUNDIALS4/cvode_interface.f90
Src/Extern/SUNDIALS4/farkode_arkstep_mod.f90
Src/Extern/SUNDIALS4/farkode_butcher_mod.f90
Src/Extern/SUNDIALS4/farkode_mod.f90
Src/Extern/SUNDIALS4/fcvode_mod.f90
Src/Extern/SUNDIALS4/fnvector_mod.f90
Src/Extern/SUNDIALS4/fnvector_serial_mod.f90
Src/Extern/SUNDIALS4/fsundials_types_mod.f90
Src/Extern/SUNDIALS4/fsunlinsol_dense.f90
Src/Extern/SUNDIALS4/fsunlinsol_dense_mod.f90
Src/Extern/SUNDIALS4/fsunlinsol_mod.f90
Src/Extern/SUNDIALS4/fsunmatrix_dense_mod.f90
Src/Extern/SUNDIALS4/fsunmatrix_mod.f90
Src/Extern/SUNDIALS4/fsunnonlinsol_mod.f90
Tools/CMake/AMReX_Options.cmake
Tools/CMake/FindSUNDIALS.cmake
Tools/GNUMake/Make.defs
Tools/GNUMake/packages/Make.sundials4
Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/GNUmakefile
Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/Make.package
Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/ark_analytic_f2003.f90

commit 361db6fb5599545fe20376cb68cd8dc45c6e4551
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 27 10:13:48 2019 -0700

    gpu: eb cylinder

Src/EB/AMReX_EB2_IF_Box.H
Src/EB/AMReX_EB2_IF_Cylinder.H

commit a725036afba002e616d08dc62bbef8a8c1ef21da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 27 09:14:16 2019 -0700

    include EB2_IF_Base.H in all IF headers

Src/EB/AMReX_EB2_IF_Cylinder.H
Src/EB/AMReX_EB2_IF_Difference.H
Src/EB/AMReX_EB2_IF_Ellipsoid.H
Src/EB/AMReX_EB2_IF_Extrusion.H
Src/EB/AMReX_EB2_IF_Intersection.H
Src/EB/AMReX_EB2_IF_Lathe.H
Src/EB/AMReX_EB2_IF_Plane.H
Src/EB/AMReX_EB2_IF_Polynomial.H
Src/EB/AMReX_EB2_IF_Rotation.H
Src/EB/AMReX_EB2_IF_Scale.H
Src/EB/AMReX_EB2_IF_Spline.H
Src/EB/AMReX_EB2_IF_Torus.H
Src/EB/AMReX_EB2_IF_Translation.H
Src/EB/AMReX_EB2_IF_Union.H

commit b8a5f16c381c5c5405645b2d4e68600dc59eb770
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 26 23:55:27 2019 -0400

    option to disable device sync in MFIter

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 2709cc3af73a5a32a61265abaf4d5c009b7e37fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 26 22:38:29 2019 -0400

    add prefetch to AmrLevel::writePlotFile

Src/Amr/AMReX_AmrLevel.cpp

commit ac514073416d3925c423f7dc108bd6eec5b7e9fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 26 18:44:50 2019 -0700

    add free functions prefetchToHost and prefetchToDevice for FabArray

Src/Base/AMReX_FabArrayUtility.H
Tutorials/GPU/EBCNS/Source/CNS_io.cpp

commit e4029c47ba262588c45602efd38aebe258ddba24
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 26 17:05:32 2019 -0700

    fix enable_if

Src/Base/AMReX_FabArray.H

commit bd68aaea0f048a272efbf04f5fba556930d7d39d
Merge: f55bfadfd d4bdf49c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 26 16:51:39 2019 -0700

    Merge branch 'weiqun/gpu' into development

commit 19478a3e1954d6574503ab03e6200300cda7bbd1
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Mar 26 16:28:58 2019 -0700

    Replace #if with #ifdef as per Andrew's suggestion

Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H
Src/Particle/AMReX_ParticleContainerI.H

commit d4bdf49c9fa8404deb3c7175531d1f084352d57e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 26 16:27:37 2019 -0700

    add README

Tutorials/GPU/EBCNS/README

commit 1cf9824aefe9d4491f449fb9361802af2667e5df
Merge: 959071461 a54ba21f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 26 16:24:58 2019 -0700

    Merge branch 'development' into weiqun/gpu

commit 9590714612d3d2db028b9ebcbd83ea91983e8e96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 26 14:58:23 2019 -0700

    fix enable_if and start gpu version of GeometryShop

Src/Base/AMReX_Array.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EB2_IF.H
Src/EB/AMReX_EB2_IF_Complement.H
Src/EB/AMReX_EB2_IF_Sphere.H

commit f55bfadfdcaab2feb1ee3f81903c060a2ee8d693
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Mar 26 13:38:12 2019 -0700

    Need to make the compute_dphidn* routines public

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 2f2ad19cd717ff3befffadd77173718652c58c67
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Mar 26 13:25:50 2019 -0700

    Make compute_dphidn hold the lower order stencil and create compute_dphidn_ho
    to hold the higher-order stencil.

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 9458a099ea91fd85b829549646ca7d903a0879a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 26 12:52:07 2019 -0700

    gpu: BoxIF and ComplementIF

Src/EB/AMReX_EB2_IF.H
Src/EB/AMReX_EB2_IF_AllRegular.H
Src/EB/AMReX_EB2_IF_Base.H
Src/EB/AMReX_EB2_IF_Box.H
Src/EB/AMReX_EB2_IF_Complement.H

commit a561d6b2b9cf7f5332ea87f731e5b16566dcd5cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 26 11:49:32 2019 -0700

    gpu: copyMultiFabToMultiCutFab

Src/EB/AMReX_EB2_Level.cpp
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp

commit 4e3e2e34dc1ed334ec174bed40255fee082391a9
Merge: a54ba21f1 96692c116
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Mar 26 09:18:15 2019 -0700

    Merge pull request #435 from jared321/flash_tileID
    
    local tile index

commit 96692c1161316a670b62039d4422d8e7d9dfc392
Author: Jared O'Neal <joneal@anl.gov>
Date:   Tue Mar 26 09:12:00 2019 -0500

    Add local tile index to the MFIter's Fortran interface.

Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 8e70f01672779af7b0285460f3b3cd9358a3d2f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 25 16:55:53 2019 -0700

    noexcept and inline

Src/Base/AMReX_Array.H
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp

commit 57d473196e12c1db8d272032938bc6d7740152d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 25 16:35:28 2019 -0700

    remove BoxLib MG and add noexcept

Src/Amr/AMReX_Amr.cpp
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Src/EB/AMReX_EB2_Level.H

commit af267f6bd7fc79a9a0f86428129e1d177c25df41
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Mar 25 19:16:17 2019 -0400

    CMake: change how we set PUBLIC_HEADER and CUDA properties on sources

Src/CMakeLists.txt

commit c94794ad7f60a814c7d33fc96552cebc35e08752
Merge: 870584201 a54ba21f1
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Mar 25 17:30:19 2019 -0400

    Merge branch 'development' into mr/cmake

commit 928950d460c7645f6341520c00b811d03e36bc18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 25 13:18:45 2019 -0700

    add struct XDim3

Src/Base/AMReX_Array.H

commit af6cff52f1e68ed882b20270eaf56d98211048fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 25 13:03:44 2019 -0700

    add struct GPUable that can be used as base for EB2's IF classes

Src/EB/AMReX_EB2_IF.H
Src/EB/AMReX_EB2_IF_Base.H
Src/EB/AMReX_EB2_IF_Sphere.H
Src/EB/CMakeLists.txt
Src/EB/Make.package

commit 35fdae2491647bfe60bb0866919f4059869f19a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 25 12:40:09 2019 -0700

    update plotfile

Tutorials/GPU/EBCNS/Exec/Sod/inputs
Tutorials/GPU/EBCNS/Source/CNS.H
Tutorials/GPU/EBCNS/Source/CNS.cpp
Tutorials/GPU/EBCNS/Source/CNS_io.cpp

commit c9fe9cdb78a72f593d0e84807a1e78c708709d49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 25 12:15:45 2019 -0700

    fix makefile and add noexcept

Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Tutorials/GPU/EBCNS/Exec/Make.CNS

commit a54ba21f1ae020319b2a051ad0789009aad27089
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 25 09:15:27 2019 -0700

    particle_compare: fix return type

Tools/Postprocessing/C_Src/particle_compare.cpp

commit faf5f9584bc2ab308bcec118e7321e316f2d2e01
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Mar 24 20:09:22 2019 -0700

    Print out message that we are initializing CUDA
    
    This can take a long time on the P9 platform, so this message is there
    to reassure the user that in fact something is happening, not a hang.

Src/Base/AMReX_CudaDevice.cpp

commit efd1db0afadb1144f3dbdbd3cb70a5fa99e44b52
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Mar 24 07:10:23 2019 -0700

    Fix typo

Src/Amr/AMReX_AmrLevel.cpp

commit cc6298afce527bda9d6a72db5dfa6a8bc3937758
Merge: 853e767be 0ca7e9a99
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Mar 23 16:25:42 2019 -0700

    Merge pull request #434 from AMReX-Codes/convergence
    
    some clean ups to the Richardson convergence tool

commit 0ca7e9a996281c308464688a567beeeb343ae690
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Mar 23 13:53:19 2019 -0700

    make the error files optional
    implement the verbose option

Tools/C_util/Convergence/RichardsonConvergenceTest.cpp

commit 853e767bea88841bb4ad67f710bf6d773c49c798
Merge: 72f994fa1 a27619f64
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Mar 23 13:30:35 2019 -0700

    Merge pull request #433 from cgilet/development
    
    Make public interpolate_to_face_centroid() and interpolate_to_face_ce…

commit a27619f64d822ce7588bbcd7c8988c72aec4fe7b
Author: cgilet <cgilet@gmail.com>
Date:   Sat Mar 23 15:51:24 2019 -0400

    Make public interpolate_to_face_centroid() and interpolate_to_face_centroid_per_cell()

Src/EB/AMReX_EBMultiFabUtil_2d.F90

commit 72f994fa1297e46c0c37e4cbdd3b2ce3c938cf8e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Mar 23 14:21:15 2019 -0400

    character variables should not be allocatable/managed

Tools/F_scripts/write_probin.py

commit 21e2c8c9338def6f5106f0482161111e2fc1ea43
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Mar 23 14:01:27 2019 -0400

    Only CUDA header script copies files

Tools/GNUMake/Make.rules

commit 8a597e9126774113b81e9f8db1a27f3c5c87cfae
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Mar 23 13:12:09 2019 -0400

    Add some parallelism to the GPU header script

Tools/F_scripts/write_cuda_headers.py
Tools/GNUMake/Make.rules

commit a11edc5cf92ea7c4f3c9fd1c88c39e7f35f7ba2d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Mar 23 08:32:11 2019 -0700

    Oops -- entered Friesen's ORCID wrong

paper/paper.md

commit 58b3be3c616c303ccc80c8a6313bc14fcf1e1088
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Mar 23 08:32:11 2019 -0700

    Oops -- entered Friesen's ORCID wrong

paper/paper.md

commit 839d4063e94afc48262bf76e3685c27e10a3a233
Merge: d81b324e4 802a8b6d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 22 21:48:44 2019 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d81b324e423a92d193d350fbea0303525e17e10f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 22 21:41:17 2019 -0700

    add cuda memory prefetch function

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H

commit a9a376131173b744b3f98101190ea51bd702552e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 22 16:51:15 2019 -0700

    Fix some capitalization

paper/paper.md

commit 802a8b6d9014c22c8af03e76e138b7aabb9a1338
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 22 16:51:15 2019 -0700

    Fix some capitalization

paper/paper.md

commit dcb313a925a622ab46f7a39d00eb5a617ac32728
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 22 16:47:15 2019 -0700

    Moved JOSS stuff from Docs/JOSS to paper folder so reviewers can find it.

paper/Makefile
paper/paper.bib
paper/paper.md

commit 46b637c8e6934b50c678c1713d34064d74ac1867
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 22 16:47:15 2019 -0700

    Moved JOSS stuff from Docs/JOSS to paper folder so reviewers can find it.

paper/Makefile
paper/paper.bib
paper/paper.md

commit 85ea2c5201980f8d247a6864d625d61761ea733b
Merge: a083776bd 048ec2bdf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 22 15:47:49 2019 -0700

    Merge branch 'weiqun/data_allocator' into development

commit a083776bd0cce44ff7fc76f9145ec97986efd688
Merge: 33070a65f a85a15d47
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 22 18:40:58 2019 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 33070a65f5ac4bd563a0377a52465c8c04a5535a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 22 18:40:19 2019 -0400

    set CFLAGS_FROM_HOST to CXXFLAGS_FROM_HOST because nvcc -x cu compiles as C++

Tools/GNUMake/comps/nvcc.mak

commit b321c408981ceb8dc832000a869c59f464ee53e8
Author: kngott <kngott@lbl.gov>
Date:   Fri Mar 22 15:05:17 2019 -0700

    Add Graphs to 1 MPI section of FillBoundary.

Src/Base/AMReX_FabArrayCommI.H

commit 630d8a4bbb35e7385939596b0d4419314743e2ff
Author: kngott <kngott@lbl.gov>
Date:   Fri Mar 22 15:04:27 2019 -0700

    Add LaunchRegion and GraphRegion checks to Device::Graph calls.

Src/Base/AMReX_CudaDevice.cpp

commit f2965ca3e300d0942c519c716fa0879f6cb01e35
Author: kngott <kngott@lbl.gov>
Date:   Fri Mar 22 15:03:23 2019 -0700

    Add static GraphRegion values for Graph Testing.

Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuControl.cpp

commit 048ec2bdfdf44c93435c99c49e56d05ae806bd3c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 22 14:49:09 2019 -0700

    add The_Cpu_Arena and CpuDataAllocator.  use CpuDataAllocator in parallelcopy meta-data processing

Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArrayBase.cpp

commit 158f2d9924bc0e9ec62c9a0786dcdcc036567f4b
Author: kngott <kngott@lbl.gov>
Date:   Fri Mar 22 12:24:57 2019 -0700

    Rewrite with Device's graphs functions for testing.

Tests/GPU/CudaGraphs/GraphCopy/main.cpp

commit 551014a60b2855c44e6836e8454389790e25585d
Author: kngott <kngott@lbl.gov>
Date:   Fri Mar 22 12:24:35 2019 -0700

    Change GNUmakefile-s to work with reorganization.

Tests/GPU/CudaGraphs/BuildingGraphs/GNUmakefile
Tests/GPU/CudaGraphs/GraphBoundary/GNUmakefile
Tests/GPU/CudaGraphs/GraphCopy/GNUmakefile

commit 15f59366dd13efae3137be07ca5dbc83e85ac147
Author: kngott <kngott@lbl.gov>
Date:   Fri Mar 22 12:23:25 2019 -0700

    Add first draft Graph functions to Device.

Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Tests/GPU/CudaGraphs/BuildingGraphs/GNUmakefile
Tests/GPU/CudaGraphs/BuildingGraphs/Make.package
Tests/GPU/CudaGraphs/BuildingGraphs/inputs_3d
Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp
Tests/GPU/CudaGraphs/BuildingGraphs/run.corigpu
Tests/GPU/CudaGraphs/CrazyGraphs/GNUmakefile
Tests/GPU/CudaGraphs/CrazyGraphs/main.cpp
Tests/GPU/CudaGraphs/CrazyGraphs/run.corigpu
Tests/GPU/CudaGraphs/GraphBoundary/GNUmakefile
Tests/GPU/CudaGraphs/GraphBoundary/Make.package
Tests/GPU/CudaGraphs/GraphBoundary/Prob.H
Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d
Tests/GPU/CudaGraphs/GraphBoundary/main.cpp
Tests/GPU/CudaGraphs/GraphBoundary/profile.sh
Tests/GPU/CudaGraphs/GraphBoundary/run.corigpu
Tests/GPU/CudaGraphs/GraphBoundary/run.summit
Tests/GPU/CudaGraphs/GraphCopy/GNUmakefile
Tests/GPU/CudaGraphs/GraphCopy/Make.package
Tests/GPU/CudaGraphs/GraphCopy/inputs_3d
Tests/GPU/CudaGraphs/GraphCopy/main.cpp
Tests/GPU/CudaGraphs/GraphCopy/run.corigpu

commit cabe5ab5e270ceb73a5c765a4076264833fe8918
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 22 11:10:07 2019 -0700

    add a default template paramter Allocator to BaseFab

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_TypeTraits.H

commit a85a15d470d9c24d38bd834835ed658f7403ae04
Merge: 7605b944c b70cbd660
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 22 10:49:49 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 7605b944c49c1e81eafb3969926d5c72c321990c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 22 10:47:40 2019 -0700

    1) Fixed bug in 3d version of amrex_eb_interpolate_to_face_centroid
    2) Made 2d versions of amrex_eb_interpolate_to_face_centroid and amrex_eb_interpolate_to_face_centroid_per_cell

Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_3d.F90

commit b70cbd6604f728e23edbf23d11a1034096714ee1
Merge: 3e7a68efa 10babf037
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 22 10:16:45 2019 -0700

    Merge pull request #432 from RevathiJambunathan/random_xorwow_RJ
    
    Random xorwow -- modified seed with mpi rank

commit 3e7a68efa149a5b123870ac0dc6404d47703e5ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 22 10:12:18 2019 -0700

    always use -Werror=return-type for gcc

Tools/GNUMake/comps/gnu.mak

commit 95138e359a5e814288db4e280b30fcc1b100e114
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 22 10:01:50 2019 -0700

    comment out some profilers

Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_VisMF.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit 5a0965ee69655a62a49a1fac2f22f6e1e2beaf53
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 22 08:06:54 2019 -0700

    Add a per-cell interpolate to face centroid routine (taken from mfix).

Src/EB/AMReX_EBMultiFabUtil_3d.F90

commit 0ec21fe72223ff03fba442954127d9f8e66fb091
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 21 19:50:19 2019 -0700

    Re-word the fork-join sentence

Docs/JOSS/paper.md

commit af730c3722899e6ff6d8450726daf33f64265ebd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 21 19:43:10 2019 -0700

    Fix more typos and remove "(AMR)" from the title.

Docs/JOSS/paper.md

commit 426ccaf054d7502598efacf17a5cf4d3af8f1f9c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Mar 21 21:39:43 2019 -0400

    Typos

Docs/JOSS/paper.md

commit d75df993d61d44d98b8d48e6218b292964638945
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Mar 21 21:37:36 2019 -0400

    Change my name

Docs/JOSS/paper.md

commit fab6d852f9c3a733f5f372fdd1881caf83854188
Merge: d2b8fecc8 bec83ac55
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 21 18:02:59 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit d2b8fecc801704990562ebf32692cfdf0e7d7c64
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 21 18:02:45 2019 -0700

    Oops -- forgot John on the author list

Docs/JOSS/paper.md

commit bec83ac553d60c84a62d0d5820c7dff044c03852
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date:   Thu Mar 21 18:02:10 2019 -0700

    Fix reference to Zingale et al 2018

Docs/JOSS/paper.md

commit 85c91c35d6531d1bb59e26b473babd2021a65262
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 21 17:51:21 2019 -0700

    updated references

Docs/JOSS/paper.bib

commit 20101dd54c2e819af558a128fcbaf6aeddb56dcc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 21 17:45:01 2019 -0700

    updated with references

Docs/JOSS/paper.md

commit d63824cda7535ffc054fd945e36f53878ab0893c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 21 17:22:42 2019 -0700

    re-order sections

Docs/JOSS/paper.md

commit 36b6ede4e0112f010cee71028c0a41c397014f8b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 21 17:21:49 2019 -0700

    Modify subsection headings

Docs/JOSS/paper.md

commit 29871f6440c0902f15b0df9fa0a06b91b75ffc11
Merge: e24e31f40 107452f06
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 21 17:21:09 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit e24e31f40ef5a7723a1716804a7709b56b93bf7d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 21 17:20:58 2019 -0700

    This is getting closer...

Docs/JOSS/paper.md

commit 10babf0375a16d6873c25b0617de66fd68464c9d
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Thu Mar 21 13:43:29 2019 -0700

     cleaned rand, instead of using loc_rand

Src/Base/AMReX_Utility.cpp

commit 410105913d6ce6fcbb01b3468715b87926b9862c
Merge: 595dda107 107452f06
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Thu Mar 21 13:31:38 2019 -0700

     fixed the conflict with 1D threadId and the newly added 3D threadId in Utility.cpp after merging with development

commit 595dda107b1b79dd649e46b603442043b67ce002
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Thu Mar 21 13:10:37 2019 -0700

     Modified main.cpp in the test file to check for resize and ensuring that the seed generation is working properly for the grown vector

Tests/GPU/RandomNumberGeneration/main.cpp

commit ce016ccedf633bb194afe833a1b0fd314ef74aca
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Thu Mar 21 13:09:38 2019 -0700

    Modified seed generation to depend on MyProc or mpi_rank, so that each GPU does not have the same seed. And within a GPU, given the same seed, the startsequence of random number generation is threadID dependent. Also, generalized the threadId calculation for 3D block Grid and 3D thread block. Finally, when resize is called, the seed generation is performed only for the newly added vector elements. Note that CheckSeedArraySizeAndResize() should be called to Resize()

Src/Base/AMReX_Utility.cpp

commit 4862ce28b310704faf8ea58652d42ddd18d568ac
Author: kngott <kngott@lbl.gov>
Date:   Thu Mar 21 12:57:18 2019 -0700

    Add FillBoundary Test to repo.

Tests/GPU/GraphBoundary/Prob.H
Tests/GPU/GraphBoundary/inputs_3d
Tests/GPU/GraphBoundary/main.cpp
Tests/GPU/GraphBoundary/profile.sh
Tests/GPU/GraphBoundary/run.corigpu
Tests/GPU/GraphBoundary/run.summit
Tests/GPU/GraphCopy/GNUmakefile
Tests/GPU/GraphCopy/Make.package
Tests/GPU/GraphCopy/inputs_3d
Tests/GPU/GraphCopy/main.cpp
Tests/GPU/GraphCopy/run.corigpu

commit 59f1e467bf859f4cb11d4ea9e3b9702b9e0bd7e6
Author: kngott <kngott@lbl.gov>
Date:   Thu Mar 21 12:41:59 2019 -0700

    Check changing memory layout on CudaGraphs.

Tests/GPU/GraphBoundary/main.cpp

commit ff086e99b32bb1e81c6c0b2ac6cea42671c779bc
Author: kngott <kngott@lbl.gov>
Date:   Thu Mar 21 00:11:20 2019 -0700

    Light cleanup.

Tests/GPU/GraphBoundary/main.cpp

commit d0ee253ed96ac059b73c70b5970f9845d4b9fdab
Author: kngott <kngott@lbl.gov>
Date:   Wed Mar 20 23:17:10 2019 -0700

    Test copy with cudaGraph.

Tests/GPU/GraphBoundary/main.cpp

commit 107452f062fa134cbf0f3888965122df8a6383bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 20 21:00:45 2019 -0700

    fix host version of Random

Src/Base/AMReX_Utility.cpp

commit 31bea5122c426738500bfb4836f6962ac941500a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 20 20:53:03 2019 -0700

    add ifdef to cuda function call

Src/Base/AMReX_Arena.cpp

commit 57a0d8a286ff61491e8236f83f6c74c547817950
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 20 16:12:14 2019 -0700

    add init eb function

Tutorials/GPU/EBCNS/Exec/Sod/GNUmakefile
Tutorials/GPU/EBCNS/Exec/Sod/inputs
Tutorials/GPU/EBCNS/Source/CNS_init_eb2.cpp
Tutorials/GPU/EBCNS/Source/Make.package
Tutorials/GPU/EBCNS/Source/main.cpp

commit 341f2ea1c40057cbc9f71fad77d5272fcd361108
Author: kngott <kngott@lbl.gov>
Date:   Wed Mar 20 17:43:33 2019 -0700

    Cuda graph testing on lambda-less form of FillBoundary calls.

Tests/GPU/GraphBoundary/GNUmakefile
Tests/GPU/GraphBoundary/Make.package
Tests/GPU/GraphBoundary/inputs_3d
Tests/GPU/GraphBoundary/main.cpp
Tests/GPU/GraphBoundary/run.corigpu

commit 4f0d598ec9206de6f6ccfd17ddcfb3d8023ae779
Merge: 3f0f8c36e 96b97ad5a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 20 15:48:37 2019 -0700

    Merge pull request #428 from RevathiJambunathan/random_xorwow_RJ
    
    Random number generator on GPU using CUDA - RJ

commit 3f0f8c36ed20339e4fa09bc86506035e5499a81c
Merge: 6f7684bb5 22ddd1824
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Mar 20 15:45:04 2019 -0700

    Merge pull request #431 from dpgrote/development
    
    Added plot_log_per

commit 23c94f2414b3b9331d72bccab4af58595132b4f8
Merge: fbf97ef04 96b97ad5a
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 15:41:27 2019 -0700

    Merge branch 'random_xorwow_RJ' of https://github.com/RevathiJambunathan/amrex into random_xorwow_RJ

commit fbf97ef049a77babb69731dfe51bf9f1a30adf99
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 15:40:44 2019 -0700

    deleting main.H and instead added dependencies in main.cpp file of the in Tests/GPU/RandomNumberGeneration/

Tests/GPU/RandomNumberGeneration/main.H

commit e28526881178b87e5078131421040a212f5294fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 20 15:38:38 2019 -0700

    start GPU/EBCNS

Tutorials/GPU/EBCNS/Exec/Make.CNS
Tutorials/GPU/EBCNS/Exec/Sod/GNUmakefile
Tutorials/GPU/EBCNS/Exec/Sod/Make.package
Tutorials/GPU/EBCNS/Exec/Sod/cns_prob.H
Tutorials/GPU/EBCNS/Exec/Sod/cns_prob.cpp
Tutorials/GPU/EBCNS/Exec/Sod/cns_prob_parm.H
Tutorials/GPU/EBCNS/Exec/Sod/inputs
Tutorials/GPU/EBCNS/Source/CNS.H
Tutorials/GPU/EBCNS/Source/CNS.cpp
Tutorials/GPU/EBCNS/Source/CNSBld.cpp
Tutorials/GPU/EBCNS/Source/CNS_K.H
Tutorials/GPU/EBCNS/Source/CNS_advance.cpp
Tutorials/GPU/EBCNS/Source/CNS_bcfill.cpp
Tutorials/GPU/EBCNS/Source/CNS_derive.H
Tutorials/GPU/EBCNS/Source/CNS_derive.cpp
Tutorials/GPU/EBCNS/Source/CNS_index_macros.H
Tutorials/GPU/EBCNS/Source/CNS_io.cpp
Tutorials/GPU/EBCNS/Source/CNS_parm.H
Tutorials/GPU/EBCNS/Source/CNS_parm.cpp
Tutorials/GPU/EBCNS/Source/CNS_setup.cpp
Tutorials/GPU/EBCNS/Source/CNS_tagging.H
Tutorials/GPU/EBCNS/Source/Make.package
Tutorials/GPU/EBCNS/Source/diffusion/Make.package
Tutorials/GPU/EBCNS/Source/hydro/CNS_hydro_K.H
Tutorials/GPU/EBCNS/Source/hydro/Make.package
Tutorials/GPU/EBCNS/Source/main.cpp

commit 96b97ad5a12cc97d2a4e0583113da84d90f943a9
Author: Revathi  Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Date:   Wed Mar 20 15:38:25 2019 -0700

    Delete main.H

Tests/GPU/RandomNumberGeneration/main.H

commit 22ddd18248b6223be76a2e1bd78584ee58ac8246
Author: Dave Grote <grote1@llnl.gov>
Date:   Tue Mar 19 10:46:18 2019 -0700

    Added plot_log_per

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp

commit a74ea02410ef8655c0ed214cbdec40b931838b54
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 15:30:25 2019 -0700

    removed main.H file that inluded AMReX header files and instead included them in the main.cpp file.

Tests/GPU/RandomNumberGeneration/main.cpp

commit 4476763ec0231dbb1da256b62058e18b96c6bd25
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 15:18:37 2019 -0700

    Tests/GPU/RandomNumberGeneration/main.cpp

Tests/GPU/RandomNumberGeneration/main.cpp

commit 0445d6e9b533da0a9cda9f34bc86ece2fab0ba97
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 15:05:16 2019 -0700

    I had initialized array size with Nbuffer=N*2, but initialized seed with N in for loop, instead of Nbuffer. I have fixed it with Nbuffer. Also note that this array size is to prevent frequent call for resize. the size of array could even be 3*N or 1.5*N. I have put 2*N thinking that should be enough. Either way, user can call CheckSeedArraySizeAndResize() with the required number of CUDA threads launched (N). This function will resize dynamically.

Src/Base/AMReX_Utility.cpp

commit 10b3fbe0529f77294888db06d885af2cbad4397e
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 14:54:18 2019 -0700

    adding the header file for testing random numbers

Tests/GPU/RandomNumberGeneration/main.H

commit 5b3c105478501110ea3ea6e12d713848191d8bbb
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 14:50:37 2019 -0700

    adding the modified test file which calls the Random() function implemented in AMReX_Utility.cpp using either GPU or CPU.

Tests/GPU/RandomNumberGeneration/main.cpp

commit a120937818ca60ea41cdb27c524daf13b14fb73c
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 14:49:32 2019 -0700

    removed #include<curand_kernel.h> since it is not used in AMReX_Vector.H and instead included in AMReX_CudaUtility.H.

Src/Base/AMReX_Vector.H

commit eba1aa01264c64092ec9c58fe0be42a87a9f3152
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 14:48:02 2019 -0700

     cleaned up utility.cpp such that it does not rely on using namespace amrex, or using namespace Gpu, instead using amrex:: or amrex::Gpu:: . Also included *glo_RandStates in an anonymous namespace. Finally, int NrandMax is removed as it is the size of the random seed vector. Instead, I have called dev_RandStates_Seed.size()

Src/Base/AMReX_Utility.cpp

commit 41d894d0f18e48aee3f8d68cb0daf0b7db3b36d1
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 14:45:08 2019 -0700

    included curand_kernel.h in this file, instead of in AMReX_Vector.H file

Src/Base/AMReX_CudaUtility.H

commit 6f7684bb504f1a50b6ffcc0b4fd2ea57af5b8a22
Merge: 21c13037f ef738f0d5
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Mar 20 13:46:08 2019 -0700

    Merge pull request #430 from jrood-nrel/nrel_add_rhodes
    
    Adding some specific compiler flags for the Rhodes machine at NREL.

commit b8f172155c56ab4cebab13eee39f82f284517142
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 12:59:44 2019 -0700

    deleted code (Hash_DistributionMap) in AMReX_Utility.H based on git diff random_xorwow_RJ and development

Src/Base/AMReX_Utility.H

commit ef738f0d5c7169522894235e5a0e96182f5b5fc6
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Wed Mar 20 13:53:57 2019 -0600

    Adding some specific compiler flags for the Rhodes machine at NREL.

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.nrel

commit 8e9b090d29d7051c2c26c7703b073591365f2694
Merge: 75b8f523b 21c13037f
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 12:17:50 2019 -0700

    Merge branch 'development' into random_xorwow_RJ

commit 75b8f523b569936a81b031723d3cd1d751e5e0cd
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 11:43:52 2019 -0700

    modified Utility.cpp to generalize it for runs that do not use the CUDA flag

Src/Base/AMReX_Utility.cpp

commit cecb2746f0b75e3858ae13ecfc63a995e4193ee1
Merge: edb2bcbe0 43f7771e0
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 10:55:43 2019 -0700

    Merge branch 'random_xorwow_RJ' of https://github.com/RevathiJambunathan/amrex into random_xorwow_RJ

commit edb2bcbe0325f595a5350916c04668e54b1f03f3
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Wed Mar 20 10:50:40 2019 -0700

    modified Utility.cpp to generalize it for runs that do not use the CUDA flag

Src/Base/AMReX_Utility.cpp

commit 43f7771e0b48ee0c245b00bd223149118d277120
Author: Revathi  Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Date:   Wed Mar 20 10:46:44 2019 -0700

    Delete test1.out

Tests/GPU/RandomNumberGeneration/test1.out.REMOVED.git-id

commit 504d54e4f56d18a2f2f79fda427b55fe4539c137
Author: Revathi  Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Date:   Wed Mar 20 10:46:35 2019 -0700

    Delete profilingdata_rndm.dat

Tests/GPU/RandomNumberGeneration/profilingdata_rndm.dat

commit cf09fc5072a0d143cc02f8e9e1c678a6766275eb
Author: Revathi  Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Date:   Wed Mar 20 10:46:27 2019 -0700

    Delete profile_without_skipahead.dat

Tests/GPU/RandomNumberGeneration/profile_without_skipahead.dat

commit 2794d16610a1819d506589c3ae4c0741efb11631
Author: Revathi  Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Date:   Wed Mar 20 10:46:20 2019 -0700

    Delete profile_with_skipahead.dat

Tests/GPU/RandomNumberGeneration/profile_with_skipahead.dat

commit e816387e89ea6f821d8ca4ffd824eaabc00eaef7
Author: Revathi  Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Date:   Wed Mar 20 10:46:04 2019 -0700

    Delete Backtrace.0

Tests/GPU/RandomNumberGeneration/Backtrace.0

commit 21c13037fd23097c9b890bd4360ee3eabe1d299f
Merge: 93707d252 81f80ea98
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 20 10:37:40 2019 -0700

    Merge branch 'weiqun/bestfit' into development

commit 93707d252e69572d0db671735a61416f8b936eb3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 20 13:35:11 2019 -0400

    allocate 3/4 of global memory up front in the arena.  this can be changed with parmparse parameter amrex.the_arena_init_size

Src/Base/AMReX_Arena.cpp

commit 6dcce9f1ede35b372d8e121cc8653c460974e457
Merge: 46c5abb44 cb68ed4e4
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Tue Mar 19 18:29:10 2019 -0700

    adding changes in Utility.H/.cpp after merging with the development branch

commit 81f80ea98c81bd47f3791482c90f222302befbec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 19 16:41:06 2019 -0700

    EArena: use lower bound

Src/Base/AMReX_EArena.cpp

commit 46c5abb447ee91c48e3c70608276299bb829ce90
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Tue Mar 19 16:36:47 2019 -0700

    adding changes made in Utility.H/.cpp to include random number generator for device

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_Vector.H

commit cb68ed4e415a5fcb4797e10240435a03da6d1ce9
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Mar 19 18:33:06 2019 -0400

    ReduceLongMax -> ReduceLongSum

Src/Particle/AMReX_ParticleContainerI.H

commit 04a8c7814433af86eb4643443cffb116b42d3060
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 19 15:08:33 2019 -0700

    EArena: memory allocator using best fit strategy

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_CArena.H
Src/Base/AMReX_EArena.H
Src/Base/AMReX_EArena.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 53ce1e1af65ad3e045a915bf2c6dfdda3e2a5193
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Mar 19 10:21:27 2019 -0400

    fix makefile

Docs/JOSS/Makefile

commit 325015b565ab58e05ae8dbdfb30baf9396393291
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 18 19:49:16 2019 -0700

    Fix the author ordering so it shows correctly on the web page

Docs/JOSS/paper.md

commit dee97eff1e5e544999082a583e3268f542771860
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 18 19:13:10 2019 -0700

    Add mention of BoxLib and xSDK.

Docs/JOSS/paper.md

commit e2d01db45b618b762ad1713aa80f8b3eb616396d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 18 19:09:44 2019 -0700

    A start of the JOSS paper and bibliography

Docs/JOSS/Makefile
Docs/JOSS/paper.bib
Docs/JOSS/paper.md

commit 6ef6e1da53385ea0736bebda210ec6e91dd067a9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 18 18:52:47 2019 -0700

    Remove "Overview"

Docs/sphinx_documentation/source/ForkJoin.rst

commit be72c86c9d31eb50862beba22702be73a7fae2e5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 18 18:48:40 2019 -0700

    "framework library" --> "framework"

Docs/sphinx_documentation/source/index.rst

commit 7435d470f9ed18c1a1091c732126a211bbc8080f
Merge: 3ef58a9f9 95e37900a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 18 18:41:04 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 3ef58a9f9368432e60c3f04494b1cec2cbbb0042
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 18 18:40:45 2019 -0700

    Add ForkJoin to the documentation (as well as the tutorials)

Docs/sphinx_documentation/source/ForkJoin.rst
Docs/sphinx_documentation/source/figs/fork_join_tasks.png
Docs/sphinx_documentation/source/figs/nested_fork_join_tasks.png
Docs/sphinx_documentation/source/index.rst

commit 95e37900aa57d63c60ac6bcffca61159158b31eb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Mar 18 21:31:21 2019 -0400

    keep the temporary variables around to save on memory usage with the Arena

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit e55119ef04d0551033daf8b57cb6f12c2e8c5b5a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Mar 18 21:30:40 2019 -0400

    use the managed arena for thrust's interal calculations

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaAllocators.cpp

commit 32e598ac155af8426b2d0d9b5aa4159944e4a11e
Merge: 5e41305a3 e4ca314f3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 18 14:52:11 2019 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 5e41305a3e702c1ca29435aea841eae9e76d783e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 18 14:50:45 2019 -0700

    Add disclaimer re Macs

Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst

commit 929a6e691fb45b49eb9352ae49179a5a1ee391d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 18 13:23:57 2019 -0700

    attribute weak

Src/Amr/AMReX_LevelBld.H
Src/Amr/AMReX_PROB_AMR_F.H
Src/Base/AMReX_Extension.H

commit e4ca314f3ce884bd25965bd625db440500fe7643
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 18 13:22:51 2019 -0700

    fix shadow warning

Src/Base/AMReX_BCRec.H

commit b89a8c35caa5016a19562ab4cf676178468355f1
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Mar 18 16:11:59 2019 -0400

    Edit Scratchpad to compile on Summit.

Tests/GPU/ScratchPad/main.cpp

commit a215812a690f95937b148b0e34d664da86d82f33
Merge: 801fb1c38 5a38f1f31
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 18 16:06:38 2019 -0400

    Merge branch 'weiqun/noexcept' into development

commit 5a38f1f3173e38f907ed07a0823914998228f3a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 18 16:06:13 2019 -0400

    add noexcept to lambda functions

Src/Base/AMReX_CudaLaunch.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/CNS_derive.cpp
Tutorials/GPU/CNS/Source/CNS_tagging.H
Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H

commit 801fb1c38bbeba631a5c76d0b8d129a5aa7c43e3
Merge: 68de1e853 84179b022
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 18 12:27:19 2019 -0700

    Merge branch 'weiqun/noexcept' of github.com:AMReX-Codes/amrex into weiqun/noexcept

commit 84179b0229d994070fa3d8534c294fd2313c5612
Merge: 40c411f87 14d441659
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 18 15:25:48 2019 -0400

    Merge branch 'development' into weiqun/noexcept

commit 68de1e85353f9cf72b8d87c0bd2f340df6346365
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 18 12:24:46 2019 -0700

    fix a warning

Src/Amr/AMReX_StateDescriptor.H

commit 14d4416594b17633fb58e871bb78ad8f30400828
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 18 14:20:31 2019 -0400

    fix make for olcf. Seems that cuda module no longer sets CUDAPATH.

Tools/GNUMake/sites/Make.olcf

commit 40c411f87c8f0d4a0e65a978ed3a5eec7adcc8c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 18 10:40:07 2019 -0700

    add noexcept to TinyProfiler

Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp

commit 6580c18faf16a37479a0fa0e8438ba3bed124e34
Merge: b94c3bc32 94746c971
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 18 10:25:24 2019 -0700

    Merge branch 'development' into weiqun/noexcept

commit 977b9c3bb53c9114df960a5d3108d83c31523ceb
Author: kngott <kngott@lbl.gov>
Date:   Mon Mar 18 10:15:30 2019 -0700

    Comment adjustments.

Tests/GPU/CrazyGraphs/main.cpp

commit b94c3bc3241450261b6f2bd527cd4e2c3099fe53
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 18 10:15:09 2019 -0700

    add noexcept to Amr/

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AuxBoundaryData.H
Src/Amr/AMReX_AuxBoundaryData.cpp
Src/Amr/AMReX_Derive.H
Src/Amr/AMReX_Derive.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StateDescriptor.H
Src/Amr/AMReX_StateDescriptor.cpp
Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_AmrParGDB.H
Src/AmrCore/AMReX_Cluster.H
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_ErrorList.H
Src/AmrCore/AMReX_ErrorList.cpp
Src/AmrCore/AMReX_FluxReg_1D_C.H
Src/AmrCore/AMReX_FluxReg_2D_C.H
Src/AmrCore/AMReX_FluxReg_3D_C.H
Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp

commit d11c4ddf4568c5b04048c9204bf3661ad34b575f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 15 17:00:19 2019 -0700

    add noexcept to MLMG

Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLALap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLALap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MacProjector.H

commit 45f9e7a51afd154144b1799df89c115d50436f08
Author: kngott <kngott@lbl.gov>
Date:   Mon Mar 18 01:03:39 2019 -0700

    Add lambda launch version. Still needs CUDA 10.1.

Tests/GPU/CrazyGraphs/main.cpp

commit cb86a8259b468df0b034155d6ca26aed4c3cb9a4
Author: kngott <kngott@lbl.gov>
Date:   Mon Mar 18 01:03:19 2019 -0700

    Add --expt-extended-lambda flag.

Tests/GPU/CrazyGraphs/GNUmakefile

commit 95106907a52f675201c078663ad029486769264b
Author: kngott <kngott@lbl.gov>
Date:   Sun Mar 17 21:04:15 2019 -0700

    Crazy Graphs. Attempt to reuse graphs with different parameters without re-instantiating. Needs CUDA 10.1 to test.

Tests/GPU/CrazyGraphs/GNUmakefile
Tests/GPU/CrazyGraphs/main.cpp
Tests/GPU/CrazyGraphs/run.corigpu

commit 3d5505d948240cd4e6791469d6d92c0e4021a3e7
Author: kngott <kngott@lbl.gov>
Date:   Fri Mar 15 16:58:17 2019 -0700

    Reuse a graph.

Tests/GPU/CudaGraphs/main.cpp

commit 1b4f38021623642c3d382f9c914d2a6c553b64be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 15 16:40:53 2019 -0700

    add noexcept to Boundary/

Src/Boundary/AMReX_BndryData.H
Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_BoundCond.H
Src/Boundary/AMReX_FabSet.H
Src/Boundary/AMReX_FabSet.cpp
Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_InterpBndryData_1D_K.H
Src/Boundary/AMReX_InterpBndryData_2D_K.H
Src/Boundary/AMReX_InterpBndryData_3D_K.H
Src/Boundary/AMReX_LOUtil_K.H
Src/Boundary/AMReX_MacBndry.H
Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_Mask.cpp
Src/Boundary/AMReX_MultiMask.H
Src/Boundary/AMReX_YAFluxRegister.H
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/Boundary/AMReX_YAFluxRegister_1D_K.H
Src/Boundary/AMReX_YAFluxRegister_2D_K.H
Src/Boundary/AMReX_YAFluxRegister_3D_K.H

commit 2414d66288d7cd4aaa3db6f5e1f0361c4f263520
Author: kngott <kngott@lbl.gov>
Date:   Fri Mar 15 16:05:55 2019 -0700

    Add linked graph over iterations.

Tests/GPU/CudaGraphs/main.cpp

commit 1570e0162306c01c3e83e9d547203d13ecc18ae7
Author: kngott <kngott@lbl.gov>
Date:   Fri Mar 15 15:30:11 2019 -0700

    One linked MFIter graph & cleaned output.

Tests/GPU/CudaGraphs/main.cpp

commit c3412db7c753be603b54bfe7d1437944d1f61848
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 15 15:21:17 2019 -0700

    more noexcepts. remove BroadcastDistributionMap and BroadcastBoxArray

Src/Base/AMReX_IndexType.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_Orientation.H
Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_Periodicity.H
Src/Base/AMReX_Periodicity.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp
Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_Vector.H

commit 83bc3a01625d2a6a27f154829d7da11cce054bc2
Author: kngott <kngott@lbl.gov>
Date:   Fri Mar 15 14:17:00 2019 -0700

    Individual timers.

Tests/GPU/CudaGraphs/main.cpp

commit 4b5a033fb6fe633ef9a117df7be5584857f16fe5
Author: RevathiJambunathan <revanathan@gmail.com>
Date:   Fri Mar 15 14:14:18 2019 -0700

    adding test directory for random no. generator on gpus - XORWOW

Tests/GPU/RandomNumberGeneration/Backtrace.0
Tests/GPU/RandomNumberGeneration/GNUmakefile
Tests/GPU/RandomNumberGeneration/Make.package
Tests/GPU/RandomNumberGeneration/main.cpp
Tests/GPU/RandomNumberGeneration/profile_with_skipahead.dat
Tests/GPU/RandomNumberGeneration/profile_without_skipahead.dat
Tests/GPU/RandomNumberGeneration/profilingdata_rndm.dat
Tests/GPU/RandomNumberGeneration/test1.out.REMOVED.git-id

commit a7707320340595b9e7eb890b010dd889e96bd36a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 15 14:13:51 2019 -0700

    more excepts and remove iMultiFab's own operator[]

Src/Base/AMReX_COORDSYS_1D_C.H
Src/Base/AMReX_COORDSYS_2D_C.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FilCC_1D_C.H
Src/Base/AMReX_FilCC_2D_C.H
Src/Base/AMReX_FilCC_3D_C.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuError.H
Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IArrayBox.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.H
Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H
Src/Base/AMReX_MultiFabUtil_nd_C.H
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp

commit 4bf99a9726fc37cf749b2e524a58951890aed4b1
Author: kngott <kngott@lbl.gov>
Date:   Fri Mar 15 13:11:52 2019 -0700

    Touch the memory first to get a fair timing.

Tests/GPU/CudaGraphs/main.cpp

commit 9de2e4d8587d99430c2b6660027daef46d09aef5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 15 12:40:53 2019 -0700

    more excepts

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_Array.H
Src/Base/AMReX_CudaAsyncArray.H
Src/Base/AMReX_CudaAsyncFab.H
Src/Base/AMReX_CudaAsyncFab.cpp
Src/Base/AMReX_CudaAsyncFabImpl.H
Src/Base/AMReX_CudaAsyncFabImpl.cpp
Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaElixir.H
Src/Base/AMReX_CudaElixir.cpp
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaMemory.H
Src/Base/AMReX_CudaRange.H
Src/Base/AMReX_CudaReduce.H
Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_CudaUtility.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabFactory.H
Src/Base/AMReX_LayoutData.H

commit b8e444b4bc6d379dbfb81552504fbc9b0571b2d3
Author: kngott <kngott@lbl.gov>
Date:   Thu Mar 14 22:22:45 2019 -0700

    Fix the indenting.

Tests/GPU/CudaGraphs/main.cpp

commit 4d1fd459fec0d8194977835ac3dc01fb90ddd21e
Author: kngott <kngott@lbl.gov>
Date:   Thu Mar 14 22:17:27 2019 -0700

    Stream-based graph test.

Tests/GPU/CudaGraphs/main.cpp

commit eeb4a76cc9b1080848c03457279b41f8dcd316dd
Author: kngott <kngott@lbl.gov>
Date:   Thu Mar 14 22:17:14 2019 -0700

    Access maxCudaStreams for Stream based graph test.

Src/Base/AMReX_CudaDevice.H

commit 89049698ccc008a70c25097404261bc27c587e0b
Author: kngott <kngott@lbl.gov>
Date:   Thu Mar 14 16:47:53 2019 -0700

    First draft of CUDA graphs.

Tests/GPU/CudaGraphs/GNUmakefile
Tests/GPU/CudaGraphs/Make.package
Tests/GPU/CudaGraphs/inputs_3d
Tests/GPU/CudaGraphs/main.cpp
Tests/GPU/CudaGraphs/run.corigpu

commit 16e880b73b8a75f0145570365ebc4ab08e0046a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 14 16:40:29 2019 -0700

    more noexcepts

Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCRec.cpp
Src/Base/AMReX_BaseFabUtility.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxIterator.H
Src/Base/AMReX_BoxIterator.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_IntVect.H

commit 94746c9710253fe7d674a590c22e4379daad22e5
Merge: 1b6af3cb6 83e39b436
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Mar 14 15:18:43 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 1b6af3cb63061a11df4b224cd08753f07adfb8ca
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Mar 14 15:18:32 2019 -0700

    CMake: enable linking against amrex in shared lib mode. Fixes Issue #425

Tools/CMake/AMReX_Config.cmake
Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt

commit 83e39b43627ffa272a627bde1584e33dfb618ad2
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Mar 14 17:37:36 2019 -0400

    Convert relevant amrex::launch's to amrex::ParallelFor in Advection_AmrCore tutorial.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H

commit 447f8ee955a84c1bf63b06bbd4b47e463ad04722
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Mar 12 00:18:31 2019 -0400

    Remove recursive header calls.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H

commit 4022f1dd6b6cb6398e407a731a8df5608e196f97
Merge: 40068ae16 69a51e27d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Mar 13 12:02:20 2019 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 40068ae16af0e76bf90985773aef963341b78299
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Mar 13 11:53:41 2019 -0700

    CMake: add support for SUNDIALS3

CMakeLists.txt
Docs/sphinx_documentation/source/BuildingAMReX.rst
Src/CMakeLists.txt
Src/Extern/SUNDIALS3/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Options.cmake
Tools/CMake/FindSUNDIALS.cmake
Tutorials/CMakeLists.txt
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/CMakeLists.txt
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/main.cpp
Tutorials/CVODE/SUNDIALS3_finterface/EX1/CMakeLists.txt
Tutorials/CVODE/SUNDIALS3_finterface/EX1/main.cpp

commit 69a51e27d9e281ca0e87246b1137d17107c09839
Merge: bd274459a d6464aaa5
Author: mic84 <mrosso@lbl.gov>
Date:   Tue Mar 12 14:50:10 2019 -0700

    Merge pull request #423 from Alpine-DAV/task/2019_03_ascent_and_conduit_cmake_support
    
    add amrex cmake support for including ascent and conduit

commit d6464aaa59ff624a3870430af1f2d6b63272922e
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Tue Mar 12 14:24:41 2019 -0700

    add cmake support for including ascent

Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_SetupThirdpartyLibs.cmake

commit bd274459ae6333b2f1f87997bf5097b4278c49b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 12 09:15:40 2019 -0700

    add include guard so that AMReX_Config.H can be included in C/Fortran codes

Tools/libamrex/mkconfig.py

commit a2335da0dad9747792cafd21b58217de58721b1c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Mar 11 19:28:12 2019 -0400

    Change to simplified simple launch.

Tests/GPU/Test/main.cpp
Tests/GPU/TestB/main.cpp
Tests/GPU/TestC/main.cpp

commit 6dfbde769ba2fd83915e0ed9664a6346e425caa7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Mar 11 15:41:48 2019 -0700

    Add >= note to C++ loop discussion.

Docs/sphinx_documentation/source/Basics.rst

commit 8fda8bab5655d1f86971758458e04cddce10e3d8
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Mar 11 17:21:15 2019 -0400

    Less than or equal to.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H

commit b070fbd379f232b9604b3918d917e37f300b2305
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Mar 10 15:49:08 2019 -0400

    Make grid-stride loops better aware of numThreadsMin

Src/Base/AMReX_CudaDevice.cpp

commit aa10d38781573c9dc3a94ee07d8f2540a5fb4323
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Mar 10 15:48:40 2019 -0400

    Specialize rule for AMReX_filcc_mod.F90 when using CUDA

Src/Base/Make.package
Tools/GNUMake/Make.rules

commit 99c3f5f63cc3f412409db1867fa7ed5999f21372
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Mar 10 08:58:24 2019 -0400

    Echo which path we're taking for CUDA fortran compilation

Tools/GNUMake/Make.rules

commit 99d24aa7ff7f4e7d1b0933aac8f55fca0c82c8db
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Mar 10 05:07:57 2019 -0400

    Add hook for setting Device::numThreadsMin

Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp

commit 09c15a29f407f6de2fad4cf9347254f75b53bde9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Mar 10 03:31:49 2019 -0400

    Get amrex_filccn going for the GPU pragma case

Src/Base/AMReX_filcc_mod.F90

commit 0440482d855549e36d7da6c252a92b6a19f0b016
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Mar 10 03:31:15 2019 -0400

    Add a device sync in case the user code does bndryFill on the GPU

Src/Amr/AMReX_StateData.cpp

commit 25a48bb1fba2330169b5076f1cd1e4f5089c1f2b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Mar 8 23:21:46 2019 -0500

    Update Tests/GPU/Test: PinnedData idea.

Tests/GPU/Test/main.cpp

commit ea9243d4b032ac3d132134e40df0daa10ba0d095
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Mar 8 23:17:24 2019 -0500

    Update Tests/GPU/TestC: Turning DeviceRegion on and off.

Tests/GPU/TestC/main.cpp

commit bb7acfb97d35d3b7dd8252beb7fb7daf4e3be472
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Mar 8 22:56:44 2019 -0500

    Update GPU/Test/TestB: Fortran return bug. (It's still a bug.)

Tests/GPU/TestB/main.cpp

commit f955cfd6a121a5d0d7554a4a5498c18f2cb53dc6
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Mar 6 19:28:10 2019 -0500

    Macro based launches to function based launches.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit a86a9fdb4b6db15d203f80de262954fac6b6aeb0
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Mar 6 19:27:49 2019 -0500

    Add USE_CUDA=TRUE to GPU tutorial makefile.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile

commit 38ff7c70874faa9a42d9b91413469de6ab28fc80
Merge: 65c7d13a2 af690cba3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 8 16:31:32 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 65c7d13a23f5fd2cdc170a8b29fd818b7437d83b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 8 16:31:11 2019 -0800

    need to include this header to compile with Cuda 10.1

Src/Base/AMReX_CudaAllocators.H

commit 8705842011ed616bb09eeef6430e744099ea415f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Mar 8 18:31:44 2019 -0500

    CMake: link to cuda only if ENABLE_CUDA is on

Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Config.cmake

commit af690cba3117d4f8533bd1ccd35cd919595eaf64
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 8 10:39:15 2019 -0800

    1) Don't pass inhomogeneous flag into gsrb -- we are always in residual-correction form there
    2) Make sure to use "integer, value, intent(in)" instead of just "integer, intent(in)" -- lesson learned!

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit 1039cbe3dd6d42bd67a21cb1bea66f63d9b04d6a
Merge: fe0074b9e 632be646d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Mar 8 08:40:36 2019 -0800

    Merge pull request #421 from AMReX-Codes/regrid_only
    
    Add optional flag to RegridOnly for disabling I/O

commit 632be646dfb1586519f54f4bd1b500f75b80b904
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Mar 8 01:08:36 2019 -0500

    Add optional flag to RegridOnly for disabling I/O
    
    RegridOnly is useful as a public interface to regridding for the user
    code to call. For cases where the user wants to call it during a
    simulation, rather than immediately after restart, the I/O options
    aren't meaningful, so this allows the user to disable that in their
    call to RegridOnly (while still potentially allowing it in other
    cases where plotfile_on_restart et al. are desired).

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp

commit 0ca64d47e1aa478bae61340ffc8bf2af589fe9c5
Merge: 16d4d63a5 fe0074b9e
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Thu Mar 7 21:36:26 2019 -0800

    merge from development

commit 16d4d63a594dd4fa0e25d3a94894c482d5a18290
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Thu Mar 7 21:30:00 2019 -0800

    plumbing for cmake support for including ascent and conduit

Src/CMakeLists.txt
Src/Extern/Conduit/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_SetupThirdpartyLibs.cmake

commit d992c914148a7bd1dd4993088b4157a97cdb125a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Mar 7 20:34:39 2019 -0500

    CMake: look for MPI in config file if required

Tools/CMake/AMReXConfig.cmake.in

commit 83d0a8f965bfd0f3443b97cb5c2768ac572a42b5
Merge: 95e81ecae fe0074b9e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Mar 7 18:56:04 2019 -0500

    Merge branch 'development' into mr/cmake

commit 95e81ecae130cb2e530c7ffb91694d7a7298416c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Mar 7 18:55:13 2019 -0500

    CMake: some clean-up

CMakeLists.txt
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_SetupCUDA.cmake
Tools/CMake/comps/AMReX_Cray.cmake
Tools/CMake/comps/AMReX_GNU.cmake
Tools/CMake/comps/AMReX_Intel.cmake
Tools/CMake/comps/AMReX_NVIDIA.cmake
Tools/CMake/comps/AMReX_PGI.cmake
Tutorials/GPU/NeighborList/CMakeLists.txt

commit fe0074b9e556920d692eb8f3478e80701e5242be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 7 15:29:41 2019 -0800

    add coarsen and refine to Geometry

Src/Base/AMReX_Geometry.H

commit c1a58d87db04a2a57530a9f5650dd2161bb4247a
Merge: 0b21df905 8c6a2fe3d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Mar 7 14:21:13 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 0b21df9054bbabcfb7191633fe5bd7d9e640f767
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Mar 7 14:20:51 2019 -0800

    CMake: fix typo in configuration file.

Tools/CMake/AMReXConfig.cmake.in

commit 8c6a2fe3df4258a1ae7fe3fba5240df0033772bb
Merge: caf8ada86 33f425ec3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 7 13:23:16 2019 -0800

    Merge pull request #420 from AMReX-Codes/marc/bad_rd_ptr_in_vismf
    
    Catch unhandled RealDescriptor logic in VisMf::Write

commit caf8ada86e1c0884300b38fbbc792a1604ea98e2
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Mar 7 13:03:50 2019 -0800

    Cleaned up diffmultifab's output, and got rid of segfault after amrex finalize

Tools/C_util/DiffMultiFab/diffmultifab.cpp

commit 855694b1889b274bbd359ea3b34fa3884a96d9f4
Merge: e9cbad95c cf599f630
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 7 11:52:17 2019 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit e9cbad95c70d7b2b7096b2faa45b386222a2af6c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 7 11:48:20 2019 -0800

    Add support for higher order stencils at EB boundaries with Dirichlet bc's.
    This may be unstable so by default it is not used -- to use it you must call
    setEBHODirichlet() in addition to setEBDirichlet (or setEBHomogDirichlet).
    There should be no change to the default behavior of any AMReX-based code from this commit.

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90

commit cf599f6309553b42b03ea12239c44c9fb3baef84
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Mar 7 11:48:16 2019 -0800

    Fixed the fix with DiffMultfab, doesn't work with MPI at the moment.

Tools/C_util/DiffMultiFab/diffmultifab.cpp

commit 33f425ec3e065c8ccc7c9b3d03edb3428da37f41
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Mar 7 11:15:34 2019 -0800

    Catch unhandled RealDescriptor logic in VisMf::Write

Src/Base/AMReX_VisMF.cpp

commit f7dde771e77d5a97963712cb401b32ab30a3e9f4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Mar 7 10:40:57 2019 -0800

    CMake: fix blitz dependency issue in configuration file. Fixes Issue #418

Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Options.cmake

commit 2ef7ceae55b05ffae868bbd56c3d5d6ee9363165
Merge: a3736c4ad b9e4c1ed0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Mar 7 09:34:53 2019 -0800

    Merge pull request #419 from maikel/bugfix/EB_LSCore
    
    Use AMREX_D_DECL for the 2D case.

commit b9e4c1ed002ee33446918344201bddea97c7b6dd
Author: Maikel Nadolski <maikel.nadolski@gmail.com>
Date:   Thu Mar 7 15:00:18 2019 +0100

    Use AMREX_D_DECL for the 2D case.

Src/EB/AMReX_EB_LSCoreBase.cpp

commit a3736c4ad16b43cc726470120e6515dcd7d93a20
Merge: f10afe756 f496320fa
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Mar 6 19:39:49 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f10afe7566a316587d0061b735b292d2e49bdf7f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Mar 6 19:39:14 2019 -0500

    do the same early exit in the neighbor particles as in redistribute

Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit f496320fa29dd34105849a0bf012feac8c58f8a4
Merge: 0b3acd674 66b488a07
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 6 16:15:36 2019 -0800

    Merge pull request #374 from Alpine-DAV/task/2018_11_add_blueprint_particle_support
    
    add conduit blueprint support for particles

commit 0b3acd674ece90675fcf2dbfcbf220bb3e62fe74
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Mar 6 19:05:59 2019 -0500

    only include this file if using cuda

Src/Particle/AMReX_NeighborParticles.H

commit 641f47ca2edcf78657b0d81779c50f499f85a1be
Merge: 4f0733662 b75901c20
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Mar 6 18:49:39 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4f07336627bfa6d30ba0bb447091d7fc3f274a54
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Mar 6 18:49:17 2019 -0500

    remove fortran neighbor list

Src/Particle/AMReX_Particle_mod_3d.F90

commit ba6f4f0180f6b4159e51e25cc9baacb4468ae3d1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Mar 6 18:22:18 2019 -0500

    add missing files

Src/Particle/AMReX_NeighborParticlesCPUImpl.H
Src/Particle/AMReX_NeighborParticlesGPUImpl.H

commit 3e0fd673186ee7cbd28279512942bf6ce4bb1562
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Mar 6 18:21:50 2019 -0500

    refactor neighbor list stuff so that it can be used in MFIX

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package
Tutorials/GPU/NeighborList/MDParticleContainer.H
Tutorials/GPU/NeighborList/MDParticleContainer.cpp
Tutorials/GPU/NeighborList/main.cpp

commit b75901c2032d16d455b7a836827bbe13dfa0f7a8
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Mar 6 17:35:20 2019 -0500

    Fix bugs in Advection_AmrCore GPU tutorial.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H

commit 7228e23acab84dabd5ca82d82661f6d1099dbe9b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Feb 18 14:53:53 2019 -0500

    unresolved-symbols flag

Tests/GPU/buildNotused/GNUmakefile

commit 66b488a07404b4b5a1977142c9e7714884dfc920
Merge: 3dd1d297f c716e089a
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Wed Mar 6 13:38:01 2019 -0800

    complete merge from develop (3/6/19)

commit 873613548893b41d1c4ac32cfc474f244cf619fc
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Mar 6 13:37:21 2019 -0800

    First draft of converting Advection_AmrCore to new GPU method.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp

commit 3dd1d297f762b041e95505cccc4b58d2b8e85bad
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Wed Mar 6 13:31:37 2019 -0800

    update ascent actions for plots to match current ascent api

Tutorials/Blueprint/AssignMultiLevelDensity/main.cpp
Tutorials/Blueprint/CellSortedParticles/main.cpp
Tutorials/Blueprint/HeatEquation_EX1_C/Source/main.cpp

commit ce40e1f1545fc89de0f43efb9e71f0492eb82bb5
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Wed Mar 6 13:30:59 2019 -0800

    add logic to calc unique domain ids for particle tiles

Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H

commit c716e089a9d7e149bd84e8b40bb957422a732495
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Mar 6 15:31:49 2019 -0500

    remove missing include file

Src/Particle/AMReX_NeighborList.H

commit ffea3e87ca591753ab9327fa2a4f9758f49833f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 6 09:14:30 2019 -0800

    add noexcept

Src/Base/AMReX_Arena.H
Src/Base/AMReX_Array.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp

commit 939cafc8779f20ac99cf59973b94561e158be912
Merge: 20830ed6d 695a53241
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Mar 5 18:49:48 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 20830ed6d21e3c4b721d2852feb2f902bf1c7c8c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Mar 5 18:49:32 2019 -0500

    allow arbitrary numbers of grow cells in the gpu neighbor list tutorial

Tutorials/GPU/NeighborList/MDParticleContainer.H
Tutorials/GPU/NeighborList/MDParticleContainer.cpp

commit 695a532417a57641f4e254bab803598475e54e38
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 5 15:37:01 2019 -0800

    print free gpu global memory

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp

commit c3aca0f4d35f0ecefdf283a7710b0a2385ff96ca
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Mar 5 18:03:09 2019 -0500

    CMake: fix Tutorials/GPU/neighborList

Tutorials/GPU/NeighborList/CMakeLists.txt

commit 91c45a9e3cc1bf083cc7ac79b224c2859c7e9592
Merge: 752f93116 4edf4a18e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Mar 5 17:34:52 2019 -0500

    Merge branch 'development' into mr/cmake

commit 4edf4a18e56fb882a4b4a83a89bf251319f7a650
Merge: 2edecc3dc 69e38b6d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 5 14:29:42 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2edecc3dc96d74ccce53fd68ab38aa48fc1ffd9b
Merge: 28cf6cbb0 98a411499
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 5 14:27:59 2019 -0800

    Merge branch 'weiqun/fb' into development

commit 752f93116c447feb1498a15f1a76957f5db85dd9
Merge: 39ce10987 6a434e42e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Mar 5 17:08:49 2019 -0500

    Merge branch 'mr/cmake' of https://github.com/AMReX-Codes/amrex into mr/cmake

commit 39ce10987822ac2051ce90c68c11b7bc90619682
Merge: 457ed458f 69e38b6d4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Mar 5 17:08:23 2019 -0500

    Merge branch 'development' into mr/cmake

commit 69e38b6d40586e8c84a7e54c8b541447cf6d93df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 5 12:57:48 2019 -0800

    FillBoundary: tweak local copy

Src/Base/AMReX_FabArrayCommI.H

commit 98a41149939f53f0311b327818c511db5115775b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 5 13:10:05 2019 -0800

    fix typo

Src/Base/AMReX_FabArrayCommI.H

commit 4af02f3f2f3bd375a7890b4edb86126685f16a8a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 5 12:57:48 2019 -0800

    FillBoundary: tweak local copy

Src/Base/AMReX_FabArrayCommI.H

commit 28cf6cbb0b417f95997c85214010a1d389c62132
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Mar 5 12:05:30 2019 -0800

    Fixed bug in DiffMultiFab

Tools/C_util/DiffMultiFab/diffmultifab.cpp

commit d099e051b9b04f1e4fbd9b36f9a9ed745b810452
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Mar 5 14:06:13 2019 -0500

    missed some device vectors

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit da5f394cef0e650977c9cca33ea337d52aedb75f
Merge: c7f2c7a53 7931a1a5d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Mar 5 13:37:54 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c7f2c7a536f6e1844ce0daecdcbe3368d6aaf01a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Mar 5 13:37:16 2019 -0500

    switch the device allocator back to using device memory

Src/Base/AMReX_CudaAllocators.H

commit f12f1ea1490765ffda9ad930b3f10dde449f3e91
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Mar 5 13:31:28 2019 -0500

    more Gpu::DeviceVector -> Gpu::ManagedDeviceVector

Src/Particle/AMReX_NeighborList.H
Src/Particle/AMReX_ParticleContainerI.H

commit c7f46964943da587835265a65cdd12960c508d99
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Mar 5 13:26:11 2019 -0500

    Gpu::DeviceVector -> Gpu::ManagedDeviceVector in NeighborList

Tutorials/GPU/NeighborList/MDParticleContainer.cpp

commit 7931a1a5d58f0084958ad829a79311d8234bdcef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 4 12:50:21 2019 -0800

    fix pointer consistence checking for non-BaseFab type

Src/Base/AMReX_FabArray.H

commit 8566f892f0d421defc03be8ec7f561fd4cb28dc7
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Mon Mar 4 11:31:32 2019 -0700

    fixed missing nghost declaration

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit c3751b1e67a7a9f213ab6104d9a0c4f3b1c507c6
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Sun Mar 3 18:01:04 2019 -0700

    updated to keep expected behavior for operators with nghost <= 1

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 5387506a87b12b6bcf6d53bc528bdaddba924ad1
Merge: a050e083e 6e1acca32
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Sun Mar 3 16:39:02 2019 -0700

    Merge branch 'development' into nodeghostcells

commit a050e083e27f29f30970579f7b7032b83f7c7a89
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Sun Mar 3 15:46:37 2019 -0700

    fixed error causing assertion error in ABecLaplacian_C test by updating RHS fill

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit a7fad46fb8f74f5259b19f9f4bb4e93e3435f78a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 2 12:49:11 2019 -0800

    consistence of style

README.md

commit 91323f27a020c30c004dddb71a7631f916c6694d
Merge: 749721f6c 6e1acca32
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 1 22:23:17 2019 -0800

    Merge branch 'development'

commit 6e1acca322a640b3d7290b54fb6a04d1c5455bc3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 1 22:21:45 2019 -0800

    fix gpu fillboundary

Src/Base/AMReX_FabArrayCommI.H

commit 3593511260e60172882de393f2eb0c35cc794e87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 1 21:09:39 2019 -0800

    fix launch safe guard

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit eb479b47f2f3c26ed32dcd8d82be575d44a3b507
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 1 20:09:27 2019 -0800

    assert that the pointers in FabArray are consistent

Src/Base/AMReX_BLassert.H
Src/Base/AMReX_FabArray.H

commit 749721f6cf42bcbff258b99c2cbaeef0ab2f52eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 1 16:52:44 2019 -0800

    fix FArrayBox I/O for gpu. resize is not safe.

Src/Base/AMReX_FArrayBox.cpp

commit aa4e00c0c45c22ab223996dfb80e789ce5e438f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 1 16:52:44 2019 -0800

    fix FArrayBox I/O for gpu. resize is not safe.

Src/Base/AMReX_FArrayBox.cpp

commit ab2e4b5049960ca297916d30d53f8ba827f52281
Merge: cde06a597 b25ac20f4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 1 08:49:56 2019 -0800

    Merge branch 'development' into faballocator

commit b25ac20f4e0837c700764494b3e4240dbb924421
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 1 08:48:27 2019 -0800

    update CHANGES

CHANGES

commit ef0ab0a3f52004c8c0bcb051c0e45cf36098b6ff
Merge: 65b640bc5 b99f44e73
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 28 22:13:35 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 65b640bc58babda414a291d21be698cc056dd316
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 28 22:13:15 2019 -0500

    switch the order of these resize operations - could in principle save memory when using the arena

Src/Particle/AMReX_ParticleTile.H

commit cde06a59746f6fbe5e1d38cdd49045fdfe521453
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 28 19:11:03 2019 -0800

    CArena: use unordered_set for busy list

Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp

commit b99f44e734f98648d4aa97cc03b5d4489dce248b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 28 16:00:41 2019 -0800

    Arena: removed duplicated codes, and make the memory type hard to change to avoid mistakes.  this also makes the DArena use preferred

Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_DArena.H
Src/Base/AMReX_DArena.cpp

commit 210f3ae188ac1daa74c61a7b0f6957d508c5d3a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 28 15:16:43 2019 -0800

    minor

Src/Base/AMReX_FabAllocator.cpp

commit f220d84a80691f3afe4079113d150238171bcc79
Merge: da49e80b9 5e7c36a0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 28 14:33:02 2019 -0800

    Merge branch 'faballocator' into development

commit 5e7c36a0ea135a8c3bc66c3622378f0bdd8298f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 28 14:06:43 2019 -0800

    special allocator for fab because they basically ahve the same size

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_CudaMemory.H
Src/Base/AMReX_FabAllocator.H
Src/Base/AMReX_FabAllocator.cpp
Src/Base/AMReX_FabArray.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit da49e80b9e8c2f274084978ec11d87756790b03d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 28 15:41:31 2019 -0500

    fix debug statement

Src/Particle/AMReX_ParticleContainerI.H

commit 8a579b78c11187cf9652230a5eeca3b7ed1031b2
Merge: cced122e1 77bc18001
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 28 13:35:24 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cced122e12ae28829ac32b2dd5aa304bdb556889
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 28 13:35:05 2019 -0500

    add early exit in the loop over grids in RedistributeGPU

Src/Particle/AMReX_ParticleContainerI.H

commit 77bc18001102990788fba22fc75e37c1d978cb35
Merge: 9c6146408 b11e1008d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 28 08:20:31 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9c6146408f3615d2d46f1221cd7390c2d3db4fe4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 28 08:20:13 2019 -0800

    fix for periodic boundary conditions for particles when single precision is used.

Src/Particle/AMReX_ParticleContainerI.H

commit b11e1008da794c9cc8851cbaebb14bd54c5a793a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 27 20:44:49 2019 -0500

    DArena: calculate free memory and print more information

Src/Base/AMReX_DArena.H
Src/Base/AMReX_DArena.cpp

commit 855d2edd79e28c83711968c491add583501cb6d1
Merge: e988d7c2c 6376b38d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 27 16:11:36 2019 -0800

    Merge branch 'development' into buddy-allocator

commit e988d7c2cb6d242a20c26507ade88640cc15a0eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 27 15:42:58 2019 -0800

    DArena: add gpu support

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_DArena.H
Src/Base/AMReX_DArena.cpp

commit a485365d2b4009c6808c4ae2af349abcf16cdd19
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 27 13:41:55 2019 -0800

    buddy memory allocator

Src/Base/AMReX_DArena.H
Src/Base/AMReX_DArena.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 6376b38d9de59ce1d3b998e1054365271072dc5f
Merge: 8741967ed 6a6e73896
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 27 15:18:36 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8741967ed94c4146ee2e0102cc98a14fc58db2c9
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 27 15:17:57 2019 -0500

    use The_Arena for all the particle stuff for now.

Src/Base/AMReX_CudaAllocators.H

commit 6a434e42e3149913d2134bb845c31d6f9dc1ce23
Merge: 5e41e2730 6a6e73896
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Feb 27 11:27:28 2019 -0800

    Merge branch 'development' into mr/cmake

commit 5e41e2730ed016a047d012bbe46e7511642f867b
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Feb 27 11:26:45 2019 -0800

    CMake: require version 3.14 only is CUDA is enabled

CMakeLists.txt

commit 6a6e7389666fe91fe38e08c87e81177ea5a7f9ef
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Feb 26 00:06:10 2019 -0500

    Correct spelling of fextrema

Tools/Plotfile/GNUmakefile
Tools/Plotfile/fextrema.cpp

commit 5435457b9ec13c113f4e0a930a39e4bcc37f76ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 25 13:40:17 2019 -0800

    Vector version of FillBoundary: switch back to the old way.  the new approach needs more works

Src/Base/AMReX_MultiFab.cpp

commit 540bf01170d29eadf778dabd32a4b0cd6007c54e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Feb 25 13:01:20 2019 -0800

    Update XL compiler locations at LLNL

Tools/GNUMake/sites/Make.llnl

commit 0f6bcebbe87dd4843a548b24a360d453f33fe1fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 25 11:31:37 2019 -0800

    add a new Geometry constructor for convenience

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp

commit 90c6cdca5e7d4baa247639800fcab6fb594a4199
Merge: 6a3d4a1b4 5ff892926
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 25 13:44:41 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6a3d4a1b44734176ff467e157beeb90431e856d0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 25 13:43:38 2019 -0500

    NeighborList tutorial - seperate out sorting the particles from doing the copies, so we can re-use the same neighbor list for multiple time steps.

Tutorials/GPU/NeighborList/MDParticleContainer.H
Tutorials/GPU/NeighborList/MDParticleContainer.cpp

commit 5ff892926ff215eeb377262dcb076150d4949b93
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 25 10:24:06 2019 -0800

    no need to init/finalize fortran mpi anymore

Src/Base/AMReX.cpp

commit af085c89cb3799ba001fe2c5531bfb7a2c8ef2bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 25 10:20:52 2019 -0800

    rm more Fortran BoxLib stuff

Src/Base/AMReX.cpp
Src/Base/AMReX_BLBoxLib_F.F90
Src/Base/AMReX_error_fi.cpp
Src/Base/AMReX_error_mod.F90
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 740583612b72fb025428e7eb871f6ba339d96a1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 25 09:38:30 2019 -0800

    rm more Fortran BoxLib stuff

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BLassert.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_FPC.H
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_Utility.H

commit eb18a252ca372638c28bec9eeac9946c93023711
Merge: 07352b580 dcfa51fe8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 25 09:03:45 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 07352b5804e932c59dd3fcf199a48fb4a10af189
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 25 09:02:15 2019 -0800

    rm more deprecated files

Src/Base/BL_mempool_f.f90
Src/Base/GPackage.mak

commit dcfa51fe8a95df16ab4f305fc9c84ea7847c8628
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Feb 25 11:56:49 2019 -0500

    Specialize some AMREX_USE_GPU to AMREX_USE_CUDA

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_FabArrayUtility.H

commit e70ede343b4ae1d64f3e009c1317625cb0132cbe
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Feb 25 03:47:06 2019 -0500

    Specialize some AMREX_USE_GPU to AMREX_USE_GPU_PRAGMA

Src/Base/AMReX_ArrayLim.H

commit f67e106fdbbc101b50f22042cec530b1ee1b14b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 25 08:51:44 2019 -0800

    include header

Src/Base/AMReX_MemPool.H

commit 6c233441043ca952f5c76e2f91a9757cecd8e056
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Feb 25 08:32:29 2019 -0800

    Remove F_BaseLib and parts of AMReX that used it.

Docs/Doxygen/doxygen.conf
Docs/sphinx_documentation/make_api.py
Src/Base/AMReX.cpp
Src/Base/AMReX_MemPool.H
Src/Base/AMReX_MemPool.cpp
Src/F_BaseLib/BLProfiler_f90.f90
Src/F_BaseLib/CMakeLists.txt
Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/FParallelMG2.mak
Src/F_BaseLib/FParallelMG_RNG.mak
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/MemProfiler_f.H
Src/F_BaseLib/MemProfiler_f.cpp
Src/F_BaseLib/MultiFab_C_F.H
Src/F_BaseLib/MultiFab_C_F.cpp
Src/F_BaseLib/amrex_fabio_c.f90
Src/F_BaseLib/amrex_fort_mod.f90
Src/F_BaseLib/amrex_timer_c.f90
Src/F_BaseLib/backtrace_c.cpp
Src/F_BaseLib/backtrace_f.f90
Src/F_BaseLib/bc.f90
Src/F_BaseLib/bc_functions.f90
Src/F_BaseLib/bl_IO.f90
Src/F_BaseLib/bl_constants.f90
Src/F_BaseLib/bl_error.f90
Src/F_BaseLib/bl_mem_stat.f90
Src/F_BaseLib/bl_parmparse.f90
Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/bl_prof_stubs.f90
Src/F_BaseLib/bl_random_c.H
Src/F_BaseLib/bl_random_c.cpp
Src/F_BaseLib/bl_random_f.f90
Src/F_BaseLib/bl_space.f90
Src/F_BaseLib/bl_stream.f90
Src/F_BaseLib/bl_string.f90
Src/F_BaseLib/bl_system.f90
Src/F_BaseLib/bl_timer.f90
Src/F_BaseLib/bl_types.f90
Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/box_f.f90
Src/F_BaseLib/box_util.f90
Src/F_BaseLib/boxarray_f.f90
Src/F_BaseLib/boxlib_f.f90
Src/F_BaseLib/cc_restriction.f90
Src/F_BaseLib/cluster_f.f90
Src/F_BaseLib/create_umac_grown.f90
Src/F_BaseLib/cutcells.f90
Src/F_BaseLib/define_bc_tower.f90
Src/F_BaseLib/f2kcli.f90
Src/F_BaseLib/f2kcli_crayx1.f90
Src/F_BaseLib/f2kcli_nag.f90
Src/F_BaseLib/f2kcli_win32.f90
Src/F_BaseLib/fab.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/filler.f90
Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/fourth_order_interp_coeffs.f90
Src/F_BaseLib/interp.f90
Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/list_box.f90
Src/F_BaseLib/make_new_grids.f90
Src/F_BaseLib/memprof.f90
Src/F_BaseLib/ml_boxarray.f90
Src/F_BaseLib/ml_cc_restriction.f90
Src/F_BaseLib/ml_layout.f90
Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/ml_nd_restriction.f90
Src/F_BaseLib/ml_restrict_fill.f90
Src/F_BaseLib/mt19937ar.f90
Src/F_BaseLib/multifab_c.f90
Src/F_BaseLib/multifab_f.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90
Src/F_BaseLib/multifab_physbc.f90
Src/F_BaseLib/multifab_physbc_edgevel.f90
Src/F_BaseLib/nodal_neumann_bcs.f90
Src/F_BaseLib/nodal_restriction.f90
Src/F_BaseLib/nodal_stencil_bc.f90
Src/F_BaseLib/omp.f90
Src/F_BaseLib/omp_stubs.f90
Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90
Src/F_BaseLib/particles_f.f90
Src/F_BaseLib/pingpong.f90
Src/F_BaseLib/plotfile.f90
Src/F_BaseLib/ppm_util.f90
Src/F_BaseLib/ppm_util_c.c
Src/F_BaseLib/regrid.f90
Src/F_BaseLib/sort_box.f90
Src/F_BaseLib/sort_d.f90
Src/F_BaseLib/sort_i.f90
Src/F_BaseLib/system_util_c.c
Src/F_BaseLib/tag_boxes.f90
Src/F_BaseLib/timer_c.c
Src/F_BaseLib/unittests/GNUmakefile
Src/F_BaseLib/unittests/gr0_3d.1level
Src/F_BaseLib/unittests/tests.f90
Src/F_BaseLib/vector_i.f90
Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak
Tools/F_mk/Readme
Tools/F_mk/comps/Darwin_ibm.mak
Tools/F_mk/comps/Darwin_intel.mak
Tools/F_mk/comps/Linux_cray.mak
Tools/F_mk/comps/Linux_intel.mak
Tools/F_mk/comps/Linux_lahey.mak
Tools/F_mk/comps/Linux_nag.mak
Tools/F_mk/comps/Linux_pathscale.mak
Tools/F_mk/comps/Linux_pgi.mak
Tools/F_mk/comps/Linux_sunstudio.mak
Tools/F_mk/comps/aix.mak
Tools/F_mk/comps/bgq.mak
Tools/F_mk/comps/g95.mak
Tools/F_mk/comps/gfortran.mak
Tools/F_mk/comps/xlf.mak
Tools/Postprocessing/F_Src/CMakeLists.txt
Tools/Postprocessing/F_Src/GNUmakefile
Tools/Postprocessing/F_Src/Palette
Tools/Postprocessing/F_Src/TODO_GHOST
Tools/Postprocessing/F_Src/faverage.f90
Tools/Postprocessing/F_Src/faverplot.f90
Tools/Postprocessing/F_Src/fboxinfo.f90
Tools/Postprocessing/F_Src/fcoarsen.f90
Tools/Postprocessing/F_Src/fcompare.f90
Tools/Postprocessing/F_Src/fdump.f90
Tools/Postprocessing/F_Src/fdumpdata2d.f90
Tools/Postprocessing/F_Src/fextract.f90
Tools/Postprocessing/F_Src/fextrema.f90
Tools/Postprocessing/F_Src/ffdcompare.f90
Tools/Postprocessing/F_Src/fintgvar2d.f90
Tools/Postprocessing/F_Src/fnan.f90
Tools/Postprocessing/F_Src/fsnapshot2d.f90
Tools/Postprocessing/F_Src/fsnapshot3d.f90
Tools/Postprocessing/F_Src/ftime.f90
Tools/Postprocessing/F_Src/fvarnames.f90
Tools/Postprocessing/F_Src/fwritecontents2d.f90
Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90
Tools/Postprocessing/python/README
Tools/Postprocessing/python/column_depth.py
Tools/Postprocessing/python/conv_slopes.py
Tools/Postprocessing/python/dumpparthistory.py
Tools/Postprocessing/python/eos_data.txt
Tools/Postprocessing/python/helmeos.py
Tools/Postprocessing/python/parseparticles.py
Tools/Postprocessing/python/test_helmeos.py
Tools/Postprocessing/python/test_parseparticles.py
Tools/Postprocessing/python/timestamp_00.REMOVED.git-id
Tools/Postprocessing/python/timestamp_02.REMOVED.git-id
Tools/Py_util/GNUmakefile
Tools/Py_util/README
Tools/Py_util/fsnapshot.f90

commit b870d481121651bdff9798ba17a1a14f96e880a7
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Feb 25 03:31:59 2019 -0500

    Do not attempt to set CUDA_ARCH if not defined

Tools/GNUMake/comps/pgi.mak

commit 8f309b03e211609d13e986ed473d20bdf1837af8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 23 15:23:39 2019 -0800

    fix assert message

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit 3ea117e6ff47ee358c7a6dbdbcd826b597e7bd93
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 23 12:51:14 2019 -0800

    MLCellLinOp:: metric factor

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90

commit 71331bea7b754cb09609866c2a53c1c23db28316
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 23 12:36:53 2019 -0800

    MLCellLinOp:: refactor

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90

commit 2d6cd66029000afdff1922ef05523fc7144c80d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 23 10:32:01 2019 -0800

    assertion no longer needed because of recent change in Array4

Src/Base/AMReX_BaseFab.H

commit 5d6de85d3999904f53d3f76f067984773ad8a834
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 23 10:21:37 2019 -0800

    pass by value

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/EB/AMReX_EB2_IF_Rotation.H

commit 924d2773369435c9f31efc4fb215c81bd49094e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 23 07:52:38 2019 -0800

    pass by value

Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IArrayBox.cpp
Src/Base/AMReX_LayoutData.H
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp

commit 37b6f354a3f370391cb5a40486a02c348c61d9b6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 22 15:55:52 2019 -0800

    remove f_baselib from the electrostatic pic tutorial

Tutorials/Particles/ElectrostaticPIC/GNUmakefile
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit 88be86ff6e545ef95d35ce436a7d0a7cba666380
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 22 15:30:54 2019 -0800

    remove commented out code

OldTutorials/PIC_C/solve_with_mlmg.cpp
OldTutorials/TwoGrid_PIC_C/solve_with_mlmg.cpp

commit 75454b78ee1d4650365317258fb2c090d0e698a2
Merge: 70bc6ff0d 53c1c663b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 22 15:17:12 2019 -0800

    Merge branch 'development' into f_baselib_particles_remove

commit 70bc6ff0dc70e5ae6bd1568511802464d0f2dbf0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 22 15:16:25 2019 -0800

    update TwoGrid_PIC_C for the removal of F_Baselib

OldTutorials/PIC_C/main.cpp
OldTutorials/TwoGrid_PIC_C/GNUmakefile
OldTutorials/TwoGrid_PIC_C/Make.package
OldTutorials/TwoGrid_PIC_C/main.cpp
OldTutorials/TwoGrid_PIC_C/solve_for_accel.cpp
OldTutorials/TwoGrid_PIC_C/solve_with_f90.cpp

commit 53c1c663b6f63707fc8d78e61fddc8657592d6fb
Merge: 8c7ad2c9e 1b73ccf6d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 22 15:04:15 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8c7ad2c9ec0036870f58c8f3d9dac5e8efe130b8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 22 15:03:27 2019 -0500

    make the neighbor list build function templated on check_pair function

Src/Particle/AMReX_NeighborList.H
Tutorials/GPU/NeighborList/CheckPair.H
Tutorials/GPU/NeighborList/MDParticleContainer.H
Tutorials/GPU/NeighborList/MDParticleContainer.cpp
Tutorials/GPU/NeighborList/Make.package
Tutorials/GPU/NeighborList/md_K.H

commit 1b73ccf6d8fa7e00e3152e9215546e16c2c3c069
Merge: e4cd2dff0 cad64ac43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 22 11:42:44 2019 -0800

    Merge branch 'weiqun/gpu' into development

commit cad64ac43f7820474eab8ac4091049e4882004ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 22 11:02:25 2019 -0800

    fix bug in C++ apply bc

Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H

commit adfb83418f8031dbba70adc079d2e3d627028395
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 22 09:26:14 2019 -0800

    MLCellLinOp: fix index

Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H

commit 6e5b3cfcd1894a8d0ce9ab4d38cc5f93fa5eed70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 22 08:00:36 2019 -0800

    MLCellLinOP: coef0 on gpu

Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H

commit b5ec971285a21c6d7ca5d5d3b4bd5c7aadc76d2a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 21 22:02:07 2019 -0800

    MLCellLinOp: applybc on gpu

Src/Boundary/AMReX_BoundCond.H
Src/Boundary/AMReX_FabSet.H
Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H
Src/LinearSolvers/MLMG/Make.package

commit e4cd2dff03cae2fe9917bf882c724835e8fb8bc5
Merge: dc462ddd7 891bd8138
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 21 20:31:33 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit dc462ddd7e0212dff946cee17d4ed94490f8ee38
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 21 20:31:13 2019 -0500

    start migrating the neighbor list stuff into AMReX proper

Src/Particle/AMReX_NeighborList.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package
Tutorials/GPU/NeighborList/MDParticleContainer.H
Tutorials/GPU/NeighborList/Make.package

commit d3a2968e6ab2b7c3682c2057bafb759b78586768
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 21 20:21:36 2019 -0500

    pstruct[i] -> p

Tutorials/GPU/NeighborList/MDParticleContainer.cpp

commit 822629da7ff387ce90b55b39281377b8aae7e1ef
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 21 20:17:45 2019 -0500

    allow the user to use range-based for loops for the neighbor list on the GPU

Tutorials/GPU/NeighborList/MDParticleContainer.H
Tutorials/GPU/NeighborList/MDParticleContainer.cpp
Tutorials/GPU/NeighborList/Make.package
Tutorials/GPU/NeighborList/NeighborList.H
Tutorials/GPU/NeighborList/NeighborList.cpp

commit 891bd8138d04ab017e4057ec0fcc0ff8b491b7a7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 21 16:11:04 2019 -0800

    Revert "Revert "CMake: change the way Algoim and Blitz are handled""
    
    This reverts commit d93c483d5849c678aeae36d278d169d4af62bb91.

CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_InstallExternalLibs.cmake

commit b1617f313a703c2b01b65c3ca87471597c72bdd3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 21 17:53:11 2019 -0500

    start to add the NeighborList stuff into a discrete class

Tutorials/GPU/NeighborList/MDParticleContainer.H
Tutorials/GPU/NeighborList/MDParticleContainer.cpp
Tutorials/GPU/NeighborList/Make.package
Tutorials/GPU/NeighborList/NeighborList.H
Tutorials/GPU/NeighborList/NeighborList.cpp
Tutorials/GPU/NeighborList/md_K.H

commit 02fc3c21c323e159fae9471ad2aa8c6372c46c93
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 21 13:12:15 2019 -0800

    remove the EBParticles OldTutorial

OldTutorials/EBParticles/EBParticleContainer.H
OldTutorials/EBParticles/EBParticleContainer.cpp
OldTutorials/EBParticles/GNUmakefile
OldTutorials/EBParticles/Make.package
OldTutorials/EBParticles/ebparticles_2d.f90
OldTutorials/EBParticles/ebparticles_3d.f90
OldTutorials/EBParticles/ebparticles_F.H
OldTutorials/EBParticles/inputs
OldTutorials/EBParticles/main.cpp

commit 457ed458fc1ce555b77a86696fa7f07a676c65de
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Feb 21 15:09:47 2019 -0500

    CMake: fix GPU/NeighborList example

Tutorials/GPU/NeighborList/CMakeLists.txt

commit 2aaf571eae83ca0f65c491596f8d0c64be2e2a8b
Merge: 77e2c10d5 d88e7433a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 20 20:50:25 2019 -0800

    Merge branch 'weiqun/fluxregister' into development

commit d88e7433a6890f7443406414921b72bdb717b36f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 20 19:17:02 2019 -0800

    allow different BoxArrays for average_down_nodal and average_down_edges.  new versions of average_down_edges and average_down_faces for single direction

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 77e2c10d5730334057d19fd83663aaf3485a13eb
Merge: ffe4d291a 49bd115a5
Author: Daniel Ladiges <drladiges@lbl.gov>
Date:   Wed Feb 20 18:54:52 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit ffe4d291abee82bf685d1c6351b69076a5b03593
Author: Daniel Ladiges <drladiges@lbl.gov>
Date:   Wed Feb 20 18:49:30 2019 -0800

    Made copy of .mak file in F_BaseLib so it has a sensible name before its death next week (and to keep consistency with FBoxLib).

Src/F_BaseLib/FParallelMG_RNG.mak

commit 49bd115a5c5de93a6b4179142a85d338ca711f7b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 20 17:23:28 2019 -0800

    do this interpolation from coarse in a different way.

Src/AmrCore/AMReX_AmrParticles.H
Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_PhysBCFunct.H

commit cdd7a75974c5dde27590337adce72261e18bdd41
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 20 16:29:09 2019 -0800

    reflux for given direction

Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp

commit 2409f9306917414638c82e6490ff9161623d17f6
Merge: 8d5b4864f bad1e4ec8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 20 15:54:30 2019 -0800

    Merge branch 'weiqun/gpu' into development

commit bad1e4ec86005d05eab8f115ce97bbeddf9f7f07
Merge: d150031c8 eca9364d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 20 16:12:34 2019 -0500

    Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu

commit d150031c8c77f5f1fde1fd7aacaee90be60d1877
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 20 16:12:21 2019 -0500

    Array4: add strides as members

Src/Base/AMReX_Array.H

commit eca9364d67e613e11df6bdede98132ae603db60b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 20 13:06:53 2019 -0800

    Array4: use printf for device code

Src/Base/AMReX_Array.H

commit e110ac728c34caf73f70bc0ad81cee4111aa9490
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 20 15:44:40 2019 -0500

    Array4: constexpr and const

Src/Base/AMReX_Array.H

commit fd703eded7a055513598952e006deeee64ac82df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 20 11:47:20 2019 -0800

    print out bounds when access to Array4 is out of bounds

Src/Base/AMReX_Array.H

commit 2136ee4c3bc31f5a21e25ff352da3a96873b5f94
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 20 14:20:08 2019 -0500

    do the clear before Redistribute

Tutorials/GPU/NeighborList/MDParticleContainer.H
Tutorials/GPU/NeighborList/MDParticleContainer.cpp

commit 12a3b9c45b45fd5d08ee404d51fb74f110a86fda
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 20 11:09:21 2019 -0800

    addr2line pretty print

Src/Base/AMReX_BLBackTrace.cpp

commit 45dc8550f9fc02208c6db0288790f96ae5bb6270
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 20 11:06:13 2019 -0800

    mlalaplacian on gpu

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLALap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLALap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLALap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLALap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLALap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLALap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLALap_F.H
Src/LinearSolvers/MLMG/AMReX_MLALap_K.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/Make.package

commit 8d5b4864fb0d4de5bb8746eda19ea735cf82cabf
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date:   Wed Feb 20 10:39:21 2019 -0800

    Rename EX3-CUDA to EX-CUSOLVER

Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/GNUmakefile
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/Make.CVODE
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/Make.package
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/README.md
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/extern_probin.template
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs_128
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs_256
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs_32
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs_64
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/main.cpp
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/make_cuda.sh
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/make_cuda_cusolver.sh
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/make_serial.sh
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_cuda.cpp
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_cuda_cusolver.cpp
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_serial.cpp
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_system.F90
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_utils.F90
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/test_react.H
Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/test_react_F.H

commit fcb5fc0586478c2e0d0049e53a0f84f39ce43285
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date:   Wed Feb 20 10:38:01 2019 -0800

    Remove unnecessary include line for FParallelMG

Tutorials/CVODE/SUNDIALS4/EX3-CUDA/Make.CVODE

commit 97ab5365bd8834c734b1217169745e01c30fb317
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 19 19:45:01 2019 -0500

    call clear and sort from inside fillNeighbors

Tutorials/GPU/NeighborList/MDParticleContainer.cpp
Tutorials/GPU/NeighborList/main.cpp

commit 70ea36d2cf337b27cfe999476d2767b8fcf65adf
Merge: ccd72bb1f 75d789b4b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 19 19:07:30 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ccd72bb1fb43453ca56c6157fd1e088c5a172b76
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 19 19:07:10 2019 -0500

    adding and using wrappers around Cuda's atomicInc and atomicDec functions

Src/Base/AMReX_CudaUtility.H
Tutorials/GPU/NeighborList/MDParticleContainer.cpp

commit ae5d7dad2a6d0b4dd2a6768420986ef1faa1ce0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 19 15:03:46 2019 -0800

    mlpoisson: normalize

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H
Src/LinearSolvers/MLMG/Make.package

commit 75d789b4ba32221685750b5bf621db194dcdb6c4
Author: kngott <kngott@lbl.gov>
Date:   Tue Feb 19 14:22:01 2019 -0800

    GPU docs.

Docs/sphinx_documentation/source/GPU.rst

commit 18053b1951b785f407690370ae3ad9a1b1c98ad7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 19 14:14:04 2019 -0800

    mlpoisson: gsrb

Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H

commit cd86febcbb686fd95201e8e232eb58c839a59ac7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 19 12:45:03 2019 -0800

    add a NoOpPhysBCFunct and use it in the amr assign density

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_PhysBCFunct.H

commit 6a3f565f9136847063876cbeddbeca9cc6d3bf90
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 19 12:39:41 2019 -0800

    version of InterpFromCoarseLevel that doesn't use enforce boundary conditions

Src/AmrCore/AMReX_AmrParticles.H
Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp

commit 74c07cdc728698b828acd307248f17477683cd55
Merge: 08b9b2e86 588130833
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Feb 19 10:36:40 2019 -0800

    Merge pull request #411 from mwm126/patch-2
    
    Fix USE_ACC error; refactor for readability

commit 08b9b2e867c9e69d9cac021243dd69c8a425fe78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 19 10:03:33 2019 -0800

    warning instead of ignoring

Tests/GPU/libamrex_CUDA/GNUmakefile

commit 26a14ea46f495a6d204b0023ec55a795304f7199
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 18 10:46:20 2019 -0800

    an example of using libamrex with cuda

Tests/GPU/libamrex_CUDA/GNUmakefile
Tests/GPU/libamrex_CUDA/README.md
Tests/GPU/libamrex_CUDA/main.cpp

commit f6cab9fbb5d5d802b61ecff623eb9cfdcc564a4a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 18 09:24:12 2019 -0800

    Elixir: add default constructor and move assignment

Src/Base/AMReX_CudaElixir.H

commit 58813083353a831b88afa4958c85da77172e1fb8
Author: Mark Meredith <mwm126@gmail.com>
Date:   Mon Feb 18 08:43:18 2019 -0500

    Fix USE_ACC error; refactor for readability
    
    I noticed a typo:
    https://github.com/AMReX-Codes/amrex/blob/master/Tools/libamrex/configure.py#L98
    should be "USE_ACC = TRUE". Writing each line in the Makefile with one line of source could help prevent errors like that.

Tools/libamrex/configure.py

commit cd85e39e1fc93cb06b7e21e85bf5459ef5834be6
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Feb 17 15:49:08 2019 -0800

    Generalize MFIter reduction to allow multiple reduce values

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 487b8184492dd7fb94fdc39fbf3601824f9b0043
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 17 14:32:56 2019 -0800

    MLPoisson: flux

Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H

commit da1c9cc3f9d7e0fd23192f09d0495b35a6f22163
Merge: 233e532f7 428ef09c2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun Feb 17 12:42:41 2019 -0800

    Merge pull request #406 from AMReX-Codes/plot_per_fix
    
    Add floating point awareness to the plot_per/check_per logic

commit 233e532f7b1440c791cf37144836438045207fc1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 17 12:28:21 2019 -0800

    generalize FillPatch for non-uniform grow cells

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_PhysBCFunct.H

commit 428ef09c2791a6f180caf6fbada0825a4f7371ce
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Feb 17 06:48:35 2019 -0800

    Scale epsilon to the current simulation time

Src/Amr/AMReX_Amr.cpp

commit 2733d5597adece632d7de8c51160b61b8554d2e2
Merge: c9b6dd3a8 d08450efc
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Feb 17 06:32:58 2019 -0800

    Merge branch 'development' into plot_per_fix

commit fd5ee74d7d2fb79620a9bf45ff96cd78c6eea7a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 16 21:39:04 2019 -0800

    minor change

Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H

commit e96c037c91d8ef1c5105bcb100a25493bd7a1bf6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 16 21:14:12 2019 -0800

    MLPoisson: adotx

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_K.H
Src/LinearSolvers/MLMG/Make.package

commit d08450efcc7d822a94d9822fc5bfe224b410aec7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Feb 16 19:27:11 2019 -0800

    Add the option to call EB_set_covered with ngrow > 0 so we can cover ghost
    cells of each Fab.

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit de98fb32a1726835151b55425e2b33c23f58c00a
Merge: 501b93d8a d93c483d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 16 18:39:46 2019 -0800

    Merge branch 'development' into weiqun/gpu

commit 9e94e935e84dad2a702c9d3b317eec04f0eded50
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Sat Feb 16 17:51:49 2019 -0700

    Merge branch development into nodeghostcells

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 939100c077b77845023a4a4d1d4fdf380ae0aff9
Merge: ad09ce0a7 d93c483d5
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Sat Feb 16 17:33:51 2019 -0700

    Merge branch 'development' into nodeghostcells

commit ad09ce0a75ecb9e94c6898b7744a98d954e2f308
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Sat Feb 16 17:33:24 2019 -0700

    removed some superfluous functions to be implemented elsewhere

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H

commit ffa23f2f10970f09fd2ca7566920ca353a5f61af
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Sat Feb 16 16:23:39 2019 -0700

    working - now cleaning up and updating

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit d93c483d5849c678aeae36d278d169d4af62bb91
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Feb 16 13:59:28 2019 -0800

    Revert "CMake: change the way Algoim and Blitz are handled"
    
    This reverts commit a4856755c6eabfd91b99842dac09dca8891393de.

CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_InstallExternalLibs.cmake

commit 501b93d8abe9d2437b819a829f5ef7b13abe3f65
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 16 12:10:54 2019 -0800

    1d and 2d gsrb

Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp

commit 8682902d1a9bbaf3ef7e7735ec6f01ec4c9c46ac
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 16 01:25:58 2019 -0800

    Add C++11 if PGI is nvcc host compiler

Tools/GNUMake/comps/nvcc.mak

commit 87db278ff24667ab2088aae2b557426c96441bdc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 15 23:06:51 2019 -0800

    3d gsrb

Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp

commit 7c05741cf1579d939efdf85b08b079d75be6fc25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 15 21:18:18 2019 -0800

    fix TagBox::coarsen for gpu

Src/AmrCore/AMReX_TagBox.cpp

commit 8e8c36db6b632e220b4a40316376433915f11b12
Merge: d2afe76c7 5bc08ecb8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 15 20:50:08 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c9127be61b1a13ce23267b6ef2d5147e6798542a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Feb 15 22:11:41 2019 -0500

    CMake: add GPU/NeighborList test

Tutorials/GPU/Launch/CMakeLists.txt
Tutorials/GPU/NeighborList/CMakeLists.txt

commit 413edad5376b54da483c6d9927ce9094584602a6
Merge: d464c3220 5bc08ecb8
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Feb 15 20:34:42 2019 -0500

    Merge branch 'development' into mr/cmake

commit 87b79015d434c481fddaa51d035ab8e1b308ac85
Merge: 75aaf725c 7320b9054
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Feb 15 18:25:29 2019 -0700

    Merge branch 'nodeghostcells' of https://github.com/AMReX-Codes/amrex into nodeghostcells

commit d464c32203023488ea60b20e3c73722e08511c61
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Feb 15 20:24:04 2019 -0500

    CMake: fix GPU example

Tools/CMake/AMReX_Config.cmake
Tutorials/GPU/Launch/CMakeLists.txt

commit 75aaf725c1e60f36f5a3cccd238bfa5fb71148e8
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Feb 15 18:22:42 2019 -0700

    works for multiple grids in serial, need to determine why mpi does not work

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 5bc08ecb8895ddcc20ae66052cdaaee5cba11b4c
Merge: edf1944fb 87c3cd753
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 15 19:56:03 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit edf1944fb334440087eb2c78c2a24a7cabeb10f0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 15 19:55:32 2019 -0500

    move the gpu neighbor list thing to Tutorials/GPU

Tutorials/GPU/NeighborList/Constants.H
Tutorials/GPU/NeighborList/GNUmakefile
Tutorials/GPU/NeighborList/MDParticleContainer.H
Tutorials/GPU/NeighborList/MDParticleContainer.cpp
Tutorials/GPU/NeighborList/Make.package
Tutorials/GPU/NeighborList/inputs
Tutorials/GPU/NeighborList/main.cpp
Tutorials/GPU/NeighborList/md_K.H

commit d2afe76c7052a67db2e4872c467eafc453370e82
Merge: 66499da6c 87c3cd753
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 15 16:17:07 2019 -0800

    Merge branch 'development' into weiqun/gpu

commit 87c3cd753991e06d151c35c4da9ee645f86cb351
Merge: 2e2239112 086ffeac3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 15 15:00:56 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 086ffeac3e5bb49adccef05b6986f7014a0168d7
Author: kngott <kngott@lbl.gov>
Date:   Fri Feb 15 14:59:53 2019 -0800

    Add support for OpenMPI+UCX library on CoriGPU.

Tools/GNUMake/sites/Make.nersc

commit 2e22391121acefd35c362c56fced50c0006af236
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 15 14:55:34 2019 -0800

    use always assert

Src/Base/AMReX_Array.H
Src/Base/AMReX_BLassert.H

commit f6df72bd4ea0de1e8e6fb8aa851acb6ce6a05f42
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 15 17:55:00 2019 -0500

    removing files added by mistake

Tutorials/Particles/NeighborList/AMReX_FPC.tsm
Tutorials/Particles/NeighborList/AMReX_ForkJoin.tsm
Tutorials/Particles/NeighborList/AMReX_NFiles.tsm
Tutorials/Particles/NeighborList/AMReX_SPMD.tsm
Tutorials/Particles/NeighborList/AMReX_VisMF.tsm
Tutorials/Particles/NeighborList/NeighborListParticleContainer.tsm
Tutorials/Particles/NeighborList/main.tsm

commit bfa45c0ede545c1dd42670a0c265b3bd091afeca
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 15 17:40:41 2019 -0500

    also make the cpu version work with non-cubic domains

Tutorials/Particles/NeighborList/AMReX_FPC.tsm
Tutorials/Particles/NeighborList/AMReX_ForkJoin.tsm
Tutorials/Particles/NeighborList/AMReX_NFiles.tsm
Tutorials/Particles/NeighborList/AMReX_SPMD.tsm
Tutorials/Particles/NeighborList/AMReX_VisMF.tsm
Tutorials/Particles/NeighborList/GNUmakefile
Tutorials/Particles/NeighborList/NeighborListParticleContainer.tsm
Tutorials/Particles/NeighborList/inputs
Tutorials/Particles/NeighborList/main.cpp
Tutorials/Particles/NeighborList/main.tsm

commit 5c5813d67b649f2705fa228de151e3d5eac7b78e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 15 17:32:38 2019 -0500

    let this thing have a non-cubic domain

Tests/Particles/GPUNeighborList/inputs
Tests/Particles/GPUNeighborList/main.cpp

commit 5743bcffe3af4230d801d12a479fa9569b4d2278
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 15 17:17:07 2019 -0500

    fix another parallel bug

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 725e6f1d4a754185ec7a6d9125b7ea4efc039635
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 15 16:30:21 2019 -0500

    parallel bug fix.

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit d05d25593af8b36e9035add520a85bd345f8069c
Merge: efa61ff2e faedb2fcd
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Feb 15 13:11:01 2019 -0700

    Merge branch 'nodeghostcells-instr' into nodeghostcells

commit efa61ff2ebe4c640d34fd203864addcf1c94daa0
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Feb 15 13:06:54 2019 -0700

    added nghost specification in linop

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit acc2f31d70ce1c0ca9a231be317d226cc65c35e2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 15 14:46:27 2019 -0500

    don't write anything by default in inputs

Tests/Particles/GPUNeighborList/inputs

commit faedb2fcd0f12afd3757885591b4d1209fbde275
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Feb 15 12:37:49 2019 -0700

    WIP: fillboundary surgery

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit ba563187a5a77d21704c4a0961429c46e0fb3cc8
Merge: 57b47c3b8 a4461a17c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 15 14:34:17 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into gpu_neighbor_list

commit 57b47c3b87b706a91676a42dd86fa86d8cbb6c44
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 15 14:32:33 2019 -0500

    MPI for gpu fillNeighbors

Tests/Particles/GPUNeighborList/GNUmakefile
Tests/Particles/GPUNeighborList/MDParticleContainer.H
Tests/Particles/GPUNeighborList/MDParticleContainer.cpp
Tests/Particles/GPUNeighborList/inputs
Tests/Particles/GPUNeighborList/main.cpp

commit de142a8a07b0df8060b1458c5f90dc3b14c01214
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Feb 15 10:50:17 2019 -0700

    re-instrumented and debugging fillboundary

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90

commit 03c69e55c599d6d4afcbdc384861ee9d6493b959
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Feb 14 21:17:41 2019 -0500

    CMake:semi-working CUDA support

CMakeLists.txt
Src/CMakeLists.txt
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_SetupCUDA.cmake
Tools/CMake/AMReX_Utils.cmake
Tools/CMake/comps/AMReX_GNU.cmake
Tools/CMake/comps/AMReX_NVIDIA.cmake
Tools/CMake/comps/AMReX_PGI.cmake
Tutorials/CMakeLists.txt
Tutorials/GPU/Launch/CMakeLists.txt
Tutorials/GPU/Launch/MyKernel_F.F90

commit a4461a17c6d3f09abc7e06eef05cf7d60a87ca03
Author: kngott <kngott@lbl.gov>
Date:   Thu Feb 14 15:14:27 2019 -0800

    Updated corigpu script.

Tutorials/GPU/run.corigpu

commit 7aa6daea5f7b25bf98539506061be3aae640bfd1
Author: kngott <kngott@lbl.gov>
Date:   Thu Feb 14 13:37:00 2019 -0800

    Add corigpu run script w/ environment & salloc instructions.

Tutorials/GPU/run.corigpu

commit 5d658c0ff00a077625b9263e793c13da3d32a9d3
Merge: acf33d839 28b7c7d41
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 14 16:19:57 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into gpu_neighbor_list

commit 28b7c7d4177365bd348cbcff4393e2dcb15cdad8
Merge: 895714865 99e2c1030
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 14 13:18:36 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8957148656d5b1dae1849f84403de3bf37b8340d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 14 13:18:25 2019 -0800

    routines for 3d neighbor list tutorial

Tutorials/Particles/NeighborList/inputs
Tutorials/Particles/NeighborList/main.cpp
Tutorials/Particles/NeighborList/neighbor_list_3d.f90

commit acf33d839f04564fb153ea05e13f535323765b8f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 14 15:39:07 2019 -0500

    a few bug fixes

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 99e2c1030b0814cee50df6f12154e33d71cadb15
Merge: a4856755c 02e4dc10a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Feb 14 11:47:11 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit a4856755c6eabfd91b99842dac09dca8891393de
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Feb 14 11:47:02 2019 -0800

    CMake: change the way Algoim and Blitz are handled

CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_InstallExternalLibs.cmake

commit 02e4dc10a5f1b687a0d94603e35f0db6800304e7
Merge: 8db89f69d 4ebff7a98
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 14 09:55:01 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8db89f69d062c68c364850ecfb4ed20dac8bacd2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 14 09:54:22 2019 -0800

    ParmParse: fix for IntVect

Src/Base/AMReX_ParmParse.cpp

commit 4ebff7a98034abf0eca3eb94a393eac67e8580c2
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Feb 14 12:11:23 2019 -0500

    Preprocess out -D defines in the CUDA script when searching for pragmas

Tools/F_scripts/write_cuda_headers.py

commit eb17f4907a1f9277732b6d12148822ad44f66ced
Merge: b12c7e641 84554a96f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 14 08:21:06 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b12c7e641b1ada11f000ba11aa1d02f118f28d21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 14 08:20:55 2019 -0800

    fcompare: handle empty plotfile

Src/Base/AMReX_PlotFileDataImpl.cpp
Tools/Plotfile/fcompare.cpp

commit 84554a96f47bf2a9702d1f46acfdfd3bb18a3d81
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Feb 13 17:50:07 2019 -0800

    Updated GPU kernel launch docs.

Docs/sphinx_documentation/source/GPU.rst

commit f8dd0159ec2a12b58e040c60c8c3c1de89103c6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 13 16:29:34 2019 -0800

    remove space from variable names

OldTutorials/MultiGrid_C/writePlotFile.cpp
OldTutorials/Tiling_Heat_C/writePlotFile.cpp
OldTutorials/WaveEquation_C/writePlotFile.cpp

commit 833f7dbf19f433c92c9dd2f84e1b9c17f8c52217
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 13 16:19:05 2019 -0800

    add Palette

Tools/Plotfile/Palette

commit 93057a03e97c78762fd127340cebc5c81d81354a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 13 18:47:10 2019 -0500

    gpu neighbor list running with domain decomposition

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp
Tests/Particles/GPUNeighborList/inputs
Tests/Particles/GPUNeighborList/main.cpp

commit 31177c370af888eb7597236ad214592f724cfe84
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 13 18:37:18 2019 -0500

    make OKGPU() work in the presence of neighbor particles

Src/Particle/AMReX_ParticleContainerI.H

commit 068179d7f66c18581922752bf507633fdd4b13fd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 13 18:12:42 2019 -0500

    make numParticles return the number of Real particles (excluding neighbors)

Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_StructOfArrays.H

commit 2400ac70a5389d4809df8eacdf5b8dd12c7996c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 13 14:14:27 2019 -0800

    fsnapshot: option to specify coordinates on slice

Tools/Plotfile/fsnapshot.cpp

commit 6e15ab3ef8318a8c58aa3221302ea46c5d5fd394
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 13 17:00:07 2019 -0500

    add fillNeighbors and clearNeighbors

Tests/Particles/GPUNeighborList/MDParticleContainer.H
Tests/Particles/GPUNeighborList/MDParticleContainer.cpp
Tests/Particles/GPUNeighborList/inputs
Tests/Particles/GPUNeighborList/main.cpp

commit 1095322e1005ad1bf707f5d79e5bcf9e96cf19a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 13 13:11:55 2019 -0800

    fsnapsht3d

Tools/Plotfile/GNUmakefile
Tools/Plotfile/fsnapshot.cpp
Tools/Plotfile/fsnapshot2d.cpp

commit 6464480c9d4bbb39e74b2577913973285ba4bc13
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 13 15:49:36 2019 -0500

    copy neighbor particles to their destinations

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 7cf07e9419aed2857f089e2708c6823277c0d5ed
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 13 15:34:10 2019 -0500

    starting to implement neighbor particle filling

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 10927618ba29e51c528cd0d9121b0722d323c7d7
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 13 15:33:51 2019 -0500

    Add getters for numNeighbors

Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_StructOfArrays.H

commit d6463c1d015444a491803a0895522e91989d5885
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 13 11:28:15 2019 -0800

    fsnapshot2d

Tools/Plotfile/AMReX_PPMUtil.H
Tools/Plotfile/AMReX_PPMUtil.cpp
Tools/Plotfile/GNUmakefile
Tools/Plotfile/Make.package
Tools/Plotfile/fcompare.cpp
Tools/Plotfile/fextract.cpp
Tools/Plotfile/fextreama.cpp
Tools/Plotfile/fnan.cpp
Tools/Plotfile/fsnapshot2d.cpp

commit d3e53077ec78af8250991d4b3b5703f7fac2eb90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 13 09:40:05 2019 -0800

    ParmParse: validate input by checking there are nothing left in the stream.  For example 1.5.e7 is an invalid double.  C++ istream will read it as 1.5 and leaves .e7 in the input stream.

Src/Base/AMReX_ParmParse.cpp

commit 4c5e77222095f7dd86aa005f44fa6cad445a0efc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 13 06:52:41 2019 -0800

    Elixir: fix assertion in resize; don't own the pointer if not in gpu launch region

Src/Base/AMReX_BaseFab.H

commit 7be102528a5a3d3d70dac21b70a9ba87f76ebf60
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 12 20:12:30 2019 -0500

    functions for setting the number of neighbor particles

Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_StructOfArrays.H

commit 71214b5c2a0e87ae100d69b7e1057d3ef69cbac0
Merge: 4997a9a41 9fe04abe6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 12 20:00:47 2019 -0500

    Merge branch 'development' into gpu_neighbor_list

commit 4997a9a4170b5a9ecc0e96077a5e689c3545a02f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 12 19:58:10 2019 -0500

    sorting the particles by which neighbor they need to be copied to

Tests/Particles/GPUNeighborList/MDParticleContainer.H
Tests/Particles/GPUNeighborList/MDParticleContainer.cpp
Tests/Particles/GPUNeighborList/inputs
Tests/Particles/GPUNeighborList/main.cpp

commit 7320b9054f44ad6410cb020625e481f1c21d0398
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Feb 12 17:38:27 2019 -0700

    removed instrumentation and cleanded up

GNUmakefile
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 213169d7a24f036f414f0fd32fd383d92ad15c15
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 12 18:34:50 2019 -0500

    build mask data structure for sending particles to neighbors

Tests/Particles/GPUNeighborList/MDParticleContainer.H
Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 0348ae195493be3998351b7c8fe308247a410d8a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 12 18:34:09 2019 -0500

    distinction between real and ghost particles in ParticleTile

Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_StructOfArrays.H

commit 9fe04abe6eb7a60019c03b9e43613b78da55ea88
Merge: e1a64f7a2 1318ed728
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 12 14:20:40 2019 -0800

    Merge branch 'plotfiletools' into development

commit 1318ed728e62f1525d82c67189ccfac338a2bfa9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 12 14:20:21 2019 -0800

    fextreama: make the output resemble fortran

Src/Base/AMReX_CudaLaunch.H
Tools/Plotfile/fextreama.cpp

commit d1f49fe6c85ba1ae3787aa98bb730c22262c65e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 12 12:58:20 2019 -0800

    fextract

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Tools/Plotfile/GNUmakefile
Tools/Plotfile/fextract.cpp
Tools/Plotfile/fextreama.cpp

commit 3d19d71a999bd019500a9c2ca7a6f98bed9b3a8d
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Mon Feb 11 17:37:52 2019 -0700

    initial working

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit e1a64f7a28ff6de01866388ace519fa2f59b0172
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Feb 11 16:09:46 2019 -0800

    Array4 const&

Docs/sphinx_documentation/source/Basics.rst

commit 316fcc81ece178a5050593581c56e8bbc049b7c7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Feb 11 13:01:15 2019 -0800

    Missing semicolon in example.

Docs/sphinx_documentation/source/Basics.rst

commit 334d778c3958b56716084ce9476f143e8fdb0c1e
Merge: f2d01623f 942e5d162
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Feb 11 12:07:59 2019 -0800

    Merge pull request #408 from mwm126/patch-1
    
    Fix typos

commit 942e5d162a565ee5f0425aa4d5b72f84e6f53875
Author: Mark Meredith <mwm126@gmail.com>
Date:   Mon Feb 11 14:57:42 2019 -0500

    Fix typos

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit f2d01623f721f587a41bc3033f61a7a52be7d9bb
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Feb 11 11:47:57 2019 -0800

    Update docs from FabView to Array4 style.

Docs/sphinx_documentation/source/Basics.rst

commit 27f2ac573238f3ac44b65ae106e681d2fc12ade7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 11 14:21:17 2019 -0500

    minor change of style

Tutorials/GPU/CNS/Source/CNS_advance.cpp

commit a95d72be5cc15a850a5e90837ab6adefd14c4085
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 11 14:20:27 2019 -0500

    elixir: make sure T is trivially dectructible

Src/Base/AMReX_BaseFab.H

commit 72c02bab45953baf00693773ca84da2c8c9049d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 11 14:00:07 2019 -0500

    fix fab stats

Src/Base/AMReX_BaseFab.H

commit 5bf393c2ed63c63ea5fc9ca0b429553cff3e22bf
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 11 13:34:53 2019 -0500

    tweak inputs

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp
Tests/Particles/GPUNeighborList/inputs

commit 23cb6133b1859bfc457be8b297b06c584dc72d9b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 10 11:00:01 2019 -0800

    fix array initialization for C++11

Src/Base/AMReX_PlotFileDataImpl.H

commit ef26b56015da6ca0ecc90157c93c3386c607c616
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 10 11:00:01 2019 -0800

    fix array initialization for C++11

Src/Base/AMReX_PlotFileDataImpl.H

commit 6aa0cd8cc08c14a5f9d48f45670309ec4070df1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 10 09:54:20 2019 -0800

    AsyncFab: add move ctor

Src/Base/AMReX_CudaAsyncFab.H

commit 31bdae254c5b108f62cc5e9a0c022343c0c42204
Merge: 5a9dd3393 47ab43431
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 9 22:36:53 2019 -0800

    Merge branch 'plotfiletools' into development

commit 5a9dd33939927ce2877dee639ca70d1f70f90956
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 9 22:08:55 2019 -0800

    elixir

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaElixir.H
Src/Base/AMReX_CudaElixir.cpp
Src/Base/AMReX_Gpu.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit cbdccf25628dfa1ad704ef37be94aec8c9abb37d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 9 21:43:49 2019 -0500

    Add AsyncFab function to return the host data

Src/Base/AMReX_CudaAsyncFab.H
Src/Base/AMReX_CudaAsyncFab.cpp

commit 47ab43431c4550b1d9ecb7d59ad17e46d0cadbec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 9 17:01:48 2019 -0800

    fextreams

Tools/Plotfile/GNUmakefile
Tools/Plotfile/fextreama.cpp

commit 1e173b4d6a7cd763fdf2d94bbbaf30a5c7e99200
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 9 15:02:15 2019 -0800

    finish fcompare

Tools/Plotfile/fcompare.cpp

commit 2be91abd29a622a02cecce6ecab2854691cf9312
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 9 17:10:40 2019 -0500

    Skip plotfile if there's no variables to plot

Src/Amr/AMReX_Amr.cpp

commit b91ede01d284ecd89281d80ace376765ca6fca27
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 9 17:04:33 2019 -0500

    Symmetrize small plot with full plot

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp

commit 8e5c61668d8965fa56964c39a3f7d7e649cee2c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 9 13:02:04 2019 -0800

    update to using PlotFileData in what we have so far

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_PlotFileDataImpl.H
Src/Base/AMReX_PlotFileDataImpl.cpp
Src/Base/AMReX_PlotFileUtil.H
Tools/Plotfile/AMReX_AnyDimUtil.H
Tools/Plotfile/AMReX_AnyDimUtil.cpp
Tools/Plotfile/GNUmakefile
Tools/Plotfile/Make.package
Tools/Plotfile/fboxinfo.cpp
Tools/Plotfile/fcompare.cpp
Tools/Plotfile/fnan.cpp
Tools/Plotfile/ftime.cpp
Tools/Plotfile/fvarnames.cpp

commit c9b6dd3a805345b3b40e86e684742a329ead1c8f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 9 15:39:21 2019 -0500

    Fix fp comparison logic using machine epsilon

Src/Amr/AMReX_Amr.cpp

commit 15748a2f31c297867f97d086cc27a53757413c79
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 9 10:40:49 2019 -0800

    Fix Cori build when linking with Fortran

Tools/GNUMake/sites/Make.nersc

commit 7aa5c4a58c3be9c9aa99dd139fdf22bb5a629d5d
Author: atmyers <atmyers2@gmail.com>
Date:   Sat Feb 9 10:27:40 2019 -0800

    add note that the GPU Vector classes now use the memory Arenas provided by AMReX.

Docs/sphinx_documentation/source/GPU.rst

commit 2cbc641af286607b0ab0c2cb72f3ebe5fcab84fb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 8 23:00:58 2019 -0800

    Fix bug in 3D GSRB cell-centered solve.

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit b746a889627bb5cc4e03c159d52e17a28fcee9ac
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 8 23:00:58 2019 -0800

    Fix bug in 3D GSRB cell-centered solve.

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit a84ad543870a4412c032dff3f0426ddbf01baf7b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 8 20:47:41 2019 -0800

    PlotFileData::get for single component

Src/Base/AMReX_PlotFileDataImpl.H
Src/Base/AMReX_PlotFileDataImpl.cpp
Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_VisMF.H

commit b8712014f8e896b51aca0259a4a2178f55d09299
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 8 17:02:38 2019 -0800

    revert changes to AmrData

Src/Extern/amrdata/AMReX_AmrData.H
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/Extern/amrdata/AMReX_PlotfileData.H
Src/Extern/amrdata/AMReX_PlotfileData.cpp
Src/Extern/amrdata/CMakeLists.txt
Src/Extern/amrdata/Make.package

commit 0ea1dcf85848e97fca270ee4c190d539621d6eea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 8 16:51:53 2019 -0800

    add PlotFileData for reading plotfiles

Src/Base/AMReX_PlotFileDataImpl.H
Src/Base/AMReX_PlotFileDataImpl.cpp
Src/Base/AMReX_PlotFileUtil.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tools/Plotfile/GNUmakefile
Tools/Plotfile/ftime.cpp

commit 81c63ca4e33510f65c9a7843c718b260461ce653
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Feb 8 17:49:46 2019 -0700

    modifying avergedownandsync

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 74f520d93b1f02511a9d63ad6a3656d94447d1be
Merge: e60c3dbbd 41c86612d
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Feb 8 17:17:52 2019 -0700

    Merge branch 'development' into nodeghostcells

commit b82c882750081d945471827c0d2f3e23d1500164
Merge: da798a3b1 c56e5ca23
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 8 13:43:17 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c56e5ca231eef7255f0bac72c476b97e3f9260cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 8 13:12:06 2019 -0800

    fix Machine for cori gpu and clean up make

Src/Base/AMReX_Machine.cpp
Tools/GNUMake/sites/Make.nersc

commit 9519d79d86d748099f867f2f073102c4ed4cab27
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 8 13:01:57 2019 -0800

    don't need travis wait anymore

.travis.yml

commit 3a6c8e810f44f798aec80d087a8128f1a612df47
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 8 12:44:53 2019 -0800

    disable breathe for now

build_and_deploy.sh

commit e60c3dbbd1e444087a81ddd93c1d64aa55ee87de
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Feb 8 13:36:27 2019 -0700

    modified interpCorrection to NOT include ghost cells

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 41c86612da02af7242dfe6ff3b749da8a9fe9d4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 8 10:40:36 2019 -0800

    WIP: make for cori gpu

Tools/GNUMake/Make.defs
Tools/GNUMake/sites/Make.nersc

commit 4cbbabec9fe4882d2634ce389d3702fe719cb4ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 8 08:46:02 2019 -0800

    fcompare wip

Src/Base/AMReX.cpp
Src/Extern/amrdata/AMReX_PlotfileData.H
Src/Extern/amrdata/AMReX_PlotfileData.cpp
Tools/Plotfile/GNUmakefile
Tools/Plotfile/fcompare.cpp
Tools/Plotfile/fnan.cpp
Tools/Plotfile/ftime.cpp
Tools/Plotfile/fvarnames.cpp

commit 7073ffa0f249039d7848db851eb65479797e659e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Feb 8 11:41:13 2019 -0500

    Add floating point awareness to the plot_per/check_per logic
    
    The current logic can be slightly erroneous due to floating point issues. For example,
    if the timestep is 0.01 and the plot_per is 0.1, you would expect plotfiles at
    steps that are multiples of 10, but due to roundoff errors the current logic will sometimes
    plot in the 11th step instead of the 10th. By adding a small number to both sides of the
    comparison, we can guarantee plotting on exactly the timestep we intended.

Src/Amr/AMReX_Amr.cpp

commit aaae94ccb20bb74a99bb5cbf5962b9550d450a33
Merge: cde8229d6 676cea69b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 7 16:26:30 2019 -0800

    Merge pull request #405 from MaxThevenet/development
    
    add tag to particles already split

commit 676cea69ba66b2ccdf8e6405d57eb16552e2dbf5
Author: Maxence Thevenet <mthevenet@lbl.gov>
Date:   Thu Feb 7 16:23:52 2019 -0800

    add tag to particles already split

Src/Particle/AMReX_Particle.H

commit cde8229d63cec4a52c1457daa340988d535bf421
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 18:17:14 2019 -0500

    remove unused variables

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 7d4dfa1555570b39b20673eb74f3e917b19f7384
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 17:56:39 2019 -0500

    make the nbor_list a map over tiles

Tests/Particles/GPUNeighborList/MDParticleContainer.H
Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 73df3e41c63113ead79f287f95b56ffe222fc4a6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 17:47:56 2019 -0500

    copy the neigbor list to host before printing

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 2b5d0bf90b246fc3a31ba5ef890e5e9a5ff4566f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 17:44:00 2019 -0500

    read print_neighbor_list from inputs

Tests/Particles/GPUNeighborList/inputs
Tests/Particles/GPUNeighborList/main.cpp

commit 1d345374c6f4a73ff98a55ecf1a599af6e49d08d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 17:41:19 2019 -0500

    move printNeighborList to its own method

Tests/Particles/GPUNeighborList/MDParticleContainer.H
Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 686998be828c1e71b913a110aeee3550291c7a55
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 17:38:05 2019 -0500

    move computeForces to a separate method

Tests/Particles/GPUNeighborList/MDParticleContainer.H
Tests/Particles/GPUNeighborList/MDParticleContainer.cpp
Tests/Particles/GPUNeighborList/main.cpp

commit f8a1119a38ec87eda659038334fddd60f14e2024
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 17:32:08 2019 -0500

    make the neighbor list a class member

Tests/Particles/GPUNeighborList/MDParticleContainer.H
Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 0a81cf9b12636464c5d778348672768e3bc38adf
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 17:25:11 2019 -0500

    thrust::raw_pointer_cast -> dataPtr()

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit a8d1946249c80285d96a5a426a69927e15446464
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 17:21:18 2019 -0500

    thrust::device_vector -> Gpu::DeviceVector

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 2ad5bad614f5aeb9ede4b0c4105d5185fcf5a8a8
Merge: c525335bb 6b4de63f6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 16:27:50 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c525335bb49f116b76bf38e0832d8f5a2151322f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 16:19:47 2019 -0500

    don't need a separate cached allocator now

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaAllocators.cpp

commit 48df6fcbf98363676a3c991e9774e9b573b0328c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 15:34:10 2019 -0500

    remove the remaining device_vector members from ParticleContainer; temporaries now work fine.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 9fd93ab27323c4a8492d135183726fd76b85a34e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 15:01:35 2019 -0500

    remove some more of the mutable thrust::device_vector members from the ParticleContainer

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 45fa9cd5b2561872c46424e6df82eec35886769a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 14:52:32 2019 -0500

    remove some of the mutable thrust::device_vector members from the ParticleContainer

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 6ea1bebb09f66813622055271f34a96403c2aaa2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 14:46:06 2019 -0500

    thrust::device_vector -> Gpu::DeviceVector

Src/Particle/AMReX_Particles.H

commit e8daa3c420edfd90ced989bb7696e90064451b53
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 14:34:27 2019 -0500

    use the Arena in Gpu::DeviceVector

Src/Base/AMReX_CudaContainers.H

commit d4a616dd3591b384d7104c13658888abc64d8fc6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Feb 7 14:34:05 2019 -0500

    add thrust allocators that are implemented in terms of AMReX's Arenas

Src/Base/AMReX_CudaAllocators.H

commit ffd2a3fe062fe64627686961767c8c17cebcf8f4
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Feb 7 11:12:56 2019 -0700

    fixed mlcg to be consistent

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 6b4de63f6e0434fe5c0e8e5478731bec80e65863
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 7 06:44:51 2019 -0800

    Remove IMEX_Advec_Diff_C from the Tutorials documentation

Docs/sphinx_tutorials/source/SDC_Tutorial.rst

commit 3f7088a49c3b4878052e862bcd452929f2c79756
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 7 06:44:07 2019 -0800

    Remove IMEX_Advec_Diff_C per Minion's guidance -- this is deprecated.

Tutorials/SDC/IMEX_Advec_Diff_C/GNUmakefile
Tutorials/SDC/IMEX_Advec_Diff_C/Make.package
Tutorials/SDC/IMEX_Advec_Diff_C/advance.cpp
Tutorials/SDC/IMEX_Advec_Diff_C/advance_2d.f90
Tutorials/SDC/IMEX_Advec_Diff_C/init_phi_2d.f90
Tutorials/SDC/IMEX_Advec_Diff_C/init_phi_3d.f90
Tutorials/SDC/IMEX_Advec_Diff_C/inputs_2d
Tutorials/SDC/IMEX_Advec_Diff_C/inputs_3d
Tutorials/SDC/IMEX_Advec_Diff_C/main.cpp
Tutorials/SDC/IMEX_Advec_Diff_C/myfunc.H
Tutorials/SDC/IMEX_Advec_Diff_C/myfunc_F.H

commit 53d4c0a3ed3c4159f5dbb292188f0358fbb37410
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 20:50:44 2019 -0800

    clean up

Src/Extern/amrdata/AMReX_PlotfileData.H
Src/Extern/amrdata/AMReX_PlotfileData.cpp

commit 8ca1dbc065049971094b6fcc92561df0382b4962
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 17:55:57 2019 -0800

    fnan

Src/Extern/amrdata/AMReX_PlotfileData.H
Src/Extern/amrdata/AMReX_PlotfileData.cpp
Tools/Plotfile/GNUmakefile

commit a265c0a1d5d92f64d20becb798556f2049ec54c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 16:30:33 2019 -0800

    ftime

Tools/GNUMake/Make.rules
Tools/Plotfile/GNUmakefile
Tools/Plotfile/fboxinfo.cpp
Tools/Plotfile/ftime.cpp
Tools/Plotfile/fvarnames.cpp

commit 8c80a3299957af0e361a74ff632bd6e8caaf08b4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 6 19:20:42 2019 -0500

    restore cuda-aware mpi option to the particle container.

Src/Particle/AMReX_Particles.H

commit 6afc477f607378656b05a74b467fe2ae767a8abd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 6 19:20:25 2019 -0500

    a vector based on same

Src/Base/AMReX_CudaContainers.H

commit 3ca4c173bc132007de204fddd50d661b2c2ab591
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 6 19:20:14 2019 -0500

    a new allocator that can toggle between pinned and device memory at runtime

Src/Base/AMReX_CudaAllocators.H

commit 8ea054eb4e6b465637f5a3e9a63876a2cae1872f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 16:11:05 2019 -0800

    fvarnames

Tools/Plotfile/GNUmakefile
Tools/Plotfile/fvarnames.cpp

commit 46bf0a6c851968ab671b92f41eb99796bd061926
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 15:47:18 2019 -0800

    dimension agnostic fboxinfo

Src/Extern/amrdata/AMReX_PlotfileData.H
Src/Extern/amrdata/AMReX_PlotfileData.cpp
Tools/Plotfile/AMReX_AnyDimUtil.H
Tools/Plotfile/AMReX_AnyDimUtil.cpp
Tools/Plotfile/GNUmakefile
Tools/Plotfile/Make.package
Tools/Plotfile/fboxinfo.cpp

commit 3714926b9508f01f79a602a0d8f1c9efc23b01b5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 6 18:45:26 2019 -0500

    some reorganization

Tests/Particles/GPUNeighborList/MDParticleContainer.H
Tests/Particles/GPUNeighborList/MDParticleContainer.cpp
Tests/Particles/GPUNeighborList/main.cpp

commit 3e078c66a2ef6df8518dea6daf043c1da42a3e54
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 6 18:33:14 2019 -0500

    fix bug

Tests/Particles/GPUNeighborList/MDParticleContainer.H
Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 2f4e526bc2bc5903ab01b666d985cb62cb82e385
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 6 18:06:33 2019 -0500

    removing is_per

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 1c042152ac8b10c2926eee599280d49352f22fba
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 6 18:06:00 2019 -0500

    implement looping over the neighbor list and moving the particles

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 500934cec055fa0dea360691af579db2ef17583d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 6 17:08:26 2019 -0500

    hardwire nppc to (1, 1, 1)

Tests/Particles/GPUNeighborList/inputs
Tests/Particles/GPUNeighborList/main.cpp

commit 0f677bbad39d1cda47739e225dcc188144e58271
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 6 17:07:49 2019 -0500

    tweak cutoff

Tests/Particles/GPUNeighborList/Constants.H

commit 6102c91b84f9234e29f6303ea8323e789da73d85
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Feb 6 16:28:05 2019 -0500

    workaround for relaxed constexpr bug in cuda 9.2

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit 34cad51a8538a3e421baf7ca9c52081a146566a5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 6 13:17:01 2019 -0800

    tweak build and deploy

build_and_deploy.sh

commit 9238a3e3da15f1d056144e353ed7b91040d8d1b7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 6 12:53:04 2019 -0800

    add travis_wait before running the build script

.travis.yml

commit 093e21e855dcee39d57036fe7bd0f85973f5cd3e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 6 12:27:42 2019 -0800

    hide more output

build_and_deploy.sh

commit 156800ff9a05dda14bac7ef0e7055a77d9fda363
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 6 11:56:05 2019 -0800

    hide the doxygen output, which puts us over the log file length limit on Travis CI

build_and_deploy.sh

commit 1975f1bef9f9ee4dbaffd6353a9b2adb917f85a6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 6 11:27:06 2019 -0800

    restore stuff for latexpdf

.travis.yml

commit f716c1ec7855c6d39c90a3d34884875c933ecfb4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 6 11:06:06 2019 -0800

    don't specify python3.6 in the build_and_deploy script

build_and_deploy.sh

commit 0195cc654bfa2c5d2437fa38f31295f217f035ba
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 6 10:45:16 2019 -0800

    also need libmpich-dev

.travis.yml

commit 7f334444316527fadd3affce7c2f92338726b973
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 6 10:40:50 2019 -0800

    remove extra addons entry

.travis.yml

commit e1cd32ec8d0b2c9db4c76d9359f706a4117fec0f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 6 10:22:08 2019 -0800

    tweak installed packahed

.travis.yml

commit e1bac9fba731d6ff9a4a5a84853359eca6161683
Merge: 81e1a48db 9b498798f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 6 10:14:42 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 81e1a48db7b77fd72889151db02cd0c430e50c50
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 6 10:14:30 2019 -0800

    remove ubuntu-toolchain-r-test

.travis.yml

commit cf4ad88b1907534cc7e25a8b598a81135347de1e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 5 21:45:59 2019 -0800

    add PlotfileData as a wrapper of DataServices

Src/Extern/amrdata/AMReX_AmrData.H
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/Extern/amrdata/AMReX_PlotfileData.H
Src/Extern/amrdata/AMReX_PlotfileData.cpp
Src/Extern/amrdata/CMakeLists.txt
Src/Extern/amrdata/Make.package

commit 9b498798f2b743beb4347db246e9f3671bd43c7d
Merge: c0a0a1b20 aae1e389b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 5 21:29:11 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c0a0a1b20487bc5b07f132a4643da612bdb0fcd8
Merge: f9167057d 7a51ec74f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 5 21:28:47 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit aae1e389be1fdd3f16f1cbd8f0d3e65ca4e9fbe4
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 5 18:28:38 2019 -0800

    Add sig for WritePltFile that takes an alternative prob domain array

Tools/C_util/WritePlotFile.H
Tools/C_util/WritePlotFile.cpp

commit f9167057d2ac2deea44ae4f2137ebe479fc4a47f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 5 21:28:28 2019 -0500

    fix bug involving asynchronous mem copies with Cuda

Src/Particle/AMReX_ParticleContainerI.H

commit 7a51ec74f14bdd60fd6b2d082a64fc1f32c4c13f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 5 17:53:04 2019 -0800

    specify sources

.travis.yml

commit 7b254ea26fc7685b33a71de0d08b371f2bf8e655
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 5 17:43:49 2019 -0800

    add python to PATH

.travis.yml

commit 182494f93815e1f95e79d51d17b31da0073b010c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 5 17:37:49 2019 -0800

    tweak pip install line

.travis.yml

commit 2381bba51c1eabf3a44ee65943a38c2b2723f300
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 5 17:35:46 2019 -0800

    change language.

.travis.yml

commit 6c5b69981e1528d64716ea2e4040e4af304d118f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 5 17:30:25 2019 -0800

    trying to fix the Travis build environment

.travis.yml

commit 74bc78064c0e86384345a17816cb8d63bd19b424
Merge: bae6b14c2 34e2b1e60
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 5 17:22:25 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 34e2b1e60bade5687bf02cf37e249329c0cdd02c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Feb 5 20:15:36 2019 -0500

    Get rid of 9.2.x limitation in GPU docs.

Docs/sphinx_documentation/source/GPU_Chapter.rst

commit 0795a00963a42a72f8989cb87fd82fa7637e2d15
Merge: d38878212 349a8360a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 5 17:10:00 2019 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit bae6b14c287d83d43dfb3927ddbd80e7e5777fd1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 5 17:08:06 2019 -0800

    bump python version

.travis.yml

commit 0cf8d19ba5545fa91382b2106d959550b1c64e21
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Feb 5 18:07:19 2019 -0700

    wip - crude updates to allow ghost cell based reflux

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 349a8360a13cb8af81b2df7433fa3b908809e28a
Merge: 286a739c0 dc9138bfa
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 5 17:02:52 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 286a739c0e181b708ebf7e43675981b8ea19258a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 5 17:02:41 2019 -0800

    mpich2 -> mpich

.travis.yml

commit d3887821212953f5f7a77dfeb793d4b70d0a4c9f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 5 17:02:11 2019 -0800

    Fix oops -- this now compiles.

Src/EB/AMReX_EBMultiFabUtil_3d.F90

commit dc9138bfa9ee936314e6bc5de1b361731b925984
Merge: fc76b489f 2349a8f55
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 5 16:58:56 2019 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit fc76b489f784d791a7e061fc1e1c17f7ce26569f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 5 16:58:19 2019 -0800

    Move interpolate_to_face_centroid routine from mfix into amrex since it is completely general.

Src/EB/AMReX_EBMultiFabUtil_3d.F90

commit 2349a8f55a08ee8c84a85cc540c3fef62ae7068f
Merge: 752fa858c ebe912f83
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 5 16:57:28 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 752fa858c60d06b5fe8c642d60639369572e0ecc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 5 16:57:14 2019 -0800

    update ubuntu version used by travis

.travis.yml

commit ebe912f83371535ed77fb64b7af46c9c0cf4600b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Feb 5 19:40:09 2019 -0500

    buildNotused, testing how to build AMReX as a library around user-defined functions.

Tests/GPU/buildNotused/Extern.H
Tests/GPU/buildNotused/GNUmakefile
Tests/GPU/buildNotused/MyKernel.H
Tests/GPU/buildNotused/MyKernel.cpp
Tests/GPU/buildNotused/MyKernelB.H
Tests/GPU/buildNotused/MyKernelB.cpp
Tests/GPU/buildNotused/Notused.H
Tests/GPU/buildNotused/Notused.cpp
Tests/GPU/buildNotused/Readme
Tests/GPU/buildNotused/main.cpp

commit 1fdf0538d75c0c196a273a09ad391bfd772f3d72
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 5 16:25:56 2019 -0800

    add AddParticles method and implement copyParticles in terms of that.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 80545e9c9b72f7611be0a0adb9d32932154f675c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 5 18:32:48 2019 -0500

    do custom partition by default

Src/Particle/AMReX_ParticleContainerI.H

commit 77bdd5dd53dd9fc4e538bdb555b8cd17f82d034d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Feb 5 18:32:19 2019 -0500

    add option to switch between versions of partition

Src/Particle/AMReX_ParticleContainerI.H

commit da798a3b1039eff770c4cb7a63b6d2d546ad6131
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 5 14:45:39 2019 -0800

    add Fortran 2003 style command argument functions

Src/Base/AMReX.H
Src/Base/AMReX.cpp

commit 9409b1f266c426293c8fc24fea59cd6358fb55b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 5 14:13:07 2019 -0800

    fix merge

Src/Particle/AMReX_Particles.H

commit f830c2bb95da2ac07046e9955086493e893f2256
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 5 13:39:54 2019 -0800

    fix merge

Src/Particle/AMReX_Particles.H

commit f690ecf6ca9c1c3266dc5be9fd755e521fa5b551
Merge: 2f2c3cf08 7710e67e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 5 13:32:47 2019 -0800

    Merge branch 'development' into dev-tmp

commit 7710e67e9beae8a4ff85f0061ce919e47660060e
Merge: 529e816df 95206d278
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 5 13:29:14 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2f2c3cf08ae71bfb5beff6d747b4655a6a45b2a5
Merge: 8cbed0da9 d2c67c019
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Feb 5 13:24:35 2019 -0800

    Merge pull request #403 from harpolea/doxygen
    
    Doxygen

commit 529e816df39274a47e9984bc2eaf3ede0484b2fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 5 13:23:41 2019 -0800

    add make option for multiple executables

Tools/GNUMake/Make.rules

commit 95206d278d3a4afe260856c40d9539b8c983cb65
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 5 12:53:46 2019 -0800

    Add EB_set_covered call at end of reflux routine.

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit d2c67c019deb5e1b23361b5fdc590ed45be04ccd
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Tue Feb 5 15:36:19 2019 -0500

    moves doxygen and breathe steps to build_and_deply

Docs/Doxygen/doxygen.conf
Docs/sphinx_documentation/Makefile
Docs/sphinx_documentation/source/conf.py
build_and_deploy.sh

commit 66499da6ca57cc7a53bc20124f5f30942864be5b
Merge: 2e4d7b025 42f8d1df6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 5 10:34:53 2019 -0800

    Merge branch 'development' into weiqun/gpu

commit 2e4d7b02582588776c885cf1b9f5e92b3b6e7bfa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 5 10:33:43 2019 -0800

    MLMG on GPU: fix eb and put some comments

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 42f8d1df6829f13969131126c3dc86af0c5580cc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 5 09:57:01 2019 -0800

    "OldMiniApps" was too old to be relevant.

OldMiniApps/FillBoundary/GNUmakefile
OldMiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
OldMiniApps/FillBoundary/README
OldMiniApps/FillBoundary/qsub.ipm.bat
OldMiniApps/MultiGrid_C/COEF_3D.F
OldMiniApps/MultiGrid_C/COEF_F.H
OldMiniApps/MultiGrid_C/GNUmakefile
OldMiniApps/MultiGrid_C/Make.package
OldMiniApps/MultiGrid_C/README
OldMiniApps/MultiGrid_C/RHS_3D.F
OldMiniApps/MultiGrid_C/RHS_F.H
OldMiniApps/MultiGrid_C/main.cpp
OldMiniApps/MultiGrid_C/qsub.ipm.bat

commit 435dee40d59424259c35598c30c43c8bec446047
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 5 09:42:50 2019 -0800

    Remove seriously old post-processing routines from Tools/Postprocessing/F_Src that were specific to
    certain applications.

Tools/Postprocessing/F_Src/old_flame/GNUmakefile
Tools/Postprocessing/F_Src/old_flame/fbubble_position.f90
Tools/Postprocessing/F_Src/old_flame/fbubble_position_3d.f90
Tools/Postprocessing/F_Src/old_flame/fcusp.f90
Tools/Postprocessing/F_Src/old_flame/fcylflame.f90
Tools/Postprocessing/F_Src/old_flame/fflamelength.f90
Tools/Postprocessing/F_Src/old_flame/finteg.f90
Tools/Postprocessing/F_Src/old_flame/fturbkin.f90
Tools/Postprocessing/F_Src/old_flame/fwidth.f90
Tools/Postprocessing/F_Src/tutorial/GNUmakefile
Tools/Postprocessing/F_Src/tutorial/fspeciesmass2d.f90
Tools/Postprocessing/F_Src/tutorial/fwrite2d.f90

commit bd6b8daa47cee89cd458e6a150d70c835b898d06
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 5 09:33:53 2019 -0800

    MLMG on GPU: flux

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/Make.package

commit 26604b385b9a4c96b15894f95f24fbc3dcee11a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 5 08:34:22 2019 -0800

    remove F_MG from inputs

OldTutorials/MultiGrid_C/inputs
OldTutorials/MultiGrid_C/inputs-rt-c-neu
OldTutorials/MultiGrid_C/inputs-rt-c-ord2
OldTutorials/MultiGrid_C/inputs-rt-f-neu
OldTutorials/MultiGrid_C/inputs-rt-f-ord2
OldTutorials/MultiGrid_C/inputs-rt-f-ord3
Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord2
Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord3
Tests/LinearSolvers/ComparisonTest/inputs-rt-Neu
Tests/LinearSolvers/ComparisonTest/inputs.3d

commit 4aa66c8ad9b0a6aac077fd168305eaca477ffc3b
Merge: bb07a2dcf 9c4a00ba8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 4 20:46:07 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit bb07a2dcf73d2ce9723783c5dc53c40ef3d07437
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 4 20:41:18 2019 -0500

    fixing bug with freeing the snd_buffer for pinned memory in RedistributeGPU

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit d0ebff754e8ddcce2a3748711848f2e4f0708b43
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 4 20:40:36 2019 -0500

    fixes for the ThrustPinnedAllocator

Src/Base/AMReX_CudaAllocators.H

commit 9c4a00ba82bcb2517202fbf970f9ae18ffc3464d
Merge: 1f8cf421f 14cc8c91d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 4 17:26:10 2019 -0800

    Merge pull request #404 from ylunalin/new_heat_tutorials
    
    New heat tutorials

commit 1f8cf421f18644ce9d8a4f030178f61d182ec03f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Feb 4 20:13:53 2019 -0500

    Clean up hybrid makefile.

Tests/GPU/buildHybrid/GNUmakefile

commit 529418cb0c33162b0990254ddaf9b40a41667256
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 4 20:11:01 2019 -0500

    ifdef the PinnedDeviceVector to be a regular Vector if CUDA is off

Src/Base/AMReX_CudaContainers.H

commit 83fb3f1cea7df966ea59ee5dec60da23998c1e96
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Feb 4 20:10:48 2019 -0500

    Bug fix and eliminate unneeded library and include lines when invoking nvcc and pgfortran.

Tests/GPU/buildTest/GNUmakefile

commit ce2a824764a1de6f75d77984b176969adc06902e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 4 20:10:12 2019 -0500

    add PinnedDeviceVector

Src/Base/AMReX_CudaContainers.H

commit 14cc8c91d59c003bec7237ba57f715c4152896a3
Merge: c68d326e5 bc4ed41c2
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Mon Feb 4 20:04:55 2019 -0500

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into new_heat_tutorials

commit c68d326e5cb5a5f19b57f7b5e37466fd9acb8133
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Mon Feb 4 20:04:29 2019 -0500

    Fixed a typo in the CUDA version, and the multiple lines issue in mykernel.H

Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/myfunc.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/mykernel.H

commit 0a4ba07172ac7a1c7ad2edcce55b6710b6d9f573
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 4 19:59:59 2019 -0500

    templated pinned allocator that can be used with thrust::device_vector

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaAllocators.cpp

commit 6ce0de9607f7db0a2df6e2e3de023affe2a737b4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 4 19:22:10 2019 -0500

    remove some private members that aren't used anymore from ThrustCachedAllocator

Src/Base/AMReX_CudaAllocators.H

commit f63d3f7600b083ef3c519f36f658a45aad29a99f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Feb 4 19:18:02 2019 -0500

    a Pinned allocator for use with Thrust

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaAllocators.cpp

commit bc4ed41c2a27e6b736ad2ccd98769cf35ecf1fba
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Feb 4 13:01:38 2019 -0800

    Remove F_BaseLib.

Tests/LinearSolvers/ComparisonTest/GNUmakefile

commit 6348c99eed30c106688523ec38fe2c4d6119671a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Feb 4 13:00:26 2019 -0800

    Remove F_BaseLib.

Tests/LinearSolvers/C_CellMG/GNUmakefile

commit 10e526313b3a6ea495906cae71f06565e869bce7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Feb 4 12:54:19 2019 -0800

    Remove use of F_MG solvers

OldTutorials/MultiGrid_C/GNUmakefile
OldTutorials/MultiGrid_C/main.cpp
OldTutorials/PIC_C/solve_with_f90.cpp
OldTutorials/README_F

commit edbf4c97d228111cc9f46df03a295532d84fc39e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 4 12:50:33 2019 -0800

    rename solve_with_f90

OldTutorials/PIC_C/Make.package
OldTutorials/PIC_C/solve_with_mlmg.cpp

commit 6ca892bbe00a3e7c5a17028661daf7e1d2916d8a
Merge: 47436c85b c279841a2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Feb 4 12:43:36 2019 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 47436c85bab2afe64650abd38d6c8e57ba45835c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Feb 4 12:43:23 2019 -0800

    Remove reference to F_MG or C_to_F_MG.

Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 8d8b12dbc3beefdc3cc0c36fb7d6c9633e7cce8d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 4 12:34:09 2019 -0800

    fix compilation / linking

OldTutorials/PIC_C/GNUmakefile
OldTutorials/PIC_C/main.cpp
OldTutorials/PIC_C/single_level.cpp
OldTutorials/PIC_C/solve_for_accel.cpp
OldTutorials/PIC_C/solve_with_f90.cpp
OldTutorials/PIC_C/two_level.cpp

commit 464c2bad38bb5406a448bc9af5a50ec274075ee5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 4 11:12:15 2019 -0800

    update GNUmakefile for new linear solver libraries.

OldTutorials/PIC_C/GNUmakefile

commit c279841a27ba20a3ac1acf426b3b664596d65d55
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 4 11:01:29 2019 -0800

    removed old CUDA Fortran example of PIC deposition.

Tests/Particles/ManagedCUDADeposition/GNUmakefile
Tests/Particles/ManagedCUDADeposition/Make.package
Tests/Particles/ManagedCUDADeposition/MyParticleContainer.H
Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp
Tests/Particles/ManagedCUDADeposition/cuda_deposit_3d.f90
Tests/Particles/ManagedCUDADeposition/deposit_3d.f90
Tests/Particles/ManagedCUDADeposition/deposit_F.H
Tests/Particles/ManagedCUDADeposition/inputs
Tests/Particles/ManagedCUDADeposition/main.cpp
Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp
Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp

commit 2c728f256ebdf1bed90b898c21a6fc0aab8c685f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Feb 4 10:52:13 2019 -0800

    Remove all use of F_MG solvers.

Tests/LinearSolvers/ComparisonTest/GNUmakefile
Tests/LinearSolvers/ComparisonTest/Make.package
Tests/LinearSolvers/ComparisonTest/compute_norm.cpp
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/writePlotFile.H
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp
Tests/LinearSolvers/F_MG/GNUmakefile
Tests/LinearSolvers/F_MG/bc_interp.f90
Tests/LinearSolvers/F_MG/cc_edge_coeffs.f90
Tests/LinearSolvers/F_MG/cc_multi.f90
Tests/LinearSolvers/F_MG/cc_rhs.f90
Tests/LinearSolvers/F_MG/grids_2d_1lev
Tests/LinearSolvers/F_MG/grids_2d_2lev
Tests/LinearSolvers/F_MG/grids_3d_1lev
Tests/LinearSolvers/F_MG/grids_3d_2lev
Tests/LinearSolvers/F_MG/init_cell_coeffs.f90
Tests/LinearSolvers/F_MG/inputs.2d.fcycle
Tests/LinearSolvers/F_MG/inputs.2d.fcycle.dir
Tests/LinearSolvers/F_MG/inputs.2d.nodal.cross
Tests/LinearSolvers/F_MG/inputs.2d.nodal.dense
Tests/LinearSolvers/F_MG/inputs.2d.vcycle
Tests/LinearSolvers/F_MG/inputs.2d.vcycle.dir
Tests/LinearSolvers/F_MG/inputs.3d.fcycle
Tests/LinearSolvers/F_MG/inputs.3d.fcycle.dir
Tests/LinearSolvers/F_MG/inputs.3d.nodal.cross
Tests/LinearSolvers/F_MG/inputs.3d.nodal.dense
Tests/LinearSolvers/F_MG/inputs.3d.vcycle
Tests/LinearSolvers/F_MG/inputs.3d.vcycle.dir
Tests/LinearSolvers/F_MG/main.f90
Tests/LinearSolvers/F_MG/makefile
Tests/LinearSolvers/F_MG/nodal_multi.f90
Tests/LinearSolvers/F_MG/nodal_rhs.f90
Tests/LinearSolvers/F_MG/regression
Tests/LinearSolvers/F_MG/t_smoother.f90
Tests/LinearSolvers/F_MG/t_stencil.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit 393c23276fa616a12b6e2b975d33269aa35f57dc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Feb 4 10:42:42 2019 -0800

    Remove F_MG and C_to_F_MG.

Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_stencil_types.H
Src/LinearSolvers/C_to_F_MG/Make.package
Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_interface_stencil.f90
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/coarsen_coeffs.f90
Src/LinearSolvers/F_MG/compute_defect.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_norm.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/nodal_applyop.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_enforce_dirichlet_rhs.f90
Src/LinearSolvers/F_MG/nodal_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_mask.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90
Src/LinearSolvers/F_MG/nodal_newu.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_apply.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90
Src/LinearSolvers/F_MG/nodal_sum.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90
Src/LinearSolvers/F_MG/sparse_solve.f90
Src/LinearSolvers/F_MG/stencil_types.f90
Src/LinearSolvers/F_MG/stencil_util.f90
Src/LinearSolvers/F_MG/tridiag.f90

commit 8cbed0da9fea9f0b16d86421847b24ed318e7df0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 4 08:48:31 2019 -0800

    BOUND_CHECK as an option

Src/Base/AMReX_Array.H
Tools/GNUMake/Make.defs

commit bb5e91303ac3f36b39d3261fcdfa67c9ed6dce05
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Mon Feb 4 11:09:26 2019 -0500

    fixed a few bugs and cleaned up

Src/Base/AMReX_iMultiFab.H
Src/Extern/CVODE/cvode_interface.f90
Src/Extern/CVODE/fnvector_serial.f90
Src/Extern/CVODE/sundials_fdlsmat.f90
Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H
Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F90
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F90
Src/SDC/AMReX_SDCstruct.H

commit 67485ad8beefb6a7c83ec07d5359b0f9e3ed7958
Merge: f5ec341eb 06e715811
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Mon Feb 4 10:26:06 2019 -0500

    fixed merge conflicts

commit f5ec341eb87853f79034f4a0d5375b74efa1a39e
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Mon Feb 4 10:23:41 2019 -0500

    fixed bugs in AMReX_Particles.H

Src/Particle/AMReX_Particles.H

commit 33c3b059763c55e2e25c10e21202ec3c17f3b72d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 2 16:52:02 2019 -0800

    MLMG on GPU: normalize

Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit a88ff2e992f3a70c281c158cd1a33fac2e35bd4b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 2 15:49:38 2019 -0800

    fix variable type and function name

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit a2154590230fce32ae1a4399ec44035ae6586a3d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 2 15:05:40 2019 -0800

    MLMG on GPU: MLABecLap A dot x

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H
Src/LinearSolvers/MLMG/Make.package

commit 06e715811324c5645e561030dbd3e2460416498d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 2 14:03:22 2019 -0800

    update tutorial documentation

Docs/sphinx_tutorials/source/GPU_Tutorial.rst

commit 36c163ac211be87d842ee48ef5a1d97b6ed8b8e5
Merge: 5a5b5ffc7 337767790
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Sat Feb 2 16:51:22 2019 -0500

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into new_heat_tutorials

commit 5a5b5ffc770e10c5f502b407321e3ba6b87325fc
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Sat Feb 2 16:50:49 2019 -0500

    GNUMakefile needed to be tweaked to work with new directory organization.

Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/GNUmakefile

commit 337767790e4d0d3b3b8ce7755b5624a1ca6911c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 2 13:49:44 2019 -0800

    fix 1d interpbndrydata

Src/Boundary/AMReX_InterpBndryData_1D_K.H

commit 75cd2e3dd6a7b5245c5c329eb57d04c861fe9d14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 2 13:49:44 2019 -0800

    fix 1d interpbndrydata

Src/Boundary/AMReX_InterpBndryData_1D_K.H

commit 21222a1aac8ab8e6cf4d80856307239840cf1e43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 2 13:49:28 2019 -0800

    MLMG on GPU: lin_cc_interp

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_F.H
Src/LinearSolvers/MLMG/AMReX_MLMG_K.H
Src/LinearSolvers/MLMG/Make.package

commit 34a88e4e3b0ede6bc3694cd0a89faa72fb782f17
Merge: 3eb2f4b5b 19a8211e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 2 08:51:32 2019 -0800

    Merge branch 'development' into weiqun/gpu

commit 19a8211e85b21d200bcee629a415f236842aa326
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 2 11:51:08 2019 -0500

    fix the version detection macro

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.cpp
Tutorials/GPU/CNS/Source/CNS_K.H

commit 3eb2f4b5b3880456a29510b1b156a4c0fcf6b5ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 2 08:26:13 2019 -0800

    use amrex::ParallelFor

Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/CNS_derive.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp

commit 526f31eefa29f4d8b7da017216ebb9f26804e8bd
Merge: 72f542c13 d1bee05cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 2 01:34:40 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 72f542c139ba5dfa3b1b2878f63d3a68eb381885
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 2 00:32:29 2019 -0500

    avoid using relaxed constexpr for nvcc 9.2 to get around its bug

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.cpp
Tools/GNUMake/comps/nvcc.mak
Tutorials/GPU/CNS/Source/CNS_K.H

commit d1bee05cc5dc22572123d0f374ba4be4b8d8ef81
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 1 19:58:26 2019 -0500

    std::cout -> amrex::Print()

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp

commit b575c698b306edd71a0f913cf228a407b050b849
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 1 19:54:54 2019 -0500

    add device function for checking a pair of particles

Tests/Particles/GPUNeighborList/MDParticleContainer.cpp
Tests/Particles/GPUNeighborList/Make.package
Tests/Particles/GPUNeighborList/md_K.H

commit 9313e3c985be47f719f2f5ca203b47639f79e78a
Merge: aefa439c7 ae1893aed
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 1 19:40:49 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit aefa439c75fa30665ec15e086dd7529c25d8bfee
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 1 19:40:30 2019 -0500

    Test for building neighbor list data structure using CUDA/Thrust for Nvidia GPUs

Tests/Particles/GPUNeighborList/Constants.H
Tests/Particles/GPUNeighborList/GNUmakefile
Tests/Particles/GPUNeighborList/MDParticleContainer.H
Tests/Particles/GPUNeighborList/MDParticleContainer.cpp
Tests/Particles/GPUNeighborList/Make.package
Tests/Particles/GPUNeighborList/inputs
Tests/Particles/GPUNeighborList/main.cpp

commit ae1893aed49e7c734cbb596a756ab1af15dc0391
Merge: 0c9d4855f 85b719bb3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 16:13:09 2019 -0800

    Merge branch 'weiqun/gpu' into development

commit 85b719bb35554a6eb2ab11c5bea2b25fb38cadaa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 16:11:32 2019 -0800

    change the default back to managed

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaAsyncFabImpl.H
Src/Base/AMReX_CudaAsyncFabImpl.cpp
Tools/GNUMake/Make.defs
Tools/GNUMake/sites/Make.olcf

commit e62cdd9827b835b3f8eb3d3944492c7268838184
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Fri Feb 1 18:13:15 2019 -0500

    Added OpenACC + OpenMP versions to HeatEquation_EX1_C and reorganize the tutorial directory.

Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/myfunc.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/mykernel.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/run.ascent
Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/run.nocuda.script
Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/run.summit
Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/run.summitdev
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc_F.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/mykernel.F90
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/run.summitdev
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc_F.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/mykernel.F90
Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/run.summitdev
Tutorials/GPU/HeatEquation_EX1_C/Make.HEAT
Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit 341cca3c724102193d9d22aa0490fb95237ed5a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 15:04:42 2019 -0800

    pinned version of AsyncFabImpl

Src/Base/AMReX_CudaAsyncFabImpl.H
Src/Base/AMReX_CudaAsyncFabImpl.cpp

commit d58b06e9e368eac2af3685e80f99745afcd68953
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Feb 1 14:11:22 2019 -0800

    Add zenodo badge

README.md

commit 5ab9242b5603f738790cab1d78b411ed17ee3f54
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Fri Feb 1 17:00:20 2019 -0500

    add breathe to .travis.yml file

.travis.yml

commit a077ca49290353cdba0a7ca813ad35b7cb5a4b2e
Merge: 6a4f5292e 0c9d4855f
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Fri Feb 1 16:56:05 2019 -0500

    fixed merge conflicts

commit 6a4f5292eb587b133784dd784a3f4b04f037298e
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Fri Feb 1 16:48:16 2019 -0500

    cleaned up some errors

Src/Amr/AMReX_Derive.H
Src/Amr/AMReX_Extrapolater.H
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateDescriptor.H
Src/AmrCore/AMReX_ErrorList.H
Src/AmrCore/AMReX_FluxReg_1D_C.H
Src/AmrCore/AMReX_FluxReg_2D_C.H
Src/AmrCore/AMReX_FluxReg_3D_C.H
Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_TagBox.H
Src/Base/AMReX_BCRec.H
Src/Base/AMReX_NFiles.H
Src/Base/AMReX_ParmParse.H
Src/Base/AMReX_parstream.H
Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_Mask.H
Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_Tagging.F90
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/Particle/AMReX_Particle.H

commit 04caac76676bb97a4731b4e002824abce0318174
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 13:15:02 2019 -0800

    switch to use pinned memory for fab be default

Src/Base/AMReX_BaseFab.H
Tools/GNUMake/Make.defs

commit 0c9d4855f383cb317d81c3b01a680841815bbe78
Merge: f17a237dc 4568621fa
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 1 13:12:24 2019 -0800

    Merge pull request #402 from MaxThevenet/splitting
    
    Add stuff for splitting

commit 4568621fa4bfcc07bf8f1c2afd3b125630737891
Author: MaxThevenet <mthevenet@lbl.gov>
Date:   Fri Feb 1 12:59:58 2019 -0800

    typo

Src/Particle/AMReX_Particle.H

commit b83fdf81750f8cc63b7a707c593a881160861f1b
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Fri Feb 1 15:43:50 2019 -0500

    doxygenised fortran files already containing documentation

Docs/sphinx_documentation/make_api.py
Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90
Src/Base/AMReX_io_mod.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90
Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_LO_UTIL.F90
Src/EB/AMReX_EB_Tagging.F90
Src/EB/AMReX_EB_geometry.F90
Src/EB/AMReX_EB_levelset_F.F90
Src/Extern/CVODE/cvode_interface.f90
Src/Extern/CVODE/fnvector_serial.f90
Src/Extern/CVODE/integrator_stats.f90
Src/Extern/CVODE/sundials_fdlsmat.f90
Src/Extern/Conduit/AMReX_Conduit_Blueprint.H
Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F90
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F90

commit 0e67e5d50a8f5295b46230ad013bfcdffc829521
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Feb 1 13:20:22 2019 -0700

    fixed error causing crse level to fail to converge

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit fc016c468636f68e9f5e71556b59766b8739b985
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Fri Feb 1 14:41:47 2019 -0500

    run on all header files (which already had some documentation)

Docs/Doxygen/doxygen.conf
Docs/sphinx_documentation/add_doxy_headers.py
Docs/sphinx_documentation/make_api.py
Src/Extern/amrdata/AMReX_DataServices.H
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/SDC/AMReX_SDCstruct.H

commit f17a237dc439eb89b11a642ba977eb5ad979a7d7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 1 11:34:06 2019 -0800

    Fix name of file in CMakeLists.txt

Src/Boundary/CMakeLists.txt

commit 1ab0d654104701f6443482415266e33d494eeb3c
Merge: 314e72eb9 81776d1c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 14:16:09 2019 -0500

    Merge branch 'development' into weiqun/gpu

commit 81776d1c6212c0265201bd8b2d0031c9e8d112c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 14:15:44 2019 -0500

    add -lmpi_ibm for summit

Tools/GNUMake/sites/Make.olcf

commit 314e72eb967c151183832a3454c841578d78c610
Merge: a50797f28 9ce73ae00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 13:52:48 2019 -0500

    Merge branch 'development' into weiqun/summit-comm

commit 9ce73ae00d19d1040c29f5d11cc117f96d977abc
Merge: 21aeb7306 0bb9b0cb7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 10:50:48 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 0bb9b0cb7cc8dceabfa5d7562c7034ffdb21d68e
Merge: e1d7a772f 4aa027096
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 1 13:49:19 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit e1d7a772f3b3a0d084b61ddb1f841a4af681ccb8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Feb 1 13:49:02 2019 -0500

    remove redundant code

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp

commit 21aeb730680f5062942e8e63acebdb66ef8fe229
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 10:46:48 2019 -0800

    use isGpuPtr instead of isHostPtr to allow BaseFab in pinned memory; some updates due to Array4 changes

Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_Interpolater.cpp
Src/Boundary/AMReX_InterpBndryData_1D_K.H
Src/Boundary/AMReX_InterpBndryData_2D_K.H
Src/Boundary/AMReX_InterpBndryData_3D_K.H
Src/Boundary/AMReX_MultiMask.H
Src/Boundary/AMReX_YAFluxRegister_1D_K.H
Src/Boundary/AMReX_YAFluxRegister_2D_K.H
Src/Boundary/AMReX_YAFluxRegister_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H
Tutorials/GPU/CNS/Source/CNS_bcfill.cpp

commit 5cd1a2bbfc1f6f45e615790a67c4d6e9f11d4a55
Merge: 4aa027096 286fcccd0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 10:01:09 2019 -0800

    Merge branch 'weiqun/gpu' into development

commit 4aa027096c1e07def93aeb94d159104deeda31ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 09:38:07 2019 -0800

    fix the one that is supposed to use macro

Tutorials/GPU/Launch/main.cpp

commit 29bd4e3794f36d996b989eede0d26806178ae623
Merge: a0b46cb7b d2fe706ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 09:23:01 2019 -0800

    Merge branch 'weiqun/launch' into development

commit a0b46cb7b1e6ba5447b0098fae184c24cf9ce550
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 09:00:51 2019 -0800

    update CHANGES

CHANGES

commit 4fe38fc86f5747f3b8a8347a4161d7bfe4027483
Merge: d56f96626 d20258863
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 1 08:52:14 2019 -0800

    Merge branch 'development'

commit 373f712f3d711a21c49d19bc2fa48565913a8a88
Author: MaxThevenet <mthevenet@lbl.gov>
Date:   Fri Feb 1 08:22:35 2019 -0800

    special id for splitting

Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_Particles.H

commit d20258863d3a84206404374054ce688d4e65bb3d
Merge: f08be5f7d 209018d16
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 31 17:53:54 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit f08be5f7d0fea8ea00d061e040294c6b30efba2a
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 31 17:53:49 2019 -0800

    fix spelling

Docs/sphinx_documentation/source/EB.rst

commit 209018d16ca6c154178aaade1f131f1cf311ddca
Merge: 187aacf17 77fc34b74
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jan 31 20:17:40 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 187aacf17bfe1cd33adb46993a15b9064c624077
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jan 31 20:17:20 2019 -0500

    use pinned memory for send / rcv buffers in Redistribute

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit d2fe706ba3807662b48fc488e8442d2507472db7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 31 16:29:14 2019 -0800

    change the const behavior of Array4

Src/Base/AMReX_Array.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_COORDSYS_1D_C.H
Src/Base/AMReX_COORDSYS_2D_C.H
Src/Base/AMReX_CudaAsyncFab.H
Src/Base/AMReX_CudaAsyncFab.cpp
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_FabArray.H
Src/Boundary/AMReX_FabSet.H
Tutorials/GPU/CNS/Exec/RT/cns_prob.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/CNS_tagging.H
Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Source/mykernel.H
Tutorials/GPU/Launch/main.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H

commit 77fc34b74888ca2073c98d83e9b7a41b1f96ca48
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 31 15:26:43 2019 -0800

    thiis kind of manual buffering is not necessary

Docs/sphinx_documentation/source/EB.rst
Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp

commit 3661157516ca5d3135da68df0069ff4094d3d4bd
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Thu Jan 31 17:41:55 2019 -0500

    Ran on Particles folder

Src/Particle/AMReX_LoadBalanceKD.H
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParGDB.H
Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_Particles.H

commit 101107640b2fe871ca058b426f47c60f4ef9e64b
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Thu Jan 31 17:29:27 2019 -0500

    ran on EB folder

Src/EB/AMReX_EB2_IF_Box.H
Src/EB/AMReX_EB2_IF_Cylinder.H
Src/EB/AMReX_EB2_IF_Ellipsoid.H
Src/EB/AMReX_EB2_IF_Polynomial.H
Src/EB/AMReX_EB2_IF_Spline.H
Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBFluxRegister.H
Src/EB/AMReX_EBSupport.H
Src/EB/AMReX_EB_LSCore.H
Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.H

commit 5e119782589a717649352170657fe9c986cbb035
Merge: 9158daec4 b955ea575
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 31 14:25:48 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 9158daec4f0d3c948718c6f3e14e2113e4f5b7e9
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 31 14:25:44 2019 -0800

    move volfrac tagging out of levelset core

Src/EB/AMReX_EBAmrUtil.H
Src/EB/AMReX_EBAmrUtil.cpp
Src/EB/AMReX_EBAmrUtil_F.H
Src/EB/AMReX_EBAmrUtil_nd.F90
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_Tagging.F90

commit 9ddd05f166fdd7e44bbecab6f5783bae77734ec0
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Thu Jan 31 17:15:40 2019 -0500

    ran on Boundary folder

Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BoundCond.H
Src/Boundary/AMReX_FabSet.H
Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_MacBndry.H
Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_YAFluxRegister.H
Src/EB/AMReX_distFcnElement.H

commit 8e6b7191dc1f9e5902c939987aa7ecda5b626465
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Thu Jan 31 16:58:05 2019 -0500

    ran on Base folder

Src/Base/AMReX_BLBackTrace.H
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseUmap.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxDomain.H
Src/Base/AMReX_BoxIterator.H
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CudaContainers.H
Src/Base/AMReX_CudaRange.H
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabConv.H
Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_LayoutData.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_Machine.H
Src/Base/AMReX_MemPool.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_NFiles.H
Src/Base/AMReX_Orientation.H
Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParmParse.H
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealVect.H
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_parstream.H

commit 10ad1891c6a8a6a2eca7686b62addc56600c88f3
Merge: a286d89e3 b955ea575
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 31 16:47:32 2019 -0500

    Merge branch 'development' into weiqun/launch

commit b955ea57538ad82f404690bd13ce98345e2cabb5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jan 31 16:27:41 2019 -0500

    use the same cuda aware mpi flag as the mesh data

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit a50797f28a1be09521828b8057244887cd0f5727
Merge: 3e6f43c81 4e19a67da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 31 16:18:55 2019 -0500

    Merge branch 'development' into weiqun/summit-comm
    
    Conflicts:
            Src/Base/AMReX_FabArrayBase.H

commit 4e19a67da2919f3499f5de503a12f3c63132cf1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 31 13:13:37 2019 -0800

    disabel cuda aware mpi by default

Src/Base/AMReX_ParallelDescriptor.cpp

commit 98a73b60478287ccc0b81039caf2c3124195cbb3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 31 15:59:48 2019 -0500

    Cuda --> Gpu

Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit 6397e9088c0e2769419312fb2451dc8ab5abae10
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 31 15:54:29 2019 -0500

    use pinned memory when amrex.use_cuda_aware_mpi is false

Src/Base/AMReX.cpp
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit d926ebd23ca6e925e094a72ba67c0f05cb6a5c47
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Thu Jan 31 15:43:32 2019 -0500

    ran on AmrCore folder

Docs/sphinx_documentation/add_doxy_headers.py
Docs/sphinx_documentation/make_api.py
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_Cluster.H
Src/AmrCore/AMReX_ErrorList.H
Src/AmrCore/AMReX_FluxReg_1D_C.H
Src/AmrCore/AMReX_FluxReg_2D_C.H
Src/AmrCore/AMReX_FluxReg_3D_C.H
Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_TagBox.H

commit 8715c9a730178b81800d1e375eab52aed63ae3ad
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Thu Jan 31 15:05:06 2019 -0500

    run script on Amr folder

Docs/sphinx_documentation/add_doxy_headers.py
Docs/sphinx_documentation/source/conf.py
Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_AuxBoundaryData.H
Src/Amr/AMReX_Derive.H
Src/Amr/AMReX_LevelBld.H
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateDescriptor.H
Src/Base/AMReX_FPC.cpp
Src/Base/AMReX_RealVect.H

commit 3e6f43c818537c09ac2e17fbe35ccf1413ec4d71
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 31 12:40:02 2019 -0500

    clean up unused features in fabarray communications

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Tests/FillBoundaryComparison/main.cpp

commit f69ca1ec87ebcebf0f0dbcb492a860121d4805a3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jan 30 23:35:59 2019 -0500

    add tupleAdd functor

Src/Particle/AMReX_Functors.H
Src/Particle/AMReX_ParticleContainerI.H

commit da0afe5922ad8aea53cd53021ff869db0fe11345
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jan 30 23:21:32 2019 -0500

    fix non-CUDA compilation

Src/Particle/AMReX_ParticleContainerI.H

commit ea9af061b8658aea06d2d192987987a6f08b0a54
Merge: d029f97ca 304b9670c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jan 30 22:19:01 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d029f97cac97e546421f2cd79323f9ac36938d05
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jan 30 22:13:53 2019 -0500

    implement option for non cuda-aware mpi

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 0b649b636b235e36511cf57d38b04dc9e3995f81
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jan 30 21:04:00 2019 -0500

    CMake: replace function to evaluate genex

Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Utils.cmake

commit 4e94951c1ddee644edb76f6bb4a58ccf9fd58f0e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jan 30 19:38:23 2019 -0500

    remove some misleading timers from GPU routines.

Src/Particle/AMReX_ParticleContainerI.H

commit 164ba7b59869512ff58ea1ae3bdacde3359c53e9
Merge: f5215e6fb 304b9670c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jan 30 17:53:09 2019 -0500

    Merge branch 'development' into mr/cmake

commit 62c8bea88711c7b4a90400b3050ab043d6040f69
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jan 30 17:32:08 2019 -0500

    some more async copy

Src/Particle/AMReX_ParticleContainerI.H

commit a286d89e38a14da78a633e717180e7d4bd2519db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 30 13:32:47 2019 -0800

    use auto; add profilers in launch tutorial

Src/Base/AMReX_Array.H
Src/Base/AMReX_CudaLaunch.H
Tutorials/GPU/Launch/MyKernel_F.H
Tutorials/GPU/Launch/main.cpp

commit 5ca4475bffde515ae75b1ac5c86e7908ba68543d
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Wed Jan 30 16:25:35 2019 -0500

    Fixed indentation of comments for add_doxy_headers so it now works almost correctly for Amr/AMReX_Derive.H

Docs/sphinx_documentation/add_doxy_headers.py

commit f6f4ee339c1f2fc80dd13515658e5c2db81f8c0e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jan 30 16:25:27 2019 -0500

    use some Async mem copies

Src/Particle/AMReX_ParticleContainerI.H

commit 3248bf350d2906cfc9f9d97bb78db4c13dc683bf
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Wed Jan 30 15:09:40 2019 -0500

    make_api.py is now recursive so will work if directories have subdirectories

Docs/sphinx_documentation/Makefile
Docs/sphinx_documentation/make_api.py

commit 304b9670c8b1c19463682a24812a57331500725e
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jan 30 14:24:22 2019 -0500

    Bug fix.

Tests/GPU/buildHybrid/GNUmakefile

commit 55095657e6c512721fb277eec583d7edc13756d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 30 11:17:02 2019 -0800

    add force inline

Src/Base/AMReX_CudaLaunch.H

commit 9bace973999f196d45c0d3a811a68aa016495157
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Jan 30 13:53:35 2019 -0500

    first attempt at a less thrust-intensive redistribute

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit f5215e6fb1f861dbc8d999d5e0365b92d4edfd76
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jan 30 13:03:11 2019 -0500

    CMake: move handling of SENSEI lib to config function

Src/Extern/SENSEI/CMakeLists.txt
Tools/CMake/AMReX_Config.cmake

commit 7d6750121790327e02783d831552ee872dc86c1f
Author: Alice Harpole <aliceharpole@gmail.com>
Date:   Wed Jan 30 12:14:39 2019 -0500

    Added doxygen and breathe to docs build to autogenerate the API

Docs/Doxygen/doxygen.conf
Docs/sphinx_documentation/Makefile
Docs/sphinx_documentation/make_api.py
Docs/sphinx_documentation/source/conf.py
Docs/sphinx_documentation/source/index.rst

commit 19b92da13d28436c058dfc9baf6ef14c1784a712
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 29 21:15:35 2019 -0800

    use rvalue in launch_host

Src/Base/AMReX_CudaLaunch.H

commit ca284b7d818fe9567ace743dc4199b75bfdfdd21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 29 20:49:16 2019 -0800

    use rvalue reference for lambda parameter for cpu version

Src/Base/AMReX_CudaLaunch.H
Tutorials/GPU/Launch/main.cpp

commit 7a7383a91341e9681d0c5fb0829ccaabc5d36d1e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 29 19:56:12 2019 -0800

    add amrex::launch, amrex::ParallelFor and amrex:For functions

Src/Base/AMReX_CudaLaunch.H
Tutorials/GPU/Launch/main.cpp

commit 82eb4d05fae4345a7d2a83bf30d62315de448e00
Merge: f5e0632a6 9c16d851e
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Jan 29 17:59:46 2019 -0700

    Merge branch 'nodeghostcells' of github.com:AMReX-Codes/amrex into nodeghostcells

commit f5e0632a6d76105d251aebffa5d1a8a3ae5a1a15
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Jan 29 17:59:21 2019 -0700

    wip - implementing update of ghost cells

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 9a058294e0d3734caf76d6e948f8e624d0acf2ec
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jan 29 19:08:24 2019 -0500

    remove empty entries from m_not_ours before calling RedistributeMPIGPU

Src/Particle/AMReX_ParticleContainerI.H

commit 286fcccd0d0b81285311d3cf02021185c4d0b389
Merge: e488e5777 285a4f5fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 29 15:40:23 2019 -0800

    Merge branch 'development' into weiqun/gpu

commit 816ef26cd916afdcabbbad1d7a7987ddd7e81841
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jan 29 18:19:22 2019 -0500

    CMake: refactor how compile definitions are handled.

Src/CMakeLists.txt
Src/EB/CMakeLists.txt
Src/Extern/ProfParser/CMakeLists.txt
Src/Extern/SENSEI/CMakeLists.txt
Src/F_Interfaces/CMakeLists.txt
Src/Particle/CMakeLists.txt
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_ThirdPartyProfilers.cmake
Tools/CMake/AMReX_Utils.cmake

commit e488e5777f3a8d8c37d2c2c69c09a7a3f6b1da9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 29 14:18:45 2019 -0800

    2D InterpBndryData: make it the same as Fortran

Src/Boundary/AMReX_InterpBndryData_2D_K.H
Src/Boundary/AMReX_LOUtil_K.H
Src/Boundary/CMakeLists.txt
Src/Boundary/Make.package

commit 285a4f5fd09cf2ab2642beea7752a90669dc4ecc
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jan 29 16:11:15 2019 -0500

    AMReX independent CUDA build tests: one using only C++ with lots of compiler options, one with hybrid Fortran & C++ that focuses on pgfortran, as done in AMReX.

Tests/GPU/buildHybrid/GNUmakefile
Tests/GPU/buildHybrid/MyKernel.H
Tests/GPU/buildHybrid/MyKernel.cpp
Tests/GPU/buildHybrid/MyKernelB.H
Tests/GPU/buildHybrid/MyKernelB.cpp
Tests/GPU/buildHybrid/MyKernel_F.F90
Tests/GPU/buildHybrid/MyKernel_F.H
Tests/GPU/buildHybrid/Readme
Tests/GPU/buildHybrid/main.cpp
Tests/GPU/buildHybrid/run.script
Tests/GPU/buildTest/GNUmakefile
Tests/GPU/buildTest/MyKernel.H
Tests/GPU/buildTest/MyKernel.cpp
Tests/GPU/buildTest/MyKernelB.H
Tests/GPU/buildTest/MyKernelB.cpp
Tests/GPU/buildTest/Readme
Tests/GPU/buildTest/main.cpp
Tests/GPU/buildTest/run.script

commit 47ab93461b0a3ba4ddeecf4a10d9bbf04638e538
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 29 12:59:15 2019 -0800

    InterpBndryData: fix a sign

Src/Boundary/AMReX_InterpBndryData_3D_K.H

commit 8cc4eeaa77e793b9491e640994a7fd5fe8cf1859
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 29 11:22:59 2019 -0800

    add a private pure virtual function for doing custom behavior after a particle is location is Redistribute(). Will be used in WarpX to do particle splitting /merging.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 6bca97c7d01147d1725a2193656d84ad5a0cfc6c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 29 11:12:23 2019 -0800

    InterpBndryData: fix bugs

Src/Boundary/AMReX_InterpBndryData_2D_K.H
Src/Boundary/AMReX_InterpBndryData_3D_K.H

commit d611427af9f0b0d694a11b12d5855dd9779ce7c9
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jan 29 13:52:48 2019 -0500

    CMake: more changes to support CUDA.
    
    * Add architecture detection
    * Split compiler flags over multiple files based on the compiler ID
    * Start adding GPU tests.
    
    WARNING: this commit still has a linking problem when CUDA is enabled.

CMakeLists.txt
Src/CMakeLists.txt
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_Utils.cmake
Tools/CMake/comps/AMReX_Cray.cmake
Tools/CMake/comps/AMReX_GNU.cmake
Tools/CMake/comps/AMReX_Intel.cmake
Tools/CMake/comps/AMReX_NVIDIA.cmake
Tools/CMake/comps/AMReX_PGI.cmake
Tools/CMake/select_gpu_arch.cmake
Tutorials/GPU/Advection_AmrCore/CMakeLists.txt
Tutorials/GPU/Launch/CMakeLists.txt

commit 821a673c765f05ced92c00065d8b789186b45f63
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jan 29 10:36:31 2019 -0800

    cleanup

Src/EB/AMReX_EB_LSCoreI.H

commit 3e0e9ab0feb463c3fa50ffa69ac10c34d6a49d4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 29 09:32:13 2019 -0800

    InterpBndryData: pass component index to kernels

Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_InterpBndryData_1D_K.H
Src/Boundary/AMReX_InterpBndryData_2D_K.H
Src/Boundary/AMReX_InterpBndryData_3D_K.H
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/Boundary/AMReX_YAFluxRegister_1D_K.H
Src/Boundary/AMReX_YAFluxRegister_2D_K.H
Src/Boundary/AMReX_YAFluxRegister_3D_K.H

commit 78d77f010b8975e88b0af96b5bb1bd93faa581bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 29 09:11:19 2019 -0800

    using Cuda::AsyncFab and CudaAsyncArray in amrex namespace

Docs/sphinx_documentation/source/GPU.rst
Src/Amr/AMReX_StateData.cpp
Src/AmrCore/AMReX_Interpolater.cpp
Src/Base/AMReX_CudaAsyncArray.H
Src/Base/AMReX_CudaAsyncFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_PhysBCFunct.H
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp

commit d29b926fb1632a827f8e10cec0dbf08640eb4057
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 29 09:02:01 2019 -0800

    operator<< for printing bounds of Array4

Src/Base/AMReX_Array.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp

commit 6c28e5422cfb714aa24e4fa1ba90e37690b55056
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 28 21:04:30 2019 -0800

    fix another bug in new InterpBndryData: refine is not always 2

Src/Boundary/AMReX_InterpBndryData_1D_K.H
Src/Boundary/AMReX_InterpBndryData_2D_K.H
Src/Boundary/AMReX_InterpBndryData_3D_K.H

commit b623c67cfc9641ab786f4bc1a49ad5eb037514a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 28 18:53:53 2019 -0800

    fix bug in new InterpBndryData

Src/Boundary/AMReX_InterpBndryData.cpp

commit 562a42162d69491e3a455d017f886c68b6bcf8b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 28 18:42:23 2019 -0800

    minor optimization by avoiding BoxArray's virtual function

Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_MultiMask.cpp
Src/Boundary/AMReX_YAFluxRegister.cpp

commit 90c5ee623c5bbdb8fdb3c87c65f7d67696631514
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 28 16:59:04 2019 -0800

    InterpBndryData on gpu

Src/Boundary/AMReX_BndryData.H
Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_F.H
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_InterpBndryData_1D_K.H
Src/Boundary/AMReX_InterpBndryData_2D_K.H
Src/Boundary/AMReX_InterpBndryData_3D_K.H
Src/Boundary/AMReX_InterpBndryData_K.H
Src/Boundary/AMReX_MacBndry.cpp
Src/Boundary/AMReX_MultiMask.H
Src/Boundary/CMakeLists.txt
Src/Boundary/Make.package

commit cab50940531deb87a4ec589cd6526465cd96ac61
Merge: 3521ea7b8 2b5dfff38
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jan 28 13:21:56 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 3521ea7b88ecabc1a3627713ad6602a766fc4b23
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jan 28 13:21:53 2019 -0800

    finish documenting levelset

Docs/sphinx_documentation/source/EB.rst

commit 2b5dfff38607136014c3551da1ac1af1ec0d2eb8
Merge: 5352cf9fb 8b48487ce
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 28 10:50:07 2019 -0800

    Merge pull request #401 from ylunalin/new_particle_tutorials
    
    Add OpenMP offloading directory in EMPIC.

commit a4b47d10dad55e7e042a460c2045d468c530c824
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 28 10:29:16 2019 -0800

    hopefully make omp and cuda more compatible in MFIter

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 1c1dd7a1d2e339f806acbd3daab43e1db8022966
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 27 17:43:40 2019 -0800

    YAFluxRegister: fix tiling bug

Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_YAFluxRegister.cpp

commit cd9ce18d51074c5110e471350c89e34d6aa73850
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 27 15:38:21 2019 -0800

    fix index bug in YAFluxRegister gpu kernel

Src/Boundary/AMReX_YAFluxRegister_1D_K.H
Src/Boundary/AMReX_YAFluxRegister_2D_K.H
Src/Boundary/AMReX_YAFluxRegister_3D_K.H

commit 4dc97ed6f51cab712a26426ee9b01cdb1c69fd59
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 27 13:31:24 2019 -0800

    finish YAFluxRegister on gpu

Src/Boundary/AMReX_YAFluxRegister.H
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/Boundary/AMReX_YAFluxRegister_1D_K.H
Src/Boundary/AMReX_YAFluxRegister_1d.F90
Src/Boundary/AMReX_YAFluxRegister_2D_K.H
Src/Boundary/AMReX_YAFluxRegister_2d.F90
Src/Boundary/AMReX_YAFluxRegister_3D_K.H
Src/Boundary/AMReX_YAFluxRegister_3d.F90
Src/Boundary/AMReX_YAFluxRegister_F.H
Src/Boundary/AMReX_YAFluxRegister_K.H
Src/Boundary/AMReX_YAFluxRegister_nd.F90
Src/Boundary/CMakeLists.txt
Src/Boundary/Make.package
Src/EB/AMReX_EBFluxRegister_nd.F90

commit 5352cf9fb4f9ca8fe8632b5c383e2e0b3672cb1c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jan 26 20:07:02 2019 -0800

    Revert "using async Iters for Nyx first attempt"
    
    This reverts commit db3e728709f2186a302f6558a3a95da848787ce3.

Src/LinearSolvers/MLMG/AMReX_MacProjector.H
Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp

commit 4004daf5c6fc7ee52721b4e0d0e70c49e8aac4f7
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 25 21:37:58 2019 -0800

    added explanation on using fortran level-set modules

Docs/sphinx_documentation/source/EB.rst

commit efc94c2a581cee77547fb9f096646932ef49d8f7
Merge: 1306808cc 79111defe
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 25 20:46:44 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 1306808cc9a6e2c1917beff10bce004115fed730
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 25 20:43:20 2019 -0800

    fix indentation

Docs/sphinx_documentation/source/EB.rst

commit 79111defe50aa6f6ef86eea88e31571efde4818b
Merge: 38d95b0d8 31e2d4a64
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 25 20:42:40 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 31e2d4a643a3bee6a9843ca9c76b377596849a24
Merge: 2cb5366eb ce3bb4a5b
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Jan 25 19:33:30 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2cb5366eb550611c393d056e083e2ca037f26933
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Jan 25 19:33:20 2019 -0800

    remove apps from amrex repo

Src/AmrTask/tutorials/Apps/Nyx_hydro/.gitignore
Src/AmrTask/tutorials/Apps/Nyx_hydro/CITATION
Src/AmrTask/tutorials/Apps/Nyx_hydro/Diagnostics/AmrDerive.cpp
Src/AmrTask/tutorials/Apps/Nyx_hydro/Diagnostics/GNUmakefile
Src/AmrTask/tutorials/Apps/Nyx_hydro/Diagnostics/Make.package
Src/AmrTask/tutorials/Apps/Nyx_hydro/Diagnostics/README
Src/AmrTask/tutorials/Apps/Nyx_hydro/Diagnostics/inputs
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/Figure/128/density_x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/Figure/128/eint_x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/Figure/128/pressure_x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/Figure/128/velocity_x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/Figure/512/density_x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/Figure/512/eint_x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/Figure/512/pressure_x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/Figure/512/velocity_x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/Figure/make_plots.gp
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/GNUmakefile
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/Make.package
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/Nyx_error.cpp
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/Prob_3d.f90
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/Tagging_3d.f90
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/amrvis.defaults
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/analytic/exact.ini.test2
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/analytic/exact.out
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/inputs-test2-x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/inputs-test2-y
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/inputs-test2-z
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/inputs.regtest
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/inputs.restarttest
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/probdata.f90
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/probin-test2-x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/probin-test2-y
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/DoubleRarefaction/probin-test2-z
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sedov/GNUmakefile
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sedov/Make.package
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sedov/Nyx_error.cpp
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sedov/Prob_3d.f90
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sedov/Tagging_3d.f90
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sedov/bc_fill_3d.f90
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sedov/inputs.3d.sph
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sedov/inputs.regtest
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sedov/probdata.f90
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sedov/probin.3d.sph
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Figure/density_x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Figure/density_y
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Figure/density_z
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Figure/eint_x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Figure/eint_y
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Figure/eint_z
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Figure/make_plots.gp
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Figure/pressure_x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Figure/pressure_y
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Figure/pressure_z
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Figure/velocity_x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Figure/velocity_y
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Figure/velocity_z
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/GNUmakefile
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Make.package
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Nyx_error.cpp
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Prob_3d.f90
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/Tagging_3d.f90
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/amrvis.defaults
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/analytic/exact.ini.sod
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/analytic/sod-exact.out
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/inputs-sod-x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/inputs-sod-y
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/inputs-sod-z
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/inputs.regtest
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/probdata.f90
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/probin-sod-x
Src/AmrTask/tutorials/Apps/Nyx_hydro/Exec/HydroTests/Sod/probin-sod-y
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commit ce3bb4a5bcb6f743eed82cf6849a62e76871583d
Merge: 4794806fb db3e72870
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jan 25 21:00:57 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4794806fbd8e3ab25ff4ac274059134d54c77f11
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jan 25 21:00:39 2019 -0500

    use the pooling memory allocator for thrust::gather calls as well

Src/Particle/AMReX_ParticleContainerI.H

commit 189c6d382fb1762d15b2f154e04ffe74aee95fca
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jan 25 20:42:07 2019 -0500

    cache grid_begin and grid_end arrays to avoid reallocation.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 847eb05341236bb2555b0fbd0b17d304d62bcf8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 25 17:24:52 2019 -0800

    YAFluxRegiser: more on gpu

Src/Boundary/AMReX_YAFluxRegister.cpp

commit 38d95b0d879264da3b0bc8f2d19589891baa8f93
Merge: 4ba6a33b1 db3e72870
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 25 17:21:33 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 4ba6a33b1deb448b07116ab67d83619a6b1416c8
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 25 17:21:25 2019 -0800

    update level-set docs

Docs/sphinx_documentation/source/EB.rst

commit 73a5d4163b7961a85b4cf8b96bfd46b3ce68a884
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 25 16:27:19 2019 -0800

    start YAFluxRegister on gpu

Src/Boundary/AMReX_MultiMask.cpp
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/Boundary/AMReX_YAFluxRegister_1D_K.H
Src/Boundary/AMReX_YAFluxRegister_2D_K.H
Src/Boundary/AMReX_YAFluxRegister_3D_K.H
Src/Boundary/AMReX_YAFluxRegister_K.H
Src/Boundary/CMakeLists.txt
Src/Boundary/Make.package

commit db3e728709f2186a302f6558a3a95da848787ce3
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Jan 25 16:20:31 2019 -0800

    using async Iters for Nyx first attempt

Src/AmrTask/tutorials/Apps/Nyx_hydro/.gitignore
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commit 4860a3985660d756144690cacc23a06335bfd889
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 25 15:24:20 2019 -0800

    Mask on gpu

Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_Mask.cpp
Src/Boundary/AMReX_MultiMask.cpp

commit 5076743399442d6ae12514828cae899dafc6bdff
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 25 14:59:57 2019 -0800

    remove unused file

Docs/sphinx_documentation/source/Tutorials_Chapter.rst

commit eb9857654f46c97144d8e1f9330d89463acecb1b
Merge: 49b96b3d8 62952ff0e
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 25 14:55:52 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 49b96b3d8f9642b0749f19894739b95ff9dd74f4
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 25 14:55:48 2019 -0800

    1. add levelset doxygen, 2. clean up eb docs formatting, 3. fix gpu docs code highlighting

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/EB.rst
Docs/sphinx_documentation/source/GPU.rst
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp

commit d56f96626fdbe215901260b0636d89b5388d0497
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 25 14:45:02 2019 -0800

    Last ORCID has been added

.zenodo.json

commit 2397070e13bb49890455c93f71886ffd7dd2ca65
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 25 14:38:17 2019 -0800

    Add one more ORCID

.zenodo.json

commit 62952ff0e75f8fb9383adb01f7efc0dc84233652
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 25 13:05:42 2019 -0800

    add missing grownnodaltilebox

Src/Base/AMReX_MFIter.cpp

commit 9fafa36d9e3303c61b4cb7ccbdc6f6b0c9c801ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 25 12:38:54 2019 -0800

    update FabSet and BndryRegister

Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_FabSet.cpp

commit fbc24aba9f2243d93b7a525f8fa132a070dd3624
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 25 10:34:40 2019 -0800

    fix compiler warning about shadow

Src/Base/AMReX_RealBox.H

commit 8b48487ced78e91e87f06f833082bb7bdf64a9cc
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Fri Jan 25 13:05:15 2019 -0500

    Add OpenMP offloading directory in EMPIC. Moved C++ header files to Source/ to be shared. Got rid of FTOC macro (use name binding), as well as function definition for PushParticlePosition (never used) in OpenACC/.

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/EMParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/inputs
Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/run.summitdev
Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Source/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Source/Make.package

commit 11062d60fd9177d888925da44843d8092c7633a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 16:12:29 2019 -0800

    fix virtual override

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H

commit 1d3c6392029ce7639ae6ab01dd72713a468302b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 16:09:59 2019 -0800

    some fixes

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit b6a0bd3f9a1b1adfa21cdcd74e46be7a72c31a27
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 16:00:50 2019 -0800

    make functions public for cuda

Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H
Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H

commit 207ae1aa7e77c1f09f86725ad36a6e04a770725e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 24 15:24:31 2019 -0800

    Re-add comma that I accidentally deleted

.zenodo.json

commit 23d46f80adb51aa2fb1d1844028ac9e31cd39cbb
Merge: 32243243a 33f404284
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 24 15:21:36 2019 -0800

    Merge branch 'master' of https://www.github.com/amrex-codes/amrex

commit 32243243a0774b3123aabb708f000d7620cc1399
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 24 15:19:53 2019 -0800

    add more data

.zenodo.json

commit 33f40428415b4e52781953c7201b1f522f0f5820
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 15:12:53 2019 -0800

    fix format

.zenodo.json

commit 34ae846e9bedb74a7ff270b20f12d1ad050bf536
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 24 15:06:43 2019 -0800

    Updated with Graves, Williams and more ORCIDs

.zenodo.json

commit e448fdd84de5133d1d12bc579ee10da92949d2d2
Merge: 752bf973e 3abc9b37c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 24 15:06:31 2019 -0800

    Merge branch 'master' of https://www.github.com/amrex-codes/amrex

commit c83302eaa83156ab01dcbbf530e3eab4a17ce220
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 15:01:51 2019 -0800

    mg interp on gpu

Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 752bf973eb33e695d2b6ecee997ec095f49d851d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 24 12:01:01 2019 -0800

    Update with names and ORCID

.zenodo.json

commit 3abc9b37cb83b060caddd3355c3de273ff077216
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 11:26:40 2019 -0800

    add a link to license in README

README.md

commit 859b0a79e25d00a416eabad75127a8b39c8b9750
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 11:26:40 2019 -0800

    add a link to license in README

README.md

commit 0955e4841851357ac38401a8c34572540d8408e7
Merge: 07e3136de 47ede8794
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 11:20:25 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9b4aca9757ac875ac54bc65acc1673caa56a9364
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 11:20:20 2019 -0800

    mg_interp in C++

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H
Src/LinearSolvers/MLMG/AMReX_MG_K.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/Make.package

commit a4573f98fbea7fa6adf9283988082697a393bd0a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 24 11:15:38 2019 -0800

    Update README

README.md

commit 8981cdabdb748c474c166392583f72ab9f97bd0b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 24 11:13:25 2019 -0800

    README.txt --> README.md

README.txt

commit db4668da1bf030036507702297a45fe5c93332a0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 24 11:09:48 2019 -0800

    Update with information about being a "core developer"

README.md

commit 47ede8794259c7de8c5ae35b9c0c115c3249b755
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 24 11:13:25 2019 -0800

    README.txt --> README.md

README.txt

commit c37afca4373963d39d792a25a3d65a6eb992728f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 24 11:09:48 2019 -0800

    Update with information about being a "core developer"

README.md

commit 07e3136de07eeefa629fb8dea5e634c0d9ff5a54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 10:00:37 2019 -0800

    add assertion

Src/Base/AMReX_Array.H

commit 8ac7dc95be9b764394ac58c4f51cc87642c699b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 12:07:10 2019 -0500

    ibm compiler flags and pragma

Src/Base/AMReX_Extension.H
Tools/GNUMake/comps/ibm.mak

commit 82bfae30b1f821ba92c8d872616c01ebc55e196c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 09:30:14 2019 -0800

    add zenodo json

.zenodo.json

commit 17ff5f93cf4411d1cb88e66e252c5bab4091dd81
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jan 23 19:58:16 2019 -0500

    CMake: Fortran interfaces are now disabled by default

Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/CMake/AMReX_Options.cmake

commit 6c2006882368e06e50e8979d1715dfd04be19a81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 23 14:38:15 2019 -0800

    mismatched #if

Src/Base/AMReX_Extension.H

commit fbe137949dab71f5728bee9e65e16132c745e446
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 23 14:36:31 2019 -0800

    comment out omp simd

Src/Base/AMReX_Extension.H

commit 22c15748370d5b8bf46c454b6a1aa56b7aca6338
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 23 14:15:02 2019 -0800

    add AMREX_PARALLEL_FOR_?D

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_GpuLaunch.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/CNS_derive.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/Launch/main.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp

commit c7589644d7dfe0011a8e3abf6dbd3a104685e3eb
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jan 23 13:11:08 2019 -0800

    Docs rewording.

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit c2fd3948a30b3b269be96ad95e1525866c8cf491
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 23 10:46:53 2019 -0800

    fix the Poisson test

Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H

commit 31416813931ed1102866f1fff932dec6a8bcebf2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 23 10:39:37 2019 -0800

    fix bug in ProbHiArray

Src/Base/AMReX_Geometry.H

commit c4efc5569fba1af31a426a1f8afd7105f1d4c268
Merge: 2f19745ea b58f86b4e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jan 22 20:34:04 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b58f86b4e457b72db16fff43417913a96ef8647a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 22 17:03:56 2019 -0800

    some fixes for cuda

Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H
Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H

commit 2f19745ea3b64f046b67464df0fb56f43ead7b53
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jan 22 19:56:42 2019 -0500

    swap data pointers instead of making temporary copies when reordering particles in RedistributeGPU

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 57b1fb4405cc00ea55d919e93575c41f1d772ed8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 22 16:37:40 2019 -0800

    update Tutorials/LinearSolvers/ABecLaplacian_C for gpu

Tutorials/LinearSolvers/ABecLaplacian_C/Make.package
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest_F.H
Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H
Tutorials/LinearSolvers/ABecLaplacian_C/init_prob.F90

commit 8bc605aaecf8f759d34ddcf6e5359a527b226621
Merge: b26c112f7 6510416c5
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jan 22 15:40:56 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit b26c112f7baf03b58a97a0f1855a561b535f112b
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jan 22 15:40:48 2019 -0800

    allow users to specify coarsening level when creating eblevels

Src/EB/AMReX_EB_LSCore.H
Src/EB/AMReX_EB_LSCoreI.H

commit 6510416c5835ee8675649d23cd3100f21817aed0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 22 15:05:46 2019 -0800

    remove numpts from BaseFab.  After dlen and numpts are removed, the size of BaseFab went down from 80 to 56 bytes

Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseUmap.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FabArray.H
Tests/BaseFabTesting/main.cpp
Tests/C_BaseLib/tUMap.cpp

commit 60caa39d6e297fe92a95183dad71944ce0339c50
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 22 14:09:07 2019 -0800

    remove dlen from BaseFab

Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BaseFab.H

commit cf2ab418a49f402570eb1c95e122bbb54f709fba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 22 14:04:29 2019 -0800

    fix some shadows

Src/Base/AMReX_FabArrayCommI.H

commit 5dd4679f54a7bfe5da6aaa0ad0e0f6187dc73ed2
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 20 22:18:23 2019 -0800

    fill boundary not needed

Src/EB/AMReX_EB_levelset.cpp

commit 0d93c4c68435991f4bfd32cbff35088c54750463
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 20 22:05:38 2019 -0800

    added static level-set intersection

Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_levelset_F.F90

commit 07e28e1904336703804abe5f61e1510812d90c04
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 19 11:26:01 2019 -0800

    add a new interface to InterpCrseFineBndryEMfield

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_Interpolater.cpp

commit 3136ee631154630237ee29ff51ef1e3d47e049db
Merge: e7d9d9054 6818acd1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 18 23:05:26 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit e7d9d905477fe503282456ec7965dca75dd52068
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 18 23:05:01 2019 -0500

    pic cuda: optimization and simplification

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H

commit 6818acd1fa8d0c2243dd4b19b4114b166cfa2104
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Jan 18 13:42:59 2019 -0800

    AsyncArray example.

Docs/sphinx_documentation/source/GPU.rst

commit bcb60c4be062e1cf9ea6a9788c119a94ad3b878d
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 18 13:27:25 2019 -0800

    make consistent fucntion signatures

Src/Base/AMReX_MultiFabUtil.H

commit 889320c21d662cd02b78fe7f694472a7470ce05c
Merge: 8840413b3 cf0b4ab87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 18 09:22:41 2019 -0800

    Merge branch 'weiqun/pic_cuda' of github.com:AMReX-Codes/amrex into weiqun/pic_cuda

commit cf0b4ab87692d6c000b3774c2c4e611fb6471c16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 18 12:15:01 2019 -0500

    add RedistributionLocal

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.H

commit e6343dcadd5ed413acd643309c5cca0d9c0d3f6f
Merge: f48fd529f 2840039ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 18 11:59:15 2019 -0500

    Merge branch 'development' into weiqun/pic_cuda

commit 2840039ad2af1f2ad907b4e9e15af2561ec7d2f5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 18 01:38:26 2019 -0800

    call local form of Redistribute in the pic tutorial

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Source/main.cpp

commit 8840413b37c9ff9c8f64dfe787372d4a63217046
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 20:56:46 2019 -0800

    rm Fortran files in the cuda version of empic

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/Source/main.cpp

commit f48fd529f61ffbdbb575dcd92f4ae6d705426aab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 16:58:59 2019 -0800

    forgot a new file

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H

commit 3d4af362e720eb31bfb955376dfcd35c82d5b2b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 16:52:05 2019 -0800

    set cuda stream in particle iterator

Src/Particle/AMReX_Particles.H

commit e8623494feb2227cf81207b67fdecf8a13e03a62
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 16:16:16 2019 -0800

    current deposition on gpu

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp

commit 75a00ef248be27cb4d38af42b256a4cedfe7fa0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 15:37:40 2019 -0800

    push e and b in cuda

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp

commit 16e3c2c1d5fc41fc0beadd7809fb791d320a296e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 15:17:14 2019 -0800

    field gather and momentum push in cuda

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp

commit 0402d2d3db66c0e818a63dae18c4db7f9aefd280
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 15:16:45 2019 -0800

    make functions in Paticle struct host and device

Src/Particle/AMReX_Particle.H

commit 4a1c7e9f3f136f7fac0dbf06f7bfff8b84e2b45d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jan 17 14:44:13 2019 -0800

    CMake: begin adding CUDA support

CMakeLists.txt
Src/CMakeLists.txt
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake

commit 9ffb13852aea5e6b8ba2a73f5c545802dc4cb381
Merge: b31cfadf4 49baf862f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 13:38:08 2019 -0800

    Merge branch 'development' into weiqun/pic_cuda

commit 28d4ae18825395793621f5d9f5334c46edd1b3f7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Jan 17 13:31:09 2019 -0800

    AsyncFab Example.

Docs/sphinx_documentation/source/GPU.rst

commit 49baf862fe129b58c313a51b863accdec2ef761d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 13:06:51 2019 -0800

    simplification

Src/Base/AMReX_MultiFabUtil.H

commit 90d945b5c7d53fb0071c1c9ea87269f228ed639f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 12:38:11 2019 -0800

    EBFArrayBoxFactory cannot be used unless it's inside ifdef AMREX_USE_EB

Src/Base/AMReX_MultiFabUtil.H

commit 6df4f859355d1467cb06a68e657d7ae44bdd7185
Merge: 95627e723 fdb20be70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 15:21:44 2019 -0500

    Merge branch 'weiqun/mpi' into development

commit fdb20be7053c8f3aa64b2301a96db3810a53e126
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 15:20:46 2019 -0500

    get around gcc-4

Src/Base/AMReX_ParallelDescriptor.cpp

commit 95627e7238fc012b5469a9e25a69602628352f33
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 17 12:18:05 2019 -0800

    add helper functions fore regridding

Src/Base/AMReX_MultiFabUtil.H

commit b2cf854bb3821f3d0311830789366289dafb0810
Merge: 2905f466a 1a6daf926
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jan 17 12:09:34 2019 -0800

    Merge branch 'development' into mr/cmake

commit 0a781554559c1d0f7431fa55a88620cc7abd77e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 11:31:28 2019 -0800

    new Mpi_typemap to replace the old implementation using removed MPI constructs

Src/Base/AMReX_ParallelDescriptor.cpp

commit 0a922f158eff7788bab6f9cd41498e7dc44600f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 17 11:20:35 2019 -0800

    missing amrex::

Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H

commit 1a6daf926c4147bec50abcaa62d79f635cb08787
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 16 20:47:23 2019 -0800

    derive variables in AmrLevel and CNS tutorial

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_Derive.H
Tutorials/GPU/CNS/Exec/Sod/inputs
Tutorials/GPU/CNS/Source/CNS_derive.H
Tutorials/GPU/CNS/Source/CNS_derive.cpp
Tutorials/GPU/CNS/Source/CNS_setup.cpp
Tutorials/GPU/CNS/Source/Make.package

commit 29fa904a249822198921bef7358b89dfee7af02b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 16 17:32:33 2019 -0800

    add Fab version of derive function

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_Derive.H
Src/Amr/AMReX_Derive.cpp

commit fb5b7f82a6f25871ea3084f7bada5d1db2184579
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 16 15:42:01 2019 -0800

    add fabPtr to AuxBoundaryData

Src/Amr/AMReX_AuxBoundaryData.H

commit f0f450c2d545d9575b7b952f9ae41de22f777222
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 16 15:20:40 2019 -0800

    add Gpu::notInLaunchRegion()

Src/Amr/AMReX_AmrLevel.cpp

commit 7b0189cb7b73dd608b0b08fb9bb8d516c7e2b6ec
Merge: 19cf22c4f 349b39be1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 16 12:55:13 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 19cf22c4f7dd1191eb916cff54ddb5abb8421fca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 16 12:55:06 2019 -0800

    Revert "Readability adjustment."
    
    This reverts commit 1ff7c6331398fc5eda770f65ab11910fccf7c2c6.

Src/Base/AMReX_ParallelContext.H

commit 36baee528d4ca0adcb353abf0757cc85f52df1e5
Merge: 1dec5e7c5 1ff7c6331
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 16 12:51:46 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 349b39be1cd08a53c00071581a3c12df063921d7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jan 16 12:48:30 2019 -0800

    Edit GPU Tutorials to explicitly cite correct the useable cuda modules on summit and summitdev.

Docs/sphinx_tutorials/source/GPU_Tutorial.rst

commit 1dec5e7c54333679a48fa36d6723734cc89dd994
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 16 12:43:09 2019 -0800

    more on amr gpu

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/Base/AMReX_BaseFab.H
Src/Boundary/AMReX_FabSet.H

commit 1ff7c6331398fc5eda770f65ab11910fccf7c2c6
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jan 16 11:30:11 2019 -0800

    Readability adjustment.

Src/Base/AMReX_ParallelContext.H

commit cdbbb1e4ff8d3d178da864dfe79961caf0b50758
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jan 16 11:29:52 2019 -0800

    Bit more on ParallelContext.

Docs/sphinx_documentation/source/Basics.rst

commit fb33a5e6407cc6cc0abd8c72927dd9f634e53876
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jan 16 11:28:37 2019 -0800

    Edit GPU Tutorials Docs.

Docs/sphinx_tutorials/source/GPU_Tutorial.rst

commit cb35f06d8ae3a8cdd8b674ede5a322bf5b1e9f9e
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jan 16 11:27:35 2019 -0800

    Comment on ParallelContext.

Docs/sphinx_documentation/source/Basics.rst

commit aa6a1fa5fa148d58cd1f6df9f01bf719e6294596
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jan 16 11:15:23 2019 -0800

    typo

Docs/sphinx_documentation/source/Particle.rst

commit fc1e3f13fd72e57b0d26ca8a5da207cc672b727e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 16 13:23:05 2019 -0500

    add ldg function for Array4

Src/Base/AMReX_Array.H
Src/Base/AMReX_CudaUtility.H

commit c8a816b619aa3439b869d3d3e422b5381bb9adfd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 16 11:43:16 2019 -0500

    add restrict the pointer member in Array4 and FabView

Src/Base/AMReX_Array.H
Src/Base/AMReX_BaseFab.H

commit 2905f466a3c716e3901b4dbb09deffe3ee0e83a6
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jan 15 21:12:24 2019 -0800

    CMake: treat Algoim and Blitz as imported interfaces

CMakeLists.txt
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_InstallExternalLibs.cmake

commit fe0eddd1a42004fcd9c1d1abf2a580f3d835397a
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jan 15 18:43:34 2019 -0800

    make static interfaces more portable

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp

commit f5587131003dafef3baceaa58775cc2ca131a45d
Merge: a11b75742 074506b49
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jan 15 17:17:01 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit a11b75742ffb0409e55db357d7bb034da41e4a88
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jan 15 17:16:58 2019 -0800

    expose more LSCore as static functions

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_levelset.H

commit 074506b49d01eed4c231c43dfd1973199f528cd4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 15 16:46:48 2019 -0800

    fix another new bug

Src/Base/AMReX_FabArrayUtility.H

commit 12248ca0894bb41c81851a9816e2f26ccf0dffb9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 15 16:27:12 2019 -0800

    fix a new bug

Src/Base/AMReX_MultiFab.cpp

commit da2f89d84e7dad1d67551d7d21ef3551f3e8d16d
Merge: 53405a9d4 488429efb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 15 15:59:34 2019 -0800

    Merge branch 'weiqun/gpu' into development

commit 53405a9d45a792123c9c515b9d920362f95cc3f7
Merge: 27cc720bd 66649b6ab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 15 15:59:23 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 488429efb62ca3add617728de518d0930e9417f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 15 15:54:18 2019 -0800

    view -> array

Tutorials/GPU/CNS/Source/CNS_K.H

commit 12486464eac455700b834831b171970d7c3096d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 15 14:32:00 2019 -0800

    remove some duplicated codes in MultiFab and iMultiFab

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.cpp

commit 1ae7a566d0ab6f679a5df7dedb3cc1a646ec28dd
Merge: 5e84be4cd 27cc720bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 15 13:14:00 2019 -0800

    Merge branch 'development' into weiqun/gpu

commit 5e84be4cdf01db1556427b30d34a4a3b0e9b4022
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 15 13:13:54 2019 -0800

    update FillBoundary

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit 27cc720bd213ff6f94ed84e4d5e1ac5563b2b0bf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 15 12:26:22 2019 -0800

    update Geometry

Src/Base/AMReX_COORDSYS_1D_C.H
Src/Base/AMReX_COORDSYS_2D_C.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_Geometry.cpp

commit eaae1503f11708d3eaa1b659cd7c36725a1b50e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 15 11:58:37 2019 -0800

    change Array4 so that it can be easily passed to Fortran

Src/Base/AMReX_Array.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H

commit 66649b6abe940bcd7857959431044ca5690324a9
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jan 15 11:11:34 2019 -0800

    Update GPU docs: needs picture change & AsyncFab/AsyncArray examples (w.r.t. new Array4 style)?

Docs/sphinx_documentation/source/GPU.rst

commit 784f8b45098c1d4b85534273c839608f4be81666
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 15 10:34:37 2019 -0800

    add profilers

Tutorials/GPU/Launch/main.cpp

commit 9251a1ead2c8489409a851622739a7c37f1cb2b6
Merge: e420ecc2d 1746f0702
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jan 15 09:45:24 2019 -0800

    Merge branch 'development' into mr/cmake

commit e420ecc2d77f388f3d72a6f1af7e43d3ed81a993
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jan 15 09:32:55 2019 -0800

    CMake: finalize move to CMake 3.11

Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake

commit 1746f0702952ec6fb722a9779d57aa2a6673a576
Merge: d40cb1e8b 16f627fbd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 14 20:09:39 2019 -0800

    Merge branch 'weiqun/gpu' into development

commit f428d6fc2fd1fe6c1e88cf8cc916f1eeb07a228e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jan 14 16:47:09 2019 -0800

    CMake: move to CMake 3.11

CMakeLists.txt
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tutorials/Amr/Advection_F/CMakeLists.txt
Tutorials/Amr/Advection_octree_F/CMakeLists.txt

commit d40cb1e8b6b244171688fc7e402826b957e33bf5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 14 15:57:31 2019 -0800

    fix bug in AMREX_FOR

Src/Base/AMReX_CudaLaunch.H

commit 16f627fbde5bf81f29bd899eab159d4614ef6cd5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 14 15:57:31 2019 -0800

    fix bug in AMREX_FOR

Src/Base/AMReX_CudaLaunch.H

commit 3116021ccfb93de3731241f524ff3ee2ed444dd6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 14 18:28:57 2019 -0500

    use AMREX_FOR in ParallelCopy

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MultiFab.cpp

commit b5a9dea8e03d4a7ac2d56a27e9833c2e4655630d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 14 13:58:12 2019 -0500

    use AMREX_FOR

Src/Base/AMReX_MultiFab.cpp

commit 7e5a55ba86eff616a1ff03af70d508df4801a77f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 14 10:54:04 2019 -0800

    fix template for no BaseFab type

Src/Base/AMReX_FabArray.H

commit 31738fbff948219d3704c4e09fa7ffd1d86761a1
Merge: 5f47b8881 7799e6bc4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 14 10:41:50 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5f47b8881419d17b8544df0477971edb20e11d76
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 14 10:41:42 2019 -0800

    remove the unused buggy code for now

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit 7799e6bc4dca73beba082701d0badd780b5aebb1
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Jan 14 08:47:25 2019 -0800

    Comments on proper use of tilebox and dynamic tiling overview.

Docs/sphinx_documentation/source/Basics.rst

commit ce493a179efefa337043efec26bfb0f45b46c2e6
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Jan 14 08:46:33 2019 -0800

    Note on ~/amrex in GNUMakefile

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit 7296686dc0fafd9e19b2fe9cb1a3c8a67f907196
Merge: 06ccd53db 116129ca9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 14 09:41:20 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 06ccd53db2f591ded35cc650ba1eb02ec32f90c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 14 09:41:12 2019 -0800

    forgot a file

Tutorials/GPU/HeatEquation_EX1_C/Source/mykernel.H

commit 116129ca93a16391bb40ba4c45c79188905b71b4
Author: Tan Nguyen <tannguyen@cs-it-6767056.local>
Date:   Mon Jan 14 11:20:54 2019 -0600

    update known limitations

Docs/sphinx_documentation/source/AsyncIter.rst

commit 87e0bd0aa5ce76f3b554e2b469b2d7ee1af80232
Author: Tan Nguyen <tannguyen@cs-it-6767056.local>
Date:   Mon Jan 14 11:13:41 2019 -0600

    update known limitation

Docs/sphinx_documentation/source/AsyncIter.rst

commit 6bdb52349e27ebd0c37ffabd0dcc80eda1a8f845
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Jan 14 09:08:46 2019 -0800

    add known limitation of the async runtime to the userguide

Docs/sphinx_documentation/source/AsyncIter.rst

commit 6fa0a6a0a1b58257662ae55160634f0e5ef5a099
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 14 06:51:06 2019 -0800

    fix compilation

Src/Base/AMReX_CudaAsyncFabImpl.cpp

commit 41e7728d4287e8958ef490e5879283c6ff02a5ea
Merge: 8a3284459 9f177bbe5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 13 20:51:10 2019 -0800

    Merge branch 'weiqun/for' into development

commit 8a3284459d5edc50654f6eb11963c8087cb3b567
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 13 20:33:48 2019 -0800

    Merge branch 'weiqun/for' into development

Src/Base/AMReX_Array.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaAsyncFab.H
Src/Base/AMReX_CudaAsyncFab.cpp
Src/Base/AMReX_CudaAsyncFabImpl.H
Src/Base/AMReX_CudaAsyncFabImpl.cpp
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_IntVect.H
Tutorials/GPU/CNS/Exec/RT/cns_prob.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/CNS_tagging.H
Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d
Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H
Tutorials/GPU/Launch/MyKernel.H
Tutorials/GPU/Launch/main.cpp

commit 9f177bbe5379c596a3992145c761fc4a5b3a4c58
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 13 20:29:16 2019 -0800

    update GPU heat equation example

Src/Base/AMReX_FArrayBox.H
Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d
Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H

commit 0f121a87c50b568c96312970c459a7383f091739
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 13 14:42:30 2019 -0800

    use AMREX_FOR in CNS tutorial

Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H
Tutorials/GPU/Launch/MyKernel.H

commit df86f0c113e6748691b2317ca9a0169d63e141db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 13 11:24:12 2019 -0800

    simplification of AMREX_FOR and more examples in launch tutorial

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_GpuLaunch.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/Launch/main.cpp

commit bf0c52e83f61ed72c556a683e409ff0dea73c909
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 13 10:17:27 2019 -0800

    expand implicit function filling

Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp

commit 0eb174ebf63e011e9a1c8ec42ce08bc81817955d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 12 22:56:57 2019 -0800

    start using AMREX_FOR in CNS tutorial

Tutorials/GPU/CNS/Exec/RT/cns_prob.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_tagging.H

commit 7172492bc7d3cc94aabc5c236ffc1439169c31e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 12 22:44:37 2019 -0800

    update Launch

Tutorials/GPU/Launch/main.cpp

commit f37659e5be01f1688de8947e089fd48d52130340
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 12 22:44:13 2019 -0800

    reorder BaseFabData structure

Src/Base/AMReX_BaseFab.H

commit 0d6158e1e1cd7189ce3816a93074311703942ae8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 12 22:05:16 2019 -0800

    AMREX_FOR_1D, 3D and 4D

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_GpuLaunch.H

commit c577887e653b4aa801c55ffd92b193f461028a41
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 12 18:31:03 2019 -0800

    add AsyncFab::array and fix const of Array4

Src/Base/AMReX_Array.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaAsyncFab.H
Src/Base/AMReX_CudaAsyncFab.cpp
Src/Base/AMReX_CudaAsyncFabImpl.H
Src/Base/AMReX_CudaAsyncFabImpl.cpp
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_IntVect.H
Tutorials/GPU/Launch/main.cpp

commit be4ad4e6b3b91897bb4fc090f170edbb4cb9c7a5
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 12 17:53:18 2019 -0800

    cleanup

Src/EB/AMReX_EB_LSCoreI.H

commit ca034f75210a435ed4bd79b5548c78378ecd3324
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 12 17:48:16 2019 -0800

    expose ebis level building as a static template class

Src/EB/AMReX_EB_LSCore.H
Src/EB/AMReX_EB_LSCoreI.H

commit 1ac82b4de33988d707ccb76658126655a607dc3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 12 15:11:39 2019 -0800

    AMREX_FOR: a new kernel launch approach

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_GpuLaunch.H
Tutorials/GPU/Launch/main.cpp

commit 48d6dcefd2113537f3ecb50fa9a2169e6255aaa7
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 12 14:46:56 2019 -0800

    fix eb_pad error

Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.cpp
Tutorials/EB/Donut/Exec/inputs

commit 85010e19e632f5150df7cb57a8643ac2eda4b692
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jan 12 13:40:23 2019 -0800

    Fix typo in push_position_boris -- we were using uxp for all directions instead of uxp, uyp, uzp

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90

commit 6837cc7a65ed2989bcbdec34ac580e5a3664ebbd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jan 12 13:38:52 2019 -0800

    Fix typo in push_position_boris code example.

Docs/sphinx_documentation/source/GPU.rst

commit 14eaaba4befca5bdf4fee5dc8ae18db4d430c5c3
Merge: 119d8f6ba 9268abc0e
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 12 12:21:52 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 119d8f6ba7ec0b14f36388c8a3288bcc43044333
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 12 12:21:40 2019 -0800

    add profiling

Src/EB/AMReX_EB_LSCoreBase.cpp

commit 9268abc0ec2b4444c05acb4fc1151debde2ba0ad
Merge: 4fcd10905 9b75dd527
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jan 12 11:51:18 2019 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 4fcd1090557b086b14ac44079777166b193da933
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jan 12 11:51:06 2019 -0800

    Add brackets to fcompare.cpp as well.

Tools/Postprocessing/C_Src/fcompare.cpp

commit 9b75dd527dfb814e939e2a5dab399e5acf930d67
Merge: b5691424e 778731020
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 12 11:49:30 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit b5691424ebfc804f6a64a97600db7d2e8c7a8e0f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 12 11:49:27 2019 -0800

    make sure boxarrays are nodal/cc and ensure this works when DIM!=3

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H

commit 77873102077f01e201fd7174ac9c1d61d5575ee6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jan 12 11:36:32 2019 -0800

    Needed to add brackets between Initialize and Finalize so this doesn't segfault.

Tools/Postprocessing/C_Src/fextract.cpp

commit b31cfadf4e84050a523ce231f512153a87b93486
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 11 22:53:01 2019 -0800

    cuda: check solution and push e field

Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/inputs
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Source/main.cpp

commit 9610f70749ca11fb9b16d9a593d9997ff718eb43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 11 21:32:01 2019 -0800

    fix memory leak in pic tutorial

Tutorials/Particles/ElectromagneticPIC/Make.EMPIC
Tutorials/Particles/ElectromagneticPIC/Source/main.cpp

commit 04f57cbd41bfe9ac4bce7d2420cd1d3aebad3fd3
Merge: adbc9e96b ff13edfb2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 11 19:43:28 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ff13edfb2d6ff0f4c3df0f77aea6883d900a56c7
Merge: d12d5ee8d 4513af878
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 11 16:30:59 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit d12d5ee8d7f923f22a350d0f5aa9724ebb466e2a
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 11 16:30:57 2019 -0800

    expose multi-level filling

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H

commit e9428b5df55002b954921edb1f2da574ba208fa1
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 11 15:23:35 2019 -0800

    static EBSearchBox, needed to expose multi-level filling

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp

commit adbc9e96bfd82386a8fe611a128d38d417aaf9bf
Merge: ed4dc8d60 4513af878
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 11 16:58:22 2019 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ed4dc8d600b3f66349d5c17d5255710516006fbb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 11 16:58:13 2019 -0500

    add nvcc argument -maxrregcount

Tools/GNUMake/comps/nvcc.mak

commit 4513af8782cb901a6bcb7e5e93cfcd5f3462bb98
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jan 11 15:42:40 2019 -0500

    turn off OMP_OFFLOAD by default

Tutorials/GPU/Launch/GNUmakefile

commit 4532950a5c77b7679991e3385c59af86d85894bb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Jan 11 15:42:02 2019 -0500

    restoring the USE_OMP_OFFLOAD option and adding an example to the launch Tutorial

Tools/GNUMake/Make.defs
Tutorials/GPU/Launch/GNUmakefile
Tutorials/GPU/Launch/MyKernel_F.F90
Tutorials/GPU/Launch/MyKernel_F.H
Tutorials/GPU/Launch/main.cpp

commit f02acdce177f3c9fa03b510ffefa7dbe7538e945
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 11 09:22:27 2019 -0800

    exclude initilizations including cuda and openacc that could take a long time from tiny profiler

Src/Base/AMReX.cpp
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_TinyProfiler.cpp

commit 9c16d851e4927f6bb423ec76a277f1c361f172c4
Merge: 1b39670db c7224c8b7
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Jan 11 09:46:32 2019 -0700

    Merge branch 'development' into nodeghostcells

commit c7224c8b7ca8a9e7f3574d3cd39498864702afe5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 10 16:27:53 2019 -0800

    inline some RealBox functions

Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp

commit d96739520a9e049c9a50b106d708521bd0ce866f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 10 16:12:50 2019 -0800

    more constexpr

Src/Base/AMReX_Orientation.H

commit 02482a8ba14b2545b6364b84b50310882ed8d54d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 10 15:44:16 2019 -0800

    make the implementation of print_state template

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_MultiFabUtil.cpp

commit c12ec7afff5421481307deea6d464550ad8d5949
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 10 15:24:16 2019 -0800

    optional ghost cell argument in print_state

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 41da65c5c4909977bec12f587063346b18784d2f
Merge: 1e1898d16 78905bf26
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jan 10 15:43:30 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 1e1898d16b83b9fbf30b9cb37e54095c4544f8fc
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jan 10 15:43:19 2019 -0800

    CMake: completely drop support for F_Baselib

Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Options.cmake

commit 78905bf2629807e1766454a7ae50ed4a4b3bcd17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 10 15:08:13 2019 -0800

    amrex::cast for MultiFab kind types

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit e1ede7dc6dfc5b1ca5ff37f0d5c5b11745b5a693
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 10 14:40:30 2019 -0800

    make some functions constexpr

Src/Base/AMReX_Box.H
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H

commit bf8713d2a348d4f17dd3cb20b3af6e2f8183f978
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 10 13:36:54 2019 -0800

    rm deprecated functions

Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IArrayBox.cpp

commit 61ab029d5ea82a8a20224cfbe7581bd9dea173c4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jan 10 15:05:57 2019 -0800

    CMake: change how the build type is set

Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_InstallExternalLibs.cmake
Tools/CMake/AMReX_Options.cmake

commit 58344d7f338f598c0b5205d4b500f1ca0c72d2db
Merge: 29557b19b d43b14257
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 10 13:43:49 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit d43b1425749931c1b7ed84ff10711850a3358b6c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 10 13:09:09 2019 -0800

    use new BaseFab interface in various places

Src/Base/AMReX_Box.H
Src/Base/AMReX_CudaRange.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp

commit ed4e217d248c54712b276cf789fc477e3078a66d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 10 13:08:20 2019 -0800

    mod gpu launch tutorial to show generic loop launch

Tutorials/GPU/Launch/main.cpp

commit a7596bcd007a13a8314de2311fa14baab13aef6f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 10 09:54:53 2019 -0800

    safeguard some CoordSys functions

Src/AmrCore/AMReX_Interpolater.cpp
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_GpuControl.H

commit 014c616c7066e688ef1a6c2d45353103d96f55de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 10 09:27:34 2019 -0800

    inline setBC function

Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCRec.cpp

commit e042ce4d7ed38a3ac85c0baaacd7cada2e01849f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 10 09:17:53 2019 -0800

    rm deprecated BaseIndex class and changed the interface of BaseFab cast

Src/Base/AMReX_BaseFabUtility.H
Src/Base/AMReX_BaseIndex.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 1a1d7dc8889656cec14742a180b84b3ea9e8ccf8
Merge: 525322786 ceb381c36
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 9 19:28:16 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ceb381c364698ec869d5baaa977b48ba776bd23f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 9 17:37:57 2019 -0800

    Make a link back from Tutorials to Documentation

Docs/sphinx_documentation/source/index.rst
Docs/sphinx_tutorials/source/index.rst

commit 9f8ef5e605b30d23b5b7fbea891411b8bd1ee460
Merge: b1ce16671 48994bfac
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 9 17:33:46 2019 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit b1ce166714e2bb69cb82ef360190dabca5064384
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 9 17:33:03 2019 -0800

    Add link to Tutorials page from the front page.

Docs/sphinx_documentation/source/index.rst

commit 29557b19bd3d586bb59737643ea29a73da800335
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 10 02:17:24 2019 +0100

    exposed level-set and volfrac box tagging

Src/EB/AMReX_EB_F.H
Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp

commit 525322786ee305840e8516f9c9d00dfb1fc8ee02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 9 17:03:57 2019 -0800

    compiles

Src/Base/AMReX_BaseFab.H

commit b63b18806dcb5cfe264300a769ec8b5e234fce6e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 9 16:49:31 2019 -0800

    more on the new interface in BaseFab

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArrayBase.H

commit 48994bfac9c80345c45bd06bee3c85677d283aa5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 9 12:02:14 2019 -0800

    add missing atomic add

Src/Base/AMReX_FabArrayUtility.H

commit c6a245ed23b8d71fb208ef27311980a4e7b5e206
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 9 11:58:27 2019 -0800

    optimization of reuction on summit

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_FabArrayUtility.H

commit ae6d2a04b8901454bed8857e9d51e7788d5cf600
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 9 10:53:05 2019 -0800

    add profilers and minor changes

Src/Base/AMReX_CudaLaunch.H
Tutorials/GPU/CNS/Source/CNS.cpp

commit c822650fa14cd90793c0dc0bcf5ece2b7d3d76cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 9 10:50:34 2019 -0800

    add copyToHost function to AsyncArray

Src/Base/AMReX_CudaAsyncArray.H

commit 0a68a6092d7f19946714ce3a4d2bb5344481844c
Merge: 5e6f40dd5 3a3aa9be1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 9 10:30:26 2019 -0800

    Merge branch 'weiqun/gpu' into development

commit 5e6f40dd5f800a6dbbc1771f4f132b7a5819c6ea
Merge: 1282e9cd9 cc7ae04e8
Author: Guy Moore <gmoore@lbl.gov>
Date:   Tue Jan 8 21:45:09 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 1282e9cd950a36f37c0e200362b0da2144a6e4f4
Author: Guy Moore <gmoore@lbl.gov>
Date:   Tue Jan 8 21:43:58 2019 -0800

    Corrected intersphinx with URL

Docs/sphinx_documentation/source/conf.py
Docs/sphinx_tutorials/source/conf.py

commit cc7ae04e8861b04bc59fc2983bc0e6d8a69d49e4
Merge: 840d13a79 d759360fd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 8 17:41:58 2019 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 840d13a79368c473d43697d55d2d5a9d5f2d2f5b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 8 17:35:25 2019 -0800

    "to be ran" --> "to be run"

Docs/sphinx_documentation/source/GPU.rst

commit d759360fd1a1c99d2bb482083827c55702cbb517
Merge: b005bb320 c41f123dd
Author: Guy Moore <gmoore@lbl.gov>
Date:   Tue Jan 8 17:21:50 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit b005bb32078ab02eb2e9320b7b29edf24c29d498
Author: Guy Moore <gmoore@lbl.gov>
Date:   Tue Jan 8 17:19:30 2019 -0800

    Added intersphinx extension to cross-ref between sphinx_documentation and sphinx_tutorials

Docs/sphinx_documentation/source/SWFFT.rst
Docs/sphinx_documentation/source/Tutorials_Chapter.rst
Docs/sphinx_documentation/source/conf.py
Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst
Docs/sphinx_tutorials/source/conf.py
Docs/sphinx_tutorials/source/index.rst

commit c41f123ddc94e4fec8fca7c0503dac56e5efff82
Merge: 50846e460 2df279092
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jan 8 16:54:01 2019 -0800

    Merge pull request #388 from AMReX-Codes/cy-perf
    
    Bunch of changes to support MLMG performance analysis and tuning

commit 50846e4609a3337e9ad67e35a71816f6a56e1cd5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 8 16:05:31 2019 -0800

    use cuda driver api to avoid cuda-memcheck error

Src/Base/AMReX_CudaUtility.H
Tools/GNUMake/Make.defs

commit ae3c8f4b5da22d33cbc94c15dd1e8d9865560a56
Merge: d707c001a ff09a41b9
Author: Cy Chan <cychan@lbl.gov>
Date:   Tue Jan 8 14:26:21 2019 -0800

    Merge branch 'development' into forkjoin

commit d707c001a49fc536a5f42df64742422ee0b18b22
Author: Cy Chan <cychan@lbl.gov>
Date:   Tue Jan 8 14:14:51 2019 -0800

    simplify ForkJoin interface a bit
      remove ngrow argument from reg_mf()
      number of grow cells in forked MultiFab now matches original MultiFab by default
      can customize after registration via modify_ngrow() function
      add overloads to modify_comp_split() and modify_ngrow() for no index argument

Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp
Tutorials/ForkJoin/MLMG/main.cpp
Tutorials/ForkJoin/Simple/MyTest.cpp

commit ff09a41b921589115bf39a8ba264fc61ef3795d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 8 11:02:07 2019 -0800

    add SafeLaunchGuard and use it in Interpolaters so that they work with old style FillPatch

Src/AmrCore/AMReX_Interpolater.cpp
Src/Base/AMReX_GpuControl.H

commit 5f9c1b5530b4c73f1a881ecf1fe997ba551e4a8f
Merge: 2d189f02d 54d0ed8cd
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Jan 8 02:33:26 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2d189f02d98b68ce44ad52efef71fd1f43836985
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Jan 8 02:33:18 2019 -0800

    fix a bug in the upcxx banckend that could lead to deadlock

Src/Amr/AMReX_Amr.cpp
Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp

commit 54d0ed8cd9839598e139d2361a3e5c3ea8fca6a2
Merge: 97dc2ca6f 3a977f510
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 7 17:36:20 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 97dc2ca6f0e28970560b9e1ecee6b6970fc20e65
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 7 17:36:10 2019 -0800

    only allow this early exit in RedistributeGPU if allPeriodic

Src/Particle/AMReX_ParticleContainerI.H

commit 3a977f5103fe98f57ca5ae641c4959579bba1a42
Merge: 351c9d504 3e819ca91
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jan 8 00:07:58 2019 +0100

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 351c9d504a883054dc0d7f15f7c51e8d68146f87
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jan 8 00:07:33 2019 +0100

    expand level-set documentation

Docs/sphinx_documentation/source/EB.rst

commit 3e819ca91b968389e1150282ae1f0e56a0d7979f
Merge: 90a7039ef c24b44c86
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Jan 7 14:19:15 2019 -0800

    Merge branch 'development' into forkjoin

commit 90a7039ef294d16018bceb0baa2a5808582ebaa9
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Jan 7 14:18:30 2019 -0800

    ForkJoin Tutorial documentation edits and formatting

Docs/sphinx_tutorials/source/AMR_Tutorial.rst
Docs/sphinx_tutorials/source/ForkJoin_Tutorial.rst
Docs/sphinx_tutorials/source/conf.py

commit 63b7c8603bd48042a93dea4bc5f2c0856576b88e
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Jan 7 11:41:43 2019 -0800

    updates to ForkJoin/MLMG tutorial and documentation

Docs/sphinx_tutorials/source/ForkJoin_Tutorial.rst
Docs/sphinx_tutorials/source/figs/fork_join_tasks.png
Docs/sphinx_tutorials/source/figs/mf_remap_hires.png.REMOVED.git-id
Docs/sphinx_tutorials/source/figs/nested_fork_join_tasks.png
Tutorials/ForkJoin/MLMG/inputs
Tutorials/ForkJoin/MLMG/main.cpp

commit c24b44c86dc3d24bd0e95b2efb41afe82aa9cfee
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jan 7 20:09:03 2019 +0100

    expand level-set documentation

Docs/sphinx_documentation/source/EB.rst
Src/EB/AMReX_EB_levelset.H

commit 242bf5b84765f18e60337033d80c614facdf17c7
Merge: 8aa7e758d 40fb2da31
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jan 7 19:16:41 2019 +0100

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8aa7e758de1a1d620f0b708d7f7755cc05297ad3
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jan 7 19:15:50 2019 +0100

    start adding level-set documentation

Docs/sphinx_documentation/source/EB.rst
Docs/sphinx_documentation/source/EB/loc_ls_ex.png

commit 1e9d32267810772919863880c1c141ad9b7bb6ab
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Jan 7 10:04:30 2019 -0800

    working on ForkJoin Tutorial

Docs/sphinx_tutorials/source/ForkJoin_Tutorial.rst
Tutorials/ForkJoin/Simple/MyTest.cpp

commit 40fb2da3149671227ed067e7808d6f2e4e5fb726
Merge: 6b9176dd4 9766347b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 7 08:56:01 2019 -0800

    Merge branch 'weiqun/interp-3' into development

commit 6b9176dd451a4328dcd20ab1b9a86c52ebd95e90
Merge: bbbe2f15c 8bdaa2184
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jan 7 17:16:10 2019 +0100

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit bbbe2f15c660e918ce10ac9bc6d084fcdf4f1225
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jan 7 17:16:04 2019 +0100

    added more profiling

Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp

commit 8bdaa21841e3cf5db422d3b8493e20b4c679dacc
Merge: 799338c03 4617c45d5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 7 06:48:29 2019 -0800

    Merge pull request #395 from khou2020/ncmpi
    
    Add PnetCDF benchmark

commit 4617c45d5b93b713e9b4360282125feb6d4e67f2
Merge: 369b5cfb2 799338c03
Author: Kaiyuan Hou <khou2020@outlook.com>
Date:   Mon Jan 7 06:04:19 2019 -0600

    Merge branch 'development' into ncmpi

commit 369b5cfb2db3150aed9e6e2b8e36837ba3ce1c50
Merge: 5a7aaa21c 03d99cd92
Author: Kaiyuan Hou <khou2020@outlook.com>
Date:   Mon Jan 7 06:03:22 2019 -0600

    Merge branch 'master' into ncmpi

commit 799338c03d58da812d85ea100014b819afc373dd
Merge: e230d2cd3 d8cecb46e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 6 18:47:40 2019 -0800

    Merge branch 'weiqun/interp-2' into development

commit e230d2cd379d9ce7035106f727371b185302c935
Merge: b016bb92d 22d3e2008
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Jan 6 17:31:59 2019 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit b016bb92d988cc40c9b60e948d390d56b8e6fbba
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Jan 6 17:31:32 2019 -0800

    Add non-const access functions for the level set arrays.

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_levelset.H

commit 22d3e200897c8f8a084d5070050923b167b6e1dd
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sun Jan 6 17:25:26 2019 -0800

    a small change in metadata extraction

Src/Amr/AMReX_Amr.cpp

commit beecea767c42c93e7580ff77e1a24b0360c7f32c
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sun Jan 6 14:27:11 2019 -0800

    fix a bug to avoid potential deadlocks

Src/Amr/AMReX_Amr.cpp
Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.H
Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.H

commit 7d4ad2430aaf8e62ea496bf8bc5cfc7dc9f0c96e
Author: Cy Chan <cychan@lbl.gov>
Date:   Sat Jan 5 21:29:26 2019 -0800

    Move existing ForkJoin tutorial to Tutorials/ForkJoin/Simple
      demonstrates various ways of passing MultiFabs into forked tasks
      demonstrates setting task output directory
    Add second ForkJoin tutorial based on modified OldTutorials/MultiColor_C tutorial
      demonstrates reusing and nesting fork-joins
      demonstrates customizing component split across tasks for split MultiFabs

Tutorials/ForkJoin/GNUmakefile
Tutorials/ForkJoin/MLMG/GNUmakefile
Tutorials/ForkJoin/MLMG/Make.package
Tutorials/ForkJoin/MLMG/ff.f90
Tutorials/ForkJoin/MLMG/inputs
Tutorials/ForkJoin/MLMG/main.cpp
Tutorials/ForkJoin/Simple/GNUmakefile
Tutorials/ForkJoin/Simple/Make.package
Tutorials/ForkJoin/Simple/MyTest.H
Tutorials/ForkJoin/Simple/MyTest.cpp
Tutorials/ForkJoin/Simple/MyTest_F.H
Tutorials/ForkJoin/Simple/inputs
Tutorials/ForkJoin/Simple/main.cpp

commit f36e9298107dbd0aaa60c582696e79e6cdce841d
Author: Cy Chan <cychan@lbl.gov>
Date:   Sat Jan 5 12:50:58 2019 -0800

    modifications to ForkJoin:
      task_output_dir set through member function instead of constructor
      defaults to empty string (don't write task output files)
      dir created in fork_join invocation instead of constructor
      append to task output files instead of creating unique filenames
      simplify ComponentBounds()

Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp
Src/Base/AMReX_ParallelContext.H
Tutorials/ForkJoin/MyTest.cpp

commit 3a3aa9be1d5864bc133809d8667dd086fd67e4c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 5 10:50:02 2019 -0800

    rm performCopy because it is no longer used

Src/Base/AMReX_BaseFab.H

commit aee02c254ce241a3b2f8f7148c65e4618be21d43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 5 08:56:09 2019 -0800

    start new BaseFab interface

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H

commit e258be2164cb5006a61b9f74e12a1cc87ee4726a
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 5 15:46:12 2019 +0100

    implicit function filling now also has the option to apply threshold

Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_utils.cpp

commit 54be91cf66bec6696758f6b084e5a63770900812
Merge: 2d7782f63 4ac5219e5
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 5 12:18:47 2019 +0100

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 4ac5219e5d34199ae0be7c48c44f26c05328494f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 4 16:12:42 2019 -0800

    minor tweaks

Docs/sphinx_tutorials/source/Particles_Tutorial.rst

commit 5b24c5a595c2d90e7b5672e4eb8e0f199016f955
Merge: f9863f1c5 7f9ed04ca
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 4 15:55:12 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f9863f1c5e075300f9d639786679859b802bfa2c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 4 15:54:59 2019 -0800

    add description of the CellSortedParticles tutorial

Docs/sphinx_tutorials/source/Particles_Tutorial.rst

commit 7f9ed04ca4ffa54878a9612e6073708b87ecb173
Merge: 36f2fa27d b24cb033c
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jan 4 15:36:17 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 36f2fa27d8f0e98b1cd30a40c24d16d84265ed0f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jan 4 15:36:00 2019 -0800

    Tutorials/Amr README files copied into documentation

Docs/sphinx_tutorials/source/AMR_Tutorial.rst
Docs/sphinx_tutorials/source/Basic_Tutorial.rst

commit b24cb033cbaedbaeb3d230e2c7beb55e190fa011
Merge: cbf38081c c7105c198
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 4 15:04:51 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cbf38081ca11fd4a635414eafcc080d544675e5c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 4 15:00:10 2019 -0800

    move LoadBalance from Tutorials to Tests - it's not really a full Tutorial.

Tests/Particles/LoadBalance/GNUmakefile
Tests/Particles/LoadBalance/Make.package
Tests/Particles/LoadBalance/create_binary_particle_file.py
Tests/Particles/LoadBalance/inputs
Tests/Particles/LoadBalance/main.cpp
Tests/Particles/LoadBalance/visualize_output.ipynb

commit ea919c0e3399b7d4585c9c5b008255a40f97002c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 4 14:59:25 2019 -0800

    minor changes

Docs/sphinx_tutorials/source/Particles_Tutorial.rst

commit cdbc60cf0114d67e37c536489ab4a2049ef91e57
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 4 14:50:31 2019 -0800

    add a section on the ElectromagneticPIC tutorial

Docs/sphinx_tutorials/source/Particles_Tutorial.rst

commit ddb3dba437e4deeaa3e6afe6c8e1cc55e400bc15
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 4 14:21:03 2019 -0800

    update sphinx documentation for particle tutorials

Docs/sphinx_tutorials/source/Particles_Tutorial.rst

commit b5f7b0a98a550e6edbd5dae337dabc4bda5de933
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 4 14:20:22 2019 -0800

    merge the two NeighborList Tutorials into one

Tutorials/Particles/NeighborList/NeighborListParticleContainer.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborList/compare.py
Tutorials/Particles/NeighborList/inputs
Tutorials/Particles/NeighborList/inputs.mr
Tutorials/Particles/NeighborList/main.cpp
Tutorials/Particles/NeighborList/neighbor_list_3d.f90
Tutorials/Particles/NeighborListMR/GNUmakefile
Tutorials/Particles/NeighborListMR/Make.package
Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.H
Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborListMR/main.cpp
Tutorials/Particles/NeighborListMR/neighbor_list_2d.f90
Tutorials/Particles/NeighborListMR/neighbor_list_F.H

commit c7105c1982d7d9e676746c8804964c6d238aa49f
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jan 4 13:58:32 2019 -0800

    Add text for SENSEI tutorial

Docs/sphinx_tutorials/source/SENSEI_Tutorial.rst

commit 7597f3ab273028bcf8b771017a6a28a587015b7e
Merge: 994fefcb6 076ae6e9b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jan 4 13:15:21 2019 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 994fefcb6ec44a23927f2052d7e459b76866a0e3
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jan 4 13:14:56 2019 -0800

    add link to amrex documentation

Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst

commit 076ae6e9b1218fa59d16d225a9b5d8417e432302
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 4 11:15:31 2019 -0800

    add a function to set the static data for periodicity in Geometry

Src/Base/AMReX_Geometry.H

commit 2d7782f63864e958b2ae729d55b1a4ad07a7f58a
Merge: 87f49051e a17cb6ca8
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 4 11:11:23 2019 +0100

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit a17cb6ca86aadec41a9e204b993232051453f76b
Merge: 7925f4eaf aa60ee134
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 3 16:50:07 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 7925f4eafd7368e47f03409fe28f16183180908d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 3 16:49:05 2019 -0800

    add caveat about one of the code snippets in the GPU docs

Docs/sphinx_documentation/source/GPU.rst

commit 3b40521414f09929237b437b146e37f0dbfd2012
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 3 16:43:12 2019 -0800

    docs typo fix

Docs/sphinx_documentation/source/GPU.rst

commit aa60ee1349d24bb4da0f1ba5f3a910750c150c59
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 3 15:20:47 2019 -0800

    removed the unroll line I accidently left there

Tutorials/GPU/Launch/MyKernel.H

commit ea87277b39073d21b1bbe08abb1f9b23df3ca927
Merge: 9277f4a7e 9766347b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 3 14:55:30 2019 -0800

    Merge branch 'weiqun/interp-3' into weiqun/gpu

commit 9277f4a7efa7c5cd3156e1cc22dd411b4d5e3f08
Merge: 336720d0d 82311957c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 3 14:55:16 2019 -0800

    Merge branch 'development' into weiqun/gpu

commit 82311957c1888777aab400b2e4042d9ca9ea6154
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 3 14:47:20 2019 -0800

    minor changes to gpu documentation

Docs/sphinx_documentation/source/GPU.rst

commit 21eef7c643d09d00a64b7b5840661275779f1f43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 3 14:46:43 2019 -0800

    add a new constructor to AsynArray so that it can be used as scratchpad

Src/Base/AMReX_CudaAsyncArray.H

commit 1b574ea8936e264bb218e3136af421ff74c055b7
Author: Tan Nguyen <tannguyen@cs-it-6767056.local>
Date:   Thu Jan 3 13:36:52 2019 -0800

    minor changes in asyncIter guide

Docs/sphinx_documentation/source/AsyncIter_Chapter.rst

commit 2df2790926f33c787b2851d78aed0a81b26d13be
Author: Cy Chan <cychan@lbl.gov>
Date:   Thu Jan 3 12:58:49 2019 -0800

    remove MLMG::Initialize/Finalize
    init MLLinOp the first time MLLinOp::define is called

Src/Base/AMReX.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 8b7cc41c747ef9cebc7af508955ebd72d97c5aa2
Merge: ec0fe6fc2 70c2cdb80
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 3 13:00:43 2019 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ec0fe6fc2a727891b3b1a90983e2b175d5e96f84
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 3 13:00:27 2019 -0800

    some double -> Real

Tools/C_util/WritePlotFile.cpp

commit 87f49051ebd5bfb8a145261a2d0fc10091f53c69
Merge: 5822778fe 70c2cdb80
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 3 21:21:57 2019 +0100

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 5822778fed303d45aa8dc895ce2da5ea8d07d96b
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 3 21:21:25 2019 +0100

    clean up method naming convention and doxygen

Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp

commit 70c2cdb80efb6d7fc18b28535309510b319b0680
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Jan 3 10:42:23 2019 -0800

    Profiling and summary GPU docs with pictures.

Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_documentation/source/GPU/Streams.pdf
Docs/sphinx_documentation/source/GPU/Streams.png
Docs/sphinx_documentation/source/GPU/Streams.pptx
Docs/sphinx_documentation/source/GPU/gpu_1.pdf
Docs/sphinx_documentation/source/GPU/gpu_1.png
Docs/sphinx_documentation/source/GPU/gpu_2.pdf
Docs/sphinx_documentation/source/GPU/gpu_2.png
Docs/sphinx_documentation/source/GPU/gpu_3.pdf
Docs/sphinx_documentation/source/GPU/gpu_3.png

commit 6f0c2169a7d99dbd49aa01781c366f385992fc19
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Jan 3 10:41:25 2019 -0800

    Doc warnings.

Docs/sphinx_documentation/source/AmrCore.rst

commit 686bdc061c0c61827a49ae15df7b0a16ab8d3c2b
Merge: 97d5e06b8 64cccb5b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 3 09:55:55 2019 -0800

    Merge branch 'weiqun/interp-1' into development

commit 84ebe89a1f52b40feec48207fd6b2ab19840cd4a
Author: Cy Chan <cychan@lbl.gov>
Date:   Wed Jan 2 17:48:02 2019 -0800

    fix some issues with performance analysis / tuning features
      add MLMG::Initialize/Finalize
        move MLCellLinOp software performance counters to static class member
        clears counters on Finalize
      add MLLinOp::Initialize/Finalize
        use unique_ptr to manage comm_cache
        clears MPI communicator cache via destructor on Finalize
      add machine::Finalize
        use unique_ptr to manage machine object
        clears neighborhood cache via destructor on Finalize
      add optional argument to DistributionMapping::makeSFC to allow selecting old behavior

Src/Base/AMReX.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_Machine.H
Src/Base/AMReX_Machine.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/GNUmakefile
Tests/LinearSolvers/MLMG/main.cpp

commit 97d5e06b801075109aaf15b99a8702e8aea2f450
Author: Tan Nguyen <tannguyen@cs-it-6767056.local>
Date:   Thu Jan 3 01:09:43 2019 -0800

    update online guide for async Iters

Docs/sphinx_documentation/source/AsyncIter.rst
Docs/sphinx_documentation/source/AsyncIter_Chapter.rst

commit d91c35b047b0303df10d76d68b63cce201764b6c
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jan 2 17:15:52 2019 -0800

    some more details on ghost cells and fillpatch

Docs/sphinx_documentation/source/AmrCore.rst
Docs/sphinx_documentation/source/Basics.rst

commit d3ccf6512f8c9df75ed3ae97c11e9e61f82c5cd0
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Jan 2 14:25:59 2019 -0800

    adding another early exit to copyParticles

Src/Particle/AMReX_ParticleContainerI.H

commit 8bc2586ec7820d4640fb40599130b3a4de4ba4d0
Merge: 2facfd56c 7b96d51e4
Author: Cy P Chan <cychan@lbl.gov>
Date:   Wed Jan 2 12:51:02 2019 -0800

    Merge pull request #393 from AMReX-Codes/weiqun/perf
    
    Weiqun/perf

commit 7b96d51e407ad4f4247f54124591c254ab0f76f4
Merge: ae91167d5 2facfd56c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jan 2 12:12:52 2019 -0800

    Merge branch 'cy-perf' into weiqun/perf

commit 2facfd56cdb17978d6b65b1cec0158ce66d93f20
Merge: d4019b35b 7e4a22107
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jan 2 11:29:03 2019 -0800

    Merge pull request #392 from AMReX-Codes/development
    
    Development

commit ae91167d561904b724bf8d74935a67272d708db2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 2 11:26:10 2019 -0800

    minor changes: boost license, cmake, etc.

Src/Base/AMReX_Machine.H
Src/Base/AMReX_Machine.cpp
Src/Base/AMReX_Utility.H
Src/Base/CMakeLists.txt

commit 4aab69a1d009f36bf1318d62cc510715d08df57c
Merge: d4019b35b 7e4a22107
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 2 10:11:26 2019 -0800

    Merge branch 'development' into pr-388

commit 7e4a2210727b98a5b2e540d1b322200687120791
Merge: 03d99cd92 ba634257b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 2 10:08:52 2019 -0800

    Merge branch 'weiqun/fluxregister' into development

commit 03d99cd9283fa024693a3c8efd199a68e223c065
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 2 10:06:55 2019 -0800

    update changes

CHANGES

commit 1b39670dbfe93d0d90a6e5481ce3a3f3ba46cb96
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Jan 2 10:46:27 2019 -0700

    tidied up

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 7fc583984437beaec4c06ade30dabae8a4c1c875
Merge: adc620037 d31416936
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Jan 2 10:21:22 2019 -0700

    Merge branch 'development' into nodeghostcells

commit d3141693601906450d3554bd168c3c7c8a7f4c93
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jan 1 14:19:09 2019 +0100

    add utility function automating levelset__eb_pad

Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp

commit df6b70dfb4bfda92b18bc551f2ef207c3aa20fe9
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jan 1 14:00:55 2019 +0100

    update Doxygen

Src/EB/AMReX_EB_levelset.H

commit a4840fd52b2d48efab3ad40c5ac123ddea5908f7
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Dec 30 17:44:46 2018 +0100

    fix level-set thresholding

Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp

commit 8f99cdded774ee1057c60fd3effd634a101d7445
Merge: 969527484 2d2b33bfe
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Dec 30 12:19:21 2018 +0100

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 9695274843cae98cbae0a238bc28f1185340dd2c
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Dec 30 12:19:17 2018 +0100

    clean up function name and doxygen

Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp

commit 2d2b33bfe362b4b25631553911629d4e84215563
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Dec 29 21:58:46 2018 -0800

    remove async metadata at stop time

Src/Amr/AMReX_Amr.cpp
Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp

commit e3c16e043d25bc0d26dc4b881328ef64eaa8d450
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Dec 29 17:50:37 2018 -0800

    Replace std::cout by amrex::Print()

Src/Extern/Algoim/AMReX_algoim_integrals.cpp

commit 59027dd9fd3e9e1638d0bd519b18a604f475265c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sat Dec 29 15:45:45 2018 -0800

    Fix numbered list for GPU docs.

Docs/sphinx_documentation/source/GPU.rst

commit f3afb4965b2e5acd896354e58ad1aa885796526f
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Dec 29 14:04:50 2018 -0800

    fix a memory leak bug in the upcxx backend

Src/Amr/AMReX_Amr.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.H
Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.H
Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx.pthreads

commit d4f3f9d9b3e328dba7399cd9946c5c93d59e50be
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Dec 29 15:45:28 2018 +0100

    update level-set doxygen

Src/EB/AMReX_EB_levelset.H

commit 5f62d9cb720160078d9f86670e22ee0f65826190
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Dec 29 15:40:07 2018 +0100

    fix sign error in local leve-set filling

Src/EB/AMReX_EB_levelset.cpp

commit 6c69eae69baea227af0b7ff40ffe1f550c271cea
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Dec 29 15:21:53 2018 +0100

    clean up LSFactory function names

Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp

commit 3183325087590b2040f2b6e116a06ef85b968f9a
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Dec 29 15:14:28 2018 +0100

    profile LSFactory fill local

Src/EB/AMReX_EB_levelset.cpp

commit cb26be15632c37a8e654ca544b7a330582b22649
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Dec 29 15:12:26 2018 +0100

    document level-set doxygen

Src/EB/AMReX_EB_levelset.H

commit eb448815a463f08a325409041364467f81202748
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Dec 29 14:59:51 2018 +0100

    make eb_facets public

Src/EB/AMReX_EB_levelset.H

commit 639a1c8c6a1ce7e7d42044702c84c2e1cd218b27
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Dec 29 12:09:37 2018 +0100

    start adding profiling the level-set

Src/EB/AMReX_EB_levelset.cpp

commit fdb37a29f28d7970aa2dcebd1eec6e0ad59ea879
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Dec 29 11:54:31 2018 +0100

    continue documenting more level-set stuff

Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp

commit 7492c3a7e01a8c2e67e6909991c758e4ca88ad13
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Dec 28 20:03:49 2018 -0800

    Change so that we only print "Bottom solve failed" when mg_verbose > 1 not >= 1

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit c12eddb13f32e06367dbfce1fe7414704b15aac3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Dec 28 19:01:06 2018 -0800

    If the BiCG bottom solver fails then sets the "solution" it found to 0 before
    going into the "bottom smooth" (if nub > 0).   This enables certain solves to
    converge which don't otherwise.

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 28936ea736654798fbc8f9f0a23c5465c9d96272
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Dec 27 15:46:34 2018 -0800

    Generic loop launch GPU streams docs.

Docs/sphinx_documentation/source/GPU.rst

commit ba634257bd78b4e9577f1d5c19f348ea14eee069
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 25 15:59:28 2018 -0800

    gpu: BndryRegister

Src/AmrCore/AMReX_FluxReg_2D_C.H
Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BndryRegister.cpp

commit 697d794942e94f576bbf360a31cee583fea10bd1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 25 12:57:16 2018 -0800

    fix component index in FineAdd

Src/AmrCore/AMReX_FluxReg_1D_C.H
Src/AmrCore/AMReX_FluxReg_2D_C.H
Src/AmrCore/AMReX_FluxReg_3D_C.H

commit 27c84ca0b2dddbfffacf135759ba319bad213342
Author: Johannes Blaschke <johannes.blaschke@gmail.com>
Date:   Tue Dec 25 03:15:56 2018 -0800

    this used to fail in debug, even though subsequent checks catch bad EB, this cange makes it safe in debug also

Src/EB/AMReX_EB_levelset.cpp

commit a445e88fa5aad15fe9a7722a749142f010e1d4dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 24 19:35:44 2018 -0800

    gpu: FluxRegister in 1D and 2D

Src/AmrCore/AMReX_FLUXREG_1D.F90
Src/AmrCore/AMReX_FLUXREG_2D.F90
Src/AmrCore/AMReX_FLUXREG_3D.F90
Src/AmrCore/AMReX_FLUXREG_F.H
Src/AmrCore/AMReX_FluxReg_1D_C.H
Src/AmrCore/AMReX_FluxReg_2D_C.H
Src/AmrCore/AMReX_FluxReg_3D_C.H
Src/AmrCore/CMakeLists.txt
Src/AmrCore/Make.package

commit e7243f899d714ccd1a7956c9b9e11430a27dbcae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 24 18:04:21 2018 -0800

    gpu: FluxRegister in 3D

Src/AmrCore/AMReX_FluxReg_3D_C.H
Src/AmrCore/AMReX_FluxRegister.cpp

commit adc620037e161e02da9a5b8950f017f5efc58dc8
Merge: c89645cf1 6dbeea20e
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Mon Dec 24 16:05:47 2018 -0700

    Merge branch 'development' into nodeghostcells

commit c89645cf17964b98e81905c9dbaaefb9b25fbebf
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Mon Dec 24 16:04:58 2018 -0700

    removed unnecessary ghost cell copy for rhs fab

GNUmakefile
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 6dbeea20ecc7ade3f85e9606c422aa8dcde4d3f0
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Dec 24 02:09:16 2018 -0800

    a few small updates on the upcxx backend

Src/Amr/AMReX_Amr.cpp

commit 5a7aaa21c77b2dca9c2c0a48e978fca29abc121e
Author: Kaiyuan Hou <khou2020@outlook.com>
Date:   Mon Dec 24 00:19:33 2018 -0600

    add performance result

Tests/PnetCDFBenchmark/ReadMe

commit 2923e3caf18114367784f2007d6c1dd5bb6c079e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 23 15:54:58 2018 -0800

    WIP: FluxRegister::FineAdd on gpu

Src/AmrCore/AMReX_FluxReg_1D_C.H
Src/AmrCore/AMReX_FluxReg_2D_C.H
Src/AmrCore/AMReX_FluxReg_3D_C.H
Src/AmrCore/AMReX_FluxReg_C.H
Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/CMakeLists.txt
Src/AmrCore/Make.package

commit afad6ee6a21bb6ce18dee0df3a24c2b670c72ec5
Merge: 5f85e048f 80bf6f9fb
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sun Dec 23 14:49:01 2018 -0800

    Merge branch 'development' into gpu

commit 5f85e048f2f78feb4ed9874f1701b88d5d0c162e
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sun Dec 23 14:48:28 2018 -0800

    Doc bugs fix.

Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_tutorials/source/ForkJoin_Tutorial.rst
Docs/sphinx_tutorials/source/MUI_Tutorial.rst
Docs/sphinx_tutorials/source/SDC_Tutorial.rst

commit d8d95b6f910d5ec989b2d625ee5b4321bf08e47f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sun Dec 23 14:37:44 2018 -0800

    GPU how-to tutorial doc.

Docs/sphinx_tutorials/source/GPU_Tutorial.rst

commit a81c3909a6f8796f709a84b0138d36f8431ee825
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sun Dec 23 14:37:18 2018 -0800

    First draft of GPU docs.

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/GPU.rst

commit fd8d0ab2bbcffd5e3f9f259edeb93e449b72a13c
Author: Kaiyuan Hou <khou2020@outlook.com>
Date:   Sun Dec 23 02:00:01 2018 -0600

    add comment

Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp

commit 8a0b1ca51d7ae9a83472c43ae42c884a5ac0cfd5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 22 20:50:14 2018 -0800

    WIP: FluxRegister on gpu

Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/Boundary/AMReX_FabSet.H

commit e6e03c8e271ffc0750e9963e7ba883925b8c9021
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 22 16:40:22 2018 -0800

    gpu: FabSet

Src/Boundary/AMReX_FabSet.H
Src/Boundary/AMReX_FabSet.cpp

commit 80bf6f9fbb2e16a93d88194c773c8d200bc4f76c
Merge: 2edfa63bc 1276a8713
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Dec 22 23:24:57 2018 +0100

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 2edfa63bcd5a114e95c193229407fad9f56d1d88
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Dec 22 23:24:52 2018 +0100

    expose level-set filling functions as static functions. This makes incorporating level-sets without LSFactory easier

Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp

commit 1276a87130770a1da6b9f1c3d81df8063c293d87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 22 12:31:17 2018 -0800

    add fabHostPtr and fabDevicePtr to FabArray and make fabPtr's return depends on whether it is in gpu launch region

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_iMultiFab.cpp

commit dab9ac7fef26ab4a2456d15eaba7295ddb5317a7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sat Dec 22 01:13:24 2018 -0500

    Add synch.

Tutorials/GPU/Launch/main.cpp

commit c96c9525557719492b995926a592a5802d2b5e3e
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sat Dec 22 01:11:40 2018 -0500

    Loop lambda works. Remove check.

Tutorials/GPU/Launch/main.cpp

commit a1a9a28110e9b8af5ccbd337ca9ffab38666fdf8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 21 20:25:17 2018 -0800

    make stop time smaller

Tutorials/GPU/CNS/Exec/RT/inputs

commit 9766347b4f31d8ddb2f59ae1f2c7e8e283473bf4
Merge: de06e07b5 d8cecb46e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 21 20:24:14 2018 -0800

    Merge branch 'weiqun/interp-2' into weiqun/interp-3

commit d8cecb46e3a1a07dc2e037a3003add561996c928
Merge: 58b722a43 64cccb5b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 21 20:23:19 2018 -0800

    Merge branch 'weiqun/interp-1' into weiqun/interp-2

commit 64cccb5b39609a20c64799675ce0a803e08f3e41
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 21 20:22:46 2018 -0800

    fix a new bug in interpolater

Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H

commit 988f2a9c91a143f7f5feda9df183d981a221881a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Dec 21 17:37:33 2018 -0800

    Loop launch example.

Tutorials/GPU/Launch/main.cpp

commit d6be58c7820ce6a3e631f81a02352d6d40cd34b3
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Dec 21 17:14:52 2018 -0700

    implemented amrex_mlmg_lin_nd_interp for 3D

GNUmakefile
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90

commit 8b258a92614987b4e715b1b883203246d53dbd89
Merge: 2b2d5fef3 c8e601a89
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 21 15:17:24 2018 -0800

    Merge branch 'development' into weiqun/interp-1

commit c8e601a891915888ca553133551da332738eebd2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 21 14:39:06 2018 -0800

    Tutorials/GPU/CNS: compute T

Tutorials/GPU/CNS/Exec/RT/inputs
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_parm.H
Tutorials/GPU/CNS/Source/CNS_parm.cpp

commit d409b0552662092662b025ca06229c83c31af89d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 21 14:12:11 2018 -0800

    Tutorials/GPU/CNS: store runtime parameters as managed variables

Src/Base/AMReX_GpuQualifiers.H
Tutorials/GPU/CNS/Exec/RT/Make.package
Tutorials/GPU/CNS/Exec/RT/cns_prob.H
Tutorials/GPU/CNS/Exec/RT/cns_prob.cpp
Tutorials/GPU/CNS/Exec/RT/cns_prob_parm.H
Tutorials/GPU/CNS/Exec/RT/inputs
Tutorials/GPU/CNS/Exec/Sod/Make.package
Tutorials/GPU/CNS/Exec/Sod/cns_prob.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp
Tutorials/GPU/CNS/Exec/Sod/cns_prob_parm.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_parm.H
Tutorials/GPU/CNS/Source/CNS_parm.cpp
Tutorials/GPU/CNS/Source/Make.package
Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H

commit c98a3cf483da6c95acdb872a3b73849fc89f66bd
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Dec 21 15:01:11 2018 -0700

    BR

GNUmakefile

commit 5bdb87fe2fc8764fdb53254d044d7e433bbbeec8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 21 12:50:09 2018 -0800

    need to ifdef

Src/AmrCore/AMReX_TagBox.cpp

commit c4bec517ad89de6de6b85a92a06b2494fb85675d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 21 12:48:35 2018 -0800

    TagBox on gpu: we must coarsen both device and host fabs

Src/AmrCore/AMReX_TagBox.cpp

commit c24e38c249711d23be669aa36e0596fefcc57b9b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 20 17:04:58 2018 -0800

    Tutorials/GPU/CNS: add RT test

Tutorials/GPU/CNS/Exec/RT/GNUmakefile
Tutorials/GPU/CNS/Exec/RT/Make.package
Tutorials/GPU/CNS/Exec/RT/cns_prob.H
Tutorials/GPU/CNS/Exec/RT/cns_prob.cpp
Tutorials/GPU/CNS/Exec/RT/inputs

commit 0e443ced430393f1adfc8fca4b5eb7f598d85a7f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 20 17:04:03 2018 -0800

    Tutorials/GPU/CNS: add gravity

Tutorials/GPU/CNS/Source/CNS.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp

commit 2d4c124e449c406c0f0c9f789b664c898d06f789
Author: Kaiyuan Hou <khou2020@outlook.com>
Date:   Fri Dec 21 03:21:35 2018 -0600

    update to dev branch

Tests/HDF5Benchmark/GNUmakefile
Tests/PnetCDFBenchmark/ReadMe
Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp
Tests/PnetCDFBenchmark/inputs
Tests/PnetCDFBenchmark/main.cpp

commit 50c89dde3e522d84fc7455646bf1f2e926a3b003
Merge: 76fdccab2 90af069af
Author: Kaiyuan Hou <khou2020@outlook.com>
Date:   Fri Dec 21 00:13:44 2018 -0600

    Merge remote-tracking branch 'upstream/development' into ncmpi

commit 0e84e413df05b85ae58ebe922796aa0b366afdec
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Dec 20 18:12:45 2018 -0700

    updated ghost cell copy and streamlined some of the code

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90

commit 336720d0dc9624860149d92799d806603ed1d754
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 20 17:04:58 2018 -0800

    Tutorials/GPU/CNS: add RT test

Tutorials/GPU/CNS/Exec/RT/GNUmakefile
Tutorials/GPU/CNS/Exec/RT/Make.package
Tutorials/GPU/CNS/Exec/RT/cns_prob.H
Tutorials/GPU/CNS/Exec/RT/cns_prob.cpp
Tutorials/GPU/CNS/Exec/RT/inputs

commit 7b90fe03c41436bc22c2f685ef9e81854dbe2e28
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 20 17:04:03 2018 -0800

    Tutorials/GPU/CNS: add gravity

Tutorials/GPU/CNS/Source/CNS.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp

commit de06e07b56cf0588b659e97b2c2cc9d4e9fdb573
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 20 15:54:13 2018 -0800

    clean up and comments

Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/AmrCore/AMReX_INTERP_F.H
Src/AmrCore/AMReX_Interpolater.cpp

commit d80cd7b341df1735ecfb3bed6e267d6b73532d48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 20 15:31:32 2018 -0800

    NodeBilinear on gpu

Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/AmrCore/AMReX_Interpolater.cpp

commit 58b722a4324b8c943bc7438a2a38e34066b5ceaf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 20 11:14:15 2018 -0800

    rm old fortran routines for pcinterp

Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/AmrCore/AMReX_INTERP_F.H

commit 72a5fc476a795200e806f62ceeee126bea350fb8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 20 11:08:18 2018 -0800

    fix volume coordinates for 1d spherical coordinates.  note that this is a long-standing issue we never bothered to fix.

Src/Base/AMReX_CoordSys.cpp

commit ac155134d5449ad31757edb46529bc75dfdc9062
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 20 10:45:51 2018 -0800

    PCInterp on gpu

Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/AmrCore/AMReX_Interpolater.cpp

commit 2b2d5fef3af8e5abdf2e0191165d41b0cd72bab1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 20 10:32:30 2018 -0800

    minor optimization

Src/AmrCore/AMReX_Interp_3D_C.H

commit 90af069af705f73c84ae263d96cd25f5fd3bc94a
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Dec 20 17:27:50 2018 +0100

    update gitignore

.gitignore

commit 4186034aba5d3533bbbbea9b04b57cdd76cb7df3
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Dec 19 17:50:43 2018 -0800

    Fix documentation warnings.

Docs/sphinx_documentation/source/Tutorials_Chapter.rst
Docs/sphinx_documentation/source/index.rst

commit f0954a6972273971405de2980b6e742b2266bd43
Merge: 7e2a0b55c 7c722c158
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Dec 19 17:23:09 2018 -0800

    Merge branch 'development' into gpu

commit 7e2a0b55c973fa6438816c2d0b2123cdce883fc8
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Dec 19 17:16:30 2018 -0800

    Plane docs

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_documentation/source/GPU_Chapter.rst

commit 96ed170ed2eef47253734c81d235b7e68e1a648c
Merge: 3aaa7c630 7c722c158
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 19 16:53:01 2018 -0800

    Merge branch 'development' into weiqun/interp-1

commit 7c722c158203ef9f03e1fb36961df85471390c28
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Dec 19 16:44:42 2018 -0800

    bugfix in avgdown_faces... was only operating on component 0

Src/Base/AMReX_MultiFabUtil.cpp

commit 8d2cbe4df7ffb80a989a9a5d1b0baa6012e8856a
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Dec 19 17:06:19 2018 -0700

    initial working version in 2D

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90

commit fadf6d74ee26c83e5a32a587b03e86fe8329ba96
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Dec 20 00:06:54 2018 +0100

    act on Weiqun's advice

Src/Base/AMReX_MultiFabUtil.H

commit a113022a3afbfb1da819b5eee5ed4f65ce6969e8
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Dec 20 00:06:36 2018 +0100

    fix comment

Src/Base/AMReX_MultiFabUtil.H

commit 3aaa7c630bae0905e37ea389567f3e2655700b1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 19 14:57:08 2018 -0800

    partially updated CellConservativeProtected

Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/AmrCore/AMReX_INTERP_F.H
Src/AmrCore/AMReX_Interpolater.cpp

commit 5a7adf8f329199c131a70c83394b160f970977e8
Merge: b5d488a97 39f6e38bc
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Dec 19 23:40:41 2018 +0100

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit b5d488a9749ada77f2388585556f26c44eb25e56
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Dec 19 23:40:36 2018 +0100

    move multifab utils used by LSCore to a better place and document in doxygen

Src/Base/AMReX_MultiFabUtil.H
Src/EB/AMReX_EB_LSCoreBase.H

commit d4019b35b099a8432fc0c7869be7dae6c07644a5
Author: Cy Chan <cychan@lbl.gov>
Date:   Wed Dec 19 13:55:52 2018 -0800

    some cleanup

Src/Base/AMReX_DistributionMapping.cpp
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit e4e8b51d5e130d9dcdcd3f96dc0fb97ab666b1d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 19 13:41:46 2018 -0800

    linccinterp in 1d and 2d

Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/Base/AMReX_CoordSys.cpp

commit 39f6e38bcbf6cb0b75211f307e07b10d8d3c45f6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 19 13:46:31 2018 -0800

    Adding clearParticles and copyParticles method to ParticleContainer.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit f78d7709b2c6e0a26811b134010d5e17f796ffdc
Merge: 226897f28 7cb1250d6
Author: Cy Chan <cychan@lbl.gov>
Date:   Wed Dec 19 13:29:35 2018 -0800

    Merge branch 'development' into cy-perf

commit 1129a742654c177e8d56006ed7f2b04cec7ea02c
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Dec 19 14:28:16 2018 -0700

    updating C/F interpolation to update ghost cells as well as other cells

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90

commit 988ba4e5b3aaf0d83c5f298bf9a0c4d7bd2593bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 19 12:35:03 2018 -0800

    add some comments and clean up

Src/AmrCore/AMReX_Interp_3D_C.H
Src/AmrCore/AMReX_Interpolater.cpp

commit 02b09c7c0bf35cf665e33c180411f36ef1d642a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 19 11:13:04 2018 -0800

    fix issues in 3D CellConservative Interpolater

Src/AmrCore/AMReX_Interp_3D_C.H
Src/AmrCore/AMReX_Interpolater.cpp

commit 20d2344592debb97c2903b0805398d1a2502a15c
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Dec 19 18:12:37 2018 +0100

    clean up comments and formatting

Src/Base/AMReX_MultiFabUtil.H

commit 7cb1250d63e26db700d43595a13b23af7854f89b
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Dec 19 00:39:15 2018 -0800

    partially fix a memory leak bug in the upcxx backend

Src/Amr/AMReX_Amr.cpp
Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.cpp
Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.H
Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/pthreads_common/LocalConnection.H
Src/AmrTask/rts_impls/pthreads_common/PerillaMemCheck.cpp
Src/AmrTask/rts_impls/pthreads_common/RemoteConnection.H
Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.H
Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.H
Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp

commit 8635e3f992a4fde24fd8bdb5b57d50ac87cc907c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Dec 19 00:37:30 2018 -0800

    WIP: GPU docs.

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_documentation/source/GPU_Chapter.rst

commit 6088dea81fe1597b8c42f5d3366fbb3623874125
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 18 21:15:58 2018 -0800

    fix omp performance in atomicAdd

Src/Base/AMReX_BaseFab.H

commit dd1313d67cd4e8989cedc7788774d3f86bb2cfae
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Dec 18 20:24:10 2018 -0500

    Add flag to script to turn off GPUDirect.

Tutorials/GPU/run.summit

commit 226897f287539d0800b1621099d837e57e1b223a
Author: Cy Chan <cychan@lbl.gov>
Date:   Tue Dec 18 14:07:32 2018 -0800

    clean up performance analysis a bit

Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_Machine.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Tests/LinearSolvers/MLMG/inputs
Tools/Backtrace/parse_bt.py

commit c7919313813ebebcd00fbd612ce256dfbbefdae7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 18 13:48:24 2018 -0800

    get the in and out file names from the command line

Tools/Postprocessing/C_Src/cube_extract.cpp

commit cfa3bebc62a8b554dc687064c2c493a38de5dd86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 18 13:47:22 2018 -0800

    3D CellConservative Interpolater on gpu

Src/AmrCore/AMReX_INTERP_3D.F90
Src/AmrCore/AMReX_Interp_3D_C.H
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_Interpolater.cpp

commit abe0fcd94cedb32d6a0f156faa7dcd77db7ed0fe
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 18 13:27:33 2018 -0800

    a utility for extracting a sub-region from a plotfile.

Tools/Postprocessing/C_Src/GNUmakefile
Tools/Postprocessing/C_Src/cube_extract.cpp

commit 98b7ad8eeaa293a07acd006aab7caef41101f7c4
Merge: eac94b9fd 4ac48958f
Author: Cy Chan <cychan@lbl.gov>
Date:   Tue Dec 18 13:14:55 2018 -0800

    Merge branch 'development' into cy-perf

commit 4ac48958f368193ba58a6ee347e0f8b6f8548d47
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 15:58:02 2018 -0800

    tweak snippet slightly

Docs/sphinx_documentation/source/GPU.rst

commit aa160e6801c53842600326f0319f58a11f7cbb89
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 15:56:30 2018 -0800

    add examples of Cuda::HostVector and Cuda::DeviceVector

Docs/sphinx_documentation/source/GPU.rst

commit 05bb1b845d3a492d142f35446c9f943335e52f9d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 15:39:17 2018 -0800

    fix markdown

Docs/sphinx_documentation/source/GPU.rst

commit 55371d8ba1f3774e2e42f28f6b2b295dfb79d85c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 15:38:38 2018 -0800

    fix highlight section

Docs/sphinx_documentation/source/GPU.rst

commit 01d1ed13ee76a4c64cef9f139ff6d5460252dc43
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 15:36:31 2018 -0800

    add OpenACC example to GPU documentation

Docs/sphinx_documentation/source/GPU.rst

commit 98cdd291b1f75d6a9e2249ad0a08173c3b0908d2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 15:23:18 2018 -0800

    remove Cuda Fortran version of EM PIC tutorial

Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/inputs
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/script.sh

commit 534be3a98969b9a5650f379511f764ffa82f65bd
Merge: cc9096849 8a9c0becd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 15:17:48 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cc90968496f95991d17601a6f1a1decf9f890130
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 15:00:09 2018 -0800

    these variables are no longer managed

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90

commit eac94b9fd96bf2ab5b8913ea80243b6192746588
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Dec 17 14:34:12 2018 -0800

    DistributionMapping: use ParallelAllGather functions

Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_ParallelReduce.H

commit ecbf70c3332e80aae3687376e4b901ec6cf8330d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Dec 17 14:25:40 2018 -0800

    WIP: GPU docs edit.

Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_documentation/source/GPU_Chapter.rst

commit 0f96430ac540fb2a70c559a4834f6cce52320f1c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Dec 13 15:32:26 2018 -0800

    Adjust to remove warning in docs.

Docs/sphinx_documentation/source/SWFFT.rst

commit 2755085a4e3590fee9a74f7cbc7e605145c9746c
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Dec 17 14:11:18 2018 -0800

    add current subgroup ranks to comm cache hash key

Src/Base/AMReX_Machine.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 92102881fe33912e0c3333e9f091426f3359d447
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 17 13:59:43 2018 -0800

    2d compiles

Src/AmrCore/AMReX_Interpolater.cpp

commit 48072327dc4416ae6f85341dafb53c85a4f3a957
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 13:51:34 2018 -0800

    can't use ParticlesAt here

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp

commit d4f1f425d358a9b41d7cccb6375636d435176519
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 17 13:51:23 2018 -0800

    fix assertion

Src/AmrCore/AMReX_Interpolater.cpp

commit 48edc0e4f20bd88f983a4f8a6c432bce5a7ee8b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 17 13:45:58 2018 -0800

    fix 2d and minor tweak

Src/AmrCore/AMReX_Interp_3D_C.H
Src/Base/AMReX_IntVect.H

commit 4c3bf4571959d275a652dcc1542612164007b666
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 13:45:07 2018 -0800

    Tutorial compiles again

Src/Particle/AMReX_Particles.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Source/main.cpp

commit 7512f78bd89785f15cb5492266be3e24302b7e42
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 13:02:59 2018 -0800

    remove unused include

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H

commit a54d11284dc68611cf0f2f76f05325866bec9072
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Dec 17 13:00:46 2018 -0800

    move hash_combine() and hash_vector() to AMReX_Utility.H

Src/Base/AMReX_Machine.cpp
Src/Base/AMReX_Utility.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 429488a8e56d3944ae630f6fc90786fa98bfcc76
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 12:58:27 2018 -0800

    fix tabs / spaces issue in emacs

Tutorials/Particles/ElectromagneticPIC/Make.EMPIC

commit f93c7ab15ef0d86ab54737058e60ec6339b9dfe9
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Dec 17 12:47:57 2018 -0800

    move AMReX_Machine files

Src/Base/AMReX_Machine.H
Src/Base/AMReX_Machine.cpp
Src/Base/Make.package
Src/LinearSolvers/MLMG/Make.package

commit 8e4e40245bb98b652a9a9be24735583f12bad12f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 12:46:09 2018 -0800

    update fortran subroutines

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H

commit 55e873ac40d08263b65b20278fe0e0a188eda1ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 17 12:37:25 2018 -0800

    Unlimited 3D CellConservative Interpolater on gpu

Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_Interp_3D_C.H
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_IntVect.H

commit cc6412f5a38541f913800b626f3f55b25fad890a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 12:22:19 2018 -0800

    update EMParticleContainer.cpp

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp

commit 381137eb2a5cb881e1993903bdef0f572d2d67b8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 11:57:02 2018 -0800

    new form of ParticlesAt that is templated on Iterator type

Src/Particle/AMReX_Particles.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp

commit 4886dcf9c6f669b804f5a477e91ab3d20c3f8f50
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 11:49:50 2018 -0800

    use MakeMFIter instead of iterating over the mask

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp

commit 0b0624df3535093be7d97f16874e0d7ff8f77064
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Dec 17 11:47:47 2018 -0800

    updates to support non-MPI build

Src/LinearSolvers/MLMG/AMReX_Machine.cpp
Tests/LinearSolvers/MLMG/inputs

commit 49026564f65f731205ad5895fd6aaacb6972ae8c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 11:25:40 2018 -0800

    forgot namespace

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp

commit 438dd3ac6e9734bfb33fdfb924972e931835f643
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 11:22:37 2018 -0800

    thrust::copy -> thrust_copy

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp

commit ff5ae4bb57c09f1635ff4fde7f5c75490d3c8109
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 11:15:15 2018 -0800

    some renaming

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package
Tutorials/Particles/ElectromagneticPIC/Source/main.cpp

commit 5b163f85fc10dd335b58f58477e9b89f83411d3a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 17 11:11:18 2018 -0800

    add EMParIter

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H

commit 8a9c0becdca7696a177f0a3a8be68396fac35c8a
Merge: 86e1e1278 33efa5749
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 16 18:03:34 2018 -0800

    Merge branch 'weiqun/gpu' into development

commit 86e1e127848f5c03bf28056f64c5520186dbbff8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 15 15:48:22 2018 -0500

    add extra -lmpi_ibm on summitdev

Tools/GNUMake/sites/Make.olcf

commit 33efa574931cd198b5719f36fbef6fb1d08bad9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 14 22:18:16 2018 -0800

    remove FabArray constructor that takes FAB::value_type

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/EB/AMReX_EB2_MultiGFab.cpp

commit 6b5318e9031d621186ce0c8370ef52e720b2f808
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 14 16:37:39 2018 -0800

    add some empty files for interpolater in C++

Src/AmrCore/AMReX_Interp_1D_C.H
Src/AmrCore/AMReX_Interp_2D_C.H
Src/AmrCore/AMReX_Interp_3D_C.H
Src/AmrCore/AMReX_Interp_C.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrCore/CMakeLists.txt
Src/AmrCore/Make.package

commit 29403bfaad219002d7f56e504efac895e7027c7a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 14 16:26:24 2018 -0800

    put interpolation in time on gpu

Src/AmrCore/AMReX_FillPatchUtil.cpp

commit a1c11e222bba7164184bbfbf82e77bd60417be65
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 14 15:57:35 2018 -0800

    Tutorials/GPU/CNS: amr

Tutorials/GPU/CNS/Exec/Sod/inputs
Tutorials/GPU/CNS/Exec/Sod/inputs.amr
Tutorials/GPU/CNS/Source/CNS.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/CNS_bcfill.cpp
Tutorials/GPU/CNS/Source/CNS_io.cpp
Tutorials/GPU/CNS/Source/CNS_setup.cpp
Tutorials/GPU/CNS/Source/CNS_tagging.H
Tutorials/GPU/CNS/Source/Make.package

commit b514f590c3f5f91f5d12d61b8191091504b7d23e
Merge: 2259b720c 5955acf3c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Dec 14 18:22:43 2018 -0500

    Merge branch 'development' into gpu

commit 2259b720c08dc4ca1f22e0e87da2fe23bd03bc19
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Dec 14 18:19:37 2018 -0500

    summit run script works. Turns off GPUDirect.

Tutorials/GPU/run.summit

commit 5955acf3c08794c5b26a8eb2510426640f606076
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Dec 14 14:56:46 2018 -0800

    Oops -- forgot "Real" when I added the brackets.

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 33f4175f837cce0775069a6b8603fbfc1d9085a6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Dec 14 14:45:56 2018 -0800

    Update "Amr Task" --> "Asynchronous Iterators (Amr Task)"

Docs/sphinx_documentation/source/AsyncIter_Chapter.rst

commit 98141c4de2db01919f80592254095fa8b0771674
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 14 14:06:39 2018 -0800

    minor

Src/Amr/AMReX_AmrLevel.H
Tutorials/EB/CNS/Source/CNS_setup.cpp

commit 15b9610f8577a49610cf6f9a6c91881907cfdc5b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Dec 14 13:50:32 2018 -0800

    Change formatting of norm output when verbose >= 4.  No change
    in functionality, only in output.

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 6855d54c7b7126dc4d89646cb9333312344382a1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Dec 14 13:44:34 2018 -0800

    Zero out the "res" array right after we create it in the nodal solve
    so that we can use the ghost nodes as a convenience in the stencil
    (knowing they are now zero)

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 4ec23424d41c4c79c475786c8aff01d700a6f4bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 14 13:30:49 2018 -0800

    get rid of some warnings

Src/Base/AMReX_CoordSys.cpp

commit 79bba81388f7bb806810dbc89e18d1cbbc26b491
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 14 13:29:02 2018 -0800

    variadic template for amrex::min and max

Src/Base/AMReX_Utility.H

commit 376a50367d1fd5594a4218060fb6d3c0ea3b5cea
Merge: b3cb198d6 33e2e0e2e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 14 11:58:09 2018 -0800

    Merge pull request #386 from jrood-nrel/update_nrel_site
    
    Update makefiles for NREL machines

commit b3cb198d61ba3c51d38f3775bc57dd49a2913f16
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Dec 14 11:29:02 2018 -0800

    Add Lassen @ LLNL

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.llnl

commit 88595df7b35926eab7f7faf4ea0dc545bc3ea250
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Dec 14 11:28:57 2018 -0800

    Cuda -> CUDA

Src/Base/AMReX_GpuError.H

commit 33e2e0e2ed2798e3898f381db0a8ee5373132011
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Fri Dec 14 12:21:56 2018 -0700

    Adding note about older compilers on NREL machines.

Tools/GNUMake/sites/Make.nrel

commit 592f6c9138db37396758b12cab80f203dc5f726c
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Fri Dec 14 12:07:00 2018 -0700

    Using same compiler flags for gcc, gnu, and llvm on NREL's Eagle machine.

Tools/GNUMake/sites/Make.nrel

commit 0921500fa2b88e6fd331e0e1b48254d82e3cda2f
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Fri Dec 14 11:49:42 2018 -0700

    Updating makefiles for NREL machines.

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.nrel

commit fee6bc5709185d72aa711e8c6a2505b410fffdfe
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Dec 14 09:49:25 2018 -0800

    In the nodal solve -- if we set CoarseningStrategy to RAP rather than Sigma -- which is
    what we do when AMREX_USE_EB is defined -- then we should always use the restriction_rap
    routine (based on "sten") rather than the standard restriction which sees no geometric
    information

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit bd9b0f998f8e9b58c9127d2292f5bca4921791f3
Merge: d879a7798 130485b8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 14 07:22:02 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d879a7798e3aef61bd9a6033cd1039c8e13f8b26
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 14 07:21:32 2018 -0800

    fix some AMREX_PRAGMA_SIMD issues

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_COORDSYS_1D_C.H

commit 130485b8c27072622d5cabfd1172c3cefe1d682a
Merge: e5a4d595a 40b6b76ca
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 13 16:50:44 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit e5a4d595a6bca5d078b7808ec4adc5cab126f66d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 13 16:50:24 2018 -0800

    fix typo

Docs/sphinx_documentation/source/index.rst

commit 3a0a157a38e2aec5d5bd71a50f154c62f0e61fec
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 13 16:49:29 2018 -0800

    rename chapters in sphinx documentation

Docs/sphinx_documentation/source/AMReX_Profiling_Tools_Chapter.rst
Docs/sphinx_documentation/source/AmrCore_Chapter.rst
Docs/sphinx_documentation/source/AmrLevel_Chapter.rst
Docs/sphinx_documentation/source/AsyncIter_Chapter.rst
Docs/sphinx_documentation/source/Basics_Chapter.rst
Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst
Docs/sphinx_documentation/source/EB_Chapter.rst
Docs/sphinx_documentation/source/External_Frameworks_Chapter.rst
Docs/sphinx_documentation/source/External_Profiling_Tools_Chapter.rst
Docs/sphinx_documentation/source/Fortran_Chapter.rst
Docs/sphinx_documentation/source/GPU_Chapter.rst
Docs/sphinx_documentation/source/GettingStarted_Chapter.rst
Docs/sphinx_documentation/source/IO_Chapter.rst
Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst
Docs/sphinx_documentation/source/Particle_Chapter.rst
Docs/sphinx_documentation/source/Visualization_Chapter.rst
Docs/sphinx_documentation/source/index.rst

commit 2e0e870f254672fabb5c81f010a294e55c0a7c79
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 13 16:31:40 2018 -0800

    make corresponding changes to the OpenACC version

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp

commit 30cdec5c20c43040ef800aed150cd2288a55b138
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 13 15:47:27 2018 -0800

    formatting changes

Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp

commit 40b6b76ca5ba9ac05e0090ce66784541bde823eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 13 13:17:18 2018 -0800

    small changes

Src/Base/AMReX_BaseFab.H
Src/EB/AMReX_EB2_GeometryShop.H

commit c386e845a6765f9adb34087aee301d84455b30dd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 13 12:29:29 2018 -0800

    update generating initial conditions with the changes from WarpX

Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp

commit e2d985ba82924987764b0b9988bb1768de310e7b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 13 12:17:45 2018 -0800

    Just call the base class constructor.

Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp

commit 54b8d3d0792b0ea06fbe57cf9b5e43e687ad72a9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 13 12:13:35 2018 -0800

    move PIdx to the ParticleContainer subclass; do not need Particles.H any more

Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Source/Particles.H

commit 5ed16936ba364ad5001aca03848b737b03e71b2b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 13 12:11:15 2018 -0800

    Redistribute Strategy is not a thing any more.

Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H

commit 10d35ebdc4f8b4d65e2e69668db67a8251319663
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 13 12:09:20 2018 -0800

    restoring the ElectromagneticPIC Tutorial

Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/inputs
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/script.sh
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/inputs
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/script.sh
Tutorials/Particles/ElectromagneticPIC/Make.EMPIC
Tutorials/Particles/ElectromagneticPIC/Source/Constants.H
Tutorials/Particles/ElectromagneticPIC/Source/IO.H
Tutorials/Particles/ElectromagneticPIC/Source/IO.cpp
Tutorials/Particles/ElectromagneticPIC/Source/Make.package
Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/Source/Particles.H
Tutorials/Particles/ElectromagneticPIC/Source/main.cpp

commit 0f01a9b6e2108735d09f5c5fdb81e5ac89b634a8
Merge: 604d5b9c5 f91c594c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 13 11:09:25 2018 -0800

    Merge branch 'development' into gpu

commit f91c594c22d698c0ced60d47da786846b89d6e20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 13 10:32:54 2018 -0800

    no need to pass GeometryData if it is not needed

Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit 163ad2ae5da1172d93017e6b420469c9310931fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 13 10:21:49 2018 -0800

    rm functions we don't really need

Src/Base/AMReX_COORDSYS_3D_C.H
Src/Base/AMReX_CoordSys.cpp

commit e44a56772a408cb06e785e9d843533b73e8fae2b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 13 10:11:34 2018 -0800

    add Geometry::isPeriodicArray that returns gpu friendly array

Src/Base/AMReX_Geometry.H

commit 8e6db26ca163cec4cfbec1b12fdd3e7d532320f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 13 10:00:33 2018 -0800

    move AsyncFab dtor to header

Src/Base/AMReX_CudaAsyncFab.H
Src/Base/AMReX_CudaAsyncFab.cpp

commit bb332cdcbc97a4628210c2c36d816238399265ca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 13 09:46:04 2018 -0800

    add amrex_multifab_read

Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Tools/CompileTesting/compiletesting.py

commit f8022a5146cbe21e6389afb0b5e1ec0dd38397b9
Merge: 5a2549870 ce38c3953
Author: Guy Moore <gmoore@lbl.gov>
Date:   Thu Dec 13 07:42:23 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 5a254987032c60a2ae70b2751a192db06cd091c5
Author: Guy Moore <gmoore@lbl.gov>
Date:   Thu Dec 13 07:39:04 2018 -0800

    Moved SWFFT tutorials into separate sub-directories, and updated documentation to reflect change
    Filled MUI documentation

Docs/sphinx_documentation/source/SWFFT.rst
Docs/sphinx_tutorials/source/MUI_Tutorial.rst
Docs/sphinx_tutorials/source/SWFFT/iface_rect.png
Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst
Tutorials/SWFFT/SWFFT_poisson/GNUmakefile
Tutorials/SWFFT/SWFFT_poisson/Make.package
Tutorials/SWFFT/SWFFT_poisson/README
Tutorials/SWFFT/SWFFT_poisson/SWFFT_Test.H
Tutorials/SWFFT/SWFFT_poisson/SWFFT_Test.cpp
Tutorials/SWFFT/SWFFT_poisson/SWFFT_Test_F.F90
Tutorials/SWFFT/SWFFT_poisson/SWFFT_Test_F.H
Tutorials/SWFFT/SWFFT_poisson/inputs.128
Tutorials/SWFFT/SWFFT_poisson/inputs.32
Tutorials/SWFFT/SWFFT_poisson/inputs.64
Tutorials/SWFFT/SWFFT_poisson/main.cpp
Tutorials/SWFFT/SWFFT_poisson/run_me
Tutorials/SWFFT/SWFFT_poisson/swfft_solver.cpp
Tutorials/SWFFT/SWFFT_simple/GNUmakefile
Tutorials/SWFFT/SWFFT_simple/Make.package
Tutorials/SWFFT/SWFFT_simple/README
Tutorials/SWFFT/SWFFT_simple/SWFFT_Test.H
Tutorials/SWFFT/SWFFT_simple/SWFFT_Test.cpp
Tutorials/SWFFT/SWFFT_simple/SWFFT_Test_F.F90
Tutorials/SWFFT/SWFFT_simple/SWFFT_Test_F.H
Tutorials/SWFFT/SWFFT_simple/inputs.multipleGrids
Tutorials/SWFFT/SWFFT_simple/inputs.oneGrid
Tutorials/SWFFT/SWFFT_simple/main.cpp
Tutorials/SWFFT/SWFFT_simple/run_me_2d
Tutorials/SWFFT/SWFFT_simple/run_me_3d
Tutorials/SWFFT/SWFFT_simple/swfft_compute.cpp

commit ce38c395377c154cab7fd2caed3f58f8f68087f4
Merge: c01a1bebe 56c0c4815
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 13 06:55:49 2018 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit c01a1bebe7e5bb89d362aa94c4451fc1416cab27
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 13 06:55:33 2018 -0800

    Wrap EB_set_covered inside ifdef AMREX_USE_EB

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 604d5b9c5960302ffce3581a224b539678f83899
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Dec 13 01:47:36 2018 -0500

    Tweaks to get AmrCore compiling on Summit + making H files for converted Fortran->C++ functions.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/GPU/Advection_AmrCore/Source/Kernels_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp

commit ff4ed0a50b480638077eba5a0714467f04475e88
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Dec 13 01:42:57 2018 -0500

    Add non const bracket operator to GpuArray.

Src/Base/AMReX_Array.H

commit 56c0c48156fb17d029455c19a3b0fc05f256ae53
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Dec 12 20:49:37 2018 -0800

    add code to detect memory leak

Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.cpp
Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp
Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.H
Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp
Src/AmrTask/rts_impls/pthreads_common/LocalConnection.H
Src/AmrTask/rts_impls/pthreads_common/Make.package
Src/AmrTask/rts_impls/pthreads_common/PerillaMemCheck.H
Src/AmrTask/rts_impls/pthreads_common/PerillaMemCheck.cpp
Src/AmrTask/rts_impls/pthreads_common/RemoteConnection.H
Src/AmrTask/rts_impls/pthreads_common/perilla.mak
Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/main.cpp

commit 8314cc2abadb314624c44fdf1e86007005f594b9
Merge: 9f6039c08 73f6f6c5f
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Dec 12 20:44:30 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 73f6f6c5f44222d627d44b32dad6f81d500d8320
Merge: d39e23b0a 556c7a140
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 12 20:05:16 2018 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit d39e23b0a928c70cbc1de64cbbb4cad2f351f4e4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 12 20:03:45 2018 -0800

    1) Some clean-up of nodal restriction
    2) Grow nodal domain by 1000 so that we don't double at Neumann boundaries
    in divu_cf_contrib when using CoarseningStrategy::RAP

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 556c7a1400d8ed2e194c55447e1deb5c884bf851
Merge: f19b2d4a7 7cefc273e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 12 17:09:34 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f19b2d4a7003061d8c32f45dc0bf0c5a07ebad91
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 12 17:09:03 2018 -0800

    Make sure to remove particles that leave the problem domain when running on the GPU.

Src/Particle/AMReX_ParticleContainerI.H

commit 9f6039c082720cd5e10da0bb3783dbff3388cc24
Merge: 417bccec1 7cefc273e
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Dec 12 16:54:26 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 7cefc273efb4a20bc17481a59af735fd779554b9
Merge: 6cac804d9 18a08df95
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 12 19:02:22 2018 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6cac804d91b0cb93953296d548ad9adc6b4157fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 12 19:01:59 2018 -0500

    more inline

Src/Base/AMReX_MultiFabUtil_1D_C.H
Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H
Src/Base/AMReX_MultiFabUtil_nd_C.H

commit 461c2a4da9d5fddd6ce6662c617a59eebcbcef18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 12 18:41:41 2018 -0500

    inline in FArrayBox

Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp

commit 0df85b933526720f51d717a258827ab22603be53
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 12 18:29:01 2018 -0500

    inline in Box

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp

commit dd80d505869c7d3981bd12e462619230ba4ab950
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 12 17:50:03 2018 -0500

    clean up

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp
Src/Base/AMReX_CudaReduce.H
Src/Base/AMReX_FabArrayUtility.H

commit f74a7d3bc543f15517e4cb6da0540cfe816588e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 12 16:53:32 2018 -0500

    move MultiFabUtil kernels to headers for inline

Src/Base/AMReX_MultiFabUtil_1D_C.H
Src/Base/AMReX_MultiFabUtil_2D_C.H
Src/Base/AMReX_MultiFabUtil_3D_C.H
Src/Base/AMReX_MultiFabUtil_C.H
Src/Base/AMReX_MultiFabUtil_nd_C.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 12879796224bfe4a382972fd3ea14b0bd715d1f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 12 16:22:21 2018 -0500

    return by value to save registers

Src/Amr/AMReX_StateData.cpp

commit 153b056fea37d23b14d8e10ccb206d869b56eba9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 12 16:05:06 2018 -0500

    move CoordSys kernels to headers for inline

Src/Base/AMReX_COORDSYS_1D_C.H
Src/Base/AMReX_COORDSYS_2D_C.H
Src/Base/AMReX_COORDSYS_3D_C.H
Src/Base/AMReX_COORDSYS_C.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 3573170c6eaf1561d6332ee944a23f836c0cbc22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 12 15:47:26 2018 -0500

    move FillCC to headers for inline

Src/Base/AMReX_FilCC_1D_C.H
Src/Base/AMReX_FilCC_2D_C.H
Src/Base/AMReX_FilCC_3D_C.H
Src/Base/AMReX_FilCC_C.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tutorials/GPU/CNS/Source/CNS_bcfill.cpp

commit d70fd98a1e5550d57375ebd9d33581cb8ee9dee4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 12 15:06:31 2018 -0500

    clean up

Tutorials/GPU/CNS/Source/CNS_setup.cpp

commit 417bccec1aa6c8967d7c5d2fc34ae90195eec81e
Merge: 2ddab9c12 18a08df95
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Dec 12 11:32:29 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6d8e898b19e4ebb4a72dbb055202d8ecb4189f62
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 12 13:08:19 2018 -0500

    add AMREX_FORCE_INLINE macro

Src/Base/AMReX_Extension.H

commit 58d8061409fbc6da1140022f59eb093485fc790d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 12 12:59:47 2018 -0500

    reorganize Tutorials/GPU/CNS for inline

Tutorials/GPU/CNS/Exec/Sod/cns_prob.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_K.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/Make.package
Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H
Tutorials/GPU/CNS/Source/hydro/Make.package
Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp

commit 18a08df955e39789ee8efb474e23a86459bcb806
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Dec 12 08:04:11 2018 -0800

    remove inconsistent definition of Real in AMReX_ParticleTile.H

Src/Particle/AMReX_ParticleTile.H

commit 2ddab9c1201a96dece6e434e1f371e36ba18673c
Merge: b4bfc5dd3 56d4adc73
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Dec 11 21:35:30 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 56d4adc7388751ac692ca55d8648c29128436f9c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 11 16:28:59 2018 -0800

    want to tile this loop

Src/Particle/AMReX_NeighborParticlesI.H

commit 2e2daa13aa1cb52f8ba353c64d89054f6cd5b975
Merge: 657b85fac 4efce4926
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Dec 11 19:19:21 2018 -0500

    Merge branch 'development' into gpu

commit 4efce4926f95c65cf849e5ae1fd14cf5094ab730
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 11 15:43:47 2018 -0800

    same thing here

Src/Particle/AMReX_NeighborParticlesI.H

commit a9a5ed28c4050aa2a9d8fd0598b0bec79d3e81d6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 11 15:39:21 2018 -0800

    the relevant dmap here is the one associated with the dst level, not the src level

Src/Particle/AMReX_NeighborParticlesI.H

commit b4bfc5dd327d23e920e0cbb434ca881573f8ef8e
Merge: 5dc2627f7 df5c4bc9d
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Dec 11 14:48:50 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5dc2627f79f872704a3c10439ab8a740e8798393
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Dec 11 14:48:35 2018 -0800

    abc

Src/Amr/AMReX_Amr.cpp

commit df5c4bc9dae068d278020e7af301d546a68a99eb
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Dec 11 14:46:23 2018 -0800

    fix BA type

Src/EB/AMReX_EB_LSCoreBase.cpp

commit 152bbeb13938add4c9ca4e20cf091323df34bb1b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 11 14:17:20 2018 -0800

    add section label

Docs/sphinx_documentation/source/GPU.rst

commit f4306c14658e2678439f10c670d7866f71211275
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 11 14:13:37 2018 -0800

    use cpp formatting

Docs/sphinx_documentation/source/GPU.rst

commit 00e4b1a68cfa147e4ff32c57317832f93bd5894f
Merge: fdc2ced27 1fb29b45e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 11 13:58:11 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit fdc2ced272031945c27d1fc08ea6bac036c92cde
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 11 13:57:57 2018 -0800

    add section on GPU particles to the docs.

Docs/sphinx_documentation/source/GPU.rst

commit 1fb29b45e7e4123dfeb35340745b634ac910a9a0
Merge: 8e54310cb f03cf4470
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Dec 11 13:22:08 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8e54310cb1136955ed38a09eaa9bb71c72ae1015
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Dec 11 13:22:04 2018 -0800

    LSCore uses a local level-set paradigm now

Src/EB/AMReX_EB_F.H
Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset_F.F90

commit f03cf44709dca78388ec95e01956b9a8870f365a
Merge: be8c8a5ed 7cf30f602
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 11 12:40:17 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit be8c8a5ed81ca7457ee3f8312974f918847d8fb9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 11 12:39:40 2018 -0800

    proofreading pass of GPU documentation

Docs/sphinx_documentation/source/ChapterGPU.rst
Docs/sphinx_documentation/source/GPU.rst

commit 7cf30f602c879ce0ba9c6df28e508b989276f521
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 11 12:26:32 2018 -0800

    Remove memory leak - changes per Weiqun's suggestion.

Src/AmrCore/AMReX_Cluster.cpp

commit 657b85fac6aa5b73c190a632d94ed7a4808ddaf5
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Dec 11 11:57:32 2018 -0800

    Removed print statement. AmrCore GPU rewrite tutorial now works on CPUs.

Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp

commit 35826e1be096ff6479c731c5dcb89c9cbf1c8895
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Dec 11 11:50:14 2018 -0800

    inputs

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs

commit f7d9446ace14faba0ca587e4117b0a195b8d00fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 11 13:19:13 2018 -0500

    add USE_FORCE_INLINE

Src/Base/AMReX_Extension.H
Tools/GNUMake/Make.defs

commit af791bbe18f2838d91291c30ae61a01c2ceaff3d
Merge: 359181abe 90fba2864
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Dec 10 21:41:15 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 359181abeda0dbb087babb41839a780b24ea065d
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Dec 10 21:41:08 2018 -0800

    implement tiling for local level-set creation

Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.cpp

commit c8114b085ce7eb6542e49578a78f48d67f085cce
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 10 18:32:19 2018 -0800

    Fix some bounds problems

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 76fdccab2b1874cc53b49670cb7d801ca8ba3784
Author: Kaiyuan Hou <khou2020@outlook.com>
Date:   Mon Dec 10 19:16:54 2018 -0600

    update timer name

Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp

commit a18a99be53f7ef245e602fb8f0188bcefddda903
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Dec 10 17:09:03 2018 -0800

    Turn off tiling in AmrCore tutorial for testing.

Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90

commit 055aa82b815f9aa08953e3ea0224ca0328c8933f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Dec 10 17:08:30 2018 -0800

    Continuing to fix Core. Has prints.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp

commit 90fba286422f13501100288331350086e5c79b16
Merge: 8decd6850 a5d28e316
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 10 16:35:57 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8decd6850e21a5d2232e9193d9f47e84bc273e47
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 10 16:35:47 2018 -0800

    this needs to be 'class' instead of 'typename' to keep gcc < 5 happy

Src/EB/AMReX_EB_LSCoreBase.H

commit a5d28e3166947e5b72e204cb86a2262bd7980520
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 10 16:16:23 2018 -0800

    more gpu doc

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_documentation/source/LinearSolvers.rst

commit 399dcd8913e0538d4c70e485f6a826fe6c55ce17
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Dec 10 16:06:22 2018 -0800

    Remove GPU macros prior to typecheck

Tools/GNUMake/Make.rules

commit a885e41bfe1b324a5da2d605547513a3be83728c
Merge: 48cfa38d7 701100a8a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 10 16:04:26 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 48cfa38d7bf074feb2137613e46393a152caceee
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 10 16:04:08 2018 -0800

    fix Tutorial

Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborList/main.cpp

commit f33171737b9408800c3566ce4ad29925a02a2b15
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 10 15:35:38 2018 -0800

    also communicate the level information in the MPI send data for neighbor particles

Src/Particle/AMReX_NeighborParticlesI.H

commit 701100a8adb47db7432ff9a35b534977cf0beb20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 10 15:02:19 2018 -0800

    minor fixes

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/EB.rst
Docs/sphinx_documentation/source/GPU.rst

commit e563f593bb5e71083095e6c21268d69d499b94f9
Merge: b049cd144 806109417
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 10 14:12:30 2018 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit b049cd1443dc07a17985f1e2f884963d2b66f0d4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 10 14:11:20 2018 -0800

    Allow multilevel solves with CoarseningStrategy::RAP.  Note there is a default
    assumption that the EB boundary does not cross the coarse-fine interface because
    the coarse-fine stencil is NOT defined using the EB-aware stencils.

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 56179041ee6d4af62d6483cae02c783caa661f96
Author: kngott <kngott@lbl.gov>
Date:   Mon Dec 10 13:45:10 2018 -0800

    Ann found compute flux was wrong.

Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp

commit 7f7523272294f43e68979dc078d3532a4d64e83e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 10 16:07:00 2018 -0500

    minor: add some consts

Src/Base/AMReX_CudaLaunch.H

commit 8061094178c4d024fb8894fee46ff6752b958aa0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 10 12:43:47 2018 -0800

    Tutorials/GPU/Launch: inline the C++ kernel

Tutorials/GPU/Launch/Make.package
Tutorials/GPU/Launch/MyKernel.H
Tutorials/GPU/Launch/MyKernel.cpp

commit a243d2553a2e453b8cbc69a7be814e20c771bdc4
Author: kngott <kngott@lbl.gov>
Date:   Mon Dec 10 11:33:31 2018 -0800

    Fixing errors in fluxes.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp

commit 2b74acc14df6d5e390029a288500b993f66aed1c
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Dec 10 00:35:57 2018 -0800

    extend the upcxx backend to support RGIter

Src/Amr/AMReX_Amr.cpp
Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.H
Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/PerillaConfig.H
Src/AmrTask/rts_impls/upcxx_pthreads/Perilla_common.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.H
Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp

commit 9179da9376d6ef9358084390f3a897d776a13362
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Dec 9 15:06:42 2018 -0800

    Remove "mfix" from routine names

Tutorials/EB/Donut/Src/EB_F.H
Tutorials/EB/Donut/Src/eb_to_pvf.F90
Tutorials/EB/Donut/Src/main.cpp

commit 166efca9be6696735057160895577b10eca695e3
Merge: 45a1d5729 6c3968287
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Dec 9 10:27:29 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 45a1d572980a2044bd1c7cad7b140456259074b4
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Dec 9 10:27:22 2018 -0800

    use tiling to fill level-set

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.cpp

commit 6c39682876b673e69e5ba63e9ed63994ca926737
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Dec 8 22:41:44 2018 -0800

    fit a small bug in the mpi backend

Src/Amr/AMReX_Amr.cpp
Src/AmrTask/rts_impls/mpi_pthreads/Perilla.H
Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp
Src/AmrTask/rts_impls/pthreads_common/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_advance.cpp

commit af2371d62e4df80ee92c32673a35a72cd4822364
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 8 21:38:44 2018 -0800

    on limitations.  this finishes my first pass of gpu documentation

Docs/sphinx_documentation/source/GPU.rst

commit 643710d9bbb9c4e4455c9f9e48d676cfc4c19149
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 8 21:19:34 2018 -0800

    on assetion, error check and reduction

Docs/sphinx_documentation/source/GPU.rst

commit 377204509dc7c279cd8b901f7dc2621e8726ad46
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 8 20:44:53 2018 -0800

    on AsyncFab

Docs/sphinx_documentation/source/GPU.rst

commit 32b072068e887465f63389374e15551cdbb5ad47
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Dec 8 22:11:41 2018 -0500

    pout -> amrex::Print()

Tools/C_util/Convergence/RichardsonConvergenceTest.cpp

commit 0786ecfefe1890c8c40a9745e8cf543578efc2fe
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Dec 8 18:58:00 2018 -0800

    Add error message if we reach the end of the new_chop routine without returning the new grids.

Src/AmrCore/AMReX_Cluster.cpp

commit 22538f570f9d023cd9d52e9152a46e424e15835d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 8 18:36:47 2018 -0800

    try again

Src/AmrCore/AMReX_Cluster.cpp

commit 742d53a4efc79608548600aada4316e5db3a0c36
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 8 18:35:13 2018 -0800

    not sure it's the right fix for ClusterList, but it compiles now

Src/AmrCore/AMReX_Cluster.cpp

commit 96e6bffb24a7ceddb0a15f5f457430c156e62fec
Merge: 3eb0140f2 d65c17104
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 8 18:28:17 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 3eb0140f2b7da485368ae0246e14bab4da5257a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 8 18:28:08 2018 -0800

    rm FabArray::getDomain and comment out some debug code using it

Src/Base/AMReX_FabArray.H
Tools/C_util/Convergence/DebugOut.cpp

commit d65c17104b7d96b8026ea644b61a9643aee4e7c4
Merge: 72e6867e7 c3989d642
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Dec 8 18:18:51 2018 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 72e6867e7963dfcd0e3dd942d701256db5cd02cd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Dec 8 18:17:01 2018 -0800

    Update the creation of the grids for the level set by
    1) removing the iteration -- we shoudln't need it
    2) Introducting a modified "chop" function which doesn't accept cuts
       if they don't imporove the grid efficiency.  This is available to
       all grid creation routines if they set the flag use_new_chop to true.
       The level set routines now do that by default.

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_Cluster.H
Src/AmrCore/AMReX_Cluster.cpp
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H

commit c3989d642e74767c6f02632e2d5738f2517a2cc1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 8 13:21:44 2018 -0800

    on gpu safe classes

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/GPU.rst

commit 66fd6db75fb1cf013c23bacc126e7a355b29031e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 8 12:02:30 2018 -0800

    add writing C++ kernel

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_documentation/source/index.rst

commit b26f007e07daf2e4b6614e8d01315f9a9188e854
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 7 22:21:57 2018 -0800

    Merge branch 'gpu-docs' into development

Docs/sphinx_documentation/Makefile
Docs/sphinx_documentation/source/AsyncIter.rst
Docs/sphinx_documentation/source/ChapterGPU.rst
Docs/sphinx_documentation/source/GPU.rst
Docs/sphinx_documentation/source/index.rst
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BLFort.H
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_fort_mod.F90
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/nvcc.mak
Tools/GNUMake/comps/pgi.mak
Tutorials/GPU/Launch/GNUmakefile
Tutorials/GPU/Launch/Make.package
Tutorials/GPU/Launch/MyKernel.H
Tutorials/GPU/Launch/MyKernel.cpp
Tutorials/GPU/Launch/MyKernel_F.F90
Tutorials/GPU/Launch/MyKernel_F.H
Tutorials/GPU/Launch/Readme.md
Tutorials/GPU/Launch/main.cpp

commit 2a66f8ac162d3e39ac17cf4232c192121bf37655
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 7 18:10:27 2018 -0800

    fix bug involving periodic boundary conditions and NeighborCopyTags

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 7f8ec36d662e9e92352658b2e2c205459ffa8156
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Dec 7 18:00:55 2018 -0800

    change buffer

Src/EB/AMReX_EB_LSCoreBase.cpp

commit 8983bdb0ca2355be515b086439541f865f65bacf
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 7 16:40:56 2018 -0800

    need to remove duplicates whether or not mask is used.

Src/Particle/AMReX_NeighborParticlesI.H

commit 6854d23eb85a0d711f0fb90c2c3ff1df8e5d1e46
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 7 16:38:54 2018 -0800

    change order of output for << operator

Src/Particle/AMReX_NeighborParticles.H

commit 6499818d6b1b301dada4a1be596ecc17e9c21abe
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Dec 7 15:22:44 2018 -0800

    finished volfrac tagging

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCore_F.H
Src/EB/AMReX_EB_Tagging.F90

commit e17f89a09d6e8f85760f12aaa88dfc9e32c726b7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 7 15:22:19 2018 -0800

    add << operators for NeighborIndexMap and NeighborCommTag

Src/Particle/AMReX_NeighborParticles.H

commit ffd0e1a397c62c963b3f2cab2c6b0dac040ee870
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 7 14:24:01 2018 -0800

    change the neighbor list print format

Src/Particle/AMReX_NeighborParticlesI.H

commit fb897c4254587f1387a50f57eb31558dc93dbea6
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Dec 7 13:39:06 2018 -0800

    get ready for volfrac tagging

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp

commit 9678d9b2d767abdb10578f671a9bd0dff3554238
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 7 13:32:13 2018 -0800

    need to always bin the particles for the nl on level 0

Src/Particle/AMReX_NeighborParticlesI.H

commit 54c7c99114366779955a792fbda007785ccbdcdf
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 7 13:28:37 2018 -0800

    have printNeighborList take a prefix argument

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 3321757431b634e01c86dbdb4400cb4875e76a96
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 7 13:20:11 2018 -0800

    add method to print out nbor list for debugging.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 45d39b390b623545633c8af1ff4118cc4621e116
Author: kngott <kngott@lbl.gov>
Date:   Fri Dec 7 11:39:55 2018 -0800

    Fix slope.cpp

Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp

commit 3c9896f25ab52e009d1ad2f6390b2bea1a34edda
Merge: 49b121b59 835ba726c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 7 11:36:21 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 835ba726c125d7c32478b2a9ac32f880ef6cfa68
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Dec 7 11:19:18 2018 -0800

    level-set tagging now seperately declared as such

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCore_F.H
Src/EB/AMReX_EB_Tagging.F90

commit 5a231bb8379a467721dc6d8bfdada02088da45bf
Merge: b45f9c279 329c2aab5
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Dec 7 11:12:33 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit b45f9c279b471a3ed6f53030c8f1e0b84bf8c78d
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Dec 7 11:12:26 2018 -0800

    clean up tagging

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCore_F.H
Src/EB/AMReX_EB_Tagging.F90

commit 329c2aab522d94cb3c2d21b4565486d0d6c5238e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 7 10:25:11 2018 -0800

    make AsyncFab copy constructor device function only and use_cuda=true only

Src/Base/AMReX_CudaAsyncFab.H

commit 20c68a15154a438635e265304b3844a8ccf332e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 7 10:05:16 2018 -0800

    Make AsyncFab interface nicer thanks to Marc's suggestion.  AsyncFab can be captured by value and AsyncFab::fab() will return a reference to Fab.

Src/Base/AMReX_CudaAsyncFab.H
Src/Base/AMReX_CudaAsyncFab.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp

commit 94c81be3cd56420cfdb2c08a026f611bded89b7e
Merge: b2296e0a5 833b9e123
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 6 16:56:12 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b2296e0a56466e3e230913f192cf443561e91831
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 6 16:55:59 2018 -0800

    separate out the printing stuff from Arena::Finalize so it can be used for debugging.

Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp

commit 833b9e123a86ab12148d37b6329a9ffddd5ef76a
Merge: 10be78bd4 47ec80ee8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 6 16:45:11 2018 -0800

    Merge branch 'weiqun/fabptr' into development

commit 47ec80ee8ed2e6d14dd776e8438156a39fdc9ce3
Merge: 92b013a41 26feb5529
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 6 19:32:21 2018 -0500

    Merge branch 'weiqun/fabptr' of github.com:AMReX-Codes/amrex into weiqun/fabptr

commit 26feb5529352bad23b222b445ac1591d80d8eaf8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 6 16:31:57 2018 -0800

    update particle functors to use device ptr

Src/Particle/AMReX_ParticleContainerI.H

commit 54fa626db5eb4f8f5f13e82de30814db21729fce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 6 16:31:28 2018 -0800

    add __FILE__ and __LINE__ as arguments ot Cuda::ErrorCheck

Src/Base/AMReX_GpuError.H

commit 10be78bd43029961d55fc2166e06d6da79b32924
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Dec 6 16:29:11 2018 -0800

    avg_down with region graph iterator

Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_advance.cpp

commit 49b121b59522c725a8818ab5fe4f24f8f963877a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 6 15:31:01 2018 -0800

    this at least runs to completion in serial

Src/Particle/AMReX_NeighborParticlesI.H

commit a5c895158c3c014a89d437efd3170eb72b6cf84f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Dec 6 15:23:53 2018 -0800

    don't regrid LSCore if BA/DM don't change

Src/EB/AMReX_EB_LSCoreBase.cpp

commit 289ffa8fd9a2150ff0e8e6fdb058c79ece840b17
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 6 15:15:44 2018 -0800

    fix bug that involved confusing the src level with the dst level

Src/Particle/AMReX_NeighborParticlesI.H

commit 6ecfce3531cba8b37fc435dfc48bc21f14bfbaf5
Author: Cy Chan <cychan@lbl.gov>
Date:   Thu Dec 6 15:03:17 2018 -0800

    add consolidation threshold parameter to MLLinOp

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Tests/LinearSolvers/MLMG/main.cpp

commit e4638572aa927e0cfeaf137efc8d24a8ac0b044a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 6 14:35:57 2018 -0800

    clean up resize containers

Src/Particle/AMReX_NeighborParticlesI.H

commit 2d3b071b7c2230ab5171cdb2dcda04e7199cc785
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 6 14:33:19 2018 -0800

    the buffer tag cache also needs to be an array over levels

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit b193ce6db2741b3f4f219c13546590a9e195f003
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 6 14:04:42 2018 -0800

    tweak inputs

Tutorials/Particles/NeighborListMR/inputs

commit 267c8745b3e1da8d061230add6b8bcedcb270978
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 6 13:45:26 2018 -0800

    remove some hard-coded 'const int lev = 0'

Src/Particle/AMReX_NeighborParticlesI.H

commit 24a1c4eb1402fa2886b5b6b00a7e68dc236ca143
Merge: 9b9370fb9 28a79294b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 6 13:33:23 2018 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 9b9370fb9b72422033dfd4eb85c65cd3b23ad09c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 6 13:30:26 2018 -0800

    Abort in the case when the entire domain is covered.  Previously this
    case ended up being viewed as "all_regular"

Src/EB/AMReX_EB2_Level.H

commit 563859211b05601fcacb1c844dd6778a0277b50a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 6 13:12:51 2018 -0800

    use the mask if max_level = 0

Src/Particle/AMReX_NeighborParticlesI.H

commit 28a79294bd091b4cccd3473d4d7e5df32245086f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Dec 6 13:12:05 2018 -0800

    completed local level-set

Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Tutorials/EB/LevelSet/Exec/inputs
Tutorials/EB/LevelSet/Src/make_cylinder.cpp

commit c17cd9ec8214db613424d1ecaa6f738b8f0c710f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 6 13:07:36 2018 -0800

    remove unused stuff from NeighborListParticleContainer

Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.H
Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborListMR/inputs
Tutorials/Particles/NeighborListMR/main.cpp

commit c1954c6c466bf22c31a3b9adff21e3dabac370b9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 6 13:04:23 2018 -0800

    fix and simplify periodic boundary adjustment for neighbors

Src/Particle/AMReX_NeighborParticlesI.H

commit f2dc968984d447fb2410365f836b424fbc4402a0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 6 13:03:50 2018 -0800

    overload << operator for NeighborCopyTag for ease of debugging

Src/Particle/AMReX_NeighborParticles.H

commit 6b4083716254764bd1357327a978b510d77ebf06
Author: kngott <kngott@lbl.gov>
Date:   Thu Dec 6 13:02:02 2018 -0800

    Properly use cell number.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp

commit fbe5dd7e75fabea3cc86fc7d5d38620254348db1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 6 12:39:12 2018 -0800

    fixing a couple more bugs

Src/Particle/AMReX_NeighborParticlesI.H

commit 92b013a41a4045792eea2cc5fe00f6329ca11456
Merge: 6b6714d4c a1fbe4d5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 6 14:01:17 2018 -0500

    Merge branch 'development' into weiqun/fabptr

commit 8e63ca33d415ce6452dd6e349e717aec0050114d
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Dec 6 10:53:12 2018 -0800

    fix typo

Src/EB/AMReX_EB_levelset_F.F90

commit 251007d69631f036729031d31a7e38790e2b3812
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Dec 6 10:52:01 2018 -0800

    fix level-set thresholding

Src/EB/AMReX_EB_F.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_levelset_F.F90

commit a1fbe4d5ab7d023c7adfb2e553fbabb482592a1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 6 09:44:47 2018 -0800

    make gcc happy

Src/Base/AMReX_MultiFab.H

commit 45812fe55627685d4e58016ebe715dc07ed26f57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 6 09:39:10 2018 -0800

    get rid of warning in version checking when users set their own CXX

Tools/GNUMake/comps/gnu.mak

commit 1fce9884601e59e8be6609470efc52af277d1ce2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 6 06:34:45 2018 -0800

    Instead of IntVect{0,0,0} use IntVect{AMREX_DECL(0,0,0)}

Src/EB/AMReX_EB_levelset.cpp

commit cf15c194ca04d905ae57462c36489a86f74c29a6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 6 06:10:16 2018 -0800

    Need to return something from eb_facets routine

Src/EB/AMReX_EB_levelset.cpp

commit 30370232770a99c9700e1d273069136373666cd0
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Dec 6 01:43:37 2018 -0800

    Advection code using RGIter

Src/AmrTask/rts_impls/pthreads_common/RGIter.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/._Exec
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/._README
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/._Source
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/._Make.Adv
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/._SingleVortex
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/._UniformVelocity
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi.omp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi.pthreads
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx.pthreads
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._face_velocity_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._probin
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/Backtrace.0
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/face_velocity_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/probin
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._probdata.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/._probin
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/probdata.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/UniformVelocity/probin
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/README
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._AdvBld.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv_F.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv_advance.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv_dt.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv_io.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Adv_setup.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Src_2d
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Src_3d
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._Src_nd
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/._main.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/AdvBld.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_F.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_advance.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_dt.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_io.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_setup.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/._Adv_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/._compute_flux_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/._slope_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/Adv_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/compute_flux_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/slope_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._Adv_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._compute_flux_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._slope_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/Adv_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/compute_flux_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/slope_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._Adv_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._Tagging_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._tagging_params.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Adv_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Tagging_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/tagging_params.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/main.cpp

commit 95dc5a109e8beec698671e9f7b71c9824e84ff59
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Dec 5 21:50:40 2018 -0800

    hack level-set threshold

Src/EB/AMReX_EB_levelset_F.F90

commit c26ddfe28bea62a27b7c000360cd2dd9ccd09cca
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 19:04:58 2018 -0800

    use AMREX_D_TERM so this works in 2D

Src/Particle/AMReX_NeighborParticles.H

commit 0496ea055b9b572cdcabfbab1828838659ee597d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 19:00:53 2018 -0800

    fix a couple of bugs

Src/Particle/AMReX_NeighborParticlesI.H

commit 4945f2609dad0be78b7e6cefe584f5156c9788ef
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Dec 5 18:37:43 2018 -0800

    bug fixes for eb_search

Src/EB/AMReX_EB_levelset.cpp

commit f79179671feb76431ceddc098c04fbab43b18ff5
Merge: e3666bf3f 2e0d85ee3
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Dec 5 18:06:08 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit e3666bf3f1c54a018961f8a8645a2e3cf6f0a402
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Dec 5 18:06:04 2018 -0800

    work on local level-set filling

Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp

commit 6b6714d4c5eebc46de9ce78a6854b1a1e5a5a589
Merge: 080924d89 159bcfb4a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 5 16:51:26 2018 -0800

    Merge branch 'development' into weiqun/fabptr

commit 080924d89e9b7f73880570ee5418d7cbc8155949
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 5 16:51:14 2018 -0800

    udpate gpu codes ot use fabPtr

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_iMultiFab.cpp
Tests/GPU/AsyncFab/main.cpp
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit 2e0d85ee351e00f76622a13d00425ade5e60f607
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Dec 5 16:44:53 2018 -0800

    add link to tutorial documentation

Docs/sphinx_documentation/source/Chapter4a.rst
Docs/sphinx_documentation/source/index.rst

commit 0ebea50a0cc6c86e823190f72b990d0431ac3601
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 16:23:59 2018 -0800

    finish non-mask version of GetNeighborCommTags

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 3d5c5669b37d39eb3e96e5fbb781575eb13b698b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 16:10:26 2018 -0800

    fix bug in computeRefFac

Src/Particle/AMReX_NeighborParticlesI.H

commit c8072408cf1ec6904181b691d5da375a568fb5b9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 15:58:44 2018 -0800

    add a numLevels() method to ParticleContainer and use it

Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_Particles.H

commit a29a8a440f6ef7f17b9599cb79762032233f092e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 15:51:47 2018 -0800

    function to compute net ref ratio between two levels

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 68667ee56e5072e10bbd22c1f363a78a7819f494
Author: Cy Chan <cychan@lbl.gov>
Date:   Wed Dec 5 15:30:09 2018 -0800

    fix bug in remap neighborhoods

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 159bcfb4a4b501df991f2bfe7fe96ce754c31984
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 5 14:26:20 2018 -0800

    fix fortran function name so that the gpu script works

Src/Base/AMReX_filcc_mod.F90
Src/Base/AMReX_fort_mod.F90

commit 6939d3b3f3652663c498e3c2504c9967cd620962
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 5 14:14:33 2018 -0800

    WIP: add host alias fabs to FabArray

Src/Base/AMReX_FabArray.H

commit 9651e2bca7d067810b3a95ed59dc3c6e2f911f44
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 5 13:37:47 2018 -0800

    add createHostAlias for fab

Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabFactory.H
Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IArrayBox.cpp
Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_Mask.cpp
Src/EB/AMReX_EBFArrayBox.H
Src/EB/AMReX_EBFArrayBox.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_MultiCutFab.H

commit e4d9589667341ed28ab6f9ef2ace56e905ca0b19
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 12:57:05 2018 -0800

    some more refactoring

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit fea2ec1fb5156ba8d821bb2eeeb63f8efcd16eee
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 5 12:36:03 2018 -0800

    move Parallel/ForkJoin --> ForkJoin

Tutorials/ForkJoin/GNUmakefile
Tutorials/ForkJoin/Make.package
Tutorials/ForkJoin/MyTest.H
Tutorials/ForkJoin/MyTest.cpp
Tutorials/ForkJoin/MyTest_F.H
Tutorials/ForkJoin/inputs
Tutorials/ForkJoin/main.cpp

commit fbdaec2bbd1aab300c72dd638cb0755acbbea557
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 12:25:15 2018 -0800

    do_mask -> use_mask

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit bf19a639fc15653083081bb3fb5385c9adc5208b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 12:04:47 2018 -0800

    split up BuildMasks into two different methods

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 4b27017ece63155b26612be907b9c8bbe8e49d05
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 5 12:01:17 2018 -0800

    1) Copy the current Tutorials that use SENSEI into a new Tutorials/SENSEI directory.
    2) Remove mentions of SENSEI from Tutorials/Amr.
    3) Add items in the sphinx documentation for each Tutorials subdirectory.

Docs/sphinx_tutorials/source/Blueprint_Tutorial.rst
Docs/sphinx_tutorials/source/Forkjoin_Tutorial.rst
Docs/sphinx_tutorials/source/GPU_Tutorial.rst
Docs/sphinx_tutorials/source/MUI_Tutorial.rst
Docs/sphinx_tutorials/source/SDC_Tutorial.rst
Docs/sphinx_tutorials/source/SENSEI_Tutorial.rst
Docs/sphinx_tutorials/source/index.rst
Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt
Tutorials/Amr/Advection_AmrLevel/Exec/Make.Adv
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs
Tutorials/SENSEI/Advection_AmrCore/CMakeLists.txt
Tutorials/SENSEI/Advection_AmrCore/Exec/Make.Adv
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/Make.package
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/Prob.f90
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/inputs
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_catalyst.py
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml
Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml
Tutorials/SENSEI/Advection_AmrCore/README
Tutorials/SENSEI/Advection_AmrCore/README_SENSEI.md
Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/SENSEI/Advection_AmrCore/Source/Make.package
Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/Adv_2d.f90
Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/Make.package
Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90
Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/slope_2d.f90
Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/Adv_3d.f90
Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/Make.package
Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90
Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/slope_3d.f90
Tutorials/SENSEI/Advection_AmrCore/Source/Src_nd/Make.package
Tutorials/SENSEI/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90
Tutorials/SENSEI/Advection_AmrCore/Source/bc_fill_nd.F90
Tutorials/SENSEI/Advection_AmrCore/Source/main.cpp
Tutorials/SENSEI/Advection_AmrLevel/CMakeLists.txt
Tutorials/SENSEI/Advection_AmrLevel/Exec/Make.Adv
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/Make.package
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/Prob.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/probin
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_catalyst.py
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.session
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.session
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_libsim.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/write_vtk.xml
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/Make.package
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/inputs
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90
Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/probin
Tutorials/SENSEI/Advection_AmrLevel/README
Tutorials/SENSEI/Advection_AmrLevel/README_SENSEI.md
Tutorials/SENSEI/Advection_AmrLevel/Source/Adv_F.H
Tutorials/SENSEI/Advection_AmrLevel/Source/AmrLevelAdv.H
Tutorials/SENSEI/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Tutorials/SENSEI/Advection_AmrLevel/Source/LevelBldAdv.cpp
Tutorials/SENSEI/Advection_AmrLevel/Source/Make.package
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/Make.package
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/slope_2d.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/Make.package
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/slope_3d.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Make.package
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/tagging_params.f90
Tutorials/SENSEI/Advection_AmrLevel/Source/main.cpp

commit 541ed4233e0c7193a5e931fef74c6183f5a1c4ab
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 11:57:26 2018 -0800

    make BuildMasks protected

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 2a096d00330dd2eae80660ce0a1d6a3d4c75558c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 11:32:44 2018 -0800

    give NeighborCopyTag explicity default constructor as well

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 0a2a0957d3c83479ed0289fc147e89c287025419
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 11:27:53 2018 -0800

    finish implementation of non-mask getNeighborTag

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit ca10e0c715a4a2bdd1063f799c72cbe56b86997b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 11:17:46 2018 -0800

    give NeighborCopyTag a non-default constructor

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit c922fc4d354aa24c357be6df0a0c49719a574f23
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 11:13:42 2018 -0800

    some work towards implementing the non-mask neighbor tag function

Src/Particle/AMReX_NeighborParticlesI.H

commit a5b5e0c1b649f8bea398dd705e29ee775bf8736b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 10:55:06 2018 -0800

    some refactoring

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit cf4c1245e5a487efbfac34bbe3a629a97df6bd6f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 5 10:52:09 2018 -0800

    Remove HYPRE tutorial -- there isn't a separate one

Docs/sphinx_tutorials/source/HYPRE_Tutorial.rst
Docs/sphinx_tutorials/source/index.rst

commit a9ec9af6b6c99208e99dfc2ec8556cb30f822957
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 5 10:35:56 2018 -0800

    Update with the three specific Tutorial names.

Docs/sphinx_tutorials/source/LinearSolvers_Tutorial.rst

commit aa84bcfd6a881834a9bc8f0fd4643b9819e335ba
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 10:04:22 2018 -0800

    correct comment

Src/Particle/AMReX_NeighborParticlesI.H

commit 0742cfff6b9fcc322f5180da1a0a49c7ab9f8f11
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 09:55:30 2018 -0800

    selectively switch off building the mask

Src/Particle/AMReX_NeighborParticlesI.H

commit 54ea4b2ce52c5fec225eba14cb24d687bfd282a5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 5 09:53:43 2018 -0800

    add a static member variable to disable the mask approach

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 893da9b9bc77b5f61d0f8b21a852da15a79513f4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 5 09:15:35 2018 -0800

    make distFcnElement2d pure virtual

Src/EB/AMReX_distFcnElement.H
Src/EB/AMReX_distFcnElement.cpp

commit 293aa3d64405d04a21f6e8c9021f22d050f7b746
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 5 09:00:22 2018 -0800

    FabArray::fabPtr functions to return pointer to fab

Src/Base/AMReX_FabArray.H

commit fc87026de68a2496bd70d9e419c909408b56b296
Author: kngott <kngott@lbl.gov>
Date:   Wed Dec 5 00:37:47 2018 -0800

    Fix initialization error.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp

commit 6fa10a22fbc9a54931b13dcb191fe64dc54ee2a9
Author: kngott <kngott@lbl.gov>
Date:   Tue Dec 4 15:49:34 2018 -0800

    Fix boxes.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit c1c1c7c6b5b8eaed9b20b3c95695556fbcb01085
Author: kngott <kngott@lbl.gov>
Date:   Tue Dec 4 15:48:32 2018 -0800

    Fix conversion of single-plane psi into three dimensional loop.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp

commit 9302eb9e840fd3fede4ee80344d497b3845859e9
Merge: 8fde8801a febd8ccc7
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Dec 4 15:44:58 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8fde8801aaa7cc997f8d829b70c6538d287cfc0b
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Dec 4 15:44:55 2018 -0800

    make EBSearchBox compatible of infs and nans

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp

commit febd8ccc77bb83db370651c2dd0500f0ab554234
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Dec 4 14:45:50 2018 -0800

    change RTS name

Src/AmrTask/rts_impls/mpi_omp/PerillaRts.H
Src/AmrTask/rts_impls/mpi_omp/PerillaRts.cpp
Src/AmrTask/rts_impls/mpi_pthreads/Make.package
Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.H
Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp
Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/pthreads_common/Make.package
Src/AmrTask/rts_impls/upcxx_pthreads/Make.package
Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.H
Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.omp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.pthreads
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.upcxx.pthreads
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/main.cpp
Src/Base/AMReX_MultiFabUtil_Perilla.cpp

commit b9e907bb831414a7da81e3c8b81b59c478db23e1
Merge: fb717eaea 53249b043
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 4 14:30:48 2018 -0800

    Merge branch 'weiqun/comm' into development

commit fb717eaea0e77eb5f4a5e2bb91d6224847dce917
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Dec 4 14:06:50 2018 -0800

    change directory name for rts backends

Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/mpi_omp/Barrier.H
Src/AmrTask/rts_impls/mpi_omp/Barrier.cpp
Src/AmrTask/rts_impls/mpi_omp/LocalConnection.H
Src/AmrTask/rts_impls/mpi_omp/Make.package
Src/AmrTask/rts_impls/mpi_omp/PackageQueue.H
Src/AmrTask/rts_impls/mpi_omp/PackageQueue.cpp
Src/AmrTask/rts_impls/mpi_omp/Perilla.H
Src/AmrTask/rts_impls/mpi_omp/Perilla.cpp
Src/AmrTask/rts_impls/mpi_omp/PerillaConfig.H
Src/AmrTask/rts_impls/mpi_omp/PerillaRts.H
Src/AmrTask/rts_impls/mpi_omp/PerillaRts.cpp
Src/AmrTask/rts_impls/mpi_omp/RegionGraph.H
Src/AmrTask/rts_impls/mpi_omp/RegionGraph.cpp
Src/AmrTask/rts_impls/mpi_omp/RegionQueue.H
Src/AmrTask/rts_impls/mpi_omp/RegionQueue.cpp
Src/AmrTask/rts_impls/mpi_omp/RemoteConnection.H
Src/AmrTask/rts_impls/mpi_omp/WorkerThread.H
Src/AmrTask/rts_impls/mpi_omp/WorkerThread.cpp
Src/AmrTask/rts_impls/mpi_omp/perilla.mak
Src/AmrTask/rts_impls/mpi_pthreads/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/mpi_pthreads/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/mpi_pthreads/Barrier.H
Src/AmrTask/rts_impls/mpi_pthreads/Barrier.cpp
Src/AmrTask/rts_impls/mpi_pthreads/LocalConnection.H
Src/AmrTask/rts_impls/mpi_pthreads/Make.package
Src/AmrTask/rts_impls/mpi_pthreads/Makefile
Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.H
Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.cpp
Src/AmrTask/rts_impls/mpi_pthreads/Perilla.H
Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/mpi_pthreads/PerillaConfig.H
Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.H
Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp
Src/AmrTask/rts_impls/mpi_pthreads/RGIter.H
Src/AmrTask/rts_impls/mpi_pthreads/RGIter.cpp
Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.H
Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp
Src/AmrTask/rts_impls/mpi_pthreads/RegionQueue.H
Src/AmrTask/rts_impls/mpi_pthreads/RegionQueue.cpp
Src/AmrTask/rts_impls/mpi_pthreads/RemoteConnection.H
Src/AmrTask/rts_impls/mpi_pthreads/WorkerThread.H
Src/AmrTask/rts_impls/mpi_pthreads/WorkerThread.cpp
Src/AmrTask/rts_impls/mpi_pthreads/mylock.h
Src/AmrTask/rts_impls/mpi_pthreads/perilla.mak
Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/pthreads_common/Barrier.H
Src/AmrTask/rts_impls/pthreads_common/Barrier.cpp
Src/AmrTask/rts_impls/pthreads_common/LocalConnection.H
Src/AmrTask/rts_impls/pthreads_common/Make.package
Src/AmrTask/rts_impls/pthreads_common/RGIter.H
Src/AmrTask/rts_impls/pthreads_common/RGIter.cpp
Src/AmrTask/rts_impls/pthreads_common/RegionQueue.H
Src/AmrTask/rts_impls/pthreads_common/RegionQueue.cpp
Src/AmrTask/rts_impls/pthreads_common/RemoteConnection.H
Src/AmrTask/rts_impls/pthreads_common/WorkerThread.H
Src/AmrTask/rts_impls/pthreads_common/WorkerThread.cpp
Src/AmrTask/rts_impls/pthreads_common/mylock.h
Src/AmrTask/rts_impls/pthreads_common/perilla.mak
Src/AmrTask/rts_impls/upcxx_pthreads/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/upcxx_pthreads/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/Barrier.H
Src/AmrTask/rts_impls/upcxx_pthreads/Barrier.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/LocalConnection.H
Src/AmrTask/rts_impls/upcxx_pthreads/Make.package
Src/AmrTask/rts_impls/upcxx_pthreads/Makefile
Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.H
Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.H
Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/PerillaConfig.H
Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.H
Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/Perilla_common.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/RGIter.H
Src/AmrTask/rts_impls/upcxx_pthreads/RGIter.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.H
Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/RegionQueue.H
Src/AmrTask/rts_impls/upcxx_pthreads/RegionQueue.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/RemoteConnection.H
Src/AmrTask/rts_impls/upcxx_pthreads/WorkerThread.H
Src/AmrTask/rts_impls/upcxx_pthreads/WorkerThread.cpp
Src/AmrTask/rts_impls/upcxx_pthreads/mylock.h
Src/AmrTask/rts_impls/upcxx_pthreads/perilla.mak

commit 603522f96e977817b4d9109987896ccea342ad1c
Author: kngott <kngott@lbl.gov>
Date:   Tue Dec 4 13:45:12 2018 -0800

    Change inputs file for GPU testing.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs

commit e634cb0cfd110c7db064f937019c35cb277d7348
Author: kngott <kngott@lbl.gov>
Date:   Tue Dec 4 13:44:51 2018 -0800

    clean up false comment

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp

commit 8c30a284a6f94b57c0309214ca4b5716fdc0bdf6
Author: kngott <kngott@lbl.gov>
Date:   Tue Dec 4 13:44:30 2018 -0800

    Fix swapped function arguments.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 2824565f9fa1d831d159e1e73a2bcd855e420e7a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 4 13:28:52 2018 -0800

    change periodic shift logic to be more forgiving

Src/Particle/AMReX_NeighborParticlesI.H

commit d2efcdd01ebebafae3366721ecd42bd72b42939e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 4 13:27:54 2018 -0800

    use and IntVect for the periodic_shift member of NeighborCopyTag

Src/Particle/AMReX_NeighborParticles.H

commit 9f12fbf90fe74d8021d0d6fbcaa56d8799afc4be
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Dec 4 13:27:21 2018 -0800

    change variable name to be more consistent

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit a9ff55753417d4d66986a097e2c6a4a6e7cdcd29
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Dec 4 13:09:13 2018 -0800

    added std::move symmantics to regridding and tweake coarsening

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H

commit 53249b0431c42f00d3fc82d9e4702ff85f448b42
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 4 15:10:02 2018 -0500

    add profiler

Src/Base/AMReX_FabArrayCommI.H

commit 12366cea00e7daf8a63d74d3e6a5926705f12c09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 4 11:31:34 2018 -0800

    AsyncArray: return earlier if size is zero

Src/Base/AMReX_CudaAsyncArray.H
Src/Base/AMReX_FabArrayCommI.H

commit 8d52683c9df4c51121544324d1248477a0d84c74
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 4 11:13:48 2018 -0800

    merged fillboundary: gpu version of local copy

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_GpuLaunch.H

commit 4f1a2802cf03eba1f69f5b8b86c27f34797c44aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 4 10:27:31 2018 -0800

    merged fillboundary: omp version of local copy

Src/Base/AMReX_FabArrayCommI.H

commit 00ab644ad28d92c7a1fb2dae8a2cdbaab2b61cdc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 4 10:05:38 2018 -0800

    remove TagVols because they have not been used. gpu version copyFromMem in the new merged fillboundary

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayCommI.H

commit 2a70e1a68457ff428f6ac473eaedaa3de9d3a656
Merge: 50d4f05b1 17bc6666f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Dec 3 18:58:17 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 50d4f05b103f0ca4b1cb740c23e24def6cf73159
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Dec 3 18:58:10 2018 -0800

    add regrid (i.e. update MF and DM of particular level) to LSCore

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp

commit 17bc6666fcb31aba3a702d289d05e1091cd8aeb3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 3 17:21:36 2018 -0800

    != operator for NeighborCopyTag

Src/Particle/AMReX_NeighborParticles.H

commit eda764d93a4241cfc22da051b48ac4d6ea01acd0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 3 13:44:16 2018 -0800

    first pass of merged FillBoundary

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit 90fd57696784afdce96d496629aab77c61529064
Merge: 5614e2154 886fa6f08
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 3 16:56:59 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5614e215443af02aedd1b4473d02d3341303d79b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 3 16:56:42 2018 -0800

    on-the-fly computation of neighbor particles in a multi-level setting.

Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.H
Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborListMR/inputs
Tutorials/Particles/NeighborListMR/main.cpp

commit fb08de8539446cdacff7bffce033e85effb4c65e
Author: kngott <kngott@lbl.gov>
Date:   Mon Dec 3 16:50:47 2018 -0800

    Primary MFIter loop done and compiling.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp

commit 886fa6f08839b2dac38f08e9e15999e33d9bd11d
Author: rgrout <rgrout@users.noreply.github.com>
Date:   Mon Dec 3 16:44:12 2018 -0700

    Replaces #375 Spline Implicit function for EB (#380)
    
    * Added Spline implicit function for EB2
    
    * Testing the FORD Scorpion piston bowl generation
    
    * Cleaned up spline implicit function
    
    * Modified the case to test the spline functionality
    
    * Resolve conflicts and address @WeiqunZhang comments
    
    * add missing amrex namespace

Src/EB/AMReX_EB2.cpp
Src/EB/AMReX_EB2_IF.H
Src/EB/AMReX_EB2_IF_Spline.H
Src/EB/AMReX_distFcnElement.H
Src/EB/AMReX_distFcnElement.cpp
Src/EB/CMakeLists.txt
Src/EB/Make.package
Tutorials/EB/GeometryGeneration/main.cpp

commit 95a76aed24ab217fdd5c5d889e04be58f1e7e2c4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 3 12:29:54 2018 -0800

    don't forget to define the dmaps

Tutorials/Particles/NeighborListMR/main.cpp

commit 7d57eec2aaa2a54893c3e9cca4b4a91886a0bcb4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 3 12:28:05 2018 -0800

    fix parameter shadowing

Src/Particle/AMReX_NeighborParticlesI.H

commit 7f9d039c612e28deb1d3f1607b94568632786718
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 3 12:25:47 2018 -0800

    update inputs file

Tutorials/Particles/NeighborListMR/inputs

commit 0e6d8b9b4d7bed6c89cde53a4c33562727603f3c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 3 12:24:32 2018 -0800

    fix another typo.

Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp

commit 18cd34acc3ede2e14bda49704916491120d34d06
Author: kngott <kngott@lbl.gov>
Date:   Mon Dec 3 12:23:17 2018 -0800

    Advection broken into functions. Compute_flux & slope left.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp

commit c9b75dedf5f691f517aa4f8c68786a7919575470
Merge: ab9a9f810 4bd856071
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 3 12:22:38 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ab9a9f81030a2ec4d49eb31d3fa6975fca354f29
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 3 12:22:06 2018 -0800

    fix typo

Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp

commit 4bd85607144c08b67ec9630e19dc2c472f20a661
Author: Tan Nguyen <tannguyen@cs-it-6767056.local>
Date:   Mon Dec 3 11:56:06 2018 -0800

    add ref guide for RegionGraph Iterator

Docs/sphinx_documentation/source/AsyncIter.rst
Docs/sphinx_documentation/source/Chapter6aa.rst

commit 9fb7c521ea93f576aa043fe4d819d4f295b535b8
Merge: 4f40d3d4f fdccb8348
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 3 10:30:20 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4f40d3d4f44df8ba0fa14eb036a067adf1b9d76f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 3 10:29:47 2018 -0800

    fix issue involving component names

Tests/HDF5Benchmark/main.cpp

commit b835b9b0c34290e7596ac5c8558cc97401f9bd81
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 3 10:24:27 2018 -0800

    fix assertion re: containing_bx in InitRandom.

Src/Particle/AMReX_ParticleInit.H

commit 66445f87db5964cf8fae9aad09e751314f936a59
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 3 10:23:57 2018 -0800

    remove unused variable

Tests/HDF5Benchmark/main.cpp

commit 0c7f8cfd4056ff1bb522ad421aa5521e72a036c4
Merge: b3734c4bc fdccb8348
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 3 08:47:26 2018 -0800

    Merge branch 'weiqun/gpu' into weiqun/comm

commit fdccb8348c485b91bee559bf736e6ca5469e509c
Merge: 35cc09c0f 4677ac986
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 3 08:46:01 2018 -0800

    Merge branch 'weiqun/gpu' into development

commit 35cc09c0fc7725207614449cbefee972515581e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 3 08:44:35 2018 -0800

    update CHANGES

CHANGES

commit 273ca8bb066dd252efe5c3d07199a13155519061
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Dec 2 22:21:50 2018 -0800

    oopsie

Src/EB/AMReX_EB_LSCoreBase.H

commit de5cb48a498414ae2be633c72daeaaa7f8e57292
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Dec 2 22:15:38 2018 -0800

    added valid flags to LSCore class

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H

commit 9ee09d5489def9a8ce26b51bbec1955b491a03f3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Dec 2 21:12:43 2018 -0500

    Restore some code that was deleted in 70befea

Src/Amr/AMReX_Amr.cpp

commit d773698da9a4c6af6b89a8c733cd8458a9092de1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Dec 2 17:55:44 2018 -0500

    make the extrema use a mask to find the true extrema in the domain (#378)
    
    closes #291

Tools/Postprocessing/F_Src/fextrema.f90

commit ab503ef7c6e96820c03ae0b7a4473fdfb34adcf9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Dec 2 13:31:02 2018 -0500

    increase width of box and zone output

Tools/Postprocessing/F_Src/fboxinfo.f90

commit b3734c4bc4b6cbc6935f96109ea99aba2f350acc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 1 19:08:00 2018 -0500

    shift the lo box the big end and do copy too

Src/Base/AMReX_FabArrayCommI.H

commit 596a137de63b0c976bb11d5c14fd94998be0186a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 1 16:03:31 2018 -0500

    add profilers

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit 38540fba4289e16a9ac10148c7b3f9980d13485e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 1 15:32:51 2018 -0500

    fewer kernels in FillBoundary

Src/Base/AMReX_FabArrayCommI.H

commit 7324ec21e899e11f2336685d41bd001f28ce635c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 1 13:38:57 2018 -0500

    fix typo

Src/Base/AMReX_FabArray.H

commit 9697f6eb7ad7a5ba99354ba553cb70b11303b604
Merge: 4677ac986 7c7f14410
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 1 13:31:40 2018 -0500

    Merge branch 'development' into weiqun/comm

commit 7c7f14410b3bce9fab77b4bcf7c4674cf415903f
Merge: 2e26882a4 853174938
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 1 13:24:28 2018 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2e26882a4a789d23bc3ad7c4537c230aec48c51c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 1 13:23:56 2018 -0500

    add function to help MPI progress

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit 4677ac986cd9e20b6a259b21f914ab3c48514c73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 1 07:40:30 2018 -0800

    filcc: multiple passes so that the corners can be dealt

Src/Base/AMReX_PhysBCFunct.H

commit e0f621eafc69e61e5c03f17893790e668b3586f6
Author: kngott <kngott@lbl.gov>
Date:   Fri Nov 30 18:08:32 2018 -0800

    face velocities into MFIter loop.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 85317493856cdd979424dab660606a4695aa9800
Merge: 4b4c53cc8 223e67a50
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 30 13:51:00 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 4b4c53cc8f3f520709665d0f977450919818d6b4
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 30 13:50:56 2018 -0800

    updated amrex build info for macOS

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit 0df67f14e0ce47a2c11a5a17c18b3f2d1f817b7a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 30 13:36:34 2018 -0800

    add hoextrap to filcc3d

Src/Base/AMReX_FilCC_3D_C.cpp

commit 223e67a509d4325ada1fb91ec777a720a2d881d6
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Nov 30 12:00:54 2018 -0800

    ref guide for AMFIter

Docs/sphinx_documentation/source/Chapter6aa.rst
Docs/sphinx_documentation/source/index.rst

commit b21ba19363a3b7904cef88c5b6cd2bcaa0574498
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 30 11:26:23 2018 -0800

    filcc 2d

Src/Base/AMReX_FilCC_1D_C.cpp
Src/Base/AMReX_FilCC_2D_C.cpp

commit 59728376b8df6d3953397a7110ad44498e07a71f
Author: kngott <kngott@lbl.gov>
Date:   Thu Nov 29 16:49:20 2018 -0800

    Init and EstTimeDt

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 3bf5d8b14126ba3dc091ab01fbc32ba87620101b
Author: kngott <kngott@lbl.gov>
Date:   Thu Nov 29 16:49:00 2018 -0800

    Init and EstTimeDt

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H

commit b848f5689f4d9920500c71e92cdb5c5234b54f82
Author: kngott <kngott@lbl.gov>
Date:   Thu Nov 29 16:48:41 2018 -0800

    Break apart face velocity.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp

commit 13132f838d089941d54b4bf5b25aedcd4b451e1c
Author: kngott <kngott@lbl.gov>
Date:   Thu Nov 29 16:47:09 2018 -0800

    Clean up init function.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp

commit 2f59c4138627e5b3301537a5e79a4945e899216a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Nov 29 19:29:44 2018 -0500

    add special case early exit to RedistributeGPU

Src/Particle/AMReX_ParticleContainerI.H

commit 4a629d4f75560f1620dabfe211c66f980cef9f76
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 29 15:48:33 2018 -0800

    fix bug

Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MultiFabUtil_1D.cpp
Src/Base/AMReX_MultiFabUtil_2D.cpp
Src/Base/AMReX_MultiFabUtil_3D.cpp

commit cf026a508c996a49490afe3f1f3a16bbf5afa865
Author: Cy Chan <cychan@lbl.gov>
Date:   Thu Nov 29 14:54:14 2018 -0800

    added Backtrace parser script to Tools/Backtrace/

Tools/Backtrace/parse_bt.py

commit 5770dff76889fda6969490719df1893127ec87b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 29 14:02:19 2018 -0800

    make gcc on cori knl happy

Src/Base/AMReX.H

commit 7f815e30aedb1aea8bd3d0afe6987668181c49d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 29 13:43:55 2018 -0800

    remove all fortran codes in EBMultiFabUtil

Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2D.cpp
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3D.cpp
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_MultiFabUtil_Perilla.cpp
Src/Base/AMReX_MultiFabUtil_nd.cpp
Src/Base/AMReX_iMultiFab.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/EB/AMReX_EBMultiFabUtil.cpp

commit 2939f7ff6c9a45f51283050275502c8c795ba04c
Merge: 3f83a4231 3a9783ffc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 29 13:31:42 2018 -0800

    Merge branch 'development' into weiqun/gpu

commit 3f83a4231344d7ef9c93ceedfe7b12fae13fe2e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 29 13:23:19 2018 -0800

    get_loop_bounds -> amrex_get_loop_bounds for the c bind name because it's global

Src/Base/AMReX_fort_mod.F90

commit c65a496813d271079151b6d5cbbb89c442966685
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 29 13:06:47 2018 -0800

    gpu: amrex_avgdown_with_vol

Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/Perilla_omp/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/Pthread_Common/AsyncMultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.cpp
Src/Base/AMReX_MultiFabUtil_2D_C.cpp
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3D_C.cpp
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_C.H
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_MultiFabUtil_Perilla.cpp
Src/EB/AMReX_EBMultiFabUtil.cpp

commit 2cbb5a911175f02baafe2eee231e7caefcd864e1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 29 12:34:56 2018 -0800

    start work on making BuildMasks multi-level

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 8e5293a45748cccccc659e0cb3fbf0c3651b6b02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 29 12:16:41 2018 -0800

    gpu: amrex_compute_divergence

Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.cpp
Src/Base/AMReX_MultiFabUtil_2D_C.cpp
Src/Base/AMReX_MultiFabUtil_3D_C.cpp
Src/Base/AMReX_MultiFabUtil_C.H
Src/Base/AMReX_MultiFabUtil_F.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit 7814aec884a8967da78409a411258bac49ecb9da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 29 11:41:00 2018 -0800

    gpu: amrex_avgdown and amrex_avgdown_nodes

Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/Perilla_omp/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/Pthread_Common/AsyncMultiFabUtil.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2D_C.cpp
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3D_C.cpp
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_C.H
Src/Base/AMReX_MultiFabUtil_F.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit 3a9783ffc1541b97198111dd7b67734f5c10a828
Author: Donald Willcox <eugene.willcox@gmail.com>
Date:   Thu Nov 29 14:33:57 2018 -0500

    Integrate to dt/2 then to dt to show example of reinitializing CVODE.

Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_cuda_cusolver.cpp

commit 332785a5570ef304c147a43c0715593a8aec2b6e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 29 11:30:25 2018 -0800

    update Tutorial

Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborListMR/main.cpp

commit 8155e58910e0ac2c994fe6003d1b54440fc55b95
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 29 11:30:15 2018 -0800

    don't make the neighbor particle methods take a lev argument

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit af76352c6fcf2e6545d05a0f699386a5ae917ff3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 29 10:52:10 2018 -0800

    gpu: amrex_avgdown_edges

Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.cpp
Src/Base/AMReX_MultiFabUtil_2D_C.cpp
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3D_C.cpp
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_C.H

commit 74f5fa3b2919da1f7481fe04a639163da15a1939
Merge: 222703fbc d0c3db03f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 29 10:35:38 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 222703fbcdf898ccb31d47e96f399443e115b8b0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 29 10:35:21 2018 -0800

    add new Test for multi-level neighbor lists

Tutorials/Particles/NeighborListMR/GNUmakefile
Tutorials/Particles/NeighborListMR/Make.package
Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.H
Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborListMR/inputs
Tutorials/Particles/NeighborListMR/main.cpp
Tutorials/Particles/NeighborListMR/neighbor_list_2d.f90
Tutorials/Particles/NeighborListMR/neighbor_list_F.H

commit 70f5ad5da1fdf6b03356073668b89f1e8fb01086
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 29 10:33:42 2018 -0800

    gpu: amrex_avgdown_faces

Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2D_C.cpp
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3D_C.cpp
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_C.H
Src/Base/AMReX_MultiFabUtil_F.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit 4d035ec1bf113e5f00809e0876cfe410a1e2227f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 29 10:32:56 2018 -0800

    add additional constructor to NeighborParticleContainer

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit d0c3db03f12b6568a4e7292341b6a195e351c330
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 29 13:14:47 2018 -0500

    make BL_NO_FORT compile

Src/Base/AMReX_iMultiFab.cpp

commit bacd9a0d99aabad3adb07f09f4cdaf344a1e8bb4
Merge: 3d77c2d8a eb1403f84
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 29 09:23:52 2018 -0800

    Merge branch 'development' into weiqun/gpu

commit 3d77c2d8a498ba64f883b3c7ec75817497c9a60f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 28 16:59:02 2018 -0800

    Revert "Tutorials/GPU/CNS: fuse launches"
    
    This reverts commit 775aee5056e47cd50247f280e10cbd0069c9c90f.

Tutorials/GPU/CNS/Source/CNS_advance.cpp

commit 775aee5056e47cd50247f280e10cbd0069c9c90f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 28 16:25:12 2018 -0800

    Tutorials/GPU/CNS: fuse launches

Tutorials/GPU/CNS/Source/CNS_advance.cpp

commit 6913553acf820cd15c1bb0a80806df9c207dc06f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 28 16:24:37 2018 -0800

    capability of fusing independent kernels

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_GpuLaunch.H

commit eb1403f84bf5768c6a18abd34b557c6cb2fbd1d4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 28 14:30:10 2018 -0800

    remove unused function

Src/Base/AMReX_MFIter.H

commit 2a70d5953a9831818c15eb0e8a7d431921c2fe9b
Author: kngott <kngott@lbl.gov>
Date:   Wed Nov 28 13:17:05 2018 -0800

    cleanup

Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp

commit 3c32aa4aa643e88b16e458768e19ba3a54f4b5a2
Author: kngott <kngott@lbl.gov>
Date:   Wed Nov 28 13:16:54 2018 -0800

    Ignore TagBox for now.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H

commit bd92538a478e727db6e8dd0468e3b370c3f32555
Author: kngott <kngott@lbl.gov>
Date:   Wed Nov 28 13:16:00 2018 -0800

    Add maxabs to BaseFab.

Src/Base/AMReX_BaseFab.H

commit 8e1f6638e228153ca11f8f0f7f5acd2a4ea77c00
Author: Cy Chan <cychan@lbl.gov>
Date:   Wed Nov 28 13:12:53 2018 -0800

    some performance analysis updates

Src/Base/AMReX_DistributionMapping.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_Machine.cpp

commit e935a2d0230ffccb89dd7f4993e88aa5cb3e9ee0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 28 11:59:10 2018 -0800

    fix index bug

Src/Base/AMReX_MultiFabUtil.cpp

commit 35e074ed0413949d496cdde65f75a163cb69638c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 28 11:42:22 2018 -0800

    renaming

Src/Base/AMReX_Box.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 5986850555d51ccd6bb8f0946d04aa06403cfc0b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 28 10:36:43 2018 -0800

    turn off simd for debug

Src/Base/AMReX_Extension.H

commit b6489523615c349b9cfe2fa8af921b16e053016b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 28 10:36:25 2018 -0800

    fix bug in iMultiFab::sum

Src/Base/AMReX_iMultiFab.cpp

commit 7ed4eede7f6ce513b25996175be30ba422ba5139
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 28 10:28:58 2018 -0800

    consolidate functions for casting from one type of fab to another

Src/Base/AMReX_BaseFabUtility.H
Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_C.H
Src/Base/AMReX_MultiFabUtil_nd_C.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 161eed763bd62ae71ecd71209a6398bd27e9535e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 28 09:55:04 2018 -0800

    add iMultiFab::sum to return long

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_C.H
Src/Base/AMReX_MultiFabUtil_nd_C.cpp
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp

commit b9a14d5546dee0bf37a067136aba2b4c5969541a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 23:05:34 2018 -0800

    fix bug in case of tiling

Src/Base/AMReX_Box.H
Src/Base/AMReX_MultiFabUtil.cpp

commit b6e71d2d8cff9c2939f05b044c867380fe5113be
Merge: 425673b76 98f9a18d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 16:41:16 2018 -0800

    Merge branch 'weiqun/gpu' into development

commit 98f9a18d6c077ffac0207160ec1da047fdd7b9c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 16:39:59 2018 -0800

    gpu: amrex_avg_cc_to_fc

Src/Base/AMReX_Box.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2D_C.cpp
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3D_C.cpp
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_C.H
Src/Base/AMReX_MultiFabUtil_F.H

commit 425673b76142d3bd14be7be6aedaa87749974d96
Merge: 858a1ca7e c33dd3c5a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 16:33:21 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c33dd3c5a2d46f3fa6bb68361d827599c6265f5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 16:28:01 2018 -0800

    avoid using omp simd with pgi

Src/Base/AMReX_Extension.H

commit 42174424dac4f8ac95f7deb539df20c4fcf11470
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 16:28:01 2018 -0800

    avoid using omp simd with pgi

Src/Base/AMReX_Extension.H

commit 858a1ca7eea9112b6df32dc4431d0ff90f75730f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 16:17:35 2018 -0800

    make the neighbors and neighbor_list protected

Src/Particle/AMReX_NeighborParticles.H

commit be85716aeaa293d4bb7b463b4cfd789e950e3207
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 16:16:49 2018 -0800

    add some accessor functions for neighbors and neighbor lists

Src/Particle/AMReX_NeighborParticles.H

commit 1704af23aab2dc4204233a4674f4b158330b280b
Author: Cy Chan <cychan@lbl.gov>
Date:   Tue Nov 27 16:12:13 2018 -0800

    Add neighborhood cache
    Add machine model input parameter parsing
    Add baseline score for neighborhood comparison

Src/Base/AMReX.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_Machine.H
Src/LinearSolvers/MLMG/AMReX_Machine.cpp

commit 218d5ed53c7222595f63f7773adb17c681aa29f5
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Tue Nov 27 15:25:01 2018 -0800

    add conduit blueprint support for particles

Src/Extern/Conduit/AMReX_Conduit_Blueprint.H
Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp
Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H
Tutorials/Blueprint/AssignMultiLevelDensity/GNUmakefile
Tutorials/Blueprint/AssignMultiLevelDensity/main.cpp
Tutorials/Blueprint/CellSortedParticles/CellSortedPC.H
Tutorials/Blueprint/CellSortedParticles/CellSortedPC.cpp
Tutorials/Blueprint/CellSortedParticles/GNUmakefile
Tutorials/Blueprint/CellSortedParticles/Make.package
Tutorials/Blueprint/CellSortedParticles/cell_sorted_3d.F90
Tutorials/Blueprint/CellSortedParticles/cell_sorted_F.H
Tutorials/Blueprint/CellSortedParticles/inputs
Tutorials/Blueprint/CellSortedParticles/main.cpp
Tutorials/Blueprint/README.txt

commit 1661318478bb5d082fb729ee8a3658b512bd98e6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 15:12:08 2018 -0800

    add the level to the internal structs used for keeping track of copies

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 0e6d5d45f11ea8370759c9c1ee9eb8aa097a9c48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 15:00:48 2018 -0800

    fix eb and comp issues in two previous commits

Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.cpp
Src/Base/AMReX_MultiFabUtil_2D_C.cpp
Src/Base/AMReX_MultiFabUtil_3D_C.cpp
Src/Base/AMReX_MultiFabUtil_C.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit 98acf69a9cf77d05c28cad4b8ff85190704a22ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 14:34:21 2018 -0800

    gpu: amrex_avg_fc_to_cc

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2D_C.cpp
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3D_C.cpp
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_C.H
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_RealBox.H

commit b20e6c6b2e934b3efe1297b0cd41ce826b287b78
Author: kngott <kngott@lbl.gov>
Date:   Tue Nov 27 14:06:14 2018 -0800

    Spelling error.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 55b17631bdf14acb116eea9f1a00b50d982df68c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 13:26:20 2018 -0800

    also keep track of the level information in the mask

Src/Particle/AMReX_NeighborParticlesI.H

commit 525f2fd3e12fb2549a7e7c348b26b8297fac558b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 13:22:21 2018 -0800

    use an enum to keep mask comps straight

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 51613d67b0fe83522e9f1f147edd99ebbb87c7df
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 13:12:37 2018 -0800

    BL_ASSERT -> AMREX_ASSERT

Src/Particle/AMReX_NeighborParticlesI.H

commit 60b6b9caaa4f2ed87e1410f5320128efc5c36ab9
Author: kngott <kngott@lbl.gov>
Date:   Tue Nov 27 13:12:31 2018 -0800

    Adjust for new PhysBCFunct.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 5f7314cbb63e4508b88b2d68fe4f719d20b9b0fc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 13:11:14 2018 -0800

    some additional regrid functions

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 7374c1845ad9566b4391e1fb576e8a748d429dc8
Author: kngott <kngott@lbl.gov>
Date:   Tue Nov 27 13:09:03 2018 -0800

    DeviceFab -> AsyncFab

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp

commit 34c9e668709088ed9626250ea727c91e1de8c4fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 13:00:51 2018 -0800

    gpu: amrex_avg_eg_to_cc

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.cpp
Src/Base/AMReX_MultiFabUtil_2D_C.cpp
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3D_C.cpp
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_C.H
Src/Base/AMReX_MultiFabUtil_F.H

commit 37696df94f38392aa66e55ffef50b095e82fa866
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 12:59:24 2018 -0800

    minor

Src/Particle/AMReX_NeighborParticlesI.H

commit 145a358f304070d1ec142942a0819bbf1d6825d9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 12:53:13 2018 -0800

    include mask_ptr in the resizeContainers call

Src/Particle/AMReX_NeighborParticlesI.H

commit 647ec7ccca607aea8011ed947e494a2c6215b215
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 12:50:55 2018 -0800

    also make the level mask structure multi-level

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 84359ac2dbb98fb025e46e10b441f60bc122fb7e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 12:32:01 2018 -0800

    fix off-by-one error

Src/Particle/AMReX_NeighborParticlesI.H

commit a8f0abde115e2d9eaaf312f95416978f5fc9e821
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 12:31:46 2018 -0800

    fix scoping issue in Tutorial

Tutorials/Particles/NeighborList/main.cpp

commit 5025167f4a7150dd1471452be49fbb0dc355d459
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 12:25:13 2018 -0800

    fix the call to get

Src/Base/AMReX_FabArrayCommI.H

commit 52dcac78ada4d441b813876a0a4d9d983d615270
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 12:21:46 2018 -0800

    remove unused variable

Src/Base/AMReX_PhysBCFunct.cpp

commit 2f1ca551bc3807d81e632a5bbce2249c3eb3123b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 12:18:07 2018 -0800

    add call to resize containers to the appropriate size

Src/Particle/AMReX_NeighborParticlesI.H

commit b3e6e8a36a4d89cccf53340d340f9135e8170486
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 12:10:59 2018 -0800

    add method for syncing up the size of neighbors and neighbor_list

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 423f1639185ce324797edbf13894e70b7d16b0ef
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 12:05:38 2018 -0800

    remove the fortran version of buildNeighborList

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit e22fb203cb8f3b77ce7728018f6bf56a2bda6291
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 12:03:23 2018 -0800

    also update the neighbor_list structure for multilevel

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp

commit 9e5d32f9353014d03e29bf500209797c25875672
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 11:56:20 2018 -0800

    update Tutorial

Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp

commit 3445d53662b553bfeadbee22d2ed67d5b54f71e7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 27 11:55:34 2018 -0800

    make the neighbor particle data structure a vector over levels

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 881e74d519892a8e7e1f6ef3bd55864d2f1c30a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 11:54:01 2018 -0800

    gpu: amrex_avg_nd_to_cc

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2D_C.cpp
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3D_C.cpp
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_C.H

commit c60bfca40bcc92a439390bdb2a6ced4b3031ef27
Merge: 4910e319b ddf01ba96
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Nov 27 10:40:16 2018 -0800

    Merge pull request #369 from burlen/sensei_init_ghost_zones
    
    Sensei init ghost zones

commit 4910e319be95dca91be17997552adb359eefa13a
Merge: 60588d2d1 8bc68a05c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Nov 27 10:28:16 2018 -0800

    Merge pull request #372 from knutsvk/development
    
     use VisIt compatible plotfile heading

commit 8bc68a05ce98c067a3f758e5bb2b80863ac63051
Merge: 5433d9588 60588d2d1
Author: knutsvk <ksk38@cam.ac.uk>
Date:   Tue Nov 27 18:07:40 2018 +0000

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 5433d9588db554d36cb11a4c82f26235f65ca7a0
Author: knutsvk <ksk38@cam.ac.uk>
Date:   Tue Nov 27 18:06:14 2018 +0000

    use VisIt compatible plotfile heading

Tutorials/EB/CNS/Source/CNS.H

commit 60588d2d1206151e96684d8fb568e0ec53d88aa6
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Nov 26 22:49:33 2018 -0800

    fix spelling mistake

Src/Base/CMakeLists.txt

commit df50c313bbce1203b68ad87b86dc74a52dbcd2a0
Merge: a3c796db7 b8f7450c2
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Nov 26 22:22:01 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit a3c796db779ce362469fde641190998084c4e811
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Nov 26 22:21:56 2018 -0800

    coarsen ghost cells as well

Src/EB/AMReX_EB_levelset.cpp

commit efb81b1d09de3979f511af9aa547b63dbd10e14a
Author: kngott <kngott@lbl.gov>
Date:   Mon Nov 26 17:50:01 2018 -0800

    Fix merge error.

Src/Base/AMReX_BaseFab.H

commit b8f7450c293ea8d0452ec25a64421dfbe107011c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 26 17:48:23 2018 -0800

    more inline

Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H

commit 97e4ed5eefb54713df5b7effd25e5d60f7757a90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 26 17:42:43 2018 -0800

    MultiFabUtil: fill slice on gpu

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_C.H
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_MultiFabUtil_nd.F90
Src/Base/AMReX_MultiFabUtil_nd_C.cpp
Src/Base/AMReX_RealBox.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 65cbb1576a8754d39bc5fadb184997f9c8df62d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 26 16:09:09 2018 -0800

    MultiFabUtil: start gpu

Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1D_C.cpp
Src/Base/AMReX_MultiFabUtil_2D_C.cpp
Src/Base/AMReX_MultiFabUtil_3D_C.cpp
Src/Base/AMReX_MultiFabUtil_C.H
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_MultiFabUtil_nd.F90
Src/Base/AMReX_MultiFabUtil_nd_C.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 213635d6775844d294568646f8c9af8a2e4b91af
Merge: 5d4ce9dcd c37f49b21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 26 18:05:32 2018 -0500

    Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu

commit c37f49b219da98a28d3b44f3ac56f15670dd7117
Merge: ed44f743b 2e7e32e68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 26 14:52:50 2018 -0800

    Merge branch 'weiqun/gpu' into development

commit 2e7e32e683e3203cf418ce7636c006cca52c126f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 26 13:45:58 2018 -0800

    remove unused norm0 function

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit 5d4ce9dcd4bbae263210024442f46500cafb9874
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 26 16:04:50 2018 -0500

    cudaMallocHost -> cudaHostAlloc

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CudaDevice.cpp

commit 191d4c715f847dc013109884d11bd4c96663d0d4
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Nov 26 12:41:14 2018 -0800

    added remap neighborhoods to MLLinOp

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_Machine.H
Src/LinearSolvers/MLMG/AMReX_Machine.cpp
Src/LinearSolvers/MLMG/Make.package
Tests/LinearSolvers/MLMG/AMReX_Machine.H
Tests/LinearSolvers/MLMG/Make.package
Tests/LinearSolvers/MLMG/inputs
Tests/LinearSolvers/MLMG/main.cpp

commit cd2f7c0f58f44ed7aa8405224a90619e61fe2a83
Merge: 055ef5b2b 52ee04e9d
Author: kngott <kngott@lbl.gov>
Date:   Mon Nov 26 12:06:18 2018 -0800

    Merge branch 'weiqun/gpu' into gpu

commit 055ef5b2b717aa6c07342f92d02dfbdbef9c928c
Author: kngott <kngott@lbl.gov>
Date:   Mon Nov 26 12:00:19 2018 -0800

    Remove .f90. Now CPU compiling. (WIP).

Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.f90

commit c1615e607ea2bef18bbd9b4ddace82e42f0cb7af
Author: kngott <kngott@lbl.gov>
Date:   Mon Nov 26 11:51:50 2018 -0800

    First attempt at slope_3d.cpp.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp

commit ed44f743bfcb09aa8c117276d2a91db0a3158ab5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 26 11:32:41 2018 -0800

    Add the brackets between amrex::Initialize() and amrex::Finalize()

Tests/HDF5Benchmark/main.cpp

commit 1c5e13e81cdec0ba12b0304b400f6764718d4684
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Nov 26 10:36:50 2018 -0800

    bug fixes and cleanup

Tests/LinearSolvers/MLMG/AMReX_Machine.cpp

commit 52ee04e9d3d5185992e34b22b6236f1f3ef075cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 26 09:35:37 2018 -0800

    change the interface of WriteMLMF to take Vector of MultiFab const*

Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_PlotFileUtil.cpp

commit 58646d3278b37b1cd6ff858014c581f479d66bdb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 26 08:56:17 2018 -0800

    rm iMultiFab norm funcitons

Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp

commit 1c6606ac457a79403fe6a12c1294da77847f1f5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 26 11:32:40 2018 -0500

    make: add USE_CUDA_FAST_MATH so that we could turn off fast math

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/nvcc.mak

commit 1532d6054a5dcdefb481b93f3d5dd923d8dfae19
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 26 11:23:51 2018 -0500

    set shared memory bank size

Src/Base/AMReX_CudaDevice.cpp

commit 3ac5023b4bc5d8504014b17ba40a3d2fd4d75cda
Merge: c8012139e b7f54ed1f
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Nov 26 08:09:05 2018 -0800

    Merge pull request #273 from Alpine-DAV/task/2018_06_add_blueprint_and_ascent
    
    add optional blueprint and ascent support to AMReX

commit c8012139ee40261ad0da31f1d19b2d52d31de375
Merge: 6f0792c81 6898aee6f
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Nov 26 08:06:54 2018 -0800

    Merge pull request #371 from knutsvk/development
    
    MLNodeLaplacian: overload define() with EBFArrayBoxFactory as input

commit 6898aee6f836b21cea251388c67eb980f5616f27
Merge: a8052b700 6f0792c81
Author: knutsvk <ksk38@cam.ac.uk>
Date:   Mon Nov 26 10:44:26 2018 +0000

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 3a0dabb5b8bf8f7044bf44fcfdda26aa9dce4711
Author: Kaiyuan Hou <khou2020@outlook.com>
Date:   Sun Nov 25 23:56:27 2018 -0600

    remove hdf5 code

Tests/HDF5Benchmark/GNUmakefile
Tests/PnetCDFBenchmark/GNUmakefile
Tests/PnetCDFBenchmark/Make.package
Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp
Tests/PnetCDFBenchmark/main.cpp

commit 8cab06ca66be3c1d96ebb33d453c5227b726cc16
Author: kngott <kngott@lbl.gov>
Date:   Sun Nov 25 20:03:26 2018 -0800

    slope left (WIP).

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package

commit 02a9024ea8a6a15d27a5100690096ba79c5f009b
Author: kngott <kngott@lbl.gov>
Date:   Sun Nov 25 19:59:19 2018 -0800

    cpp versions

Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp

commit 6f0792c81782661fa04e758df452b5afbf5c6822
Merge: 9f8303ba4 141666f10
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 25 18:18:08 2018 -0800

    Merge branch 'weiqun/comm' into development

commit 9f8303ba4b32902bca974450e97def9620012382
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sun Nov 25 16:42:13 2018 -0800

    update destructors for AMFIter related classes

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AsyncFillPatch.cpp
Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp
Src/AmrTask/rts_impls/Perilla/Perilla.H
Src/AmrTask/rts_impls/Perilla/Perilla.cpp
Src/AmrTask/rts_impls/Perilla/RegionGraph.H
Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp
Src/AmrTask/rts_impls/Pthread_Common/LocalConnection.H

commit 141666f108e526ebad2f8caf018b41a8a6cf3fab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 25 15:14:30 2018 -0800

    fix bug: forgot for after omp parallel

Src/Base/AMReX_FabArrayCommI.H

commit 12847a471aaae4315ffe246be9a3653222042258
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 25 11:28:39 2018 -0800

    fix bugs in the new ParallelCopy

Src/Base/AMReX_FabArrayCommI.H

commit c4f3a77cb90158ab89e43e17c26dd5cab08d926a
Merge: 69372fdca 7b357feba
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Nov 24 22:01:54 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 69372fdca700c154aa3ba03ef2e0893a123ec449
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Nov 24 22:01:45 2018 -0800

    some cleanup and fixing parameters

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/EB/AMReX_EB_LSCoreBase.cpp
Tutorials/EB/Donut/Exec/inputs

commit ecd7645fecddd8ae75ea498f5b81045afc417c72
Merge: a191785e3 7b357feba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 24 21:17:11 2018 -0800

    Merge branch 'development' into weiqun/comm

commit 7b357feba36aaf0dba217d952aff62fde65e1342
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 24 21:14:28 2018 -0800

    add scope

Tests/LinearSolvers/ComparisonTest/main.cpp

commit 7077ee903422fa6af136c7d2fa45288083f688ab
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Nov 24 21:07:47 2018 -0800

    make use of BL_TO_FORTRAN macros

Src/EB/AMReX_EB_LSCoreI.H
Tutorials/EB/Donut/Exec/inputs

commit f6bce80ee9a3d4c1c7f05555bcdcf6d2c77869ea
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Nov 24 20:28:46 2018 -0800

    higher blocking factor

Tutorials/EB/Donut/Exec/inputs

commit a191785e3b535b1f406ed259a4815a64c33819e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 24 19:40:04 2018 -0800

    update ParallelCopy

Src/Base/AMReX_FabArrayCommI.H

commit 82f932bcfee120573ee9cad039dac8019893320e
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Nov 24 18:14:36 2018 -0800

    added adaptive mesh around donut

Src/EB/AMReX_EB_LSCoreI.H
Tutorials/EB/Donut/Exec/inputs
Tutorials/EB/Donut/Src/main.cpp

commit fa30aa76a1da0d9d523509372d8b101a52658a8e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 24 18:11:10 2018 -0800

    update FillBoundary

Src/Base/AMReX_FabArrayCommI.H

commit a6fbd66f7d1da4234fd677311253634ca2c81114
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 24 17:03:25 2018 -0800

    fix bug: unpacking must be consistent with packing

Src/Base/AMReX_FabArrayCommI.H

commit eee869a81c46974c498c94871f1da92f259d3653
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 24 16:58:55 2018 -0500

    wip: fix race condition in ParallelCopy unpacking

Src/Base/AMReX_FabArrayCommI.H

commit 6cca89f4130cfbaea2894d0aebee9211d8acdaf9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 24 16:07:07 2018 -0500

    clean up

Src/Base/AMReX_FabArrayCommI.H

commit c427998b8b467b9c7579461366e094d142b823eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 24 15:38:45 2018 -0500

    split local copy in ParallelCopy into multiple versons

Src/Base/AMReX_FabArrayCommI.H

commit 40de547ab972f2adbd79cae73de08648e28131f7
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Nov 24 12:16:17 2018 -0800

    added bite make to donut

Tutorials/EB/Donut/Exec/inputs
Tutorials/EB/Donut/Src/eb_to_pvf.F90
Tutorials/EB/Donut/Src/main.cpp

commit a154ef0b0736c13881f8f7495f1b564bd5eb4fd0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 24 14:41:22 2018 -0500

    change operator< for locality

Src/Base/AMReX_FabArrayBase.H

commit 216f6e6ab1fd7d2fc373f7e27ceca671c9b2022d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 24 14:39:35 2018 -0500

    print version

Src/Base/AMReX.cpp

commit 86b5351631e1db31f2531560c5723b4a1d9cc548
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 23 23:20:52 2018 -0800

    yay this is a donut... but some of the ebgrids are missing :(

Tutorials/EB/Donut/Exec/inputs
Tutorials/EB/Donut/Src/main.cpp

commit edfb23d23c22b834f95921546038d9992aeaeaf1
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 23 23:09:12 2018 -0800

    added rudimentary inputs file

Tutorials/EB/Donut/Exec/inputs

commit 79836c5a8b12da60cea5108b21d9611dee33b9d0
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 23 23:04:49 2018 -0800

    debug donut example

Src/EB/AMReX_EB2_IF_Torus.H
Tutorials/EB/Donut/Exec/GNUmakefile
Tutorials/EB/Donut/Src/Make.package
Tutorials/EB/Donut/Src/main.cpp

commit f4662aaf5c04590451a3f70ae689a4eacf9adacc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 24 01:47:40 2018 -0500

    reorder local copy in ParallelCopy

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit 254f0c0ed0d88896257f2222e456c6a1cd4aaec7
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 23 22:42:16 2018 -0800

    make use of BL_TO_FORTRAN macros

Tutorials/EB/Donut/Src/main.cpp

commit d5601f3052a793399b24e8fc3e5c182591e8fe3a
Merge: 10377ee12 7d49e97eb
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 23 22:34:22 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 10377ee120f955aefeeac9d3d2219c8d908dde1b
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 23 22:34:15 2018 -0800

    start working on donut example

Tutorials/EB/Donut/Exec/GNUmakefile
Tutorials/EB/Donut/Src/EB_F.H
Tutorials/EB/Donut/Src/Make.package
Tutorials/EB/Donut/Src/eb_to_pvf.F90
Tutorials/EB/Donut/Src/main.cpp
Tutorials/EB/LevelSet/Src/main.cpp

commit 7d49e97ebbe2b0d3b29ab511b56031f7bf5502c1
Merge: cda07930c d3ec30436
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 23 17:06:15 2018 -0800

    Merge branch 'development' into weiqun/gpu

commit d3ec3043682ad03ab9c063a45471701150457555
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 23 17:02:46 2018 -0800

    rm using std::min and std::max

Src/Extern/amrdata/AMReX_DataServices.cpp

commit 3a31aedf82b30b227f00ac836e741528a3f798b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 23 17:00:55 2018 -0800

    remove start_profiler

Src/Amr/AMReX_Amr.cpp

commit cda07930c4898d91c9a678372b50e7b508bab4d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 23 16:04:11 2018 -0800

    ifdef cuda specific stuff

Src/Base/AMReX_CudaMemory.H

commit 5405e9559e5b398c30a36c1619e8595351037366
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 23 16:02:17 2018 -0800

    gpu reduce in MultiFab

Src/Base/AMReX_MultiFab.cpp

commit 53053dcee83e4e69cf041af80b02d2d42cae8948
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 23 15:38:50 2018 -0800

    fix extern shared for templates

Src/Base/AMReX_CudaMemory.H
Src/Base/AMReX_FabArrayUtility.H

commit 0e52972d59f9241cd47c82f3a98ced1d4e516021
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 23 14:51:49 2018 -0800

    Gpu reduce in iMultiFab. Removed norm functions from iMultiFab. don't think we need them.  If they are indeed needed by codes, we will put them back.

Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IArrayBox.cpp
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp

commit 8aeef50cd914e32e9f52b57cdd46a2d653fcc4a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 23 14:47:32 2018 -0800

    remove init from reduce

Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_MultiFab.cpp
Tutorials/GPU/CNS/Source/CNS.cpp

commit fd0af808d81c66deac2c925a0f26fb14667685e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 23 13:34:46 2018 -0800

    add more FabArray reduce and put them in FabArrayUtility

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayUtility.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tutorials/GPU/CNS/Source/CNS.cpp

commit 570f9e7ff41c5030f712cfa8bdd80ee932637346
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 23 11:30:09 2018 -0800

    add indentation when printing unused parmparse parameters

Src/Base/AMReX_ParmParse.cpp

commit 314c43e64a131106ab3e39e304d9cf62881be593
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 23 11:20:25 2018 -0800

    print out a message after initialize and finalize

Src/Base/AMReX.cpp

commit a8052b7008cc187061651c4aa4c04be81a2fc550
Author: knutsvk <ksk38@cam.ac.uk>
Date:   Fri Nov 23 14:00:14 2018 +0100

    use the ebfactory version of define in the ebfactory version of constructor

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit d76df14022fa9e5e1a183b558c4688feaf77457b
Author: knutsvk <ksk38@cam.ac.uk>
Date:   Fri Nov 23 13:54:28 2018 +0100

    use c++14

Tools/GNUMake/comps/llvm.mak

commit 6e52f7b571f92c39cdc2d9a1aef21c5a52ba16c4
Merge: 5f174ee0a 7d6811caf
Author: knutsvk <ksk38@cam.ac.uk>
Date:   Fri Nov 23 13:53:39 2018 +0100

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 5f174ee0a55cb46c167461745a5fed86ba0b565c
Author: knutsvk <ksk38@cam.ac.uk>
Date:   Fri Nov 23 13:53:19 2018 +0100

    overload define() to work when given EBFArrayBoxFactory instead of FabFactory<FArrayBox> as input

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 5324e8a457cb94c90d245c52ab55c7adfeca1459
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 21 21:33:40 2018 -0800

    add typename

Src/Base/AMReX_FabArray.H

commit 287365b7b75eedf3ef301d540451be0b342198c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 21 20:57:21 2018 -0800

    more FabArray::reduce*

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.cpp

commit bc7d54352020990ce4d25e24abaed7ad0729061a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 21 19:05:18 2018 -0800

    move MultiFab reduction into FabArray templates

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.cpp
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_K.cpp

commit 7d6811caf7cd1be6800a18847d07abb4d30d8d9c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 21 18:49:20 2018 -0800

    give more information before aborting

Src/AmrCore/AMReX_AmrMesh.cpp

commit dcb1401d5637d7c11330d7840d355f17e8510ee0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 21 16:39:23 2018 -0800

    Tutorials/GPU/CNS: fast reduction

Src/Amr/AMReX_AmrLevel.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.H
Tutorials/GPU/CNS/Source/CNS.H
Tutorials/GPU/CNS/Source/CNS.cpp

commit fc73948ef7829210048bbb60f64c6a2d6b292015
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 21 16:06:22 2018 -0800

    add more reduce functions

Src/Base/AMReX_CudaReduce.H

commit f272cc68a61be9cb3007c214671c3a818918efaf
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Nov 21 13:06:06 2018 -0800

    extract metadata after regridding on a non-base AMR level

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AsyncFillPatch.cpp

commit 96568cfaebc631f1d9c7dd8e017e15eac18bfb7d
Author: kngott <kngott@lbl.gov>
Date:   Wed Nov 21 12:18:15 2018 -0800

    Put changes into Src_3d until 3d and 2d combined.

Tutorials/GPU/Advection_AmrCore/Source/Src/Adv_3d.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src/Adv_3d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src/compute_flux_3d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src/slope_3d.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src/slope_3d.f90

commit 3ff668716381aa3f4d915e07ee81fbfbcbf09667
Author: kngott <kngott@lbl.gov>
Date:   Wed Nov 21 12:15:03 2018 -0800

    Wrap OpenMP pragma.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp

commit b6e4e28f7477014f1b820a2879d85dbdab0606ed
Merge: b8241914a 7027401f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 20 21:01:50 2018 -0500

    Merge branch 'weiqun/gpu' into development

commit 7027401f5607381901d20c1d2285a46c41d96a15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 20 19:52:13 2018 -0500

    back to use device pagable memory

Src/Base/AMReX_CudaAsyncArray.H
Src/Base/AMReX_CudaAsyncArray.cpp
Src/Base/AMReX_CudaAsyncFabImpl.H
Src/Base/AMReX_CudaAsyncFabImpl.cpp

commit b7f54ed1fa3d118356bcf71c934bc2363b643fdf
Merge: f6a412b1b b8241914a
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Tue Nov 20 11:22:35 2018 -0800

    Merge branch 'development' into task/2018_06_add_blueprint_and_ascent

commit b8241914a423708507954a0771be46418abac297
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Tue Nov 20 01:47:57 2018 -0500

    Clarify CUDA and PGI versions as well as the make command in the Readme.

Tutorials/CVODE/SUNDIALS4/EX3-CUDA/README.md

commit 62fad37ef1ecb74879b1210497f0a25765220e87
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Tue Nov 20 01:38:03 2018 -0500

    Update call to cv_cuSolver_SetLinearSolver to support additional arguments.

Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_cuda_cusolver.cpp

commit 0b1275d18317dcc1fc37db13ab38186a0d64ba06
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Nov 19 22:46:01 2018 -0500

    Write out small plotfile in addition to full plotfile

Src/Amr/AMReX_Amr.cpp

commit 6c05cb3948c24480e79a18b00f69d5a30fd4b9bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 19 15:56:22 2018 -0800

    split warpReduceSum into two versions

Src/Base/AMReX_CudaReduce.H

commit 6a89dcadb9396b9ea219e1d19d44860b0355796b
Merge: f61b78ac8 ef6f45eee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 19 15:28:49 2018 -0800

    Merge branch 'development' into weiqun/gpu

commit f61b78ac8c566ca12aa237e0f09ee637a99e6ce4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 19 15:28:02 2018 -0800

    preallocate some memory in amrex::Initialize; switch to using pinned memory for cudaMemcpyAsync

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_CudaAsyncArray.H
Src/Base/AMReX_CudaAsyncArray.cpp
Src/Base/AMReX_CudaAsyncFabImpl.H
Src/Base/AMReX_CudaAsyncFabImpl.cpp

commit ef6f45eeed154138153a30abef31abf2eec200f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 19 10:50:29 2018 -0800

    call __syncwarp for volta

Src/Base/AMReX_CudaReduce.H

commit 23cd99ddc27b1b5a9ea38b38eea01264a48fdc51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 19 10:23:08 2018 -0800

    ifdef

Src/Base/AMReX_CudaLaunch.cpp

commit 0cb37e1aeaf16a4967dbe70fd5e335c7b373c7ed
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 19 09:41:34 2018 -0800

    AMREX_CudaReduce.H --> AMReX_CudaReduce.H

Src/Base/CMakeLists.txt

commit d5aaebe623f794b424be322222f937993cd5be4f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 19 09:20:17 2018 -0800

    Tutorials/GPU/CNS: set USE_CUDA to TRUE by default

Tutorials/GPU/CNS/Exec/Sod/GNUmakefile

commit f7a7d8637179b4a892932206acf5a6c038a5b270
Merge: 1c5d1e1d2 e18f6904a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 19 08:53:16 2018 -0800

    Merge branch 'weiqun/gpu' into development

commit 927389db6eef77a3ac707e649dfead863cec18c5
Author: kngott <kngott@lbl.gov>
Date:   Mon Nov 19 01:24:20 2018 -0800

    Fix: phi -> psi.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp

commit 1c5d1e1d27b127299d248d24b54344f54ea840a7
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Nov 18 22:32:08 2018 -0800

    LSCoreBase returns level-set data

Src/EB/AMReX_EB_LSCoreBase.H

commit e18f6904a7b79877cf85bc09faa93c85655b1e75
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 18 21:46:55 2018 -0800

    minor

Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaReduce.H
Src/Base/AMReX_MFIter.cpp

commit ddf01ba968fd62c6dfcb8341617cee30c4785c86
Author: Burlen Loring <bloring@lbl.gov>
Date:   Fri Nov 16 12:55:14 2018 -0800

    add option to pin mesh
    
    this forces mesh origin to 0,0,0. this works around
    a bug in visit enabling visualization of moving meshes
    it's off by deault.

Src/Extern/SENSEI/AMReX_AmrDataAdaptor.H
Src/Extern/SENSEI/AMReX_AmrDataAdaptor.cpp
Src/Extern/SENSEI/AMReX_AmrInSituBridge.cpp
Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.H
Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp
Src/Extern/SENSEI/AMReX_AmrMeshInSituBridge.cpp
Src/Extern/SENSEI/AMReX_InSituBridge.H
Src/Extern/SENSEI/AMReX_InSituBridge.cpp

commit 2c4868194d35d1506e9bec7b8479afeb70fda599
Author: Burlen Loring <bloring@lbl.gov>
Date:   Thu Nov 15 04:50:13 2018 -0800

    add functions to fill ghost cells in cell centering conversions

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 7745635a6ff976174178be663b148e24f223113f
Author: Kaiyuan Hou <khou2020@outlook.com>
Date:   Sun Nov 18 00:19:45 2018 -0600

    single thread

Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp

commit b7692f02f86fbe8520e07dd97d56a5e4cb0a4dda
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Nov 17 15:04:48 2018 -0800

    add note for macOS users

Tools/CMake/AMReX_InstallExternalLibs.cmake

commit 01f96627f44f869e6e6d7819c12e6f9155b3a46c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 17 13:27:20 2018 -0800

    redo reduction in MultiFab::sum

Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp
Src/Base/AMReX_CudaReduce.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 681241e5b72ed01ff37106743720967047824105
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sat Nov 17 12:28:56 2018 -0800

    Begin cpp version of Src

Tutorials/GPU/Advection_AmrCore/Source/Src/Adv_3d.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src/Adv_3d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src/compute_flux_3d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src/slope_3d.cpp
Tutorials/GPU/Advection_AmrCore/Source/Src/slope_3d.f90

commit f7e0342deac5407d6e0c6119ff565d227349fbea
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sat Nov 17 12:26:52 2018 -0800

    Adjustments.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H

commit 20d4d4532a20b2e2c31f6dc5f16f59fa6de27b50
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sat Nov 17 12:25:20 2018 -0800

    Clean up face_velocity.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90

commit af23e716c8398e8e92570be8ae78bc4246b63e21
Author: Kaiyuan Hou <khou2020@outlook.com>
Date:   Fri Nov 16 23:50:23 2018 -0600

    compile passed

Tests/PnetCDFBenchmark/GNUmakefile
Tests/PnetCDFBenchmark/Make.package
Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.H
Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp
Tests/PnetCDFBenchmark/inputs
Tests/PnetCDFBenchmark/main.cpp

commit 74c6f2462571a476d12f48e16915f2249e0d8de6
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 16 20:40:15 2018 -0800

    enable ls core to read external tag-levels (needed for mfix)

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp

commit 0a34e27f6d3d9c4e57848ffb6b47c4664a293e64
Merge: b598d8053 364afd71f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 16 19:10:06 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit b598d8053d478f7985a0e9d33a1cfc430355cd8f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 16 19:09:31 2018 -0800

    no longer need to store extra level_set_cc mf vector

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H
Tutorials/EB/LevelSet/Src/main.cpp

commit e6816d454b9a3b7586109eb87b23b26722d784d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 16 20:44:04 2018 -0500

    add some inline

Src/Base/AMReX_CudaUtility.H

commit 1b825e8c39e633bcb4e4c4e71cfc63a10806a977
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 16 16:20:33 2018 -0800

    put setComplement on gpu

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_PhysBCFunct.H

commit 364afd71f5daa53770eaf54e73888d3e8d34f199
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 16 14:25:56 2018 -0800

    fix makefile logic

Tools/GNUMake/comps/pgi.mak

commit a316a11474297f18c1e013a5d384e2fa0af7e20c
Author: Cy Chan <cychan@lbl.gov>
Date:   Fri Nov 16 13:24:47 2018 -0800

    add local neighborhood calculation

Tests/LinearSolvers/MLMG/AMReX_Machine.H
Tests/LinearSolvers/MLMG/AMReX_Machine.cpp
Tests/LinearSolvers/MLMG/main.cpp

commit 4d461681b1f7f3fc49ac456d1d8b8ff9f052e9ed
Merge: b00ce98ac d598e3a3c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 16 14:10:20 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b00ce98ac9872b43e5dcf523c9a505a841c6f62c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 16 14:10:12 2018 -0800

    fix merge error

Tools/GNUMake/comps/pgi.mak

commit d598e3a3ce46a590eeb973849835f5b475ec3d2b
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 16 13:57:29 2018 -0800

    get rid of unused variable

Src/EB/AMReX_EB_levelset.cpp

commit 992757b9f19a86085a4c42aa542bd4b0f8188c0a
Merge: 151a1f1d0 6742063eb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 16 13:16:34 2018 -0800

    merging

commit 151a1f1d07a870b12202219b1b260a7e004995c7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 16 13:14:27 2018 -0800

    turn on c++14 for pgi if the gcc version is new enough

Tools/GNUMake/comps/pgi.mak

commit 71b71551097e8c58ea519666987428b0a47f067c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 16 12:49:32 2018 -0800

    also parse pgi major and minor version numbers in pgi.mak

Tools/GNUMake/comps/pgi.mak

commit 6742063eb4e27f72b2c87b3ddc7a7ef4fe032264
Merge: 81df91a3f 825e8e1bb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 16 12:04:49 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 81df91a3fd05e71e2d8f065a11c5680f0a9aeb2b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 16 12:04:34 2018 -0800

    do not serialize the initial conditions in the HDF5 benchmark

Tests/HDF5Benchmark/main.cpp

commit 825e8e1bbc4a0259f45a29b7f18bd4f3e6d04df8
Merge: 3f66e38d0 4aeeccd82
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 16 10:40:46 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 3f66e38d01e50e046d248363e34cc4f0e2d226db
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 16 10:40:39 2018 -0800

    fix pointer pass-by-reference

Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_Tagging.F90
Tutorials/EB/LevelSet/Exec/inputs
Tutorials/EB/LevelSet/Src/main.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp
Tutorials/EB/LevelSet/Src/make_shapes.H

commit 4aeeccd8223b9c4cd00777982bd055f912ec143a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Nov 16 09:32:49 2018 -0800

    Add absolute tolerance to MAC projector

Src/LinearSolvers/MLMG/AMReX_MacProjector.H
Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp

commit 931363df02c9613e25af9bb83fd2c05d6efe9dfb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 22:58:51 2018 -0800

    move the change to libraries to the end of Make.defs

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/nvcc.mak

commit 39e2b48541fadb9c6afa3f5d43e87543bf469e8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 22:53:31 2018 -0800

    fix linking with nvcc

Tools/GNUMake/Make.rules
Tools/GNUMake/comps/nvcc.mak

commit a3675430d9635710805c03c86f7266714790089c
Author: Cy Chan <cychan@lbl.gov>
Date:   Thu Nov 15 17:55:13 2018 -0800

    performance analysis:
      added AMReX_Machine.H/.cpp utilities to determine location on machine

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Tests/LinearSolvers/MLMG/AMReX_Machine.H
Tests/LinearSolvers/MLMG/AMReX_Machine.cpp
Tests/LinearSolvers/MLMG/GNUmakefile
Tests/LinearSolvers/MLMG/Make.package
Tests/LinearSolvers/MLMG/main.cpp

commit 24c3033f66a3fb425be7eaede019bdca0fa36908
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 16:32:10 2018 -0800

    respect NVCC_HOST_COMP

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/nvcc.mak

commit 2d2ac366e0c66226b846befddb9997382c314729
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 18:03:35 2018 -0500

    fix ibm.mak

Tools/GNUMake/comps/ibm.mak

commit 86e33d764bdf6880b96281d4d7ff43f9777c3c91
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 14:56:47 2018 -0800

    rename for clarity and update make help

Tools/GNUMake/Make.rules

commit 9301c8eb784190c0529738a2bbaf5160c76e1b28
Merge: dc76962de 989c90b83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 14:45:07 2018 -0800

    Merge branch 'development' into weiqun/gpu

commit 989c90b838042ca14327537b90ad6e7b5bc09284
Merge: 5403edfe1 244a5374d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 14:44:01 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit dc76962de8ceb9bd5f2d90c98b0c818de2097a77
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 14:37:35 2018 -0800

    add openacc to ignore list

Tools/F_scripts/dep.py

commit b5dcbd075be89b210fbfc0ab2bbb10d82d862ab2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 13:55:56 2018 -0800

    modify make so that we can compile with nvcc+gcc without pgi or ibm

Src/Base/AMReX_fort_mod.F90
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/ibm.mak
Tools/GNUMake/comps/nvcc.mak
Tools/GNUMake/comps/pgi.mak

commit fff82f1cde2c01671af29024338f26115ce0b0c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 11:30:35 2018 -0800

    a bug in make

Tools/GNUMake/comps/nvcc.mak

commit 495bb2b38fcf31aeafb7c33162f3561c5e53eea2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 11:19:27 2018 -0800

    add --ptxas-options=-O3

Tools/GNUMake/comps/nvcc.mak

commit 5f7e0e25c123f868646c3a8162cf7982755f3fc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 11:18:22 2018 -0800

    add comments

Tools/GNUMake/sites/Make.unknown

commit 244a5374dfcadd27ba0e51c98d19388bef61514a
Merge: 149755ad7 b24fd785b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 15 10:18:30 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 149755ad7ee8b75d5cf09d162ff5aa5ba3fc1adb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 15 10:17:52 2018 -0800

    whitelist nec compiler as well

Tools/libamrex/configure.py
Tools/libamrex/mkconfig.py

commit 481a8d5bbd423e824de2b8bcdcd33c7b10ba0c7b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 09:47:18 2018 -0800

    typo

Src/Base/AMReX_CudaDevice.cpp

commit 7e65ef96421d8abcc3a327f1b4d21ca7f89cf82d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 09:46:31 2018 -0800

    move openacc stuff into fortran

Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_acc_mod.F90
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit b952c36d843e69c9341b357728a156136bc8ddc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 09:23:40 2018 -0800

    update script

Tools/F_scripts/write_cuda_headers.py

commit 1dee311c510843954f5b8850445f56b3c9f48dbe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 15 09:00:06 2018 -0800

    move the initialiation and finalization of arenas to amrex::Initialize and Finalize so that these arenas will be deleted before cuda shuts down its runtime

Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp

commit b24fd785bb2138b778f7d67b4c88b6e2fc2dc617
Merge: 1a0fdf0e5 0e3e59bf9
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Nov 14 21:44:40 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 1a0fdf0e57de03dd5237f98aacc3c3f862de82ee
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Nov 14 21:44:29 2018 -0800

    modernizing ls core tutorial

Tutorials/EB/LevelSet/Exec/inputs
Tutorials/EB/LevelSet/Src/main.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp
Tutorials/EB/LevelSet/Src/make_shapes.H

commit 12e2b6257d187045b22f6f66f79b173b0b58b7b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 14 16:49:30 2018 -0800

    migrated fortran function threads_and_blocks

Src/Base/AMReX_CudaDevice.cpp

commit 6062586795fe10a66bd8857cff7616bb6b3727b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 14 15:51:14 2018 -0800

    remove AMReX_CudaFort.F90

Src/Base/AMReX_CudaFort.F90
Src/Base/Make.package

commit 014aac3b699387d2d6e1ab725fa00d662bcf6409
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 14 15:50:15 2018 -0800

    remove dependence on cuda fortran

Src/Amr/AMReX_Amr.cpp
Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_BArena.H
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaFort.F90
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaUtility.cpp
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_fort_mod.F90

commit 0e3e59bf9c2cb9846870d9579d41001a11183b6d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Nov 14 17:42:59 2018 -0500

    support ibm compiler for libamrex

Tools/GNUMake/Make.rules
Tools/libamrex/configure.py
Tools/libamrex/mkconfig.py

commit 9eca4f9b5920505fb247be6a6dc1d50fcf41b69a
Author: Guy Moore <gmoore@lbl.gov>
Date:   Wed Nov 14 13:51:42 2018 -0800

    fix sphynx error message

Docs/sphinx_tutorials/source/AMR_Tutorial.rst
Docs/sphinx_tutorials/source/Basic_Tutorial.rst
Docs/sphinx_tutorials/source/Tutorials/Tutorials.rst
Docs/sphinx_tutorials/source/index.rst

commit 3f8fbd5952a0244dd3abd4f7a8abcfb526af57cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 14 13:28:16 2018 -0800

    initialize device in C++

Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaAsyncArray.H
Src/Base/AMReX_CudaAsyncFab.cpp
Src/Base/AMReX_CudaAsyncFabImpl.cpp
Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaRange.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuError.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tools/GNUMake/Make.defs

commit 9269430f6af19b370879c9040f0110dff529ea55
Merge: 4ae646b24 13839ccba
Author: Guy Moore <gmoore@lbl.gov>
Date:   Wed Nov 14 12:30:27 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 4ae646b24546608f8df262c350d464261c92d751
Author: Guy Moore <gmoore@lbl.gov>
Date:   Wed Nov 14 12:27:38 2018 -0800

    Fixed LaTex equation for building HTML

Docs/sphinx_documentation/source/SWFFT.rst

commit 13839ccba64a754a06f6674a533fe58770512495
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 14 09:00:17 2018 -0800

    don't include EB_LSCore* in 2D because it doesn't compile.  cmake not fixed

Src/EB/AMReX_EB_LSCore.H
Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/Make.package

commit 301d001b4e3178b0ec1c461cf1a2e3f012301b47
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Nov 14 08:06:39 2018 -0800

    update AMReX CMake system

Src/EB/CMakeLists.txt

commit 6662a685164dba4d91052fb2e5cd5b0593f07903
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Nov 13 22:31:16 2018 -0800

    LSCore accepts amr parameters during initialization

Src/EB/AMReX_EB_LSCore.H
Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H

commit e8ce21a11132840663386dce33361fb2346fcce9
Author: Guy Moore <gmoore@lbl.gov>
Date:   Tue Nov 13 19:56:10 2018 -0800

    Updated SWFFT documentation, and moved SWFFT and CVODE documentation into a single chapter titled "External Frameworks"

Docs/sphinx_documentation/source/CVODE.rst
Docs/sphinx_documentation/source/CVODE_top.rst
Docs/sphinx_documentation/source/Chapter14.rst
Docs/sphinx_documentation/source/SUNDIALS3.rst
Docs/sphinx_documentation/source/SWFFT.rst
Docs/sphinx_documentation/source/SWFFT/figs/grid_1x4x2.png
Docs/sphinx_documentation/source/SWFFT/figs/grid_2x2x2.png
Docs/sphinx_documentation/source/SWFFT/figs/grid_4x1x2.png
Docs/sphinx_documentation/source/SWFFT/figs/grid_4x2x1.png
Docs/sphinx_documentation/source/SWFFT/figs/grid_4x4x4.png
Docs/sphinx_documentation/source/SWFFT/figs/grid_8x8x1.png
Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst

commit a7c60915d533f55978e970a008ced42bf6e444f1
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Nov 13 16:32:49 2018 -0800

    store ls checkpoint

Src/EB/AMReX_EB_LSCoreBase.H
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp

commit 5403edfe1f9a1af7e4240672d5021d06e76baf8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 13 16:25:16 2018 -0800

    some name changes for xSDK

Src/Base/AMReX.cpp
Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaAsyncArray.H
Src/Base/AMReX_CudaAsyncFab.cpp
Src/Base/AMReX_CudaAsyncFabImpl.cpp
Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaLaunch.H
Tools/F_scripts/write_cuda_headers.py

commit 26cf216493e22141e1217569a17130d3be91a3a3
Merge: e6cb569f5 13e8e89ec
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Nov 13 16:20:34 2018 -0800

    Merge branch 'development' into jpb/ls-core

commit e6cb569f53ebcb2f28546d8b744b879fb93003ef
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Nov 13 16:19:52 2018 -0800

    update inputs

Tutorials/EB/LevelSet/Exec/inputs

commit baf0e5c43352670ac7ce1abb3f4dc5c1cbd86afb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 13 15:33:40 2018 -0800

    remove some unused stuff

Src/Base/AMReX_BLFort.H
Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaFort.F90

commit 13e8e89ec3867625bf925fb6edac1d82bc240b54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 13 14:40:53 2018 -0800

    in BndryFuncArray, we need to loop over components

Src/Base/AMReX_PhysBCFunct.cpp

commit d09c41f3452f33c72de04631af4d6bfd27e5644d
Author: kngott <kngott@lbl.gov>
Date:   Tue Nov 13 13:49:23 2018 -0800

    AMREX_RESTRICT non SIMD BaseFab loops. Try dot and sum for now to test.

Src/Base/AMReX_BaseFab.H

commit 46d920a8e843793fa4873f04cb5e1c2929d11b2a
Author: kngott <kngott@lbl.gov>
Date:   Tue Nov 13 13:07:44 2018 -0800

    Clear DeviceFab pointer after use.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp

commit ecf30f6568be4f1be3d2d027e401957973660889
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 13 12:45:16 2018 -0800

    fix a new bug in PhysBCFunct

Src/Base/AMReX_PhysBCFunct.H

commit 3ace8106fc8fda2dd42de84042f237e05c834737
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Nov 13 11:47:10 2018 -0800

    update levelset amr to be compatible with new changes

Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 42affd166f379dfb73785dc84611a0467354c3b1
Merge: 2606dd961 56860a708
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Nov 13 11:15:25 2018 -0800

    Merge branch 'development' into jpb/ls-core

commit 56860a7080f63952b30e1aac7a46b8faac0efcdf
Merge: 6f0ce3844 2b59ea10d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 13 11:14:11 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2b59ea10dda8a2f158393f8034ef0611df07fd84
Merge: 836940d8b 139230c2c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Nov 13 11:13:31 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 836940d8b6561353795ecf0eed49a3e3290ff940
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Nov 13 11:13:22 2018 -0800

    Algoim: output runtime info only in debug mode

Src/Extern/Algoim/AMReX_algoim_integrals.cpp

commit 6f0ce38441d1536c2f6c0ac5c793851174005015
Merge: c4513513c a124074bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 13 10:10:45 2018 -0800

    Merge branch 'weiqun/gpu' into development

commit c4513513cc83906b7b6691f2eb6ca8ffd5fd8ae9
Merge: 645163829 139230c2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 13 10:08:19 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a124074bc97376d72f7c7b5ff507354cfe5123ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 13 10:07:54 2018 -0800

    fix out of bound

Src/Base/AMReX_CudaDevice.cpp

commit 139230c2c9193a8827459952f315a49d17025d6a
Merge: de52e0213 29d1afb48
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Nov 13 08:51:32 2018 -0800

    Merge pull request #366 from AMReX-Codes/SDC
    
    cleaning up redundant MG assignments

commit 2606dd961bc05f631c871129895020e7388805b0
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Nov 12 23:16:02 2018 -0800

    Updated fortran subroutine names to match amrex convention

Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCore_F.H
Src/EB/AMReX_EB_Tagging.F90
Src/EB/AMReX_EB_bc_fill_nd.F90

commit 9f5872b7d189b371341c8c3b09c028c6423a8c4c
Merge: fbcd628b7 de52e0213
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Nov 12 22:57:54 2018 -0800

    Merge branch 'development' into jpb/ls-core

commit fbcd628b7f8b57ef4430e4db7d312fbea3e357dd
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Nov 12 22:56:30 2018 -0800

    clean up

Src/EB/AMReX_EB_LSCore.H
Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_utils.H
Src/EB/AMReX_EB_utils.cpp
Src/EB/Make.package

commit 9b45fdf8816a297260958bd7fd8c5001f673e2ea
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Nov 12 15:14:41 2018 -0800

    yay, fixed performance problem

Src/Base/AMReX_Box.H
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_EB_LSCore.H
Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.cpp
Tutorials/EB/LevelSet/Exec/inputs

commit a750223aa2e18b78885b22d54352db574520d573
Author: kngott <kngott@lbl.gov>
Date:   Mon Nov 12 14:40:51 2018 -0800

    Implement deviceFab.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp

commit de52e0213f95c973f854bda0648f0663cebb83af
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Nov 12 14:25:04 2018 -0800

    fixing a memory leak bug in the upcxx backend

Src/AmrTask/rts_impls/Perilla_upc++/PackageQueue.H
Src/AmrTask/rts_impls/Perilla_upc++/PackageQueue.cpp
Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.H
Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.cpp

commit 29d1afb480828792cb81696d5ba80c256bc7ccc2
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Mon Nov 12 14:12:00 2018 -0800

    cleaning up redundant MG assignments

Tutorials/SDC/MISDC_ADR_2d/Exec/inputs_2d
Tutorials/SDC/MISDC_ADR_2d/README
Tutorials/SDC/MISDC_ADR_2d/Source/SDC_sweeper.cpp
Tutorials/SDC/MISDC_ADR_2d/Source/main.cpp

commit 4cec047ae74d9c5c87950f8e51e97e91e66a2e07
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Nov 12 13:37:09 2018 -0800

    fixing a memory leak bug

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/AmrTask/rts_impls/Perilla/PackageQueue.H
Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp
Src/AmrTask/rts_impls/Perilla/RegionGraph.H
Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp
Src/AmrTask/rts_impls/Pthread_Common/LocalConnection.H
Src/AmrTask/rts_impls/Pthread_Common/RGIter.cpp
Src/AmrTask/rts_impls/Pthread_Common/RegionQueue.H
Src/AmrTask/rts_impls/Pthread_Common/RegionQueue.cpp
Src/AmrTask/rts_impls/Pthread_Common/RemoteConnection.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp

commit 66e583b6a229cf8eff1a8c47f237111426b1297f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 12 12:34:56 2018 -0800

    white spaces

Src/Amr/AMReX_AmrLevel.cpp

commit 37c555f7799f5ea5fd909a5a59c6ad80d98a1f07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 12 12:25:53 2018 -0800

    filcc 1D

Src/Base/AMReX_FilCC_1D_C.cpp
Src/Base/AMReX_FilCC_3D_C.cpp

commit f04ac545a884605446d82702400af89a42ecc8dc
Author: kngott <kngott@lbl.gov>
Date:   Mon Nov 12 09:32:39 2018 -0800

    c++ version of face_velocity compiles.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 3c40447fd9e067b87db3bfabf43573e196e4f664
Author: kngott <kngott@lbl.gov>
Date:   Mon Nov 12 09:31:07 2018 -0800

    Protect Prob.cpp.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp

commit bd93aa9dccfc888c4c6acfda10d63ea5b66b4f9c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sun Nov 11 21:50:29 2018 -0800

    First attempt at C++ version of face_velocity. Not compile tested. WIP.

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H

commit ba96dac22ee09f36dacc9912c7a69be8cf133ae7
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Nov 11 17:47:24 2018 -0800

    sync wip

Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H

commit 216a674a793688347d6bdc921dc1729473a710aa
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Nov 11 17:15:55 2018 -0800

    work on improving performance of multi-level level-set

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_MultiFab.H
Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Tutorials/EB/LevelSet/Exec/inputs

commit 03b4bc385914062a3464baebbfc70e0afd9f890e
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Nov 11 13:59:13 2018 -0800

    fix problem where eb_padding wil to small... this does not perform well though

Src/AmrCore/AMReX_AmrMesh.cpp
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.cpp
Tutorials/EB/LevelSet/Exec/inputs

commit ba4a01b0a3be1838f2ee666f5f4507a2bddf80e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 11 16:54:06 2018 -0500

    use functor instead of function pointer so that we can pass user provided function to kernels

Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp
Tutorials/GPU/CNS/Source/CNS_bcfill.cpp

commit 5e9a90d4dc045d737e1239a21948872b7fa9fd1f
Author: kngott <kngott@lbl.gov>
Date:   Sun Nov 11 11:08:50 2018 -0800

    Define C version of get_face_velocity.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H

commit 2f7fa5cf220d176eca7ff3dcdbedc7cd2fa9d247
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 11 01:00:02 2018 -0500

    have to create a local copy of the member variable for the lambda to capture

Src/Base/AMReX_PhysBCFunct.cpp

commit d8275704d766f98c4e872b5f2c3cff9342862c76
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 10 23:13:43 2018 -0500

    no need to use mutex in AsynArray anymore because carena has one

Src/Base/AMReX_CudaAsyncArray.cpp

commit d6c4708803740e47bc939b3bd6ae384e88f25511
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 10 23:10:21 2018 -0500

    fix mutex in AsyncFab

Src/Base/AMReX_CudaAsyncFab.cpp
Src/Base/AMReX_CudaAsyncFabImpl.H
Src/Base/AMReX_CudaAsyncFabImpl.cpp

commit 891df864fc4c0e5209698d1157792ca5a8b9659d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 10 22:57:47 2018 -0500

    mutex in CArean

Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp

commit 9284aa8120d8fe07dbcaea24d300701528ed6ae2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 10 22:47:27 2018 -0500

    avoid using fab.box() in assertion

Src/Amr/AMReX_StateData.cpp

commit cbca02b9656ec0dda83d7bb22c4c78304551af4f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 10 22:46:21 2018 -0500

    comment out set nan on gpu for now. will move it to multifab in the future.

Src/Base/AMReX_FArrayBox.cpp

commit 3d82ea9529f5d193a9ee94a70711a7b1159d48fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 10 19:13:41 2018 -0500

    StateData: option to fill domain bc on gpu

Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_FilCC_3D_C.cpp
Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuControl.cpp

commit aa2cb3b7ccae91ef9ce043e3523c18b8e9ee2f83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 10 16:53:49 2018 -0500

    first pass of filcc in 3d w/o high-order extrapolation

Src/Base/AMReX_FilCC_3D_C.cpp

commit d702c2078e00f75f5ecd09b51dfe313d1f2713b0
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Nov 10 13:34:27 2018 -0800

    going to nodal level-set

Src/AmrCore/AMReX_AmrMesh.H
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_Tagging.F90

commit bf68bb5eeefdd16fb61a5d0cca677b3f9aae3414
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 10 16:21:23 2018 -0500

    inline some BCRec functions

Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCRec.cpp

commit 5131f12f2777e643a10e67e8ca14bb1bfdc41286
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 10 01:27:04 2018 -0500

    more work on GpuBndryFuncFab

Src/Base/AMReX_FilCC_1D_C.cpp
Src/Base/AMReX_FilCC_2D_C.cpp
Src/Base/AMReX_FilCC_3D_C.cpp
Src/Base/AMReX_FilCC_C.H
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 4ebf5a62b1b475468e2d959b7e03e4cd031fe4f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 10 00:12:02 2018 -0500

    add ___host__ __device__ to BCRec

Src/Base/AMReX_BCRec.H

commit b9d825e25fdec9499f40611eb09ac55fe155c388
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 9 23:53:45 2018 -0500

    make sure nvcc use the same std version as gcc in case gcc version > 5

Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/nvcc.mak

commit 2cc5bd3432c52a2f93b937f4a8f41365c5986925
Author: kngott <kngott@lbl.gov>
Date:   Fri Nov 9 19:48:40 2018 -0800

    Define new initprob and change implementation.

Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H

commit c18a5a31516b46ea4670da5d1c33d30dd28820af
Author: kngott <kngott@lbl.gov>
Date:   Fri Nov 9 19:46:47 2018 -0800

    Update make system.

Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv
Tutorials/GPU/Advection_AmrCore/Source/Make.package

commit da72b81451b36fa1b8c85f594249760c2d6cf7e1
Author: kngott <kngott@lbl.gov>
Date:   Fri Nov 9 19:31:52 2018 -0800

    C++ version of Prob

Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.f90

commit 93bc1a8d1196b798dca948fe7b321e4c9521e4c1
Author: kngott <kngott@lbl.gov>
Date:   Fri Nov 9 19:27:16 2018 -0800

    Remove exec.

Tutorials/GPU/Advection_AmrCore/Source/a.out

commit 4f786e3a8598480c20ea8f7148b3af1b2cf48af1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 9 16:46:44 2018 -0800

    use --std=c++14 when using gcc as the host compiler if the gcc version is new enough

Tools/GNUMake/comps/nvcc.mak

commit dc20014e5ed82974225e11f5657132b7a65c17cb
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Nov 9 15:19:04 2018 -0800

    sync wip while debug

Src/AmrCore/AMReX_Interpolater.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_Tagging.F90
Src/EB/AMReX_EB_levelset.cpp
Tutorials/EB/LevelSet/Exec/inputs

commit 5c302080b5cfdef3343cffcc1d1add944403afb9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 9 14:23:13 2018 -0800

    GpuBndryFuncFab WIP

Src/Base/AMReX_PhysBCFunct.cpp

commit 2642312a28662b1c1534fbf34596d67a72076e20
Merge: 7230b398f e0d4403c1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 9 14:00:04 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 520eb6f0ded91f75d690748808bf4fc22275bb04
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 9 13:54:31 2018 -0800

    some work on CpuBndryFuncFab

Src/Amr/AMReX_StateDescriptor.H
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp
Tutorials/GPU/CNS/Source/CNS.H
Tutorials/GPU/CNS/Source/CNS_bcfill.cpp
Tutorials/GPU/CNS/Source/CNS_setup.cpp

commit 7230b398f44968a1f1eafe52892b41b1343975ca
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 9 13:33:06 2018 -0800

    correct neighbor size in NeighborListParticleContainer.cpp

Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp

commit 894a26aeaba6d4e8f6cae2cd51cb11face8a9535
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 9 13:10:55 2018 -0800

    switch the neighbor list structure to use ParticleType instead of char

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 7e05e67e640c307279364e99a3945b1e552e47f5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 9 13:08:01 2018 -0800

    remove neighbor_t from the NeighborList tutorial

Tutorials/Particles/NeighborList/neighbor_list_3d.f90

commit 5d698f830eaedc3e92e7b86a0e8628a65849a9ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 9 10:08:01 2018 -0800

    add default constructor for StateDescriptor::BndryFunc

Src/Amr/AMReX_StateDescriptor.H

commit 8c6654f13ef82c244bd51e00e8fefdf11fa94924
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 9 09:50:52 2018 -0800

    clean up

Src/Amr/AMReX_StateDescriptor.H
Src/AmrCore/AMReX_AmrParticles.H
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit fca63428c271d9bfa11b7145d438e3914133bc13
Merge: ed068ed15 645163829
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 9 08:40:31 2018 -0800

    Merge branch 'development' into weiqun/gpu

commit 6451638295dbb15766039fc440650905e66da801
Merge: 2400749ea e0d4403c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 9 08:37:18 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b2c847ac8de1d9601669269712b1ca7e6081041e
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Nov 8 22:51:12 2018 -0800

    yay! level-sets

Src/EB/AMReX_EB_LSCore.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H
Tutorials/EB/LevelSet/Exec/inputs
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp

commit d91e6bdae9aeca1d657f36977648111548b5012a
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Nov 8 21:53:13 2018 -0800

    split basic amr core behaviour and specialized eb-geometry

Src/AmrCore/AMReX_AmrCore.H
Src/EB/AMReX_EB_LSCore.H
Src/EB/AMReX_EB_LSCoreBase.H
Src/EB/AMReX_EB_LSCoreBase.cpp
Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_LSCore_F.H
Src/EB/AMReX_EB_bc_fill_nd.F90
Src/EB/Make.package
Tutorials/EB/LevelSet/Exec/inputs
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp

commit ed068ed159b290507fd4c2907feeec42e064e7ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 8 21:51:54 2018 -0800

    update due to change in FillPatch

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StateDescriptor.H
Src/Amr/AMReX_StateDescriptor.cpp
Src/AmrCore/AMReX_AmrParticles.H
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp
Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp
Src/F_Interfaces/Base/AMReX_FPhysBC.H
Src/F_Interfaces/Base/AMReX_FPhysBC.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex
Tutorials/Amr/ScalarAdvectionDiffusion/Doc/references.bib
Tutorials/Amr/ScalarAdvectionDiffusion/Doc/working_notes.tex
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Make.Adv.Diff
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs.tracers
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/probin
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/debug.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.2d.convtest.sh
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.3d.convtest.sh
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/probdata.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/probin
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/face_velocity_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/probdata.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/probin
Tutorials/Amr/ScalarAdvectionDiffusion/README
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugDump.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/LevelBldAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/slope_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/slope_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Adv_nd.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Tagging_nd.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/tagging_params.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/main.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/fourthOrderCFInterpTest.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/test.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_mpi_driver.py
Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_serial_driver.py
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit 62238fcd6a45ad8dcfe7f963c0200cf257bbdd35
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Nov 8 20:24:12 2018 -0800

    LSCore needs to be a template class (so that it can hold gshop objects)

.gitignore
Src/EB/AMReX_EB2_IF_Intersection.H
Src/EB/AMReX_EB_LSCore.H
Src/EB/AMReX_EB_LSCoreI.H
Src/EB/AMReX_EB_levelset.H

commit e0d4403c13e952ea50d2b43b111842ed5ae2b16b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 8 18:07:51 2018 -0800

    Fix error statements to correctly reflect the routine they're from

Src/Particle/AMReX_ParticleContainerI.H

commit 8f81d49d7e114dde3cf571c054c6ab726f3495f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 8 16:45:05 2018 -0800

    Redo the FillPatch interface.  The change is not backward compatible for AmrCore based codes that use FillPatch

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 5a5fdfc2117756e82a080547a5ad349cf322091f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Nov 8 13:57:40 2018 -0800

    sync wip

Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_EB_LSCore.H
Src/EB/AMReX_EB_LSCore.cpp

commit 589e8326270086d33049bd8d3b875d4d4eea33c7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Nov 8 16:23:19 2018 -0500

    AdvCore added to Tutorials/GPU and being worked on.

Tutorials/GPU/Advection_AmrCore/CMakeLists.txt
Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.f90
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_catalyst.py
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml
Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml
Tutorials/GPU/Advection_AmrCore/README
Tutorials/GPU/Advection_AmrCore/README_SENSEI.md
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/GPU/Advection_AmrCore/Source/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src_2d/Adv_2d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src_2d/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src_2d/slope_2d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.f90
Tutorials/GPU/Advection_AmrCore/Source/Src_nd/Make.package
Tutorials/GPU/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90
Tutorials/GPU/Advection_AmrCore/Source/a.out
Tutorials/GPU/Advection_AmrCore/Source/bc_fill_nd.F90
Tutorials/GPU/Advection_AmrCore/Source/main.cpp

commit 921aa68296411b9b94bea79de8ab2194bf253024
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Nov 8 16:22:14 2018 -0500

    fix .x issue

Src/Base/AMReX_COORDSYS_2D.cpp

commit c41e57a74b5ce5eb40e3407b71d3b748ecc11fb5
Merge: 7e5bf5a24 48c89300c
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Nov 8 10:20:00 2018 -0800

    Merge branch 'development' into jpb/ls-core

commit 48c89300cb7eb6ee80c58b966413dcef153d490d
Merge: 2d6d876fa bbcca5e8d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Nov 8 09:32:11 2018 -0800

    Merge pull request #362 from AMReX-Codes/f2py-microphysics
    
    Add compile flags for building a code using the AMReX build system as an f2py library

commit 7e5bf5a241b9eb92530acbbe36ee70828b5bb7bc
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Nov 7 21:16:15 2018 -0800

    added first pass at AMR for level-set

Src/EB/AMReX_EB_LSCore.H
Src/EB/AMReX_EB_LSCore.cpp
Src/EB/AMReX_EB_LSCore_F.H
Src/EB/AMReX_EB_Tagging.F90
Src/EB/AMReX_EB_bc_fill_nd.F90

commit b6af74e3774537b4cc66a37036082f39a21d8a79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 21:15:03 2018 -0800

    DeviceFab -> AsyncFab

Src/Base/AMReX.cpp
Src/Base/AMReX_CudaAsyncFab.H
Src/Base/AMReX_CudaAsyncFab.cpp
Src/Base/AMReX_CudaAsyncFabImpl.H
Src/Base/AMReX_CudaAsyncFabImpl.cpp
Src/Base/AMReX_CudaFab.H
Src/Base/AMReX_Gpu.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tests/GPU/AsyncFab/GNUmakefile
Tests/GPU/AsyncFab/Make.package
Tests/GPU/AsyncFab/main.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp

commit e993a388e508359bbc9c55baf310fc37ca827142
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 21:03:27 2018 -0800

    fix bug in CudaAsyncArray

Src/Base/AMReX_CudaAsyncArray.H
Src/Base/AMReX_CudaAsyncArray.cpp

commit 2d6d876fa68e3a7310bf7d57a9a34234a11d0354
Merge: 3e352a3a1 157ec60a5
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Nov 7 20:55:53 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 3e352a3a1c339b8bfd1880e7f6277c3b02802014
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Nov 7 20:54:48 2018 -0800

    these aren't needed after all

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp

commit 157ec60a565ef66c8a6ae9115c9b0e77e4d863a4
Merge: 1689fedb8 4cc74b6f6
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Nov 7 17:26:58 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 1689fedb8be006ab6bc4031471bcfae6f4615108
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Nov 7 17:26:23 2018 -0800

    CMake: add hack to compile blitz on nersc machines

Tools/CMake/AMReX_InstallExternalLibs.cmake

commit bbcca5e8d1d450445808d4091df615c8d8cbfd9d
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date:   Mon Oct 22 21:59:11 2018 -0700

    Support for building StarKiller Microphysics as a library with f2py.
    
    WIP support for building StarKiller Microphysics as a library with f2py.
    
    Add default setting USE_COMPILE_PIC?=FALSE

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/gnu.mak

commit 0378e2e7bb3e476f672ac97e47d7aceb9b1bf901
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Nov 7 17:01:11 2018 -0800

    CMake: fix mispelled variable

Tools/CMake/AMReX_Machines.cmake

commit 2400749ea351353c9aba2cae87e5711f6560c2cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 17:00:07 2018 -0800

    Gpu::AsyncArray

Src/Base/AMReX_CudaAsyncArray.H
Src/Base/AMReX_CudaAsyncArray.cpp
Src/Base/AMReX_CudaFab.cpp
Src/Base/AMReX_Gpu.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tutorials/GPU/CNS/Source/CNS_bcfill.cpp

commit 4cc74b6f6bdee3db88ebc22b9e450d7e276861b7
Merge: 2cb5fbbd2 afc57e26d
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Nov 7 15:46:35 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 4480374724ff0010688c2cd805376ab5b8883565
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 14:57:46 2018 -0800

    new bndry fill function in StateData

Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StateDescriptor.H
Src/Amr/AMReX_StateDescriptor.cpp
Src/Base/AMReX_BCRec.cpp

commit 2cb5fbbd2569442d6340f9fab063b7078c5ce9d5
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Nov 7 14:09:09 2018 -0800

    added FillPatch operations for constant-in-time MFs

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp

commit 39f2c54ec9c65aa8c0a252db84efa032d62bbd04
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Nov 7 17:07:48 2018 -0500

    protected_divide with zeros BaseFab test.

Tests/BaseFabTesting/main.cpp

commit 368f0ac66f691ea82d4e88a398e97092fd89802c
Author: kngott <kngott@lbl.gov>
Date:   Wed Nov 7 13:38:16 2018 -0800

    Convert remaining stridedPtr to FabView.

Src/Base/AMReX_COORDSYS_1D.cpp
Src/Base/AMReX_COORDSYS_2D.cpp
Src/Base/AMReX_COORDSYS_3D.cpp
Src/Boundary/AMReX_Mask.cpp
Src/EB/AMReX_EB2_GeometryShop.H

commit b7d5b539263e518247847b07370e99db2f2af52b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Nov 7 15:53:21 2018 -0500

    Merge errors.

Src/Base/AMReX_BaseFab.H

commit ef32672a25c20d0e50e38f0f202ebbb5aca07fef
Merge: 8a66b2ed1 cd88e66c4
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Nov 7 15:32:54 2018 -0500

    Merge branch 'weiqun/gpu' into gpu
    
    Conflicts:
            Src/Base/AMReX_BaseFab.H

commit cd88e66c447964a6006728f39a4b15806c170f9a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Nov 7 15:30:28 2018 -0500

    BaseFab with FabView.

Src/Base/AMReX_BaseFab.H

commit afc57e26d93cfed07ae622f42950f2a905154aae
Merge: 278be0da1 052a1912e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 7 12:09:49 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 278be0da114a97cdf9180ed73907abad9690803e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 7 12:09:33 2018 -0800

    when running with CUDA, construct the neighbor on the host, then copy it into managed memory.

Src/Particle/AMReX_NeighborParticlesI.H

commit 052a1912e284ade8dd57bdee86b9b35b6ccb7ccd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 14:24:45 2018 -0500

    fix set_covered for nodal

Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_3d.F90
Src/EB/AMReX_EBMultiFabUtil_F.H

commit ad91fa40a76c8f29171f6a0bddf782cd3957d7f0
Merge: 5ddfcf284 656bf0073
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Nov 7 14:00:10 2018 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5ddfcf28403c075ec58e9f19d3e183a61a73f3c9
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Nov 7 13:59:43 2018 -0500

    remove uneccesary casts from these thrust calls.

Src/Particle/AMReX_ParticleContainerI.H

commit cffccd5ee946a03457b3494877be941a11029317
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Nov 7 13:32:15 2018 -0500

    prettify thrust calls

Src/Particle/AMReX_ParticleContainerI.H

commit 656bf007387dde4f5d337c59e217012f9ce7ba27
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 13:31:33 2018 -0500

    setVal: return if Box is not ok.  This is the traditional behavior

Src/Base/AMReX_BaseFab.H

commit 5c4a95ea5cf0746a00a6c7e76ef46d4ad4da27b7
Merge: e57ab30cd 696793a25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 09:07:17 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 696793a25c52fcc1d15c7c6d5851a838738cc380
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 09:06:33 2018 -0800

    fix omp

Src/Base/AMReX_MultiFab.cpp

commit 94868ad6070836834234ae6d94b55ab0d53cfd5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 08:53:26 2018 -0800

    include cmath

Src/EB/AMReX_EB2_IF.H
Src/EB/AMReX_EB2_IF_Torus.H

commit e57ab30cdc6601ad94f0820e0800e4356d3bf8ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 08:51:46 2018 -0800

    include cmath

Src/EB/AMReX_EB2_IF.H
Src/EB/AMReX_EB2_IF_Torus.H

commit 7e84b9446f645a814eff111cef10b51fccb6f67d
Merge: f753145ca 4ef56b859
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 07:18:14 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4ef56b859a1c0ff96f9c50758c834bf68439e2d2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 7 06:51:44 2018 -0800

    sqrt --> std::sqrt

Src/EB/AMReX_EB2_IF_Torus.H

commit 480615462d8c6490b6a2dc5ebf49e91a14b8521e
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Nov 7 02:40:10 2018 -0800

    fixing a memory leak bug

Src/Amr/AMReX_AmrLevel.cpp

commit 4648de6723b8346b77e8b5232e68146871801446
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Nov 7 02:24:05 2018 -0800

    fixing a few memory leak bugs

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp

commit 1527a835783221623c68f7a249df0e55dce60065
Merge: 96c62cf90 5fc026813
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 6 17:45:45 2018 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 96c62cf90e52fe13d0a80f91ea48a2f44d846aef
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 6 17:45:22 2018 -0800

    Add torus

Src/EB/AMReX_EB2.cpp
Src/EB/AMReX_EB2_IF_Torus.H
Src/EB/Make.package

commit 5fc0268137e1dce781ed2a0e687d6719c55da57e
Merge: 4e0870f5c 1abf13141
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Nov 6 17:37:55 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 4e0870f5c2d038844d9c885b6dec1d67dfdc1e73
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Nov 6 17:37:49 2018 -0800

    CMake: update documentation

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit 1c1596f418ec375b2be8056dce5238cfba05142c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Nov 6 17:25:36 2018 -0800

    Cmake: implement small improvements

Src/CMakeLists.txt
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_InstallExternalLibs.cmake

commit f753145caa7d153dbd44052ea483e319f18134c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 6 17:12:24 2018 -0800

    add Fab version of Bndry Func

Src/Amr/AMReX_StateDescriptor.H
Src/Amr/AMReX_StateDescriptor.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp
Tutorials/GPU/CNS/Exec/Sod/inputs
Tutorials/GPU/CNS/Source/CNS_bcfill.cpp
Tutorials/GPU/CNS/Source/CNS_setup.cpp
Tutorials/GPU/CNS/Source/Make.package

commit 266b16903c2288daacfcacbce56cfa820e50a68a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Nov 6 16:53:56 2018 -0800

    CMake: add support for 3D nodal projection.
    
    Add support for Algoim and Blitz libraries if nodal projection is
    required. CMake will download and install these libraries if
    no installation paths is given for them.

CMakeLists.txt
Src/CMakeLists.txt
Src/Extern/Algoim/CMakeLists.txt
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_InstallExternalLibs.cmake
Tools/CMake/AMReX_Options.cmake

commit 6475a69c8424e3731a5a0c4f9cbdeb4266a986b4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Nov 6 16:49:26 2018 -0800

    CMake: refactor CMakeLists hierarchy in Extern subdir

Src/CMakeLists.txt
Src/Extern/CMakeLists.txt
Src/Extern/ProfParser/CMakeLists.txt
Src/Extern/amrdata/CMakeLists.txt

commit 1abf13141b8a223dd267efcf493bf4de7b99eb4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 6 14:36:15 2018 -0800

    remove some unused print functions

Src/Amr/AMReX_StateDescriptor.H
Src/Amr/AMReX_StateDescriptor.cpp
Src/Base/AMReX_PhysBCFunct.cpp

commit 07330e81f3af4f20cd540306016f10fd50684dd1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 6 14:07:13 2018 -0800

    fix a bug in StateData FillBoundary

Src/Amr/AMReX_StateData.cpp

commit d3b48480666eeaec5691be2febc1a6572e51ce1b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 6 12:52:32 2018 -0800

    fix omp

Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_MultiFab.cpp
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90

commit e8eb1251d9019e2bbc6b0a084f691a81b886751e
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Nov 6 15:31:56 2018 -0500

    First draft of GPU minIndex and maxIndex. Needs atomic IntVect assignment to complete thread-safety.

Src/Base/AMReX_MultiFab.cpp

commit 9a601bd32f68b9dabb943cd8cc6873790fa2a468
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Nov 6 15:29:27 2018 -0500

    Change DeviceScalar from is_pod to is_trivially_copyable.

Src/Base/AMReX_CudaMemory.H

commit d4154d60b8f9c27cc4c545a71cee9b6beb1cd877
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Nov 6 15:28:49 2018 -0500

    BaseFab::indexFromValue. Need tolerance checking.

Src/Base/AMReX_BaseFab.H

commit 970e5649b8d6cb5023dd1105abe6de79d3de3933
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Nov 5 19:37:26 2018 -0500

    Thin wrapper around thrust::copy.

Src/Base/AMReX_CudaContainers.H

commit 9aa1c559f82d3878fd29aacb8e4fd407954fdbc3
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Nov 5 18:54:14 2018 -0500

    Cuda -> Gpu & first attempt at minIndex.

Src/Base/AMReX_MultiFab.cpp

commit c8efaca8355b05c599971f0d278b34b68fb8437e
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Nov 5 13:12:35 2018 -0500

    Remaining norm Multifab funcs outlined. Won't compile with USE_CUDA=FALSE until thrust::copy is wrapped.

Src/Base/AMReX_MultiFab.cpp

commit 90d0f2c358b136194366f1717aef280d996b4cad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 6 10:52:19 2018 -0800

    use amrex::min and max

Src/Base/AMReX_Utility.H
Tutorials/GPU/CNS/Source/CNS_K.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp

commit 62ca4039c4eb9ac9769bebc857ea3626bf6c0c83
Merge: e125a7593 8a66b2ed1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 6 09:55:14 2018 -0800

    Merge branch 'gpu' into development

commit e125a75934e3819c668eb1f731e6471fb25f7457
Merge: 35dd527c2 27cc2ebfb
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Nov 6 09:38:39 2018 -0800

    Merge pull request #356 from AMReX-Codes/SDC
    
    Sdc

commit 35dd527c2a5d6df11c30cfb14f1bbd647cf7d312
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 5 18:31:53 2018 -0800

    missed a few.

Tools/Postprocessing/C_Src/fcompare.cpp

commit 20ca7d5725807ac9d28ab7a2a373318a4f7377e5
Merge: 0db027a65 86beaeb50
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 5 18:27:40 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 0db027a65383317601e9bec40c565020182bd8a9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 5 18:27:21 2018 -0800

    specifiy amrex::min and amrex::max

Tools/Postprocessing/C_Src/fcompare.cpp

commit 86beaeb50b73367f9aec6bba3460c850f6c4b163
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 5 17:56:17 2018 -0800

    print out the maximum discrepancy in volume fraction but don't abort when
    the volume fraction or centroids don't match.

Src/Extern/Algoim/AMReX_algoim_integrals.cpp

commit 8a66b2ed1f59bd676e26d57a4a9e7ec53588e4e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 5 16:08:53 2018 -0800

    bug fixes

Src/Base/AMReX_BaseFab.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp

commit 27cc2ebfb8c3946f61277e3c33970ee9bab45547
Merge: 6ff294752 d9ba6482f
Author: Minion <mlminion@lbl.gov>
Date:   Mon Nov 5 14:58:55 2018 -0800

    Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC

commit 6ff294752c60571cf293e6b0779d1dff41417c98
Author: Minion <mlminion@lbl.gov>
Date:   Mon Nov 5 14:57:43 2018 -0800

    fixing size of quad matrices

Src/SDC/AMReX_SDCstruct.cpp

commit 7849aeef9a58058eac20aa99d677cc17e0563280
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 5 14:54:19 2018 -0800

    fix bound checking

Src/Base/AMReX_BaseFab.H

commit 1ab045832bfc6997894b2185c0439b6107df3998
Merge: f6640d572 396cf411e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 5 14:36:32 2018 -0800

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit f6640d5729429dd2889a1634fd9dc0cb75b1b611
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 5 14:36:24 2018 -0800

    Fix typos in comments

Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H

commit 396cf411e231d73e0c66a92d705149b838c1fe8f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 5 16:50:02 2018 -0500

    and use the new utility functions in the getParticleTile function

Src/Particle/AMReX_ParticleUtil.H
Src/Particle/AMReX_ParticleUtil.cpp

commit 5cff8b641a72ac78bba27343b62ac479d4d3404b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Nov 5 16:49:23 2018 -0500

    add min and max utility functions that work in both host and device code

Src/Base/AMReX_Utility.H

commit 71c7c23a7856fb9f53b9989a8262d2c28f258ba0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 5 13:43:18 2018 -0800

    ostream for Dim3

Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp

commit 7dbdea31990e192644286fa88a26278c4806b563
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 5 13:38:32 2018 -0800

    Riemann solver and reset eint

Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_K.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp

commit d9ba6482f59029626061df80b8771e869172754e
Merge: fbcda5bbb 559cb7099
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Mon Nov 5 12:07:59 2018 -0800

    Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC

commit fbcda5bbbf7a477b433650a08f579007cd1a35bd
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Mon Nov 5 12:06:56 2018 -0800

    removing outdated example

Tutorials/Basic/SDCAdvDiffusion_C/Exec/.#advance.cpp
Tutorials/Basic/SDCAdvDiffusion_C/Exec/GNUmakefile
Tutorials/Basic/SDCAdvDiffusion_C/Exec/inputs_2d
Tutorials/Basic/SDCAdvDiffusion_C/Source/Make.package
Tutorials/Basic/SDCAdvDiffusion_C/Source/advance.cpp
Tutorials/Basic/SDCAdvDiffusion_C/Source/advance_2d.f90
Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_2d.f90
Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_3d.f90
Tutorials/Basic/SDCAdvDiffusion_C/Source/inputs_3d
Tutorials/Basic/SDCAdvDiffusion_C/Source/main.cpp
Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc.H
Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc_F.H
Tutorials/Basic/SDCAdvDiffusion_C/Source/pf_quadrature.f90

commit 4b10e6cde42032343633f328ca97451c2da68874
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 5 11:22:47 2018 -0800

    GPU/CNS: slopes

Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_K.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp

commit cc698315696eacde71ac9c4b4563f0c7f4554537
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 5 09:45:36 2018 -0800

    Update the ALGOIM stuff to be in AMReX namespace and change the
    convention so ALGOIM_HOME points to the external Algoim directory.

Src/Extern/Algoim/AMReX_algoim_integrals.H
Src/Extern/Algoim/AMReX_algoim_integrals.cpp
Src/Extern/Algoim/Make.package
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tests/LinearSolvers/NodeEB/GNUmakefile
Tests/LinearSolvers/NodeEB/MyTest.cpp

commit 4db7d9076d6940b0d83f51cd1bd1be04c8622e1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 4 17:55:41 2018 -0500

    add Dim3 struct and this helps pgi in vectorization

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_IntVect.H
Tests/Vectorization/kc.H

commit 03da503f09d2a91c7c5ab5d2f560a20c242922af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 4 17:19:27 2018 -0500

    use the correct pragma for pgi

Src/Base/AMReX_Extension.H

commit bfea64a2b853e85343a86eef8063c625cd98efd5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 4 13:13:56 2018 -0800

    minor tweak

Tests/Vectorization/kc.H

commit 9b8478d68633dd4542f2d69fcd7547e7f62c0612
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 4 11:04:28 2018 -0800

    use FabView

Tests/Vectorization/kc.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp
Tutorials/GPU/CNS/Source/CNS_K.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/CNS_index_macros.H
Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp

commit 4507c0d643e73538c917730564cc29de8f7c20d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 4 13:37:57 2018 -0500

    rewrite ctoprim

Tests/Vectorization/kc.H

commit e46edc98424401e496ffd19ca2611cbd0139a6db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 3 21:19:46 2018 -0700

    use the new version

Tests/Vectorization/kc.H

commit 75f55ac6e98cd8d14adad496bbd5ae8d7eaa05bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 3 21:16:32 2018 -0700

    FabView: clean up and add bound checking in debug

Src/Base/AMReX_BaseFab.H

commit 847eed93191f974b07a99bb33d930fb7694a54cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 3 16:48:27 2018 -0700

    fix intel deprecaion warning

Src/Base/AMReX_Extension.H

commit 9a9fa778058b0876aa1240eea7e59c637258351f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Nov 3 16:47:27 2018 -0700

    Update the regression tests so we test 2d and 3d -- in 3d we test cylinder with
    the axis in three coordinate directions

Tests/LinearSolvers/NodeEB/GNUmakefile
Tests/LinearSolvers/NodeEB/MyTest.H
Tests/LinearSolvers/NodeEB/MyTest.cpp
Tests/LinearSolvers/NodeEB/inputs
Tests/LinearSolvers/NodeEB/inputs.rt.2d
Tests/LinearSolvers/NodeEB/inputs.rt.3d.x
Tests/LinearSolvers/NodeEB/inputs.rt.3d.y
Tests/LinearSolvers/NodeEB/inputs.rt.3d.z

commit 4d8ae5b55f2e367b692ac6807193ad4352d6fede
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Nov 3 16:45:56 2018 -0700

    Had to change the coarsening since the stencils pointing to the faces
    are 0 for regular cells when dx = dy = dz.   This messes with the
    coarsening when a full cell is near an almost full cell.  We should
    probably make the same change in the interpolation but for now this
    works on simple test cases (ie cylinders)

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 5de8f04d317e9aad91ed4c7a385fa435b2ef6a9a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Nov 3 16:45:24 2018 -0700

    Remove extra printing

Src/Extern/Algoim/Algoim_integrals.cpp

commit f52ba695a77004906d8e9f8560896c9a26f1f1a5
Merge: 2ec929062 a255044ab
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Nov 3 15:05:12 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 2ec9290625ba18996253928611d12fa6b4e91b79
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Nov 3 15:04:49 2018 -0700

    Comment out print statement and setprecision statement

Src/Extern/Algoim/Algoim_integrals.cpp

commit a255044abf0e9f99e2a7e584d7700cf78b4dd5f8
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Nov 3 17:20:44 2018 -0400

    Fix some divide by zero issues in DistributionMapping

Src/Base/AMReX_DistributionMapping.cpp

commit 1bd9aad69291f96e693d30c5a7d6e90a5835cc00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 3 13:33:49 2018 -0700

    add warm up to the test

Tests/Vectorization/main.cpp

commit cb5a968b2079859107e45f1bca4a1b9af87ee79c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 3 13:01:04 2018 -0700

    new headers

Tests/Vectorization/kc.H
Tests/Vectorization/kdecl.H

commit 67fbc910637eb5c1d7f4e74b33d06170faa0a0fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 3 12:57:50 2018 -0700

    add ctoprim test

Tests/Vectorization/kf.F90
Tests/Vectorization/main.cpp

commit 074384fb55c5660a04499cb804ec11b280b8035e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 3 12:06:37 2018 -0700

    add non-simd version

Tests/Vectorization/GNUmakefile
Tests/Vectorization/Make.package
Tests/Vectorization/kc.cpp
Tests/Vectorization/main.cpp

commit 96e21c5d0c6485003b93eab900cbb405ea5db7fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 3 11:35:18 2018 -0700

    minor

Tests/Vectorization/main.cpp

commit 2c320d49efda86e0c3f64c09a41a6b5ce9b0e467
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 3 11:32:46 2018 -0700

    compiler extension macros

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaFab.cpp
Src/Base/AMReX_Extension.H
Src/Base/AMReX_REAL.H
Src/Base/AMReX_RESTRICT.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tools/GNUMake/comps/gnu.mak

commit 65055b9a8d68575e4c9304e7b6e1fab85133a18b
Merge: d482be48a 8ff58db6e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Nov 3 10:54:17 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit d482be48ab310ad3c4a805dea28a2d3256cbd2d8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Nov 3 10:53:36 2018 -0700

    Fix indexing problem in 3D EB nodal restriction operator.
    (There is still a different issue but this does fix some problems)

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 8ff58db6ef8cad54fa9e2ccbd1435904734106df
Merge: 37db0ea10 57572bec8
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Nov 3 10:45:10 2018 -0700

    Merge pull request #359 from AMReX-Codes/mkatz/last_checkpoint
    
    Fill in last_checkpoint/last_plotfile after a restart

commit 37db0ea1037a689cf1987be1c77eaa6a63f46a3f
Merge: 24f5ab414 f1afba2e3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Nov 3 10:43:03 2018 -0700

    Merge pull request #358 from AMReX-Codes/mkatz/minimalbox_overflow_fix
    
    Fix a potential numerical overflow in BoxArray::minimalBox

commit 57572bec8ca30d710fb78b6e2e35088e3ba35e29
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Nov 3 03:05:46 2018 -0400

    Fill in last_checkpoint/last_plotfile after a restart
    
    Castro and Nyx have logic in main.cpp that says to only dump a checkpoint
    if the coarse timestep of the last checkpoint is older than the current
    coarse timestep. In the edge case where the simulation doesn't actually
    take any timesteps after a restart, this results in a checkpoint and plotfile
    being written from the same data we restarted from, which unnecessarily clobbers
    the old data and creates a duplicate checkpoint/plotfile.
    
    If the user explicitly wants a new checkpoint on restart, perhaps because
    they are doing some kind of transformation, they can still take advantage
    of the flags checkpoint_on_restart and plotfile_on_restart.

Src/Amr/AMReX_Amr.cpp

commit b522d30ad60b1ce1ee5ae8939b2a46a0276a3d42
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 23:10:12 2018 -0700

    vectorization test

Tests/Vectorization/GNUmakefile
Tests/Vectorization/Make.package
Tests/Vectorization/kc.cpp
Tests/Vectorization/kf.F90
Tests/Vectorization/main.cpp

commit 72353b69b5b3c47324c22318620b3dc256344b9b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 23:03:34 2018 -0700

    AMREX_PRAGMA_SIMD

Src/Base/AMReX_RESTRICT.H
Tools/GNUMake/comps/ibm.mak
Tools/libamrex/configure.py
Tools/libamrex/mkconfig.py

commit ebd4680eab65547ae7d3ec713a4ea4a8a28410a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 23:02:13 2018 -0700

    FabView

Src/Base/AMReX_BaseFab.H

commit f1afba2e3e8e91c2f656c2dadc03578816551a3e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Nov 3 00:11:07 2018 -0400

    Fix a potential numerical overflow in BoxArray::minimalBox
    
    If the number of points per dimension N is such that N^3 is larger than
    a 32-bit integer (or N^2, for 2D), then this implementation of minimalBox
    will overflow when accumulating into an n_pts variable. Solved by replacing
    the value holding the number of points with a long, which is consistent with
    similar calculations elsewhere in BoxArray.
    
    Fixes #357

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.cpp

commit 4a7f8c24c3538a0f6e8cfd0f980b3bc4084f0fbb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 16:31:32 2018 -0700

    flux to dudt

Tutorials/GPU/CNS/Source/CNS.H
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp

commit 24f5ab414fc5312670f7d096df879aec8e607e83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 15:27:26 2018 -0700

    std::isnan and isinf -> amrex::isnan and isinf

Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp

commit d9d6d67b68a7985af087dc2d00b964b5183a5458
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 15:25:26 2018 -0700

    ptxas info

Tools/GNUMake/comps/nvcc.mak

commit 78916ca8b6f217a9dad4de8bb3efe45081836b60
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 14:48:12 2018 -0700

    fix omp

Src/Base/AMReX_MultiFab.cpp

commit 0bf4d42d74e00460875e2741945b8fec23d9b1ef
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Nov 2 15:02:33 2018 -0400

    Turn off OpenMP+GPU in contains_inf/nan.

Src/Base/AMReX_MultiFab.cpp

commit 0d5156bc2868aa82b46bdc6fd1c1de88ce4f7224
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Nov 2 14:54:32 2018 -0400

    MultiFab::contains_nan and contains_inf to gpu.

Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_MultiFab.cpp

commit d1f45911e128a754458427d6d43f8989e6f9ff54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 11:11:49 2018 -0700

    add AMREX_LAUNCH_DEVICE_LAMBDA_BOXIV

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_GpuLaunch.H

commit 4970b9cdcf8e660872a9636bbd673eccd6d7544f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 12:28:58 2018 -0400

    fix merge

Src/Base/AMReX_BaseFab.H

commit deaf67f925e3471cafa2d9ddb887a150c43a2d23
Merge: 41d0cebb2 aefa9f75e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 12:26:42 2018 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development
    
    Conflicts:
            Src/Base/AMReX_BaseFab.H

commit 41d0cebb2b1644b1b633e0abb780b0abfab87405
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 12:23:08 2018 -0400

    hopefully mfic can now compile with USE_CUDA=TRUE

Src/Base/AMReX_BaseFab.H
Src/EB/AMReX_EBCellFlag.H

commit aefa9f75e8d9ca83aa17cba0b564e414a3e7b977
Merge: e68664152 da111633c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 09:15:27 2018 -0700

    Merge branch 'development' into weiqun/merge-b-devicefab

commit da111633cb9c2f9892c7122e0228824781c1bb34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 21:05:00 2018 -0700

    in debug mode, add -Werror=return-type to gcc

Tools/GNUMake/comps/gnu.mak

commit d3f00ab7f6384bbc363ccbdf86303a3f4792a97b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 21:00:34 2018 -0700

    fix a bug

Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp

commit 9701371299cd7d302ef2e5c3c568ca7c0e0d5da9
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Nov 1 20:30:07 2018 -0400

    use thrust::sort here if running with Cuda

Src/Particle/AMReX_NeighborParticlesI.H

commit 4da37600c2a33f437266cfb71d0af2fcd159c522
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 17:25:25 2018 -0700

    add ctoprim

Src/Amr/AMReX_Amr.cpp
Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp
Tutorials/GPU/CNS/Exec/Sod/inputs
Tutorials/GPU/CNS/Source/CNS.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_K.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/CNS_index_macros.H
Tutorials/GPU/CNS/Source/CNS_io.cpp
Tutorials/GPU/CNS/Source/Make.package
Tutorials/GPU/CNS/Source/hydro/Make.package
Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp

commit 68ffefb5c31d0037e36b2a38bd3a6b9246e27206
Merge: 055b4d653 9a141b726
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Nov 1 18:44:50 2018 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 055b4d653a9697143de86ee7425b05b2eecdc76e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Nov 1 18:40:10 2018 -0400

    remove the index conversion stuff for now.

Src/Particle/AMReX_ParticleUtil.H
Src/Particle/AMReX_ParticleUtil.cpp

commit 9e10e0fe306c1d64063bcdd4ca2b533eacbe7bdb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 15:26:57 2018 -0700

    fix sum

Tutorials/GPU/CNS/Source/CNS.cpp

commit dd6a5812423f073cc262aa7b004a98d738b0cf03
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 15:20:59 2018 -0700

    estimate dt

Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_Geometry.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp
Tutorials/GPU/CNS/Exec/Sod/inputs
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_K.cpp
Tutorials/GPU/CNS/Source/CNS_io.cpp
Tutorials/GPU/CNS/Source/CNS_setup.cpp
Tutorials/GPU/CNS/Source/Make.package

commit 8b2e6de470d95e8e1ba024e8b4a88c592cfc335f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Nov 1 17:45:33 2018 -0400

    fix compilation error

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit d301ef0ab2fde61d449ff1736204c154dbebc708
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Nov 1 17:45:15 2018 -0400

    forgot to add these files.

Src/Particle/AMReX_ParticleUtil.H
Src/Particle/AMReX_ParticleUtil.cpp

commit 5c285c1d271f9e53a13b645a2546e380e6de07b5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Nov 1 17:30:11 2018 -0400

    pass the bin start and stop indices into the SortParticlesByBin method

Src/Particle/AMReX_ParticleContainerI.H

commit 76cf6ac992aabc9c91a8b07e2afb7c0afb7a9ff3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 14:10:44 2018 -0700

    vectorization

Src/Base/AMReX_BaseFab.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp

commit c49b2777758c9dab3f8524ab542f9ba2d124c98d
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Nov 1 17:07:17 2018 -0400

    add stub for SortParticlesByBin

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit dc7b453c7cbee9b6ca0b8316b08627fb6977dcb8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Nov 1 16:58:56 2018 -0400

    add new functor for binning particles on a sub-grid basis

Src/Particle/AMReX_Functors.H

commit e68664152dc5a4384b711df2c7b87eae5ef33692
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 13:46:44 2018 -0700

    comment out resize because it contains cuda api calls thus not safe as callback.  add mutex in delete to protect the memory pool

Src/Base/AMReX_CudaFab.H
Src/Base/AMReX_CudaFab.cpp

commit 2481746147bc49310e9ae29a0d35b3e5b8dccb82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 13:46:44 2018 -0700

    comment out resize because it contains cuda api calls thus not safe as callback.  add mutex in delete to protect the memory pool

Src/Base/AMReX_CudaFab.H
Src/Base/AMReX_CudaFab.cpp

commit ee81d5436e727349e22873e17918060164e92494
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Nov 1 16:06:15 2018 -0400

    move getTileIndex to a separate file, make it run on both host and device

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 471441486a7cd0ec151372ed5d1fb70a098542dc
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Nov 1 15:06:47 2018 -0400

    mark getTileIndex as __host__ __device__

Src/Particle/AMReX_Particles.H

commit 2a7244f12c1727450f53e5f850d0ffe6e708dcc8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Nov 1 15:05:46 2018 -0400

    refactor getTileIndex to not use static members so that it can be called from device code.

Src/Particle/AMReX_ParticleContainerI.H

commit 9a141b726296a74f658486274a99ec7e05bafd38
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Nov 1 12:00:41 2018 -0700

    Reset minIndex.

Src/Base/AMReX_MultiFab.cpp

commit 02cda9da632126a2eb41622636e05f6105ff8ae9
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Nov 1 14:58:23 2018 -0400

    Continuing to convert MultiFab functions.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_MultiFab.cpp

commit ef6c98f00690eeebd7451b61bd37e1191eeb758f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 11:05:22 2018 -0700

    add cns_initdata

Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp
Tutorials/GPU/CNS/Exec/Sod/inputs
Tutorials/GPU/CNS/Source/CNS.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNS_K.H
Tutorials/GPU/CNS/Source/CNS_index.H
Tutorials/GPU/CNS/Source/CNS_setup.cpp
Tutorials/GPU/CNS/Source/Make.package

commit 6e60b0edda955502ae3d628b867d05fccb726a35
Merge: 76b781001 862170c8a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 1 10:00:41 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 76b781001a19174cafad337e7be787be3d852b4d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 1 10:00:31 2018 -0700

    remove unused variables

Src/Particle/AMReX_Particles.H

commit aca87d9b0772f981b41cacf13cdea4299b3c47fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 09:06:02 2018 -0700

    DeviceFab:: add async clear and resize

Src/Base/AMReX_CudaFab.H
Src/Base/AMReX_CudaFab.cpp
Src/Base/AMReX_CudaFabImpl.cpp

commit 3bdf3c82872608e34a4cf9198e2e2d67ed8c1bfd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 09:06:02 2018 -0700

    DeviceFab:: add async clear and resize

Src/Base/AMReX_CudaFab.H
Src/Base/AMReX_CudaFab.cpp
Src/Base/AMReX_CudaFabImpl.cpp

commit 9e0461f904c549452b19d5c207a2510e3c3549b0
Merge: 5a7046a12 294fb430e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 08:40:17 2018 -0700

    Merge branch 'development' into weiqun/gpu

commit 294fb430e2448ac2b43c10f0442e216cebd4ddbc
Merge: dcbfdc0b0 0d5866916
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 08:39:40 2018 -0700

    Merge branch 'weiqun/merge-a-coord' into development

commit 862170c8af86ebca67fff989878e281db94c37e5
Merge: aabb2e131 294fb430e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 1 08:38:50 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit aabb2e1316726c9adbc5e48c5f96c35812cc9f06
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 1 08:38:37 2018 -0700

    Remove VisMF::Write call.

Src/Extern/Algoim/Algoim_integrals.cpp

commit dcbfdc0b0e0e97e8c58696d98c60522ba2d4d8d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 1 08:38:20 2018 -0700

    update CHANGES

CHANGES

commit 2ae376784842324b2bf54babe24d2ded7016f542
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 1 08:30:50 2018 -0700

    Fix typo in 3d version of mknewu_eb

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 730c383e3fe892f73828491e85f805c1845b7760
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 1 07:15:42 2018 -0700

    Make sure to enforce periodicity of 3d nodal EB integrals

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 715c875afff6a23cda4b21c5f60cbcc9776f704c
Merge: 187123e5f 3130c7cd0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 1 07:13:44 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 187123e5f7b2688b51a01f5fa6e582a243ca5cdd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 31 21:16:12 2018 -0700

    Fix some sign errors and the scaling of the 3D EB nodal stencil

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 1033b29fe3b4a568890d1a6ff543b9af78316b89
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 31 18:19:24 2018 -0700

    Initialize the ghost cells of the intg array elements as well

Src/Extern/Algoim/Algoim_integrals.cpp

commit 3130c7cd0fe04cc5e52ae3e68590cd3e9c00ea7c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 31 19:40:40 2018 -0400

    Update HeatEquation GPU example.

Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H

commit 0d5866916aac5cd7a5e868c701f6643506b50126
Merge: b1258d42d 864aa38b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 31 16:29:24 2018 -0700

    Merge branch 'development' into weiqun/merge-a-coord

commit 864aa38b1967a9b25724b32126a77ff86ffd7881
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 31 16:24:52 2018 -0700

    remove now-unused file

Src/Particle/AMReX_RedistributeStrategy.H

commit b63298b7f0eeb6f02ee4afa2dd6c1d3e233bf349
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 31 16:18:37 2018 -0700

    remove broken tutorials - will fix these and add them back later.

Tutorials/GPU/ElectromagneticPIC/Constants.H
Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.H
Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC/Evolve.H
Tutorials/GPU/ElectromagneticPIC/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC/GNUmakefile
Tutorials/GPU/ElectromagneticPIC/IO.H
Tutorials/GPU/ElectromagneticPIC/IO.cpp
Tutorials/GPU/ElectromagneticPIC/Make.package
Tutorials/GPU/ElectromagneticPIC/NodalFlags.H
Tutorials/GPU/ElectromagneticPIC/NodalFlags.cpp
Tutorials/GPU/ElectromagneticPIC/Particles.H
Tutorials/GPU/ElectromagneticPIC/StructOfArrays.H
Tutorials/GPU/ElectromagneticPIC/em_pic_3d.F90
Tutorials/GPU/ElectromagneticPIC/em_pic_F.H
Tutorials/GPU/ElectromagneticPIC/inputs
Tutorials/GPU/ElectromagneticPIC/main.cpp
Tutorials/GPU/ElectromagneticPIC/script.nompi.sh
Tutorials/GPU/ElectromagneticPIC/summit.sh
Tutorials/GPU/ElectromagneticPIC/summitdev.sh
Tutorials/GPU/ElectromagneticPIC/test.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/inputs
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/script.sh
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/inputs
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/script.sh
Tutorials/Particles/ElectromagneticPIC/Make.EMPIC
Tutorials/Particles/ElectromagneticPIC/Source/Constants.H
Tutorials/Particles/ElectromagneticPIC/Source/IO.H
Tutorials/Particles/ElectromagneticPIC/Source/IO.cpp
Tutorials/Particles/ElectromagneticPIC/Source/Make.package
Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/Source/Particles.H
Tutorials/Particles/ElectromagneticPIC/Source/main.cpp

commit 3f9a7412690dbef0e8abfe0d78ba0e5ad5b0b302
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 31 16:07:07 2018 -0700

    remove debug print statement

Src/Particle/AMReX_ParticleContainerI.H

commit 1b07b2acaa0fe4d1455fc638e232d90aa8de0953
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 31 16:03:27 2018 -0700

    force rebuilding the redistribute mask when you ask for more ghost cells than it currently has

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit b1258d42d9e6773d3f2620328e5d79b5fe105f84
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 31 12:59:21 2018 -0700

    fix offset

Src/Base/AMReX_COORDSYS_1D.cpp
Src/Base/AMReX_COORDSYS_2D.cpp

commit 5a7046a12054a18a6375d07070454a31b99e684e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 31 11:04:36 2018 -0700

    minor

Tutorials/GPU/CNS/Exec/Sod/GNUmakefile

commit ab1eb7de8cfaff45bb4c5be10646328d30f5faae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 31 10:32:46 2018 -0700

    skelton for CNS

Tutorials/GPU/CNS/Exec/Make.CNS
Tutorials/GPU/CNS/Exec/Sod/GNUmakefile
Tutorials/GPU/CNS/Exec/Sod/Make.package
Tutorials/GPU/CNS/Exec/Sod/cns_prob.H
Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp
Tutorials/GPU/CNS/Exec/Sod/inputs
Tutorials/GPU/CNS/Source/CNS.H
Tutorials/GPU/CNS/Source/CNS.cpp
Tutorials/GPU/CNS/Source/CNSBld.cpp
Tutorials/GPU/CNS/Source/CNS_advance.cpp
Tutorials/GPU/CNS/Source/CNS_io.cpp
Tutorials/GPU/CNS/Source/CNS_setup.cpp
Tutorials/GPU/CNS/Source/Make.package
Tutorials/GPU/CNS/Source/diffusion/Make.package
Tutorials/GPU/CNS/Source/hydro/Make.package
Tutorials/GPU/CNS/Source/main.cpp

commit b5b603c3434040d7812e9d319f94375b1cecd6b8
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Oct 31 01:49:47 2018 -0700

    refactoring AMFIter codes

Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/Perilla/Barrier.H
Src/AmrTask/rts_impls/Perilla/Barrier.cpp
Src/AmrTask/rts_impls/Perilla/LocalConnection.H
Src/AmrTask/rts_impls/Perilla/Make.package
Src/AmrTask/rts_impls/Perilla/PackageQueue.H
Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp
Src/AmrTask/rts_impls/Perilla/Perilla.cpp
Src/AmrTask/rts_impls/Perilla/PerillaRts.cpp
Src/AmrTask/rts_impls/Perilla/RGIter.H
Src/AmrTask/rts_impls/Perilla/RGIter.cpp
Src/AmrTask/rts_impls/Perilla/RegionQueue.H
Src/AmrTask/rts_impls/Perilla/RegionQueue.cpp
Src/AmrTask/rts_impls/Perilla/RemoteConnection.H
Src/AmrTask/rts_impls/Perilla/WorkerThread.H
Src/AmrTask/rts_impls/Perilla/WorkerThread.cpp
Src/AmrTask/rts_impls/Perilla/mylock.h
Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/Perilla_upc++/Barrier.H
Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp
Src/AmrTask/rts_impls/Perilla_upc++/LocalConnection.H
Src/AmrTask/rts_impls/Perilla_upc++/Make.package
Src/AmrTask/rts_impls/Perilla_upc++/Perilla.H
Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp
Src/AmrTask/rts_impls/Perilla_upc++/PerillaRts.cpp
Src/AmrTask/rts_impls/Perilla_upc++/Perilla_common.cpp
Src/AmrTask/rts_impls/Perilla_upc++/RGIter.H
Src/AmrTask/rts_impls/Perilla_upc++/RGIter.cpp
Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.H
Src/AmrTask/rts_impls/Perilla_upc++/RegionQueue.H
Src/AmrTask/rts_impls/Perilla_upc++/RegionQueue.cpp
Src/AmrTask/rts_impls/Perilla_upc++/RemoteConnection.H
Src/AmrTask/rts_impls/Perilla_upc++/WorkerThread.H
Src/AmrTask/rts_impls/Perilla_upc++/WorkerThread.cpp
Src/AmrTask/rts_impls/Perilla_upc++/mylock.h
Src/AmrTask/rts_impls/Perilla_upc++/perilla.mak
Src/AmrTask/rts_impls/Pthread_Common/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/Pthread_Common/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/Pthread_Common/Barrier.H
Src/AmrTask/rts_impls/Pthread_Common/Barrier.cpp
Src/AmrTask/rts_impls/Pthread_Common/LocalConnection.H
Src/AmrTask/rts_impls/Pthread_Common/Make.package
Src/AmrTask/rts_impls/Pthread_Common/RGIter.H
Src/AmrTask/rts_impls/Pthread_Common/RGIter.cpp
Src/AmrTask/rts_impls/Pthread_Common/RegionQueue.H
Src/AmrTask/rts_impls/Pthread_Common/RegionQueue.cpp
Src/AmrTask/rts_impls/Pthread_Common/RemoteConnection.H
Src/AmrTask/rts_impls/Pthread_Common/WorkerThread.H
Src/AmrTask/rts_impls/Pthread_Common/WorkerThread.cpp
Src/AmrTask/rts_impls/Pthread_Common/mylock.h
Src/AmrTask/rts_impls/Pthread_Common/perilla.mak

commit 52e2ab6955876934add9610ada119485be14d2a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 30 20:51:40 2018 -0700

    forgot to add files

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaFab.H
Src/Base/AMReX_CudaFab.cpp
Src/Base/AMReX_CudaFabImpl.H
Src/Base/AMReX_CudaFabImpl.cpp

commit c21604554eada56ab7e4843b983569042032be18
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 30 18:31:48 2018 -0700

    Fix oops

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 8a5253cdbb5754d8739368be177948938134408b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 30 18:30:17 2018 -0700

    Remove extra print

Src/Extern/Algoim/Algoim_integrals.cpp

commit e37bb3fc5a1b7092a2b3be1b46c7d96cd468a1ca
Merge: e7a7de58b 79c269324
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 30 18:29:21 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit e7a7de58b7ad03d817b553a5842dfa2b92c89bb8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 30 18:28:53 2018 -0700

    In preparation for being able to use Algoim to construct the 3d EB nodal integrals
    for use in the 3d nodal projection

Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFabFactory.H
Src/Extern/Algoim/Algoim_integrals.H
Src/Extern/Algoim/Algoim_integrals.cpp
Src/Extern/Algoim/Make.package
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 64112f8eaba07d5427d11a86a6959fb9f77387d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 30 18:08:58 2018 -0700

    add an example of using DeviceFab

Tests/GPU/DeviceFab/GNUmakefile
Tests/GPU/DeviceFab/Make.package
Tests/GPU/DeviceFab/main.cpp

commit 559cb7099a392e36c34bbe81d10b868fcf2464e6
Author: Minion <mlminion@lbl.gov>
Date:   Tue Oct 30 17:03:16 2018 -0700

    Moving files to look like other tutorials

Tutorials/SDC/MISDC_ADR_2d/Exec/GNUmakefile
Tutorials/SDC/MISDC_ADR_2d/Exec/inputs_2d
Tutorials/SDC/MISDC_ADR_2d/README
Tutorials/SDC/MISDC_ADR_2d/Source/Make.package
Tutorials/SDC/MISDC_ADR_2d/Source/SDC_sweeper.cpp
Tutorials/SDC/MISDC_ADR_2d/Source/functions_2d.f90
Tutorials/SDC/MISDC_ADR_2d/Source/init_phi_2d.f90
Tutorials/SDC/MISDC_ADR_2d/Source/main.cpp
Tutorials/SDC/MISDC_ADR_2d/Source/myfunc.H
Tutorials/SDC/MISDC_ADR_2d/Source/myfunc_F.H

commit 64cd99e24675a0d43b1ed21cba5ad35a4aaa24c5
Author: Minion <mlminion@lbl.gov>
Date:   Tue Oct 30 16:46:50 2018 -0700

    made Nnodes adjustable and cleaner quadrature matrices

Src/SDC/AMReX_SDCstruct.H
Src/SDC/AMReX_SDCstruct.cpp

commit f29ceb098636e9816a066fb4f345c06c7c54b8be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 30 16:39:14 2018 -0700

    DeviveFab: add new constructor for the omp fab resize idiom

Src/Base/AMReX_CudaFab.H
Src/Base/AMReX_CudaFab.cpp
Src/Base/AMReX_CudaFabImpl.H
Src/Base/AMReX_CudaFabImpl.cpp

commit 1189de10d9bdac07a73be61fc7409d34aa7bed2a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 30 18:54:52 2018 -0400

    add profiler to CudaFab

Src/Base/AMReX_CudaFab.cpp
Src/Base/AMReX_CudaFabImpl.cpp

commit 79c26932410322f359b88005181f15c26d55ddd4
Author: Jean Sexton <jmsexton@lbl.gov>
Date:   Tue Oct 30 18:31:28 2018 -0400

    Remove old example

Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/GNUmakefile
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/Make.package
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/SetIC.f90
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/inputs
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/main.cpp
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/myfunc_F.H
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/ode_mod.f90

commit 58e2b03f69bcb96cb0e35eb8078545c461d660e6
Author: Cy Chan <cychan@lbl.gov>
Date:   Tue Oct 30 14:03:15 2018 -0700

    add flag to turn on/off new features for A/B comparison within the same run
      want to compare under same node assignment from job scheduler
    print SLURM_NODELIST in MLLinOp

Src/Base/AMReX_DistributionMapping.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 0ff2813e18e4573bbcaa7b4b2656c8b4e11ec6e9
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 30 13:55:22 2018 -0700

    Add to documentation: Fortran cannot be instrumented when using Tiny Profiling.

Docs/sphinx_documentation/source/AMReX_Profiling_Tools.rst

commit ef86702ef4cc330b6e47f7edbef1c0ca63204372
Merge: c28684d89 7a3148cb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 30 16:38:10 2018 -0400

    Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu

commit 7a3148cb43c04cebc358d45bbb2142e894a508c8
Merge: de25ba1dd 227f62499
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 30 13:38:19 2018 -0700

    Merge branch 'development' into weiqun/gpu

commit de25ba1ddc488deb87a29ae0dd95a92a3e95746f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 30 13:24:49 2018 -0700

    fix non-cuda build

Src/Base/AMReX_CudaFabImpl.cpp

commit c28684d893d8190c9bafe36dd70828ff5d89a329
Merge: ad2baf40d de25ba1dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 30 16:24:47 2018 -0400

    Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu

commit ad2baf40d1cfc77b709733bd038e4f852eceb48c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 30 16:16:33 2018 -0400

    use AMREX_CUDA_MAX_THREADS instead of hardwired number 256

Src/Base/AMReX_CudaDevice.cpp

commit dd63bad3479ccf8e07c44209e36869a862d0d2e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 30 13:11:44 2018 -0700

    implement DeviceFab

Src/Base/AMReX.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaFab.H
Src/Base/AMReX_CudaFab.cpp
Src/Base/AMReX_CudaFabImpl.H
Src/Base/AMReX_CudaFabImpl.cpp
Src/Base/AMReX_CudaUtility.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 227f62499c8a58f1721d564f82490bdafb67a67a
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Oct 30 06:49:03 2018 -0700

    use resize instead of clear

Src/Particle/AMReX_ParticleContainerI.H

commit 7f66c6de69b9887306a1b3aa1e87031ade2acfab
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Oct 30 06:29:11 2018 -0700

    need to clear ghosts / virtuals after adding them

Src/Particle/AMReX_ParticleContainerI.H

commit 4cff527c6663b493706041d73ddad14346d1213f
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Oct 30 01:13:29 2018 -0700

    correct AMFIter metadata after regridding

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AsyncFillPatch.cpp
Src/AmrTask/rts_impls/Perilla/Perilla.H
Src/AmrTask/rts_impls/Perilla/Perilla.cpp
Src/AmrTask/rts_impls/Perilla/PerillaRts.cpp
Src/AmrTask/rts_impls/Perilla/RGIter.cpp
Src/AmrTask/rts_impls/Perilla_upc++/Perilla_common.cpp

commit c0fda2f9f235f67337fbfd6662345ab4583244c8
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Mon Oct 29 23:39:35 2018 -0700

    fix mfi ordering bug

Src/SDC/AMReX_SDCstruct.cpp

commit c548b64158c7b342142d00989a9b818992a60351
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Mon Oct 29 23:10:49 2018 -0700

    Adding MISDC example with exact solution

Tutorials/SDC/MISDC_ADR_2d/GNUmakefile
Tutorials/SDC/MISDC_ADR_2d/Make.package
Tutorials/SDC/MISDC_ADR_2d/SDC_sweeper.cpp
Tutorials/SDC/MISDC_ADR_2d/functions_2d.f90
Tutorials/SDC/MISDC_ADR_2d/init_phi_2d.f90
Tutorials/SDC/MISDC_ADR_2d/inputs_2d
Tutorials/SDC/MISDC_ADR_2d/main.cpp
Tutorials/SDC/MISDC_ADR_2d/myfunc.H
Tutorials/SDC/MISDC_ADR_2d/myfunc_F.H

commit 8e51d61cf72771fc5faf0fac1f729af0a6612ea1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 29 18:06:00 2018 -0700

    make BaseFab's data trivially copyable

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaFab.H
Src/Base/AMReX_CudaFab.cpp
Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_Gpu.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 175f0dc150bcb596292d84faeab3e62a71d46693
Merge: 6b66db074 4aa3cf096
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 29 17:33:18 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 6b66db074f11e4e400c94f218aa77bb45be207af
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 29 17:33:04 2018 -0700

    Remove unused "auto sfab = ..." lines

Src/EB/AMReX_EBAmrUtil.cpp
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EB_levelset.cpp

commit 4aa3cf09644db7f269d2c5b4a88d47506d8bc04a
Merge: 6f5f3bede 22f04e44a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Oct 29 20:30:54 2018 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6f5f3bede1ae09268f7ec225e37fdb001f0e136a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Oct 29 20:30:11 2018 -0400

    changes needed for Nyx to compile with USE_CUDA=TRUE

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H

commit 22f04e44a39c692e524a4542a705e9df4a50b504
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 29 20:00:56 2018 -0400

    Consolidate and cleanup GPU tutorials.

Tests/GPU/ScratchPad/GNUmakefile
Tests/GPU/ScratchPad/Make.package
Tests/GPU/ScratchPad/inputs_3d
Tests/GPU/ScratchPad/main.cpp
Tests/GPU/ScratchPad/run.script
Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC/inputs
Tutorials/GPU/ElectromagneticPIC/summitdev.sh
Tutorials/GPU/ElectromagneticPIC_1/Constants.H
Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.H
Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC_1/Evolve.H
Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_1/GNUmakefile
Tutorials/GPU/ElectromagneticPIC_1/IO.H
Tutorials/GPU/ElectromagneticPIC_1/IO.cpp
Tutorials/GPU/ElectromagneticPIC_1/Make.package
Tutorials/GPU/ElectromagneticPIC_1/NodalFlags.H
Tutorials/GPU/ElectromagneticPIC_1/NodalFlags.cpp
Tutorials/GPU/ElectromagneticPIC_1/Particles.H
Tutorials/GPU/ElectromagneticPIC_1/StructOfArrays.H
Tutorials/GPU/ElectromagneticPIC_1/em_pic_3d.F90
Tutorials/GPU/ElectromagneticPIC_1/em_pic_F.H
Tutorials/GPU/ElectromagneticPIC_1/inputs
Tutorials/GPU/ElectromagneticPIC_1/main.cpp
Tutorials/GPU/ElectromagneticPIC_1/make.out
Tutorials/GPU/ElectromagneticPIC_1/summit.sh
Tutorials/GPU/ElectromagneticPIC_1/summitdev.sh
Tutorials/GPU/ElectromagneticPIC_1/test.cpp
Tutorials/GPU/ElectromagneticPIC_2/Constants.H
Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.H
Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC_2/Evolve.H
Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_2/GNUmakefile
Tutorials/GPU/ElectromagneticPIC_2/IO.H
Tutorials/GPU/ElectromagneticPIC_2/IO.cpp
Tutorials/GPU/ElectromagneticPIC_2/Make.package
Tutorials/GPU/ElectromagneticPIC_2/NodalFlags.H
Tutorials/GPU/ElectromagneticPIC_2/NodalFlags.cpp
Tutorials/GPU/ElectromagneticPIC_2/Particles.H
Tutorials/GPU/ElectromagneticPIC_2/StructOfArrays.H
Tutorials/GPU/ElectromagneticPIC_2/em_pic_3d.F90
Tutorials/GPU/ElectromagneticPIC_2/em_pic_F.H
Tutorials/GPU/ElectromagneticPIC_2/inputs
Tutorials/GPU/ElectromagneticPIC_2/main.cpp
Tutorials/GPU/ElectromagneticPIC_2/script.nompi.sh
Tutorials/GPU/ElectromagneticPIC_2/summit.sh
Tutorials/GPU/ElectromagneticPIC_2/summitdev.sh
Tutorials/GPU/ElectromagneticPIC_2/test.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d
Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Exec/run.ascent
Tutorials/GPU/HeatEquation_EX1_C/Exec/run.nocuda.script
Tutorials/GPU/HeatEquation_EX1_C/Exec/run.summit
Tutorials/GPU/HeatEquation_EX1_C/Exec/run.summitdev
Tutorials/GPU/HeatEquation_EX1_C/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H
Tutorials/GPU/HeatEquation_EX1_C/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/init_phi_2d.f90
Tutorials/GPU/HeatEquation_EX1_C/init_phi_3d.f90
Tutorials/GPU/HeatEquation_EX1_C/inputs_2d
Tutorials/GPU/HeatEquation_EX1_C/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H
Tutorials/GPU/HeatEquation_EX1_C/physbc.cpp
Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/run_summit_1node.sh
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/Make.package
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance_2d.f90
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance_3d.f90
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/init_phi_2d.f90
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/init_phi_3d.f90
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/main.cpp
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/myfunc_F.H
Tutorials/GPU/Readme.txt

commit dfe4c1f2640676e3c1f0f11c615fcd4fff8355fe
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Oct 29 14:31:35 2018 -0700

    MLMG: add cache for bottom-solve MPI sub-communicators
      MPI_Comm_create() is expensive and is called for every gravity solve
    remove some BL_PROFILE_REGION

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 1d4a4d3d6ee78c53a056850caa8d70ce9834f20e
Merge: d94ad31fc d27b3cc50
Author: Guy Moore <gmoore@lbl.gov>
Date:   Mon Oct 29 16:38:38 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit d94ad31fce36a5ee41e3d69e45eefc6ab68d3aaa
Author: Guy Moore <gmoore@lbl.gov>
Date:   Mon Oct 29 16:36:44 2018 -0700

    First commit of MUI-coupling tutorial

Tutorials/MUI/Exec_01/GNUmakefile
Tutorials/MUI/Exec_02/GNUmakefile
Tutorials/MUI/Exec_coupled/cmd_mpirun
Tutorials/MUI/Exec_coupled/inputs
Tutorials/MUI/Source_01/Make.package
Tutorials/MUI/Source_01/init_phi_3d.f90
Tutorials/MUI/Source_01/main_01.cpp
Tutorials/MUI/Source_01/myfunc.H
Tutorials/MUI/Source_01/myfunc_F.H
Tutorials/MUI/Source_02/Make.package
Tutorials/MUI/Source_02/main_02.cpp
Tutorials/MUI/Source_02/myfunc.H
Tutorials/MUI/doc/GNUmakefile
Tutorials/MUI/doc/MUIcouplingNotes.tex
Tutorials/MUI/doc/iface_rect.png
Tutorials/MUI/doc/vis_interface.m

commit b5d89747b553ecfd1cd4a6079c0f5b69d15c0087
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Oct 29 14:29:43 2018 -0700

    change makeSFC() to use box volume instead of just 1.0 for weights
      should improve load balancing for consolidated multigrid levels

Src/Base/AMReX_DistributionMapping.cpp

commit 97f573ddbb0ae90750c9465f5344967735d38f1c
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Mon Oct 29 14:12:56 2018 -0700

    Added multi-implicit capability

Src/SDC/AMReX_SDCstruct.H
Src/SDC/AMReX_SDCstruct.cpp

commit d27b3cc50a475b3b5cc7136ec73c1161f3dd11e6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 29 12:22:37 2018 -0700

    "conn" in 3d has 27 not 12 components

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit f8d7261bfe3c3b7e5cf04a1223fbf898b018ca59
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 29 12:22:06 2018 -0700

    Formatting for easier reading

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit 220edd81a33de8fc7d956cf9c3d256e5d1c008b8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 29 12:21:49 2018 -0700

    Fix typo: "coarest" --> "coarsest"

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 87fbee771c1478aa2d40b4d9923f3a5947649b74
Merge: d68355726 7c3d66689
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 29 12:20:58 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit d6835572664f4733464c3e2f19123501b7dbf1e7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 29 12:20:15 2018 -0700

    1) Fix typo in newu -- should be (i,j,k,2) not (i,j,2,k)
    2) add eps to the denominator when we create sten(i,j,k,ist_inv) -- mimicing 2d

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit cc6dfa6944f44bc7ddbdbed75c2b93a6dcae973e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 29 11:54:09 2018 -0700

    update

Src/Base/AMReX_Box.H
Src/Base/AMReX_COORDSYS_1D.cpp
Src/Base/AMReX_COORDSYS_2D.cpp
Src/Base/AMReX_COORDSYS_3D.cpp
Src/Base/AMReX_COORDSYS_C.H
Src/Base/AMReX_CoordSys.cpp

commit 7c3d66689a88c322a0412e755a1165c323a6af6a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Oct 29 10:30:39 2018 -0700

    Fix typo in Makefile

Src/Particle/Make.package

commit b1f02a0859fa6fd6d98d18d519ae1ab7ebd90a0d
Merge: 4e72e97a1 42ffc8db8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 29 10:18:09 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 4e72e97a10cd1117d0622fb0b31156ec62159b37
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 29 10:17:45 2018 -0700

    Make sure that the direction of a cylinder is in the range [0:AMREX_SPACEDIM-1]
    not [0:AMREX_SPACEDIM]

Src/EB/AMReX_EB2.cpp

commit 42ffc8db86f762970117a633e649a861ff0c7ab0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Oct 29 09:55:32 2018 -0700

    fix restart

Src/Particle/AMReX_ParticleContainerI.H

commit 68ea7185e42798f79f1381fa8e745368d0150b18
Merge: 4052ff7cc 70cce32aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 29 09:50:43 2018 -0700

    Merge branch 'development' into weiqun/gpu

commit 2359a078fcaf37495375831f1e990dccb40e1e3c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 28 20:21:29 2018 -0700

    Add the 3D EB nodal stencil.  Note that we haven't yet computed the integrals -- this just
    goes from the 19 core integrals to "conn" to "sten" -- we still need to include the computation
    of the vol, S_x, S_x^2 integrals etc.

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 70cce32aaf0e0168e46c2d8fa591570b78a72395
Merge: d862ef5a6 ebddada4a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 27 20:39:37 2018 -0700

    Merge branch 'gpu-merge-test' into development

commit ebddada4a291268b52f0dd12be4b8286ac790e16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 27 20:30:25 2018 -0700

    udpate build

Src/Base/CMakeLists.txt
Tools/libamrex/configure.py

commit 0e5f8945fd19006a5428eff67d6e520c9a924801
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 27 23:17:28 2018 -0400

    simplification

Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_GpuLaunch.H

commit d24f58a66cfb9802d44bb317d4960e580216d10f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 27 21:16:57 2018 -0400

    add cpu and device version for the range macro

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_GpuLaunch.H

commit 6486e1c3851ebc70cecff34a70e3819e3b224529
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 27 17:57:26 2018 -0700

    add Cuda::Range so that we can use the same macro for int and Box

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaRange.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit b8264404121ff350877f968283d05b14d764cc7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 27 11:50:47 2018 -0700

    some renaming

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.cpp

commit 76529b6a8f255ae870c9e819f30d304a24e89c28
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Fri Oct 26 17:18:29 2018 -0700

    Nuking old Heat Equation Example

Tutorials/SDC/HeatEquation_EX1_C/GNUmakefile
Tutorials/SDC/HeatEquation_EX1_C/Make.package
Tutorials/SDC/HeatEquation_EX1_C/advance.cpp
Tutorials/SDC/HeatEquation_EX1_C/advance_2d.f90
Tutorials/SDC/HeatEquation_EX1_C/advance_3d.f90
Tutorials/SDC/HeatEquation_EX1_C/init_phi_2d.f90
Tutorials/SDC/HeatEquation_EX1_C/init_phi_3d.f90
Tutorials/SDC/HeatEquation_EX1_C/inputs_2d
Tutorials/SDC/HeatEquation_EX1_C/inputs_3d
Tutorials/SDC/HeatEquation_EX1_C/main.cpp
Tutorials/SDC/HeatEquation_EX1_C/myfunc.H
Tutorials/SDC/HeatEquation_EX1_C/myfunc_F.H
Tutorials/SDC/HeatEquation_EX1_C/pf_quadrature.f90

commit 6fd46648612398aa0afdbe74d34127b2066e2069
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Fri Oct 26 17:16:13 2018 -0700

    Changing example name to reflect IMEX advection diffusion

Tutorials/SDC/IMEX_Advec_Diff_C/GNUmakefile
Tutorials/SDC/IMEX_Advec_Diff_C/Make.package
Tutorials/SDC/IMEX_Advec_Diff_C/advance.cpp
Tutorials/SDC/IMEX_Advec_Diff_C/advance_2d.f90
Tutorials/SDC/IMEX_Advec_Diff_C/init_phi_2d.f90
Tutorials/SDC/IMEX_Advec_Diff_C/init_phi_3d.f90
Tutorials/SDC/IMEX_Advec_Diff_C/inputs_2d
Tutorials/SDC/IMEX_Advec_Diff_C/inputs_3d
Tutorials/SDC/IMEX_Advec_Diff_C/main.cpp
Tutorials/SDC/IMEX_Advec_Diff_C/myfunc.H
Tutorials/SDC/IMEX_Advec_Diff_C/myfunc_F.H

commit 209b3e457cd24bccc48bdf8176179a5ec6ea6568
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Fri Oct 26 17:14:27 2018 -0700

    Reworked Tutorial to have a modular SDC form

Src/SDC/AMReX_SDCquadrature.F90
Src/SDC/AMReX_SDCstruct.H
Src/SDC/AMReX_SDCstruct.cpp
Src/SDC/Make.package
Tutorials/SDC/HeatEquation_EX3_C/Make.package
Tutorials/SDC/HeatEquation_EX3_C/advance.cpp
Tutorials/SDC/HeatEquation_EX3_C/advance_2d.f90
Tutorials/SDC/HeatEquation_EX3_C/init_phi_2d.f90
Tutorials/SDC/HeatEquation_EX3_C/inputs_2d
Tutorials/SDC/HeatEquation_EX3_C/main.cpp
Tutorials/SDC/HeatEquation_EX3_C/myfunc.H
Tutorials/SDC/HeatEquation_EX3_C/myfunc_F.H

commit d862ef5a626632494d7c3b4f33943098ace97459
Merge: 221058e0a cb4f4ef55
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 26 16:52:39 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 221058e0a78fb149d277556563a5bd44d991ad70
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 26 16:45:52 2018 -0700

    Cleaned up notation a little -- no functional change

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit cb4f4ef552936f1d063bc352cdef0f892c1e8672
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 26 16:25:28 2018 -0700

    add regression test inputs

Tests/LinearSolvers/NodeEB/inputs.rt.2d

commit 193b1566f1e34dc65a2a7025d6e4cf69de667baf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 26 16:08:36 2018 -0700

    Nodal EB test

Tests/LinearSolvers/NodeEB/GNUmakefile
Tests/LinearSolvers/NodeEB/Make.package
Tests/LinearSolvers/NodeEB/MyTest.H
Tests/LinearSolvers/NodeEB/MyTest.cpp
Tests/LinearSolvers/NodeEB/initEB.cpp
Tests/LinearSolvers/NodeEB/inputs
Tests/LinearSolvers/NodeEB/main.cpp

commit 00b7e49a0478811c4ac706c345a619f4984ea751
Merge: 15562f403 bddce1ae4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Oct 26 13:41:30 2018 -0700

    Merge pull request #333 from AMReX-Codes/gpu-merge-test
    
    gpu-mm branch into development.

commit bddce1ae4b70b44b74b8b84a4cda228621d5da78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 26 16:34:03 2018 -0400

    fix include in BLFort.H

Src/Base/AMReX_BLFort.H

commit e9d5b69c9c33b899baa0abb051e457669132acd8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 26 12:43:05 2018 -0700

    fix some remaining issues of the reorganization

Src/Base/AMReX_CudaContainers.H
Src/Base/AMReX_CudaMemory.H
Src/Base/AMReX_GpuLaunch.H

commit 37ec77f6e1d9b5b95d1fb304542bacf2da4df4d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 26 11:17:45 2018 -0700

    update cuda qualifier

Src/Base/AMReX_CudaUtility.H

commit a18a8ff4dc9eda681db983d96cd4f6a0f3840a11
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 26 11:14:22 2018 -0700

    update the cuda script

Tools/F_scripts/write_cuda_headers.py

commit 429ff4e534c52968c983a31f1934a678f70ba1a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 26 10:54:51 2018 -0700

    fix the merge

Src/Base/AMReX_Geometry.H
Src/Particle/AMReX_Functors.H

commit 4321f8876b232e7e6de9d7c9a0817f302afb0cc8
Merge: 0975bc242 11ab1fd53
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 26 10:51:21 2018 -0700

    Merge branch 'gpu-merge-test2' into gpu-merge-test

commit 0975bc2420f2f7edaabb89ffc9896a1ca10b00e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 26 10:48:43 2018 -0700

    add namespace alias Gpu and hide the name cuda from users

Src/Base/AMReX_GpuControl.cpp

commit 583cfe5fac9b29cfc019b79e6333f72184dfa77d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 26 10:42:23 2018 -0700

    add namespace alias Gpu and hide the name cuda from users

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_GpuControl.H

commit 44c96b8b1358ae94f1d4bdf56a5b6625a5303b6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 26 10:34:18 2018 -0700

    add namespace alias Gpu and hide the name cuda from users

Src/Amr/AMReX_Amr.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_Array.H
Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BArena.H
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_Box.H
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_Cuda.H
Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaContainers.H
Src/Base/AMReX_CudaDevice.H
Src/Base/AMReX_CudaDevice.cpp
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp
Src/Base/AMReX_CudaMemory.H
Src/Base/AMReX_CudaQualifiers.H
Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_CudaUtility.cpp
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Gpu.H
Src/Base/AMReX_GpuControl.H
Src/Base/AMReX_GpuControl.cpp
Src/Base/AMReX_GpuLaunch.H
Src/Base/AMReX_GpuQualifiers.H
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_Orientation.H
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_iMultiFab.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/EB/AMReX_MultiCutFab.H
Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_StructOfArrays.H
Tests/GPU/TestC/main.cpp
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/F_scripts/write_cuda_headers.py
Tools/GNUMake/Make.defs
Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/main.cpp
Tutorials/GPU/HelloWorld_C/main.cpp

commit 11ab1fd530bf3bc6a4a526c8850f81af506cd54d
Merge: c45c0c007 48b783e2e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Oct 26 10:50:25 2018 -0400

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit c45c0c00782361ec5d2323cf5a4aeba2e42f2aea
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Oct 26 10:50:03 2018 -0400

    start to work on particle tiling for GPU

Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_ParticleContainerI.H

commit 48b783e2e5d9a32d887597af2859a51c38ac04bf
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Oct 25 23:35:23 2018 -0400

    fix NumberOfParticlesAtLevel

Src/Particle/AMReX_ParticleContainerI.H

commit 946a55341764f3806dd46284d6577f6dce43e1b7
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 25 23:00:05 2018 -0400

    remove functors from AMReX_Particles.H

Src/Particle/AMReX_Particles.H

commit 458a627db851770a1a0a0c39fec247ed18a27c41
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 25 22:52:11 2018 -0400

    template the setPosition functor on particle type

Src/Particle/AMReX_ParIterI.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 029cfc794b3b82ebc2d7dc4d983e937c69aef66e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 25 22:51:40 2018 -0400

    move functors to separate file

Src/Particle/AMReX_Functors.H

commit 159ecac124273e9e328bdf8557731ebe11efc6b6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 25 22:51:11 2018 -0400

    fix bug introduced

Src/Particle/AMReX_ParticleContainerI.H

commit 85f313f053b2e1a741ab45e7b60cbfd5529d1380
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 25 22:11:31 2018 -0400

    use the new managed objects in the thrust functors

Src/Particle/AMReX_ParticleContainerI.H

commit 4defed6eb6865b62d322a95807c677e1c6567ba9
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 25 22:11:14 2018 -0400

    add isPeriodic to GeometryData

Src/Base/AMReX_Geometry.H

commit 3d1112a3283d180bf71826d565485ee2b597a3f7
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 25 21:25:32 2018 -0400

    use the AMREX_CUDA_HOST_DEVICE macro

Src/Particle/AMReX_ParticleContainerI.H

commit d727d151f1adf9317cd3b81e939bd49c045ce04e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 25 17:39:44 2018 -0700

    tidy

Src/Base/AMReX_Arena.cpp

commit 57f827bf4c9b86331d5fc4c2c0a4f76b52935922
Merge: 857e66cf0 c4ef60b1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 25 20:25:44 2018 -0400

    Merge branch 'gpu-merge-test2' into gpu-merge-test

commit 857e66cf0f83e048fae4b7d279093368005b36fe
Merge: abf9034ea 15562f403
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 25 20:25:33 2018 -0400

    Merge branch 'development' into gpu-merge-test

commit c4ef60b1cb2eba17a6ec4de3b77d4126f3184564
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 25 20:24:03 2018 -0400

    reorganize arenas. Managed class uses the managed arena. remove BaseFab Fortran functions

Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90
Src/Base/AMReX_CudaMemory.H
Src/Base/Make.package

commit ea6ced7f1eb5a3b2bd4b7f7cf29633c0c55257f9
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 25 16:01:25 2018 -0400

    do not sort the grids here.

Src/Particle/AMReX_ParticleContainerI.H

commit a123f49d050b06be390db88d97ef0c67f618f918
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 25 15:41:48 2018 -0400

    function to sort particles be cell if desired

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 966d62ac8e39bb60b34d979b1c9fbdca4da931f5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 25 10:32:43 2018 -0400

    also use it in the call to sort_by_dest

Src/Particle/AMReX_ParticleContainerI.H

commit 2e3b85ad28def29b81b2fd0b869966e5afc4c5b8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 25 10:32:24 2018 -0400

    simply use The_Cuda_Arena() internally for thrust

Src/Base/AMReX_CudaAllocators.H

commit e276b2f674f6bcfdaf2ae138fbf80efaf76c2c27
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 24 14:44:53 2018 -0700

    make sure communication work with non-cuda-aware mpi

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 9b76e70da6c5de2de9a640c71c58b3782ac23edf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 24 14:27:06 2018 -0700

    arena reorganization

Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit cf1044754d3019f4d608ae5258d24ceac76cc8d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 24 16:49:42 2018 -0400

    the cuda arena based on CArena and cudaMalloc

Src/Base/AMReX_Arena.H
Src/Base/AMReX_FabArrayBase.cpp

commit 481b22acb6859717fefbba0f3140ea50b7ee7d6a
Author: Minion <mlminion@lbl.gov>
Date:   Wed Oct 24 13:35:45 2018 -0700

    Creating SDCstruct library in Src

Src/SDC/AMReX_SDCstruct.H
Src/SDC/AMReX_SDCstruct.cpp
Src/SDC/Make.package

commit 25af27aa1131cfc1dbb3a27ebdeb889718d13511
Author: Minion <mlminion@lbl.gov>
Date:   Wed Oct 24 13:34:25 2018 -0700

    moving SDC arrays into struct

Tutorials/SDC/HeatEquation_EX3_C/GNUmakefile
Tutorials/SDC/HeatEquation_EX3_C/Make.package
Tutorials/SDC/HeatEquation_EX3_C/SDCstruct.H
Tutorials/SDC/HeatEquation_EX3_C/advance.cpp
Tutorials/SDC/HeatEquation_EX3_C/main.cpp
Tutorials/SDC/HeatEquation_EX3_C/myfunc.H

commit 8985423a70482bdfd6624bbde945a169a98c4e55
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 16:21:01 2018 -0400

    also keep the recv buffers around to avoid cudaMalloc costs

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 15562f40333022082971643914ea32ead93abd4a
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Oct 24 12:44:50 2018 -0700

    regular AMFiter update

Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AsyncFillPatch.cpp
Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/Perilla/Barrier.cpp
Src/AmrTask/rts_impls/Perilla/Make.package
Src/AmrTask/rts_impls/Perilla/Perilla.H
Src/AmrTask/rts_impls/Perilla/Perilla.cpp
Src/AmrTask/rts_impls/Perilla/PerillaConfig.H
Src/AmrTask/rts_impls/Perilla/PerillaRts.H
Src/AmrTask/rts_impls/Perilla/PerillaRts.cpp
Src/AmrTask/rts_impls/Perilla/RGIter.H
Src/AmrTask/rts_impls/Perilla/RGIter.cpp
Src/AmrTask/rts_impls/Perilla/RegionGraph.H
Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp
Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp
Src/AmrTask/rts_impls/Perilla_upc++/Make.package
Src/AmrTask/rts_impls/Perilla_upc++/Perilla.H
Src/AmrTask/rts_impls/Perilla_upc++/PerillaConfig.H
Src/AmrTask/rts_impls/Perilla_upc++/RGIter.H
Src/AmrTask/rts_impls/Perilla_upc++/RGIter.cpp
Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.H
Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp
Src/Base/AMReX_MultiFabUtil_Perilla.cpp

commit ca5a1b5d488c51a2298835c44593d8672879c60f
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Wed Oct 24 11:51:28 2018 -0700

    making constructor for SDCstruct

Tutorials/SDC/HeatEquation_EX3_C/SDCstruct.H
Tutorials/SDC/HeatEquation_EX3_C/advance.cpp
Tutorials/SDC/HeatEquation_EX3_C/main.cpp
Tutorials/SDC/HeatEquation_EX3_C/myfunc.H
Tutorials/SDC/HeatEquation_EX3_C/myfunc_F.H

commit d2c37a6bddbad40fc835a231a025baa77848dc19
Merge: 21f3c2902 0f1a9106e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 13:30:34 2018 -0400

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit 21f3c290232f9e5ea240214a68dfd7accb996e27
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 13:30:00 2018 -0400

    fix DEBUG build for gpu

Src/Particle/AMReX_ParticleContainerI.H

commit 0f1a9106e248609acf36b4c1c0eff352020f323d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 24 13:27:59 2018 -0400

    Wrap nvvp naming with appropriate directives.

Src/Base/AMReX.H
Src/Base/AMReX.cpp

commit df72a2ccb8c36f978b9c680ad0280e497e293181
Merge: 78fefbd31 568e27881
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 13:21:35 2018 -0400

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit 78fefbd319dcdb6303de0ce68bc8ce945ec0cd23
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 13:18:49 2018 -0400

    fix circular includes

Src/Base/AMReX_CudaAllocators.H

commit 568e27881588acf262de1b2a3f93e29d9b4225a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 24 08:41:23 2018 -0700

    check thread safety when using cuda

Src/Base/AMReX_FabArrayBase.cpp

commit cb6eed9802b8fdc6c87302074ab1304e8f3f4dc0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 24 08:41:00 2018 -0700

    these static functions are host only

Src/Base/AMReX_BaseFab.H

commit 9b9a0f908574b80a17c7e357f15a3edd4dde2fbe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 24 08:35:10 2018 -0700

    remove unused variable

Src/Base/AMReX_FabArrayBase.cpp

commit 8fb644a297bbf498d571ec0d45842314aa01c22b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 24 11:44:19 2018 -0400

    Add profiler wrapper to Device's init to clearly identify Cuda driver and Cuda API startups in nvvp.

Src/Base/AMReX.H
Src/Base/AMReX.cpp

commit df0b032a69535b20960eb50011bfa66bf64cfc39
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 11:20:51 2018 -0400

    clean up a little bit.

Src/Base/AMReX_CudaAllocators.cpp

commit 64b6423d6b80fdbcabc329f859d2af055da1e9de
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 11:10:06 2018 -0400

    comments

Src/Base/AMReX_CudaContainers.H

commit 16d6e6fa8e4c641807c66051c1e79ee1b4a62b88
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 11:07:32 2018 -0400

    restore the managed version of std::vector (could be useful elsewhere)

Src/Base/AMReX_CudaContainers.H

commit 782063c0f304ae362fa6ebff699072d46b505553
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 11:02:29 2018 -0400

    rename ManagedVector -> ManagedDeviceVector

Src/Base/AMReX_CudaContainers.H
Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_StructOfArrays.H

commit 68008a55e388abec76c3240f91464bb4dd61b2bd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 10:55:49 2018 -0400

    add missing ifdef

Src/Base/AMReX_CudaAllocators.cpp

commit fd99d6db63b9592595455b6838d72f8ad0582453
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 10:49:06 2018 -0400

    add stub from compiling fcompare in Tools/Postprocessing/C_Src

Tools/Postprocessing/C_Src/GNUmakefile

commit 3f9f9d8afcec96eb19fc2b419de7e1a9b982e3dc
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 10:42:01 2018 -0400

    use preallocated buffer for mpi communication in RedistributeGPU

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 711b34abef843e73a5427cf0c1162c7fcc70d1f6
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 10:40:57 2018 -0400

    use the ThrustManagedAllocator in the Thrust calls in RedistributeGPU

Src/Base/AMReX.cpp
Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaAllocators.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit c3ade82e32b101b02a9d6df3cd4823890ad7ab02
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 24 10:03:52 2018 -0400

    adding a ThrustCachedAllocator for calls to thrust::sort and thrust::partition

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaContainers.H

commit 8d6d1aafe0e19a704152a7f0d1aa56739d6f4943
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 23 21:36:45 2018 -0700

    fix thread safety

Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_CudaUtility.cpp
Src/Base/AMReX_FabArrayCommI.H

commit 75609195c1a49f540acec202ac6bb70dd045b716
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 23 17:00:58 2018 -0700

    fix omp for StreamIter

Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_CudaUtility.cpp
Src/Base/AMReX_FabArrayCommI.H

commit e98d97fe2a10df573aa454eec1a626f5ede33c44
Merge: 219379b0d 6ae02409e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 23 19:32:36 2018 -0400

    Merge branch 'gpu-fb' into gpu-merge-test2

commit 219379b0d58230d2fc6ffa2daf65ca8b93bf9303
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 23 19:31:16 2018 -0400

    make The_FA_Arena used the managed CArena (from weiqun)

Src/Base/AMReX_FabArrayBase.cpp

commit 6ae02409e2f6c25966fc3d82d82650aa4341d950
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 23 15:24:35 2018 -0700

    use one buffer for all send data

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayCommI.H

commit 1db5bb236e7532896fc7281c128cffdec8e03678
Merge: 175892ee0 8e1f65055
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Tue Oct 23 14:50:20 2018 -0700

    Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC

commit 175892ee07460f89a3d6add0aaa1250ec8bd0a3b
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Tue Oct 23 14:49:42 2018 -0700

    changing example size

Tutorials/SDC/HeatEquation_EX1_C/GNUmakefile
Tutorials/SDC/HeatEquation_EX1_C/inputs_2d

commit 5df963c75abb7cb68f31136c75c9e67273d3b079
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 23 14:44:56 2018 -0700

    use one buffer for all recv data

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit a26f208d29bc3c364e55fc5409698f5dbee51459
Merge: 6aac4a682 a48788daa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 23 14:20:06 2018 -0700

    Merge branch 'gpu-comm-malloc' into gpu-fb

commit a48788daae005f7f2ace89af4940bee03dbd8551
Merge: abfc3af25 07678f261
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 23 14:17:15 2018 -0700

    Merge branch 'gpu-merge-test2' into gpu-comm-malloc

commit 07678f261460570ceef8665484a9edd3aa8736a9
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 23 16:15:56 2018 -0400

    changes needed by the new Cuda::ManagedVector

Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_TracerParticles.cpp

commit 375a7eb1d08b1c9b6d0e8e8835aa24e9473e0de8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 23 16:14:55 2018 -0400

    use thrust as the underlying container type for Cuda::ManagedVector

Src/Base/AMReX_CudaContainers.H

commit 4d051de0de43b28d43e5fcb4bd48a200b01f9595
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 23 16:14:17 2018 -0400

    add custom allocator for use with thrust::device_vector

Src/Base/AMReX_CudaAllocators.H

commit b30cff0eb5020083e47515fb2ba27bafa58e18d3
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 23 16:10:08 2018 -0400

    Revert "Async FillBoundary kernel calls. Further testing/tweaking required."
    
    This reverts commit 0b9070719e7e3a7092e9f3c33d60b3e1bb561d1a.

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit bbf7beabf891fb796f83a090744c055dcfc9007d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 23 16:09:46 2018 -0400

    Revert "Revert "Add first draft of ASYNC macro and CPU versions of other macros.""
    
    This reverts commit 901d17cc2d19fc768fe05db37fc5ef4de6e0cb17.

Src/Base/AMReX_CudaLaunch.H

commit 901d17cc2d19fc768fe05db37fc5ef4de6e0cb17
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 23 16:07:23 2018 -0400

    Revert "Add first draft of ASYNC macro and CPU versions of other macros."
    
    This reverts commit 8ef30be7967b6b6f17e5b955bd882c398103a230.

Src/Base/AMReX_CudaLaunch.H

commit 6aac4a68291278826ba14874ce93eed08d720678
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 23 15:54:07 2018 -0400

    remove _async

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit 4cadfd66fb5eda07b2120ebbb8cedda5f5b04a88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 23 15:29:58 2018 -0400

    WIP: StreamIter

Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_FabArrayCommI.H

commit 0b9070719e7e3a7092e9f3c33d60b3e1bb561d1a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 23 12:32:49 2018 -0400

    Async FillBoundary kernel calls. Further testing/tweaking required.

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit 8ef30be7967b6b6f17e5b955bd882c398103a230
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 23 12:31:10 2018 -0400

    Add first draft of ASYNC macro and CPU versions of other macros.

Src/Base/AMReX_CudaLaunch.H

commit fdd5414712f73b59bac54f2c6049bcbde25444ed
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 23 12:29:59 2018 -0400

    GPU-ize another norm function.

Src/Base/AMReX_MultiFab.cpp

commit 080cee792c32bfd834dc8a91fa7ae54ec79402d6
Merge: 590c60434 f4acc9482
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 23 00:04:26 2018 -0400

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit 590c604348604f6054ef2fb5378e245f46bd4d43
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 23 00:03:42 2018 -0400

    further reduce the number of memory allocations in RedistributeGPU

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 4052ff7cc86202a043df479cd09077e2a1b98618
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 22 18:15:47 2018 -0700

    update header name

Src/Base/AMReX_CoordSys.cpp

commit c4ef333919b53a8a6c16478d4067eab62bb217b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 22 18:15:07 2018 -0700

    rename for typecheck

Src/Base/AMReX_COORDSYS_C.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit fcc1923854b31bcb0c78bc1d22137bbfcbd786c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 22 17:58:51 2018 -0700

    CoordSys: Fortran -> C++ and GPU

Src/Base/AMReX_Box.H
Src/Base/AMReX_COORDSYS_1D.F90
Src/Base/AMReX_COORDSYS_1D.cpp
Src/Base/AMReX_COORDSYS_2D.F90
Src/Base/AMReX_COORDSYS_2D.cpp
Src/Base/AMReX_COORDSYS_3D.F90
Src/Base/AMReX_COORDSYS_3D.cpp
Src/Base/AMReX_COORDSYS_F.H
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_Geometry.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 085375494e9a3cb8bb24abf338344cdc723849f9
Merge: 22cd090c5 276cba540
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Oct 22 17:31:29 2018 -0700

    Merge pull request #351 from burlen/sensei_adaptor_bugfix
    
    sensei data adaptor fixes

commit 276cba5406a18909371a7739b9135e9228dd5e77
Author: Burlen Loring <bloring@lbl.gov>
Date:   Mon Oct 22 15:15:27 2018 -0700

    sensei data adaptor fixes
    
    * set data set origin, fixes issue with simulations where the lower left
      corner in physical space is not at 0,0,0
    * fix a memory leak in AmrMeshDataAdaptor
    * let simulations set control parameters explicilty
    * validate control parameters during initialization

Src/Extern/SENSEI/AMReX_AmrDataAdaptor.cpp
Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp
Src/Extern/SENSEI/AMReX_InSituBridge.H
Src/Extern/SENSEI/AMReX_InSituBridge.cpp

commit f4acc948295f4198c4d60efc4219ad4e3a81614b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 22 17:31:09 2018 -0400

    First attempt at a triple macro for (i, j, k) equivalent flux calls.

Src/Base/AMReX_CudaLaunch.H

commit b51f0192d92313b4db6a66358dec546489bd0b50
Merge: d6ae25ec3 ac6e1ed2f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Oct 22 16:15:32 2018 -0400

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit d6ae25ec3fa9d583a04f60f074a8739d8213f2a5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Oct 22 16:15:08 2018 -0400

    avoid repeatedly reallocating memory on the GPU

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit abfc3af258d9a434237102570bf76273bf6ed213
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 22 13:08:25 2018 -0700

    rm deprecated upc++ stuff

OldTutorials/PGAS_HEAT/GNUmakefile
OldTutorials/PGAS_HEAT/Make.package
OldTutorials/PGAS_HEAT/advance_3d.f90
OldTutorials/PGAS_HEAT/init_phi_3d.f90
OldTutorials/PGAS_HEAT/inputs_3d
OldTutorials/PGAS_HEAT/main.cpp
OldTutorials/PGAS_HEAT/test-mpi3/main.cpp
OldTutorials/PGAS_HEAT/writePlotFile.H
OldTutorials/PGAS_HEAT/writePlotFile.cpp
Src/Base/AMReX.cpp
Src/Base/AMReX_BLPgas.H
Src/Base/AMReX_BLPgas.cpp
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tests/FillBoundaryComparison/GNUmakefile
Tests/FillBoundaryComparison/main.cpp

commit de3b4ba84680bc73301c1493250b7206c7bb3056
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Oct 22 14:57:49 2018 -0400

    remove page faults from RedistributeGPU

Src/Particle/AMReX_ParticleContainerI.H

commit 22cd090c5a70c7028cac4b63d1751e70fdcccc04
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 22 11:10:08 2018 -0700

    fix a bug in 1d interpolation thanks to Zhonglin Li

Src/AmrCore/AMReX_INTERP_1D.F90

commit ac6e1ed2f99d832ab59d345ae7cd03cb4ca8513e
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 22 12:55:59 2018 -0400

    Fix MultiFab reduction locations in some functions.

Src/Base/AMReX_MultiFab.cpp

commit 03eb03560a147443fa7e0654946f4aa3d15a2d79
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 22 12:45:34 2018 -0400

    Add Cuda namespace to HeatEquation & add script for OLCF Ascent.

Tutorials/GPU/HeatEquation_EX0_C/Exec/run.ascent
Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp

commit 3bc91be1e84697f5d19352d847a5dcdb2640af99
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 22 09:23:17 2018 -0700

    fix typo

Src/Base/AMReX_CudaLaunch.H

commit 05db02e4f2c9c233c153e7244a68dd7df8f52769
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 21 17:50:23 2018 -0700

    Add the gradient operation for 3D EB nodal -- this is in the mknewu routine.

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit f97f4ab56ab9f8f415ef84f74cc258673e5e53cd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 21 13:44:05 2018 -0700

    Add the 3D EB divergence stencil

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 97a5dd17bd075df3c8a0fb046dda629636ae9df5
Merge: e649272b2 302e474d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 21 13:22:08 2018 -0700

    Merge branch 'gpu-merge-test3' into gpu-merge-test2

commit 302e474d0f8177966d78be760e400419eb52f665
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 21 16:15:46 2018 -0400

    tweak threading trying to be more page friendly

Src/Base/AMReX_CudaLaunch.H

commit e649272b2ec910548f8d9cff09df442bdf875f33
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sun Oct 21 13:15:16 2018 -0400

    Small, partial changes.

Src/Base/AMReX_MultiFab.cpp

commit 2031ff34f7d85a26aae73595bd2b339bbd25dc88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 20 13:38:35 2018 -0700

    rm Managed as Base of Box and RealBox. namespace reorganization: amrex::Cuda::Atomic::Add etc.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_CudaMemory.H
Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_RealBox.H

commit a7a5389cc5b7b4579cb7fa2a674015c9fb29a82f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 20 10:46:13 2018 -0700

    try to avoid potential name conflict

Src/Base/AMReX_CudaLaunch.H

commit 86bd00c115fbd2b7ce7c27ab6ccdec3f3d9e205e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 20 10:42:49 2018 -0700

    put Strategy and getThreadBox into namespace Cuda

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp
Src/Base/AMReX_FArrayBox.cpp

commit acd6f6eb50482e1ec3f662d4fd1c8ced659d3455
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 19 21:52:02 2018 -0700

    int -> long and inline

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp

commit 717229b4389df56ef99c973a04253a7561290783
Merge: 323671933 d14cb41c3
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 19 22:17:33 2018 -0400

    Merge branch 'gpu-merge-test3' of https://github.com/AMReX-Codes/amrex into gpu-merge-test3

commit 323671933165ee0faf87281affc95ce061644740
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 19 22:17:25 2018 -0400

    Better/(fixed(?)) version of the 1D thread box.

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp

commit 0f86f9e4a1d789013c423ca2b87635af78046969
Merge: b7a041012 5a7cfbb9d
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Oct 19 17:44:31 2018 -0700

    Merge pull request #346 from burlen/amrmesh_bug_fix
    
    fix a bug in sensei AmrMeshDataAdaptor

commit d14cb41c3b12df8221ed6dc7c02f87251b72bb72
Merge: 957b7a77a fb62a1051
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 19 17:39:03 2018 -0700

    Merge branch 'gpu-merge-test2' into gpu-merge-test3

commit fb62a10513e70c1a7326007c848e9fce88262a15
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 17:23:53 2018 -0700

    make ManagedVector<T>::assign run either on the CPU or GPU depending on Cuda::inLaunchRegion

Src/Base/AMReX_CudaContainers.H

commit bac6d84b580ae3f8acb9d3eb61f8aa5743e96d35
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 17:21:18 2018 -0700

    double -> Real

Src/Particle/AMReX_Particles.H

commit dc8a7ec2d17ef85950a0533c638ebd664ec159b9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 17:15:41 2018 -0700

    fix get / set particles for 2D

Src/Particle/AMReX_Particles.H

commit 21f44b57b662cf1c9a8a42dc1bf7f9f38fef1744
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 16:56:22 2018 -0700

    use Cuda::ManagedVector in Particles

Src/Base/AMReX_CudaContainers.H
Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_StructOfArrays.H

commit 5a7cfbb9d9f7580b9629228a1193ed27cf6b7b4c
Author: Burlen Loring <bloring@lbl.gov>
Date:   Fri Oct 19 16:53:08 2018 -0700

    fix a bug in sensei AmrMeshDataAdaptor
    
    ref ratios may be empty if only 1 level, and cleanup some
    code in the tutorial that should not have been committed.

Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit c5b8482936911115e08bcb14955df710a89f75f6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 16:32:35 2018 -0700

    add HostVector and ManagedVector, move to a different file.

Src/Base/AMReX_Cuda.H
Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_CudaContainers.H
Src/Base/AMReX_Vector.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 45d993a958fd2166fa0abf17c7fab9564fc83710
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 16:27:51 2018 -0700

    remove executable permissions from these source files.

Src/Base/AMReX_MultiFabUtil_Perilla.H
Src/Base/AMReX_MultiFabUtil_Perilla.cpp

commit 6909852e0aff465bfbab5e322151fb8fcdbec3ab
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 16:16:39 2018 -0700

    add dataPtr() wrapper to ArrayOfStructs

Src/Particle/AMReX_ArrayOfStructs.H

commit 144acd74bfa3f0a68212f85012894c8ff1c136b8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 15:59:09 2018 -0700

    use a template function to reduce code duplication

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H

commit 43091486b26ade527b27067260cffb324db3a1c8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 15:55:37 2018 -0700

    mn -> mx again

Src/Base/AMReX_MultiFab.cpp

commit 5fa5fb94448150cf5319a6ac3ce67cfd936eeb1e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 15:55:13 2018 -0700

    mn -> mx

Src/Base/AMReX_MultiFab.cpp

commit 8aee1a4ebd11d2ca2f1a836faba9418720a89784
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 15:54:45 2018 -0700

    add missing if

Src/Base/AMReX_MultiFab.cpp

commit bcd324f4355d180fba5c6726c05916e2d054dff6
Merge: 12dba2753 b698d8041
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 15:53:22 2018 -0700

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit 957b7a77a85b9779740835016c6e73c8b528eb4c
Merge: f18587738 b698d8041
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 19 15:14:53 2018 -0700

    Merge branch 'gpu-merge-test2' into gpu-merge-test3

commit f18587738b4dc832d733659c0a7ea7f2f26cbd8a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 19 18:12:26 2018 -0400

    fix launches.

Src/Base/AMReX_CudaLaunch.H

commit 12dba2753d8cecd90597f1ec32aaf60b59a6c32e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 14:52:31 2018 -0700

    give DeviceVector an assign method

Src/Base/AMReX_Vector.H

commit 2f9f814d4043abd5161a256a63903518d6222581
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 19 17:47:29 2018 -0400

    Launch macros with striding.

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp

commit b698d8041c054b33eea3ee9e79807eeae22693f3
Merge: 02c26860e 7fecc0778
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 19 14:40:42 2018 -0700

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit 93d79691c115e91cb3822bf645f3689c2f2b3fe1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 14:31:22 2018 -0700

    give both device and managed versions of Get / Set Position to ParIter

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H

commit 7cc3f09db4a2240068e783cd3d7bad60be1384e1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 14:08:07 2018 -0700

    use DeviceVector in the ParIter

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H

commit e7c6863a72955c9b8d0e713aaf586850192fa034
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 19 14:07:34 2018 -0700

    add a wrapper around thrust::device_vector that does the raw_pointer_cast for you

Src/Base/AMReX_Vector.H

commit ba94b412bd0e2c355efcd6a6831e441032be815a
Merge: 872f8a9b5 b7a041012
Author: Cy Chan <cychan@lbl.gov>
Date:   Fri Oct 19 13:57:02 2018 -0700

    Merge branch 'development' into cy-perf

commit 872f8a9b5c0308421d192fcb2c6839bc332b5411
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Oct 15 16:22:54 2018 -0700

    add verbose_mapper flag and detailed messages for DistributionMapping

Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_ParallelContext.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 7fecc07780a93d019a4c275e1723433ba579f808
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 19 16:31:54 2018 -0400

    Testing safe for USE_CUDA=FALSE

Tutorials/GPU/HelloWorld_C/main.cpp

commit 704563169e97a82ce030a91ac432427c55c28b76
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 19 16:30:09 2018 -0400

    Starting MultiFab::norm conversions with norm0.

Src/Base/AMReX_MultiFab.cpp

commit fb50d2d3fc798c4a6ad78962a2bca52dc77d2a84
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 19 16:19:46 2018 -0400

    new strategy

Src/Base/AMReX_Box.H
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp

commit 02c26860e66ccc0f277971c4a261b6c0323903f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 19 10:52:32 2018 -0700

    add AMReX_Cuda.H so that the user only needs to include this one header.  add operator<< for printing dim3.

Src/Base/AMReX_Cuda.H
Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_CudaUtility.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 91fb0604d7fe316aa763dc7be2c83711abd90848
Merge: 999aafb91 9ddc51039
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 18 21:22:55 2018 -0400

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit 999aafb91c3e85652db4e9c8949e888b6c827997
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 18 21:22:28 2018 -0400

    add a nice hack to the Ascent makefile so you don't have to mess with CPATH to build

Tools/GNUMake/sites/Make.olcf

commit 9ddc51039f96f19e5f5d1ff4961b1e1862059c0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 18 17:40:31 2018 -0700

    move ptr identification functions to amrex::Cuda:: in AMReX_CudaUtility.H

Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 1669e0edffd6592e190cb497b758f109ab9d00fb
Merge: f17b7cff7 d988fb9a0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 18 17:19:46 2018 -0700

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit d988fb9a01087d2fcb5b42457605a8c0d69f1f70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 18 13:31:06 2018 -0700

    fix bugs

Src/Base/AMReX_CudaLaunch.cpp
Src/Base/AMReX_Device.cpp

commit f17b7cff75f9f3faf4ea3398fe6a0b16dc60394b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 18 17:15:38 2018 -0700

    only use thrust::device_vector in Get / Set Position if Cuda is on.

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H

commit 3c7e91f2bf58ebd09e379c16da18f557ce6438a5
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 18 19:51:53 2018 -0400

    Wrap Utility for USE_CUDA=FALSE

Src/Base/AMReX_CudaUtility.H

commit ec5cccb6d2bca2d126184caf93afb56dcd4201e5
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 18 19:50:57 2018 -0400

    Fix DeviceScalar.

Src/Base/AMReX_CudaMemory.H

commit d9e78c5bf5a84911afce8bd1ca6b1497c71c5d0d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 18 19:30:41 2018 -0400

    Max and Min changes and test case.

Src/Base/AMReX_MultiFab.cpp
Tutorials/GPU/HelloWorld_C/main.cpp

commit 11a82011642e64207a366413b531044db62e2012
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 18 09:35:21 2018 -0700

    add inline so that it compiles

Src/Base/AMReX_CudaUtility.H

commit b8d3fbd36798179dec64a36f0fdaf94c0ed05ad0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 18 09:32:41 2018 -0700

    fix typo

Src/Base/AMReX_CudaUtility.H

commit e0031fdc03cc2a21a7f91ccd73f437cc421b9368
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 18 03:17:15 2018 -0400

    First draft of GPU MultiFab::min and max. Needs testing. Fix in sum.

Src/Base/AMReX_MultiFab.cpp

commit 56f503d94988bef27d85fe0cda2d55623eb3257a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 18 03:15:13 2018 -0400

    atomicMin and atomicMax for float and double.

Src/Base/AMReX_CudaUtility.H

commit 89dfa8dae8fdadc186dd952c108a80bf7003b1b4
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 17 20:12:39 2018 -0400

    GPU versions of Dot, Dotmask, initVal and Sum.

Src/Base/AMReX_MultiFab.cpp

commit 02b616ff13b7659e1b6754d5c4d3e1f4d9d38310
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 17 17:04:38 2018 -0700

    Device::inLaunchRegion() -> Cuda::inLaunchRegion()

Src/Base/AMReX_MultiFab.cpp

commit 4f1b0acf4720db5a7e3e87694e39002392578b05
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 17 19:55:20 2018 -0400

    use macro instead of template thing here

Src/Base/AMReX_TypeTraits.H
Src/Particle/AMReX_ParticleContainerI.H

commit 73aa1732e163651435704121a6f47db41ecc3cbb
Merge: d0dacb8cb 4a513d311
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 17 16:42:46 2018 -0700

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit d0dacb8cbf9f154501ea25719e97ae6f7c500cc3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 17 16:42:21 2018 -0700

    always have this compile-time check return true if the gcc version is too old to support it

Src/Base/AMReX_TypeTraits.H

commit 4a513d311d21cc3ce7d1be9c37ddee889dc1699d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 17 16:14:03 2018 -0700

    put FabArray::initVal on GPU

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.cpp

commit 9b65ce6b35ab79bd7f7a356edac29db03a12884d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 17 16:12:50 2018 -0700

    int -> long in 1d Strategy

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 340f216f6bd5e58fe98488f62019130c880c90e6
Merge: 1cae99ebb abf9034ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 17 15:40:51 2018 -0700

    Merge branch 'gpu-merge-test' into gpu-merge-test2

commit abf9034ea967600f2b9d58cc98a8ff08325eb292
Merge: 382da09d1 b7a041012
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 17 15:40:28 2018 -0700

    Merge branch 'development' into gpu-merge-test

commit b7a041012fe6d5008221d88d453423bf57d1ddb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 17 15:38:09 2018 -0700

    CArena: make sure memory blocks from different allocations are not coalesced, otherwise cuda complains about invalid argument in cudaMemcpy.

Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp

commit 1cae99ebbbcd84b331f9bf0a839a916dafd1a967
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 17 15:38:09 2018 -0700

    CArena: make sure memory blocks from different allocations are not coalesced, otherwise cuda complains about invalid argument in cudaMemcpy.

Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp

commit 0f1802b78f7c015e4d31c6ddf7a23d0c49f8237d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 17 11:31:04 2018 -0700

    add some Cuda error checks

Src/Base/AMReX_CudaLaunch.H

commit f3a969c20371115f4e024741366a13042b7a073a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 17 15:07:45 2018 -0700

    Fix a problem that was causing us to lose particles in a triply periodic
    domain.  In the case that required this fix, which used single precision
    particles, the particle's location was only slightly outside the low domain,
    but the periodic shift put the particle exactly on the high boundary. The
    solution is to move the particle to the low boundary when the domain
    is periodic and the particle lies exactly on the high boundary.  The
    particle will then live in the first cell along the low boundary rather
    than being labeled as out of bounds outside the high boundary.

Src/Particle/AMReX_ParticleContainerI.H

commit 787cf9e517ec4cd79b1f4c88719d48d2b86f29a1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 17 15:06:03 2018 -0700

    fix typo in new constructor

Src/Particle/AMReX_Particles.H

commit a1be7990e9a8e5444ca5e853ae51443e257256f6
Merge: d64e02e11 cdf6166a6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 17 14:13:08 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d64e02e119b0ebeb6d37456f08251492e126fd50
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 17 14:12:55 2018 -0700

    add some ifdefs for when HDF5 is not on

Tests/HDF5Benchmark/WritePlotfileHDF5.H
Tests/HDF5Benchmark/WritePlotfileHDF5.cpp
Tests/HDF5Benchmark/main.cpp

commit cdf6166a68c8a69579bac11bd2e8a1f0a2b7ad11
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 17 14:03:52 2018 -0700

    read nppc from inputs file

Tests/HDF5Benchmark/inputs

commit d28a262e6625bd766bf095a1ce89997a533ecd31
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 17 14:01:53 2018 -0700

    change default compiler to intel

Tests/HDF5Benchmark/GNUmakefile

commit 9acea847f51ef0da20a83e19e5f92fb746da11b0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 17 14:00:35 2018 -0700

    add Particle IO to the HDF5Benchmark

Tests/HDF5Benchmark/GNUmakefile
Tests/HDF5Benchmark/main.cpp

commit 8749a22e939225d7dbdc09a0f7a01dfbc4fdbad5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 17 14:00:17 2018 -0700

    add new constructor to ParticleContainer

Src/Particle/AMReX_Particles.H

commit 94fccde71b7d8e86d07d429bdb013697cbeb42da
Merge: 78fcf19b0 db5bdb0fd
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 17 15:14:01 2018 -0400

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit 78fcf19b0329b53a1d467774678949adfb9a09cb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 17 15:13:33 2018 -0400

    also assert that the particle type is trivially copyable

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 02f5889df37f82bd18a39e1277e80f9360144250
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 17 15:13:12 2018 -0400

    add a new template to work around the fact that gcc < 5 doesn't have std::is_trivially_copyable

Src/Base/AMReX_TypeTraits.H

commit 4fef58f691c78e05cebcbc6f7ecc49b4f4c97572
Merge: 205402177 d90470823
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Oct 17 10:25:36 2018 -0700

    Merge pull request #344 from jared321/intersectionInFortran
    
    Intersection in fortran

commit db5bdb0fd32cccc4fe31f17fc7f8abad9543bab6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 17 10:03:45 2018 -0700

    change strides back to 1 again

Src/Base/AMReX_CudaLaunch.H

commit 78bec173fbc0f24f02de6780de8f1f106a2d8737
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 17 09:38:05 2018 -0700

    shift the box so that the smallend is zero.  this will make threading consistent for same size boxes

Src/Base/AMReX_CudaLaunch.H

commit d90470823ca01cd42d2f998a30f3666d45cc39ad
Author: Jared O'Neal <joneal@anl.gov>
Date:   Wed Oct 17 11:31:31 2018 -0500

    Intersection is no longer done by using C++ routines.  It is handled directly in
    the Fortran box module.

Src/F_Interfaces/Base/AMReX_box_fi.cpp
Src/F_Interfaces/Base/AMReX_box_mod.F90

commit 37cc4a75827a7125e2bfdcdc284db3a7d940a938
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 17 00:13:38 2018 -0400

    change strides to 1 till we fix the bug

Src/Base/AMReX_CudaLaunch.H

commit 26b06d8c80d0dc9489f10db68af8e57de9f8610b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 16 17:25:31 2018 -0700

    new Strategy giving more work to threads

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp
Src/Base/AMReX_MultiFab.cpp
Tutorials/GPU/HelloWorld_C/inputs_3d
Tutorials/GPU/HelloWorld_C/main.cpp

commit f4f3e55573fdc97ff44aba52f06d61ffd373b5ab
Merge: cf624acfd 382da09d1
Author: Andrew Myers <atmyers@login1.ascent.olcf.ornl.gov>
Date:   Tue Oct 16 20:08:31 2018 -0400

    Merge branch 'gpu-merge-test' into gpu-merge-test2

commit cf624acfd26ee16baa96e8318ecdb687854eb34a
Merge: 8441d60c0 6f760d0ec
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 16 19:54:12 2018 -0400

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit 8441d60c0abe46bb5b7fed10ca221d60e32009d8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 16 19:53:41 2018 -0400

    relax the assumption that the particle type must be POD

Src/Particle/AMReX_ParticleContainerI.H

commit 82ce7f89a3e5a4c96b7dc74abc2d912fbea4c709
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 16 19:53:20 2018 -0400

    give particle a constructor marked host/device

Src/Particle/AMReX_Particle.H

commit 6f760d0ec37a566dc7f99680cd9f17e763ac4ac4
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 16 19:42:04 2018 -0400

    Correct inputs for Dot test.

Tutorials/GPU/HelloWorld_C/inputs_3d
Tutorials/GPU/HelloWorld_C/inputs_geometry

commit 03ed3958d489030b33f1b986f4a71561635d3159
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 16 19:39:27 2018 -0400

    Dot test.

Tutorials/GPU/HelloWorld_C/main.cpp
Tutorials/GPU/HelloWorld_C/run.script

commit 7484adcf0898370821765d94a13ea123866e4bc5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 16 15:21:19 2018 -0700

    update DeviceScalar so that it works outside launch region

Src/Base/AMReX_CudaMemory.H

commit c8d689c15c126dcfc0e6c2a43ce3273a28de3e5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 16 15:16:32 2018 -0700

    Device::inLaunchRegion -> Cuda::inLaunchRegion so that we can access the flag without including AMReX_Device.H

Src/Base/AMReX_CudaControl.H
Src/Base/AMReX_CudaControl.cpp
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tools/F_scripts/write_cuda_headers.py

commit 20540217751f596024a8eb255cd4c13486e9e25d
Merge: 5776d2e9a eb175b3f2
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Oct 16 14:57:25 2018 -0700

    Merge pull request #339 from burlen/sensei_insitu_development
    
    Sensei insitu development

commit 5ad081e62f9418bd23caff646ac34c77b1ed7207
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 16 17:33:28 2018 -0400

    make MultiFab::OverrideSync() launchable

Src/Base/AMReX_MultiFab.cpp

commit 5687b90a780e97b6861625c60d2dad1b3932d084
Merge: e5050cd53 35dc98d1e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 16 17:23:30 2018 -0400

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit 35dc98d1ee85fb721518e0c3f8b0217b77e421d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 16 13:08:39 2018 -0700

    remove HostDeviceScalar

Src/Base/AMReX_CudaMemory.H

commit 7ae5f75f3dda2743603794d9241d9dfe2d1756c4
Author: Jared O'Neal <joneal@anl.gov>
Date:   Tue Oct 16 15:04:39 2018 -0500

    Added box intersection routine in Fortran interface.

Src/F_Interfaces/Base/AMReX_box_fi.cpp
Src/F_Interfaces/Base/AMReX_box_mod.F90

commit e5050cd5391f5868ad5934ead3b34f31e44d5f59
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 16 15:59:12 2018 -0400

    fix parameter shadowing

Src/Particle/AMReX_ParticleContainerI.H

commit 978d92586e50236804043c4af188c6639da7fb52
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 16 14:30:22 2018 -0400

    remove AtomicAccumulate method from ParticleContainer in favor of the one from BaseFab.

Src/Particle/AMReX_Particles.H

commit 6227feebab8967d50b30ba0a8147c37a16dc84b9
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 16 14:27:27 2018 -0400

    fix atomicAdd implementation

Src/Base/AMReX_BaseFab.H

commit d230a70253e0cd352b2b6bc2e801eeec07472dd2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 16 14:24:24 2018 -0400

    finish implementing atomicAdd for BaseFab

Src/Base/AMReX_BaseFab.H

commit 77a7e6b23225e0c4b1d617f8a2d63e4b76f50711
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 16 14:16:43 2018 -0400

    start to implement atomicAdd for BaseFab

Src/Base/AMReX_BaseFab.H

commit 34b8900f58e0182fbb143f04a14d8564f8654cfc
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Oct 15 15:09:23 2018 -0700

    CMake: fix bug in STRIP macro

Tools/CMake/AMReX_Utils.cmake

commit 458408072accab686366256a2237e8e2fd92162d
Merge: 8edfba50e fe7c86fae
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 16 13:56:58 2018 -0400

    Merge branch 'gpu-merge-test' into gpu-merge-test2

commit 8edfba50e8a07523da463313aa3e8f88c9cb3c16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 16 10:52:51 2018 -0700

    move atomics to CudaUtility.H, add DeviceScalar, and simplify reduction for MultiFab::Dot

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaMemory.H
Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_TypeTraits.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit fe7c86faed89ee9e6099bc59b2b3ecd204d2e489
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 16 02:11:40 2018 -0400

    more timers in Multifab

Src/Base/AMReX_MultiFab.cpp

commit f2c767a1f9abe65cd73ee910fcec86fcb9aee0ac
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 16 00:24:53 2018 -0400

    C++ version of amrex_atomic_accumulate

Src/Particle/AMReX_Particles.H

commit 382da09d11ea2c91c25fcd4e110004047d169433
Merge: b35ad2e44 ed34b99cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 15 17:50:28 2018 -0700

    Merge branch 'gpu-merge-test' of github.com:AMReX-Codes/amrex into gpu-merge-test

commit b35ad2e4468aa3166a0cd2b7619f26807a1b5ba3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 15 17:50:12 2018 -0700

    add some Device:synchronize calls to the two step version of parallel copy

Src/Base/AMReX_FabArrayCommI.H

commit ed34b99cf09e3054af439545117283cd850b81cb
Author: Kevin Gott <kngott@login1.ascent.olcf.ornl.gov>
Date:   Mon Oct 15 20:28:30 2018 -0400

    Preliminary GNUMake system for Ascent. Just copy of summit for now.

Tools/GNUMake/Make.machines
Tools/GNUMake/comps/nvcc.mak
Tools/GNUMake/sites/Make.olcf

commit 5776d2e9a6d891fef75a173ad7069803e9e0b99a
Merge: 463427ba1 d6ee42371
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Mon Oct 15 17:21:14 2018 -0700

    Merge branch 'development' of github.com:amrex-codes/amrex into development

commit 463427ba1c3b3ae8f0f888b0d33ba5b3556f68a6
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Mon Oct 15 17:20:34 2018 -0700

    Add basic documentation for new flags

Docs/sphinx_documentation/source/CVODE.rst
Docs/sphinx_documentation/source/SUNDIALS3.rst

commit d6ee423712f49dc8e74993c8cec38d9da8949be0
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Oct 15 17:09:25 2018 -0700

    wrote a helpful debugging utility, "WriteMLMF" that writes a multilevel plotfile to disk given only:
     -plotfile name
     -vector of MultiFabs
     -vector of Geometrys
     variable names are written as "Var0", "Var1", etc.
     refinement ratio is computed from the Geometry vector
     "time" and "level_steps" are set to zero

Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_PlotFileUtil.cpp

commit 9b14a25dcc9f0cc48f4d87de2e58151dfb6d43c2
Merge: d92e74784 f67363da4
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Mon Oct 15 17:04:25 2018 -0700

    Merge branch 'development' of github.com:amrex-codes/amrex into development

commit d92e7478496e6da6bd7278c5d357a09a04850df9
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Mon Oct 15 17:04:18 2018 -0700

    Updated make system with new sundials compile flags

Src/Extern/SUNDIALS3/Make.package
Tools/GNUMake/Make.defs
Tools/GNUMake/packages/Make.cvode
Tools/GNUMake/packages/Make.sundials3
Tutorials/CVODE/SUNDIALS2_finterface/EX1/GNUmakefile
Tutorials/CVODE/SUNDIALS2_finterface/EX2/GNUmakefile
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/GNUmakefile
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/main.cpp
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/GNUmakefile
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/main.cpp
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/GNUmakefile
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/SetIC.f90
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/main.cpp
Tutorials/CVODE/SUNDIALS3_finterface/EX1/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/Make.package
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/GNUmakefile

commit f67363da4459beeb5110409045f9fd7907a857af
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Oct 15 15:50:43 2018 -0700

    Replace macro D_DECL() with AMREX_D_DECL to comply with XSDK defaults

Src/Base/AMReX_ForkJoin.H

commit 3e4e560889d6de8fca8c3f2eb34d499144a31d1e
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Oct 15 15:43:22 2018 -0700

    added software performance counters for MLMG operations
      smooth, apply, restrict, interpolate
      turn on with -DAMREX_SOFT_PERF_COUNTERS
    added some profiling regions for detailed MLMG analysis
      regions used to tag sends/receives when used with amrprofvis -srlist
      separate out different MG levels

Src/Base/AMReX_MultiFabUtil.cpp
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/main.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit 3e4375fe5fdef8e145b10c899857c884309b7aec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 15 15:44:57 2018 -0700

    add addFromMem and use it for FabArray::ADD

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArrayCommI.H

commit 8b576d579c67d845c7def29acce06fec469fc160
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Oct 15 15:09:23 2018 -0700

    CMake: fix bug in STRIP macro

Tools/CMake/AMReX_Utils.cmake

commit f62009be796fffa9c080d744ca5eec8e57889ec4
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Mon Oct 15 14:37:25 2018 -0700

    Rearranged Sundials tutorials

Tutorials/CVODE/SUNDIALS2_finterface/EX1/GNUmakefile
Tutorials/CVODE/SUNDIALS2_finterface/EX1/Make.package
Tutorials/CVODE/SUNDIALS2_finterface/EX1/inputs
Tutorials/CVODE/SUNDIALS2_finterface/EX1/integrate_ode.f90
Tutorials/CVODE/SUNDIALS2_finterface/EX1/main.cpp
Tutorials/CVODE/SUNDIALS2_finterface/EX1/myfunc_F.H
Tutorials/CVODE/SUNDIALS2_finterface/EX1/ode_mod.f90
Tutorials/CVODE/SUNDIALS2_finterface/EX2/GNUmakefile
Tutorials/CVODE/SUNDIALS2_finterface/EX2/Make.package
Tutorials/CVODE/SUNDIALS2_finterface/EX2/inputs
Tutorials/CVODE/SUNDIALS2_finterface/EX2/integrate_ode_no_jac.f90
Tutorials/CVODE/SUNDIALS2_finterface/EX2/integrate_ode_with_jac.f90
Tutorials/CVODE/SUNDIALS2_finterface/EX2/main.cpp
Tutorials/CVODE/SUNDIALS2_finterface/EX2/myfunc_F.H
Tutorials/CVODE/SUNDIALS2_finterface/EX2/ode_mod.f90
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/GNUmakefile
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/Make.package
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/SetIC.f90
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/inputs
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/main.cpp
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/myfunc_F.H
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/ode_mod.f90
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/GNUmakefile
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/Make.package
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/SetIC.f90
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/inputs
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/main.cpp
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/myfunc_F.H
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/ode_mod.f90
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/GNUmakefile
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/Make.package
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/inputs
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/inputs_2box
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/inputs_non_vectorized
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/main.cpp
Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/myfunc_F.H
Tutorials/CVODE/SUNDIALS3_finterface/EX1/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX1/Make.package
Tutorials/CVODE/SUNDIALS3_finterface/EX1/inputs
Tutorials/CVODE/SUNDIALS3_finterface/EX1/integrate_ode.f90
Tutorials/CVODE/SUNDIALS3_finterface/EX1/main.cpp
Tutorials/CVODE/SUNDIALS3_finterface/EX1/myfunc_F.H
Tutorials/CVODE/SUNDIALS3_finterface/EX1/ode_mod.f90
Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/Make.package
Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/ark_analytic_fp.f90
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/Make.package
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/cv_analytic_fp.f90
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/cv_analytic_fp.out
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/Make.package
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/cv_analytic_sys_dns.f90
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/cv_analytic_sys_dns.out
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/Make.package
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/cv_analytic_sys_dns_jac.f90
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/cv_analytic_sys_dns_jac.out
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/GNUmakefile
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/Make.package
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/cv_brusselator_dns.f90
Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/cv_brusselator_dns.out
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/GNUmakefile
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/Make.CVODE
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/Make.package
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/README.md
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/extern_probin.template
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs_128
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs_256
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs_32
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs_64
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/main.cpp
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/make_cuda.sh
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/make_cuda_cusolver.sh
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/make_serial.sh
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_cuda.cpp
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_cuda_cusolver.cpp
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_serial.cpp
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_system.F90
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_utils.F90
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/test_react.H
Tutorials/CVODE/SUNDIALS4/EX3-CUDA/test_react_F.H

commit fdb9416dddcecc10a4fb891be3e4df56734ba452
Merge: 042eb98aa c63ecbbb6
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 15 17:15:07 2018 -0400

    Merge branch 'gpu-merge-test' of https://github.com/AMReX-Codes/amrex into gpu-merge-test

commit 042eb98aa4d695c7eaae776567a9e50457c646de
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 15 17:14:50 2018 -0400

    Update tutorials to new macros and library names. All successfully compile.

Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp
Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/GNUmakefile

commit c63ecbbb62193f6a30f6fa693ff4f6e6797825e6
Merge: b026bc74f 2d8237714
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Oct 15 16:41:01 2018 -0400

    Merge branch 'gpu-merge-test' of github.com:AMReX-Codes/amrex into gpu-merge-test

commit 2d82377143a41210873c1c21fc8b3a908ce1e9e2
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 15 16:24:44 2018 -0400

    AMReX_Device.H included in AMReX_CudaAllocators.H

Src/Base/AMReX_CudaAllocators.H

commit b026bc74f57a8323ce5df371d1bf901cdcd3e7dc
Merge: 5ab12ea9e d0ab3db30
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Oct 15 16:05:39 2018 -0400

    Merge branch 'development' into gpu-merge-test

commit d0ab3db30f947619139f348881f2662595fd6101
Merge: ef472d7f8 1c1376aea
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Oct 15 15:43:18 2018 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ef472d7f8f4072a7d12f5c63a28f3d4942f518c5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Oct 15 15:42:51 2018 -0400

    add a few dimension macros to silence unused variable warnings.

Src/Base/AMReX_BaseFab.H

commit 5ab12ea9eb0e457e1c8ea20e632e480321c5ca5f
Merge: 6b3c9038c 1b2f3bc43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 15 12:11:15 2018 -0700

    Merge branch 'gpu-merge-test2' into gpu-merge-test

commit 1b2f3bc436a6b40b6bfbe4672080071dbe27569f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 15 12:10:46 2018 -0700

    fix the_FA_arena initializaiton

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit a980d1266d7aa506ee448e41359eac9b91944a2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 15 11:58:17 2018 -0700

    back to the usual version

Src/Base/AMReX_FabArrayCommI.H

commit e0460837bb02dec767d96efd76f5416b45cceb2b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 15 10:39:19 2018 -0700

    add NOBOX version of launch macro

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_FabArrayCommI.H

commit eb175b3f238729e00aa6b2579e5ab9e30baac979
Author: Burlen Loring <bloring@lbl.gov>
Date:   Thu Oct 11 15:09:26 2018 -0700

    SENSEI sphinx documentation

Docs/sphinx_documentation/source/Visualization.rst
Docs/sphinx_documentation/source/Visualization/rt_2048_paraview_000500.png.REMOVED.git-id
Docs/sphinx_documentation/source/Visualization/rt_2048_visit_000500.png.REMOVED.git-id
Docs/sphinx_documentation/source/Visualization/sensei_amrex_arch_sm_824.png

commit b346e122b757753aa1ea0f4c992d554859c1afc0
Author: Burlen Loring <bloring@lbl.gov>
Date:   Thu Apr 19 15:47:10 2018 -0700

    SENSEI
    
    Integrates the SENSEI in situ framework with AMReX. Adds SENSEI data
    adaptors, and bridge codes for Amr and AmrMesh classes, and is
    demonstrated through the Advection AmrLevel and AmrCore SingleVortex
    Tutorial.

.gitignore
GNUmakefile.in
Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/AmrCore/Make.package
Src/CMakeLists.txt
Src/Extern/SENSEI/AMReX_AmrDataAdaptor.H
Src/Extern/SENSEI/AMReX_AmrDataAdaptor.cpp
Src/Extern/SENSEI/AMReX_AmrInSituBridge.H
Src/Extern/SENSEI/AMReX_AmrInSituBridge.cpp
Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.H
Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp
Src/Extern/SENSEI/AMReX_AmrMeshInSituBridge.H
Src/Extern/SENSEI/AMReX_AmrMeshInSituBridge.cpp
Src/Extern/SENSEI/AMReX_InSituBridge.H
Src/Extern/SENSEI/AMReX_InSituBridge.cpp
Src/Extern/SENSEI/AMReX_InSituUtils.H
Src/Extern/SENSEI/AMReX_InSituUtils.cpp
Src/Extern/SENSEI/CMakeLists.txt
Src/Extern/SENSEI/Make.package
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/GNUMake/Make.defs
Tools/GNUMake/sites/Make.nersc
Tools/GNUMake/tools/Make.sensei
Tools/libamrex/configure.py
Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/Amr/Advection_AmrCore/Exec/Make.Adv
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_catalyst.py
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml
Tutorials/Amr/Advection_AmrCore/README_SENSEI.md
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt
Tutorials/Amr/Advection_AmrLevel/Exec/Make.Adv
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_catalyst.py
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.session
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.session
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_libsim.xml
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/write_vtk.xml
Tutorials/Amr/Advection_AmrLevel/README_SENSEI.md
Tutorials/Amr/Advection_AmrLevel/Source/main.cpp

commit 1c1376aeaa8b3251d3506545b890aab48c343ea6
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Oct 15 05:50:06 2018 -0700

    Catch errors in the launch configuration

Tools/F_scripts/write_cuda_headers.py

commit 64b662227120480dc10a9be2305585f43f09431b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 13 16:50:11 2018 -0700

    wrap atomic min and max

Src/Base/AMReX_CudaLaunch.H

commit d9aec518529b384d95beb41a5eb900722aa36dab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 13 19:01:39 2018 -0400

    abort if not in launch region

Src/Base/AMReX_CudaLaunch.H

commit c1fcbea770435b7493c489e8184937a14b3dac9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 13 13:35:55 2018 -0700

    add some ifdef AMREX_USE_CUDA so that it compiles without cuda

Src/Base/AMReX_CudaMemory.H

commit 9641d8fefb372ae5a4e0bb50528dece44a3449f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 13 13:19:29 2018 -0700

    add a helper function for reduction

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaMemory.H
Src/Base/AMReX_MultiFab.cpp

commit 3a3c7cd7368b76464b5c437c25c3dca761dabc9b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 13 12:29:58 2018 -0700

    more gpu stuff to MultiFab and iMultiFab

Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.cpp

commit d7b016a27e8792e75b1ab4927ebe574135471be2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 13 11:17:45 2018 -0700

    fix typo; avoid new when copying

Src/Base/AMReX_FabArrayCommI.H

commit 7f490160f5db8bba272414cbdbdb2e97f9f0325f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 13 10:18:02 2018 -0700

    simplification: as long as we pack and unpack the same way, the buffer does not have to preserve the order in memory

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit 299c527c8cc6e2018d6e1c6b8542b8903bd03d58
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 13 10:00:53 2018 -0700

    fix EB CutFab

Src/EB/AMReX_MultiCutFab.H

commit 06433412e4e4e0ba04461a801283c8c7149e6e9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 13 00:08:04 2018 -0700

    FArrayBox -> FAB in template

Src/Base/AMReX_FabArrayCommI.H

commit 6b3c9038c15be4fee16cb0588005d6bd5bfdb86a
Merge: 05dfa0416 104d3c10d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 13 00:03:15 2018 -0700

    Merge branch 'development' into gpu-merge-test

commit 104d3c10d757a21458f50d034b514ef865c8f152
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 13 00:01:45 2018 -0700

    fix particle for 1 and 2d

Src/Particle/AMReX_ParIterI.H

commit 23de189c82239f2d499d7db29d9b6e0720fb5dee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 13 00:01:45 2018 -0700

    fix particle for 1 and 2d

Src/Particle/AMReX_ParIterI.H

commit c820a303cba10ee13353157ae2be5760c932d22d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 13 00:01:27 2018 -0700

    fix macro name

Src/Base/AMReX_FabArrayCommI.H

commit 55668f1511d0bedf7607b4bd357539d50940758f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 12 23:39:42 2018 -0700

    finish FabCommI

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit 95ae2381b9382b602156f12e6d7d7b2d14078b1d
Merge: 3bdfdb7b3 c81138ce7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 12 21:51:32 2018 -0700

    Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2

commit 3bdfdb7b3ecc5f89d25b88a159e68bdc31375219
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 12 21:50:48 2018 -0700

    add AMREX_LAUNCH_HOST_DEVICE_LAMBDA

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_MultiFab.cpp

commit c81138ce7a97aecd30e1fa70f4607e576b25a0b3
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 12 17:03:50 2018 -0400

    First version of ManagedMemory object for testing.

Src/Base/AMReX_CudaMemory.H

commit 7dfe10bb942bfad1d726bfbdc6b3954a743f2d9a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 11 19:31:18 2018 -0400

    AMReX_CudaManaged.H -> AMReX_CudaMemory.H

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_CudaMemory.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tests/GPU/Test/main.cpp
Tests/GPU/TestB/main.cpp
Tests/GPU/TestC/main.cpp

commit 8fe374828b1b363aca08f1d89b6e04d0295b8f2d
Merge: 421376b26 05dfa0416
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 12 16:41:07 2018 -0700

    Merge branch 'gpu-merge-test' into gpu-merge-test2

commit 05dfa0416ddd949027dc0baee69844f920c573ca
Merge: 5bedd3b42 6a22de47d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 12 16:40:26 2018 -0700

    Merge branch 'development' into gpu-merge-test

commit 421376b262062be5d432e471f50155dca4296495
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 12 19:32:34 2018 -0400

    Fix MultiFab::Dot launch macro name.

Src/Base/AMReX_MultiFab.cpp

commit acc2c42ebdc8a2a2d351c862b87a8ce3176fa0f6
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 12 19:31:10 2018 -0400

    First draft of MultiFab::Dot. Included test in GPU/HelloWorld.

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_MultiFab.cpp
Tutorials/GPU/HelloWorld_C/main.cpp
Tutorials/GPU/HelloWorld_C/run.script

commit e9cdcaa87a9303ea757507e6512533dee660c805
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 12 19:28:37 2018 -0400

    rename launch macros and add AMREX_USE_BASEFAB_CPP

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_MultiFab.cpp

commit 6a22de47d1d5a60fe9ba57483cf602415a9fbabc
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Oct 12 18:26:58 2018 -0400

    a testbed for profiling the particle redistribute on GPUs

Tests/GPU/Particles/Redistribute/Constants.H
Tests/GPU/Particles/Redistribute/GNUmakefile
Tests/GPU/Particles/Redistribute/Make.package
Tests/GPU/Particles/Redistribute/TestParticleContainer.H
Tests/GPU/Particles/Redistribute/TestParticleContainer.cpp
Tests/GPU/Particles/Redistribute/inputs
Tests/GPU/Particles/Redistribute/main.cpp
Tests/GPU/Particles/Redistribute/test_3d.F90
Tests/GPU/Particles/Redistribute/test_F.H

commit 5b218293bd1e361904495bdec31c48cfe88f85bc
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Oct 12 17:48:21 2018 -0400

    cut down on the number of temporary memory allocations in RedistributeGPU

Src/Particle/AMReX_ParticleContainerI.H

commit 57299b36f51e4a8e9749595254112814be50ec81
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Oct 12 17:35:41 2018 -0400

    add finer-grained profiling information to RedistributeGPU

Src/Particle/AMReX_ParticleContainerI.H

commit 8db1b1742630690ee7074148256d820e7f4d05ec
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Oct 12 17:34:52 2018 -0400

    minor

Src/Particle/AMReX_ParIterI.H

commit 93eb7509f07b90bfcc15712e3c47c35da617f479
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Oct 12 17:34:15 2018 -0400

    use cudaMemAdvise to set the preferred location of managed vector data to the GPU

Src/Base/AMReX_CudaAllocators.H

commit 5bedd3b426b4f309caf109ac3d55708acd9a207b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 12 17:03:50 2018 -0400

    First version of ManagedMemory object for testing.

Src/Base/AMReX_CudaMemory.H

commit 0503f8d585bcbd67fd14b03c2fe54499cc0028a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 12 16:12:30 2018 -0400

    use ThreadBox instead of ThreadComponentBox

Src/Base/AMReX_FabArrayCommI.H

commit 7743284d3868a878a7209dee6df0591d9b67b58c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 12 14:33:53 2018 -0400

    lambda launch setVal

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_FabArray.H

commit e21d4a8154649ea85f80ab6cce344b2a27338551
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 12 13:33:43 2018 -0400

    new ThreadComponentBox function

Src/Base/AMReX_CudaLaunch.cpp
Src/Base/AMReX_Device.cpp

commit 50efa757a5dcb219628f856ebcbd4d099db28d1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 12 01:38:11 2018 -0400

    ComponentBox

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp
Src/Base/AMReX_FabArrayCommI.H

commit 613bce24e2125fec22cb2b177f8e54319c6a1fdf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 11 22:34:12 2018 -0700

    fix plus

Src/Base/AMReX_FabArrayCommI.H

commit e41c77b68fdefc9c0665c4c9ff10c01ed9653cae
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Oct 11 19:31:18 2018 -0400

    AMReX_CudaManaged.H -> AMReX_CudaMemory.H

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_CudaMemory.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tests/GPU/Test/main.cpp
Tests/GPU/TestB/main.cpp
Tests/GPU/TestC/main.cpp

commit f0bb27fc923267a4ead57d04ad65ee0bba7fc348
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 11 16:09:35 2018 -0700

    use C++ copy

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayCommI.H

commit 4d3b6781d16fd62e453b56eeabadc0d12eb335d4
Merge: 5f4c36d08 39fb3524c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 11 18:21:16 2018 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5f4c36d087f2363959c0a1b1ca6d2d725520a5a1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 11 18:20:50 2018 -0400

    GPU-enabled version of get / set particle position

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H

commit c801250adab2e507c917b9c106a02af1677649f2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 11 17:19:10 2018 -0400

    early exit if there are no particles to redistribute

Src/Particle/AMReX_ParticleContainerI.H

commit 5d71fc3db924fce08ee5c7ecf343e7afe8a707ed
Merge: 4b76bef0c 39fb3524c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 11 11:01:34 2018 -0700

    Merge branch 'development' into gpu-merge-test

commit 39fb3524c1418698b2423ed9c2af068b7ed720f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 11 10:55:17 2018 -0700

    fix OMP

Src/F_Interfaces/Base/AMReX_fab_mod.F90
Tutorials/Amr/Advection_F/Source/compute_dt_mod.F90
Tutorials/Amr/Advection_F/Source/evolve_mod.F90
Tutorials/Amr/Advection_octree_F/Source/compute_dt_mod.F90
Tutorials/Amr/Advection_octree_F/Source/evolve_mod.F90

commit 2d847d219480a67c1bf9c431f0a15a1b3b066a99
Merge: ddcf7e8e7 6735da6ba
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 10 19:38:03 2018 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ddcf7e8e7572c3391b77c8eee0e0e876147529dc
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 10 19:29:17 2018 -0400

    remove early exits, they are wrong

Src/Particle/AMReX_ParticleContainerI.H

commit 01cbfe8503d08c56af4badf2298ac2b08819b730
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 10 19:28:43 2018 -0400

    correct for domain offset in assignParticle(), for consistency with CPU version

Src/Particle/AMReX_ParticleContainerI.H

commit 4b76bef0c2b4fbf2ad1fdfc1285fdf69eb785506
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 10 12:41:52 2018 -0700

    fix omp compilation

Src/Base/AMReX_Device.cpp
Src/Base/Make.package

commit 51764b9aad17cc4d354495e37145151eddc002a4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 10 15:39:46 2018 -0400

    fix copy/paste error

Src/Particle/AMReX_ParticleContainerI.H

commit 5581114564e42fb859fac8e22c04a9b69d46037d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 10 12:06:03 2018 -0700

    fix fortran boxlib compilation

Src/Base/AMReX_CArena.cpp

commit e0c35e7f4b8a762c261422dee19cb81d14ebb6e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 10 12:00:58 2018 -0700

    revert change to TinyProfiler

Src/Base/AMReX_TinyProfiler.cpp

commit b8d38d39dc893bc76b245cd43973b7869a565642
Merge: 09ea88f37 6735da6ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 10 11:57:41 2018 -0700

    Merge branch 'development' into gpu-merge-test

commit 6735da6ba490f12790a5c74936101ed90cf81743
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Oct 10 09:56:37 2018 -0700

    fix fortran fcompare crash when given nComp=0 plotfile

Src/F_BaseLib/bl_IO.f90
Src/F_BaseLib/plotfile.f90
Tools/Postprocessing/C_Src/fcompare.cpp
Tools/Postprocessing/F_Src/GNUmakefile
Tools/Postprocessing/F_Src/fcompare.f90

commit 9d6ec0320214d47148e6b3d30d830d775b810c0e
Merge: 9bb651294 fd15682cc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 9 20:35:43 2018 -0700

    Merge pull request #334 from RemiLehe/cuda_system
    
    Set SYSTEM_CUDA_PATH for unknown machine

commit fd15682ccb694dc06cf6d1621440eaf633ba2c4f
Author: Remi Lehe <remi.lehe@normalesup.org>
Date:   Tue Oct 9 20:14:40 2018 -0700

    Set SYSTEM_CUDA_PATH for unknown machine

Tools/GNUMake/sites/Make.unknown

commit 9bb65129461a14162f955238fa0495f07086aa89
Merge: ad3bfc62b 9931dbd8c
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Oct 9 19:19:13 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit ad3bfc62b899b82b92f5ec17faba2d9dd39f0636
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Oct 9 19:19:10 2018 -0700

    Add feature to write 'just' the header files <- helpful for postprocessing particle-only plotfiles

Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp

commit 9931dbd8c7e180fb7f6cae4a83ac5fab4379826b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 9 21:17:06 2018 -0400

    make sure the requested device number gets passed in to acc_set_device

Src/Base/AMReX_CUDA.F90

commit ad814efeb63a130428b4df40e9bbe4c1d75ce285
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 9 21:09:26 2018 -0400

    fix RedistributeMPIGPU.

Src/Particle/AMReX_ParticleContainerI.H

commit d2a76cc8973ce80a3c0f13e022f8f7119e885be6
Merge: 17cbd2f21 7ddd6b8b4
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Tue Oct 9 20:14:46 2018 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 17cbd2f21d503c9c36ce08663e68231b4fcec70a
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Tue Oct 9 20:14:29 2018 -0400

    Add sample compile lines.

Tutorials/CVODE/EX3-CUDA/make_cuda.sh
Tutorials/CVODE/EX3-CUDA/make_cuda_cusolver.sh
Tutorials/CVODE/EX3-CUDA/make_serial.sh

commit 343e8f993ed27420c79cd219b5e75983a0b809c5
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Tue Oct 9 20:14:13 2018 -0400

    Add a react example using cuSolver linear algebra for CUDA CVODE.

Tutorials/CVODE/EX3-CUDA/GNUmakefile
Tutorials/CVODE/EX3-CUDA/Make.CVODE
Tutorials/CVODE/EX3-CUDA/Make.package
Tutorials/CVODE/EX3-CUDA/README.md
Tutorials/CVODE/EX3-CUDA/react_cuda.cpp
Tutorials/CVODE/EX3-CUDA/react_cuda_cusolver.cpp
Tutorials/CVODE/EX3-CUDA/react_serial.cpp
Tutorials/CVODE/EX3-CUDA/test_react.H
Tutorials/CVODE/EX3-CUDA/test_react_F.H

commit 4bc4a617d17040cf9030d96ac68fc5d1d3eba0fa
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Tue Oct 9 19:31:44 2018 -0400

    Add optional Fortran RHS or C++ RHS to mimic the Fortran RHS interface in StarKiller Microphysics.

Tutorials/CVODE/EX3-CUDA/Make.package
Tutorials/CVODE/EX3-CUDA/react_cuda.cpp
Tutorials/CVODE/EX3-CUDA/react_system.F90
Tutorials/CVODE/EX3-CUDA/react_utils.F90
Tutorials/CVODE/EX3-CUDA/test_react_F.H

commit 29f35729a3db89922f5911bc9db6583e4661a5a5
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Tue Oct 9 19:30:44 2018 -0400

    Add CVODE libraries to rpath. Define CPP_RHS.

Tutorials/CVODE/EX3-CUDA/GNUmakefile
Tutorials/CVODE/EX3-CUDA/Make.CVODE

commit 09ea88f37021db9aff687e5be99010150e3673eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 16:14:08 2018 -0700

    rm Arena_Initialize from amrex::Initialize

Src/Base/AMReX.cpp

commit 5336f025e0e634fe71bf15702d6bd7570c8aff8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 16:09:55 2018 -0700

    revert changes to the_arena

Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp

commit 3bddee5508dfc865c0d311939e6c91aa541e4472
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 15:35:09 2018 -0700

    fix cmake

Src/Base/CMakeLists.txt

commit 59d93fa2419e58a8d6d4451428d519e4e220aecf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 15:16:11 2018 -0700

    fix typo

Tools/GNUMake/Make.defs

commit e9cb3d4c7e0088c70c1c9b085e9b15c26a7a6866
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 15:07:03 2018 -0700

    move device finalization later after memory poll finalization

Src/Base/AMReX.cpp

commit 9cb1bdaaca4ce6d0591c50567b6df0a82120d159
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 15:01:03 2018 -0700

    comment out a version of getThreadBox

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp
Src/Base/AMReX_FabArrayCommI.H
Tutorials/GPU/ElectromagneticPIC/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp

commit 8447a27b89a31bae901f3d48b3b61bbaf32331f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 14:42:39 2018 -0700

    Revert "Adjust Box+Type launch to match surroundingNodes method."
    
    This reverts commit 40baf4661bb13768125dc12a7d0dabb14e3b72de.

Src/Base/AMReX_CudaLaunch.cpp

commit 379d6028bfdd474cf075552c17a8deaac1a6c4f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 14:25:51 2018 -0700

    add more AMREX_CUDA_HOST_DEVICE

Src/Base/AMReX_Box.H

commit 40baf4661bb13768125dc12a7d0dabb14e3b72de
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 9 16:16:35 2018 -0400

    Adjust Box+Type launch to match surroundingNodes method.

Src/Base/AMReX_CudaLaunch.cpp

commit aaef2ffd2429204aa3051e324c3775254b35592a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 12:51:22 2018 -0700

    update ThreadComponentBox

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_FabArrayCommI.H

commit df915ce13aa09f49ef7d1819054dc636954fd286
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 11:24:06 2018 -0700

    add another simple Strategy

Src/Base/AMReX_CudaLaunch.H

commit 2e4e03813188b7a3df5fbceba233576801ea3391
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 10:21:39 2018 -0700

    fix copy between fab and buffer in FillBoundary

Src/Base/AMReX_FabArrayCommI.H

commit abc2f40ead07c07d18160734b367052ed4205fcf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 10:01:51 2018 -0700

    for clarity add ()

Src/Base/AMReX_FabArrayCommI.H

commit d48fb6cfa0b5f4376d3d4e76f4a9f388cc08ca3b
Merge: 8cef75de2 8c2029d14
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 9 12:38:27 2018 -0400

    Merge branch 'gpu-merge-test' of https://github.com/AMReX-Codes/amrex into gpu-merge-test

commit 8cef75de2b44d0e6985bcfe1d24c9b954b2836ac
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 9 12:38:06 2018 -0400

    Add both boxes to the check. Instead add an initial ASSERT or is that done elsewhere?

Src/Base/AMReX_FabArrayCommI.H

commit 8c2029d1459e2dd0583e19cb9bc330a2e5bfcde7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 09:18:27 2018 -0700

    We can still do OMP and tiling if not in launch region and not using pragma gpu

Src/Base/AMReX_Device.cpp
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_MultiFab.cpp

commit 09e96fd311d128432cfde8a545613cd39c428107
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 9 11:41:17 2018 -0400

    Add missed Box checks to kernel launch functions.

Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_MultiFab.cpp

commit 7ddd6b8b45cc274b5f5eea0c32845818d4bbf3d0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 8 18:45:58 2018 -0700

    Update the nodal linear solvers so that we can now call the
    operator to compute the multilevel nodal divergence, and can
    call MLMG::getFluxes for nodal as well as cell-centered data.

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H

commit 22640e07ba33c4eac3de36a429016c62bab10452
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 8 20:25:30 2018 -0400

    Update Function tutorial with new version of launch macro.

Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp

commit fcd9a283447dd39904e54c29dc725c1c4f2be36d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 8 17:17:07 2018 -0700

    AMREX_CUDA_LAUNCH_FUNCTION -> AMREX_CUDA_LAUNCH_GLOBAL

Src/Base/AMReX_CudaLaunch.H

commit dc4235160656c2978e7c4de89c66fba6170af015
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 8 20:11:17 2018 -0400

    Changing lambda launch function.

Src/Base/AMReX_CudaLaunch.H

commit 841dd9f6be8a046d97bbd9c21fabc8dcf6f1e0ba
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 8 20:10:52 2018 -0400

    More changes to Tutorials.

Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_1/make.out
Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp
Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp

commit ec786baa04e7235a27cbba514f5d6467cdfbad6c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 8 16:07:19 2018 -0700

    Simplify launching macros

Src/Base/AMReX_CudaLaunch.H
Src/Base/AMReX_CudaLaunch.cpp
Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 4f69bcc6d630e89d14a1ef724e5be03c60d193ae
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 8 17:25:31 2018 -0400

    Adjust GPU tutorials for new changes and update Readme.

Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC/em_pic_3d.F90
Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_1/em_pic_3d.F90
Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_2/em_pic_3d.F90
Tutorials/GPU/Readme.txt

commit 26039d1db6ec3a4351aed4ed326b7cf49e463a15
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 8 17:05:06 2018 -0400

    Fix HeatEquation0.

Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp

commit afed7d6fdfe7422d203d30aebe9693bd1ad30867
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 8 17:03:48 2018 -0400

    Add threading strategy to FillBoundary lambda calls.

Src/Base/AMReX_FabArrayCommI.H

commit 71d033aeea8ae81cf79f475c67ed83f92f8cb740
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 8 17:02:53 2018 -0400

    Add map to Allocators

Src/Base/AMReX_CudaAllocators.H

commit 2d6325144bc5021acd9d96c74e9df30359388733
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 8 16:59:47 2018 -0400

    verbose fortran attributes

Tools/GNUMake/Make.defs

commit 025a8d02f1de07f6a0ffa53c782dc5885a04021b
Merge: f41b57d8f 3ab4676ee
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 8 15:47:06 2018 -0400

    Merge branch 'gpu-merge-test' of https://github.com/AMReX-Codes/amrex into gpu-merge-test

commit f41b57d8fe17df85f3d192f527bc6a6e4b4836b0
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 8 15:46:49 2018 -0400

    AMREX_CUDA_DEVICE to AMREX_CUDA_HOST_DEVICE for lambda launches.

Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_MultiFab.cpp

commit 3ab4676ee2c172cdf82ede68daeb07db1a3c1edf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 8 12:05:50 2018 -0700

    minor

Src/Base/AMReX_Device.H
Tools/F_scripts/write_cuda_headers.py

commit c692b0b10addda79c3cdf0e94ac3037aca34a7cf
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 8 14:53:35 2018 -0400

    Add threading strategy to all MultiFab functions currently using lambdas.

Src/Base/AMReX_MultiFab.cpp

commit 6c8a5a057baffe7d38a718e18a44418f54f320e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 8 10:41:52 2018 -0700

    TilingIfNotGPU()

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MultiFab.cpp

commit c7112eebaf2170e029cd39b8ca8f9e0d1385b82c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 8 10:33:35 2018 -0700

    remove RunOn

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_MultiFab.cpp
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Tests/C_BaseLib/tFB.cpp

commit f68de2156859b851e95e2823ace9c423dd4b7945
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 8 09:47:58 2018 -0700

    more reorganization

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_CudaFort.F90
Src/Base/AMReX_CudaManaged.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit b9125f167b6134519d256abd7dfde5dd4d6fecc8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 8 09:33:25 2018 -0700

    reorganization

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_Array.H
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CudaQualifiers.H
Src/Base/AMReX_CudaUtility.H
Src/Base/AMReX_CudaUtility.cpp
Src/Base/AMReX_Device.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_Managed.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_Orientation.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tools/F_scripts/write_cuda_headers.py

commit 9aacfad9647025a96ab544be8197cfc00ef4fc74
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 7 12:24:16 2018 -0700

    move SetPreferred to where the arena is built now

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BaseFab.cpp

commit 74180285cd558896432d2f2e441e77b41381d220
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 22:36:07 2018 -0700

    fix omp

Src/Base/AMReX_FabArrayCommI.H

commit 02935819661be0764900ed948ff41b7879d7ca25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 22:09:52 2018 -0700

    fix some warnings

Src/Base/AMReX.cpp
Src/Base/AMReX_BaseFab.cpp

commit 2e1491a597d7966d7e3d399f5749c779aaa96a36
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 21:49:49 2018 -0700

    put OKGPU inside AMREX_USE_CUDA

Src/Particle/AMReX_ParticleContainerI.H

commit b7acd64f34d54e91bc5eeb1ba8e8dc7d9ac93014
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 21:49:49 2018 -0700

    put OKGPU inside AMREX_USE_CUDA

Src/Particle/AMReX_ParticleContainerI.H

commit c05916b696c30001439e2ccd005bb850c60ad18a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 21:31:09 2018 -0700

    fix compilation for USE_CUDA=FALSE

Src/Base/AMReX_CUDA_Utility.H
Src/Base/AMReX_Managed.H

commit 78ce066f560e88cdedc7dff09078f50b01d2d8db
Merge: 56c4304d2 93309ae58
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 21:22:55 2018 -0700

    Merge branch 'development' into gpu-merge-test

commit 56c4304d2dc92adbac29722a6a61eb110b6390a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 21:21:41 2018 -0700

    revert some changes to Arena

Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_FabArrayBase.cpp

commit 5dc41cb42fbc29bbd453e55aefa4e6a600b9e113
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 17:43:07 2018 -0700

    minor changes for easy comparison

Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp

commit 235a743f226323feffe3bbd7db5f18786c0b23a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 17:29:23 2018 -0700

    return old value when set

Src/Base/AMReX.H
Src/Base/AMReX.cpp

commit 078bafef55427e408054bc8fe878932884c22925
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 17:27:07 2018 -0700

    function to set where to run

Src/Base/AMReX.H
Src/Base/AMReX.cpp

commit 8a0269c0797c89a1d57c5eea1a03b15dd9520fcd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 17:08:03 2018 -0700

    WhereToRunDefault -> WhereToRun

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_FabArray.H
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Tests/C_BaseLib/tFB.cpp

commit 9c6225fb02b46a8db8649b0892c2e421c49fecde
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 16:41:07 2018 -0700

    simplify Geometry::data

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp

commit 93309ae58ea8f7ca91e2531ce18084b344f9b8cc
Merge: 949322724 4526c78e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 16:33:24 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9493227240ed26b35b95d15c9617884fec31e763
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 1 20:41:06 2018 -0400

    toLower and toUpper Utility functions.

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit 5a2f4642515d8d30b4a2c32826c5168e630eb067
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 15:47:19 2018 -0700

    minor changes for readability

Src/Base/AMReX_Array.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_Orientation.H

commit 7dc4054face985d3a054a9888a6baa0d043fca4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 14:29:48 2018 -0700

    Managed: remove the device version

Src/Base/AMReX_Managed.H

commit b1a7b28b4407b9c847efd9f0d53f7b4e16c73296
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 6 11:30:13 2018 -0700

    reorganization

Src/Base/AMReX_Box.H
Src/Base/AMReX_CUDA_Utility.H
Src/Base/AMReX_CUDA_Utility.cpp
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_Managed.H

commit 4526c78e8b606e9e8465f14108d301a3584c42c6
Merge: a7d412fcf 69813c7fe
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Oct 6 13:50:17 2018 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a7d412fcf262d9b977e473097639b208a2b3b7e3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Sat Oct 6 13:49:48 2018 -0400

    correctly enforce periodic boundary conditions in the GPU form of Redistribute()

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit bf907665e3be2a65169a949ab6d7f7e96a8a0560
Merge: 699ee4d64 4d2e9fb05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 5 21:00:43 2018 -0700

    Merge branch 'gpu-merge-test' of github.com:AMReX-Codes/amrex into gpu-merge-test

commit 699ee4d641fb4612804b8b274652fef445bb0c13
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 5 20:58:54 2018 -0700

    fix conflict

Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d
Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script
Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H

commit 910460fe48550f9821872d8acde5813e25c316a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 5 20:54:08 2018 -0700

    fix conflict

Tutorials/Particles/ElectromagneticPIC/Particles.H
Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H
Tutorials/Particles/ElectromagneticPIC/script.sh
Tutorials/Particles/ElectromagneticPIC/test.cpp

commit 4d2e9fb05be6058be66a1cb99d6b943b8d526b5d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 5 20:30:20 2018 -0400

    Add threading strategy for copy to match Castro's Sedov. Rest of MultiFab to come soon.

Src/Base/AMReX_MultiFab.cpp

commit 932cf60bf9145da50b7e00cd920e85a69a65e51c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 5 15:13:51 2018 -0700

    hide some codes from Fortran BoxLib

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BArena.cpp
Src/Base/GPackage.mak

commit c81591a31b371f793c0ff73a17f5b1a902836608
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Oct 5 17:35:40 2018 -0400

    Library adjustments.

Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_CArena.cpp

commit 74895195147221873572a92f4fdee8e093002589
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Oct 5 16:22:04 2018 -0400

    implement OK() routine that can be run on either the GPU or the CPU.

Src/Particle/AMReX_ParticleContainerI.H

commit d9610df11327256c6fceed0bafcb997dfccaea15
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Oct 5 16:21:39 2018 -0400

    make these data members mutable

Src/Particle/AMReX_Particles.H

commit 69813c7fe7086f60932ad8a7375fc50e4a504530
Merge: c028a005c f5c7d46e8
Author: Jean Sexton <jmsexton@lbl.gov>
Date:   Fri Oct 5 13:57:21 2018 -0400

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit c028a005c2732286b4711cc92d8571bcbcc728fa
Author: Jean Sexton <jmsexton@lbl.gov>
Date:   Fri Oct 5 13:56:58 2018 -0400

    Single cell successfully passed through to f90 device function

Tutorials/SUNDIALS3/EX1_CUDA_NVEC/Make.package
Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp
Tutorials/SUNDIALS3/EX1_CUDA_NVEC/myfunc_F.H
Tutorials/SUNDIALS3/EX1_CUDA_NVEC/ode_mod.f90

commit ea43473d94a33a2e8c042f59a34bb5c519fbfca8
Author: Jean Sexton <jmsexton@lbl.gov>
Date:   Fri Oct 5 13:55:39 2018 -0400

    c rhs calls user-defined kernel

Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp

commit f5c7d46e8ebf276781d0152c71884a09714ddc19
Merge: 7ab4fc97b b98e8650d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Oct 5 10:46:26 2018 -0700

    Merge pull request #331 from AMReX-Codes/mc-nodelinop
    
    Mc nodelinop

commit b98e8650daa512ba00386064a73c57c79fb08322
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Oct 5 11:40:28 2018 -0600

    Update AMReX_MLMG.cpp
    
    Removed `setVal`

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 7ab4fc97bf575142b9604c878d8432882c9c9039
Merge: 116f12b06 b9157c8ef
Author: Jean Sexton <jmsexton@lbl.gov>
Date:   Fri Oct 5 13:07:00 2018 -0400

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 116f12b06b8910c0830dfe4b81937e6c7e83fcad
Author: Jean Sexton <jmsexton@lbl.gov>
Date:   Fri Oct 5 13:06:50 2018 -0400

    Added serial C++ driven version of EX1, differences between vectorized version and non-vectorized approaches precision level as tolerances are tightened

Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp
Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/GNUmakefile
Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/Make.package
Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/inputs
Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/inputs_2box
Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/inputs_non_vectorized
Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/main.cpp
Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/myfunc_F.H

commit 3ce0c9e15a073dfd35aa1c7ae7ac57bb4cc4b526
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Oct 5 11:03:53 2018 -0600

    Update AMReX_MLMG.cpp
    
    bug fix

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit e0c5cceb5b883d6e967d37945e861341ab6aa022
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Oct 5 10:54:49 2018 -0600

    Update AMReX_MLLinOp.cpp
    
    Removed setVal

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 494a5516420d280115992b1c47d4fd49194cd7b6
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Oct 5 10:53:35 2018 -0600

    Update AMReX_MLMG.cpp

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit e6b57819f0431a63100eeade921f453935c49818
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Oct 5 10:39:44 2018 -0600

    Made n inside loop

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90

commit b9157c8eff2c0b9b95641fe52dd1c0c6f0e0a4b6
Merge: 54f5cc49f 402e7396a
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Oct 5 09:26:58 2018 -0700

    Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into development

commit 402e7396ac7ce88890b6f709c9d1e3b6f4e133bc
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Oct 5 09:19:45 2018 -0700

    Commented out unnecessary subtractions

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit 54f5cc49f441ffc3c3aac1ab82d63d7919d0a571
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 5 08:04:56 2018 -0700

    Revert "Put the makeSolvable (ie subtract off the mean) back into the BiCG solver - this"
    
    This reverts commit aeea5d24835e5a570c9866e32191906222e6669e.

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit fb81213bf4c0ff8d8c2f56fb044afedf68c0f199
Merge: f373cdcf9 aeea5d248
Author: sireeveslbl <sireeves@ucsc.edu>
Date:   Thu Oct 4 18:00:27 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mlmg

commit f373cdcf99ee29b0d612eb321e0c9befa8ddf0a0
Author: sireeveslbl <sireeves@ucsc.edu>
Date:   Thu Oct 4 17:59:15 2018 -0700

    Changed MLCG makeSolvable to MLMG makeSolvable, changed computeVolInv to kill bug that was not inverting volume for use EB but all_Regular geometry

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit aeea5d24835e5a570c9866e32191906222e6669e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 4 17:55:54 2018 -0700

    Put the makeSolvable (ie subtract off the mean) back into the BiCG solver - this
    should help.

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit acbb76613b59ad8d375162547aa633c97d20e475
Merge: 1aacac585 ad21d22af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 4 17:41:51 2018 -0700

    Merge branch 'development' into gpu-merge-test

commit ad21d22af6549ec2bb24887fd11f5c270ba52c2c
Merge: 760562cba bec746bdb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 4 17:05:46 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 760562cbaa6857681a3fdb2b73bd80bb55a3bc5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 4 17:02:20 2018 -0700

    Call mlmg's makeSolvable. Calls are commented out because it may not work.

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit bec746bdbdbb0c9be94dae84a5fe5f9362538b82
Author: Jean Sexton <jmsexton@lbl.gov>
Date:   Thu Oct 4 20:01:06 2018 -0400

    Cleaned up some comments

Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp
Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/GNUmakefile
Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/Make.package
Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/SetIC.f90
Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/inputs
Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/main.cpp
Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/myfunc_F.H
Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/ode_mod.f90

commit 2bd65af115038f2f92a54687fe913c855b2cbc2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 4 16:58:04 2018 -0700

    make MLCGSolver a friend of MLMG and pass MLMG pointer into MLCGSolver ctor

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 747396b6d8303dfe4e1ebe661488bbc929ed879c
Author: Jean Sexton <jmsexton@lbl.gov>
Date:   Thu Oct 4 19:56:38 2018 -0400

    Updated sundials library include statements, seperated N_Vector cuda example from AMREX_GPU_PRAGMA example

Src/Extern/SUNDIALS3/Make.package
Tools/GNUMake/packages/Make.sundials3
Tutorials/SUNDIALS3/EX1/GNUmakefile
Tutorials/SUNDIALS3/EX1/integrate_ode.f90
Tutorials/SUNDIALS3/EX1/ode_mod.f90
Tutorials/SUNDIALS3/EX1_CUDA_NVEC/GNUmakefile
Tutorials/SUNDIALS3/EX1_CUDA_NVEC/Make.package
Tutorials/SUNDIALS3/EX1_CUDA_NVEC/SetIC.f90
Tutorials/SUNDIALS3/EX1_CUDA_NVEC/inputs
Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp
Tutorials/SUNDIALS3/EX1_CUDA_NVEC/myfunc_F.H
Tutorials/SUNDIALS3/EX1_cuda/GNUmakefile
Tutorials/SUNDIALS3/EX1_cuda/Make.package
Tutorials/SUNDIALS3/EX1_cuda/SetIC.f90
Tutorials/SUNDIALS3/EX1_cuda/main.cpp
Tutorials/SUNDIALS3/EX1_cuda/myfunc_F.H
Tutorials/SUNDIALS3/EX_ark_analytic_fp/GNUmakefile
Tutorials/SUNDIALS3/EX_cv_analytic_fp/GNUmakefile
Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/GNUmakefile
Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/GNUmakefile
Tutorials/SUNDIALS3/EX_cv_brusselator_dns/GNUmakefile

commit 4100cf0305db0ae3f9969f966765dc2f19ca5837
Merge: 09885864b 59a45f297
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 4 19:34:51 2018 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 09885864b24699d2865152906cd8eacc9100df77
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 4 19:34:23 2018 -0400

    dispatch redistribute to the GPU when possible when compiling with AMREX_USE_CUDA=TRUE

Src/Particle/AMReX_ParticleContainerI.H

commit 59a45f2976e86c40b64ce51a2d4de243f369f0dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 4 16:23:55 2018 -0700

    comment out some new codes

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit a30152418e3e7c97d1fdaad331dd6ffb0d365e87
Merge: 862bb4133 7f0603dae
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Oct 4 15:32:48 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 862bb41336da19fc1094b35d81b6a36804eefc8d
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Oct 4 15:32:27 2018 -0700

    Some clean up in AMReX_MLCGSolver.cpp. Removed leftovers from debugging bicgstab

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit 7f0603dae75ca684d63bdd8819f26a6149a94d4e
Merge: 43cd3bf6c fd085f2c4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 4 15:32:18 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 43cd3bf6c74b21f081daf520660c0f727d359fd1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 4 15:32:04 2018 -0700

    work-around for pgi in how we handle OMP in the particle container

Src/Particle/AMReX_ParticleContainerI.H

commit fd085f2c484a14bb2cd98ae198cc1595efe6fcb2
Merge: 7b83fbb4f 832f4f97c
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Oct 4 15:29:14 2018 -0700

    Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into development

commit 7b83fbb4f7fdfce6c6d474d0ec18144d62ac425a
Merge: 935b3fc79 001814001
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Oct 4 15:17:57 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 832f4f97ce9af9365612bc138c21110e30fa4c64
Merge: 3e3d093ac 001814001
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Oct 4 15:17:44 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mlmg

commit 3e3d093acd124732a250e7c121006a899d1945b8
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Oct 4 15:16:59 2018 -0700

    Changed BiCGStab to include subtracting out the Mean residual for singular linear operators only. This solved the issue with the sinusoidal RHS on the 5x5x5 problem. I also tested it with the classic CellEB problems, that the original BiCGstab solved. Each test yeilded good results.

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit 1aacac585964495cc54114ab67e7485e8639fd8a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 4 14:20:01 2018 -0700

    make more device functions

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Managed.H
Src/Base/AMReX_TinyProfiler.cpp

commit 001814001a21c3f079ade6c641c850445a5cef81
Merge: 420fdc62c 0bc5aae12
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 4 16:49:03 2018 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 420fdc62ccbfe259977043b2bcf8e5c0d2b69554
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 4 16:32:41 2018 -0400

    disambiguate timer

Src/Particle/AMReX_ParticleContainerI.H

commit 0f0bb696ee1bf012fb7d2e8b346c61c025896025
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Oct 4 16:30:00 2018 -0400

    a thrust particle redistribute for both soa and aos data

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit d7e40df50ca45270bbd8bc3ec5ea10e14ab4d27b
Merge: b221f49d0 0bc5aae12
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Oct 4 13:59:06 2018 -0600

    Merge branch 'development' into mc-nodelinop

commit 935b3fc79ce52b2ba8097e34e4bfbdfb673facc9
Merge: 0b8ab21da 0bc5aae12
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Oct 4 12:48:32 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mlmg

commit 0b8ab21da033bcc1a6111864b8eb9b05ca233ca3
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Oct 4 12:31:06 2018 -0700

    Changed BiCGStab to subtract out the mean residual, solves the periodic 5x5x5 problem along with the regular problems.

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit 664bd2655517ae4ea11006fec645b48eebbf5120
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 4 12:10:35 2018 -0700

    add AMREX_CUDA_HOST_DEVICE to more functions

Src/Base/AMReX_Box.H
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_Orientation.H

commit 0bc5aae12ced26910d5f7ab13c743a4bc1b013a1
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Oct 4 11:33:45 2018 -0700

    CMake: start GPU support

Src/Base/CMakeLists.txt
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake

commit 5a4985f51cb3556367a6aaac3992579ea928e9a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 4 10:38:38 2018 -0700

    Fix for codes with Fortran main.  Add AMREX_CUDA_HOST_DEVICE to some functions

Src/Base/AMReX_Box.H
Src/Base/AMReX_IntVect.H
Tools/GNUMake/comps/pgi.mak

commit 97444e555579354a7804fc9fe856ffb9af7a5928
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 4 10:37:39 2018 -0700

    make amrex::Assert host and device function

Src/Base/AMReX.H
Src/Base/AMReX.cpp

commit 30a9752716584d5a21ccb77919eaf3ffb33c82d3
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Oct 4 09:52:35 2018 -0700

    CMake: fix misspelled file name

Src/Particle/CMakeLists.txt

commit 0ad85a1132c248700851e1a9e0c7ffebbc7b05db
Merge: 5f33ded5b b128b0933
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 4 09:20:12 2018 -0700

    Merge branch 'development' into gpu-merge-test

commit b128b0933e38fb449f7813c0bffc9d954ed35ae5
Merge: c02a8019a 3e87fcabf
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Oct 4 09:19:13 2018 -0700

    Merge pull request #315 from AMReX-Codes/devirtualize-fab
    
    Devirtualize fab

commit 5f33ded5bcb296c8d1d1e6a1859a53c8eb3e3049
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 22:06:05 2018 -0700

    fix some tests

Tests/C_BaseLib/tFB.cpp
Tests/FillBoundaryComparison/main.cpp

commit 28aef88f9087c748d52e3697c3916ab9faad942b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 21:44:50 2018 -0700

    pragma gpu script: add call to device function

Tools/F_scripts/write_cuda_headers.py

commit 38e820704b1c5e6ffae00f236aaabba370120cac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 21:42:03 2018 -0700

    comment out a specialization

Src/Base/AMReX_BaseFab.H

commit ba261dba2aba2f9cd585148b79e6bcadc409e801
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 21:29:49 2018 -0700

    remove duplicated declarations and fix missing definition of variable

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Device.cpp

commit 3cb7a8f59b6860d5cda9efb552c878763723bb18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 21:16:58 2018 -0700

    rm BF_init. we initialize The Arena in amrex::Initialize

Src/Base/AMReX_BaseFab.H

commit 5e667e10e33fcc6b6bfa2517924c9f1191053031
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 21:08:42 2018 -0700

    remove a number of BaseFab Fortran calls because they don't use gpu pragama anyway.  so we can simpply use c++ versions

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp

commit a324899bd04c0d4810fc83b2f8de6fd6d9a37ac9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 17:30:51 2018 -0700

    more fixes

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BoxArray.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit b3648c6ff384f05139b6e10a5ddaf7e0a882c31f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 3 20:19:50 2018 -0400

    start porting over the thrust redistribute from the tutorial

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 892d73abf2a7f12099553507a00a99de1c3b6ed1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 3 20:19:15 2018 -0400

    add a wrapper around resize for the ArrayOfStructs

Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_ParticleTile.H

commit b3fef8c905e9a5eb883fda188464db74f4b04be8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 16:47:25 2018 -0700

    fix ArrayLim

Src/Base/AMReX_ArrayLim.H

commit f9c073cb88e2e2844cb1def9753760cfd9b1b0f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 16:19:26 2018 -0700

    fix some FillBoundary arguments

Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit d18c260bb475aa23753ef9a842eaa2c2fe03f9bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 16:05:49 2018 -0700

    fix F_Interfaces

Src/F_Interfaces/Base/AMReX_multifab_fi.cpp

commit 60d94252634b7336503f7bcfba116d337e6aea42
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 16:00:38 2018 -0700

    HelloWorld compiles

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_ForkJoin.H

commit 804a444a0d3fc4b1e157053bbba47ee17b09ea4a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 3 15:42:21 2018 -0700

    Fix namespace brackets.

Src/Base/AMReX_BaseFab.cpp

commit 861cbf80d38447fe48473c84d1c78f079816bfae
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 3 15:38:50 2018 -0700

    Add back TrueUnlessGPU.

Src/Base/AMReX_MFIter.H

commit 333f65d7ba5290273d62b2f7d3e8b7effff59508
Merge: 94b72209c 3e87fcabf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 15:29:15 2018 -0700

    Merge branch 'devirtualize-fab' into gpu-merge-test

commit 3e87fcabf1159442abb99fc0ab3ca5dde5f570e9
Merge: 559affd67 c02a8019a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 15:26:15 2018 -0700

    Merge branch 'development' into devirtualize-fab

commit 94b72209c9d7c1abf35151fff6d132376a77a170
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 3 18:25:30 2018 -0400

    Adjust arena to match both branches.

Src/Base/AMReX_Arena.H

commit 037e8896b05b53985b4ca964874c8c6d05fbb6a8
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 3 18:12:13 2018 -0400

    Wrap Device::synchronizes.

Src/Base/AMReX_FabArrayCommI.H

commit c8bf8c76bec5cdebc0522b3f3401f0f0f1f22b61
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 3 18:09:38 2018 -0400

    Add missing commas to macros.

Src/Base/AMReX_Managed.H

commit 9a1bd281aa59e2751c866db45be7007cf03225bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 13:50:20 2018 -0700

    fix conflicts in Base

Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCUtil.H
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_CudaAllocators.H
Src/Base/Make.package

commit ad99e9fd35d745b0241669df89820627b1913f0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 13:23:06 2018 -0700

    fix conflicts in make

Src/Particle/AMReX_NeighborParticlesI.H
Tools/F_mk/GMakedefs.mak
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.local.template
Tools/GNUMake/comps/nvcc.mak
Tools/GNUMake/packages/Make.cvode
Tools/GNUMake/tools/Make.craypat
Tools/GNUMake/tools/Make.vtune

commit c02a8019aee5cb38176893d2666156c004babd02
Author: Jean Sexton <jmsexton@lbl.gov>
Date:   Wed Oct 3 15:51:12 2018 -0400

    Added SUNDIALS3 EX1 tutorial using CVODE Cuda N_Vector and amrex copyToMem

Src/Extern/SUNDIALS3/cvode_interface.f90
Tools/GNUMake/packages/Make.sundials3
Tutorials/SUNDIALS3/EX1_cuda/GNUmakefile
Tutorials/SUNDIALS3/EX1_cuda/Make.package
Tutorials/SUNDIALS3/EX1_cuda/SetIC.f90
Tutorials/SUNDIALS3/EX1_cuda/inputs
Tutorials/SUNDIALS3/EX1_cuda/main.cpp
Tutorials/SUNDIALS3/EX1_cuda/myfunc_F.H
Tutorials/SUNDIALS3/EX1_cuda/ode_mod.f90

commit 45a91b002cc94d6cb3a16774932e235ac44d3c5c
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Wed Oct 3 15:24:04 2018 -0400

    Add CUDA CVODE example EX3-CUDA.

Tutorials/CVODE/EX3-CUDA/GNUmakefile
Tutorials/CVODE/EX3-CUDA/Make.CVODE
Tutorials/CVODE/EX3-CUDA/Make.package
Tutorials/CVODE/EX3-CUDA/README.md
Tutorials/CVODE/EX3-CUDA/extern_probin.template
Tutorials/CVODE/EX3-CUDA/inputs
Tutorials/CVODE/EX3-CUDA/inputs_128
Tutorials/CVODE/EX3-CUDA/inputs_256
Tutorials/CVODE/EX3-CUDA/inputs_32
Tutorials/CVODE/EX3-CUDA/inputs_64
Tutorials/CVODE/EX3-CUDA/main.cpp
Tutorials/CVODE/EX3-CUDA/react_cuda.cpp
Tutorials/CVODE/EX3-CUDA/react_serial.cpp
Tutorials/CVODE/EX3-CUDA/react_utils.F90
Tutorials/CVODE/EX3-CUDA/test_react.H
Tutorials/CVODE/EX3-CUDA/test_react_F.H

commit 66d1f6482b9a71c235ce99caa74a1327194a9cd0
Merge: 2150dc4b1 f6f7a4c0c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 3 15:13:55 2018 -0400

    Merge branch 'development' into gpu-merge-test
    
    Conflicts:
            Src/Base/AMReX_Arena.H
            Src/Base/AMReX_ArrayLim.H
            Src/Base/AMReX_BArena.H
            Src/Base/AMReX_BArena.cpp
            Src/Base/AMReX_BaseFab.H
            Src/Base/AMReX_BaseFab.cpp
            Src/Base/AMReX_BaseFab_f.H
            Src/Base/AMReX_BaseFab_nd.F90
            Src/Base/AMReX_CUDA.F90
            Src/Base/AMReX_CudaAllocators.H
            Src/Base/AMReX_Device.H
            Src/Base/AMReX_Device.cpp
            Src/Base/AMReX_FabArray.H
            Src/Base/AMReX_FabArrayCommI.H
            Src/Base/AMReX_MFIter.H
            Src/Base/AMReX_MFIter.cpp
            Src/Base/AMReX_fort_mod.F90
            Src/Particle/AMReX_ParticleContainerI.H
            Src/Particle/AMReX_Particles.H
            Tests/Particles/StructOfArrays/GNUmakefile
            Tools/F_mk/GMakedefs.mak
            Tools/F_mk/comps/Linux_pgi.mak
            Tools/GNUMake/Make.defs
            Tools/GNUMake/Make.machines
            Tools/GNUMake/Make.rules
            Tools/GNUMake/comps/gnu.mak
            Tools/GNUMake/comps/ibm.mak
            Tools/GNUMake/comps/nvcc.mak
            Tools/GNUMake/comps/pgi.mak
            Tools/GNUMake/sites/Make.llnl
            Tools/GNUMake/sites/Make.olcf
            Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
            Tutorials/Particles/ElectromagneticPIC/Evolve.H
            Tutorials/Particles/ElectromagneticPIC/Evolve.cpp
            Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H
            Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90
            Tutorials/Particles/ElectromagneticPIC/em_pic_F.H
            Tutorials/Particles/ElectromagneticPIC/inputs
            Tutorials/Particles/ElectromagneticPIC/main.cpp

commit f6f7a4c0c6391e8fcc809538970f5c0d5bfbbf5b
Merge: 06f905d40 17a7f5045
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Oct 3 13:15:32 2018 -0400

    merging.

commit 17a7f50456bb629c6584a0be3f58fd33595055c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 10:00:27 2018 -0700

    put Nvar_Arena into AMREX_USE_GPU_PRAGMA

Src/Base/AMReX_Arena.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp

commit 2150dc4b15837d421feac033e0b217c315cd8583
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 3 12:33:09 2018 -0400

    Rename for runOn variable for easy searching/renaming later.

Src/Base/AMReX_FabArray.H

commit 77b02d212ae2be0801af9e6b1cdd1fee32d3001c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 08:56:36 2018 -0700

    fix cmake

Src/Particle/CMakeLists.txt

commit c5e355508e8c6297f5abfda2fa140e6dc0bc513c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Oct 3 11:48:48 2018 -0400

    FillBoundary and EnforcePeriodicity converted to RunOn selection.

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit b221f49d0672e59a8452a78799a60b88d5277522
Merge: 0213b99d9 dcc46f612
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Oct 3 07:41:58 2018 -0600

    Merge branch 'development' into mc-nodelinop

commit 06f905d40830f966a0965e040cf93d4faa236e05
Merge: aa5e5ee97 dcc46f612
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 2 20:02:40 2018 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit dcc46f612ec32a199f7e1076720d10e60ed711af
Merge: c4a48a12f 238d6764f
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Oct 2 16:41:06 2018 -0700

    Merge branch 'marc/forkjoin_dev' into development

commit 238d6764f362ed79287c9e89a395f77e4d4aed60
Merge: 352e295ac c4a48a12f
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Oct 2 16:39:14 2018 -0700

    resolve trivial conflict

commit 352e295ac130c2503bca0c70484c3cb43d1a4fab
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Oct 2 16:37:21 2018 -0700

    Remove commented code lines

Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp

commit c4a48a12f0ef08943e92349c5a1235208d3e4685
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 2 16:34:13 2018 -0700

    add NVCC_HOST_COMP

Tools/GNUMake/comps/nvcc.mak

commit 7821e732f3c4ac6156228ce785f4517f60bba3c2
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Oct 2 16:32:26 2018 -0700

    Add some functionality to the test code

Tutorials/Parallel/ForkJoin/MyTest.H
Tutorials/Parallel/ForkJoin/MyTest.cpp

commit 14ccb0cd040c6e9dac2f9f0b9c211ccd4b01f75f
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Oct 2 16:20:31 2018 -0700

    Add name of output folder to fj ctr, allow to be empty string and to overwrite existing output

Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp

commit 6dc5b422406cf144f2582689dfaeadd59b162e0d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 2 18:52:16 2018 -0400

    Slight renaming.

Src/Base/AMReX.cpp

commit a733e05e598350542f093e1eb60f2184a6b89ec4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 2 15:40:51 2018 -0700

    use linop getFluxes

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit aa5e5ee97bc31da8e26d08c5f11fd9192c85657b
Merge: 7f1ceb460 12683828a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 2 18:13:29 2018 -0400

    Merge branch 'atmyers-gpu_particles_reorg' into development

commit 7f1ceb460bfefee34295fa696c76c51495d32e16
Merge: a800d462d 654b518fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 2 14:46:41 2018 -0700

    Merge branch 'gpu' into development

commit cf152a29122e5970665ee4b5e3b9b1c608cc803e
Merge: d9a06831d a800d462d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 2 17:43:34 2018 -0400

    Merge branch 'development' into gpu-mm

commit 0005734598ce96d8970b82c89ff9a26c64b8b74d
Merge: a776e26d4 a800d462d
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Oct 2 14:30:24 2018 -0700

    Merge branch 'development' into marc/forkjoin_dev

commit a800d462d702607e6689a45db8c8ba2485d8e9de
Merge: 3d5d930a6 3bbda25ac
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Oct 2 14:28:33 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d9a06831d2d910d3e664bd394436f7fae8150565
Merge: 45502483d 3bbda25ac
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 2 17:06:31 2018 -0400

    Merge branch 'development' into gpu-mm

commit 654b518fcca82cfe010f4bb460aa07467061ade4
Merge: 7132db3e7 3bbda25ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 2 14:01:36 2018 -0700

    Merge branch 'development' into gpu

commit 3bbda25ac3aea96302db5e3979ecda0f999620cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 2 13:59:54 2018 -0700

    remove some old unused functions

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 7132db3e7219411ca55ddb2f0d26ce62cfe8cb5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 2 13:35:57 2018 -0700

    fix cmake

Src/Base/AMReX_BaseFab_nd.F90
Src/Base/CMakeLists.txt

commit 45502483d826de993dbf04599efab2298d47dd65
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 2 16:33:30 2018 -0400

    Reorganize FillBoundary and EnforcePeriodicity calls.

Src/Base/AMReX_FabArray.H

commit 3cb09f17abda23bbcae89f26ba64f9dd010b9be2
Merge: 0cf71283e 0330434c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 2 13:15:23 2018 -0700

    Merge branch 'development' into gpu

commit 0cf71283e9ac113a943425455a5694f4bd8df72d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 2 12:25:00 2018 -0700

    minor changes in MFIter

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 2e2af66c997418451c3397501275d2f6cd1432fe
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 2 15:26:17 2018 -0400

    Move RunOn and CopyFromTo to AMReX.H

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_Managed.H

commit aef0d1ec6ff58682367b0a3a812235d7785ac30c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 2 15:19:31 2018 -0400

    Make AMReX_Managed.H called under any circumstances.

Src/Base/AMReX_Array.H
Src/Base/AMReX_MultiFab.cpp

commit 29a0ada8d2b3dcf8122b7fea9d13f9388f9afc0a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Oct 2 15:18:43 2018 -0400

    Addition of runOn/CopyFromTo runtime default and slight renaming.

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_Managed.H

commit 12683828a1a10fe9d6f62ae1aa1ba8e0f2b643b7
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 2 15:12:48 2018 -0400

    remove variadic tuple stuff from particle tile - taking a different approach

Src/Particle/AMReX_ParticleTile.H

commit d06d06c9a7990ab248b4bada0352420407c32a75
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 2 15:07:34 2018 -0400

    using the managed particle vector in Redistribute

Src/Particle/AMReX_ParticleContainerI.H

commit 1cd8f16db1ade888455c479a404333378fe03b53
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Oct 2 15:06:47 2018 -0400

    use managed vectors in the particle iterator for get / set position

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H

commit 0330434c8d7a9681ad6cff72dbf4d759e27bdcec
Merge: 1b629dd98 4d3b30304
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Oct 2 11:59:32 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 1b629dd98b7fcac7696a4e649018d81ba6b9a2d9
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Oct 2 11:58:50 2018 -0700

    update asyncFP

Src/Amr/AMReX_AsyncFillPatch.cpp

commit 6c1766a1eaa64a7cedff1eac9beaaa30e668fb85
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 2 10:49:46 2018 -0700

    use AMREX_USE_GPU_PRAGMA in the script

Tools/F_scripts/gpu_fortran.py
Tools/F_scripts/write_cuda_headers.py

commit c5e29cc4c67dff939c89cc760c4a7f4e35a91f42
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 1 18:10:50 2018 -0700

    make make have the old behavior when USE_GPU_PRAGMA is not TRUE

Src/Base/AMReX_fort_mod.F90
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 4d3b303046ebc98271d0c00173962396f6c429d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 1 18:17:31 2018 -0700

    fix compilation

Src/Amr/AMReX_AsyncFillPatch.cpp

commit 167c0257de002c6c29f8937e506142f0cdab1d11
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 1 20:41:06 2018 -0400

    toLower and toUpper Utility functions.

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit 3adf9557c2c6938f7efd0202defec3d02de1bd50
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 1 20:40:44 2018 -0400

    Small fix.

Src/Base/AMReX.cpp

commit 4ac83d76293b50ce797e90979b91edf08af08d5a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 1 20:35:00 2018 -0400

    Temporary fill of RunOn in lambdas to allow compile testing while default and function interfaces are adjusted.

Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_MultiFab.cpp

commit d28b38eb592c0a18b51f9f2cf801869fdaa2002b
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Oct 1 15:28:29 2018 -0700

    create a separate file for asyncMFIter code

Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AsyncFillPatch.cpp
Src/Amr/Make.package

commit 0c48c88bdbab0d054e28ef3f332ccf749c2758b5
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 1 15:51:03 2018 -0400

    Small GPU Readme to remind difference between tutorials.

Tutorials/GPU/Readme.txt

commit 1c20672825570473608470350b4c63911fbd126c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Oct 1 15:37:29 2018 -0400

    First pass at runtime selection of location of lambdas. Should run poorly with HeatEquation_EX0 (lambda version).

Src/Base/AMReX.cpp
Src/Base/AMReX_Managed.H
Tests/GPU/TestC/main.cpp
Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp

commit 4c9866ecce59bc9cf165696c300effff6fbfc422
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Oct 1 15:32:01 2018 -0400

    add some useful typedefs to the ParIter

Src/Particle/AMReX_Particles.H

commit 8c4ee539038d5aee876b4923589dfd6ac6146064
Merge: 5a057d085 dc4a6267b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 1 12:25:41 2018 -0700

    Merge branch 'eb-grow' into development

commit dc4a6267bf68a17be3ffb3cda542a6ddd6a1cd89
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 1 12:18:48 2018 -0700

    update CellEB2 test

Tests/LinearSolvers/CellEB2/MyTest.cpp

commit ffbaa2c6d5cefc49afd06859f2a5fad4b23786e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 1 12:02:17 2018 -0700

    update EB doc

Docs/sphinx_documentation/source/EB.rst
Tutorials/EB/CNS/Source/CNS_init_eb2.cpp

commit 67b34cc2aaafac1eaadac5327e3fcdf0853a23e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 1 11:10:28 2018 -0700

    finish implementation of ngrow for eb

Src/EB/AMReX_EB2.H
Src/EB/AMReX_EB2_IndexSpaceI.H
Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_EB2_Level.cpp

commit 5a057d085a36027b02d2fc4e26f1e5df656db5fd
Merge: 4911f909e 8e073533b
Author: Guy Moore <gmoore@lbl.gov>
Date:   Mon Oct 1 09:18:10 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8e073533b0cffe6dc78847dd4ec93cfed7907549
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 1 08:52:00 2018 -0700

    update CHANGES

CHANGES

commit e56c28918788293fcffce7beaa7a2286dda9502e
Merge: 9d22e2340 a11cf25db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 1 08:51:10 2018 -0700

    Merge branch 'development'

commit c0e7ad998388be0527ab23b620ae4ef66b6b2e54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 30 16:40:43 2018 -0700

    add aoptional ngrow argument to EB2::Build and start implementation

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/EB/AMReX_EB2.H
Src/EB/AMReX_EB2.cpp
Src/EB/AMReX_EB2_IndexSpaceI.H
Src/EB/AMReX_EB2_Level.H

commit 9215f1d22b4ca60f96fdc0820467442b88d3717b
Merge: cfb661c22 a11cf25db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 29 11:24:50 2018 -0700

    Merge branch 'development' into mlmg

commit a11cf25dbd5e6f771c7f6cedfbdea368f9559261
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 29 11:24:33 2018 -0700

    Merge branch 'mlmg' into development

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit cfb661c226012d1a36242e0bdfb54a9fda0492b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 29 11:23:34 2018 -0700

    fix hypre: make sure to exclude non-valid cells

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit 4911f909e46ded55ccd6ba25f73c845ccab5f69c
Merge: 6f3b4eb63 afc4caed3
Author: Guy Moore <gmoore@lbl.gov>
Date:   Fri Sep 28 16:32:19 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 6f3b4eb6349709beedc3e350a406fc9253bda002
Author: Guy Moore <gmoore@lbl.gov>
Date:   Fri Sep 28 16:29:12 2018 -0700

    Added more comments to README

Tutorials/SWFFT_simple/README

commit 86104f6fbad729c10ab37b7b825bc691c7bbd89f
Merge: 051c791c4 afc4caed3
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 28 18:53:06 2018 -0400

    Merge branch 'development' into gpu-mm

commit 051c791c4dabc7a466d964c9f969764074dab5c7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 28 18:48:59 2018 -0400

    AMREX_CUDA_HOST_DEVICE added.

Src/Base/AMReX_Array.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_CUDA_Utility.H
Src/Base/AMReX_CUDA_Utility.cpp
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_Managed.H
Src/Base/AMReX_RealBox.H

commit 0db41995ca04dd9562c0090922657e289cc2bc86
Author: Guy Moore <gmoore@lbl.gov>
Date:   Fri Sep 28 14:53:27 2018 -0700

    Added scaling comment to README

Tutorials/SWFFT_simple/README

commit 5d0d7e204007e8e7de4827b8565cc2f212fc15e6
Author: Guy Moore <gmoore@lbl.gov>
Date:   Fri Sep 28 14:48:56 2018 -0700

    Confirmed FFT scaling

Tutorials/SWFFT_simple/SWFFT_Test.cpp
Tutorials/SWFFT_simple/SWFFT_Test_F.F90
Tutorials/SWFFT_simple/inputs.multipleGrids
Tutorials/SWFFT_simple/inputs.oneGrid

commit afc4caed3bf642c0f27b088f431d9261e03fd72c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 28 14:46:06 2018 -0700

    Revert "use git pull instead of clone to avoid polluting the download statistics"
    
    This reverts commit d8ee1ef0d9211f7d8615b04883bf145166b2a0e3.

build_and_deploy.sh

commit 6d6782004db272be88559bc9f2c5396a06114161
Merge: d8ee1ef0d af73f93d4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 28 14:36:55 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d8ee1ef0d9211f7d8615b04883bf145166b2a0e3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 28 14:32:45 2018 -0700

    use git pull instead of clone to avoid polluting the download statistics

build_and_deploy.sh

commit af73f93d49a0d6d21b10c599078af850a2b3e8d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 28 14:26:14 2018 -0700

    port BoxArray DistributionMapping version of MFIter constructor to Fortran

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 8ca61396525f121934aba97a1a1dd05f419e2508
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 28 14:19:19 2018 -0700

    fix typo

build_and_deploy.sh

commit ffd3e55b04ed026571cfb2d911a7e18188adeac8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 28 14:07:03 2018 -0700

    generate pdf and copy it into source before building html

build_and_deploy.sh

commit a2f0d4ddcea8bab3266219e7a6032a70508d1bd4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 28 13:43:36 2018 -0700

    build pdf of the docs and link to it from the html version on every commit to development

.travis.yml
Docs/sphinx_documentation/source/index.rst
Docs/sphinx_tutorials/source/index.rst
build_and_deploy.sh

commit d17314c4029e5a7f4127e6e44e17c03e32c9db6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 28 13:38:55 2018 -0700

    attempt to set computability with deviceQuery

Tools/GNUMake/sites/Make.unknown

commit 19d17692e4233bf5b9725627a32cda9372184bea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 28 13:37:36 2018 -0700

    make sure C++ standards are consistently set

Tools/GNUMake/comps/nvcc.mak

commit 32e0e3917cc5d46f7c0390e2af04c896d38aaa56
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 28 13:29:26 2018 -0700

    fix shadows

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_Device.H

commit 2c355925414b55dd95ff232184192643b3f705e4
Author: Guy Moore <gmoore@lbl.gov>
Date:   Fri Sep 28 12:39:53 2018 -0700

    Updated README

Tutorials/SWFFT_simple/README
Tutorials/SWFFT_simple/SWFFT_Test.cpp

commit f1a2277801fa0fa90e62d6e796bf3358e3dcbbc1
Merge: f4009f86e 8aaa6483c
Author: Guy Moore <gmoore@lbl.gov>
Date:   Fri Sep 28 12:06:13 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit f4009f86e4c29215fafdce056a787ab73e04efb4
Author: Guy Moore <gmoore@lbl.gov>
Date:   Fri Sep 28 12:04:24 2018 -0700

    Adapted for 2D

Tutorials/SWFFT_simple/SWFFT_Test.H
Tutorials/SWFFT_simple/SWFFT_Test.cpp
Tutorials/SWFFT_simple/SWFFT_Test_F.F90
Tutorials/SWFFT_simple/SWFFT_Test_F.H
Tutorials/SWFFT_simple/run_me
Tutorials/SWFFT_simple/run_me_2d
Tutorials/SWFFT_simple/run_me_3d
Tutorials/SWFFT_simple/swfft_compute.cpp

commit 65a241c969fcf345de52d02b0e829de11de305bf
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 28 14:16:54 2018 -0400

    Adjust C+ BaseFab merge to get GPU HeatEquation Running.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_nd.F90
Src/Base/AMReX_Box.H

commit 8aaa6483cd179413394054e663e204b68a846ae4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 28 11:15:10 2018 -0700

    Fix VisMF for the case where the number of ghost cells can be different in each direction

Src/Base/AMReX_VisMF.cpp

commit 9bfafef0daaf2e140f8786f1c143ffb2730047eb
Author: Guy Moore <gmoore@lbl.gov>
Date:   Fri Sep 28 10:53:59 2018 -0700

    Cleaned up SWFFT_simple - removed unecessary code from original SWFFT tutorial

Tutorials/SWFFT_simple/Make.package
Tutorials/SWFFT_simple/README
Tutorials/SWFFT_simple/SWFFT_Test.H
Tutorials/SWFFT_simple/SWFFT_Test.cpp
Tutorials/SWFFT_simple/SWFFT_Test_F.F90
Tutorials/SWFFT_simple/SWFFT_Test_F.H
Tutorials/SWFFT_simple/inputs.multipleGrids
Tutorials/SWFFT_simple/main.cpp
Tutorials/SWFFT_simple/swfft_compute.cpp

commit 497e6621cc4a5d35f91c1a8cc657c5ba681cc058
Author: Guy Moore <gmoore@lbl.gov>
Date:   Fri Sep 28 10:11:00 2018 -0700

    First commit of SWFFT_simple tutorial, in which only a forward FFT is performed

Tutorials/SWFFT_simple/GNUmakefile
Tutorials/SWFFT_simple/Make.package
Tutorials/SWFFT_simple/README
Tutorials/SWFFT_simple/SWFFT_Test.H
Tutorials/SWFFT_simple/SWFFT_Test.cpp
Tutorials/SWFFT_simple/SWFFT_Test_F.F90
Tutorials/SWFFT_simple/SWFFT_Test_F.H
Tutorials/SWFFT_simple/inputs.multipleGrids
Tutorials/SWFFT_simple/inputs.oneGrid
Tutorials/SWFFT_simple/main.cpp
Tutorials/SWFFT_simple/run_me
Tutorials/SWFFT_simple/swfft_solver.cpp

commit e40b2daf7e64d90326351fbcad0f9306f80ee415
Merge: 7de9ae558 8447e9ac2
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Sep 27 20:21:26 2018 -0400

    Merge branch 'development' into gpu-mm:
    cpp versions of BaseFab funcs
    
    Conflicts:
            Src/Base/AMReX_BaseFab.H
            Src/Base/AMReX_BaseFab.cpp
            Src/Base/AMReX_BaseFab_f.H
            Src/Base/AMReX_BaseFab_nd.F90

commit 7de9ae558e5c578bf361f581125bfa1dda40d204
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Sep 27 13:08:22 2018 -0400

    Move GPU tests from Tutorials to Test.

Tests/GPU/Test/GNUmakefile
Tests/GPU/Test/Make.package
Tests/GPU/Test/main.cpp
Tests/GPU/Test/run.exitcode
Tests/GPU/Test/run.script
Tests/GPU/TestB/GNUmakefile
Tests/GPU/TestB/Make.package
Tests/GPU/TestB/main.cpp
Tests/GPU/TestB/return_test.F90
Tests/GPU/TestC/GNUmakefile
Tests/GPU/TestC/Make.package
Tests/GPU/TestC/main.cpp
Tests/GPU/TestC/run.summit
Tests/GPU/TestC/run.summitdev

commit 8447e9ac2512dd6cc1b6ee999ce87c2f8594ad2a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 26 18:11:14 2018 -0700

    add an assertion

Src/Base/AMReX_BaseFab.H

commit 75db0e761bf2f35b323e5b7277770493fe20b36d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Sep 26 14:02:31 2018 -0400

    Prefix CUDA_MAX_THREADS with AMREX

Src/Base/AMReX_CUDA.F90
Tools/GNUMake/Make.defs

commit d0e3ad5d9cf15e507af4b49e80a3b23f75ec756b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Sep 26 13:57:48 2018 -0400

    Prefix GPUS_PER_SOCKET/NODE with AMREX

Src/Base/AMReX_Device.cpp
Tools/GNUMake/Make.defs

commit 98b121dd9c38d344dfeecf9679f58a0ac794a4f2
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Sep 26 13:56:07 2018 -0400

    Remove CUDA_UM

Src/Base/AMReX_BArena.cpp
Tools/GNUMake/Make.defs

commit 18e9ac7ec6c290757730ca09ef1e9147fabd2535
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Sep 26 13:54:25 2018 -0400

    Remove unused OMP_OFFLOAD

Tools/GNUMake/Make.defs

commit f8fea4918c11a70d755e725f8ac0f61d5700a5da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 26 10:48:15 2018 -0700

    make sure global operators are used

Src/Base/AMReX_BArena.cpp

commit f50cf2263719cf4e8d0732f7bf89121bc3845034
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 26 10:44:17 2018 -0700

    remove unused variables

Src/Base/AMReX_MultiFab.cpp

commit 6fc69832298173ec1f48d1a152e8e596a308eb61
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 26 10:40:37 2018 -0700

    remove unused variable

Src/Base/AMReX_FabArray.H

commit 83823afa804e5ea85cffbae71c73ae27b3cc90ad
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Sep 25 20:10:21 2018 -0400

    Free local communicator

Src/Base/AMReX_Device.cpp

commit ee231f076d9f8a752000d2c7d3ad458d3f8beef6
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Sep 25 20:03:39 2018 -0400

    Use PD Communicator

Src/Base/AMReX_Device.cpp

commit 85e7ad8867dae516e0e1a357757d89c142a6e769
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Sep 25 20:00:43 2018 -0400

    Remove unused variable

Src/Base/AMReX_Device.H

commit 4e24b2a4d9edb3782225dfb9ddf32f3d21a03a03
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Sep 25 19:59:56 2018 -0400

    Add a definition for max_cuda_streams

Src/Base/AMReX_Device.cpp

commit d9dc8bcec4dcd84506c17b0eef533b1fb72f4435
Merge: 8a4cbe149 0e1878ce1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 25 15:26:31 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8a4cbe14900b1b266d4e57f9b8a17503247df70f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 25 15:26:12 2018 -0700

    add ba / dmap access functions to EBFArrayBoxFactory

Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp

commit 0e1878ce1167b371baeca7cf44c1f5c9ffe99a8c
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Sep 25 14:33:04 2018 -0700

    update async version of FillPatchIter

Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Base/AMReX_MultiFabUtil_Perilla.H
Src/Base/AMReX_MultiFabUtil_Perilla.cpp

commit 502418e1bad5cf43df47360bc6f799f9590cc00b
Merge: 0cd513b29 b9d703f47
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 25 12:56:33 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 0cd513b29e72257b8f72939c30008b026121218d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 25 12:54:24 2018 -0700

    EB: fix roundoff error issues

Src/EB/AMReX_eb2_3d.F90

commit b9d703f4759a2374c0eb721d1606c376aeed0b62
Merge: 8a901fed8 ea6dbf258
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 25 12:11:21 2018 -0700

    Merge pull request #324 from zingale/development
    
    work around intel compiler crash

commit ea6dbf2589e60ecc95b351056f1d03c6cf80e94a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 25 11:54:47 2018 -0700

    work around intel compiler crash

Tools/F_scripts/write_probin.py

commit 8a901fed8156e588e65f15b60b27476cbcb98a5f
Merge: 1c0141d7b bf54f74c3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 25 09:23:03 2018 -0700

    Merge pull request #322 from wolfram-schmidt/development
    
    Development

commit 0213b99d98d51171ddb1429cdedd24a77769c77c
Merge: 9b435a2b6 1c0141d7b
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Sep 25 09:58:04 2018 -0600

    Merge branch 'development' into mc-nodelinop

commit 9b435a2b60674969fb4c5570de5b78959d7888b3
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Sep 25 09:57:36 2018 -0600

    updated MLMG solver for multicomponent solve

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit bf54f74c3cf2ae0947c77f47cf4e51e62b38558a
Author: Wolfram Schmidt <wolfram.schmidt@uni-hamburg.de>
Date:   Tue Sep 25 11:52:20 2018 +0200

    Cleaned up nec.mak

Tools/GNUMake/comps/nec.mak

commit a0c1442b6fec3c03ec44e81fd2c9aeaa2ffd3116
Merge: 919594fe8 1c0141d7b
Author: Wolfram Schmidt <wolfram.schmidt@uni-hamburg.de>
Date:   Tue Sep 25 10:14:15 2018 +0200

    Merge remote-tracking branch 'upstream/development' into development

commit 1c0141d7b3a9ececcf4d91da3d7e3ff57d8cc09b
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Mon Sep 24 17:53:47 2018 -0700

    Added ARKODE interface for Sundials 3.X from CVODE interface, used with USE_ARKODE=TRUE and USE_SUNDIALS3=TRUE

Docs/sphinx_documentation/source/SUNDIALS3.rst
Src/Extern/SUNDIALS3/Make.package
Src/Extern/SUNDIALS3/arkode_interface.f90
Src/Extern/SUNDIALS3/farkode.f90
Tools/GNUMake/packages/Make.sundials3
Tutorials/SUNDIALS3/EX_ark_analytic_fp/GNUmakefile
Tutorials/SUNDIALS3/EX_ark_analytic_fp/Make.package
Tutorials/SUNDIALS3/EX_ark_analytic_fp/ark_analytic_fp.f90

commit d30eea1ac4319202d52a7013cab16ed7f808aafd
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Mon Sep 24 14:00:08 2018 -0700

    Added initial documentation for added Sundials version 3.X support

Docs/sphinx_documentation/source/CVODE.rst
Docs/sphinx_documentation/source/Chapter14.rst
Docs/sphinx_documentation/source/SUNDIALS3.rst

commit 045c46bed4c8e0a844746342cdee75ee2e904a1b
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date:   Mon Sep 24 13:18:34 2018 -0700

    USE_SUNDIALS3=TRUE links in David's updated fcvode interface for Sundials 3.X, 5 new example added to Tutorials

Src/Extern/SUNDIALS3/Make.package
Src/Extern/SUNDIALS3/cvode_interface.f90
Src/Extern/SUNDIALS3/fcvode.f90
Src/Extern/SUNDIALS3/fnvector_serial.f90
Src/Extern/SUNDIALS3/fnvector_serial_fprefix.f90
Src/Extern/SUNDIALS3/fsunlinsol_dense.f90
Src/Extern/SUNDIALS3/fsunmat_dense.f90
Tools/GNUMake/Make.defs
Tools/GNUMake/packages/Make.sundials3
Tutorials/SUNDIALS3/EX1/GNUmakefile
Tutorials/SUNDIALS3/EX1/Make.package
Tutorials/SUNDIALS3/EX1/inputs
Tutorials/SUNDIALS3/EX1/integrate_ode.f90
Tutorials/SUNDIALS3/EX1/main.cpp
Tutorials/SUNDIALS3/EX1/myfunc_F.H
Tutorials/SUNDIALS3/EX1/ode_mod.f90
Tutorials/SUNDIALS3/EX_cv_analytic_fp/GNUmakefile
Tutorials/SUNDIALS3/EX_cv_analytic_fp/Make.package
Tutorials/SUNDIALS3/EX_cv_analytic_fp/cv_analytic_fp.f90
Tutorials/SUNDIALS3/EX_cv_analytic_fp/cv_analytic_fp.out
Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/GNUmakefile
Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/Make.package
Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/cv_analytic_sys_dns.f90
Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/cv_analytic_sys_dns.out
Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/GNUmakefile
Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/Make.package
Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/cv_analytic_sys_dns_jac.f90
Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/cv_analytic_sys_dns_jac.out
Tutorials/SUNDIALS3/EX_cv_brusselator_dns/GNUmakefile
Tutorials/SUNDIALS3/EX_cv_brusselator_dns/Make.package
Tutorials/SUNDIALS3/EX_cv_brusselator_dns/cv_brusselator_dns.f90
Tutorials/SUNDIALS3/EX_cv_brusselator_dns/cv_brusselator_dns.out

commit 919594fe85584419743e72e1adf25c91a4b4161c
Merge: 9d0fe16b1 b9a5b6547
Author: Wolfram Schmidt <wolfram.schmidt@uni-hamburg.de>
Date:   Mon Sep 24 12:19:18 2018 +0200

    Merge remote-tracking branch 'upstream/development' into development

commit 9d0fe16b15bca67976994acb28439ec81d96e2d9
Author: Wolfram Schmidt <wolfram.schmidt@uni-hamburg.de>
Date:   Mon Sep 24 12:18:31 2018 +0200

    Another fix for NEC.

Src/F_BaseLib/fabio_c.c
Tools/GNUMake/sites/Make.hs

commit cf475a3fb6f0482a576fcfe6a11cc376797c194e
Merge: da04fa61a b9a5b6547
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Sep 22 09:21:02 2018 -0400

    Merge branch 'development' into gpu

commit b9a5b6547326c5186a089cbde76ea217919116e8
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sat Sep 22 02:06:51 2018 -0400

    Fix timer.

Tests/BaseFabTesting/main.cpp

commit ddb2d87ad21a17e89ba88cab835d4153de2f6d29
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sat Sep 22 01:55:30 2018 -0400

    Small change to BaseFabTest.

Tests/BaseFabTesting/main.cpp

commit 877f48ac235bb136ee84f85128b5da2b8b84e0bc
Merge: 87aa025f6 55033748a
Author: kngott <kngott@lbl.gov>
Date:   Fri Sep 21 22:48:07 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-codes/amrex into development

commit 87aa025f6614068722ac64e56a7bdbaa9e5c7de5
Author: kngott <kngott@lbl.gov>
Date:   Fri Sep 21 22:47:55 2018 -0700

    BaseFab edit for 1 iter.

Tests/BaseFabTesting/inputs
Tests/BaseFabTesting/main.cpp

commit 55033748a0fdd1f979c016449294a54354b02a0a
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Sep 21 14:18:17 2018 -0700

    update RGIter

Src/Base/AMReX_FabArrayBase.H

commit 088a8bb0879f2defd8ea490c43bd19fd7ac823ef
Merge: edc3de713 8ad443b0b
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Sep 21 13:43:39 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit edc3de713afe364c18c7b77522e16252b60ab3ca
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Sep 21 13:43:25 2018 -0700

    update AsyncFillPatchIter

Src/AmrTask/rts_impls/Perilla/Perilla.H
Src/AmrTask/rts_impls/Perilla/Perilla.cpp
Src/AmrTask/rts_impls/Perilla/PerillaConfig.H
Src/AmrTask/rts_impls/Perilla/RegionGraph.H
Src/Base/AMReX_MultiFabUtil_Perilla.H
Src/Base/AMReX_MultiFabUtil_Perilla.cpp
Src/Base/Make.package

commit 8ad443b0b88f347bd907ce70059bc3898155361b
Author: kngott <kngott@lbl.gov>
Date:   Fri Sep 21 12:40:03 2018 -0700

    Update to BaseFabTest: some results fixed and masks set randomly.

Tests/BaseFabTesting/main.cpp

commit afe6fe57a8fa34c6b642061ec6431ab1bcb26e69
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 21 10:51:34 2018 -0700

    For portability, static_cast std::streampos to std::streamoff for comparison with long

Src/Base/AMReX_VisMF.cpp

commit f44f5798c915c1032b6f30f6350e2176ff8d9fc8
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Sep 21 13:32:36 2018 -0400

    wip - beging reorg of gpu particle code

Src/Particle/AMReX_ArrayOfStructs.H
Src/Particle/AMReX_Particle.H
Src/Particle/AMReX_ParticleTile.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_StructOfArrays.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit da04fa61af9f6cd04ebb1613be70478efa9146a8
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Sep 21 10:33:01 2018 -0400

    Use PGI as host compiler when using OpenACC

Tools/GNUMake/comps/nvcc.mak
Tools/GNUMake/comps/pgi.mak

commit 25179b7eb1b28cb7543554e19d6164d95853bb04
Merge: 26917c856 aab9bd1cd
Author: Wolfram Schmidt <wolfram.schmidt@uni-hamburg.de>
Date:   Fri Sep 21 12:01:19 2018 +0200

    Merge remote-tracking branch 'upstream/development' into development

commit 559affd6750bdc3bb30939e0ea7c37f53700323d
Merge: 8f5e38c7c aab9bd1cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 20 21:15:04 2018 -0700

    Merge branch 'development' into devirtualize-fab

commit aab9bd1cdeff7f5d90c6c28d4fa7f7d3a3a71a8c
Merge: 98cda28ca b538009df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 20 21:13:52 2018 -0700

    Merge branch 'development' into basefab_T

commit b538009dfb3dfbfaac82de97ed785b1f6063a2aa
Merge: 695feee9c b33076b85
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 20 18:01:15 2018 -0700

    Merge branch 'development' into mlmg

commit 695feee9cccbec6c60bf5870a71ef889cf62b0d7
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Sep 20 15:53:30 2018 -0700

    Fixed PETSC

Src/Extern/PETSc/AMReX_PETSc.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit b33076b85c82f4b7e769a98145388fddc31d485e
Merge: 86850afe1 ee28ee67c
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Sep 20 15:51:12 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 86850afe17051fdecd07b6d55744f19eb3350b64
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Sep 20 15:51:10 2018 -0700

    levelset factory now outputs eb-geometry

Src/EB/AMReX_EB_levelset.H

commit a776e26d4553a4e0ae8500696078bf6171fc894a
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 20 15:36:29 2018 -0700

    pass flux call down to linop

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 98cda28ca016bf0d7e50f79d95d7530b009d42b8
Author: kngott <kngott@lbl.gov>
Date:   Thu Sep 20 15:24:16 2018 -0700

    remove whitespace

Tests/BaseFabTesting/inputs

commit 6a53f4c5881c80d5a5f194333e8fb8e144ff4b83
Merge: 800520ffc 3d5d930a6
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 20 15:13:06 2018 -0700

    Merge branch 'development' into marc/forkjoin_dev

commit 3d5d930a667650b623a3c9dd84c3084822ba2681
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 20 15:12:32 2018 -0700

    Add a getFluxes function that takes a solution rather than using the internal one, which may not exist unless solve is called.

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit f61302f3e1c8a39797cd6faf233485122b999aa3
Author: kngott <kngott@lbl.gov>
Date:   Thu Sep 20 14:34:34 2018 -0700

    mask fix

Tests/BaseFabTesting/inputs
Tests/BaseFabTesting/main.cpp

commit 8b08251d15b729e2ae043538e5a5db62576e016e
Author: kngott <kngott@lbl.gov>
Date:   Thu Sep 20 13:43:52 2018 -0700

    More BaseFabTest adjustments.

Tests/BaseFabTesting/main.cpp

commit 479adf60df8260c6f4afedd4ec67809d10698fb5
Author: kngott <kngott@lbl.gov>
Date:   Thu Sep 20 13:37:35 2018 -0700

    Less iterations, all basefab routines.

Tests/BaseFabTesting/inputs
Tests/BaseFabTesting/main.cpp

commit f0a8cffdf88921e2fa36f8efc0fd6b3c106f1fa2
Merge: 43a972fe4 224cc1bb3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 20 13:25:49 2018 -0700

    Merge branch 'basefab_T' of github.com:AMReX-Codes/amrex into basefab_T

commit fa84c2fbcaff3e4e00162a2d2ee96eb62fb842d5
Merge: 8f4772b8c ee28ee67c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Sep 20 16:14:19 2018 -0400

    Merge branch 'development' into gpu

commit ee28ee67c98502018c5a98335f267572a0ab3de5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Sep 20 16:11:34 2018 -0400

    Add template for max reduction

Src/Base/AMReX_BLFort.H

commit 8f4772b8c5fd75be4046ee1626c27da32417fcf1
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Sep 20 16:10:23 2018 -0400

    Add max reduction

Src/Base/AMReX_BLFort.H

commit 43a972fe4839dcf0b5398dc284c980ef246c91e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 20 12:54:02 2018 -0700

    minor

Src/Boundary/AMReX_Mask.cpp
Src/EB/AMReX_EB2_GeometryShop.H

commit 9611046defbadb9c89aac3e2b56b38e08d6a0a61
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Sep 20 15:21:54 2018 -0400

    Split up kernel launch line

Tools/F_scripts/write_cuda_headers.py

commit ca76cd28ba3cf787ed6773f4775418b05a3a446e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Sep 20 15:10:08 2018 -0400

    Throw an error if not using PGI or XL with CUDA

Tools/GNUMake/Make.defs

commit 224cc1bb3ea3ee70d92ddc954fc8e0406e316992
Author: kngott <kngott@lbl.gov>
Date:   Thu Sep 20 11:41:46 2018 -0700

    Clean up prints.

Tests/BaseFabTesting/main.cpp

commit 32cb991f357f9575e09ad4d9192950c186db64ba
Author: kngott <kngott@lbl.gov>
Date:   Thu Sep 20 11:28:03 2018 -0700

    Partial test update.

Tests/BaseFabTesting/main.cpp

commit b693d59c64e5e150837f8c1f2f4d476559d6d26e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 20 11:17:57 2018 -0700

    fix uninitialized value

Src/Base/AMReX_BaseFab.H

commit 723017c6c3fd931b7335c2f94ec8dfee279a2d42
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 20 10:18:12 2018 -0700

    add StridedPtr and use it

Src/Base/AMReX_BaseFab.H

commit 9412dda96792c9ff6907b4d3a7bdf4b70f59fadc
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Thu Sep 20 10:18:18 2018 -0400

    preserve case for gpu targets in public statements

Tools/F_scripts/gpu_fortran.py

commit ce13ef65cb4328aa9bb8337ccc560f9a9f7d5452
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date:   Thu Sep 20 09:19:09 2018 -0400

    Add charstring compiler flag (#321)
    
    Adds -Mcuda=charstring flag to pgi.mak. This is needed for offloading some of the gravity routines to GPU in Castro.

Tools/GNUMake/comps/pgi.mak

commit 00647e6e08c35ccbce3a0d4ff74f054d62073552
Merge: 3dcf17588 dd674416e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 19 21:54:56 2018 -0700

    Merge branch 'basefab_T' of github.com:AMReX-Codes/amrex into basefab_T

commit 3dcf17588edd71026a3ad401d96a7afc305e8b38
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 19 21:54:07 2018 -0700

    clean up

Src/Base/AMReX_BaseFab.H

commit a325765e6900d19e7a6aa8d0994e0283ee6d3ad3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 19 21:39:19 2018 -0700

    new version of BaseFab function templates

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_c.H
Src/Base/AMReX_BaseFab_c.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit dd674416e89f8ecbcee267ad713aa51f9c96c487
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Sep 19 23:45:23 2018 -0400

    Compile worked on BaseFab test.

Tests/BaseFabTesting/GNUmakefile
Tests/BaseFabTesting/inputs
Tests/BaseFabTesting/main.cpp

commit fd99cf50edacf595fd9704ecef097be8d1e83a18
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Sep 19 20:47:35 2018 -0400

    Add number of components to test.

Tests/BaseFabTesting/inputs
Tests/BaseFabTesting/main.cpp

commit bd1d0fcef3e91ce39005abb9e6bf1d2fb9261c05
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Sep 19 16:52:04 2018 -0700

    add asyncFillPatchIter

Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/Perilla/Perilla.H
Src/AmrTask/rts_impls/Perilla/Perilla.cpp
Src/AmrTask/rts_impls/Perilla/RGIter.H
Src/AmrTask/rts_impls/Perilla/RGIter.cpp

commit 8b96839601ff76af8c16e25903b8c8cdde96ea1f
Merge: 1113463c8 5f973b8a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 19 16:39:58 2018 -0700

    Merge branch 'basefab_c' into basefab_T

commit 1113463c85c25d67028b43b2d4bef2f4181f19a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 19 16:38:07 2018 -0700

    another version of linComb

Src/Base/AMReX_BaseFab.H

commit bbf511bad712b50ccf21c9337f8b839808a8b130
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Sep 19 17:01:20 2018 -0600

    minor changes to fix NAN errors

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 6e7c60160418782843b3d67372941ed004c164d6
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Sep 19 18:46:17 2018 -0400

    Fix macros

Src/Base/AMReX_ArrayLim.H

commit 1ceb9772e90672f0a040bb2fc23d32ce81987025
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 19 15:42:31 2018 -0700

    an alternative version of linComb

Src/Base/AMReX_BaseFab.H

commit 494c0567ec8aa6274d7955012ad070deb0bca053
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 19 15:02:12 2018 -0700

    fix bug

Src/Base/AMReX_BaseFab.H

commit d615236dd7919def5556f9da18e3c38e8b576be2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 19 14:27:33 2018 -0700

    Add the option to set the bottom_solver_type through the MacProjector.

Src/LinearSolvers/MLMG/AMReX_MacProjector.H
Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp

commit 9409d21e570f0dce6089481f1b210b36646071eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 19 13:14:30 2018 -0700

    first pass to template implementation

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_REAL.H
Src/Base/AMReX_RESTRICT.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit e6fcfa6ea1cb38ea075277a1039f6c432aa340c0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Sep 19 16:44:04 2018 -0400

    Revert "Respect the COMP choice when compiling with CUDA"
    
    This reverts commit 8a597a3c41342058eacfe889f8d7be04e517c4c0.

Tools/GNUMake/comps/nvcc.mak

commit b3cdcaa69bed05aa595cd8afef18b1c60e8d8ec3
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Sep 19 16:22:24 2018 -0400

    remove un-needed boilerplate from CudaManagedAllocator; let compiler define constructors

Src/Base/AMReX_CudaAllocators.H

commit 5f973b8a913ff3208da9ed085e7996553c431af4
Author: kngott <kngott@lbl.gov>
Date:   Wed Sep 19 12:14:30 2018 -0700

    Working BaseFab test suite.

Tests/BaseFabTesting/GNUmakefile
Tests/BaseFabTesting/inputs
Tests/BaseFabTesting/main.cpp

commit 3a49e2eff77a524d45f2be519759d4bdefe562f8
Merge: b93c11e60 dd1fe920a
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Sep 19 12:46:59 2018 -0600

    Merge branch 'development' into mc-nodelinop

commit b93c11e60938aec9fddba956eb05902335edbd16
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Sep 19 12:46:25 2018 -0600

    updated MLMG for multicomponent solve

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 5a78f5027a4cf0e7848a28c0fee3575e437df936
Author: kngott <kngott@lbl.gov>
Date:   Wed Sep 19 11:32:57 2018 -0700

    First draft of BaseFab Test.

Tests/BaseFabTesting/GNUmakefile
Tests/BaseFabTesting/Make.package
Tests/BaseFabTesting/main.cpp

commit dd1fe920a6a9a154ec0506fdf97d238ac0c693d6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 19 11:30:07 2018 -0700

    protect against floating point exceptions in DistributionMapping::makeKnapSack

Src/Base/AMReX_DistributionMapping.cpp

commit 8a597a3c41342058eacfe889f8d7be04e517c4c0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Sep 19 13:02:42 2018 -0400

    Respect the COMP choice when compiling with CUDA

Tools/GNUMake/comps/nvcc.mak

commit 98ab6e68bdbc3d83178b2421f3c21f4f8605a6ad
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Sep 19 13:01:59 2018 -0400

    Always use gcc for the preprocessing

Tools/GNUMake/Make.rules

commit 3923f2a42ceea4f894a006b5d8296b6c4213a090
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 19 08:52:07 2018 -0700

    expose MLMG and LinOp from MacProjector

Src/LinearSolvers/MLMG/AMReX_MacProjector.H

commit 26917c8566c617299c669df204cba1c7cdb1c467
Author: Wolfram Schmidt <wolfram.schmidt@uni-hamburg.de>
Date:   Wed Sep 19 17:21:11 2018 +0200

    Added configuration for NEC Aurora (only serial) to GNUMake and excluded GNU extensions not supported by NEC compiler via __NEC__ preprocessor symbol.

Src/Base/AMReX.cpp
Src/Base/AMReX_BLBackTrace.H
Src/Base/AMReX_BLBackTrace.cpp
Src/F_BaseLib/backtrace_c.cpp
Src/F_BaseLib/fabio_c.c
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.machines
Tools/GNUMake/comps/nec.mak
Tools/GNUMake/sites/Make.hs

commit 9b3ac6265189e60f897a73da7a2d54ffaf357121
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Sep 19 11:10:33 2018 -0400

    Catch numbers in subroutine names

Tools/F_scripts/write_cuda_headers.py

commit 1edfb306cd715bcb7e0d25cb6fd91ed9a3a0a857
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 21:28:39 2018 -0700

    rm slowCopy

Src/Base/AMReX_BaseFab.H

commit 31c9e7997968a194e5fd1f678c8e0f8933468027
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 21:08:00 2018 -0700

    ifdef out specialization

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp

commit 2d333ab237a90a31297478c7e00b024e7cdae0f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 20:28:09 2018 -0700

    remove trailing space

Tools/GNUMake/Make.defs

commit ba21ae6d170ae1ef70813b51599d23f7277048fa
Merge: daaf0c641 c679ba5d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 20:26:19 2018 -0700

    Merge branch 'basefab_c' of github.com:AMReX-Codes/amrex into basefab_c

commit daaf0c6414f39ed340fbbc8c886659b4c3fbb109
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 20:26:05 2018 -0700

    c -> cpp

Src/Base/AMReX_BaseFab_c.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit e44304858370f9b238cfec8cbab66a58dd040fca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 20:18:20 2018 -0700

    add AMREX_RESTRICT

Src/Base/AMReX_BaseFab_c.H
Src/Base/AMReX_BaseFab_c.c
Src/Base/AMReX_REAL.H

commit c679ba5d75eb114ac07b81d4b474ccf6d3f011cc
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Sep 18 20:18:31 2018 -0400

    Add USE_GPU_PRAGMA option to GNUMakefile.

Tools/GNUMake/Make.defs

commit 690812fd1516bd03b5861ba63d5a0001829fae0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 17:14:43 2018 -0700

    fix a test

Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit f85a5d7d1dbabdaadab7fa9aae0149e646d866d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 16:41:24 2018 -0700

    missing fabs

Src/Base/AMReX_BaseFab_c.c

commit 3d1cffe4dffc632d363a1c7652af6fee9ad0c35d
Merge: 7f0845305 58a9fb74d
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Sep 18 15:41:06 2018 -0600

    Merge branch 'development' into mc-nodelinop

commit 7f08453057b766cd852d39549c38c509fccc75f1
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Sep 18 15:38:16 2018 -0600

    initial update of mllinop for multicomponent solves

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 31ab19c4bd3fb0487485d3f35f4eecce2db3b80b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 14:17:41 2018 -0700

    removed some BL_NO_FORT's

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_MultiFab.cpp

commit 9a047f1dc19781dc0d8e7dc34efddb3e081a1fb6
Merge: 35c790dd9 58a9fb74d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Sep 18 17:03:50 2018 -0400

    Merge branch 'development' into gpu-mm
    
    Conflicts:
            Src/Base/AMReX_BaseFab_nd.F90

commit bc204686d7022b9ee421b3fd162086bac98e1eab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 14:02:24 2018 -0700

    update setval_ifnot

Src/Base/AMReX_BaseFab.cpp

commit 35c790dd9f666f18dc6cfa89b890f7b146e5ada4
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Sep 18 16:56:43 2018 -0400

    Remove CPU versions of now Device functions.

Src/Base/AMReX_Managed.H

commit 510b7bdd549820a1fa26fc0d7e3989ed7bcffd87
Merge: ca28e06da 4fe77f7a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 13:54:03 2018 -0700

    Merge branch 'development' into basefab_c

commit 4fe77f7a5232dedce2860bf568d25f1d37fe064d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 13:49:38 2018 -0700

    add BaseFab::setValIfNot

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.f90
Src/Base/AMReX_MultiFab.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit ca28e06da54daa46cea53139aeda89458fdc53eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 13:19:10 2018 -0700

    use c versions in BaseFab

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_c.H
Src/Base/AMReX_BaseFab_c.c
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.f90

commit b2e8221755bc42c94296318d669c18aca26fc4c1
Merge: 2f75c9c7e 3fbc6ecb5
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Tue Sep 18 20:06:31 2018 +0000

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 2f75c9c7e7b82020933505d45f6c41576d7d0e4f
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Tue Sep 18 20:06:26 2018 +0000

    AMREX_ARLIM_ARG with CUDA always returns 3 arguments.

Src/Base/AMReX_ArrayLim.H

commit 3fbc6ecb5453ec621ebaa526f989c411f2bf3c98
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Tue Sep 18 15:47:28 2018 -0400

    Replace procedure with procedure_device, preserving the case of procedure.

Tools/F_scripts/gpu_fortran.py

commit ecb145dae43f7bc7f088b2fbd7b02575594d0cf5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 11:34:01 2018 -0700

    tidy

Src/Base/AMReX_BaseFab_c.c

commit 7931efa03a80ae63f6e072554162377df8b9d93d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 11:21:20 2018 -0700

    first pass

Src/Base/AMReX_BaseFab_c.H
Src/Base/AMReX_BaseFab_c.c
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.f90
Src/Base/AMReX_MultiFab.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 58a9fb74d69855f8049ca393ebb5b2c38d27d248
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 18 10:40:51 2018 -0700

    eb: add more protection against roundoff errors

Src/EB/AMReX_eb2_3d.F90

commit 56c7b28131266cbc1d5baabf2eb71b8df795e245
Merge: e0efa7a19 e9a3e4ed2
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Sep 18 12:43:47 2018 -0400

    Merge branch 'development' into gpu

commit e0efa7a1994122f73ac089d342f19f0a06e5b927
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Tue Sep 18 12:31:34 2018 -0400

    Fix a subroutine-detecting bug.

Tools/F_scripts/gpu_fortran.py

commit e9a3e4ed228b9f80e055c90c7be3b994296db33a
Merge: 69c592b88 ba870923e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 18 09:09:00 2018 -0700

    Merge pull request #311 from AMReX-Codes/statedata
    
    Statedata

commit f0c9a6df5c0f2f6b3f7f1a2974940ce118cbfd6e
Merge: df4ba45de 03877e801
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Tue Sep 18 05:52:48 2018 +0000

    Merge branch 'gpu-fortran-update' into gpu to support StarKiller Microphysics.

commit 03877e8018fd1c181fdd4120b5d29e0ba01d72be
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date:   Tue Sep 18 05:52:27 2018 +0000

    GPU Fortran preprocessing script supports StarKiller.

Tools/F_scripts/gpu_fortran.py

commit 203a75c9fe9e12cbbb26dda1bf26a926cf798021
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 17 22:04:47 2018 -0700

    more on BaseFab C functions

Src/Base/AMReX_BaseFab_c.H
Src/Base/AMReX_BaseFab_c.c
Src/Base/AMReX_BaseFab_f.H

commit 69c592b88479d7f561e6378a0b8324f858f8ff80
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Sep 17 17:12:49 2018 -0700

    regular updates

Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp
Src/AmrTask/rts_impls/Perilla/PerillaConfig.H
Src/AmrTask/rts_impls/Perilla_upc++/PerillaConfig.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile

commit 9bfe9492a9e478ec3d7d507bb91197b1fa3c3bab
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Sep 17 20:05:18 2018 -0400

    Test showing Fortran return problem.

Tutorials/GPU/TestB/GNUmakefile
Tutorials/GPU/TestB/Make.package
Tutorials/GPU/TestB/main.cpp
Tutorials/GPU/TestB/return_test.F90

commit 6963ebf53a03d3e4a589d1092bd1eb438ac79dd5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 17 16:59:18 2018 -0700

    tweak macros

Src/Base/AMReX_BaseFab_c.c

commit 03fcaeb687b347e8ea127b7c9602c7ec4d21af5f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Sep 17 19:30:44 2018 -0400

    Missed parenthesis.

Src/Base/AMReX_MultiFab.cpp

commit df4ba45debfeb765d07298cf4b0e782e26817d9e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Sep 17 17:15:57 2018 -0400

    Function signatures should be case sensitive in C++

Tools/F_scripts/write_cuda_headers.py

commit e195cf01917ba3864a20444a3af162c37a6964a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 17 13:48:44 2018 -0700

    tidy and check in new files

Src/Base/AMReX_BaseFab_c.H
Src/Base/AMReX_BaseFab_c.c

commit 855fef569cb1b0cd1518e4fe0618011e8256f9de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 17 13:24:10 2018 -0700

    start BaseFab_c

Src/Base/AMReX_BaseFab.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit f43c2192d19b84e5ffc30ce09ec0f3292d7973e7
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Sep 17 12:46:06 2018 -0700

    just regular updates

Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp
Src/AmrTask/rts_impls/Perilla/Perilla.cpp
Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile
Src/Base/AMReX_MemPool.cpp

commit 01d1ea223b406dfe500438c8059cbe75b8c60034
Merge: 6ba2b8b7d e167f1a03
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 17 11:15:04 2018 -0700

    Merge branch 'mlmg' into development

commit 6ba2b8b7d02b9770afa785d12cb874bd977baade
Merge: 2360e2e86 5b66f1cd9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 17 11:14:55 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit e167f1a0377ce543296a09a8cf0398a3c44cc92c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 17 11:13:02 2018 -0700

    CellEB2 test: more general at boundary

Tests/LinearSolvers/CellEB2/MyTest.cpp
Tests/LinearSolvers/CellEB2/MyTest_F.H
Tests/LinearSolvers/CellEB2/mytest_f.F90

commit a0bdf76d92a105cabfe45ea682eded3087370607
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Mon Sep 17 14:01:59 2018 -0400

    Update GPU script for StarKiller Microphysics.

Tools/F_scripts/gpu_fortran.py

commit 5b66f1cd92eacf48fecdc14861220ca4ab6dea90
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Sep 17 10:54:51 2018 -0700

    adding overloaded versions of get_particles, num_particles, and add_particle to the Fortran interfaces

Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90

commit 2360e2e86b3d1c71297d9c50ffbfc02dca2bd303
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 17 09:38:58 2018 -0700

    add a new geometry type to CellEB2 test

Tests/LinearSolvers/CellEB2/initEB.cpp

commit 12352aaebd2d166edf2043e1ce984d8705668a9e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 16 15:43:55 2018 -0700

    fix path

Tools/CompileTesting/compiletesting.py

commit 3e9257ed949477fd3e6c83a0da2d22e783c8fa79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 16 15:38:30 2018 -0700

    update compile testing

Tools/CompileTesting/compiletesting.py

commit 038b48f8306fd9857277491951f864c3348f3fcd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 16 15:21:48 2018 -0700

    inputs for new EB regression tests

Tests/LinearSolvers/CellEB/inputs.rt.2d
Tests/LinearSolvers/CellEB/inputs.rt.2d.petsc
Tests/LinearSolvers/CellEB/inputs.rt.3d

commit 117db3c591c39893524130ad3cffe51a3b900101
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 16 15:17:29 2018 -0700

    fix return

Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit a5fdd7aa11e311315de7eae83b96033e71eb30c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 15 23:08:56 2018 -0700

    writePlotfile

Tests/LinearSolvers/CellEB/MyTest.H
Tests/LinearSolvers/CellEB/MyTest.cpp
Tests/LinearSolvers/CellEB/main.cpp

commit 6b930dcb6a6e3b3ac27fa16ab14eb074b4260a8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 15 21:32:36 2018 -0700

    inputs for new EB regression tests

Tests/LinearSolvers/CellEB2/inputs.rt.2d
Tests/LinearSolvers/CellEB2/inputs.rt.3d
Tests/LinearSolvers/CellEB2/inputs.rt.hypre

commit b5ffcd71223d5dc71bd9108b3e2d865eb705bfdf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 15 21:10:59 2018 -0700

    add a test for BL_NO_FORT

Tests/NoFort/GNUmakefile
Tests/NoFort/Make.package
Tests/NoFort/main.cpp

commit 2016e2e80b4ab73ecafe77c70b69d491f1ec1ba8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 15 18:13:06 2018 -0700

    doc: make it clear the command line argument is optional.

Docs/sphinx_documentation/source/GettingStarted.rst

commit ba870923e51245b61864407034db187175957f4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 15 18:13:06 2018 -0700

    doc: make it clear the command line argument is optional.

Docs/sphinx_documentation/source/GettingStarted.rst

commit 8e50c24c72b29678e414aa31eb2545bb27936a5e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 15 11:43:08 2018 -0700

    more changes for NEC

Src/Base/AMReX_ParallelDescriptor_F.F90
Src/Base/AMReX_parmparse_mod.F90

commit 7ca91d255b5204826043d548ae2cfca8bc3630e8
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Sat Sep 15 13:30:23 2018 -0400

    Hack for importing functions and logic for distinguishing function calls.

Tools/F_scripts/gpu_fortran.py

commit 24e83eb300a073bbca8643f6cda4cb36a307d491
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 15 07:31:13 2018 -0700

    fix missing prefix

Src/Base/AMReX_BaseFab_nd.f90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90

commit 9d0b09d5b52bdf093f96f622c24ffdff5ecf8a76
Merge: 74ca9348f 87e26603e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Sep 14 22:54:51 2018 -0700

    Merge pull request #313 from kweide/development
    
    More changes for per-fab fluxregister fineadd use from FLASH

commit 8f5e38c7cd342f0267485bf22e6e60ed142adb4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 21:47:40 2018 -0700

    fix more casts

Src/EB/AMReX_EBAmrUtil.cpp
Src/EB/AMReX_EBFluxRegister.cpp

commit fa2e2a74d68975527fd8973b1337a0aab3c7345d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 21:33:33 2018 -0700

    fix cast

Tutorials/EB/CNS/Source/CNS.cpp

commit 9060af7bb4d9aaca020ea1bd722af2b3ff620bc5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 21:22:26 2018 -0700

    explicitly write move constructor for StateData hoping to make NEC happy

Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp

commit cdd3243e262c2f36b5ebf45e5289e40599938ff2
Merge: 1c51ec0df 74ca9348f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 21:08:30 2018 -0700

    Merge branch 'development' into statedata

commit 1978a0dec2bed815f9fe999ed5c37f1f64f2f400
Merge: e55a70c3d 74ca9348f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 21:03:04 2018 -0700

    Merge branch 'development' into devirtualize-fab

commit 74ca9348f9dbe4a7898cba7bbcf765efe050df08
Merge: 64bcc3f87 9081c0836
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 21:01:00 2018 -0700

    Merge branch 'development' into mlmg

commit c6db1630b726416b1c5683a51e2be308ec8801ab
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 14 21:45:34 2018 -0400

    BaseFab add, subtract, multiply and divide GPU-ized, including Multifab calls.

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_MultiFab.cpp

commit 64bcc3f87c0cb141211dfcfc34e8fa21b15684ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 18:02:04 2018 -0700

    use dx_eb from module

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit dcc2ab9c8e0b79d9300bfdbc436fe683a67ef38b
Merge: 17c31e631 a9cfb02a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 17:56:19 2018 -0700

    Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg

commit 17c31e631f144e66d02a27453f1dcc41f7341ea0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 17:56:14 2018 -0700

    add makePETSc

Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit a9cfb02a8b7e99196e725597491b0b1dfe99bbd7
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Sep 14 17:29:13 2018 -0700

    Hypre Routines for EB Dirichlet complete. Works for 2D and 3D

Src/Extern/HYPRE/AMReX_HABEC_3D.F90

commit cf1b212547734e3569183dcc289ce9dd66c67817
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 14 19:23:12 2018 -0400

    Make HeatEquation0 lambdas inlined. EmPIC keeps the separate lambdas/macro example.

Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp

commit 22936b3c4cba678e0cfc89489e8a5af729f42448
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 14 19:17:07 2018 -0400

    Change Remaining BaseFab<Real> -> FArrayBox

Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit 1c96532d375e9436ef7e77f89f403a10b86ac521
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 14 19:02:27 2018 -0400

    Rename and distinguish run scripts.

Tutorials/GPU/HeatEquation_EX0_C/Exec/run.summit
Tutorials/GPU/HeatEquation_EX0_C/Exec/run.summitdev

commit 6514c79e4cf2770e924720e9f0f6d1c1601c701e
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 14 19:01:45 2018 -0400

    Change BaseFab<Real> to FArrayBox for lambda capture. First test. Need to explicitly label all FArrayBox functions that use static class objects AMREX_DEVICE_HOST for safety.

Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp

commit d55fe127d8f2dc17f12a7a8656b12da60dd839d9
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 14 19:00:43 2018 -0400

    Variable and test to turn tiling off if on GPU.

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MultiFab.cpp

commit cf588c4b48d6cc9a817a1910ac1f64b4588069e7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 14 18:59:23 2018 -0400

    First Multifab function to GPU: copy. HeatEquation now has negligible page faults.

Src/Base/AMReX_MultiFab.cpp

commit 61d759c232d86ac5025e810dd06347ac403bb187
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 14 18:57:35 2018 -0400

    Change inputs

Tutorials/GPU/HeatEquation_EX0_C/Exec/inputs_3d

commit 9171a5b2b9329b1328f6f6f2cae8e797c1e6172e
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 14 18:56:46 2018 -0400

    EmPIC with Lambdas inlined.

Tutorials/GPU/ElectromagneticPIC_2/Constants.H
Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.H
Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC_2/Evolve.H
Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_2/GNUmakefile
Tutorials/GPU/ElectromagneticPIC_2/IO.H
Tutorials/GPU/ElectromagneticPIC_2/IO.cpp
Tutorials/GPU/ElectromagneticPIC_2/Make.package
Tutorials/GPU/ElectromagneticPIC_2/NodalFlags.H
Tutorials/GPU/ElectromagneticPIC_2/NodalFlags.cpp
Tutorials/GPU/ElectromagneticPIC_2/Particles.H
Tutorials/GPU/ElectromagneticPIC_2/StructOfArrays.H
Tutorials/GPU/ElectromagneticPIC_2/em_pic_3d.F90
Tutorials/GPU/ElectromagneticPIC_2/em_pic_F.H
Tutorials/GPU/ElectromagneticPIC_2/inputs
Tutorials/GPU/ElectromagneticPIC_2/main.cpp
Tutorials/GPU/ElectromagneticPIC_2/script.nompi.sh
Tutorials/GPU/ElectromagneticPIC_2/summit.sh
Tutorials/GPU/ElectromagneticPIC_2/summitdev.sh
Tutorials/GPU/ElectromagneticPIC_2/test.cpp

commit 08b4e950e26a03a65a530425912440931ebe2195
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 14 18:43:16 2018 -0400

    CUDA ifdef wrapper fix.

Src/Base/AMReX_Device.cpp

commit 887029a32da87a8f3917a119cc0e6ac95c8b7d0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 13:58:10 2018 -0700

    explicitly use final override. makeHypre linop

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H

commit 729f866edaa63eb22b4f78fba1d515633090442b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 11:33:32 2018 -0700

    move getFluxes from MLMG to MLCellABecLap

Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 39368764212dbf082bf8ba8fb10aa27fea00774f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 10:52:32 2018 -0700

    add abstract MLCellABecLap class

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/Make.package

commit f560e2e1c7084ace63e48668a2e94ce1c1364598
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 09:28:54 2018 -0700

    fix typo

Src/Extern/HYPRE/AMReX_HABEC_2D.F90

commit 800520ffcbae0867abe6e04871666da777f85691
Merge: 6abf70666 9081c0836
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 13 23:45:13 2018 -0700

    Merge branch 'development' into marc/forkjoin_dev

commit 9081c0836c93cc6d8e957a7f9f65c9534bf98bcd
Author: Cy Chan <cychan@lbl.gov>
Date:   Thu Sep 13 23:10:50 2018 -0700

    added ForkJoin::set_task_output_file()
    enabled appending to task output files
    enabled changing task output files in the middle of tasks
    updates to MultiColor_C

OldTutorials/MultiColor_C/main.cpp
Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ParallelContext.cpp

commit 6abf70666957254eef4dfb293a55be7e27dbaa87
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 13 19:41:36 2018 -0700

    Make C_CellMG collectives Fork-Join friendly

Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp

commit 76c295b9d6f27d3729f0fdecaa4da4cf87320838
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 13 18:28:01 2018 -0700

    Add not-equal for BERec

Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCRec.cpp

commit db88a39487d7d82f357b2c33678d3e73b96bca3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 13 17:19:16 2018 -0700

    add use_petsc

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H
Src/Extern/PETSc/AMReX_PETSc.H
Src/Extern/PETSc/AMReX_PETSc.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/CellEB2/GNUmakefile
Tests/LinearSolvers/CellEB2/MyTest.H
Tests/LinearSolvers/CellEB2/MyTest.cpp

commit 53cf63c8f2ee5bbb89e43e5104f71a55c222d763
Merge: 42a912f6d 7d5d2a064
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 13 16:20:58 2018 -0700

    Merge branch 'development' into mlmg

commit 7d5d2a0648092f814a1d82d0c8fa3c7ebae62a2a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 13 16:20:38 2018 -0700

    fix a bug in test set up

Tests/LinearSolvers/CellEB2/mytest_f.F90

commit b08840c7355f50f6e5b11fc84ab21ce67b780dca
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Sep 13 19:08:01 2018 -0400

    script and input adjustments

Tutorials/GPU/ElectromagneticPIC/summitdev.sh
Tutorials/GPU/HeatEquation_EX0_C/Exec/GNUmakefile
Tutorials/GPU/HeatEquation_EX0_C/Exec/inputs_3d
Tutorials/GPU/HeatEquation_EX0_C/Exec/run.script
Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script

commit 9e13a75c3fa55756919edb91a232462579b47633
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Sep 13 19:00:14 2018 -0400

    Addition of non-sync cudaMemcpy wrappers.

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit fff0bcf0df12e46119744fd628be33c911310d17
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Sep 13 18:51:52 2018 -0400

    Additional Device::synch

Src/Base/AMReX_FabArrayCommI.H

commit 47e8febfbe1f94c1b3dc4a2fea0fd06b15acbdf3
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Sep 13 18:51:15 2018 -0400

    CUDA wrapper adjustment.

Src/Base/AMReX_fort_mod.F90

commit 74e89954c1a6fd97ecd97ce12e466191bb19a833
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Sep 13 18:49:19 2018 -0400

    include fix

Src/Base/AMReX_CudaAllocators.H

commit 226c0b530b07b4305105ec5d72337fdc869f8c40
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Sep 13 18:47:24 2018 -0400

    amrex_malloc and amrex_free library fix.

Src/Base/AMReX_CUDA_Utility.cpp

commit 42a912f6de0375726a6eb4f7f26a36d31702e184
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 13 15:16:32 2018 -0700

    fix a few things

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H

commit 3c742ce8528b48486ac99d127cf1170083eb6237
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 13 13:04:21 2018 -0700

    some clean up

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit 54f2c1d315923d27359cb9107dfffb1094c12024
Merge: 765ee8812 cb4c49653
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 13 13:16:47 2018 -0700

    Merge remote-tracking branch 'origin/development' into marc/forkjoin_dev

commit cb4c4965357714e2104558b30e10090eb0136e31
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 13:08:50 2018 -0700

    tweak .travis.yml again...

.travis.yml

commit 4be5e4cda0c8356477f12c5c1046bef23bac7da7
Merge: 08423fb65 0f48f3d8f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 13:03:55 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 08423fb655f62b8e15155493ebdb8d531d766fee
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 13:03:44 2018 -0700

    assume 'yes' to queries since this is happening in a script

.travis.yml

commit 0f48f3d8f0b449464963b1f921f6490821a99e96
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 13 13:03:30 2018 -0700

    Add (another) multifab diff tool that includes grow cells

Tools/C_util/DiffMultiFab/GNUmakefile
Tools/C_util/DiffMultiFab/diffmultifab.cpp

commit c9748733bc2d6519a06d0d085797f1193b9f2077
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 12:55:18 2018 -0700

    try to use 3.6 instead of 3.4

.travis.yml
build_and_deploy.sh

commit 305dd23f6a32645b8e82b5162c7ae4b5a0fa24f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 13 12:54:40 2018 -0700

    pass EB b coefficients to hypre

Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_Hypre.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 490ec265a35da5b0a4983aab18ff8ba88340b3de
Merge: f35bc44c0 694f36947
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 12:30:46 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f35bc44c0d8c74c0a80dcf184bfc9aca3bf5aed7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 12:30:28 2018 -0700

    specifiy that we want python3 in the build_and_deploy script

build_and_deploy.sh

commit 3bdae5afa87c01a6755c00a30f65514f6560730d
Merge: f0c8a3f51 694f36947
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 13 12:27:03 2018 -0700

    Merge branch 'development' into mlmg

commit 694f369470dbc66a4b81e4224bf06c00cf0294cd
Merge: 158d6507a cac96c8e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 13 12:24:18 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 158d6507a992564c02dbc14450c534b37b636c16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 13 12:24:10 2018 -0700

    add a tutorial for geometry generation

Tutorials/EB/GeometryGeneration/GNUmakefile
Tutorials/EB/GeometryGeneration/Make.package
Tutorials/EB/GeometryGeneration/main.cpp

commit cac96c8e2b0a68a96183a78a72f69ae40af2d429
Merge: 9490c479e 4ac061964
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 12:18:39 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8752fe6d3a2acc1618e7bec02346ea227b08fba2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 13 12:18:36 2018 -0700

    add functions for writing plotifles with EB

Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_PlotFileUtil.cpp

commit 9490c479e34b6e6e7a7e3d622d071af8e1e7b3ca
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 12:18:22 2018 -0700

    try explicitly using pip3

.travis.yml

commit 4ac061964b57b3869f46a100779215b88dc21242
Merge: 648a451c5 9af05c8b4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 12:03:13 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 648a451c508b771abae0e2c0012b01e3f54b461a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 12:02:54 2018 -0700

    turn on TINY_PROFILING

Tests/HDF5Benchmark/GNUmakefile

commit b82a57fc6e309521fcfee3ead70f283b0c79136d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 12:02:43 2018 -0700

    also add the native write plot file to the benchmark

Tests/HDF5Benchmark/main.cpp

commit 9af05c8b48fd0d9da59fe4848576f9605c6ec948
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 11:28:06 2018 -0700

    tweak travis.yml again

.travis.yml

commit 87e26603e9f7349f36ecba288bab639faa7836e7
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Thu Sep 13 13:27:00 2018 -0500

    add short comment and cleanup

Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp

commit 5be85d84a77bd17e72683507c45eacb72806e43c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 11:14:05 2018 -0700

    switch to using python 3 with travis

.travis.yml

commit 67a21df1345eb29e2217f639746a0276cd8b668b
Merge: ef6847645 a117dcb32
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 11:06:23 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ef684764583043db2e8df29093f68cbb67e6c0df
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 11:06:12 2018 -0700

    change python version in travis config

.travis.yml

commit 94696a5eaa856a7a57ba8ca9c91a56460f462978
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Thu Sep 13 12:59:56 2018 -0500

    Changes for per-FAB fluxregister use from Fortran
    
    Added optional argument to amrex_fluxregister_fineadd_1fab for
    requesting zeroing of the coresponding fluxregister data storage
    before flux data from the current fab are added.
    
    Added FineSetVal method to FluxRegister class.

Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90

commit a117dcb32631725a4856a660a0ab4a36905d50e2
Merge: 504ea405e 94f19e3ea
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 10:52:55 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 504ea405e48bbe2d27bc2110cfb93ee0c7fec57c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 13 10:52:43 2018 -0700

    add an HDF5 IO Benchmark test, based on the writer fron Nyx

Tests/HDF5Benchmark/GNUmakefile
Tests/HDF5Benchmark/Make.package
Tests/HDF5Benchmark/WritePlotfileHDF5.H
Tests/HDF5Benchmark/WritePlotfileHDF5.cpp
Tests/HDF5Benchmark/inputs
Tests/HDF5Benchmark/main.cpp

commit 5b11781aa3cfa70568d06b2c7a67119426e4dabb
Merge: 1b6d906fd 94f19e3ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 13 09:26:39 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 94f19e3eaba8fed0c871287de277e7d8c9a4bcdd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 13 09:20:41 2018 -0700

    CylinderIF: fix sign bug and clean up

Src/EB/AMReX_EB2.cpp
Src/EB/AMReX_EB2_IF_Cylinder.H

commit 1b6d906fdb8042328399c1b716881a9d68c1d95a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 12 21:16:15 2018 -0700

    add Difference and Extrusion for EB

Src/Base/AMReX_Array.H
Src/EB/AMReX_EB2_IF.H
Src/EB/AMReX_EB2_IF_Complement.H
Src/EB/AMReX_EB2_IF_Difference.H
Src/EB/AMReX_EB2_IF_Extrusion.H
Src/EB/AMReX_EB2_IF_Lathe.H
Src/EB/AMReX_EB2_IF_Rotation.H
Src/EB/AMReX_EB2_IF_Scale.H
Src/EB/CMakeLists.txt
Src/EB/Make.package
Tests/LinearSolvers/CellEB/initEB.cpp
Tests/LinearSolvers/CellEB2/initEB.cpp
Tutorials/EB/CNS/Source/CNS_init_eb2.cpp
Tutorials/EB/MacProj/initEB.cpp

commit 26815f1868c9eeb93fe348f216366a52a9443073
Merge: a2ca8fdaa b5192cc64
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Sep 12 21:07:32 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit a2ca8fdaaa8e69eea54f74d65ad3801e05a0e79f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Sep 12 21:07:29 2018 -0700

    added infinite CylinderIF by overloading constructor

Src/EB/AMReX_EB2.cpp
Src/EB/AMReX_EB2_IF_Cylinder.H

commit b5192cc641da8bd0f3cb84e2e421eeae424005c4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 12 13:58:39 2018 -0700

    always have at least ref_ratio ghost cells for the fine levels in AssignDensity

Src/AmrCore/AMReX_AmrParticles.H

commit 3df57fd5df9ced3d74918dfc628ef14e42f1e5bd
Merge: c025461cd 9be9dbdc5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 12 12:33:34 2018 -0700

    merging

commit c025461cdb5a40c801e1c54737f683a5a87646a5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 12 12:25:54 2018 -0700

    allow callers to pass in an ngrow parameter into AssignDensity

Src/AmrCore/AMReX_AmrParticles.H
Src/Particle/AMReX_Particles.H

commit 0667aaa150e375ea0a7660af740978b352f9940d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Sep 12 13:46:42 2018 -0400

    Add CUDA initialization output

Src/Base/AMReX_Device.cpp

commit f0c8a3f51e5532e70f40334efd44ebd388e3419c
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Wed Sep 12 10:28:43 2018 -0700

    Hypre Dirichlet main routines compile, but need to get the eb_b multifab.

Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit a1ff7fde3720992374d5fe3c871c3a3d4366d2a1
Merge: ac636be78 b6e7c9a3f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Sep 12 12:56:39 2018 -0400

    Merge branch 'development' into gpu

commit 9be9dbdc52fa40bf431545fa4826c71447297b8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 12 09:23:38 2018 -0700

    because C++ has double pow(double base, int iexp), there is no reason we don't use it

Src/EB/AMReX_EB2_IF_Polynomial.H

commit cd0f7c5c5df63b11e92d29fe68b2569d58a7992c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 12 08:57:26 2018 -0700

    more ParallelDescriptor::second -> amrex::second

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AuxBoundaryData.cpp
Src/Base/AMReX_VisMF.cpp
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_TracerParticles.cpp
Tutorials/Amr/Advection_AmrCore/Source/main.cpp
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Tutorials/Amr/Advection_AmrLevel/Source/main.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX3_C/Source/main.cpp
Tutorials/CVODE/EX1/main.cpp
Tutorials/CVODE/EX2/main.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/main.cpp

commit a7192fababe911204e0e9b41729d3a1c26af9b67
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 12 08:21:05 2018 -0700

    ParallelDescriptor::second -> amrex::second in profiler

Src/Base/AMReX_BLProfiler.cpp

commit 88a9f4406d13763401e5e3b619d5977a0338beea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 12 08:17:36 2018 -0700

    update doc

Docs/sphinx_documentation/source/GettingStarted.rst

commit 38f09b7c31d5b5a0f63c5b6397740ae1f1cf9421
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 12 08:08:56 2018 -0700

    turn on verbosity by default

Src/Base/AMReX.cpp
Src/Base/AMReX_Utility.cpp

commit 80027298c8a5076f0b17c492cdb1318aa8d3228d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 11 22:10:02 2018 -0700

    use double in tiny profiler

Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp

commit dc719276cb06b3d2950c37198017e99866000732
Merge: 272502a25 8a1c247e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 11 21:07:54 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 272502a2520b00f5bb26330928ee15332e5ac992
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 11 20:54:01 2018 -0700

    double precision -> real(amrex_real)

Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Prob.f90
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_2d/slope_2d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/slope_3d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90

commit ac636be78ec8e492f9878a2567c03ac9e77152a8
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Sep 11 23:33:21 2018 -0400

    Fix string concatenation

Src/Base/AMReX_Device.cpp

commit edf541c301c70579ca77bb018adcb8999e605570
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Sep 11 16:04:03 2018 -0700

    Still working on Hypre EB Dirichlet. Some more compilation errors to work out.

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_Hypre.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H

commit 8a1c247e2d1c50ac9ed4e4955eb05220d6c19de9
Merge: 1d6cefea0 3ed45f021
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Sep 11 15:04:23 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 1d6cefea03f3bd00a53e21cceaa466d6b9425d64
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Sep 11 15:04:13 2018 -0700

    elaborate on gcc and cmake

Docs/sphinx_documentation/source/BuildingAMReX.rst
Docs/sphinx_documentation/source/Visualization.rst

commit 3ed45f021a41ba598b9632906743739c7c551fa6
Merge: 4ff794c13 a442ae307
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 11 14:37:00 2018 -0700

    Merge pull request #310 from kweide/development
    
    Fortran build routine for non-owning fab

commit a442ae30741a7d992b58f6d97bc140505df565e8
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Tue Sep 11 16:34:23 2018 -0500

    Use amrex_error not ERROR STOP

Src/F_Interfaces/Base/AMReX_fab_mod.F90

commit 4ff794c134555354e5d181ca5e27850c45156249
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Sep 11 14:19:46 2018 -0700

    rephrase homebrew install isntructions slightly

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit c6cd321bd93512fb29fdf73e10533ccdcc9d6062
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Sep 11 14:10:18 2018 -0700

    elaborate more on gcc install for macOS

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit aa14dd880da135357c086606a3ecc4814cbfa2f6
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Sep 11 14:05:15 2018 -0700

    elaborate more on Amrvis install for macOS

Docs/sphinx_documentation/source/Visualization.rst

commit 35a4e9585cb693453b4dbd7396ad57a73bacb618
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Sep 11 13:53:37 2018 -0700

    update docs to give more info about building on macOS

Docs/sphinx_documentation/source/BuildingAMReX.rst
Docs/sphinx_documentation/source/GettingStarted.rst
Docs/sphinx_documentation/source/Visualization.rst

commit 7c6c11bb79ae85cc2b8b559d5f895db3777205c4
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Tue Sep 11 13:27:17 2018 -0500

    rename a Fortran routine, add argument error checking
    
    Changed specific name from amrex_fab_build to amrex_fab_build_alloc.
    Added some argument size error checking, subject to ifdef AMREX_DEBUG;
    uses ERROR STOP.

Src/F_Interfaces/Base/AMReX_fab_mod.F90

commit 1c51ec0df435c3e4c12fe317375244a86ffac472
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 11 11:20:16 2018 -0700

    StateData: use unique_ptr internally; declare all five explicitly

Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp

commit 54fdc8b923f5baa38d0f22795a530c879ef1e842
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 11 11:11:45 2018 -0700

    fix AssignDensity for ref_ratio != 2

Src/AmrCore/AMReX_AmrParticles.H

commit 38bb56457c82096fae6c141ea845124fedb664e2
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Tue Sep 11 09:25:12 2018 -0500

    Add amrex_fab_build_install
    
    New specific subroutine that builds a non-owning (Fortran) FAB
    from a given (Fortran) data pointer.

Src/F_Interfaces/Base/AMReX_fab_mod.F90

commit 2d43c56fffd550061dd96955bd9c6c2ccf677cdb
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Sep 11 01:43:07 2018 -0700

    fix a synchronization bug

Src/AmrTask/rts_impls/Perilla/Barrier.H
Src/AmrTask/rts_impls/Perilla/Barrier.cpp
Src/AmrTask/rts_impls/Perilla/PackageQueue.H
Src/AmrTask/rts_impls/Perilla/Perilla.cpp
Src/AmrTask/rts_impls/Perilla/PerillaConfig.H
Src/AmrTask/rts_impls/Perilla/RegionGraph.H
Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp
Src/AmrTask/rts_impls/Perilla/RegionQueue.H
Src/AmrTask/rts_impls/Perilla/RegionQueue.cpp
Src/AmrTask/rts_impls/Perilla/WorkerThread.H
Src/AmrTask/rts_impls/Perilla/WorkerThread.cpp
Src/AmrTask/rts_impls/Perilla_omp/Perilla.cpp
Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.H
Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.cpp
Src/AmrTask/rts_impls/Perilla_upc++/Barrier.H
Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp
Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.omp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.pthreads
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.upcxx.pthreads
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp

commit 2b3dd45e332cae694de1f4d6aa8a506927841fea
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Mon Sep 10 19:56:01 2018 -0500

    The 1-FAB fineadd now takes a 0-based boxno (aka gridIdx) argument
    
    Don't convert from a 1-based to a zero-based index.
    The new behavior is more consistent with other multifab functions in
    the Fortran interface that either take or return a grid_index.

Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90

commit 497c421b669d3fd532c1c6a4c1896428c783b2a0
Merge: 1b89a5016 33c0aede0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Sep 10 10:33:59 2018 -0700

    Merge pull request #309 from AMReX-Codes/endian
    
    use __BYTE_ORDER__ to detect endianess

commit 1b89a5016ac44d4b056669339dd9f8d60d241795
Merge: 946ba2856 8568150e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 10 10:30:10 2018 -0700

    Merge branch 'pr-308' into development

commit 946ba2856ff1c86a20da406a838f430e7794fc0a
Merge: b6e7c9a3f 4a97e1adf
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Sep 10 10:30:00 2018 -0700

    Merge pull request #308 from kweide/development
    
    Add per-fab version of FineAdd to fluxregister's Fortran interface

commit 8568150e63b4948f4749b6a0ebf57bd91a70c496
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 10 10:29:15 2018 -0700

    cleanup

Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp

commit 33c0aede0ad5a0665a82d7e960d5f3bbb3f9fe85
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 10 09:45:19 2018 -0700

    use __BYTE_ORDER__ to detect endianess

Src/Base/AMReX_FPC.cpp
Src/F_BaseLib/fabio_c.c

commit a5b0908e1f3e28e26f4c12799ca9fd7b75b103d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Sep 9 10:05:31 2018 -0400

    remove ref to interface block

Tools/F_scripts/gpu_fortran.py

commit 376ffe28c7a26e3e3a0be9617e4b9f231d814c37
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Sep 9 09:58:16 2018 -0400

    Update comments for gpu_fortran.py

Tools/F_scripts/gpu_fortran.py

commit 9803fde5adc7a248cafd226d389a8d3cc9f5728d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sun Sep 9 00:53:00 2018 -0400

    Add NVML to Summit, Sierra.

Tools/GNUMake/sites/Make.llnl
Tools/GNUMake/sites/Make.olcf

commit b8d2ab388a347fec687ef008baa60e3410b87d1f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sun Sep 9 00:47:25 2018 -0400

    String comparison fix.

Src/Base/AMReX_Device.cpp

commit b6e7c9a3fc03601e9ea1267aa074c45880e45e21
Merge: fc3b1ef98 9c8f9ecf6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 8 20:50:54 2018 -0700

    Merge branch 'streampos' into development

commit fc3b1ef98ae13150e5986c9affd0cc871ade9d17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 8 18:57:21 2018 -0700

    minor cleanup

Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp
Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp

commit 9e460548db6a5791519b078078f2fb0ba50ca81d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 8 18:43:56 2018 -0700

    add ErrorHandler

Src/Base/AMReX.H
Src/Base/AMReX.cpp

commit b6b402b005434da02a52b9933715018eca6e5422
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 8 18:06:10 2018 -0700

    clean up Print

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit eb1971c42fd363e4a51ffe784cf7fbef69c2e5d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 8 17:44:35 2018 -0700

    rm unused Serialize/UnSerialize functions

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit 7caa763a3277ae90c19bf836b2de7e5973e5ce31
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 8 17:30:18 2018 -0700

    change tolerance of nodal Poisson solver test

Tutorials/LinearSolvers/NodalPoisson/MyTest.H
Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp

commit ff7c6ce78169ed262d434163e3d2dc027c688b44
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 8 17:28:48 2018 -0700

    add amrex::SetVerbose function

Src/Base/AMReX.H
Src/Base/AMReX.cpp

commit 4a9a07fd16b0f8421cfc689d942a55642dc4d45c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 8 11:41:17 2018 -0700

    Nodal Poisson solver tutorial

Tutorials/LinearSolvers/NodalPoisson/GNUmakefile
Tutorials/LinearSolvers/NodalPoisson/Make.package
Tutorials/LinearSolvers/NodalPoisson/MyTest.H
Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp
Tutorials/LinearSolvers/NodalPoisson/MyTest_F.H
Tutorials/LinearSolvers/NodalPoisson/init_prob.F90
Tutorials/LinearSolvers/NodalPoisson/main.cpp

commit 0dbfbb6db95bcdb19e74609f42d05d4f0839f479
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Sep 8 11:20:02 2018 -0700

    Add warning if oversubscribing GPUs

Src/Base/AMReX_Device.cpp

commit c9da4bc1bc040eb786edd0dda46f888a83c774a1
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Sep 8 10:39:45 2018 -0700

    Simplify and make more robust the logic for mapping ranks to GPUs

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 4e7e43a162f027a9ca566f1a0d69bc3e2942505c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Sep 8 10:39:21 2018 -0700

    Provide GPU configuration on known systems

Tools/GNUMake/Make.defs
Tools/GNUMake/sites/Make.llnl
Tools/GNUMake/sites/Make.olcf

commit 2727dccb4ad116be2cab494c511fecb50c94d094
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Sep 8 07:03:54 2018 -0700

    Move Sierra to the rolling MPI release

Tools/GNUMake/sites/Make.llnl

commit 8bb157fff8433368b9104ffbd83fa3a189f34c66
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Sep 8 07:03:45 2018 -0700

    Add NVML to Summit, Sierra

Tools/GNUMake/sites/Make.llnl
Tools/GNUMake/sites/Make.olcf

commit 47f72ef3af5e0e61d7dd88817cb09f6cc4e22eef
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Sep 8 07:02:23 2018 -0700

    Fix string comparison issue

Src/Base/AMReX_Device.cpp

commit e229e2c2cf0c2fd09532aad5d16eb4bd14341fb9
Merge: 20d09285f 78d4e0d72
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 7 22:26:08 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 20d09285f1ce2aada904ba2ef3924d8281753901
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 7 22:25:54 2018 -0700

    fix due to change of average_center_to_face

Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp

commit 78d4e0d7242717c09fa67c3c779f5f3358ad2f0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 7 22:23:13 2018 -0700

    fix new typo

Src/Base/AMReX_mempool_mod.F90

commit a6e632c34e3ea7a3d2df0645fcdc97dea2a02ca0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 7 22:11:42 2018 -0700

    use pointer bound remapping to avoid an intel compiler bug

Src/Base/AMReX_mempool_mod.F90
Src/Base/BL_mempool_f.f90
Src/Base/CMakeLists.txt
Src/Base/GPackage.mak
Src/Base/Make.package

commit d6f295c941890949e22f702bb0709935c7f7d4eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 7 15:06:04 2018 -0700

    remove duplication

Src/Base/AMReX_MultiFabUtil.cpp

commit 9103fd1fe7ab33b49cf3aaddab02ae20da165e7a
Merge: cda692808 518a6d2bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 7 14:06:35 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cda692808a71a00251d9bf92463504098cd7d93d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 7 14:05:48 2018 -0700

    avoid calling popen when intel is used with omp

Src/Base/AMReX.cpp
Src/Base/AMReX_BLBackTrace.cpp

commit 518a6d2bb6bea387b0c0e3688e6503fd4f673d5c
Merge: 2f3091ff2 d48662d16
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 7 12:11:46 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d48662d169a2cd4f1a534141e4dd1e0a5717a16e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Sep 7 12:11:53 2018 -0700

    Add ome more conversion subroutine for vector of array of ptrs

Src/Base/AMReX_Array.H
Src/Base/AMReX_Vector.H

commit 2f3091ff23d1e798ac0caa78261726d000a97c17
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 7 12:11:30 2018 -0700

    only allow this version of GetArrOfPtrs to be chosen if T has a FABType

Src/Base/AMReX_Array.H

commit 189078e82e665f94314ef8d1e74a1155731fe5fd
Merge: bf3cb995c 6bab5d322
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Sep 7 15:06:45 2018 -0400

    Merge remote-tracking branch 'origin/development' into gpu-mm

commit 765ee88128e0f805e86be53e3aca9a0333dc59f7
Merge: 97dbf2b3b 6bab5d322
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Sep 7 11:15:10 2018 -0700

    Merge branch 'development' into marc/forkjoin_dev

commit 6bab5d322b1cfc34091ea6d46ebd11daebb90edf
Merge: 18888cdbb 25e12c549
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Sep 7 11:12:36 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 18888cdbb723a3a904d190d0bbe95fdba4a5741c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Sep 7 11:12:31 2018 -0700

    Add signature for average_cellcenter_to_face()

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 97dbf2b3b30461c27286e29086b8b9b664a66a94
Merge: 6d38b7022 25e12c549
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 6 23:35:38 2018 -0700

    Merge branch 'development' into marc/forkjoin_dev

commit 6d38b7022619e2be6ebaf5a9563a252536553eaf
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 6 23:34:56 2018 -0700

    Add profiling info for ForkJoin overhead

Src/Base/AMReX_ForkJoin.cpp

commit 25e12c549984702cf7bf18a282e22c36aee5ce6b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 6 17:24:02 2018 -0700

    add additional constructor for MakeMFIter that knows about dynamic scheduling.

Src/Particle/AMReX_Particles.H

commit e8988c3ce7801e2edc06bae933035f0f87387e1f
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Sep 6 16:00:18 2018 -0700

    More work on Dirichlet Hypre, not finished yet.

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_Hypre.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit 4a97e1adfacc3ff40f9bb9566d0e2e8441b4baeb
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Thu Sep 6 14:24:33 2018 -0500

    add amrex_fluxregister_fineadd_1fab implementation
    
    This is a fineadd method for amrex_fluxregister that adds
    fluxes from only one fab to a fluxregister.
    Currently an amrex_fab has to be constructed by the caller
    and passed, as well as a box number (grid_index, more or less).

Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90

commit e55a70c3d4f320c6c9f013be18f01967f97a961a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 6 09:29:06 2018 -0700

    use factory to delete FAB

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabFactory.H
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp

commit bf3cb995cb6cf0bafa7d7e65f05791a1a6815b16
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Sep 6 05:29:40 2018 -0400

    Threading strategy fix.

Src/Base/AMReX_BaseFab.cpp

commit b0db9113eb67d7ec05ed19052956014f6507c50d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 5 21:27:05 2018 -0700

    const_cast for MPI-2

Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_ParallelReduce.H

commit da8f86e068d7395f014bdfcaaa93983016a89c84
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Sep 5 17:38:25 2018 -0700

    Add signature for GetArrOfConstPtrs()

Src/Base/AMReX_Array.H

commit e2e7973d73101f226957d7165dc25938a331aba5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 5 16:58:23 2018 -0700

    remove vitual from BaseFab

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_IArrayBox.H
Src/EB/AMReX_EBAmrUtil.cpp
Src/EB/AMReX_EBFArrayBox.H
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBInterpolater.cpp
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_MultiCutFab.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/fortran/CNS_nd.F90

commit 3fec85546799f531714fac8ba3869e4030395662
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Wed Sep 5 16:00:10 2018 -0700

    Changed Makefile to reflect location in amrex download

Tests/LinearSolvers/CellEB2/GNUmakefile

commit 96634380423f2df196b85b91fe96f1cc4109ea74
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Wed Sep 5 15:55:59 2018 -0700

    More progress on Hypre EB-dirichlet. Bogus compiler flags are included as to not break anything

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit f6a412b1b93c2394f81dd780852eced063facb3d
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Wed Sep 5 15:37:27 2018 -0700

    restore missing endif

Tools/GNUMake/Make.defs

commit bed34b12ecfc9fdce32f1b1ef4a3491a37002849
Merge: 2d6ef4f3a 5a997fec0
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Wed Sep 5 15:33:53 2018 -0700

    merge development branch and resolve conflict

commit 2d6ef4f3a57a831550dcd7c27b730e9b2d535175
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Wed Sep 5 15:28:46 2018 -0700

    add build system var for ascent

Tools/GNUMake/Make.defs

commit 8d24b366e297457f81b9875a71cda8792eb0034d
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Wed Sep 5 15:22:24 2018 -0700

    move blueprint support

Src/Base/Make.package
Src/Extern/Conduit/AMReX_Conduit_Blueprint.H
Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp
Src/Extern/Conduit/Make.package
Tools/GNUMake/Make.defs
Tools/GNUMake/packages/Make.ascent
Tools/GNUMake/packages/Make.conduit
Tutorials/Blueprint/AssignMultiLevelDensity/GNUmakefile
Tutorials/Blueprint/HeatEquation_EX1_C/Exec/GNUmakefile

commit 5a997fec0db563b25a6dbc83910d3cf0204cfae1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 5 14:16:21 2018 -0700

    rm SPMD

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_SPMD.H
Src/Base/AMReX_SPMD.cpp
Src/Base/AMReX_SPMDI.H
Src/Base/AMReX_parstream.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 481e212e678637272ba6d2b72b5ef6ff8b44abb1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 5 13:55:04 2018 -0700

    simplification

Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp

commit d7ec55af5730ff8df8121f75376d25879fa8fac4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 5 13:13:03 2018 -0700

    pass by value so that it support both rvalue and lvalue

Src/Base/AMReX_ParallelReduce.H

commit e470eec8b40eaa45db63b85737b3d84112ac880f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Sep 5 15:24:15 2018 -0400

    Mistype.

Src/Base/AMReX_BaseFab.cpp

commit d41a2c0fbea1f6f6b2778eeec9408e0d4ddb166d
Merge: 318ff60a0 1d010e28f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Sep 5 15:19:23 2018 -0400

    Merge remote-tracking branch 'origin/development' into gpu-mm
    
    Conflicts:
            Src/Base/AMReX_ArrayLim.H
            Src/Particle/AMReX_ParticleContainerI.H

commit 318ff60a06288d1ba2bfa3ccfbe45131aa59ad59
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Sep 5 15:03:45 2018 -0400

    FillBoundary rewritten onto GPUs.

Src/Base/AMReX_FabArrayCommI.H

commit 476cc89442041928d78477241eb8e2086fa7190c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Sep 5 14:48:40 2018 -0400

    Threading strategy for copy, copyTo and copyFrom.

Src/Base/AMReX_BaseFab.cpp

commit 4269eef0d683ea2d4960a12ab2bcbb2506f14a57
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Sep 5 14:27:16 2018 -0400

    Changes to GPU data class thingee.

Tutorials/GPU/Test/main.cpp

commit 70d46ab97989eaa6b283174f8640f3af9e0f3de0
Author: Steven <sireeves@ucsc.edu>
Date:   Wed Sep 5 10:17:50 2018 -0700

    Forgot this one

Src/Extern/HYPRE/AMReX_Hypre.cpp

commit 55d374bfa6a7f9a25fc9178324dd913fe81eba18
Author: Steven <sireeves@ucsc.edu>
Date:   Wed Sep 5 10:16:42 2018 -0700

    Hypre Dirichlet Additions, not complete

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_Hypre.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H

commit 9c8f9ecf6207ff7c0f025f9a816f2fba703605cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 5 10:10:26 2018 -0700

    try to fix portablity issue of std::streampos

Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_VisMF.cpp

commit ba9c6ae77ad38e4fa586607c63a297c13007599a
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Wed Sep 5 09:59:37 2018 -0700

    move Blueprint examples from Test to Tutorials

Tutorials/Blueprint/AssignMultiLevelDensity/GNUmakefile
Tutorials/Blueprint/AssignMultiLevelDensity/Make.package
Tutorials/Blueprint/AssignMultiLevelDensity/inputs
Tutorials/Blueprint/AssignMultiLevelDensity/main.cpp
Tutorials/Blueprint/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/Blueprint/HeatEquation_EX1_C/Exec/inputs_2d
Tutorials/Blueprint/HeatEquation_EX1_C/Exec/inputs_3d
Tutorials/Blueprint/HeatEquation_EX1_C/Source/Make.package
Tutorials/Blueprint/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/Blueprint/HeatEquation_EX1_C/Source/advance_2d.f90
Tutorials/Blueprint/HeatEquation_EX1_C/Source/advance_3d.f90
Tutorials/Blueprint/HeatEquation_EX1_C/Source/init_phi_2d.f90
Tutorials/Blueprint/HeatEquation_EX1_C/Source/init_phi_3d.f90
Tutorials/Blueprint/HeatEquation_EX1_C/Source/main.cpp
Tutorials/Blueprint/HeatEquation_EX1_C/Source/myfunc.H
Tutorials/Blueprint/HeatEquation_EX1_C/Source/myfunc_F.H
Tutorials/Blueprint/README.txt

commit 411209a75be742b486ac78a5e4291671374be8dd
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Sep 5 12:31:59 2018 -0400

    Fortran functions for amrex_gpu_malloc and amrex_gpu_free.

Src/Base/AMReX_fort_mod.F90

commit ce480ee80da834c5a2f2b6907dd0d99e3a824f81
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Sep 5 12:31:24 2018 -0400

    Initial attempt at Box+component threading strategy. Still need to account for very large kernels (thread > max number of threads).

Src/Base/AMReX_CUDA_Utility.H
Src/Base/AMReX_CUDA_Utility.cpp
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_Managed.H

commit 614e36ef4a7f7e0c2b11cd03814c8a5d1e23b716
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Sep 5 12:19:56 2018 -0400

    amrex_gpu_alloc, amrex_gpu_free and cudaMemCpy wrappers.

Src/Base/AMReX_CUDA_Utility.H
Src/Base/AMReX_CUDA_Utility.cpp
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit c3ca0cc94b7c8748ead180051f8c91cdc701e84b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Sep 5 12:08:19 2018 -0400

    Additional Box device functions.

Src/Base/AMReX_Box.H

commit 9b2e953f40eb55b84b9d084d0ac96e61fe611ca8
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Sep 5 12:07:36 2018 -0400

    Make main FillBoundary function public to allow kernels.

Src/Base/AMReX_FabArray.H

commit c15487420a0595c0841cf7341632ad2d9783bf95
Author: Steven <sireeves@ucsc.edu>
Date:   Wed Sep 5 07:48:59 2018 -0700

    EB Dirichlet Hypre Started. Going through Dirichlet MLMG and adapting it to the Hypre format.

Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_Hypre.cpp

commit 8bcb1fd7e53349b5b6aeff50cf931514c0abc440
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Sep 5 02:37:21 2018 -0400

    Add error checking to BArena.

Src/Base/AMReX_BArena.cpp

commit 1d010e28f59331ea45ab5e9d961059e938327c52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 4 17:17:47 2018 -0700

    add a number of BL_NO_FORTs so that part of Base can be built without Fortran

Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_MFCopyDescriptor.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_ParmParse.cpp
Src/Base/Make.package

commit 9d22e23402af27f2ea6356f67d7a64f59e192ed6
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Sep 4 11:58:18 2018 -0700

    CMake:some modification to comply with SPACK requirements

Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_Utils.cmake
Tools/CMake/MakefileConfig.export.in
Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt

commit c1052a0d749e6b9ed5c64b7ad41443a20e635e2c
Merge: e3cd0b07d 2f7682928
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 4 12:31:47 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit e3cd0b07d04691c9ed6a1fff25d541fc1c0dde25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 4 11:30:50 2018 -0700

    MLMG: cell-centered fluxes

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_3d.F90
Src/EB/AMReX_EBMultiFabUtil_F.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 2f76829284d5b68017cb55e4ad5f0c2206184c7e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Sep 4 11:58:18 2018 -0700

    CMake:some modification to comply with SPACK requirements

Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_Utils.cmake
Tools/CMake/MakefileConfig.export.in
Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt

commit 90f948159844ec45b9b2f66eaf77e65d584bf133
Merge: 75f3abe5f 4b2542dc1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 13:54:44 2018 -0700

    Merge branch 'mlmg' into development

commit 4b2542dc17b0580d104d9934d44a55da2f2fa154
Merge: f131bf762 0cf77fb99
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 13:54:24 2018 -0700

    Merge branch 'petsc' into mlmg

commit 0cf77fb9936052f7bb220bf2660e3d8acb16c629
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 13:53:28 2018 -0700

    follow convention in Extern/HYPRE

Src/Extern/PETSc/AMReX_PETSc.cpp

commit 00bdbc57a27f093f4e7cf1484bc797a58e5f5f5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 13:44:04 2018 -0700

    set one row at a time

Src/Extern/PETSc/AMReX_PETSc.cpp

commit db93a614aa26e66a834ed9ec211e01d9272ea26e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 13:34:44 2018 -0700

    white space

Src/Extern/PETSc/AMReX_PETSc.cpp

commit 2ce5087db4dae366c6d2f977ae4550dfb2c847ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 13:32:48 2018 -0700

    Not sure we can assume these petsc calls are omp thread safe.

Src/Extern/PETSc/AMReX_PETSc.cpp

commit e85e157faac36f01a757faea43bab2aa3f1cb3b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 13:30:01 2018 -0700

    adjust petsc preallocatoin. (note that the estimate is for per row, not for all rows in a process.)

Src/Extern/PETSc/AMReX_PETSc.cpp

commit bc27d78e441215d3975386c601ce7929702205bf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 12:48:19 2018 -0700

    static assert hypre and petsc have the same int

Src/Extern/PETSc/AMReX_PETSc.cpp

commit fc348441458cdc6bb95ccd04ebfee72ae67a45ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 12:43:40 2018 -0700

    comment out KSPSetFromOptions

Src/Extern/PETSc/AMReX_PETSc.cpp

commit f131bf762b6a32d0b7bb465d810839ae13acb0fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 12:32:47 2018 -0700

    update MLPoisson:FFlux

Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 75f3abe5f814140d1290a600f8354f4b2f4667aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 12:32:47 2018 -0700

    update MLPoisson:FFlux

Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit acf1898d1874debdd3c7498c889de54962f5e5d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 12:33:09 2018 -0700

    remove HYPRE_DIR/include from petsc

Tools/GNUMake/packages/Make.petsc

commit 0c3257d20711b7c3562e3570d8f4ebe2300ecc48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 12:32:47 2018 -0700

    update MLPoisson:FFlux

Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 0a7d68dece718240a0adb93c3d877c6d83fcc48f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 12:16:59 2018 -0700

    fix link to petsc on NERSC

Tests/LinearSolvers/CellEB/MyTest.cpp
Tools/GNUMake/packages/Make.petsc

commit b4eca770fa587439bfdb09d087535aae4b6c6c68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 12:10:15 2018 -0700

    the link flags for various petsc stuff have to be inside ifdef otherwise it won't compile on say NERSC because they want different flags

Tests/LinearSolvers/CellEB/inputs
Tools/GNUMake/packages/Make.hypre
Tools/GNUMake/packages/Make.petsc

commit cdd9899d02635a306ae92b1fb54018aef4f49494
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 11:51:42 2018 -0700

    remove hardwired path to petsc

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/CellEB/GNUmakefile

commit 42cbd1280d90b0bcddcc249de5f6c31a6ebbe38f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 11:43:50 2018 -0700

    use forward declaration

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Tutorials/EB/MacProj/GNUmakefile

commit 61ded76626446e35eca6748ce9922ba339758b44
Merge: 6994e0510 999851d79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 09:40:40 2018 -0700

    Merge branch 'mlmg' into petsc

commit 999851d79d974ae543af2694804ca3a31e966114
Merge: 1d9197229 04969771e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 09:39:19 2018 -0700

    Merge branch 'development' into mlmg

commit 04969771ed55bde0b575bdc47c398e4dc0fef970
Merge: e66a346e7 9ffacd1de
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Sep 3 09:36:56 2018 -0700

    Merge pull request #270 from AMReX-Codes/forkjoin
    
    Forkjoin

commit 9ffacd1de2870ca1f0fcb0300dd2affb39c53607
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 09:35:53 2018 -0700

    move -> forward

Src/Base/AMReX_ParallelReduce.H

commit e66a346e7e96fb4bfd9200a05df249c57c758f11
Merge: 2716130d8 adb09f392
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 09:31:41 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit adb09f392c21e50d6e89adf437e5b65acf6f7200
Merge: 2aba10102 5ab4e1042
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 09:30:51 2018 -0700

    Merge branch 'master' into development

commit 5ab4e1042647e4429bf55027c73be306279bd45e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 3 09:29:50 2018 -0700

    update CHANGES

CHANGES

commit b4fc255bc85c3bcd98eee5c2c22c75c5482f1700
Merge: 782009df1 2aba10102
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 3 12:19:14 2018 -0400

    Merge branch 'development' into gpu

commit 782009df11c3113593794f8a2e7bb06851f25100
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 3 12:18:59 2018 -0400

    sync encodings

Tools/F_scripts/preprocess.py

commit 2aba10102e454558ea9a0d28e2959123ef0301b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 3 12:15:45 2018 -0400

    remove unneeded module

Tools/F_scripts/dep.py

commit 6580f739038a0ecc7a9d4549fe79f65933ab9d79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 3 12:13:50 2018 -0400

    split out preprocess like we do in GPU

Tools/F_scripts/dep.py
Tools/F_scripts/preprocess.py

commit 1359cb411c9fe92c22b56453d91760ea08b09c72
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Sep 3 11:56:16 2018 -0400

    Insert a device sync in CrseInit

Src/AmrCore/AMReX_FluxRegister.cpp

commit 1d91972293fd0296cbe21717725a793f80c47af4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 2 11:30:56 2018 -0700

    MLMG: clean up flux and grad

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit ef7c79c8e24511b3431de463d769c169dd25c37b
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Sun Sep 2 00:44:44 2018 -0500

    flailing around

Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90

commit e23d0acf51aef8fe1ba289c441deea24f3492825
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Sep 1 19:28:23 2018 -0400

    Don't do MFIter reductions if not executing on device

Src/Base/AMReX_MFIter.cpp

commit 2e4c9ae01def7e7036a6ea1bf2b329c48f050f30
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Sep 1 19:28:09 2018 -0400

    Write amrex_max, etc. device versions by hand

Src/Base/AMReX_fort_mod.F90

commit 9566a0d0d857eb90dc301656ef16df9c9aab0879
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Sep 1 19:27:37 2018 -0400

    Start in device launch region

Src/Base/AMReX_Device.cpp

commit 1828b46a33f7e87a3ab7205c5ccafca6d11307f3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Sep 1 18:34:27 2018 -0400

    Add an option to disable the device offload

Tools/F_scripts/write_cuda_headers.py

commit bbbd997dd3c8a2bac0552340e8fc7e1d2e11e36c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Sep 1 18:17:36 2018 -0400

    Write out the host function signature

Tools/F_scripts/write_cuda_headers.py

commit 75c469c5b46e9ede58f325c63bb9eac0b51d81b5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Sep 1 18:04:31 2018 -0400

    Add a device synchronize in debug mode

Tools/F_scripts/write_cuda_headers.py

commit da171a0e75318528a9c23b13f38bf1d0db9ebee1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 1 14:21:33 2018 -0700

    implement the locatio option for grad phi

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit d553d266c7fdc776742f147b2641aad19ed3640a
Merge: abc62bc09 5e40c6f61
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Sat Sep 1 16:08:55 2018 -0500

    Merge branch 'development' of github.com:kweide/amrex into kw-development

commit f205aa81db6fde73ba3535d4e0ec022e43dda765
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 1 13:49:27 2018 -0700

    implement the locatio option for flux

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit 8c72f8d71d728ae3e9dbc0bed953ba8312809ad9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 1 08:24:47 2018 -0700

    add Location in preparation for getting fluxes at different locations

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp

commit 9ebd4a60d46772ff2536dd4fd71da61e4d28a6dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 1 07:49:55 2018 -0700

    simplification

Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit eccfe39f39c46def58519914b181da91021ba3a8
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Aug 31 17:26:27 2018 -0700

    Modify reductions to use parallel context comm

Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp

commit da52e980742189f75fd9ea21c1d7207b5e1800e7
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Aug 31 16:45:58 2018 -0700

    Add grow cells to ForkJoin registration.

Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp
Tutorials/Parallel/ForkJoin/MyTest.cpp

commit 62429e843d5ddde09fee4338c7401c55a35dd40e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 31 15:59:31 2018 -0700

    CellEB2 test: fix the setup of prob type 2

Tests/LinearSolvers/CellEB2/mytest_f.F90

commit ca71934e9d44c67b48a87c86e950b2eabc867c2b
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Aug 31 14:46:40 2018 -0700

    Use ComponentSet instead of std::pair, and use Redistribute instead of copy.

Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp
Tutorials/Parallel/ForkJoin/MyTest.cpp

commit 4f07fc3b4c0e9c8937df6ab3ae0edcfdf8b2ad37
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 31 14:44:59 2018 -0700

    CellEB2 test: add option for composite or level by level solve

Tests/LinearSolvers/CellEB2/MyTest.H
Tests/LinearSolvers/CellEB2/MyTest.cpp
Tests/LinearSolvers/CellEB2/inputs

commit 2716130d85e005d7bfa8985b7c0033213b3149da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 31 13:50:33 2018 -0700

    cell centered EB solver: multi-level works

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 1343e8571e138f01edbaba3871ad4196a03f2ce2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 31 13:43:24 2018 -0700

    MLMG: add StateMode so that we can properly apply EB bc

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit abc62bc09c0c8094dea77b8d4dc68339fc690c38
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Aug 31 12:39:29 2018 -0700

    restore some debugging changes I introduced.

Tools/F_scripts/dep.py

commit b755d3c2585ae57072e8a0e74710cb25728e9520
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Aug 31 12:38:05 2018 -0700

    fix some Python 3 / Unicode issues in dep.py

Tools/F_scripts/dep.py

commit 6994e0510c07fb18e53b913954d1a5951bd10b3d
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Aug 31 11:24:25 2018 -0700

    PETSC looks ok

Src/Extern/PETSc/AMReX_PETSc.H
Src/Extern/PETSc/AMReX_PETSc.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 5a060e8af09ebfbb9c01d2ba76fccd039ee8f40a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 31 10:46:15 2018 -0700

    EB dirichlet: average down for multi amr levels

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 340035c59d8c8fc2c9f6fb207b8f47d295868809
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 31 10:28:37 2018 -0700

    add Array versions of various average down functions

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit 01162e096e6fe3a6d4e442bb885d449ad4e459cd
Merge: f63c63874 61ab86d89
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Aug 30 19:09:25 2018 -0700

    Merge branch 'marc/forkjoin_dev' of github.com:AMReX-Codes/amrex into marc/forkjoin_dev

commit f63c63874a3fd24eb5217f10aa749cf1e57123fe
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Aug 30 12:07:22 2018 -0700

    Fix bug in tutorial.

Tutorials/Parallel/ForkJoin/MyTest.cpp

commit c6c76c36b2c141250976030870e2b114ca1688ec
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Aug 30 12:01:28 2018 -0700

    Add a simple ForkJoin Tutorial, add a function to the fj class. Tutorial currently gives weird result for duplicated multifabs.

Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp
Tutorials/Parallel/ForkJoin/GNUmakefile
Tutorials/Parallel/ForkJoin/Make.package
Tutorials/Parallel/ForkJoin/MyTest.H
Tutorials/Parallel/ForkJoin/MyTest.cpp
Tutorials/Parallel/ForkJoin/MyTest_F.H
Tutorials/Parallel/ForkJoin/inputs
Tutorials/Parallel/ForkJoin/main.cpp

commit d980a04ded8687bbfb7611f7198f05d407d0b43c
Merge: ab479546b 613b99c18
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Aug 30 18:59:44 2018 -0700

    Merge remote-tracking branch 'origin/development' into forkjoin

commit 613b99c18989cb425c1f0a70483e5b8f1896dd42
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 30 16:43:13 2018 -0700

    clean up

GNUmakefile.in
OldTutorials/EBParticles/GNUmakefile
Src/Base/AMReX_BCRec.cpp
Src/EB/AMReX_EB2.H
Src/EB/AMReX_EB2.cpp
Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/CMakeLists.txt
Src/EB/Make.package
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Tests/LinearSolvers/CellEB/GNUmakefile
Tests/LinearSolvers/CellEB2/GNUmakefile
Tests/LinearSolvers/EBConvergenceTest/GNUmakefile
Tests/LinearSolvers/EBflux_grad/GNUmakefile
Tutorials/EB/CNS/Exec/Make.CNS
Tutorials/EB/LevelSet/Exec/inputs_eb2
Tutorials/EB/LevelSet/Src/main.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp
Tutorials/EB/LevelSet/Src/make_poly.cpp
Tutorials/EB/LevelSet/Src/make_shapes.H
Tutorials/EB/MacProj/GNUmakefile

commit 30e876d982d807b4c6c2cd0342c3466f06745b4f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 30 16:26:04 2018 -0700

    removed old EB

Docs/Doxygen/doxygen.conf
Docs/sphinx_documentation/source/EB.rst
OldTutorials/EBParticles/EBParticleContainer.H
OldTutorials/EBParticles/EBParticleContainer.cpp
OldTutorials/EBParticles/GNUmakefile
OldTutorials/EBParticles/Make.package
OldTutorials/EBParticles/ebparticles_2d.f90
OldTutorials/EBParticles/ebparticles_3d.f90
OldTutorials/EBParticles/ebparticles_F.H
OldTutorials/EBParticles/inputs
OldTutorials/EBParticles/main.cpp
OldTutorials/GeometryGeneration/exec/GNUmakefile
OldTutorials/GeometryGeneration/exec/coveredSlabs.cpp
OldTutorials/GeometryGeneration/exec/coveredslabs.inputs
OldTutorials/GeometryGeneration/exec/parabolaWithSphere.cpp
OldTutorials/GeometryGeneration/exec/parabolaWithSphere.inputs
OldTutorials/GeometryGeneration/exec/sphere.cpp
OldTutorials/GeometryGeneration/exec/sphere.inputs
OldTutorials/GeometryGeneration/exec/surfaceOfRevolution.cpp
OldTutorials/GeometryGeneration/exec/surfaceOfRevolution.inputs
OldTutorials/GeometryGeneration/src/CommonCode.H
OldTutorials/GeometryGeneration/src/CommonCode.cpp
OldTutorials/GeometryGeneration/src/Make.package
OldTutorials/GeometryGeneration/src/WriteEBPlotFile.H
OldTutorials/GeometryGeneration/src/WriteEBPlotFile.cpp
Src/Amr/AMReX_StateData.H
Src/CMakeLists.txt
Src/EB/AMReX_EB2.H
Src/EB/AMReX_EB2.cpp
Src/EB/AMReX_EB2_F.H
Src/EB/AMReX_EB2_GeometryShop.H
Src/EB/AMReX_EB2_Graph.H
Src/EB/AMReX_EB2_IF_AllRegular.H
Src/EB/AMReX_EB2_IF_Box.H
Src/EB/AMReX_EB2_IF_Complement.H
Src/EB/AMReX_EB2_IF_Cylinder.H
Src/EB/AMReX_EB2_IF_Ellipsoid.H
Src/EB/AMReX_EB2_IF_Intersection.H
Src/EB/AMReX_EB2_IF_Lathe.H
Src/EB/AMReX_EB2_IF_Plane.H
Src/EB/AMReX_EB2_IF_Polynomial.H
Src/EB/AMReX_EB2_IF_Rotation.H
Src/EB/AMReX_EB2_IF_Scale.H
Src/EB/AMReX_EB2_IF_Sphere.H
Src/EB/AMReX_EB2_IF_Translation.H
Src/EB/AMReX_EB2_IF_Union.H
Src/EB/AMReX_EB2_IndexSpaceI.H
Src/EB/AMReX_EB2_Level.H
Src/EB/AMReX_EB2_Level.cpp
Src/EB/AMReX_EB2_MultiGFab.H
Src/EB/AMReX_EB2_MultiGFab.cpp
Src/EB/AMReX_eb2_2d.F90
Src/EB/AMReX_eb2_3d.F90
Src/EB/CMakeLists.txt
Src/EB/Make.package
Src/EB2/CMakeLists.txt
Src/EB2/Make.package
Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H
Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp
Src/EBAMRTools/AMReX_DivergenceOp.H
Src/EBAMRTools/AMReX_DivergenceOp.cpp
Src/EBAMRTools/AMReX_EBCFInterp.H
Src/EBAMRTools/AMReX_EBCFInterp.cpp
Src/EBAMRTools/AMReX_EBCoarseAverage.H
Src/EBAMRTools/AMReX_EBCoarseAverage.cpp
Src/EBAMRTools/AMReX_EBFastFR.H
Src/EBAMRTools/AMReX_EBFastFR.cpp
Src/EBAMRTools/AMReX_EBFineInterp.H
Src/EBAMRTools/AMReX_EBFineInterp.cpp
Src/EBAMRTools/AMReX_EBFortND.F90
Src/EBAMRTools/AMReX_EBFortND_F.H
Src/EBAMRTools/AMReX_EBLevelDataOps.H
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Src/EBAMRTools/AMReX_GradientOp.H
Src/EBAMRTools/AMReX_GradientOp.cpp
Src/EBAMRTools/AMReX_MeshRefine.H
Src/EBAMRTools/AMReX_MeshRefine.cpp
Src/EBAMRTools/Make.package
Src/GeometryShop/AMReX_AggStencil.H
Src/GeometryShop/AMReX_AggStencilI.H
Src/GeometryShop/AMReX_AllRegularService.H
Src/GeometryShop/AMReX_AllRegularService.cpp
Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H
Src/GeometryShop/AMReX_AnisotropicIF.H
Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_BaseEBCellFABI.H
Src/GeometryShop/AMReX_BaseEBCellFactory.H
Src/GeometryShop/AMReX_BaseEBFaceFAB.H
Src/GeometryShop/AMReX_BaseEBFaceFABI.H
Src/GeometryShop/AMReX_BaseIF.H
Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFAB.cpp
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_BaseIFFactory.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/AMReX_BaseIVFactory.H
Src/GeometryShop/AMReX_CH_EBIS_ORDER.H
Src/GeometryShop/AMReX_CellEdge.H
Src/GeometryShop/AMReX_CellEdge.cpp
Src/GeometryShop/AMReX_ComplementIF.H
Src/GeometryShop/AMReX_ComplementIF.cpp
Src/GeometryShop/AMReX_ConstrainedLS.H
Src/GeometryShop/AMReX_ConstrainedLS.cpp
Src/GeometryShop/AMReX_CoordinateSystem.H
Src/GeometryShop/AMReX_CoordinateSystemImplem.H
Src/GeometryShop/AMReX_CoveredSlabs.H
Src/GeometryShop/AMReX_CoveredSlabs.cpp
Src/GeometryShop/AMReX_CutCellMoments.H
Src/GeometryShop/AMReX_CutCellMoments.cpp
Src/GeometryShop/AMReX_CutCellMomentsImplem.H
Src/GeometryShop/AMReX_DivNormalRefinement.H
Src/GeometryShop/AMReX_DivNormalRefinementImplem.H
Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBArith.cpp
Src/GeometryShop/AMReX_EBCellFAB.H
Src/GeometryShop/AMReX_EBCellFAB.cpp
Src/GeometryShop/AMReX_EBCellFactory.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBDataFactory.H
Src/GeometryShop/AMReX_EBDataVarMacros.H
Src/GeometryShop/AMReX_EBDebugDump.H
Src/GeometryShop/AMReX_EBDebugOut.H
Src/GeometryShop/AMReX_EBDebugOut.cpp
Src/GeometryShop/AMReX_EBFaceFAB.H
Src/GeometryShop/AMReX_EBFaceFAB.cpp
Src/GeometryShop/AMReX_EBFluxFAB.H
Src/GeometryShop/AMReX_EBFluxFAB.cpp
Src/GeometryShop/AMReX_EBFluxFactory.H
Src/GeometryShop/AMReX_EBFluxFactory.cpp
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISBox.H
Src/GeometryShop/AMReX_EBISBox.cpp
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Src/GeometryShop/AMReX_EBLevelGrid.H
Src/GeometryShop/AMReX_EBLevelGrid.cpp
Src/GeometryShop/AMReX_EBLevelRedist.H
Src/GeometryShop/AMReX_EBLevelRedist.cpp
Src/GeometryShop/AMReX_EBLoHiCenter.H
Src/GeometryShop/AMReX_EBLoHiCenter.cpp
Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H
Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp
Src/GeometryShop/AMReX_EB_TYPEDEFS.H
Src/GeometryShop/AMReX_Ellipsoid.cpp
Src/GeometryShop/AMReX_EllipsoidIF.H
Src/GeometryShop/AMReX_EllipsoidIF.cpp
Src/GeometryShop/AMReX_ExtrudeIF.H
Src/GeometryShop/AMReX_ExtrudeIF.cpp
Src/GeometryShop/AMReX_FabArrayIO.H
Src/GeometryShop/AMReX_FabArrayIO.cpp
Src/GeometryShop/AMReX_FaceIndex.H
Src/GeometryShop/AMReX_FaceIndex.cpp
Src/GeometryShop/AMReX_FaceIterator.H
Src/GeometryShop/AMReX_FaceIterator.cpp
Src/GeometryShop/AMReX_Factorial.H
Src/GeometryShop/AMReX_FixedRefinement.H
Src/GeometryShop/AMReX_FixedRefinementImplem.H
Src/GeometryShop/AMReX_FlatPlateGeom.H
Src/GeometryShop/AMReX_FlatPlateGeom.cpp
Src/GeometryShop/AMReX_GenericArithmetic.H
Src/GeometryShop/AMReX_GenericArithmeticI.H
Src/GeometryShop/AMReX_GeomIntersectUtils.H
Src/GeometryShop/AMReX_GeomIntersectUtils.cpp
Src/GeometryShop/AMReX_GeometryService.H
Src/GeometryShop/AMReX_GeometryService.cpp
Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_GraphNode.H
Src/GeometryShop/AMReX_GraphNode.cpp
Src/GeometryShop/AMReX_IFData.H
Src/GeometryShop/AMReX_IFData.cpp
Src/GeometryShop/AMReX_IFDataImplem.H
Src/GeometryShop/AMReX_IFSlicer.H
Src/GeometryShop/AMReX_IFSlicer.cpp
Src/GeometryShop/AMReX_IFSlicerImplem.H
Src/GeometryShop/AMReX_IndexTM.H
Src/GeometryShop/AMReX_IndexTMI.H
Src/GeometryShop/AMReX_IndexedMoments.H
Src/GeometryShop/AMReX_IntVectSet.H
Src/GeometryShop/AMReX_IntVectSet.cpp
Src/GeometryShop/AMReX_IntersectionIF.H
Src/GeometryShop/AMReX_IntersectionIF.cpp
Src/GeometryShop/AMReX_IrregFAB.H
Src/GeometryShop/AMReX_IrregFAB.cpp
Src/GeometryShop/AMReX_IrregFABFactory.H
Src/GeometryShop/AMReX_IrregFABFactory.cpp
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_IrregNode.cpp
Src/GeometryShop/AMReX_KDStruct.H
Src/GeometryShop/AMReX_KDTree.H
Src/GeometryShop/AMReX_KDTree.cpp
Src/GeometryShop/AMReX_LSProblem.H
Src/GeometryShop/AMReX_LSProblem.cpp
Src/GeometryShop/AMReX_LSProblemImplem.H
Src/GeometryShop/AMReX_LSquares.H
Src/GeometryShop/AMReX_LSquares.cpp
Src/GeometryShop/AMReX_LatheIF.H
Src/GeometryShop/AMReX_LatheIF.cpp
Src/GeometryShop/AMReX_LoHiSide.H
Src/GeometryShop/AMReX_LoHiSide.cpp
Src/GeometryShop/AMReX_MetaPrograms.H
Src/GeometryShop/AMReX_MinimalCCCM.H
Src/GeometryShop/AMReX_MinimalCCCM.cpp
Src/GeometryShop/AMReX_MinimalCCCMImplem.H
Src/GeometryShop/AMReX_MomentIterator.H
Src/GeometryShop/AMReX_MomentIteratorImplem.H
Src/GeometryShop/AMReX_Moments.H
Src/GeometryShop/AMReX_Moments.cpp
Src/GeometryShop/AMReX_MonomialPowers.H
Src/GeometryShop/AMReX_MultiIndex.H
Src/GeometryShop/AMReX_MultiIndexImplem.H
Src/GeometryShop/AMReX_NoRefinement.H
Src/GeometryShop/AMReX_NoRefinementImplem.H
Src/GeometryShop/AMReX_NormalDerivative.H
Src/GeometryShop/AMReX_NormalDerivative.cpp
Src/GeometryShop/AMReX_NormalDerivativeNew.H
Src/GeometryShop/AMReX_Notation.H
Src/GeometryShop/AMReX_PXStuff.H
Src/GeometryShop/AMReX_PXStuff.cpp
Src/GeometryShop/AMReX_PlaneIF.H
Src/GeometryShop/AMReX_PlaneIF.cpp
Src/GeometryShop/AMReX_PolyGeom.H
Src/GeometryShop/AMReX_PolyGeom.cpp
Src/GeometryShop/AMReX_PolynomialIF.H
Src/GeometryShop/AMReX_PolynomialIF.cpp
Src/GeometryShop/AMReX_RedistStencil.H
Src/GeometryShop/AMReX_RedistStencil.cpp
Src/GeometryShop/AMReX_RefinementCriterion.H
Src/GeometryShop/AMReX_STLAsciiReader.H
Src/GeometryShop/AMReX_STLAsciiReader.cpp
Src/GeometryShop/AMReX_STLBox.H
Src/GeometryShop/AMReX_STLBox.cpp
Src/GeometryShop/AMReX_STLExplorer.H
Src/GeometryShop/AMReX_STLExplorer.cpp
Src/GeometryShop/AMReX_STLIF.H
Src/GeometryShop/AMReX_STLIF.cpp
Src/GeometryShop/AMReX_STLMesh.H
Src/GeometryShop/AMReX_STLMesh.cpp
Src/GeometryShop/AMReX_STLReader.H
Src/GeometryShop/AMReX_STLUtil.H
Src/GeometryShop/AMReX_STLUtil.cpp
Src/GeometryShop/AMReX_SmoothAbsoluteValue.H
Src/GeometryShop/AMReX_SmoothAbsoluteValue.cpp
Src/GeometryShop/AMReX_SmoothIntersection.H
Src/GeometryShop/AMReX_SmoothIntersection.cpp
Src/GeometryShop/AMReX_SmoothUnion.H
Src/GeometryShop/AMReX_SmoothUnion.cpp
Src/GeometryShop/AMReX_SphereIF.H
Src/GeometryShop/AMReX_SphereIF.cpp
Src/GeometryShop/AMReX_Stencils.H
Src/GeometryShop/AMReX_Stencils.cpp
Src/GeometryShop/AMReX_TransformIF.H
Src/GeometryShop/AMReX_TransformIF.cpp
Src/GeometryShop/AMReX_UnionIF.H
Src/GeometryShop/AMReX_UnionIF.cpp
Src/GeometryShop/AMReX_VoFIterator.H
Src/GeometryShop/AMReX_VoFIterator.cpp
Src/GeometryShop/AMReX_VolIndex.H
Src/GeometryShop/AMReX_VolIndex.cpp
Src/GeometryShop/AMReX_WrappedGShop.H
Src/GeometryShop/AMReX_WrappedGShop.cpp
Src/GeometryShop/AMReX_ZCylinder.H
Src/GeometryShop/AMReX_ZCylinder.cpp
Src/GeometryShop/CMakeLists.txt
Src/GeometryShop/Make.package
Src/GeometryShop/_save/AMReX_GeometryShop.H
Src/GeometryShop/_save/AMReX_GeometryShop.cpp
Tests/EBAMRTools/README
Tests/EBAMRTools/regression/GNUmakefile
Tests/EBAMRTools/regression/Make.package
Tests/EBAMRTools/regression/aggpwlfp.inputs
Tests/EBAMRTools/regression/aggpwlfpTest.cpp
Tests/EBAMRTools/regression/divergenceOpTest.cpp
Tests/EBAMRTools/regression/divop.inputs
Tests/EBAMRTools/regression/ebCoarseAveTest.cpp
Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp
Tests/EBAMRTools/regression/ebFineInterpTest.cpp
Tests/EBAMRTools/regression/ebcoarave.inputs
Tests/EBAMRTools/regression/ebfineinterp.inputs
Tests/EBAMRTools/regression/fluxRegTest.cpp
Tests/EBAMRTools/regression/fluxreg.inputs
Tests/EBAMRTools/regression/gradientOpTest.cpp
Tests/EBAMRTools/regression/gradop.inputs
Tests/EBAMRTools/regression/meshref.inputs
Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp
Tests/EBAMRTools/regression/nwoebquadcfi.inputs
Tests/EBAMRTools/regression/regFluxRegTest.cpp
Tests/EBAMRTools/regression/runalltests.mpi.sh
Tests/EBAMRTools/regression/runalltests.serial.sh
Tests/EBAMRTools/regression/simpleMeshRefine.cpp
Tests/EBAMRTools/regression/sphere.inputs
Tests/EBEB2/GNUmakefile
Tests/EBEB2/Make.package
Tests/EBEB2/MyTest.H
Tests/EBEB2/MyTest.cpp
Tests/EBEB2/initEB.cpp
Tests/EBEB2/inputs
Tests/EBEB2/main.cpp
Tests/EBbcent/GNUmakefile
Tests/EBbcent/Make.package
Tests/EBbcent/main.cpp
Tests/GeometryShop/README
Tests/GeometryShop/STLGeom/GNUmakefile
Tests/GeometryShop/STLGeom/bad.cylinder.inputs
Tests/GeometryShop/STLGeom/bad.reactor.inputs
Tests/GeometryShop/STLGeom/cylinder.stl
Tests/GeometryShop/STLGeom/good.cylinder.inputs
Tests/GeometryShop/STLGeom/good.reactor.inputs
Tests/GeometryShop/STLGeom/good.sphere.inputs
Tests/GeometryShop/STLGeom/reactor.stl
Tests/GeometryShop/STLGeom/sphere.stl
Tests/GeometryShop/STLGeom/stl.inputs
Tests/GeometryShop/STLGeom/stlgeom.cpp
Tests/GeometryShop/ebgraphDistributed/GNUmakefile
Tests/GeometryShop/ebgraphDistributed/Make.package
Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp
Tests/GeometryShop/ebgraphDistributed/sphere.inputs
Tests/GeometryShop/ebgraphSingleGrid/GNUmakefile
Tests/GeometryShop/ebgraphSingleGrid/Make.package
Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp
Tests/GeometryShop/ebgraphSingleGrid/sphere.inputs
Tests/GeometryShop/flatPlate/GNUmakefile
Tests/GeometryShop/flatPlate/Make.package
Tests/GeometryShop/flatPlate/flatPlateTest.cpp
Tests/GeometryShop/flatPlate/flatplate.inputs
Tests/GeometryShop/ramp/GNUmakefile
Tests/GeometryShop/ramp/Make.package
Tests/GeometryShop/ramp/inputs
Tests/GeometryShop/ramp/main.cpp
Tests/GeometryShop/regression/GNUmakefile
Tests/GeometryShop/regression/Make.package
Tests/GeometryShop/regression/dataArith.cpp
Tests/GeometryShop/regression/dataarith.inputs
Tests/GeometryShop/regression/ebio.2.inputs
Tests/GeometryShop/regression/ebio.cpp
Tests/GeometryShop/regression/ebio.inputs
Tests/GeometryShop/regression/ebnormalizeTest.cpp
Tests/GeometryShop/regression/ebnormtest.inputs
Tests/GeometryShop/regression/fabfromif.cpp
Tests/GeometryShop/regression/fabio.cpp
Tests/GeometryShop/regression/fabio.inputs
Tests/GeometryShop/regression/levelRedistTest.cpp
Tests/GeometryShop/regression/levelredist.inputs
Tests/GeometryShop/regression/momentConvTest.cpp
Tests/GeometryShop/regression/momentconvtest.inputs
Tests/GeometryShop/regression/multicelllev.cpp
Tests/GeometryShop/regression/multicelllev.inputs
Tests/GeometryShop/regression/runalltests.mpi.sh
Tests/GeometryShop/regression/runalltests.serial.sh
Tests/GeometryShop/regression/serialization.cpp
Tests/GeometryShop/regression/serialization.inputs
Tests/GeometryShop/regression/simpleMomentExample.cpp
Tests/GeometryShop/regression/simplemomentexample.inputs
Tests/GeometryShop/runalltests.mpi.sh
Tests/GeometryShop/runalltests.serial.sh
Tests/GeometryShop/sparseDataSingleGrid/GNUmakefile
Tests/GeometryShop/sparseDataSingleGrid/Make.package
Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp
Tests/GeometryShop/sparseDataSingleGrid/sphere.inputs
Tests/GeometryShop/sphere/GNUmakefile
Tests/GeometryShop/sphere/Make.package
Tests/GeometryShop/sphere/sphere.inputs
Tests/GeometryShop/sphere/sphereConvTest.cpp
Tests/GeometryShop/sphere/sphereTest.cpp
Tests/GeometryShop/sphereEBISBox/GNUmakefile
Tests/GeometryShop/sphereEBISBox/Make.package
Tests/GeometryShop/sphereEBISBox/sphere.inputs
Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp
Tests/GeometryShop/stencilTestbed/exec/GNUmakefile
Tests/GeometryShop/stencilTestbed/exec/Make.package
Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp
Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90
Tests/GeometryShop/stencilTestbed/exec/dirichletTest_F.H
Tests/GeometryShop/stencilTestbed/exec/sphere.inputs
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_2d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_3d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_F.H
Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H
Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.H
Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp
Tests/GeometryShop/stencilTestbed/src/Make.package
Tests/GeometryShop/stencilTestbed/src/lapl_nd.F90
Tests/GeometryShop/stencilTestbed/src/lapl_nd_F.H
Tests/GeometryShop/vofStructures/AMReX_EBRedist.H
Tests/GeometryShop/vofStructures/AMReX_EBStruct.H
Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90
Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/README.txt
Tests/GeometryShop/vofStructures/flatplate.inputs
Tests/GeometryShop/vofStructures/nbrsTest.cpp
Tests/GeometryShop/vofStructures/nbrsTest_mod.F90
Tests/GeometryShop/vofStructures/nbrsTest_nd.f90
Tests/GeometryShop/vofStructures/sphere.inputs
Tests/GeometryShop/vofStructures/umapTest.H
Tests/GeometryShop/vofStructures/umapTest.cpp
Tests/GeometryShop/vofStructures/umapTest_mod.f90
Tests/GeometryShop/vofStructures/umapTest_nd.f90
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/EBSurfaceTools/GNUmakefile
Tools/GNUMake/Make.defs
Tutorials/EB/CNS/Exec/Make.CNS
Tutorials/EB/LevelSet/Exec/GNUmakefile

commit 9774819404e1caf31dac39309be4016a2158fe34
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Aug 30 16:10:43 2018 -0700

    odd stencil behavior for generating the matrix. Some regions do not have the penta-diagonal design it should have. Looking to investigate this.

Src/Extern/PETSc/AMReX_PETSc.cpp

commit b926f8d6b4c9530f26add30c72b58cb5001f11dc
Author: Ray Grout <ray.grout@nrel.gov>
Date:   Thu Aug 30 16:10:01 2018 -0600

    Change how vfrac threshold is written out so that amrvis and visit are both happy

Tutorials/EB/CNS/Source/CNS_io.cpp

commit 473ba9b58ef84aa571712ed706b37acb9de7bd59
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 30 13:46:38 2018 -0700

    CellEB2: add fine grids

Src/EB2/AMReX_EB2_Level.H
Tests/LinearSolvers/CellEB2/MyTest.H
Tests/LinearSolvers/CellEB2/MyTest.cpp
Tests/LinearSolvers/CellEB2/inputs

commit 427ed65caafa636d9e47f80ec88eb62943eadf82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 30 13:32:33 2018 -0700

    add CellEB2 test for Dirichlet bc

Tests/LinearSolvers/CellEB2/GNUmakefile
Tests/LinearSolvers/CellEB2/Make.package
Tests/LinearSolvers/CellEB2/MyEB.H
Tests/LinearSolvers/CellEB2/MyTest.H
Tests/LinearSolvers/CellEB2/MyTest.cpp
Tests/LinearSolvers/CellEB2/MyTest_F.H
Tests/LinearSolvers/CellEB2/initEB.cpp
Tests/LinearSolvers/CellEB2/inputs
Tests/LinearSolvers/CellEB2/main.cpp
Tests/LinearSolvers/CellEB2/mytest_f.F90

commit 61ab86d89ddc80106e9a4d89bac4cdf2881fa17f
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Aug 30 12:07:22 2018 -0700

    Fix bug in tutorial.

Tutorials/Parallel/ForkJoin/MyTest.cpp

commit 9e4329c64a588c19373b39fd2349a2080a9372ac
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Aug 30 12:01:28 2018 -0700

    Add a simple ForkJoin Tutorial, add a function to the fj class. Tutorial currently gives weird result for duplicated multifabs.

Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp
Tutorials/Parallel/ForkJoin/GNUmakefile
Tutorials/Parallel/ForkJoin/Make.package
Tutorials/Parallel/ForkJoin/MyTest.H
Tutorials/Parallel/ForkJoin/MyTest.cpp
Tutorials/Parallel/ForkJoin/MyTest_F.H
Tutorials/Parallel/ForkJoin/inputs
Tutorials/Parallel/ForkJoin/main.cpp

commit 21ddc4f0cce1ba86d6b5ce35574bb74a84e81619
Merge: bb9c90e6c 16c4af11a
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Aug 30 10:34:44 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit bb9c90e6ce3f370471655e43577755898bce1805
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Aug 30 10:34:41 2018 -0700

    Add == op for BCRec

Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCRec.cpp

commit 16c4af11a566bafc3652dd63e73cebb6430b6099
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 30 10:29:14 2018 -0700

    new iMultiFab constructor taking IntVect ngrow

Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp

commit ab479546b2a79ff0139df460555f97ed9ebbfeb3
Author: Cy Chan <cychan@lbl.gov>
Date:   Wed Aug 29 22:05:39 2018 -0700

    ParallelReduce.H: for MPI_Op lookup, change unordered_map to array

Src/Base/AMReX_ParallelReduce.H

commit b9724be8936687d03d9b7d23ea79570b898197d0
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Wed Aug 29 16:02:57 2018 -0700

    Matrix appears to be correctly populating. However, the KSB solver is throwing a floating point exception. Will continue to debug. Possible culprits: RHS and Sol vectors not correctly being loaded, petsc not being correctly initialized, or something I haven't thought of.

Src/Extern/PETSc/AMReX_PETSc.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit e1e5eff32eb1f793c5a1a631cba9ed39c8eb74c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 29 15:59:00 2018 -0700

    put limit on eb max coarsening level

Src/EB2/AMReX_EB2_IndexSpaceI.H

commit 5fef32336b5bac633cba0a89ddda600d7ccab3ca
Merge: ed915ae84 2a8625c73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 28 17:15:27 2018 -0700

    Merge branch 'development' into mlmg

commit ed915ae84fc32db432e5761f6c016744ee67a522
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 28 17:15:08 2018 -0700

    remove unused variables

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit d3aba2ded4ef78375dd25a69511201e155bd8f0b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 28 16:08:34 2018 -0700

    3d eb dirichlet: gsrb and normalize

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 657d4cf3a5aa820e79b5a92ef2136e198a39ab82
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Aug 28 15:59:47 2018 -0700

    Removed unneeded function

Src/Extern/PETSc/AMReX_PETSc.H

commit b1ac6e77a5e1405d39f9ad17f54efaef003dc693
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Aug 28 15:57:23 2018 -0700

    Wrote the function to connect applications and PETSc routines. There are bugs in the execution that will need to be flushed out.

Src/Extern/PETSc/AMReX_PETSc.H
Src/Extern/PETSc/AMReX_PETSc.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 6d6c53c958e74fca3e10b89189d8f16fbc6365c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 28 15:45:34 2018 -0700

    3d eb dirichlet a dot x

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit ef35e87ce9f378eb00c4d6b1c73d65e9417c7e66
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Aug 28 14:26:48 2018 -0700

    Proper build of Petsc, returned Make.petsc to previous version, single include directory. KSP solver not converging, need to iron out bugs.

Tests/LinearSolvers/CellEB/GNUmakefile
Tests/LinearSolvers/CellEB/inputs
Tools/GNUMake/packages/Make.petsc

commit 7ab674867475643a895854b83d723ce75b54f419
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Aug 28 13:32:55 2018 -0700

    Switched things a bit

Tests/LinearSolvers/CellEB/GNUmakefile
Tools/GNUMake/packages/Make.petsc

commit 5b3ef7c78c7744e94e0b0ee0f24eb8947e48e2dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 28 13:28:15 2018 -0700

    update normalize

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit 06aed25d7028e47ce3ef0402681d2b9266f027b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 28 13:03:33 2018 -0700

    eb dirichlet: use the simple version

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit 7b5d037c980373df3b86533f2031a34bfe909378
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Aug 28 13:02:59 2018 -0700

    AMReX with PETSC bottom solve works. Going to go through and remove any unneccessary links/ directories

Src/Extern/PETSc/AMReX_PETSc.cpp
Tests/LinearSolvers/CellEB/GNUmakefile
Tools/GNUMake/packages/Make.petsc

commit 17cd9fa57c34931c83fe7cb24e8504fef50c475f
Author: sireeveslbl <sireeves@ucsc.edu>
Date:   Mon Aug 27 14:16:51 2018 -0700

    Killing compilation issues, got the proper linkage. However now am having pointer issues. Will try and fix those. Note this does not compile yet for USE_PETSC=TRUE

Src/Extern/PETSc/AMReX_PETSc.cpp
Tests/LinearSolvers/CellEB/MyTest.H
Tests/LinearSolvers/CellEB/MyTest.cpp
Tests/LinearSolvers/CellEB/inputs

commit 2a8625c73cd0d0eb4eb76e9a26f4e047d9736b2b
Merge: d149d24fe dc64d08fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 27 12:30:38 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d149d24fea679f0b8f3c1a3db04edbbe1e10c793
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 27 12:28:30 2018 -0700

    VisMF::Read can read lower-dimensional files with ghost cells

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_VisMF.cpp

commit 0d7547cacee0ddb2fb4cb969b5b5961ecf13356a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 27 12:27:25 2018 -0700

    mfiter: support no IntVect number of ghost cells

Src/Base/AMReX_MFIter.cpp

commit dc64d08fe1812add24fac348a49696d4c0a42b48
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Aug 27 12:24:17 2018 -0700

    fix a small buf in the custom Barrier

Src/AmrTask/rts_impls/Perilla/Barrier.cpp
Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp

commit 098043097935058b039fdff6d252f497315e8723
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 27 10:34:07 2018 -0700

    make IntVect operator>> work for data of any dimensions

Src/Base/AMReX_IntVect.cpp

commit 3d9c8f52f32179e6bc672372ad64a7ca21498e70
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 25 15:45:15 2018 -0700

    Fix up the heat equation GPU tutorial

Tutorials/GPU/HeatEquation_EX1_C/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/advance.cpp

commit 18e000996386064d540416a819201889be2a5946
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 25 15:33:42 2018 -0700

    Fix typo

Tools/F_mk/GMakeMPI.mak

commit a7e16417e1b2e93131a0f60312709b678f49b151
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 25 15:30:35 2018 -0700

    Sync up some more with development

Src/Base/AMReX.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_Geometry.cpp

commit 5ee56f711fc7fc3209a0dd6192129aaeaaba2af3
Merge: 565e7c377 156bb1bb1
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 25 14:42:40 2018 -0700

    Merge branch 'development' into gpu
    
    Conflicts:
            Src/Base/AMReX_ArrayLim.H

commit 565e7c3771bbd494ab6c5027e26fb2fdc28795f5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 25 14:35:04 2018 -0700

    Sync up RealBox with development

Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp

commit 26b56028a437604079b2d2ed9e5c1b7c8e02e3a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 25 13:54:00 2018 -0700

    dirichlet eb: clean up

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit d301f6c31caa7974058af6691508b09be9766354
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 25 11:09:55 2018 -0700

    eb dirichlet: version that avoids extrapolation

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit eb95fb356ad43d101e342f079457eb13f6ca3136
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 24 22:30:10 2018 -0700

    CellEB test: print out the smallest cut cell's volume fraction

Tests/LinearSolvers/CellEB/MyTest.cpp

commit ea9f5ab9649a63a770bd31b798fe9ff16b74d42e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 24 22:03:49 2018 -0700

    eb dirichlet: tweak parameters

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit b8990a8d64a17745869fa3978498ee62c1d917cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 24 21:40:24 2018 -0700

    eb dirichlet: fix blend function

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Tests/LinearSolvers/CellEB/MyTest.cpp

commit e14fe5af840268e43554aab9d241238408145c57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 24 17:15:51 2018 -0700

    eb dirichlet: 2d gsrb

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit 2e5eee253ec02b7d767b512fb9224b18a1a69fe4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 24 17:15:38 2018 -0700

    CellEB test: add parameters for scalars

Tests/LinearSolvers/CellEB/MyTest.H
Tests/LinearSolvers/CellEB/MyTest.cpp

commit 915d961dd8112f90a4e9a0d79e1843c446130bdc
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Aug 24 15:57:28 2018 -0700

    Linking issues between PETSc HYPRE and AMReX. Will route out the problem.

Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Tests/LinearSolvers/CellEB/GNUmakefile
Tools/GNUMake/packages/Make.petsc

commit f5470d8f155663022d8ad1260aa9e1e0d014ee83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 24 15:53:30 2018 -0700

    pass dirichlet information into gsrb

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit 0da813407d405f445e71e135ee41f08d4fddaedb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 24 15:43:59 2018 -0700

    change the CellEB test initial data

Tests/LinearSolvers/CellEB/MyTest.cpp

commit d5c81011f62382aaa2b062eee5a270f0a12ca810
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 24 15:17:11 2018 -0700

    eb dirichlet: a dot x

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit 156bb1bb193b01259f6ac6ba4b596b74337e7db0
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Aug 24 13:48:16 2018 -0700

    Typo fix

Docs/sphinx_documentation/source/EB.rst

commit 619d79ca1c04e9c002bb5bf2a3c1df4c1709a20d
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Aug 24 13:45:35 2018 -0700

    Use Vec functions from PETSc

Src/Extern/PETSc/AMReX_PETSc.cpp

commit 29f66535b8e88fcece80b1f77fb0c5d3d7417f07
Author: Cy Chan <cychan@lbl.gov>
Date:   Fri Aug 24 01:27:33 2018 -0700

    fixed issue in ParallelReduce for non-integer MPI_Op implementations

Src/Base/AMReX_ParallelReduce.H

commit e233ff9b869badd71f4b4ebce9d41563004c36e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 23 17:53:10 2018 -0700

    WIP: eb dirichlet

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit 0034073b463b89ad2c90c2a219795f9854eeea79
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Aug 23 17:47:38 2018 -0700

    fix problem with levelset bcs and avoid unncessary tiling

Src/EB/AMReX_EB_levelset.cpp
Tutorials/EB/LevelSet/Src/main.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp

commit 03b21c46093244c7a9a5948d726dde4de4c76026
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Aug 23 16:03:31 2018 -0700

    Working on PETSc availability for the bottom solve. Currently am preallocating based on the stencil for our problem. Might be an over estimate, but could also be cheaper than looping through the solution to dictate what is in the diagonal blocks and what is not. Load vector and get solution vector is being modeled after the HYPRE ones, but will change to utilize the PETSc routines.

Src/Extern/PETSc/AMReX_PETSc.cpp

commit c89bb1c4ec83013aed093cf950933d3d4112e4f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 23 14:57:44 2018 -0700

    pass eb area and beta coefficient into Fortran

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit 454aa22ac3b16bd3e7c9cb04b5f4b227055df284
Merge: 65e91937d 0ebe1f0c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 23 13:37:26 2018 -0700

    Merge branch 'development' into forkjoin

commit 31df60ec85c47f479ec7bbb58f0dcff9bbd55dcc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 23 10:23:13 2018 -0700

    add a blend function for EB dirichlet

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit 0ebe1f0c5d7d44a5199c5e082573842b9880182f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Aug 23 10:11:21 2018 -0700

    bug fix: EB tutorial now works without DAMREX_USE_GEOMETRYSHOP

Src/EB2/AMReX_EB2_IF_Polynomial.H
Tutorials/EB/LevelSet/Src/main.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp
Tutorials/EB/LevelSet/Src/make_poly.cpp
Tutorials/EB/LevelSet/Src/make_shapes.H

commit c0ae1e8caff7bfbe092e662557de26af8a29f6a5
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Aug 23 13:03:38 2018 -0400

    Pinned allocator adjustment.

Src/Base/AMReX_CudaAllocators.H

commit 50ea23a19028c0ddfe44c882d74bcbf7a9e0095c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Aug 23 13:01:55 2018 -0400

    PinnedData object draft.

Tutorials/GPU/Test/GNUmakefile
Tutorials/GPU/Test/main.cpp
Tutorials/GPU/Test/run.script

commit 4b148a197587e7eef5b99cd88abb605cfa2b2430
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Aug 22 21:56:32 2018 -0700

    update level set tutorial => user can specify eb or eb2

Src/EB/AMReX_EBTower.H
Tutorials/EB/LevelSet/Exec/inputs_eb2
Tutorials/EB/LevelSet/Src/main.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp
Tutorials/EB/LevelSet/Src/make_poly.cpp
Tutorials/EB/LevelSet/Src/make_shapes.H

commit 708cb6da6f481deaec9f95c42b941877ea29eba2
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Aug 22 17:49:35 2018 -0700

    replace pow function in IF_Polynomial with integer-specific version

Src/EB2/AMReX_EB2_GeometryShop.H
Src/EB2/AMReX_EB2_IF_Plane.H
Src/EB2/AMReX_EB2_IF_Polynomial.H
Tutorials/EB/LevelSet/Exec/inputs
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp

commit 0f747c64853aed5fef900c20262902967f49fa0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 22 11:21:31 2018 -0700

    fix bug

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 42bcd87b86137830793d62c98c603ad187a4b28f
Merge: 491cc8f0f 45d69788f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Aug 22 10:48:03 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 491cc8f0f9c52ce4227e3c1fc4cfc5a04dc0d7b0
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Aug 22 10:47:54 2018 -0700

    upgrade LSFactory to work with EB2

Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2_IF_Plane.H
Src/EB2/AMReX_EB2_IF_Polynomial.H
Src/EB2/AMReX_EB2_IF_Translation.H
Src/EB2/AMReX_EB2_IF_Union.H
Src/EB2/AMReX_EB2_IndexSpaceI.H
Src/EB2/CMakeLists.txt
Src/EB2/Make.package
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Tutorials/EB/LevelSet/Src/main.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp
Tutorials/EB/LevelSet/Src/make_shapes.H

commit 45d69788fd625dfa182c2f85275a98e05eaff732
Author: sireeveslbl <sireeves@ucsc.edu>
Date:   Wed Aug 22 10:40:31 2018 -0700

    Last of the EB proofreading.

Docs/sphinx_documentation/source/EB.rst

commit e10d7a767b26d073038331c7129b994441e7980a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 22 06:35:40 2018 -0700

    GEOMETRY_SHOP-->GEOMETRYSHOP

Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake

commit 93af7689615dd9cb7ecc79f5281b1eb52260e55e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 22 06:31:32 2018 -0700

    USE_GEOMETRY_SHOP --> USE_GEOMETRYSHOP

Tools/GNUMake/Make.defs

commit 249af6290b190308bc67303f587da3633831fc40
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Aug 21 23:50:43 2018 -0700

    Fix some variable definitions for nvcc.mak

Tools/GNUMake/comps/nvcc.mak

commit c55f996a827112d8d9f9efd71f5e71cc5d9fbead
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Aug 21 21:53:23 2018 -0700

    Move the fortran preprocessing to the actual compile rule

Tools/GNUMake/Make.rules

commit f88bcca5051f173a764f98714792870deb7603d4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Aug 21 21:11:56 2018 -0700

    We no longer need the Fortran passed to the CUDA script

Tools/F_scripts/write_cuda_headers.py
Tools/GNUMake/Make.rules

commit 43b0cdef9093b9d1fdd984a79dd611c8f2ebd3f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 21 17:01:01 2018 -0700

    eb avgdown boundaries

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_3d.F90
Src/EB/AMReX_EBMultiFabUtil_F.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 2609ac24899a582ce51db176e770045a5eed6669
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 21 16:27:14 2018 -0700

    add boundary area to eb factory

Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFabFactory.H

commit f596359f6d925d83cfea9a7b1ee40aabf3dcc6d3
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Aug 21 16:06:49 2018 -0700

    Proof read edits to new EB documentation. Still working through it.

Docs/sphinx_documentation/source/EB.rst

commit 8823d007d7b75d7ef605938b6a753d129ecd960d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 21 15:53:16 2018 -0700

    add function to pass Dirichlet data for EB

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90
Tests/LinearSolvers/CellEB/MyTest.H
Tests/LinearSolvers/CellEB/MyTest.cpp

commit ba980b866fefa1e1630aa2266a7edad4926920ec
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Aug 21 15:18:59 2018 -0700

    cuda header script should also depend on CEXE_sources

Tools/F_scripts/write_cuda_headers.py
Tools/GNUMake/Make.rules

commit 94dd0a030b6d91c17949a112c39ee860ace3e16b
Merge: b3c6209d9 08995b1aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 21 14:29:32 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b3c6209d95a247ae4d3de86eb58d84b67ff40e7d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 21 14:26:34 2018 -0700

    EB documentation

Docs/sphinx_documentation/source/EB.rst

commit 08995b1aa35f3892be63923e475ccd0d00df415b
Merge: 75db2acde b3027c25b
Author: kngott <kngott@lbl.gov>
Date:   Tue Aug 21 13:12:43 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-codes/amrex into development

commit 75db2acde250c324bb26de37a39f63d6943c5209
Author: kngott <kngott@lbl.gov>
Date:   Tue Aug 21 13:12:15 2018 -0700

    Profiler adjustment to allow compile.

Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp

commit b3027c25be9da522293e185439a422d42fbdb112
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 21 12:55:15 2018 -0700

    Need to add flags for using GeometryShop directory

Tools/GNUMake/Make.defs

commit 3a2b253b66f9d883e4db50dd454471ae2feb6381
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Aug 21 10:04:12 2018 -0700

    Consistency in pronouns

Docs/sphinx_documentation/source/EB.rst

commit 2d4c2597e29d6676bcb645885e4016242bfa10b8
Merge: 16984fc1e 5283952ca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 20 17:25:08 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 16984fc1e94d781a155c29abf380c87566caf430
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 20 17:25:02 2018 -0700

    WIP: EB documentation

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/EB.rst
Docs/sphinx_documentation/source/EB/EB_example.fig.bak
Docs/sphinx_documentation/source/EB/eb_fluxes.fig.bak
Docs/sphinx_documentation/source/EB/parabsphere.pdf
Docs/sphinx_documentation/source/EB/parabsphere.png
Docs/sphinx_documentation/source/EB/parabsphere.ps.REMOVED.git-id
Docs/sphinx_documentation/source/EB/revolution.pdf
Docs/sphinx_documentation/source/EB/revolution.png
Docs/sphinx_documentation/source/EB/revolution.ps.REMOVED.git-id
Src/EB2/AMReX_EB2_IF_Scale.H

commit 65e91937d472e7dfd5ccfb674340a28afb286fc3
Merge: 290b0f152 5283952ca
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Aug 20 15:32:54 2018 -0700

    Merge branch 'development' into forkjoin

commit 290b0f152f614ddf7d08b865d9a5466d6f3ee690
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Aug 20 15:24:46 2018 -0700

    create directory for fork-join task output files

Src/Base/AMReX_ForkJoin.cpp

commit 5283952ca193bd342eb73596237eb5c607a37962
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Aug 20 14:49:44 2018 -0700

    Further Documentation Editing, reviewed Linear Solvers, will do EB next

Docs/sphinx_documentation/source/LinearSolvers.rst

commit 2d21b89308d70e7cfe142e09a8444d012a69d01a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Aug 20 11:31:39 2018 -0700

    bugfix to the fill_slice interpolation routine

Src/Base/AMReX_MultiFabUtil_nd.F90

commit eb486fd3c0b2a0eec4cbd2c02aecf949647d52cc
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Aug 20 03:19:20 2018 -0400

    Clean up lineinfo/debug differences for CUDA

Tools/GNUMake/comps/nvcc.mak
Tools/GNUMake/comps/pgi.mak

commit 795b012c53f75e7b8e6d99f41cef37a4ed22c165
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Aug 19 13:28:18 2018 -0400

    Sync up write_probin.py with gpu branch

Tools/F_scripts/write_probin.py

commit e7421210a95191f35ac3006d7a7e199c713fcc71
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Aug 19 13:25:23 2018 -0400

    Clean whitespace

Tools/F_scripts/write_probin.py

commit e1138b1e8689341485f0201dfe809d0e40661fab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Aug 19 11:04:44 2018 -0400

    fix typo in macro

Src/Base/AMReX_ArrayLim.H

commit 8a94be9e9611f539007de3bfc460d97b6fe5e812
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 23:56:43 2018 -0700

    Remove get_fortran_pointer

Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_MFIter.H

commit 9848001028fbb04d507ac5da032987614b0e8c54
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 23:55:38 2018 -0700

    Remove registerRealBox

Src/Base/AMReX_MFIter.H

commit 1e3ccf553a7ec42f6127d68275cdc0482e9b01a7
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 23:25:14 2018 -0700

    Add rzansel @ LLNL

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.llnl

commit 50d1756aa65cf9027203596b42d9c04cfd545d29
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Aug 19 01:15:49 2018 -0400

    Re-enable optimizations for PGI with CUDA

Tools/GNUMake/comps/pgi.mak

commit 5c318d01f3ccd30f021ec94f6e6a4e7812b0798b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 21:06:56 2018 -0700

    Switch to arch specification, default cc35

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/Linux_pgi.mak
Tools/GNUMake/Make.defs
Tools/GNUMake/comps/nvcc.mak
Tools/GNUMake/comps/pgi.mak
Tools/GNUMake/sites/Make.llnl
Tools/GNUMake/sites/Make.olcf

commit 08cb1d7c7691ecbca50f0cbd1b8a52835d89b7ba
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 21:01:03 2018 -0700

    Add debug flags for nvcc

Tools/GNUMake/comps/nvcc.mak

commit 7f5475151b0c01948d5578b98058837e553ed7da
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 22:04:12 2018 -0400

    Take the physical boundary fill off the GPU for now

Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90
Src/Base/AMReX_filcc_f.H
Src/Base/AMReX_filcc_mod.F90

commit 1faefc76720e9a79e1afebaea603c5c3cce11f78
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 22:03:35 2018 -0400

    Take the derives off the GPU for now

Src/Amr/AMReX_AmrLevel.cpp

commit b202afde083a8f244ae64829915dad1b23666df1
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 21:45:13 2018 -0400

    Create a preprocessed version of the C++ files for diagnostic uses

Tools/F_scripts/write_cuda_headers.py

commit 8ce7188c06c669e50b8d8fc72f0e304b531f859e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 21:23:02 2018 -0400

    ZFILL -> AMREX_ZFILL

Src/Base/AMReX_ArrayLim.H

commit ea6e4c795e5d53b6cf221d8bf4db9ef2b4371f86
Merge: 07fd20e19 115ea7c38
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 20:13:04 2018 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 115ea7c385ec0f2dd2cdd01c418578615cc01d54
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 19:56:24 2018 -0400

    Fix nvcc version check

Tools/GNUMake/comps/nvcc.mak

commit 07fd20e19d57b3668dc7fd13b20a4ed1fe9e81dc
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 19:44:17 2018 -0400

    Replace mfi.get_fortran_pointer with macro

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_ArrayLim.H

commit 6c0a6db4df51ee4a949eabbb3494d548f73aaf84
Merge: 01b9892d6 ccd3e70f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 18 13:59:17 2018 -0700

    Merge branch 'development' into petsc

commit ccd3e70f30504a16c3aa948d7bbae8a304735ffc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 18 13:58:28 2018 -0700

    no need to include GeometryShop in Tutorials

Docs/README.md
Tests/LinearSolvers/CellEB/GNUmakefile
Tests/LinearSolvers/CellEB/inputs
Tests/LinearSolvers/EBConvergenceTest/GNUmakefile
Tests/LinearSolvers/EBConvergenceTest/inputs
Tests/LinearSolvers/EBflux_grad/GNUmakefile
Tests/LinearSolvers/EBflux_grad/inputs
Tutorials/EB/CNS/Exec/Combustor/inputs
Tutorials/EB/CNS/Exec/Combustor/inputs.regt
Tutorials/EB/CNS/Exec/Make.CNS
Tutorials/EB/CNS/Exec/Pulse/inputs
Tutorials/EB/CNS/Exec/Pulse/inputs.regt
Tutorials/EB/CNS/Exec/ShockRef/inputs
Tutorials/EB/CNS/Exec/ShockRef/inputs.amr
Tutorials/EB/CNS/Exec/ShockRef/inputs.regt
Tutorials/EB/CNS/Exec/Sod/inputs
Tutorials/EB/CNS/Source/main.cpp
Tutorials/EB/MacProj/GNUmakefile

commit 5e6365b8408ef22a6692bc8f377fa5e7ea1f0512
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 18 13:42:20 2018 -0700

    put some notes into subdirectory

Docs/Notes/Notes.io_implementation
Docs/Notes/Readme.backtrace
Docs/Notes/Readme.io
Docs/Notes/Readme.profiling
Docs/Notes/Readme.typecheck
Docs/README.md
Docs/Readme.sphinx

commit 75dd369e746264ec85cdf3d3cffcac235dad9b79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 18 13:33:28 2018 -0700

    reset hypre solver in case the solver is reused

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 028acad6856c463fc82d8f0a4638c5051e19e2b4
Merge: babdc7964 06d9bacf3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 18 13:18:00 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit babdc7964de652dd4b525ac016784ff724626d56
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 18 13:16:25 2018 -0700

    ZFILL -> AMREX_ZFILL

Src/Base/AMReX_ArrayLim.H

commit ee035aade6d2e23f51108f4d89fbb1c802b05cea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 18 13:14:09 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

Src/Base/AMReX_ArrayLim.H

commit 25e95b4a3589b190b91233d147dd9178c4bea875
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 18 13:08:43 2018 -0700

    cleanup

Src/EB/AMReX_ebinterp_2d.F90
Src/EB2/AMReX_eb2_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit eedbd40e4c75758051a0eee36dbd7d3fb1c32c6c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 18 13:06:58 2018 -0700

    fix return

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H

commit 796b05b8a065031aacad1bf75a01ce5eedc6dae7
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 15:58:40 2018 -0400

    Create fewer streams to shorten initialization time

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H

commit af932c15d8134505a1dd5a15b17c8267d1b6b863
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 18 12:48:02 2018 -0700

    save parent in factory

Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_Level.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 5337abf745959056a69a42cb534b9d82387e9aff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 18 08:47:33 2018 -0700

    use AMREX_USE_GEOMETRYSHOP. add parent information to EB2::Level and Factory

Src/Amr/AMReX_StateData.H
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_IndexSpaceI.H
Src/EB2/AMReX_EB2_Level.H

commit d38840f0a943f6bde1dbc5721d454869b2857e46
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 06:18:48 2018 -0400

    GPU script learns about AMREX_REAL_ANYD

Tools/F_scripts/write_cuda_headers.py

commit 64c7aeb2eb89b48dc9dd6468e0dc44949808f2e7
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 06:18:30 2018 -0400

    Add AMREX_REAL_ANYD

Src/Base/AMReX_ArrayLim.H

commit 729c84f8bccd807cecd2249e90d7af34972ed258
Merge: a3d678573 06d9bacf3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 05:39:07 2018 -0400

    Merge branch 'development' into gpu

commit 06d9bacf35f1e3ad6b04093f991fcb4fb0cf90a8
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 05:23:01 2018 -0400

    Add macros for compatibility with GPU branch

Src/Base/AMReX_ArrayLim.H

commit a3d678573fe6d6697420daa6672238e864db2672
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 05:08:11 2018 -0400

    Remove MFIter::registerBox

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit c276cb1ae3886a75f9b12a40fc960adf744b6832
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 05:01:19 2018 -0400

    Sync up Box class with development

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp

commit fb160e974d4c7581abda1674ddf72c6e62fac44b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 05:01:07 2018 -0400

    Add some missing includes

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MFIter.H

commit c71c43536f9581b3d47af8ee10e15d8f28cf2993
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 04:49:38 2018 -0400

    Pass intvect by value for several common macros

Src/Base/AMReX_ArrayLim.H
Tools/F_scripts/write_cuda_headers.py

commit d66734b85a5aa230b17f245051c49b6d650efe92
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 03:29:15 2018 -0400

    AMREX_ARLIM_ARG -> AMREX_INT_ANYD

Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_BaseFab.cpp
Tutorials/GPU/HeatEquation_EX1_C/advance.cpp

commit a60a5e08cc59d633c44025ae4ca8f05a420fe34d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 18 03:24:23 2018 -0400

    Make GPU script aware of BL_TO_FORTRAN

Tools/F_scripts/write_cuda_headers.py

commit 0c958eb215dc875cf043a10005e66db165b19e62
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 17 18:44:41 2018 -0700

    MLMG reuse for EB too

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit cc81903911e0ffc480910ca4f6c9bc3eedcde49c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 17 18:38:09 2018 -0700

    allow MLMG being reused

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 61395dc158d6b3852b75fe5a83d5fbf579ce0339
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 17 17:09:46 2018 -0400

    change the default value of USE_CUDA in the OMP HeatEquation example.

Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/GNUmakefile

commit 5226a6a8087c46546ebac8ac4e02c0f99de5fa4c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 17 17:09:16 2018 -0400

    no longer need to do special memory allocation for OMP_OFFLOAD

Src/Base/AMReX_BArena.cpp

commit 9668e34e275994a81d5f1256bc783505f3b2b4c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 17 13:54:40 2018 -0700

    make EB2 the default

Src/EB2/AMReX_EB2.cpp

commit 001d25f8fa384a79630fa6721faa612aae1f7e23
Merge: d4a3f3c80 2edabdb09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 17 13:48:08 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 77b396421d2bc18fd73812c9f86d94f3d5c2e017
Merge: 642e93b28 cdd8cb0e2
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 17 16:44:27 2018 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 642e93b28d8814a0ce50e94b8ba41356c8d9e0f1
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri Aug 17 16:44:05 2018 -0400

    add in missing cudaDeviceSynchronize to FillBoundary (bug only affected NProcs = 1)

Src/Base/AMReX_FabArrayCommI.H

commit d4a3f3c801ebe1a8f123012a9458ba2004e51e3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 17 13:41:49 2018 -0700

    use the new GetVecOfArrOfPtrs

Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp
Tutorials/EB/MacProj/main.cpp

commit 715e0c1e4fd074f435f8ea72327e5bbe5d445ea4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 17 13:37:57 2018 -0700

    fix the new GetVecOfArrOfPtrs with enable_if

Src/Base/AMReX_Vector.H

commit 0334eca80928e427274001de58de1b93e72875d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 17 13:36:32 2018 -0700

    add IsFabArray type traits

Src/Base/AMReX_TypeTraits.H

commit 40f0c98cec9edb0e95c8c659303754b842f224db
Author: Cy Chan <cychan@lbl.gov>
Date:   Fri Aug 17 13:06:48 2018 -0700

    fix bug in ParallelReduce.H for USE_MPI=FALSE

Src/Base/AMReX_ParallelReduce.H

commit 2edabdb090fbcc0888a3cdf61ed0603a752d6f28
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 17 11:05:24 2018 -0700

    Update CMake stuff to take AMREX_ENABLE_GEOMETRY_SHOP option through CMake and
    convert it to AMREX_USE_GEOMETRY_SHOP flag

Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake

commit e33d461af4d779c26b2d1bbd1804acf9be0c9d0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 17 10:55:35 2018 -0700

    fix bug in my last commit

Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp

commit dce9b3210f27a5f02d14aa152ffbf54f005e4b6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 17 10:47:23 2018 -0700

    MacProjector: support regular geometry too

Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp

commit 2e0bde34bf37c5368855398c6b79a05db2f0f930
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 17 10:41:03 2018 -0700

    comment out VisMF::Write

Tutorials/EB/MacProj/main.cpp

commit d7c6c52f88c5aa9f476b8a3ebbbf0bc1054ac0a5
Merge: 29dfbaadc b6572b0b5
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Aug 17 10:33:59 2018 -0700

    Merge pull request #301 from jared321/flash_fluxcorrection
    
    Flux correction changes needed for FLASH

commit 6d22c43a282079b90e65fa95381fbe37e872d2e5
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Aug 17 13:03:27 2018 -0400

    Test program.

Tutorials/GPU/Test/GNUmakefile
Tutorials/GPU/Test/Make.package
Tutorials/GPU/Test/main.cpp
Tutorials/GPU/Test/run.exitcode
Tutorials/GPU/Test/run.script

commit cdd8cb0e28576d52c5b95ce50905da758657107a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Aug 17 03:36:18 2018 -0400

    GPU script now passes AMREX_INT_ANYD wrapped IntVects by value
    
    Still needs work; there is an incompatibility between the argument
    positions in the C++ and the preprocessed headers.

Src/Base/AMReX_ArrayLim.H
Tools/F_scripts/write_cuda_headers.py

commit 936f38fc48c66341bc3bb39cad3e7a68174a8e10
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Aug 17 02:33:59 2018 -0400

    Add capability for script to detect argument location of macros

Tools/F_scripts/write_cuda_headers.py

commit 29dfbaadc1adf19d96c0aa400f23f8d154f9516d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 16 21:44:12 2018 -0700

    switch to IAMR sign convention

Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp
Tutorials/EB/MacProj/main.cpp

commit c733a2a23453b4fe71a34046b7de83043e1cf6d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 16 21:35:10 2018 -0700

    add EB2::useEB2 function to update the use_eb2 flag

Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2.cpp

commit 46df61c1b19c211e9c506d6ae37d74fd9124713a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 16 18:32:12 2018 -0700

    finish MacProjector and tutorial

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_F.H
Src/EB/AMReX_EBMultiFabUtil_nd.F90
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MacProjector.H
Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp
Tutorials/EB/MacProj/main.cpp

commit 716bcc4ffea93a7242403a3adbf8c0144a0bbfb8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 16 17:24:12 2018 -0700

    remove some debug lines

Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp

commit 8e76dbc7533642dde83cbf65d78fb29421cab32d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 16 17:23:35 2018 -0700

    have to remove the new GetVecOfArrOfPtrs because it breaks the old one

Src/Base/AMReX_Vector.H

commit 687840cefbcd70b6b9b8168712bac431e82a5698
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 16 17:15:06 2018 -0700

    add new files

Src/LinearSolvers/MLMG/AMReX_MacProjector.H
Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp

commit 1696fe655d768f467fae584d701503d736703527
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Aug 16 20:10:09 2018 -0400

    Change HeatEquation_EX1 to GPU global functions version.

Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit 62d8d354723e42c30cd19c03c45be0552440f19a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Aug 16 20:05:17 2018 -0400

    Remove un-needed in linear solver heat equation tutorial... for now.

Tutorials/GPU/HeatEquation_EX2_C/Exec/GNUmakefile
Tutorials/GPU/HeatEquation_EX2_C/Exec/inputs_2d
Tutorials/GPU/HeatEquation_EX2_C/Exec/inputs_3d
Tutorials/GPU/HeatEquation_EX2_C/Source/Make.package
Tutorials/GPU/HeatEquation_EX2_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX2_C/Source/advance_2d.f90
Tutorials/GPU/HeatEquation_EX2_C/Source/advance_3d.f90
Tutorials/GPU/HeatEquation_EX2_C/Source/init_phi_2d.f90
Tutorials/GPU/HeatEquation_EX2_C/Source/init_phi_3d.f90
Tutorials/GPU/HeatEquation_EX2_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc.H
Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc_F.H

commit 2ae645f1955c692c32100c6dc26dcf1b2616be00
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Aug 16 19:59:23 2018 -0400

    Adjustment to GPU Box distribution strategy.

Src/Base/AMReX_Box.H
Src/Base/AMReX_CUDA_Utility.cpp
Src/Base/AMReX_IndexType.H

commit 7746413ba967f29ffec305f8ed2f859933b50cb4
Merge: 7b84b294d 019aa570e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 16 16:55:31 2018 -0700

    Merge branch 'development' into mlmg

commit 019aa570e4d0d47ee40b254e6a8c8c8c8113f7ea
Merge: 9bd4a028c 195666aa0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 16 16:54:51 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9bd4a028c743c7c6ac87984bfdecd4ff864a55c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 16 16:54:39 2018 -0700

    MacProjector: compute rhs and then solve

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_F.H
Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_3d.F90
Src/EB/AMReX_EBMultiFabUtil_F.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Tutorials/EB/MacProj/inputs

commit 195666aa01f03d64ebdcd22616f23c0f872faff7
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Aug 16 16:00:11 2018 -0700

    Fixed some document typos + some rewording for clarity.

Docs/sphinx_documentation/source/Basics.rst

commit e5eb1030d3f3675fe08fd7655c0dc18ddcfd3e46
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Aug 16 14:59:33 2018 -0700

    fix a small bug

Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp

commit aade9c7e7da6e8ce672645ce64e5e0383b734620
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 16 14:58:47 2018 -0700

    start MacProjector

Src/EB2/AMReX_EB2.cpp
Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/Make.package
Tutorials/EB/MacProj/GNUmakefile
Tutorials/EB/MacProj/Make.package
Tutorials/EB/MacProj/initEB.H
Tutorials/EB/MacProj/initEB.cpp
Tutorials/EB/MacProj/inputs
Tutorials/EB/MacProj/main.cpp

commit 8420a7153db30c0be76891043733b58da02a1992
Merge: 88d1fe3d8 b3392d7a5
Author: kngott <kngott@lbl.gov>
Date:   Thu Aug 16 14:01:42 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-codes/amrex into development

commit 7b84b294d6c866e6e640700daeaa34df95296bd1
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Aug 16 13:39:25 2018 -0700

    GetVecOfArrOfPtrs implemented for regular class T

Src/Base/AMReX_Vector.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Tests/LinearSolvers/EBflux_grad/MyTest.H
Tests/LinearSolvers/EBflux_grad/MyTest.cpp

commit b3392d7a50ed9dbf4d7e8066059db7542747b0f6
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Aug 16 13:29:27 2018 -0700

    fix a mem leak bug in the runtime backend

Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp

commit 88d1fe3d87f0786a2b6c8c63cbac1aae88ddf629
Author: kngott <kngott@lbl.gov>
Date:   Thu Aug 16 13:17:01 2018 -0700

    int to long in Profiler to accomodate very large profiling jobs. More similar fixes to likely come later.

Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp

commit b6572b0b5ed428d08ac1b70dc3fa53779723e5d0
Author: Jared O'Neal <joneal@anl.gov>
Date:   Thu Aug 16 14:42:35 2018 -0500

    Fixed bug in OverwriteFlux routine.  The code was coarsening the grid in the
    FluxRegister constructor and in the OverwriteFlux function.  It now just
    coarsens at construction.  For FLASH, we only need to do flux correction at
    fine/coarse boundaries.  Therefore, altered code to ignore physical boundaries.

Src/AmrCore/AMReX_FLUXREG_nd.F90
Src/AmrCore/AMReX_FluxRegister.cpp

commit 9e1f388a220b884400052789245565bcd54572b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 16 12:28:27 2018 -0700

    documentation

Docs/sphinx_documentation/source/EB.rst
Docs/sphinx_documentation/source/EB/eb_fluxes.eps
Docs/sphinx_documentation/source/EB/eb_fluxes.fig
Docs/sphinx_documentation/source/EB/eb_fluxes.fig.bak
Docs/sphinx_documentation/source/EB/eb_fluxes.pdf
Docs/sphinx_documentation/source/EB/eb_fluxes.png
Docs/sphinx_documentation/source/LinearSolvers.rst

commit dcc3a0c3f438cad6eb09ba0fa0c49c5704a89ca9
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Aug 16 10:12:19 2018 -0700

    Killed the 3D bug. EB Grad and Flux work for 2D and 3D

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H
Tests/LinearSolvers/EBflux_grad/MyTest.cpp

commit d72246a1a5e97fd4d3268fe5d501e3a8ad497802
Merge: 5132d4aa6 451d50cb8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 15 18:19:26 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5132d4aa6053822aa9d86c0ef43ac26eafbaa2ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 15 18:19:05 2018 -0700

    linear solver documentation

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/Chapter7.rst
Docs/sphinx_documentation/source/LinearSolvers.rst
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H

commit 451d50cb86d284b171d6c1e2c8e7bd572664cf6f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Aug 15 17:26:40 2018 -0700

    If you try to build and EBTower 'over' another, the second one is ingored. This is a misleading design pattern => throw error if trying to build EBTower twice (without clearing the old one first)

Src/EB/AMReX_EBTower.cpp

commit 71e48d0513d3539a68522e178f5b7846d515bb86
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Wed Aug 15 16:20:34 2018 -0700

    Flux and Grad 2D are working, flux 3D is working. Debugging Grad 3D

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H
Tests/LinearSolvers/EBflux_grad/GNUmakefile
Tests/LinearSolvers/EBflux_grad/Make.package
Tests/LinearSolvers/EBflux_grad/MyEB.H
Tests/LinearSolvers/EBflux_grad/MyTest.H
Tests/LinearSolvers/EBflux_grad/MyTest.cpp
Tests/LinearSolvers/EBflux_grad/initEB.cpp
Tests/LinearSolvers/EBflux_grad/inputs
Tests/LinearSolvers/EBflux_grad/main.cpp

commit d70359ca590e64a5c89301c6de96aa851da827f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 15 14:55:16 2018 -0700

    std::array --> Array

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp

commit 22120f0d3b037593e208dc01a3fa3582f5faab3f
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Wed Aug 15 11:32:25 2018 -0700

    amrex_mlebabeclap_flux/grad compile for both 2D and 3D

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 4c29dbfa4e52d5451babad792e5f74b77677f8f1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 15 10:04:21 2018 -0700

    Don't use ls_ba as a local variable when it's defined in the .H file

Src/EB/AMReX_EB_levelset.cpp

commit 79115e587021a0fde264828113c8fc1e9e71afb5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 14 18:13:05 2018 -0700

    remove using namespace amrex from headers

Tutorials/Basic/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.H
Tutorials/Basic/HeatEquation_EX2_C/Source/advance.cpp
Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc.H
Tutorials/Basic/HeatEquation_EX3_C/Source/advance.cpp
Tutorials/Basic/HeatEquation_EX3_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX3_C/Source/myfunc.H

commit 4e5ea54d60b983042893e6b0fb67aafe1c4fde3f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 14 18:04:40 2018 -0700

    update documentation

Docs/sphinx_documentation/source/AmrCore.rst
Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/Visualization.rst
Src/Base/AMReX.cpp

commit 0e1bf8dc0f657cb89015b8365a7fea0504c21d79
Author: sireeveslbl <sireeves@ucsc.edu>
Date:   Tue Aug 14 17:39:21 2018 -0700

    Get Gradient of solution implemented for 2D

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit c0572aa5179f0ad3f5bc07247b5515e7db6120c5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 14 16:04:05 2018 -0700

    Remove unused variables

Src/EB/AMReX_EBFluxRegister_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90

commit 768047436ac6c39ed485c77cc27eb084404957c2
Merge: 01cc5a795 b42954ee7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 14 16:02:56 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 01cc5a795b2c7727fe3d2b09c4fe9102ad33afa4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 14 16:02:32 2018 -0700

    Remove unused variable

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit b42954ee748f31aad2b759139c33f8bb3207a7c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 14 16:00:59 2018 -0700

    update documentation

Docs/Readme.typecheck
Docs/sphinx_documentation/source/Basics.rst

commit 54e23158e526ca32fb6f7378c365638878ac2089
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Aug 14 17:21:15 2018 -0400

    Setup for larger comparison testing.

Src/Base/AMReX_Box.H
Src/Base/AMReX_CUDA_Utility.cpp
Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC/inputs
Tutorials/GPU/ElectromagneticPIC/summitdev.sh
Tutorials/Particles/ElectromagneticPIC/Evolve.cpp

commit c460d7cca01d6977706dfd85ac741fa86c29b204
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 14 13:49:20 2018 -0700

    set dt_level after building bldFineLevels

Src/Amr/AMReX_Amr.cpp

commit 58af6bbbc696cf719caa35463b90169286c2f5ed
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Aug 14 16:13:31 2018 -0400

    Global function version of ElectromagneticPIC.

Tutorials/GPU/ElectromagneticPIC_1/Constants.H
Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.H
Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC_1/Evolve.H
Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC_1/GNUmakefile
Tutorials/GPU/ElectromagneticPIC_1/IO.H
Tutorials/GPU/ElectromagneticPIC_1/IO.cpp
Tutorials/GPU/ElectromagneticPIC_1/Make.package
Tutorials/GPU/ElectromagneticPIC_1/NodalFlags.H
Tutorials/GPU/ElectromagneticPIC_1/NodalFlags.cpp
Tutorials/GPU/ElectromagneticPIC_1/Particles.H
Tutorials/GPU/ElectromagneticPIC_1/StructOfArrays.H
Tutorials/GPU/ElectromagneticPIC_1/em_pic_3d.F90
Tutorials/GPU/ElectromagneticPIC_1/em_pic_F.H
Tutorials/GPU/ElectromagneticPIC_1/inputs
Tutorials/GPU/ElectromagneticPIC_1/main.cpp
Tutorials/GPU/ElectromagneticPIC_1/summit.sh
Tutorials/GPU/ElectromagneticPIC_1/summitdev.sh
Tutorials/GPU/ElectromagneticPIC_1/test.cpp

commit 8ed8342ccebd1edfb8f48a56078d5b5518523e1f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Aug 14 16:11:06 2018 -0400

    Fix size check.

Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp

commit a87cb4474b16e8e4a99951a7dd182a73e0cf7dc7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Aug 14 16:10:42 2018 -0400

    Adjusting GPU box setup.

Src/Base/AMReX_CUDA_Utility.cpp

commit ae99c03811256956b7b15af08199e80832ed3069
Merge: 7d1eb83fb b63478695
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Aug 14 12:45:35 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 7d1eb83fbb7585367902a316c89e4e6d9e693403
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Aug 14 12:45:27 2018 -0700

    first demo of the upcxx backend

Src/Amr/AMReX_Amr.cpp

commit 2dc26ef627cb38f64fee6914b7b88e54ec9ad569
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Aug 14 12:35:13 2018 -0700

    a demo version of the upcxx backend

Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp
Src/Base/AMReX.cpp

commit b634786956a5e213c38c4b865540d6177a594d54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 14 12:26:14 2018 -0700

    update documentation

Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/BuildingAMReX.rst
Docs/sphinx_documentation/source/Chapter3.rst

commit 603288e70f53d1f2c1b052b485cda343b97d4b00
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Aug 14 01:54:05 2018 -0400

    Catch a corner case in device function naming

Tools/F_scripts/gpu_fortran.py

commit 4b5b6cb9bc7dd349a01e2267d258227ebdf0a23d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 13 18:19:55 2018 -0700

    move heat equation example to the end of the chapter on base so that the readers have seen names like MultiFab, BoxArray, etc. at that time

Docs/sphinx_documentation/source/Basics.rst
Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp

commit c4da60a9355d858949286c8151fb9ed1b133fdd6
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Aug 13 20:43:15 2018 -0400

    Improved GPU thread distribution method.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CUDA_Utility.cpp
Tutorials/GPU/ElectromagneticPIC/Evolve.cpp

commit 8638ccc1e4ea90b78e0bc810a0efcb2c49fc5e2b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 13 17:41:07 2018 -0700

    update documentation

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit f14f51c97da01f3a19fd699c6598ebfa1348e048
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 13 17:40:44 2018 -0700

    add hypre to libamrex

GNUmakefile.in
Tools/libamrex/configure.py

commit 1cdf1f952f59bee27b625b11b232447d0fbd8eb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 13 17:22:21 2018 -0700

    add EB to libamrex.a as optional feature

GNUmakefile.in
Src/Amr/AMReX_StateData.H
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Tools/libamrex/configure.py
Tutorials/EB/CNS/Exec/Make.CNS
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp

commit 6b8aeddecc52f5132dd4043248620e8487231a1b
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Aug 13 20:02:03 2018 -0400

    Implement ParticlesData.

Src/Base/AMReX_Box.H
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H
Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC/Particles.H

commit 76af532cb52f723750ef09972e19b917a36d2aa5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 13 16:46:26 2018 -0700

    update documentation

Docs/sphinx_documentation/source/BuildingAMReX.rst
Docs/sphinx_documentation/source/Chapter3.rst
Docs/sphinx_documentation/source/GettingStarted.rst
Docs/sphinx_documentation/source/Introduction.rst

commit 3b54e8f672b2b7c6cdb95ec2af8e987fde448564
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Aug 13 16:10:44 2018 -0700

    Flux routine for 2D and 3D compile. Will need to test them.

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H
Tests/LinearSolvers/EBConvergenceTest/bcoef.F90

commit 528f27bfb8449dd4d405631da7f52734c6250e74
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 13 15:27:14 2018 -0700

    less verbose

Src/Base/AMReX.cpp
Src/Base/AMReX_FabArrayBase.cpp

commit 035b24af7fa8d7be46bdb26d7824f5a10be3f281
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Aug 13 14:54:34 2018 -0700

    Did 2D comp flux for EB. Didn't break anything. Now for 3D.

Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H
Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot2D.m

commit 13a08eee35bc2a0f291b0844ae40c32e306be2ae
Merge: 70ead1df8 633ab9f48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 13 14:45:28 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 70ead1df866e9093a5d12411c2a67c234b9586c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 13 14:45:01 2018 -0700

    fix a bug 3d gsrb for eb

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 633ab9f48c18d5ff9e7c3eed85b3eea34ce480e7
Merge: b2b2f044e d18bba7d1
Author: Daniel Ladiges <drladiges@lbl.gov>
Date:   Mon Aug 13 13:28:52 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit b2b2f044e97370e05a34e7419a3877937329d4d5
Author: Daniel Ladiges <drladiges@lbl.gov>
Date:   Mon Aug 13 13:25:50 2018 -0700

    Added seperate FParallelMG2.mak file for AMReX-FHDeX, to avoid conflict with existing LLNS code

Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/FParallelMG2.mak

commit d18bba7d177e5ca0f8282ecacb2d8ba406eedfa4
Merge: 5e01ae0d1 1ba80eb7f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 13 12:33:02 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5e01ae0d1ea596a1619347e80bcd0223fea892ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 13 12:30:23 2018 -0700

    weight by volume fraction in computing max-norm error

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 8dfe7773f4dfc5698f526bf0cdc14a3dc077a42a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 13 10:47:59 2018 -0700

    EB linear solver test: add periodic test

Tests/LinearSolvers/CellEB/MyTest.H
Tests/LinearSolvers/CellEB/MyTest.cpp

commit 1ba80eb7f2d6fe43f677133075f07472a5e66013
Merge: ba1934e2b ca75ca481
Author: asalmgren <asalmgren@lbl.gov>
Date:   Mon Aug 13 09:34:27 2018 -0700

    Merge pull request #298 from AMReX-Codes/initial_dt_fix
    
    Do not initialize dt_level on levels that do not yet exist

commit ce57255fc97da415162a1297fd4c3e5e5bfc71ba
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Aug 12 02:39:47 2018 -0700

    Add OpenMP GPU offload version of HeatEquation_EX1_C tutorial (#296)
    
    * Tools: add Piz Daint at CSCS to list of sites/machines
    
    * GNUmake: add OpenMP GPU offload flags for XL on Summit/summitdev
    
    * Tutorials: create HeatEquation_EX1_C using OpenMP 4.5 GPU offloading

Src/Base/AMReX_BArena.cpp
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.cscs
Tools/GNUMake/sites/Make.olcf
Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/run_summit_1node.sh
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/Make.package
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance_2d.f90
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance_3d.f90
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/init_phi_2d.f90
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/init_phi_3d.f90
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/main.cpp
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/myfunc_F.H

commit ca75ca481429819d852eaac44da9c0856d6b515b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Aug 12 05:23:07 2018 -0400

    Do not initialize dt_level on levels that do not yet exist
    
    This initialization is problematic if the level 0 timestep when the simulation
    starts is significantly different from the timestep later on in the simulation
    when we add refinement. In particular, this will happen if the simulation code
    shrinks the initial timestep by some factor. If the fine levels are only added
    later on once the timestep has caught back up to its normal limited level, then
    the first timestep on the fine level will be effectively limited by the initial
    level 0 timestep, which can sharply decrease the timestep for no reason.

Src/Amr/AMReX_Amr.cpp

commit dbb6ea07aeb5a56e1e3645dace1c7ecbefdcb57f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 10 18:28:31 2018 -0700

    effectively remove the floor on target relative tolerance so that it's easy for testing how small the residual can be

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit ba1934e2b08099a1871f95d3474e9639f783a351
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Aug 10 17:13:18 2018 -0700

    Rewrite this AmrData function in terms of mesh and data that might be provided by something like SENSEI, e.g. (although fake it using plotfile data)

Tools/Postprocessing/C_Src/IntegrateComp.cpp

commit e766f5f851129e8e99330af9b7fca1c69fc66a53
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 10 16:38:10 2018 -0700

    typo in profiler name

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit aa8ad3e5ec446a6617e041793fa5c0b104eae4e5
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Aug 10 16:00:25 2018 -0700

    Add a simple AmrData-based integrate function.

Tools/Postprocessing/C_Src/IntegrateComp.cpp

commit 43736e05292f730b43f34f26d628e149500ac266
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Aug 10 14:17:06 2018 -0700

    Forgot to add RHS

Tests/LinearSolvers/EBConvergenceTest/RHS.F90

commit 39efc55a19ea159a75c527be49cf8fa5e8fe9397
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Aug 10 14:04:56 2018 -0700

    EB convergence testing complete.

Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp
Tests/LinearSolvers/EBConvergenceTest/RHS.F90
Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot2D.m
Tests/LinearSolvers/EBConvergenceTest/bcoef.F90

commit 01b9892d66f51caff036e08c75ae15d889f3679d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 9 16:53:43 2018 -0700

    must re-assign m_factory because rhs must be a different multifab

Src/Extern/PETSc/AMReX_PETSc.cpp

commit 334fafa0ea8c179691138ab10184d02b2212741d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 9 16:52:35 2018 -0700

    hypre: must re-assign m_factory because rhs must be a different multifab

Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit fbd640ac6005004bffb48060c5e57f6e80a2b2e1
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Aug 9 16:05:38 2018 -0700

    Solution is a little off at the physical boundary. Need to fix before moving on.

Tests/LinearSolvers/EBConvergenceTest/Make.package
Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp
Tests/LinearSolvers/EBConvergenceTest/MyTest_F.H
Tests/LinearSolvers/EBConvergenceTest/RHS.F90
Tests/LinearSolvers/EBConvergenceTest/acoef.F90
Tests/LinearSolvers/EBConvergenceTest/bcoef.F90

commit 5d7796d017b32a33bff93968c5bc17b9b7583734
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 9 16:00:56 2018 -0700

    EB solvability

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 7bc7628df20629309d72e1fd60fe3ac6e40e5db9
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Aug 9 08:32:06 2018 -0700

    Corrected Convergence script, and Octave scprit. 3D constant coefficient shows 2nd Order convergence.

Tests/LinearSolvers/EBConvergenceTest/Convergence_Data_Gen.sh
Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot3D.m

commit 54f7bf7cf3aeca9824973d2fe416b2816906c354
Author: sireeveslbl <sireeves@ucsc.edu>
Date:   Wed Aug 8 19:34:41 2018 -0700

    Still ironing out some bugs. Looks like the analytic solution isn't being generated correctly for the error calculation in 3D test case.

Tests/LinearSolvers/EBConvergenceTest/BC.F90
Tests/LinearSolvers/EBConvergenceTest/Convergence_Data_Gen.sh
Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp
Tests/LinearSolvers/EBConvergenceTest/RHS_2D.F90
Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot3D.m
Tests/LinearSolvers/EBConvergenceTest/Results/mfread2.m
Tests/LinearSolvers/EBConvergenceTest/Results/mfread3.m

commit 7e7381359b61b50616103f769be0d95141ff3ed0
Merge: 1966cb81f d771bcf5d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 8 16:13:12 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 1966cb81fab9f7360c7c6ec5a5913f6b423f8cab
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 8 16:13:03 2018 -0700

    update these function names

Tests/Particles/AssignDensity/main.cpp
Tests/Particles/AssignMultiLevelDensity/main.cpp

commit d771bcf5d9d319b210a7e0c1f1355e185f913695
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 8 16:11:20 2018 -0700

    update documentation

Docs/sphinx_documentation/source/IO.rst

commit 9526d97f230c40b52527c5793cf559ad00a66cfd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 8 15:39:22 2018 -0700

    reverse the order of the IOBuffer and fstream variables.

Src/Base/AMReX_NFiles.H
Src/Base/AMReX_PlotFileUtil.cpp
Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_TracerParticles.cpp
Tools/C_util/dbgTools/crsGrids.cpp
Tools/C_util/dbgTools/intersectGrids.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 96fea6ac2a01a49cdf7fb5a2712ce15efad34b90
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Aug 8 17:48:41 2018 -0400

    MultiFab to iMultiFab + Deviceifying BaseFab functions

Src/Base/AMReX_BaseFab.H
Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.H
Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC/inputs

commit be2456344bfdbcc44f45aaa9766dd4f634afc255
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Aug 8 14:39:24 2018 -0400

    Added simple overall timer and option to output error at each step.

Tutorials/GPU/ElectromagneticPIC/main.cpp

commit 898b21240eecd7531d4c1235668f446487e9f408
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 8 11:08:09 2018 -0700

    call pubsetbuf before fstream is opened, otherwise it has no effect for some compilers

Docs/Readme.sphinx
Docs/sphinx_documentation/source/IO.rst
Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_VisMF.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit a1e5ed9ca90963776b6855b43cbd002036296aef
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Aug 8 13:30:53 2018 -0400

    Convert emPIC to use BaseFab<Real>

Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp

commit eae40da887b44424aa4fd0d9bc6168b64217a465
Author: sireeveslbl <sireeves@ucsc.edu>
Date:   Tue Aug 7 22:08:27 2018 -0700

    3D MyTest now produces results that visually look like the analytical solution. Fixed MultiFabToMatlab 3D so now the binary files aren't garbage. Updated Bash script so user can specify spacedim of test.  Todo - Matlab/Octave script for 3D scaling plot.

Tests/LinearSolvers/EBConvergenceTest/BC_3D.F90
Tests/LinearSolvers/EBConvergenceTest/Convergence_Data_Gen.sh
Tools/Postprocessing/C_Src/MultiFabToMatLab.cpp

commit 333ae3f3541bccd0df9d29ba8a8e28fc4318baad
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Aug 7 16:12:38 2018 -0700

    Working on 3D Problem. There are some kinks to work out still.

Tests/LinearSolvers/EBConvergenceTest/BC_2D.F90
Tests/LinearSolvers/EBConvergenceTest/BC_3D.F90
Tests/LinearSolvers/EBConvergenceTest/Make.package
Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp
Tests/LinearSolvers/EBConvergenceTest/MyTest_F.H
Tests/LinearSolvers/EBConvergenceTest/RHS.F90

commit 2c21c72d18e98a7d1d3cd7426edf67b0a38d85fc
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Aug 7 18:21:41 2018 -0400

    DeviceBox and DeviceDomain replaced with standard AMReX objects.

Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC/summit.sh
Tutorials/GPU/ElectromagneticPIC/summitdev.sh

commit 085a9932f10a0c02cbd5d6965baa7069885db850
Merge: 8aeb67004 b4ed7b196
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 7 14:08:46 2018 -0700

    Merge branch 'master' into development

commit b4ed7b196f9b6ba0dda353e73a6f7612bdd6c7c6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 7 13:41:41 2018 -0700

    We have added a new flag -- system::regtest_reduction -- that controls whether or not we use the
    OpenMP reduction.  In AMReX_MultiFab we have replaced
    "pragma omp parallel reduction(+:sm)"
    by
    "pragma omp parallel if (!system::regtest_reduction) reduction(+:sm)"
    so that if you set system.regtest_reduction = 1 in your inputs file (or command line), you will
    not see the OpenMP-related variability in MultiFab sum and norm1.  You can also use this in
    your application code.

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_MultiFab.cpp

commit 2ca5c5aa1e033a5190e0dc25f136d3364b60af9a
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Aug 6 16:18:53 2018 -0700

    Convergence test for 2D constant coefficient successfully illustrates second order convergence. Convergence_Data_Gen.sh is a script that generates the EB solution for 32X32 to 1024x1024 grids. In the Results folder, there is an octave script that generates a scaling plot and saves it as a .png for later viewing.

Tests/LinearSolvers/EBConvergenceTest/BC.F90
Tests/LinearSolvers/EBConvergenceTest/Convergence_Data_Gen.sh
Tests/LinearSolvers/EBConvergenceTest/RHS_2D.F90
Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot2D.m
Tests/LinearSolvers/EBConvergenceTest/Results/mfread.m
Tests/LinearSolvers/EBConvergenceTest/inputs

commit 8aeb67004327c0662229bc81c70da67a7d5eac6d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Aug 6 15:28:15 2018 -0700

    fix typo in assert

Src/Base/AMReX_Geometry.cpp

commit a51af5058c800e77804a065318f7c9dce78a440d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Aug 6 14:39:16 2018 -0400

    Corrected run script for summitdev, different version for summit.

Tutorials/GPU/ElectromagneticPIC/summit.sh
Tutorials/GPU/ElectromagneticPIC/summitdev.sh

commit ad69f1499d5a4bcef9f779f85e7aadd223a8793e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Aug 6 09:59:52 2018 -0700

    if there is no information about the particle box array in the checkpoint file (true for old checkpoints), assume dual_grid = false.

Src/Particle/AMReX_ParticleContainerI.H

commit 023bbeb6873ac9dbc21423ebd991bb4870b31408
Merge: a8fdedc53 6ba44195c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Aug 6 10:00:01 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a8fdedc538dcc0eb86848c397a554c59ecc381f4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Aug 6 09:59:52 2018 -0700

    if there is no information about the particle box array in the checkpoint file (true for old checkpoints), assume dual_grid = false.

Src/Particle/AMReX_ParticleContainerI.H

commit 1381ae45a0f532a9e48794b1dc5c48c3d4ad1c91
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Aug 6 09:10:03 2018 -0700

    The BCs appear to be fixed.

Tests/LinearSolvers/EBConvergenceTest/BC.F90
Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp

commit f7dc10b7888679d9d36b7a236dc18f7787da2c6a
Author: sireeveslbl <sireeves@ucsc.edu>
Date:   Sun Aug 5 20:23:45 2018 -0700

    Seems to be correct, but odd error for small n_cell. Need to find the answer to this problem.

Tests/LinearSolvers/EBConvergenceTest/BC.F90
Tests/LinearSolvers/EBConvergenceTest/Make.package
Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp
Tests/LinearSolvers/EBConvergenceTest/MyTest_F.H

commit 6ba44195ced11fab5632638a712a8988ab964b85
Merge: 3e916d54c ba844dbd6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 4 09:31:02 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 3e916d54cbfdc7dc5d3c2c5a817c45ee316ba87a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 4 09:30:49 2018 -0700

    make sure MLMG works when AMREX_USE_EB is defined but EB indexspace is not defined

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit ba844dbd667fd8642f7aa7a2e4e69f1dbb709551
Merge: 448ed444f 66aecd3d9
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Aug 4 02:06:27 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 448ed444f97fe611ef87a070c32919eadce3af65
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Aug 4 02:06:02 2018 -0700

    upcxx backend

Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/Perilla_upc++/Barrier.H
Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp
Src/AmrTask/rts_impls/Perilla_upc++/LocalConnection.H
Src/AmrTask/rts_impls/Perilla_upc++/Make.package
Src/AmrTask/rts_impls/Perilla_upc++/Makefile
Src/AmrTask/rts_impls/Perilla_upc++/PackageQueue.H
Src/AmrTask/rts_impls/Perilla_upc++/PackageQueue.cpp
Src/AmrTask/rts_impls/Perilla_upc++/Perilla.H
Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp
Src/AmrTask/rts_impls/Perilla_upc++/PerillaConfig.H
Src/AmrTask/rts_impls/Perilla_upc++/PerillaRts.H
Src/AmrTask/rts_impls/Perilla_upc++/PerillaRts.cpp
Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.H
Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.cpp
Src/AmrTask/rts_impls/Perilla_upc++/RegionQueue.H
Src/AmrTask/rts_impls/Perilla_upc++/RegionQueue.cpp
Src/AmrTask/rts_impls/Perilla_upc++/RemoteConnection.H
Src/AmrTask/rts_impls/Perilla_upc++/WorkerThread.H
Src/AmrTask/rts_impls/Perilla_upc++/WorkerThread.cpp
Src/AmrTask/rts_impls/Perilla_upc++/mylock.h
Src/AmrTask/rts_impls/Perilla_upc++/perilla.mak

commit 623b935ae8584a556e57e94c89469a9dfffe69e9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 3 14:30:41 2018 -0700

    streamline particle restart when dual-grid is enabled.

Src/Particle/AMReX_ParticleContainerI.H

commit 66aecd3d90e4139db2d9e25732dfb5274e8cbbba
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 3 17:26:17 2018 -0700

    remove a debug print.

Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp

commit e31ae6bddf17c3db86a9b8bfda44e0a462c18a22
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 3 17:13:13 2018 -0700

    add a bunch of debugging functions to the CellSortedPC

Tutorials/Particles/CellSortedParticles/CellSortedPC.H
Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp

commit 91677b5a9f3f2d1cdfbe53b5c263c1e71642ea2b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 3 14:45:52 2018 -0700

    fix parameter shadowing

Src/Particle/AMReX_ParticleContainerI.H

commit d80152c510c19b08af9c87b78b10d1f40b30fa1d
Merge: 964cde61a a3150ebc2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 3 14:33:55 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 964cde61a2155e45bb0e98f3dd465522f74249e4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 3 14:33:38 2018 -0700

    some work on enabling caching of the cell vectors for the DSMC code

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Tutorials/Particles/CellSortedParticles/CellSortedPC.H
Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp
Tutorials/Particles/CellSortedParticles/cell_sorted_3d.F90
Tutorials/Particles/CellSortedParticles/main.cpp

commit a3150ebc2ca6defa45d92715a4fea7e5d23a4705
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 3 14:30:41 2018 -0700

    streamline particle restart when dual-grid is enabled.

Src/Particle/AMReX_ParticleContainerI.H

commit 96b0e13760aa043fc3aa24a6c2b7fa8b6202a035
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Aug 3 09:49:16 2018 -0400

    emPIC working on Summitdev w one rank.

Src/Base/AMReX_CUDA_Utility.cpp
Src/Base/AMReX_Device.cpp
Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC/GNUmakefile
Tutorials/GPU/ElectromagneticPIC/em_pic_3d.F90
Tutorials/GPU/ElectromagneticPIC/script.nompi.sh
Tutorials/GPU/ElectromagneticPIC/script.sh

commit bdd98934e52bc425b3a4b2966af6363c0b0b8cbf
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Aug 2 11:09:18 2018 -0700

    added inputs

Tests/LinearSolvers/EBConvergenceTest/inputs

commit 50d3a4017a4a09a6f0cc876e40c10a6dc0765bab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 1 18:16:15 2018 -0700

    WIP: PETScABecLap

Src/Extern/PETSc/AMReX_PETSc.cpp

commit 4b46a85a7299892785a6c81d573bc114f419743c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 1 16:56:21 2018 -0700

    WIP: PETScABecLap

Src/Extern/HYPRE/Make.package
Src/Extern/PETSc/AMReX_PETSc.H
Src/Extern/PETSc/AMReX_PETSc.cpp
Src/Extern/PETSc/Make.package

commit 12cfbf4d1aaf371c61592e6db87acd3d0d813489
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Wed Aug 1 19:26:11 2018 -0400

    some reorganization

Src/Particle/AMReX_RedistributeStrategy.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Source/Particles.H

commit 87d8a087a4755252a94a6b864bdc8fcd3d388aec
Merge: 83b848e56 2296e58b0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 1 15:53:55 2018 -0700

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 83b848e560f9750e1ce88cbd51f72afa867b3324
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 1 15:49:29 2018 -0700

    fix compilation problem on Travis build

Src/Particle/AMReX_RedistributeStrategy.H
Src/Particle/AMReX_RedistributeStrategyCPU.cpp
Src/Particle/AMReX_RedistributeStrategyGPU.cpp
Src/Particle/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp

commit fcc76e32db54098b2d5429e4fa26c4de4af26393
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Aug 1 14:18:43 2018 -0700

    Make sure define is called when reading a coordsys

Src/Base/AMReX_CoordSys.cpp

commit a817ab604c4194200facb4cd5cc95e34e049112a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 1 14:29:35 2018 -0700

    Add the MLMG path to the new files added to CMakeLists.txt which
    are only included if ENABLE_EB is on.

Src/LinearSolvers/CMakeLists.txt

commit 9016683614915cd804cc566b1b69c23f1baf97ea
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Aug 1 14:18:43 2018 -0700

    Make sure define is called when reading a coordsys

Src/Base/AMReX_CoordSys.cpp

commit f02a1fc3f0b638220c3a2ebc94b3a717e07294be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 1 13:07:34 2018 -0700

    add Make.petsc

Tools/GNUMake/packages/Make.petsc

commit 722241e1e7f72f96194fd990c56691f316bf25ef
Merge: 1068a7da5 9ac3da07b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 1 13:03:53 2018 -0700

    Merge branch 'development' into petsc

commit 2296e58b088827667bc54ff7c3519cb57b8d5068
Merge: 42f9fbd50 7854d354d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 1 12:51:00 2018 -0700

    Merge pull request #295 from ylunalin/gpu
    
    Added collapse clause to acc directives on the triple do loops.

commit 9ac3da07b0e4b9dd7ff23b7f3497a8dfb67a278b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 1 12:18:15 2018 -0700

    minor optimization: use mfi instead of int index

Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit 7854d354dfe8ff8a0ef504a59ec4209efb500d4c
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Wed Aug 1 15:14:05 2018 -0400

    Added collapse clause to acc directives on the triple do loops.

Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90

commit ef02ea30568a89a716cf48de74eed1516996b2dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 1 11:14:49 2018 -0700

    MLMG: for multiple components, we only need to to do one allreduce

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 57c664b21a28c8549e84c1cc0164e2a59e340e88
Merge: 1a6826139 2c344fa6d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 1 11:01:51 2018 -0700

    Merge branch 'development' into hypre

commit 2c344fa6dd98aa9acf2e744983b24e4d14357a80
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 1 11:00:23 2018 -0700

    update CHANGES

CHANGES

commit 8e4c6dbd8605d2a47d43433a105d541fd0a0aa14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 31 23:18:25 2018 -0700

    reimplement LayoutData copy ctor and assignment op

Src/Base/AMReX_LayoutData.H

commit 1a68261392069580c321bd0df047800ba8d660a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 31 21:34:20 2018 -0700

    add boomeramg parameters

Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp

commit 10764c6c00bf0e1bda32dd0e48db11a06e904302
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 31 21:31:08 2018 -0700

    clean up

Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit 914dc018f9e38fc514082af6ddf47af79346090e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 31 18:24:15 2018 -0700

    remove bd key from LayoutData

Src/Base/AMReX_LayoutData.H

commit 42f9fbd50d8a0e7f4135bfef6d8ba6ec58d94db5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 31 20:20:52 2018 -0400

    put shared code into a Source directory

Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Constants.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/IO.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/IO.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Particles.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/main.cpp
Tutorials/Particles/ElectromagneticPIC/Make.EMPIC
Tutorials/Particles/ElectromagneticPIC/Source/Constants.H
Tutorials/Particles/ElectromagneticPIC/Source/IO.H
Tutorials/Particles/ElectromagneticPIC/Source/IO.cpp
Tutorials/Particles/ElectromagneticPIC/Source/Make.package
Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/Source/Particles.H
Tutorials/Particles/ElectromagneticPIC/Source/main.cpp

commit 86899895521a018893a97ade12954241395db9ff
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 31 19:53:50 2018 -0400

    move the Cuda and OpenACC problem directories into Exec

Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Constants.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/IO.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/IO.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Particles.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/inputs
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/main.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/script.sh
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Constants.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/IO.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/IO.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Particles.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/inputs
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/main.cpp
Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/script.sh

commit 78151857c38412c67439be1930ec178a3846866c
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 31 19:49:01 2018 -0400

    some slight renaming

Tutorials/Particles/ElectromagneticPIC/Cuda/Constants.H
Tutorials/Particles/ElectromagneticPIC/Cuda/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/Cuda/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Cuda/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Cuda/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/Cuda/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Cuda/IO.H
Tutorials/Particles/ElectromagneticPIC/Cuda/IO.cpp
Tutorials/Particles/ElectromagneticPIC/Cuda/Make.package
Tutorials/Particles/ElectromagneticPIC/Cuda/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/Cuda/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/Cuda/Particles.H
Tutorials/Particles/ElectromagneticPIC/Cuda/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/Cuda/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/Cuda/inputs
Tutorials/Particles/ElectromagneticPIC/Cuda/main.cpp
Tutorials/Particles/ElectromagneticPIC/Cuda/script.sh
Tutorials/Particles/ElectromagneticPIC/OpenACC/Constants.H
Tutorials/Particles/ElectromagneticPIC/OpenACC/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/OpenACC/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/OpenACC/Evolve.H
Tutorials/Particles/ElectromagneticPIC/OpenACC/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/OpenACC/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/OpenACC/IO.H
Tutorials/Particles/ElectromagneticPIC/OpenACC/IO.cpp
Tutorials/Particles/ElectromagneticPIC/OpenACC/Make.package
Tutorials/Particles/ElectromagneticPIC/OpenACC/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/OpenACC/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/OpenACC/Particles.H
Tutorials/Particles/ElectromagneticPIC/OpenACC/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/OpenACC/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/OpenACC/inputs
Tutorials/Particles/ElectromagneticPIC/OpenACC/main.cpp
Tutorials/Particles/ElectromagneticPIC/OpenACC/script.sh

commit 5957a23185e0eca03a0084477b256259911e7084
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 31 19:45:16 2018 -0400

    remove the original directory

Tutorials/Particles/ElectromagneticPIC/orig/Constants.H
Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/orig/Evolve.H
Tutorials/Particles/ElectromagneticPIC/orig/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/orig/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/orig/IO.H
Tutorials/Particles/ElectromagneticPIC/orig/IO.cpp
Tutorials/Particles/ElectromagneticPIC/orig/Make.package
Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/orig/Particles.H
Tutorials/Particles/ElectromagneticPIC/orig/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/orig/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/orig/inputs
Tutorials/Particles/ElectromagneticPIC/orig/main.cpp
Tutorials/Particles/ElectromagneticPIC/orig/script.sh

commit 1f1ac5cceb4edf074736dc87f41d5bd3856b2aa5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 31 19:44:37 2018 -0400

    finish off the merge between my stuff and Luna's

Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.cpp

commit 74667c7d8ca2f0a899e0dd2d4da4e5ad346c92bf
Merge: be215feeb 70a2b8266
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 31 19:19:55 2018 -0400

    merging gpu_particles_refactor into gpu

commit be215feebb73660e761890906b762bd67ac8e381
Merge: a3e009611 73cce6faa
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 31 16:11:18 2018 -0700

    Merge pull request #294 from ylunalin/gpu
    
    Try again to merge new GPU particles EMPIC tutorial in.

commit 73cce6faad2ddb5e6e49c586495b92d9b6e9abc3
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Tue Jul 31 18:40:51 2018 -0400

    Fixed the fortran subroutine name binding issue.

Tutorials/Particles/ElectromagneticPIC/acc/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/acc/inputs
Tutorials/Particles/ElectromagneticPIC/orig/inputs

commit 70a2b826616d01719812f444eeffb00c6fc31888
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Tue Jul 31 17:59:07 2018 -0400

    move the GPU particle redistribute code into Src/Particle

Src/Particle/AMReX_RedistributeStrategy.H
Src/Particle/AMReX_RedistributeStrategyCPU.cpp
Src/Particle/AMReX_RedistributeStrategyGPU.cpp
Src/Particle/Make.package
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Make.package

commit 02abaf3ec71b43da2184f2068b9cd7d154903cd6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 31 14:32:46 2018 -0700

    Remove deprecated Tutorial.  We now use hypre through MLMG.

Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tutorials/HYPRE/ABecLaplacian/ABL.H
Tutorials/HYPRE/ABecLaplacian/ABL.cpp
Tutorials/HYPRE/ABecLaplacian/ABL_F.F90
Tutorials/HYPRE/ABecLaplacian/ABL_F.H
Tutorials/HYPRE/ABecLaplacian/GNUmakefile
Tutorials/HYPRE/ABecLaplacian/Make.package
Tutorials/HYPRE/ABecLaplacian/inputs
Tutorials/HYPRE/ABecLaplacian/main.cpp

commit 579122c4c5ae95667754e9c038ea22c8b4a179cb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 31 14:24:18 2018 -0700

    use pair index to store particles tiles even when using the GPU

Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategy.H
Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategyCPU.cpp
Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategyGPU.cpp
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp

commit a3e00961169ade69f4b887260abcc82eb09db809
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jul 31 17:19:49 2018 -0400

    Fix a typo in the IBM makefile

Tools/GNUMake/comps/ibm.mak

commit 49edffef30469939d026363342b389300d0845f3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 31 14:10:19 2018 -0700

    seperate out the implementation strategy of Redistribute from the ParticleContainer code

Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategy.H
Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategyCPU.cpp
Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategyGPU.cpp
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Make.package

commit 6ff8e87e3419ffe6cab6e7f0eedd92601af965ee
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Jul 31 13:48:17 2018 -0700

    Testing MultiFab to MatLab converter

Tools/Postprocessing/C_Src/GNUmakefile
Tools/Postprocessing/C_Src/MultiFabToMatLab.cpp

commit ecfc630070d76ac6401472f61cff904b3c9436bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 31 13:35:14 2018 -0700

    fix memory leak in HypreABecLap

Src/Extern/HYPRE/AMReX_HypreABecLap.cpp

commit c283698c519ec51ba367f29c12053e082791222f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 31 13:19:29 2018 -0700

    HypreABecLap2: avoid memory leak due to hypre bug. Because HypreABecLap memory leak is not fixed yet, switch to HypreABecLap2 in MLMG

Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H

commit cb6238e86aa2037f1ef1b361e4d785e820fa3544
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jul 31 15:15:58 2018 -0400

    Make defines consistent

Src/Base/AMReX_filcc_mod.F90

commit de30817c36c902d993a779c3800f12b0e53a486d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jul 31 15:02:58 2018 -0400

    Use unmodified C++ defines for the CUDA script
    
    We always use g++ for host compiling when USE_CUDA=TRUE, so we
    want to use the -D defines, not the -WF defines when COMP=IBM.

Tools/GNUMake/Make.rules

commit b4fbf94f9048137260d2a52942538468f6adc41d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 31 11:14:03 2018 -0700

    normalize matrix for regular hypre too

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_Hypre.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H

commit 64062c4d9a62e9a682a593ff25eff62f26cefaae
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Tue Jul 31 09:35:53 2018 -0700

    Strip trailing whitespaces in cuda/ and orig/.

Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/cuda/Evolve.H
Tutorials/Particles/ElectromagneticPIC/cuda/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/cuda/IO.H
Tutorials/Particles/ElectromagneticPIC/cuda/IO.cpp
Tutorials/Particles/ElectromagneticPIC/cuda/Make.package
Tutorials/Particles/ElectromagneticPIC/cuda/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/cuda/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/cuda/Particles.H
Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/cuda/main.cpp
Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/orig/Evolve.H
Tutorials/Particles/ElectromagneticPIC/orig/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/orig/IO.H
Tutorials/Particles/ElectromagneticPIC/orig/IO.cpp
Tutorials/Particles/ElectromagneticPIC/orig/Make.package
Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/orig/Particles.H
Tutorials/Particles/ElectromagneticPIC/orig/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/orig/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/orig/main.cpp

commit ef58fd6eb506c705b82870d17e34859eabe4c8e7
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Tue Jul 31 09:32:27 2018 -0700

    Convert push_electric(magnetic)_field_x(y,z) subroutine to OpenACC version. Strip whitesopaces in acc/.

Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/acc/Evolve.H
Tutorials/Particles/ElectromagneticPIC/acc/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/acc/IO.H
Tutorials/Particles/ElectromagneticPIC/acc/IO.cpp
Tutorials/Particles/ElectromagneticPIC/acc/Make.package
Tutorials/Particles/ElectromagneticPIC/acc/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/acc/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/acc/Particles.H
Tutorials/Particles/ElectromagneticPIC/acc/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/acc/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/acc/main.cpp

commit def166e8b336eb9ffab71c66efc13713ac2705fc
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Tue Jul 31 08:23:24 2018 -0700

    Convert to AMREX_FORT_LAUNCH_PARTICLES functions to OpenACC.

Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/acc/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/acc/em_pic_F.H

commit 5c03b1b6c2f6110d4f6325bae51a35c92e13b0fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 30 17:51:06 2018 -0700

    refactor hypre classes to reuse the solver for different x and b

Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_Hypre.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap.H
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.H
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp

commit b4c7ca0c34dab82cb3c518ede18a3aed65cd8f0e
Merge: e569b364f e2f4d716f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 30 19:45:02 2018 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit e569b364fcf004ba0521af50a2fd485484e09cab
Merge: 94744c8be 357976971
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 30 19:42:00 2018 -0400

    fixing merge conflict

commit 357976971ecdeb5203cdaa7b1e45320438578855
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 30 19:32:52 2018 -0400

    Need to add source to INCLUDE_LOCATIONS

Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX2_C/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX3_C/Exec/GNUmakefile

commit a3ff68ef45b897bc88c018033e3e7d3a38e904f5
Merge: 8f05fe8f4 e2f4d716f
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Mon Jul 30 19:27:33 2018 -0400

    Merge remote-tracking branch 'upstream/gpu' into gpu

commit e2f4d716fe5eea7d1b126d688a3317484ba2d99f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 30 19:18:50 2018 -0400

    These flags only belong on Fortran

Tools/GNUMake/comps/ibm.mak

commit ec15cc9bd5f272f5086f70566963a05fd1cfa3f6
Merge: 2e74b893e d9733c039
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Jul 30 15:33:41 2018 -0700

    Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into mlmg

commit 2e74b893ea482f80c44a6d5901b3a9f31cc17fd6
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Jul 30 15:33:21 2018 -0700

    MLMG to generate solution for testing convergence of EB solver. Going to change PlotFile->matlab to use multifabs to illustrate convergence. The RHS is for the function phi = (x-1/2)/sqrt((x-1/2)^2+(y-1/2)^2), and should be used with the sphere geometry in 2D only, with location 1/2,1/2 and radius 0.25.

Tests/LinearSolvers/EBConvergenceTest/GNUmakefile
Tests/LinearSolvers/EBConvergenceTest/Make.package
Tests/LinearSolvers/EBConvergenceTest/MyEB.H
Tests/LinearSolvers/EBConvergenceTest/MyTest.H
Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp
Tests/LinearSolvers/EBConvergenceTest/MyTest_F.H
Tests/LinearSolvers/EBConvergenceTest/RHS_2D.F90
Tests/LinearSolvers/EBConvergenceTest/initEB.cpp
Tests/LinearSolvers/EBConvergenceTest/inputs
Tests/LinearSolvers/EBConvergenceTest/main.cpp

commit 8f05fe8f44265660134573ada5d1d8223efabbfd
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Mon Jul 30 17:03:10 2018 -0400

    Added OpenACC only version of the tutorial.

Tutorials/Particles/ElectromagneticPIC/acc/Constants.H
Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/acc/Evolve.H
Tutorials/Particles/ElectromagneticPIC/acc/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/acc/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/acc/IO.H
Tutorials/Particles/ElectromagneticPIC/acc/IO.cpp
Tutorials/Particles/ElectromagneticPIC/acc/Make.package
Tutorials/Particles/ElectromagneticPIC/acc/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/acc/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/acc/Particles.H
Tutorials/Particles/ElectromagneticPIC/acc/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/acc/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/acc/inputs
Tutorials/Particles/ElectromagneticPIC/acc/main.cpp
Tutorials/Particles/ElectromagneticPIC/acc/script.sh

commit 94744c8beb6e98aa4e04b7768e701314b166aee0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 30 16:22:19 2018 -0400

    wrap these thrust things in AMREX_USE_CUDA

Src/Particle/AMReX_StructOfArrays.H

commit b723354e84fccaba0de461a977f0a702092f1894
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Mon Jul 30 15:43:27 2018 -0400

    Fixed a few AMREX_USE_CUDA left behind.

Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_3d.F90

commit 43848e1a9e36680d2545ef98b1bd6f2d2889c659
Author: Luna Lin <y.lin2783@gmail.com>
Date:   Mon Jul 30 14:55:31 2018 -0400

    Moved tutorial files to orig/ subdirectory, create cuda/ subdir, and separate out only cuda enabled codes into it.

Tutorials/Particles/ElectromagneticPIC/cuda/Constants.H
Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/cuda/Evolve.H
Tutorials/Particles/ElectromagneticPIC/cuda/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/cuda/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/cuda/IO.H
Tutorials/Particles/ElectromagneticPIC/cuda/IO.cpp
Tutorials/Particles/ElectromagneticPIC/cuda/Make.package
Tutorials/Particles/ElectromagneticPIC/cuda/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/cuda/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/cuda/Particles.H
Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/cuda/inputs
Tutorials/Particles/ElectromagneticPIC/cuda/main.cpp
Tutorials/Particles/ElectromagneticPIC/cuda/script.sh
Tutorials/Particles/ElectromagneticPIC/inputs
Tutorials/Particles/ElectromagneticPIC/orig/Constants.H
Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/orig/Evolve.H
Tutorials/Particles/ElectromagneticPIC/orig/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/orig/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/orig/IO.H
Tutorials/Particles/ElectromagneticPIC/orig/IO.cpp
Tutorials/Particles/ElectromagneticPIC/orig/Make.package
Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/orig/Particles.H
Tutorials/Particles/ElectromagneticPIC/orig/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/orig/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/orig/inputs
Tutorials/Particles/ElectromagneticPIC/orig/main.cpp
Tutorials/Particles/ElectromagneticPIC/orig/script.sh

commit d9733c03901bd787aa123d4cb10e2c1a0e302e33
Merge: 47d2ac1f1 1b16867da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 29 21:32:28 2018 -0700

    Merge branch 'development' into hypre

commit 47d2ac1f1a57c2f971c64f5e860921545541bd73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 29 21:23:06 2018 -0700

    minor change to get rid of a compiler warning

Src/EB2/AMReX_EB2_IF_Rotation.H

commit 0c3bfc387db21629c0fb2ed14775a8a87a319f22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 28 18:24:08 2018 -0700

    normalize matrix for hypre

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H

commit ef0dfe3d7d42abb2e90751f93216702b32ef92dc
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sat Jul 28 04:46:20 2018 -0400

    Test program update.

Tutorials/GPU/HelloWorld_C/main.cpp
Tutorials/GPU/HelloWorld_C/run.script

commit 2a4c6984e2efee168167b3c1f2b7587c38b75738
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sat Jul 28 04:45:52 2018 -0400

    ElectromagneticPIC, Lamdba version. Work breakdown needs debugging.

Tutorials/GPU/ElectromagneticPIC/Constants.H
Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.H
Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/GPU/ElectromagneticPIC/Evolve.H
Tutorials/GPU/ElectromagneticPIC/Evolve.cpp
Tutorials/GPU/ElectromagneticPIC/GNUmakefile
Tutorials/GPU/ElectromagneticPIC/IO.H
Tutorials/GPU/ElectromagneticPIC/IO.cpp
Tutorials/GPU/ElectromagneticPIC/Make.package
Tutorials/GPU/ElectromagneticPIC/NodalFlags.H
Tutorials/GPU/ElectromagneticPIC/NodalFlags.cpp
Tutorials/GPU/ElectromagneticPIC/Particles.H
Tutorials/GPU/ElectromagneticPIC/StructOfArrays.H
Tutorials/GPU/ElectromagneticPIC/em_pic_3d.F90
Tutorials/GPU/ElectromagneticPIC/em_pic_F.H
Tutorials/GPU/ElectromagneticPIC/inputs
Tutorials/GPU/ElectromagneticPIC/main.cpp
Tutorials/GPU/ElectromagneticPIC/script.sh
Tutorials/GPU/ElectromagneticPIC/test.cpp

commit 2673ea4425d1591281b450ecc3494d0d11dae1c7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sat Jul 28 04:42:57 2018 -0400

    ElectromagneticPIC function version. Conversion in progress. Need Particles wrapper for GPUs.

Tutorials/Particles/ElectromagneticPIC/CudaManagedAllocator.H
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Particles.H
Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H
Tutorials/Particles/ElectromagneticPIC/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/inputs
Tutorials/Particles/ElectromagneticPIC/script.sh

commit 8e77d2188a1b4a3b4fa98f594664baf3c4a45142
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sat Jul 28 04:38:00 2018 -0400

    Adjustments for ElectromagneticPIC.

Src/Base/AMReX_Box.H
Src/Base/AMReX_CUDA_Utility.H
Src/Base/AMReX_CUDA_Utility.cpp
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H

commit 0e431a0241a4265a986a0fd8eeb65874e4cedfaa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 27 21:16:49 2018 -0700

    bug fix in eb apply bc

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90

commit e5318c77aed8f5e050b9ba9e405baf210c5f8823
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 27 18:36:39 2018 -0700

    2d high order

Src/Extern/HYPRE/AMReX_HABEC_2D.F90

commit ba155e9aed09feaba8a60b511f813292f1c5e315
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 27 18:32:08 2018 -0700

    change the parameter of two spheres so that it doesn't have multi-cuts in 3d

Tests/LinearSolvers/CellEB/initEB.cpp
Tests/LinearSolvers/CellEB/inputs

commit 2c5486753e5c2fa3f9e5d5c338ed173687314b1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 27 18:31:34 2018 -0700

    high order bc

Src/Extern/HYPRE/AMReX_HABEC_3D.F90

commit 1b16867daf4f8fd7a4e1ac3a740375c5e38cfd01
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 27 17:25:00 2018 -0700

    remove these functions for getting all particle data on a single proc - these are inefficient and not needed.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 5646bd2664540c1403a5e4c1be450e8b70657ee7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 27 16:52:52 2018 -0700

    also provide interfaces to get the particle id and cpu number when initializing particles from Fortran

Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90
Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_2d.f90
Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_3d.f90

commit e90f936dacd94ff874c34555e717f318de41e3ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 27 16:52:22 2018 -0700

    eb apply bc

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90
Src/LinearSolvers/MLMG/Make.package

commit c632af7140508f04f7a5652f44abf4f1b9fc9760
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 27 16:38:41 2018 -0700

    remove deprecated particle initialization style from the F_Interfaces

Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90

commit dc98da8edac41776802adf1afb8267531d59da26
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 27 16:33:33 2018 -0700

    add new wrappers to the F_Interfaces and set the Advection_F Tutorial to use them

Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90
Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_2d.f90
Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_3d.f90
Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/Amr/Advection_F/Source/evolve_mod.F90
Tutorials/Amr/Advection_F/Source/initdata.F90

commit fb2b4b2160703145540687e44e57210708fc573f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 26 18:39:22 2018 -0700

    fix bug

Src/EB/AMReX_EBMultiFabUtil_3d.F90

commit 76bbf24ac49a095eab5f15537b937280df2ab2b8
Merge: 6833294e4 dab364ead
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 26 20:52:43 2018 -0400

    Merge branch 'development' into gpu

commit 6833294e45fde8b4a7c9f9426905490d68155d85
Merge: c6f222489 eb38d8cd7
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 26 20:52:03 2018 -0400

    merging development into gpu

commit dab364ead6bcdbce73b8636b29078ca0f945385f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 26 17:50:23 2018 -0700

    removed unused variable

Src/Particle/AMReX_ParticleContainerI.H

commit eb38d8cd75b98b3fb061fbcfaf1514d7b4c1c4ee
Merge: 691bb57c7 f9cf22539
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 26 17:42:03 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 691bb57c70239c0022490faa1a214f63fc82b2f1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 26 17:41:51 2018 -0700

    rename these functions to reflect the fact that there are no longer C++ and Fortran versions.

Src/AmrCore/AMReX_AmrParticles.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit fe9f51fdaf3aa7bdbb6ec6a076d068c87b9bf620
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 26 17:30:41 2018 -0700

    minor.

Src/Particle/AMReX_ParticleContainerI.H

commit 1bec1218025ee99b20c364f86ddf92e7a6a326f2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 26 17:26:01 2018 -0700

    minor.

Src/Particle/AMReX_ParticleContainerI.H

commit 0a1ea32c1f5af29d3a85519504bfcf1a17e7257e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 26 15:33:07 2018 -0700

    tweak gsrb near the intersection of eb and domain boundary

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit aa7f2fa5cdbbc7b7f530423680eb34bd71db1776
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 26 12:18:37 2018 -0700

    fix corner cases

Src/Extern/HYPRE/AMReX_HABEC_3D.F90

commit c6f222489a141ca1379074a29efec59fb1519a89
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 26 14:53:36 2018 -0400

    put the detail stuff from StructOfArrays into the amrex namespace.

Src/Particle/AMReX_StructOfArrays.H

commit 7a309aa33a1fe3ec6f7624230c64abf34c01ca1f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Thu Jul 26 14:51:16 2018 -0400

    use the IndexSequence stuff Weiqun added to Base instead of rolling my own.

Src/Particle/AMReX_StructOfArrays.H

commit 72fc56637cb6ad0d6b7eecd8c2512f36287d13b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 26 10:27:20 2018 -0700

    add MLMG::setBottomTolerance

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/CellEB/MyTest.H
Tests/LinearSolvers/CellEB/MyTest.cpp

commit 74f6c3bcad387c9f07eb2477fe88a155eb7d5bae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 26 10:18:39 2018 -0700

    tweak hypre parameter

Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit a1ee2335a73f1119f781b217eee5e68d36677e6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 26 09:16:46 2018 -0700

    need to cal EB_average_down_faces

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_F.H

commit 1b1eebb25b66b7aade34bf4c4d03b54cad0406ef
Merge: 5f3c52f94 49c44894d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 26 07:59:18 2018 -0700

    Merge branch 'hypre' into mlmg

commit 49c44894d550fee0d39c0bf390ec1e5b0ea3862a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 26 07:58:22 2018 -0700

    fix bug

Src/Extern/HYPRE/AMReX_HABEC_3D.F90

commit e8c2c3051eed089c257368cc95cdcf686bfda4bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 25 16:55:49 2018 -0700

    fix bug

Src/Extern/HYPRE/AMReX_HABEC_3D.F90

commit fbbef653e65754c05453a0aa5d8412d6774a8a4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 25 16:21:30 2018 -0700

    for eb, b coefficients must have one ghost

Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit 73c6daee1bc820e36c519e6d14d1b18d32ff15f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 25 16:10:31 2018 -0700

    ij matrix for 3d eb

Src/Extern/HYPRE/AMReX_HABEC_3D.F90

commit f9cf22539b7f38a2bec076ca830f747391f4f0c7
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Wed Jul 25 15:36:47 2018 -0700

    Exiting properly the AugmentPlotfile tool if we already have divergence and vorticity already computed, and avoiding useless copy-paste of data

Tools/C_util/AugmentPlotfile/AugmentPlotfile.cpp

commit 54262806bb0317128113da335ac13db6d74ed7d2
Merge: 1733a4832 07980a98c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 25 15:04:09 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 77434b2f5a0e843d99663e06dbc5a4dcb1dd3d32
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 25 13:59:39 2018 -0700

    ij matrix for 3d all_regular eb

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Tests/LinearSolvers/CellEB/inputs

commit 1733a48323447c50e04e351ecc80a474e3c69d81
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 25 13:48:42 2018 -0700

    optimize the 'remove_if' logic in ParticleContainer::Redistribute() - note that this will affect the order of particles on the tiles and therefore will cause roundoff differences in the tests.

Src/Particle/AMReX_ParticleContainerI.H

commit 5a1a672d33ec7af1605748a16a91606ba3e7be5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 25 12:41:47 2018 -0700

    tweak hypre parameters

Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit bb75f0b6f1ee1a2e617b8272f2c4ccda302fcab7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 25 11:34:13 2018 -0700

    add rotated box to CellEB test

Tests/LinearSolvers/CellEB/initEB.cpp
Tests/LinearSolvers/CellEB/inputs

commit 44bd85db255cf1b2d9b10f18b1ef84bfd5b4dfa3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 25 10:35:09 2018 -0700

    fix typo

Src/Extern/HYPRE/AMReX_HABEC_2D.F90

commit eef5300a03bae684b9dee1324c81c5597ed63d88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 24 18:34:25 2018 -0700

    add linop_maxorder option to CellEB test

Tests/LinearSolvers/CellEB/MyTest.H
Tests/LinearSolvers/CellEB/MyTest.cpp

commit e0d37c545d590d9ca4c92461cbb524041e068703
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 24 17:11:33 2018 -0700

    fix bug

Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit 300404ac2b129ae4a7de72d1336b178b57c4e82c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 24 17:00:15 2018 -0700

    WIP: ij matrix for 2d eb

Src/Extern/HYPRE/AMReX_HABEC_2D.F90

commit 07980a98c1bab00faefdc1bb8fe057e1d87dbef4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 24 13:11:34 2018 -0700

    move the computation of indexArray and ownerShip to DistributionMapping

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArrayBase.cpp

commit c528454d6efe855a8851b4fa1b18fc1d2c459cc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 24 12:31:25 2018 -0700

    WIP: hypre for eb

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H

commit 19ad1649e251836b4aad7b0a1317a2cca60d005d
Merge: 2bf04932e bb2d9caaa
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 24 12:14:07 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2bf04932e23e378d520f8e3dcb5780a47c06caee
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 24 12:13:58 2018 -0700

    Allow for the creation of multiple particle container instances when using the Fortran interfaces.

Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90
Tutorials/Amr/Advection_F/Source/amr_data_mod.F90
Tutorials/Amr/Advection_F/Source/evolve_mod.F90
Tutorials/Amr/Advection_F/Source/initdata.F90
Tutorials/Amr/Advection_F/Source/my_amr_mod.F90
Tutorials/Amr/Advection_F/Source/plotfile_mod.F90

commit f2bac735a828fd63a2c86aa7c96595931b6a8f54
Merge: e82229495 bb2d9caaa
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 23 21:48:24 2018 -0400

    Merge branch 'development' into gpu

commit bb2d9caaa0dae9954198ac4309df8c41038c958a
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 23 21:47:29 2018 -0400

    remove unused code from Src/Particle

Src/Particle/AMReX_Particles_1D.F
Src/Particle/AMReX_Particles_2D.F
Src/Particle/AMReX_Particles_3D.F
Src/Particle/AMReX_Particles_F.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit e82229495de8101dc1553a0e6d22053a5ffd1f1c
Merge: da7ba920f 59aa1c7d5
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 23 21:44:24 2018 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit da7ba920f9afb3c5677714022d8354f9664a3365
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 23 21:36:20 2018 -0400

    move the thrust-aware struct-of-arrays to Particles so it can be reused elsewhere.

Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_StructOfArrays.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Particles.H

commit 59aa1c7d52d5ba80ee6849aeafa453d7ea20e3d2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jul 23 21:09:16 2018 -0400

    remove old function

Tools/F_scripts/write_cuda_headers.py

commit 7ba1cffe010c775c9d8343eec8128f0521b44f6b
Merge: 0247b40a2 a2aa3c63e
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 23 21:06:16 2018 -0400

    merging development into gpu

commit 0247b40a259a0a30954dbabc9ce79dbf67ea0849
Merge: 97fbf785f 001fd5350
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 23 20:44:53 2018 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 97fbf785fa1ec7c6ece0ff8be9bf607c8f255b52
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 23 20:41:03 2018 -0400

    install the CudaAllocators Header in Base

Src/Base/Make.package

commit 5e4bd1355804cdc318cb95cc97d3d5fa8d2a703b
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 23 20:35:05 2018 -0400

    update Make.packages

Src/Base/Make.package
Src/Particle/Make.package

commit 45ca10670121afafab6a8ad32b2e434a230d8050
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 23 20:34:39 2018 -0400

    use the Base version of the CudaManagedAllocator

Src/Particle/AMReX_Particles.H

commit ffe1ab70cfea689abfac439203d292fce6f9954f
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 23 20:29:28 2018 -0400

    remove old deposition example

Tests/Particles/CUDADeposition/GNUmakefile
Tests/Particles/CUDADeposition/Make.package
Tests/Particles/CUDADeposition/MyParticleContainer.H
Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/cuda_deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_F.H
Tests/Particles/CUDADeposition/inputs
Tests/Particles/CUDADeposition/main.cpp
Tests/Particles/CUDADeposition/solve_for_accel.cpp
Tests/Particles/CUDADeposition/solve_with_f90.cpp

commit cf4f6166005cbd5abb46d6546d5e3816b8b843cb
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 23 20:28:52 2018 -0400

    fix deposition test

Tests/Particles/ManagedCUDADeposition/deposit_F.H
Tests/Particles/ManagedCUDADeposition/main.cpp
Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp
Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp

commit 001fd5350e81882cb2757b121d59af50bd357dde
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jul 23 20:08:36 2018 -0400

    find the fortran targets from the C++ pragmas

Tools/F_scripts/write_cuda_headers.py

commit 8907f2bc7fd88f7612affdd05297d1079bb5add7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 23 16:50:57 2018 -0700

    HYPRE_BoomerAMGSetup only needs to be called once

Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit 0269e6cd655f65efec8caf79920c7d75d2611139
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 23 16:31:27 2018 -0700

    fix bct and bcl

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90

commit 2bb830685108627ed2d4b2224598166038668bfa
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 23 19:21:24 2018 -0400

    some Array->Vector

Src/Particle/AMReX_CudaManagedAllocator.H
Tests/Particles/CUDADeposition/main.cpp
Tests/Particles/CUDADeposition/solve_for_accel.cpp
Tests/Particles/CUDADeposition/solve_with_f90.cpp

commit e92b000e7d66506b4c4fbac140899be5b4c92690
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Jul 23 19:19:19 2018 -0400

    HeatEq1 uses standard functions. HeatEq0 uses lambda launchers.

Tutorials/GPU/HeatEquation_EX0_C/Exec/GNUmakefile
Tutorials/GPU/HeatEquation_EX0_C/Exec/inputs_2d
Tutorials/GPU/HeatEquation_EX0_C/Exec/inputs_3d
Tutorials/GPU/HeatEquation_EX0_C/Exec/run.nocuda.script
Tutorials/GPU/HeatEquation_EX0_C/Exec/run.script
Tutorials/GPU/HeatEquation_EX0_C/Source/Make.package
Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX0_C/Source/advance_2d.F90
Tutorials/GPU/HeatEquation_EX0_C/Source/advance_3d.F90
Tutorials/GPU/HeatEquation_EX0_C/Source/init_phi_2d.F90
Tutorials/GPU/HeatEquation_EX0_C/Source/init_phi_3d.F90
Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX0_C/Source/myfunc.H
Tutorials/GPU/HeatEquation_EX0_C/Source/myfunc_F.H

commit 8d160d5800f477b4b9c2d367d64b8142364ff8ea
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Jul 23 19:11:58 2018 -0400

    Done playing with lambdas in HeatEq1.

Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H

commit 90a2d71859c9fe0ad246041c658db39e80f30326
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 23 15:54:24 2018 -0700

    2d ij matrix

Src/Extern/HYPRE/AMReX_HABEC_2D.F90

commit 5f3c52f946609aba512ade99226d79e3e6c78a7c
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Jul 23 14:36:51 2018 -0700

    EB Avgdown faces works in 2D and 3D

Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_3d.F90
Src/EB/AMReX_EBMultiFabUtil_F.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit f85f8c9de400735cd5e25fab932812b1829229a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 23 13:41:13 2018 -0700

    clean up

Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit 1114d53447c9418ef8f18be0dedd15a370949c73
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Jul 23 16:37:31 2018 -0400

    move the cuda allocator for std::vector into Base so that it may be re-used (not really particle specific)

Src/Base/AMReX_CudaAllocators.H
Tutorials/Particles/ElectromagneticPIC/CudaManagedAllocator.H
Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H

commit 64717ba3f443166f7c24cc0d7c4e808c7af383a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 23 13:33:58 2018 -0700

    fix more bugs

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp

commit 2ae8ec3fae6796b37d9f54868c6b05a2389b730d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Jul 23 16:27:38 2018 -0400

    1st version of Lambda kernel wrappers. May want to rename later.

Src/Base/AMReX_Managed.H
Tools/GNUMake/comps/nvcc.mak

commit e19781312d41fed444294d4c921f7a525d23d99a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 23 12:36:14 2018 -0700

    bug fixes

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H

commit d96c3d13dcad6014eab6571a5f3ff9cf7455730d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 23 11:49:28 2018 -0700

    Merge particle support into GPU branch (#290)
    
    Adds GPU particle support to AMReX, along with several Tutorials.

Src/Base/AMReX_BLFort.H
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp
Src/Base/AMReX_Vector.H
Src/Particle/AMReX_CudaManagedAllocator.H
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Src/Particle/Make.package
Tests/Particles/CUDADeposition/GNUmakefile
Tests/Particles/CUDADeposition/Make.package
Tests/Particles/CUDADeposition/MyParticleContainer.H
Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/cuda_deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_F.H
Tests/Particles/CUDADeposition/inputs
Tests/Particles/CUDADeposition/main.cpp
Tests/Particles/CUDADeposition/solve_for_accel.cpp
Tests/Particles/CUDADeposition/solve_with_f90.cpp
Tests/Particles/ManagedCUDADeposition/GNUmakefile
Tests/Particles/ManagedCUDADeposition/Make.package
Tests/Particles/ManagedCUDADeposition/MyParticleContainer.H
Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp
Tests/Particles/ManagedCUDADeposition/cuda_deposit_3d.f90
Tests/Particles/ManagedCUDADeposition/deposit_3d.f90
Tests/Particles/ManagedCUDADeposition/deposit_F.H
Tests/Particles/ManagedCUDADeposition/inputs
Tests/Particles/ManagedCUDADeposition/main.cpp
Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp
Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp
Tests/Particles/StructOfArrays/CudaManagedAllocator.H
Tests/Particles/StructOfArrays/GNUmakefile
Tests/Particles/StructOfArrays/Make.package
Tests/Particles/StructOfArrays/StructOfArrays.H
Tests/Particles/StructOfArrays/main.cpp
Tools/GNUMake/comps/pgi.mak
Tutorials/Particles/ElectromagneticPIC/CudaManagedAllocator.H
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Particles.H
Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H
Tutorials/Particles/ElectromagneticPIC/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/inputs
Tutorials/Particles/ElectromagneticPIC/main.cpp
Tutorials/Particles/ElectromagneticPIC/script.sh

commit dafa1dd927da9cfbb96752de56efd5b1b724823a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 23 10:51:19 2018 -0700

    WIP: load vectors and get solution

Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit 5e4fbb846a2b3445a40c17a1726aea3a1f7f2712
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 22 18:02:02 2018 -0700

    WIP: finish matrix setup

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H

commit b565a7834ae4eeaa17ad55f3be23c75043144af9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 22 08:37:47 2018 -0700

    WIP: prepare ij matrix

Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit a2aa3c63e3d5b1f21b4772153272cf175f97568e
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Jul 21 23:53:42 2018 -0700

    add a routine into Perilla WorkerThread

Src/AmrTask/rts_impls/Perilla/WorkerThread.H
Src/AmrTask/rts_impls/Perilla_omp/WorkerThread.H

commit af16bf2b85ff6a683c6cb66b1aaa6831931d1e6d
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Jul 21 23:34:57 2018 -0700

    extend the memory pool to make it compatible with Perilla

Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp
Src/Base/AMReX_MemPool.cpp

commit fcd26442c0986b898f06eebf77866afe4d230b96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 21 21:47:32 2018 -0700

    WIP: prepare the solver

Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit 25cda379c532e26d68d80be695b2b7a1ae293a92
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 21 12:15:57 2018 -0400

    Fix incorrect GPU parameter

Src/Amr/AMReX_AmrLevel.cpp

commit c93f87752cb0ec69b3b97bf10bcf75f2379d8afb
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Jul 20 19:42:00 2018 -0400

    Playing with lambdas.

Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H

commit 6118c9a60308d01c11a137b2d5fd9c2e5db827b3
Merge: 51c6f9313 0e1a0f0b4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 20 13:09:34 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 0e1a0f0b437ff8f3146a12aa33617f28cbc6f9ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 20 06:39:45 2018 -0700

    #ifdef so that Vector.H is safe for BoxLib Fortran

Src/Base/AMReX_Vector.H

commit 3b8eb996bcdac9a11bf09eeb2ee6a3324a7ab3a3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 19 17:38:54 2018 -0700

    remove const I just added

Src/Base/AMReX_Array.H

commit 51c6f93138cb951ac561e0a0f946985cec5e4b0c
Merge: db4f5059e 087f7ae6c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jul 19 17:10:52 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 087f7ae6c379aa03bac714746f19d72525f165eb
Merge: f3ec0972f c2eda1404
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 19 17:07:28 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f3ec0972f868c5f995b5fc68a037e102562494cc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 19 17:07:22 2018 -0700

    function for converting from unique_ptr to ptr in the kind of containers used by MLMG to store fluxes and gradients.

Src/Base/AMReX_Array.H
Src/Base/AMReX_Vector.H

commit 88ec0b2550670c4ed4d271df89fe4c9e116a3546
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 19 16:13:58 2018 -0700

    use HYPRE_Int

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_Hypre.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap.H
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.H
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_Hypre_fort_mod.F90
Src/Extern/HYPRE/Make.package
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp

commit e351a2967839c051ba227d07a3193e9c26ce1332
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 19 14:33:58 2018 -0700

    WIP: ij matrix

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_Hypre.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.H
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H

commit 3efa9e2935f09e98c4d1a2de6443dbc84503908c
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Jul 19 16:16:46 2018 -0400

    Fixing namespaces.

Src/Base/AMReX_Array.H
Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_Managed.H

commit 4d285332766a059fd94a1f4f283595550ae5659e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 19 12:49:03 2018 -0700

    option to choose hypre_interface

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp

commit c661af65a432209ff99fc72b9ebac650d4067d9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 19 12:33:39 2018 -0700

    clean up semi-structed hypre

Src/Extern/HYPRE/AMReX_HypreABecLap.H
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.H
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit dc93ed23a4e2cd37f6ef472c1051fd7f14ff3d8d
Merge: e89fe4e66 c2eda1404
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Jul 19 14:26:41 2018 -0400

    Merge branch 'development' into gpu-mm
    
    Conflicts:
            Src/Base/CMakeLists.txt

commit db4f5059e7dd2b20d457afdaac56ab541246cc12
Merge: 3ce935aab c2eda1404
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jul 19 11:24:24 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit e89fe4e66d6d5f4ec8157a9a23fadb92493ae7ba
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Jul 19 14:11:10 2018 -0400

    Various small changes for GPU C++ particles.

Src/Base/AMReX_Array.H
Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_fort_mod.F90

commit 9e2084f31a218929eb27e01a64c65555c5cc037b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 19 11:02:00 2018 -0700

    2d structed

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90

commit 788fc5a3ce1e970b7e4135ff32ff24bceb0585e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 19 07:09:17 2018 -0700

    set hypre logging and limit linop maxorder

Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 28521c8a91c02548318fed4fae1ec461950aac7d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 19 06:48:58 2018 -0700

    match boundary maxorder

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_Hypre.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap.H
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.H
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90

commit a76e27d9076c0720267da25c2e5cdb5bdab46eea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 18 22:38:49 2018 -0700

    WIP: clean up

Src/Extern/HYPRE/AMReX_HABEC_2D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap.H
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.H
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit bb5fc714ead25c160d6e33ca6e7d996dd0fe2ef4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 18 17:01:34 2018 -0700

    make structed grid interface work

Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_Hypre.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap.H
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.H
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit 8e1f650553a87ff020e9616d85100d25c1ae0ceb
Author: Minion <mlminion@lbl.gov>
Date:   Wed Jul 18 16:04:42 2018 -0700

    input variables v and nu, fix multi-block error, improve modularity, clean up advance.dpp

Tutorials/Basic/SDCAdvDiffusion_C/Exec/GNUmakefile
Tutorials/Basic/SDCAdvDiffusion_C/Exec/inputs_2d
Tutorials/Basic/SDCAdvDiffusion_C/Source/advance.cpp
Tutorials/Basic/SDCAdvDiffusion_C/Source/advance_2d.f90
Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_2d.f90
Tutorials/Basic/SDCAdvDiffusion_C/Source/main.cpp
Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc.H
Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc_F.H

commit 1752fe40f607ed03d250dcd249b16c2dbd44a387
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 18 15:33:34 2018 -0700

    start refactoring Hypre

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_Hypre.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_3D.F
Src/Extern/HYPRE/AMReX_HypreABec_F.H
Src/Extern/HYPRE/Make.package
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/inputs
Tutorials/LinearSolvers/ABecLaplacian_C/inputs-rt-abeclap-com
Tutorials/LinearSolvers/ABecLaplacian_C/inputs-rt-poisson-lev

commit b712e71c2dc16ed122d9d8dd1b5e54175c55967f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 17 18:19:25 2018 -0700

    back to use HypreABecLap2 because HypreABecLap3 doesn't work yet

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/GNUmakefile
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit f98081877ed1128f0fa004ae574bb3c37147bfd3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 17 17:06:55 2018 -0700

    expand some macros

Src/Extern/HYPRE/AMReX_HABEC_3D.F90

commit d2d11fc3c3495b8696d5c0780670386da02dd5f4
Merge: 3413b5a76 a687aab5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 17 16:55:29 2018 -0700

    Merge branch 'mlmg' into hypre

commit 3413b5a765c05fdb17ba677ccb1df52000895c9c
Merge: 581bfd935 ce857eed2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jul 17 16:41:00 2018 -0700

    Merge pull request #246 from shashankNREL/sy/hypre
    
    Sy/hypre - HYPRE IJ matrix interface

commit a687aab5dc3cbf96fd41fc67d6f8c60758e3ef48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 17 16:40:04 2018 -0700

    fix gsrb when eb crosses domain

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit c2eda1404601ccbcb9b879088353d2e6438857ba
Merge: f4ad3e63d 8cedfa6d8
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jul 17 16:31:32 2018 -0700

    Merge pull request #288 from cdaley/development
    
    Add a makefile fragment for Clang/Flang

commit 8cedfa6d824f338ba6f6a74eecca2343a4e875d9
Author: cdaley <chrisdaley82@gmail.com>
Date:   Tue Jul 17 16:11:31 2018 -0700

    Add a makefile fragment for Clang/Flang

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/llvm-flang.mak

commit 1fba0a3328d2c57e9ca32a9310216a1ed0891156
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 17 15:39:33 2018 -0700

    use mask for EB and domain bc crosses

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit f4ad3e63dee902a7dadfced6f2c679c44eef6bd7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 17 15:10:26 2018 -0700

    fix omp bug in ABecLaplacian_F tutorial

Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90

commit 66edf60e71eebd2fe4918742138cd6834086d137
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 17 15:04:34 2018 -0700

    fix make

Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile

commit 2026409bdbe3fa4aafac7e3d11f3970595617dd0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 17 15:04:20 2018 -0700

    avoid using null as variable name

Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90

commit 2d8cbf141e9c897e53c93aeadbba37e5c747cceb
Author: Minion <mlminion@lbl.gov>
Date:   Tue Jul 17 14:56:39 2018 -0700

    IMEX advection diffusion example.  This works as long as there is only one box

Tutorials/Basic/SDCAdvDiffusion_C/Exec/.#advance.cpp
Tutorials/Basic/SDCAdvDiffusion_C/Exec/GNUmakefile
Tutorials/Basic/SDCAdvDiffusion_C/Exec/inputs_2d
Tutorials/Basic/SDCAdvDiffusion_C/Source/Make.package
Tutorials/Basic/SDCAdvDiffusion_C/Source/advance.cpp
Tutorials/Basic/SDCAdvDiffusion_C/Source/advance_2d.f90
Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_2d.f90
Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_3d.f90
Tutorials/Basic/SDCAdvDiffusion_C/Source/inputs_3d
Tutorials/Basic/SDCAdvDiffusion_C/Source/main.cpp
Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc.H
Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc_F.H
Tutorials/Basic/SDCAdvDiffusion_C/Source/pf_quadrature.f90

commit b28746163c983364f9a8b0830adbc521afbe8714
Merge: 7fc3bca4f f11605d0f
Author: Minion <mlminion@lbl.gov>
Date:   Mon Jul 16 19:55:12 2018 -0700

    Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC

commit 7fc3bca4f925bb6135c2eeff11f430d72cd252af
Author: Minion <mlminion@lbl.gov>
Date:   Mon Jul 16 19:52:36 2018 -0700

    changing to match new tutorial style

Tutorials/SDC/HeatEquation_EX1_C/GNUmakefile
Tutorials/SDC/HeatEquation_EX1_C/advance.cpp
Tutorials/SDC/HeatEquation_EX1_C/init_phi_2d.f90
Tutorials/SDC/HeatEquation_EX1_C/inputs_2d
Tutorials/SDC/HeatEquation_EX1_C/main.cpp
Tutorials/SDC/HeatEquation_EX1_C/myfunc_F.H

commit e383375cd6b6ca88884dbb69ea1b9fac0d0df0e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 16 18:24:22 2018 -0700

    pass mask to Fortran

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit 61904d01ac973ce7abc9c04227898a23bde0fea3
Merge: af7e35009 a5d5e1bf1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 16 18:11:01 2018 -0700

    Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg

commit af7e350091e953cdabca5ad3b23c462547d1900f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 16 18:10:25 2018 -0700

    add cc mask

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 15abdae568c040962b951bd781290a290cb51c4d
Merge: 79650123e f7db6b956
Author: Minion <mlminion@lbl.gov>
Date:   Mon Jul 16 17:58:59 2018 -0700

    Merge branch 'development' into SDC

commit 7d16226bf29ada54358594dd34f5ab7c40efab01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 16 17:45:26 2018 -0700

    simplification

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit a5d5e1bf1876c1597d4b09d4356c12c1008445d6
Merge: 62bf8117d f4e374564
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Jul 16 14:03:49 2018 -0700

    Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into mlmg

commit 62bf8117d37cf416d4dc8c8e65177350779838f5
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Jul 16 14:03:47 2018 -0700

    myTest for merging

Tests/LinearSolvers/CellEB/MyTest.cpp

commit 02de6ec0e3012136bd401695889b53e9f5e8dbab
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Jul 16 14:01:19 2018 -0700

    Some changes, need to investigate some bugs, put it back to non-EB face averaging for now

Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_F.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit f4e374564f12972ad8485fa9328e13072941e296
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 16 13:37:59 2018 -0700

    3d mlebabeclap and over relaxation

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit f7db6b95620b9fd9e4747d84ae911532715a3932
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Jul 16 12:45:26 2018 -0700

    fix a compile error in the OMP backend of perilla

Src/AmrTask/rts_impls/Perilla_omp/Perilla.cpp
Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.H
Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/inputs

commit 78b766b2db6b6a65d2adc23719d2cb901d32734b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 16 12:10:31 2018 -0700

    2d mlebabeclap

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit 2a62bfc383735026b566b18ffd48c0f0cbc7d32f
Merge: 48564f3b8 027cac634
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 16 10:29:58 2018 -0700

    Merge branch 'development' into mlmg

commit 027cac63420f117e0b98e02ce603d1264bc76e62
Merge: 7f76f9078 817e87bd2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 16 10:29:19 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 7f76f907835f9bd6d49d3bdcef664c47ef5843e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 16 10:28:50 2018 -0700

    move GeometryGeneration to OldTutorials

OldTutorials/GeometryGeneration/exec/GNUmakefile
OldTutorials/GeometryGeneration/exec/coveredSlabs.cpp
OldTutorials/GeometryGeneration/exec/coveredslabs.inputs
OldTutorials/GeometryGeneration/exec/parabolaWithSphere.cpp
OldTutorials/GeometryGeneration/exec/parabolaWithSphere.inputs
OldTutorials/GeometryGeneration/exec/sphere.cpp
OldTutorials/GeometryGeneration/exec/sphere.inputs
OldTutorials/GeometryGeneration/exec/surfaceOfRevolution.cpp
OldTutorials/GeometryGeneration/exec/surfaceOfRevolution.inputs
OldTutorials/GeometryGeneration/src/CommonCode.H
OldTutorials/GeometryGeneration/src/CommonCode.cpp
OldTutorials/GeometryGeneration/src/Make.package
OldTutorials/GeometryGeneration/src/WriteEBPlotFile.H
OldTutorials/GeometryGeneration/src/WriteEBPlotFile.cpp

commit 817e87bd2a74d2025340236c06e86743fb6ae119
Merge: 4a41e5fce 0b3ce7eef
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jul 16 10:23:01 2018 -0700

    Merge pull request #287 from zingale/development
    
    close math mode in latex table

commit ce857eed216d088415fab222804f9bf9d0ee279e
Author: shashankNREL <shashank.yellapantula@nrel.gov>
Date:   Mon Jul 16 08:15:28 2018 -0600

    Accomodating suggestions from Weiqun on the PR

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Tests/LinearSolvers/MLMG/GNUmakefile

commit 4a41e5fcef63c1fc7c932fe146dba7b59a16c8c7
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Jul 16 01:32:52 2018 -0700

    add perilla source code

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/Perilla/Barrier.H
Src/AmrTask/rts_impls/Perilla/Barrier.cpp
Src/AmrTask/rts_impls/Perilla/LocalConnection.H
Src/AmrTask/rts_impls/Perilla/Make.package
Src/AmrTask/rts_impls/Perilla/Makefile
Src/AmrTask/rts_impls/Perilla/PackageQueue.H
Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp
Src/AmrTask/rts_impls/Perilla/Perilla.H
Src/AmrTask/rts_impls/Perilla/Perilla.cpp
Src/AmrTask/rts_impls/Perilla/PerillaConfig.H
Src/AmrTask/rts_impls/Perilla/PerillaRts.H
Src/AmrTask/rts_impls/Perilla/PerillaRts.cpp
Src/AmrTask/rts_impls/Perilla/RegionGraph.H
Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp
Src/AmrTask/rts_impls/Perilla/RegionQueue.H
Src/AmrTask/rts_impls/Perilla/RegionQueue.cpp
Src/AmrTask/rts_impls/Perilla/RemoteConnection.H
Src/AmrTask/rts_impls/Perilla/WorkerThread.H
Src/AmrTask/rts_impls/Perilla/WorkerThread.cpp
Src/AmrTask/rts_impls/Perilla/mylock.h
Src/AmrTask/rts_impls/Perilla/perilla.mak
Src/AmrTask/rts_impls/Perilla_omp/AsyncMultiFabUtil.H
Src/AmrTask/rts_impls/Perilla_omp/AsyncMultiFabUtil.cpp
Src/AmrTask/rts_impls/Perilla_omp/Barrier.H
Src/AmrTask/rts_impls/Perilla_omp/Barrier.cpp
Src/AmrTask/rts_impls/Perilla_omp/LocalConnection.H
Src/AmrTask/rts_impls/Perilla_omp/Make.package
Src/AmrTask/rts_impls/Perilla_omp/PackageQueue.H
Src/AmrTask/rts_impls/Perilla_omp/PackageQueue.cpp
Src/AmrTask/rts_impls/Perilla_omp/Perilla.H
Src/AmrTask/rts_impls/Perilla_omp/Perilla.cpp
Src/AmrTask/rts_impls/Perilla_omp/PerillaConfig.H
Src/AmrTask/rts_impls/Perilla_omp/PerillaRts.H
Src/AmrTask/rts_impls/Perilla_omp/PerillaRts.cpp
Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.H
Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.cpp
Src/AmrTask/rts_impls/Perilla_omp/RegionQueue.H
Src/AmrTask/rts_impls/Perilla_omp/RegionQueue.cpp
Src/AmrTask/rts_impls/Perilla_omp/RemoteConnection.H
Src/AmrTask/rts_impls/Perilla_omp/WorkerThread.H
Src/AmrTask/rts_impls/Perilla_omp/WorkerThread.cpp
Src/AmrTask/rts_impls/Perilla_omp/perilla.mak
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/._Exec
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/._README
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/._Source
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/._Make.Adv
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/._SingleVortex
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/._UniformVelocity
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._face_velocity_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._probin
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/face_velocity_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/probin
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._probdata.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/._probin
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/GNUmakefile
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/Prob.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/inputs
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/probdata.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/probin
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/README
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._AdvBld.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_F.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_advance.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_dt.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_io.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_setup.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Src_2d
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Src_3d
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Src_nd
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._main.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/AdvBld.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_F.H
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_dt.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_io.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_setup.cpp
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._Adv_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._compute_flux_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._slope_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/Adv_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/compute_flux_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/slope_2d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._Adv_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._compute_flux_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._slope_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/Adv_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/compute_flux_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/slope_3d.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._Adv_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._Tagging_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._tagging_params.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/Adv_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/Make.package
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/Tagging_nd.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/tagging_params.f90
Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/main.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit 48564f3b851af0cec07ab234eb4d52862e3c5d0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 14 12:58:36 2018 -0700

    make EB2::maxCoarsening more general

Src/Base/AMReX_Box.H
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Tests/LinearSolvers/CellEB/MyTest.cpp

commit 126f39dc64a3690b7a5692a02e9e8bc15ba573dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 14 11:38:06 2018 -0700

    use EB_average_down for solution too

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 6a124e54beaec28acc72a54db8e1a4c26f6a2451
Merge: 81108c1f4 caf348a8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 14 11:33:59 2018 -0700

    Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg

commit caf348a8d6ddc30a3f33dca6dcf4571f311fcb77
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Jul 13 16:18:02 2018 -0700

    Changed one arguement

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit 41ed9f63132ef7de2e865e51548b441077e13523
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Jul 13 16:00:57 2018 -0700

    EB average down faces compiles, and doesn't break code. Still need to test

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_3d.F90
Src/EB/AMReX_EBMultiFabUtil_F.H

commit 81108c1f49aec3cbeca2a97902c472fa05ad002d
Merge: 9cc5b847a d7583ec17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 13 15:06:00 2018 -0700

    Merge branch 'development' into mlmg

commit d7583ec174a3161e9e88d60dae205931a94f0144
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 13 15:05:41 2018 -0700

    simplication

Src/EB2/AMReX_EB2.cpp

commit fcb961551ca3f4395aa4756dba684cf4d57fdaed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 13 15:02:23 2018 -0700

    ParmParse: get and query using std::array

Src/Base/AMReX_ParmParse.H

commit 53b936c73f7a8130dfd5a6f00ccfd97ac2088417
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 13 14:07:22 2018 -0700

    remove old EB from EB/CNS

Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs
Tutorials/EB/CNS/Exec/Combustor/inputs
Tutorials/EB/CNS/Exec/Combustor/inputs.regt
Tutorials/EB/CNS/Exec/Combustor/inputs.testing
Tutorials/EB/CNS/Exec/Combustor/inputs_combustor
Tutorials/EB/CNS/Exec/Pulse/inputs.regt
Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs
Tutorials/EB/CNS/Exec/ShockRef/inputs
Tutorials/EB/CNS/Exec/ShockRef/inputs.amr
Tutorials/EB/CNS/Exec/ShockRef/inputs.regt
Tutorials/EB/CNS/Source/CNS_init_eb.cpp
Tutorials/EB/CNS/Source/CNS_init_eb2.cpp
Tutorials/EB/CNS/Source/Make.package
Tutorials/EB/CNS/Source/main.cpp

commit 9cc5b847aeaf6e87712cb35cf74eea21eba16750
Author: sireeveslbl <sireeves@ucsc.edu>
Date:   Thu Jul 12 22:18:32 2018 -0700

    More work on EB average down faces

Src/EB/AMReX_EBMultiFabUtil.cpp

commit e7d309f4ca8ed1edec477e3b54dc49efd6ca8a94
Merge: 06263a738 f94437c57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 12 22:10:24 2018 -0700

    Merge branch 'development' into eb2

commit 1068a7da5333e721f7b8edd64aa8efd19948d512
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 12 18:43:48 2018 -0700

    start petsc based bottom solver

Src/Extern/PETSc/AMReX_PETSc.H
Src/Extern/PETSc/Make.package
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tools/GNUMake/Make.defs
Tools/GNUMake/packages/Make.hypre
Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp

commit 0b3ce7eef3edd346d9cfb5c91d1befbbbc7421ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 12 20:28:28 2018 -0400

    close math mode in latex table

Tools/C_util/Convergence/RichardsonConvergenceTest.cpp

commit 9fd58f1d4f594f53be9aa7e82a5e875b092aae0b
Author: sireeveslbl <sireeves@ucsc.edu>
Date:   Thu Jul 12 14:48:33 2018 -0700

    EB Average Down Faces not finished yet, but code compiles

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit 06263a73855f2995665ec5aa16c3167881cc8fc9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 12 11:16:03 2018 -0700

    change inputs back to sphere

Tutorials/EB/CNS/Exec/Sod/inputs

commit f94437c57f6867ee47113e2fa74f31ab50492407
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 11 21:42:27 2018 -0700

    update inputs

Tutorials/EB/CNS/Exec/ShockRef/inputs.regt

commit f7f117c1b8518fa2bb130c031576b8dad9eaaa71
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 11 18:26:19 2018 -0700

    fix corner case of BoxArray::maxSize

Src/Base/AMReX_BoxArray.cpp

commit a199794c47dd31982feeddae59193f71c3b58917
Merge: aaa5bc206 f7a3868cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 11 17:37:53 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit aaa5bc206fc43c23d6323ef72358f09ca3fa5ed6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 11 17:37:40 2018 -0700

    turn off SIGTERM handling by default to avoid generating tons of Backtrace files after going over the queue time limit

Src/Base/AMReX.cpp

commit 6b0dc59e25420d7a25abf4de91c56782771c1fb7
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Wed Jul 11 16:20:57 2018 -0700

    Working on EB average down faces. Not complete yet.

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit f7a3868cd01d64bf5b13d34e1579bce2621395b9
Merge: e8c5a2a14 12ad70a0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 11 16:05:30 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit e8c5a2a1428a073ec2037dc55862899df6617167
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 11 16:05:12 2018 -0700

    fix a bug in PhysBCFunct

Src/Base/AMReX_PhysBCFunct.cpp

commit 12ad70a0ca00698b8cc8d79d4b28a5eeb2f31730
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 11 13:05:02 2018 -0700

    avoid conflict with PROFILE

Src/Base/AMReX_TinyProfiler.cpp

commit f481cf4145987f6a656ae97d23174ecea886ad2c
Merge: b99f63b5e 5b46ed8d9
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jul 11 12:27:01 2018 -0700

    Merge pull request #286 from AMReX-Codes/valentina/timer
    
    added timer for MLMG::Solve

commit 5b46ed8d99e67f94721fd309cad8540216569cbf
Author: Valentina Ricchiuti <vricchiuti@lbl.gov>
Date:   Wed Jul 11 12:04:11 2018 -0700

    added timer for MLMG::Solve

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 960f19b527f9db74637b195cb1c18f5f7c2a1931
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Wed Jul 11 11:01:54 2018 -0700

    Moved to a 4 point interpolation for fluxes

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 7886ad9af152899a96e10209dbaeb469ff48031e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 10 18:01:48 2018 -0700

    add ghost cells to A coefficient

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit b99f63b5e77414c9cc46aba53184e2c17128ba86
Merge: 3f34528d4 876b0495b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 10 17:24:33 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 3f34528d43ca61c9ac17eff8ea66d508bdcac592
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 10 17:10:48 2018 -0700

    remove the allow_particles_near_boundaries parameter - no longer needed.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit d2f12e4493ec0e7285460d3f12045331735dc3c0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 10 16:50:16 2018 -0700

    remove old multi-level deposition routines (aren't used any more)

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit fbbf3b15d06786d918e5531b82a67794cd59d404
Merge: 547406ea3 876b0495b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 10 16:07:37 2018 -0700

    Merge branch 'development' into mlmg

commit 876b0495b03ec3a5fb89337c83fdbb73e56b040a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 10 16:07:13 2018 -0700

    compile with PRECISION=FLOAT

Src/EB/AMReX_EB_levelset_F.F90
Src/EB2/AMReX_EB2_GeometryShop.H
Src/GeometryShop/AMReX_FlatPlateGeom.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp

commit 547406ea3706dd92655c3d4f930371f183fc03ba
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Jul 10 15:32:03 2018 -0700

    Other Functions with centroid interpolation

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit 62e6da141a594eba627422a1f998344e71f46278
Merge: b8c1c0177 e9a939a89
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 10 15:12:57 2018 -0700

    Merge branch 'eb2' into development

commit 935b19a19f7b6022ba9430231c6686f5128109c4
Merge: 7707c8ea1 1a1c3586e
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Jul 10 14:49:05 2018 -0700

    Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into mlmg

commit 7707c8ea106b4a62d1907179a95592987ec7fb71
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Jul 10 14:49:02 2018 -0700

    merging

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 1a1c3586ec91e135a000378b1b4bd6a9fe06a2e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 10 13:54:23 2018 -0700

    fix bugs in adotx

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit c4edfa31bd98e0fde9e4b4c75706ad1b7c708c1c
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Jul 10 13:01:48 2018 -0700

    Interpolating on a*phi in 'A dot x', utilizing the centroid data

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit b8c1c0177829e56d7df24388206a544ed858dc38
Merge: 59fbdef59 179c3812b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 17:50:46 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 59fbdef595764be22bd77627598316826cedd1b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 17:17:04 2018 -0700

    catch SIGTERM

Src/Base/AMReX.cpp
Src/Base/AMReX_BLBackTrace.cpp

commit e9a939a89717495e0f2272794e86545f7140e07d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 17:47:55 2018 -0700

    need to parallel reduce the error code

Src/EB2/AMReX_EB2_Level.cpp

commit 2e1a9beff733b9e51b058fc15e4e8e8af7a85e46
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 17:17:04 2018 -0700

    catch SIGTERM

Src/Base/AMReX.cpp
Src/Base/AMReX_BLBackTrace.cpp

commit 7a0ed3f404e3c9adf6e799a69a7d4d0ef968d1bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 17:47:55 2018 -0700

    need to parallel reduce the error code

Src/EB2/AMReX_EB2_Level.cpp

commit c8e60428f7ad454ad4d9aee9b1998bd066ff639b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 17:17:04 2018 -0700

    catch SIGTERM

Src/Base/AMReX.cpp
Src/Base/AMReX_BLBackTrace.cpp

commit 179c3812b08995c500a1ce6e9518023793c34a35
Merge: a697abb10 f571114d6
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Mon Jul 9 16:49:25 2018 -0700

    Merge pull request #282 from johnpwakefield/augtool
    
    Augtool

commit b95231695b48c6d88519debbfa36b6fd0f519193
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 16:45:07 2018 -0700

    increase max_coarsening_level

Tests/LinearSolvers/CellEB/MyTest.H
Tests/LinearSolvers/CellEB/initEB.cpp

commit 8fd5ba804fa070a292ae85f691fce73919dece30
Merge: 3892da9b4 c5263e033
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 16:35:01 2018 -0700

    Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg

commit 3892da9b473dab1f345e9a47327b800058d7cfa3
Merge: ca467a7f7 7e3ae0084
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 16:34:57 2018 -0700

    Merge branch 'eb2' into mlmg

commit 7e3ae008428f38d0bbcfac8bf01b102f02979e1d
Merge: e29f0b236 a697abb10
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 16:34:25 2018 -0700

    Merge branch 'development' into eb2

commit a697abb101827533d6f11e88a3105de05bad082d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 16:34:08 2018 -0700

    cannot call MPI_Group_free after MPI_Finalize

Src/Base/AMReX_ParallelDescriptor.cpp

commit ca467a7f742a9854898d623a79d8535fffcea280
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 16:28:42 2018 -0700

    when using EB, limit max coarsening level

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit c5263e0339e25f606107fb992e0fe6950779934c
Merge: 1bf59e0c1 f1fa2557a
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Jul 9 16:26:19 2018 -0700

    Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into mlmg

commit 1bf59e0c1790cdd14e5f91769b4e1788290b19b9
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Jul 9 16:25:57 2018 -0700

    Wrong dx in interpolation in 2D for a, 3D non-zero alpha now supported. Works with sphere test.

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit f1fa2557adbce37e278738ef6349b9c9f515b21b
Merge: 150a50cf8 e29f0b236
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 15:46:42 2018 -0700

    Merge branch 'eb2' into mlmg

commit e29f0b2366be28d74e512848f21691aa3fb74ab6
Merge: d50a85528 c41536b44
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 15:46:17 2018 -0700

    Merge branch 'weiqun/eb2' into eb2

commit d50a85528036d212897b720cf1ed4aecf948995c
Merge: 0b7d415a9 d6b8a51ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 15:45:58 2018 -0700

    Merge branch 'development' into eb2

commit c41536b44d2ef2feeadf47231022e0cbb97ad902
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 15:44:57 2018 -0700

    make sure fine grids are coarsenable

Src/EB2/AMReX_EB2_Level.cpp

commit 150a50cf8a2f6d9387ed7dacc9cf3c46cbe6a840
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Jul 9 14:30:18 2018 -0700

    Minor change

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit 8ca921e23705e47e9b401a537783401b9861972b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 13:41:48 2018 -0700

    rm old comment

Src/EB2/AMReX_EB2_Level.H

commit 7543b2ecced441bd7596d195e50dc1c308cf6ab7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 13:24:16 2018 -0700

    EB2: fix maxCoarseningLevel

Src/EB2/AMReX_EB2.H

commit 17f83e874842a338228b429c194d13d9a7c4f847
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 13:09:26 2018 -0700

    finished implementation of coarsening to different grids

Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Tests/EBEB2/MyTest.cpp

commit d6b8a51aca5f3e08b473d8aae41c8cbd4b41f6e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 9 10:57:00 2018 -0700

    push communicator to ParallelContext stack earlier so that Abort could work properly

Src/Base/AMReX_ParallelDescriptor.cpp

commit de4f5c81eeb696e4f3a18a1081d49455646d2fc3
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Jul 9 10:42:49 2018 -0700

    Fixed Erroneous Arithmetic Error, and convergence, non-zero alpha is working for 2D.

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit 35d08e425180123539e697de16b25685a95a734d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 8 08:38:58 2018 -0700

    MPI_TAG_UB may only be obtained with MPI_COMM_WORLD

Src/Base/AMReX_ParallelDescriptor.cpp

commit 0a2c5a5e9483bceae1e3def2c85794e7c1cb3bf2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 7 11:09:35 2018 -0700

    Fix a bug. Even if boxarray is empty, we may still need to clear various cache.

Src/Base/AMReX_FabArrayBase.cpp

commit 3ce935aab1c2223d75ae830f3a373caee4bbc108
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 6 17:58:37 2018 -0700

    CMake: add test_install to be XSDK compliant

CMakeLists.txt
Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt
Tutorials/CMakeLists.txt

commit 5fe36a127533591063ff3bb3d09b6dd4f688e33f
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Jul 6 20:13:52 2018 -0400

    Add Summit's no CUDA-aware flag.

Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script

commit 365b953e37f7c94fd13326895bda50b95028dbaf
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Jul 6 18:48:18 2018 -0400

    run script with GPUDirect off flag.

Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script

commit 50f8a05724c91e8c05546da2ec49b9c7cadfdd65
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Jul 6 18:44:00 2018 -0400

    Rename kernel

Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit 4f80122ce8da28b2f371d9b3a96147b525c2c248
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Jul 6 15:26:57 2018 -0700

    Testing Nonzero Alpha for 2D EB MLMG

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Tests/LinearSolvers/CellEB/MyTest.cpp

commit c66be15a755697c6374658aea360d7f64c614dbf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 6 10:57:24 2018 -0700

    remove optional nmax argument from SFC

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit 0038c22528bef9d750b19e9b103a486fe300e63b
Merge: 69992f2e7 eee695a18
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 6 10:34:39 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 69992f2e771a16622ef64e5f5cb117189c8c8450
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 6 10:34:34 2018 -0700

    CMake: strip MPI and OpenMP variables before using them

Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Utils.cmake

commit eee695a1832241640ca4b7f4a4e718c020534b3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 5 18:57:26 2018 -0700

    special fix for cray, don't know why it works

Src/Base/AMReX_DistributionMapping.cpp

commit 914f62280ef31224f6d9e90a0848b5d9955875e6
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jul 5 17:01:28 2018 -0700

    CMake: fix setting for Cray compiler

Tools/CMake/AMReX_Config.cmake

commit af4f30f7828a963151380dac47777d61804b47ef
Merge: 26d69f54b 94c857384
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jul 5 13:37:09 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 26d69f54b1a99644cbb4ec17cca9b9f6feb153bd
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jul 5 13:37:02 2018 -0700

    CMake: fix problem with AppleClang compiler

Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Utils.cmake

commit 76755cce925c289170785f04f8ea0dd4c9500485
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Jul 5 01:18:14 2018 -0400

    Reorganization and small adjustments.

Src/Base/AMReX_Box.H
Src/Base/AMReX_CUDA_Utility.H
Src/Base/AMReX_CUDA_Utility.cpp
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_Managed.H
Src/Base/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit a18c5463d9bbc3c90371f05c6714ba6b6da1a37d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 4 18:34:58 2018 -0700

    WIP: coarsen to different grids

Src/EB2/AMReX_EB2_IndexSpaceI.H
Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp

commit c5a36d4abb505e37ae6a039eb9c94cc69b9ba56f
Merge: e11950623 0b7d415a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 4 07:24:13 2018 -0700

    Merge branch 'eb2' into mlmg

commit 0b7d415a9781482386bd3968cde12d7f8d1bf07b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 4 07:17:47 2018 -0700

    finish 3d version of amrex_eb2_check_mvmc

Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90

commit 5222cde56836aa9f1d26bf19b571d3aa43383991
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 22:06:40 2018 -0700

    start 3d version of amrex_eb2_check_mvmc

Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_Level.cpp
Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90

commit d1234c192a0beddd1014a7ecbbf031f967514f00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 22:05:34 2018 -0700

    init IArrayBox to INT_MAX in debug/test mode

Src/Base/AMReX_IArrayBox.cpp

commit e11950623636099ecaeb1a52adefafd2c644a382
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 4 07:17:47 2018 -0700

    finish 3d version of amrex_eb2_check_mvmc

Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90

commit 86e2f4cce80e3dd40c4876839d714e8b282be2ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 22:06:40 2018 -0700

    start 3d version of amrex_eb2_check_mvmc

Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_Level.cpp
Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90

commit 67f937aa0ca85dad70c8665874f5c8cb09bdd050
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 22:05:34 2018 -0700

    init IArrayBox to INT_MAX in debug/test mode

Src/Base/AMReX_IArrayBox.cpp

commit 94c857384eecac55b3a1a7ff42dacd0660ade13b
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Jul 3 18:31:00 2018 -0700

    Don't warn when particles are removed at non-periodic boundaries, even with verbose=true.

Src/Particle/AMReX_ParticleContainerI.H

commit 5c64814a3ec5c34ddec4dfb13257af5ebef78ef2
Merge: 1e12eef59 50ae5b12e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jul 3 17:26:52 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 1e12eef597b8545ba9fb746b6e507ec06fbef702
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jul 3 17:26:39 2018 -0700

    CMake: provide AMReX versioning even when .git is not present

CMakeLists.txt
Src/CMakeLists.txt

commit 50ae5b12ea9b1094d881478006edda5040111e12
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 17:20:34 2018 -0700

    only print when verbose is true

Src/Particle/AMReX_ParticleContainerI.H

commit f88948557dc6a8e0c0cac66be1fe08eaebe24bcc
Merge: 8696a86a9 ebad409cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 17:15:16 2018 -0700

    Merge branch 'eb2' into mlmg

commit ebad409cd08cbbb38309a205c7a4eafa1130f440
Merge: 438f1653e 2668c5a33
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 17:11:25 2018 -0700

    Merge branch 'development' into eb2

commit 8696a86a9e383858f46bc9337c40c008696a3dcf
Merge: fb03516ff 438f1653e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 17:00:03 2018 -0700

    Merge branch 'eb2' into mlmg

commit fb03516ffe4824975e5f133b20290b6a6f45d575
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 16:59:44 2018 -0700

    don't let linear solver's max_coarsening_level exceed EB2's

Tests/LinearSolvers/CellEB/MyTest.cpp

commit 2668c5a33ef1cc3991b608b101a1b266936b96f4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jul 3 16:49:11 2018 -0700

    CMake: fix bug

Tools/CMake/AMReX_Options.cmake

commit fc5d7f7f44c07a61967bfe39999489e8e142d30e
Merge: 830f6db9b b0d12e39c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 16:48:30 2018 -0700

    Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg

commit 438f1653eb09a6ca6312e69d720f6bee0cc27e67
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 16:45:03 2018 -0700

    fix m_ok

Src/EB2/AMReX_EB2_Level.H

commit f61c5298612f6b44fdb0fe1a33c9dbeea2e270fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 16:35:50 2018 -0700

    function to return max coarsening level

Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_IndexSpaceI.H
Src/EB2/AMReX_EB2_Level.H

commit 29494277c70c434d0098ef6490d6f711b820689b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 15:31:32 2018 -0700

    check for multi-cuts and multi-values

Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90

commit 830f6db9bc902f7ce1178d80b0ee4f788346b2fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 16:45:03 2018 -0700

    fix m_ok

Src/EB2/AMReX_EB2_Level.H

commit 73dddbe378c80961018f11abcc064c5d801cd231
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 16:35:50 2018 -0700

    function to return max coarsening level

Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_IndexSpaceI.H
Src/EB2/AMReX_EB2_Level.H

commit 43283ccba78472de118e3743d9fa2e42541d1c07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 15:31:32 2018 -0700

    check for multi-cuts and multi-values

Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90

commit 98bdd48c0c969b3c550ab6b6787940326a81c75f
Merge: a6d7028a5 391a3a8ad
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jul 3 14:48:39 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit a6d7028a59c6f4f05b638a461bc8b93217c65520
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jul 3 14:48:04 2018 -0700

    CMake: one more change

Src/CMakeLists.txt

commit b0d12e39cd76e394837549ab1dd5597054c00954
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Jul 3 13:11:35 2018 -0700

    Fixed Another Bug, for regular convergence

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit a98287ed04e859fe9ad5fb4abfb71ac00dd8a16f
Merge: 7bacb0186 95f7869d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 3 13:03:42 2018 -0700

    Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg

commit 391a3a8ad0da7ccb9f46322ffe2f562b9607afbc
Merge: ddbf2bd4e 90764850e
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jul 3 12:57:28 2018 -0700

    Merge pull request #279 from jrood-nrel/update_nrel_makefile
    
    Update makefile for NREL site to get higher vectorization from the Intel compiler

commit 90764850e01f8d238787ef467af13f9dc0ad64dd
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Tue Jul 3 13:37:40 2018 -0600

    Update makefile for NREL site to get higher vectorization from the Intel compiler.

Tools/GNUMake/sites/Make.nrel

commit ddbf2bd4ef4ff511bd11b1439a4cf940e432da51
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jul 3 12:06:56 2018 -0700

    CMake: some more improvements

Src/CMakeLists.txt
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Utils.cmake

commit 95f7869d38e48212832a01dfe329ef00efa10968
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Jul 3 10:12:26 2018 -0700

    MyTest Changed to allow for 3D

Tests/LinearSolvers/CellEB/MyTest.cpp

commit 17aea688ccd1371fa59e5d1aca038a3e5e31fa56
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Jul 3 10:10:18 2018 -0700

    Bug Killed, Test Case works for Sphere

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 52717e2d143e6c9d574ca42558553f2b309b2a20
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jul 2 16:19:37 2018 -0700

    CMake: bug fix

Tools/CMake/AMReX_Config.cmake

commit f2572f354c7f164bd05e27930d408bf181db6c58
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Jul 2 18:56:02 2018 -0400

    strip USE_CUDA in make file

Tools/GNUMake/Make.defs

commit 9d2c88ef119fba3ba9298953627c4c7961caec2d
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Jul 2 18:52:47 2018 -0400

    Add CUDA streams to MFIter.

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 5dcb9401d870c605c9b1667a79973379d41a69eb
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Jul 2 18:50:08 2018 -0400

    Adjust Device for AMREX_USE_CUDA=FALSE.

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/Make.package

commit 21f4a0119a9009affbd6ae847f31bdc91f5fcc9e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jul 2 15:49:31 2018 -0700

    CMake: update Doc

Docs/sphinx_documentation/source/BuildingAMReX.rst

commit 8a8b0226c15a81b115152872861b37d4189d6b0e
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Jul 2 18:45:17 2018 -0400

    Add using CudaAllocators = std allocator for USE_CUDA=FALSE.

Src/Base/AMReX_CudaAllocators.H

commit 18045ef219bbad954c724c8a8f6bead156a3200d
Merge: 8da722c6e ca45d5254
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jul 2 15:28:58 2018 -0700

    Merge branch 'development' into mr/cmake

commit 8da722c6ecaecd93c5ffd995abb3165ad8d009bb
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jul 2 15:22:22 2018 -0700

    CMake: complete transition to 'Modern CMake'

CMakeLists.txt
Src/CMakeLists.txt
Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Machines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_Utils.cmake
Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt

commit ca45d5254cc935fd6fc36e72c3b6d2f34a0af1a2
Merge: cceea4038 3caa6292f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jul 2 13:38:42 2018 -0700

    :Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit cceea40388e6cb15d0770e3f2b670a5a8af211ee
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jul 2 13:38:38 2018 -0700

    remove meaningless const

Src/EB/AMReX_EB_levelset.H

commit 3caa6292fa604e9cedeb29e098fd560dcef7ca9e
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jul 2 13:11:54 2018 -0700

    fixed dummy variable and meaningless const

Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset_F.F90

commit 14bf698934e320a63990b9ff5801dbec0fcc658d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 2 10:46:08 2018 -0700

    makeSFC: switch the order of optional arguments

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit 63c651efd555227fb44c831a42f38643abf6fa3f
Merge: 1b1fad431 a83507a0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 2 10:42:01 2018 -0700

    Merge branch 'sfc' into development

commit 1b1fad431ffe4a546ec971a01d1e6fd0b0af951b
Merge: 30149e4eb 76f5e80c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 2 10:41:34 2018 -0700

    Merge branch 'knapsack' into development

commit 30149e4ebd623991b404a2d90fc40f794d1d8ed3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 2 10:40:21 2018 -0700

    update CHANGES

CHANGES

commit 7bacb018680dac8c6c3e735b82d845828bb46d5b
Merge: 432b1218c 954032cf5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 29 18:33:28 2018 -0700

    Merge branch 'eb2' into mlmg

commit 954032cf52741606e1b92348ce924b6c4f838e2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 29 18:08:26 2018 -0700

    detect mutli-values in 2d

Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90

commit 432b1218cbdbcd908513ccd045f0afa087bd0e60
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Jun 29 16:37:01 2018 -0700

    Bugs somewhere, maybe in the interp. Gotta buscar!

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit 6c748a75abd100c8db7170139b3bf6f8913af2b9
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Fri Jun 29 15:11:45 2018 -0700

    MLEBABecLap_3d compiles, fixed interpolation to multi-D. Needs testing

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit df7b16c20911389890b5cf99171399cdc7ff8f34
Merge: c59f538af ca99e0530
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jun 29 14:15:38 2018 -0700

    Merge pull request #276 from AMReX-Codes/bugfix_Convergence_tools
    
    fix convergence tools in 1D

commit c59f538af06a54b951a9135ad7aab5d18183329c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 29 13:45:31 2018 -0700

    IntVect version of iMultiFab::define

Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp

commit d7fd2bb2b60d67c6a81fb4d63e9b133c94d244dd
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 28 17:59:26 2018 -0700

    CMake: bug fixes

Src/Extern/CMakeLists.txt
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake

commit cc6ae87b67ea697c9729b101285d9814f5ce8619
Merge: a3afb8634 796e155ac
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 28 17:01:19 2018 -0700

    Merge branch 'development' into mr/cmake

commit a3afb863409f0de3e4c664f437a4aa045ec5665c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 28 16:37:10 2018 -0700

    CMake: improve installation step

Src/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake

commit 76f5e80c7269f85ff490ac8c257ccea1a6afcd70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 28 16:34:16 2018 -0700

    knapsack: minor cleanup

Src/Base/AMReX_DistributionMapping.cpp

commit e266b425fa97afe529ffac7bcdeb2eea2f39ec8b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 28 16:04:04 2018 -0700

    knapsack swap: only need to check the end

Src/Base/AMReX_DistributionMapping.cpp

commit ca99e05308f88f9e9b2a44b0a9b1c029daf516f2
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Thu Jun 28 13:50:07 2018 -0700

    fix convergence tools in 1D

Src/Extern/ProfParser/AMReX_AVGDOWN_1D.F
Tools/C_util/Convergence/GNUmakefile

commit 3318c23dcfc0f35dc4dd3c14e7c1a514efbce471
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Thu Jun 28 13:44:42 2018 -0700

    First function compelete

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90

commit f960f6aad75366a5c211c4362e982a0e3fb692b0
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 28 11:01:00 2018 -0700

    CMake: use generator expressions when setting compiler flags

Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake

commit 0a857b49c2abd557a43160c8fac908d4a478cb68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 28 10:59:02 2018 -0700

    knapsack: timer and assertion

Src/Base/AMReX_DistributionMapping.cpp

commit 796e155ac52a07d486966a70e9e77b0ee85c12c0
Merge: bd82031a3 36ab899cc
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jun 28 10:18:38 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit bd82031a3feefd2ad499303aa4734438d6b28dff
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jun 28 10:18:34 2018 -0700

    boundary level-set initialization ignored periodic directions (filled using FillBoundary anyway)

Src/EB/AMReX_EB_F.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_levelset_F.F90

commit 4d89ac16ae29b1a611db4d78c68bb9387233dfbe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 28 07:32:34 2018 -0700

    knapsack: if the top has only one Box, there is no need to check swapping

Src/Base/AMReX_DistributionMapping.cpp

commit 49c3bb356915f00b6787168cf6fccad95b67b261
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 28 07:21:41 2018 -0700

    knapsack: switch order for performance

Src/Base/AMReX_DistributionMapping.cpp

commit aaa933a7b11cde0d084d7837be6049a455f93b30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 28 07:02:39 2018 -0700

    knapsack: list -> vector

Src/Base/AMReX_DistributionMapping.cpp

commit 36ab899cc67296f632f7da28c2a71e3713036be7
Merge: 5f0327ddc 63fbc614b
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jun 27 19:30:53 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5f0327ddc5214625981cb7fee20609d74c53a83e
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jun 27 19:30:26 2018 -0700

    Add a utility to append stuff to plotfiles...requires some care to use. following instructions on screen after plotfile modified this way.

Tools/C_util/AppendToPlotFile.H
Tools/C_util/AppendToPlotFile.cpp

commit 63fbc614b4542581114eb6ca5cdc05d2ee414ed0
Merge: e86cf5329 e31932d6d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jun 27 18:47:10 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit e86cf5329f137082f57878c0cd028c0f28838d53
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jun 27 18:46:40 2018 -0700

    force it to rebuild the CellVectors every time Redistribute is called.

Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp

commit bce53cba156f1e0bf6fd4448d8103c33d808024b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jun 27 18:44:20 2018 -0700

    lower dt

Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp

commit 6cb32e97053087b612367fbb0686982e4903461a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jun 27 18:43:55 2018 -0700

    make this loop work with tiling

Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp
Tutorials/Particles/CellSortedParticles/cell_sorted_3d.F90
Tutorials/Particles/CellSortedParticles/cell_sorted_F.H
Tutorials/Particles/CellSortedParticles/main.cpp

commit 5f44c2cc57ff22fde2c942a1f4c9adcf088b11a4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jun 27 18:38:26 2018 -0700

    typo fix

Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp

commit 9dc4c831e78cb2878e1caed03374b1395201597a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 27 17:56:22 2018 -0700

    CMake: update tutorials

Tools/CMake/AMReX_Compilers.cmake
Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt
Tutorials/Amr/Advection_F/CMakeLists.txt
Tutorials/Amr/Advection_F/Source/my_amr_mod.F90
Tutorials/Amr/Advection_octree_F/CMakeLists.txt
Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90
Tutorials/CMakeLists.txt

commit e31932d6dc751c97cd9ddbf5a153aaf9be444c56
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jun 27 17:22:12 2018 -0700

    Remove IOIOI cout statements for precreating directory struture

Src/Amr/AMReX_Amr.cpp

commit 5bd3164afa9aac1bcd5a0f375a9fa1eeed94ed6a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 27 16:16:07 2018 -0700

    CMake: set manually C++ std flags to enable transitive dependencies on this property

CMakeLists.txt
Tools/CMake/AMReX_Compilers.cmake

commit fda7766915f13e5c32c2059ea6bfd2f986445e3f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 27 15:02:41 2018 -0700

    CMake: some modifications to support different scenarios

Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_ThirdPartyProfilers.cmake

commit 3335e86bf5439539b67b235ff36df5e0566fdecd
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 27 17:27:28 2018 -0400

    Remove blockSize from particle blocks_and_threads.

Src/Base/AMReX_Device.cpp

commit 6e3b58115473de262def5164bf6f6395473041d0
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Jun 27 14:06:05 2018 -0700

    only manually fill valid non-periodic boundaries

Src/EB/AMReX_EB_F.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_levelset_F.F90

commit 13da92224793b3d6dc0518b870f8b7a7a38b8c46
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Jun 27 13:30:29 2018 -0700

    almost done eliminating all the copy-and-paste bits

Src/EB/AMReX_EB_F.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_levelset_F.F90

commit be135d7b289642ea3baa16bd223d774268ec14df
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 27 15:18:01 2018 -0400

    Direct, unedited copy of tutorial from gpu_particles.

Tutorials/Particles/ElectromagneticPIC/CudaManagedAllocator.H
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/Particles.H
Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H
Tutorials/Particles/ElectromagneticPIC/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/inputs
Tutorials/Particles/ElectromagneticPIC/main.cpp
Tutorials/Particles/ElectromagneticPIC/script.sh
Tutorials/Particles/ElectromagneticPIC/test.cpp

commit 57fbaaddf0fb317b707c19174884c4793c03c7e4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 27 10:40:36 2018 -0700

    CMake: some bug fixes

Tools/CMake/AMReX_Config.cmake

commit fbe95bbeb3ac08504451ef9b6afabeb8791275e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 27 10:34:32 2018 -0700

    add inputs

Tests/LinearSolvers/CellEB/inputs

commit 6781596a7e4f9911b57d6c3f4131df81e928cfff
Merge: d87b1da90 ef8d4bab3
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Jun 27 10:09:14 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit d87b1da904cc40e92ecc7c912fa8f561362e2619
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Jun 27 10:08:49 2018 -0700

    some more cleaning and removing unncessary arguments

Src/EB/AMReX_EB_F.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_levelset_F.F90

commit f1bcaf745d2ef0da62f4cf6fb3b99f7b4794481b
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jun 26 21:57:16 2018 -0700

    more cleaning up

Src/EB/AMReX_EB_levelset_F.F90

commit 428cb47ce2c882f80f715bc07426c081d53fce52
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jun 26 18:48:27 2018 -0700

    working on cleaning copy-and-paste

Src/EB/AMReX_EB_levelset_F.F90

commit ef8d4bab3d16885d22fafd95ba06a562a9318b83
Merge: 47b820d2f 4acffee07
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 26 17:52:20 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 47b820d2fcf730f48792b7c4ce5fbd2e8f14e14c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 26 17:52:02 2018 -0700

    periodic shift should *repeatedly* shift the particle until it is inside.

Src/Particle/AMReX_ParticleContainerI.H

commit 697426b2f17884c4356b83d246a92b003551ca06
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 26 17:49:11 2018 -0700

    CMake: further improvements

Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake

commit 4acffee07cd29abf31730e1b831aa5c5f64a0d81
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jun 26 17:36:10 2018 -0700

    fill level set manually in boundary points

Src/EB/AMReX_EB_F.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_levelset_F.F90

commit 55479a619c12754862c313aacd3a2637c2b276a4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 26 15:51:44 2018 -0700

    CMake: continue transition to 'modern CMake'

CMakeLists.txt
Src/CMakeLists.txt
Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_ThirdPartyProfilers.cmake

commit d81c618f21719fb32b8ed6b39894b3d84d6682b4
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Mon Apr 23 19:10:18 2018 -0400

    add macro and helper routine for launching particle kernels

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_Managed.H

commit 2f90deb67c9791aa38bd7f756cace75c6b3f1563
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jun 6 14:56:11 2018 -0400

    Add CharVector that can be CUDA memory managed and make neighbors now
    be managed the way particles are.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_Particles.H

commit 77805a6a638370cebb6bb917a893ed70ff9e5141
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 20 14:59:45 2017 -0800

    finish fixing gpu_particles branch

Src/Particle/AMReX_Particles.H

commit 4510dd9939ae0079bc48cc8488067c785be2e331
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 20 10:24:15 2017 -0800

    some work on fixing the gpu_particles branch.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 4836d76c7344389aa15372403b7accdace35c89c
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Jun 26 14:38:33 2018 -0700

    Pulse Inputs to use EB2 stuff

Tutorials/EB/CNS/Exec/Pulse/inputs

commit f27a6970246d7cc1b591aacfa9724be3a437737c
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Jun 26 14:26:55 2018 -0700

    MyTest.cpp

Tests/EBEB2/MyTest.cpp

commit c6f9e437b209b9836c7ca96a20735f1462002781
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Jun 26 14:14:43 2018 -0700

    Minor Format Change

Tutorials/EB/CNS/Source/CNS_init_eb.cpp

commit 73fdb7c01c564dca0a3bd47516962ea1011c037b
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Jun 26 14:11:52 2018 -0700

    Wrote combustor function for EB1 to follow same params as EB2. Edited initialize_EBIS to take additional Geometry argument, for the effective construction of the flattened corner. Removed the old polygon_revolution params in input.

Tutorials/EB/CNS/Exec/Combustor/inputs
Tutorials/EB/CNS/Source/CNS_init_eb.cpp
Tutorials/EB/CNS/Source/main.cpp

commit 99d17e26422317b6ef3a4d74876f294b15439d4a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jun 26 16:54:07 2018 -0400

    Fix after merge.

Tools/GNUMake/sites/Make.olcf

commit e6e53b92bf3770c776d45e9d73504e8add28cf6b
Merge: 2306a221e 4d8502ca3
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jun 26 16:44:37 2018 -0400

    Merge with development.

commit 2306a221e30459a8109b408ca476753d2fe0ad4a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jun 26 15:34:50 2018 -0400

    HeatEquation Inputs and run.script

Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d
Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script

commit fd8e5fefb930296d3cfe55a47ae06d5a91355895
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 26 03:03:35 2018 -0700

    Automatically generate both host and device functions

Tools/F_scripts/gpu_fortran.py
Tools/F_scripts/write_cuda_headers.py

commit 5a86ca9ba4b8e0ffac3ba1929a97a75f45345822
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 26 01:26:51 2018 -0700

    Move module use statements into subroutines

Src/Base/AMReX_BaseFab_nd.F90

commit 6b9eae69aeaf99dac5f992be0daad24e88896f1a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Jun 25 22:13:52 2018 -0400

    Split work on GPU to 1 grid cell per GPU thread.

Src/Base/AMReX_Box.H
Src/Base/AMReX_Managed.H
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp

commit e65168f1980529903d1cdc2728b4d640935d5d56
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Jun 25 16:52:17 2018 -0700

    Combustor Inputs returned to original problem

Tutorials/EB/CNS/Exec/Combustor/inputs

commit 4d8502ca3da9479df08d6244a78fe13f9b7e725d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 25 16:31:18 2018 -0700

    update the Tests and the Tutorials

Tests/Particles/AssignDensity/GNUmakefile
Tests/Particles/AssignMultiLevelDensity/main.cpp
Tests/Particles/GNUmakefile
Tutorials/Particles/CellSortedParticles/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/GNUmakefile
Tutorials/Particles/NeighborList/GNUmakefile

commit 7e2701896137e6595e3adc8c99f72ad93c500bea
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 25 16:30:13 2018 -0700

    don't need these includes any more

Src/Particle/AMReX_Particles.H

commit 75d76b10f85cd976400d472476a86d6700a4bc4e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 25 16:29:56 2018 -0700

    ... and actually remove it from Src/Particles

Src/Particle/AMReX_ParticleContainerI.H

commit 64ea0677ae3da70383052abe5b5f3e4b9fe77f0c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 25 16:29:24 2018 -0700

    move implementation of multi-level assign density into Src/AmrCore

Src/AmrCore/AMReX_AmrParticles.H

commit 99c01ca0c1dfd5657e784d96e48e692fc780b5cf
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Jun 25 16:17:25 2018 -0700

    Changed inputs for working EB2, need to translate old EB to work with new inputs

Tutorials/EB/CNS/Exec/Combustor/inputs
Tutorials/EB/CNS/Exec/ShockRef/inputs

commit 18b54728fd91f20b8dd6128b6590c44e16ab0c5e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 25 16:05:19 2018 -0700

    test for CC EB solver

Tests/LinearSolvers/CellEB/GNUmakefile
Tests/LinearSolvers/CellEB/Make.package
Tests/LinearSolvers/CellEB/MyEB.H
Tests/LinearSolvers/CellEB/MyTest.H
Tests/LinearSolvers/CellEB/MyTest.cpp
Tests/LinearSolvers/CellEB/initEB.cpp
Tests/LinearSolvers/CellEB/main.cpp

commit da3509b5d272e94e542fa2bae1a2c3c1132ae3fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 25 15:45:35 2018 -0700

    add 3d version of amrex_mlmg_eb_cc_interp to public

Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90

commit 800390ea20ede398b0ef1efac276f04c3eb3590b
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Mon Jun 25 13:14:18 2018 -0700

    CNS combustor is finished for EB2, user defines locations of planes, boxes etc

Tutorials/EB/CNS/Exec/Combustor/inputs
Tutorials/EB/CNS/Source/CNS_init_eb2.cpp

commit 50d3411a428f148d88c8032b0155726c7b4d918f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 25 12:15:40 2018 -0700

    we need to include EB2 to build now.

Tutorials/Particles/EBParticles/GNUmakefile

commit c7d4df9b54b15558aa4116b9592dfe70a0c0381b
Merge: 526b275f9 b02764fdb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 25 10:48:55 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 526b275f90f9d58976a8c4071da32883adb8cf13
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 25 10:48:36 2018 -0700

    break this timer into two

Src/Particle/AMReX_ParticleContainerI.H

commit c5358da231cb9c411fab9ed2e7d90fc0d9c323cb
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 25 01:26:58 2018 -0700

    Write out the actual CUDA code instead of using the macro

Tools/F_scripts/write_cuda_headers.py

commit a40fee086f5746bc121cb4db9eeb16171e4ecb12
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 25 01:14:17 2018 -0700

    Also capture Fortran functions

Tools/F_scripts/gpu_fortran.py

commit 58d8321f068929ed3ff6da4b7b41333b535cc358
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 25 01:07:37 2018 -0700

    Replace with attributes(device) instead of AMREX_DEVICE

Tools/F_scripts/gpu_fortran.py
Tools/F_scripts/write_cuda_headers.py

commit e46cdb267f95bb4721c16cf7d5ea420d0cde6197
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 24 23:52:37 2018 -0700

    Update script info

Tools/F_scripts/write_cuda_headers.py

commit 9cc7717649b1f07e1954987a17810f438d2f3abd
Merge: 7c70d8d29 c3161c486
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 24 23:46:44 2018 -0700

    Merge branch 'gpu' into gpu-gpu

commit c3161c48685ce68a2fee272ba993eee56cdfde77
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 24 23:37:32 2018 -0700

    Preprocess CUDA files to look for !$gpu

Tools/F_scripts/gpu_fortran.py
Tools/GNUMake/Make.rules

commit 13c037ea0aa68e0eb70976e01770b21255f2e594
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 24 23:32:32 2018 -0700

    Only do the CUDA header work in the tempdir

Tools/F_scripts/write_cuda_headers.py
Tools/GNUMake/Make.rules

commit 9ae00258b6d3228df6dcb42bfafd054ff0ff24fd
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 24 22:56:05 2018 -0700

    Really fix source term copying

Tools/GNUMake/Make.rules

commit e5cde30f59c4e060077b9e0897fb6a50b11c2391
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 24 22:39:08 2018 -0700

    Fix source file copying

Tools/GNUMake/Make.rules

commit e88588e5fb51a330c981e742efd4730cac820421
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 24 16:19:57 2018 -0700

    Use the srcTempDir for the dependency generation

Tools/GNUMake/Make.rules

commit 121bd385ccb9d57a4106772b0830686406a1ab61
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 24 16:03:43 2018 -0700

    Fix tmpbuilddir logic

Tools/GNUMake/Make.rules

commit 9406ac004c610c7d732fd27c629b8622c0a1a6b3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 24 16:00:32 2018 -0700

    Add a missing @

Tools/GNUMake/Make.rules

commit ba483a6ac97f7cef6f519d19d96529d5693d8c87
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 24 15:17:27 2018 -0700

    Always include the temp build directory first

Tools/GNUMake/Make.defs

commit e1aa87114abe50d4ad1a39bdb9f3480a08641020
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 24 15:02:59 2018 -0700

    Reverse order so that source copies occur first

Tools/GNUMake/Make.rules

commit 69bf42190ccb725ac26b33e1f036d658c6063763
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 24 14:20:48 2018 -0700

    Copy all source files to a temp build directory before compilation

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 7c70d8d29d6f30688808c3f00cab4f67652987ba
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 23 21:21:03 2018 -0700

    [WIP] Update the CUDA script description

Tools/F_scripts/write_cuda_headers.py

commit 64dfddba06ed20d4a9d4bd02827008155b31595c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 23 21:19:21 2018 -0700

    [WIP] Update the CUDA script description

Tools/F_scripts/write_cuda_headers.py

commit c8c36717097b95d6a53f85722c7457ec66a0dc91
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 23 21:14:37 2018 -0700

    Replace AMREX_DEVICE with !$gpu

Src/Base/AMReX_BaseFab_nd.F90
Src/Base/AMReX_filcc_mod.F90
Src/Base/AMReX_fort_mod.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90

commit d4bcc41b0b070404ae7a9b9ebf7bad01d2542f71
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 23 20:28:24 2018 -0700

    Add some more GPU defines

Tools/GNUMake/Make.defs

commit a702c708071cc8b600e7cfa2124ca51397ffc38f
Merge: b41bec709 b02764fdb
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 23 14:45:39 2018 -0700

    Merge branch 'development' into gpu
    
    Conflicts:
            Src/Base/AMReX_ArrayLim.H
            Src/Base/AMReX_BLFort.H
            Tools/GNUMake/sites/Make.olcf

commit b02764fdb7c19739f9bc2129b012b0afba5f0a50
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 23 14:38:28 2018 -0700

    Add reduction macros

Src/Base/AMReX_BLFort.H

commit b41bec709cfd7c6fcb3cac1e38989805f9ed4ae3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 23 14:13:48 2018 -0700

    Fix logic on the nvcc version check

Src/Base/AMReX_BLFort.H

commit 976b61db32359ab9d662516d8d08b7639fafe2ef
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 23 15:36:18 2018 -0400

    Remove legacy non-CUDA 8 code

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.cpp
Tools/GNUMake/Make.defs
Tools/GNUMake/sites/Make.olcf

commit d765df200c7dc7f7e059a9d42f15519cb8b57899
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 23 12:16:01 2018 -0700

    Disallow CUDA toolkit versions <= 8.0

Tools/GNUMake/comps/nvcc.mak

commit ad68aa1bbb697aed6846808a1a59aa2ef0640672
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 23 12:12:01 2018 -0700

    bl_error -> amrex_error for CUDA

Src/Base/AMReX_CUDA.F90

commit 568d8ad9f0c75e86ff56af90646f31fa7b5f4c43
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 23 14:20:59 2018 -0400

    Capture NVCC version

Tools/GNUMake/comps/nvcc.mak

commit cd50afa43ea0bd80afbdceb5ee381ecf2d85a69c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jun 22 18:15:30 2018 -0700

    CMake: start transition to 'modern CMake'

Src/Amr/CMakeLists.txt
Src/AmrCore/CMakeLists.txt
Src/Base/CMakeLists.txt
Src/Boundary/CMakeLists.txt
Src/CMakeLists.txt
Src/EB/CMakeLists.txt
Src/EB2/CMakeLists.txt
Src/Extern/CMakeLists.txt
Src/F_Interfaces/CMakeLists.txt
Src/GeometryShop/CMakeLists.txt
Src/LinearSolvers/CMakeLists.txt
Src/Particle/CMakeLists.txt
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_Utils.cmake
Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/CMakeLists.txt

commit f11605d0f58061cf79b32ec5ac38c45db6c9de61
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Fri Jun 22 18:05:33 2018 -0700

    Getting implicit example in SDC tutorials

Tutorials/SDC/HeatEquation_EX3_C/GNUmakefile
Tutorials/SDC/HeatEquation_EX3_C/Make.package
Tutorials/SDC/HeatEquation_EX3_C/advance.cpp
Tutorials/SDC/HeatEquation_EX3_C/advance_2d.f90
Tutorials/SDC/HeatEquation_EX3_C/init_phi_2d.f90
Tutorials/SDC/HeatEquation_EX3_C/init_phi_3d.f90
Tutorials/SDC/HeatEquation_EX3_C/inputs_2d
Tutorials/SDC/HeatEquation_EX3_C/inputs_3d
Tutorials/SDC/HeatEquation_EX3_C/main.cpp
Tutorials/SDC/HeatEquation_EX3_C/myfunc.H
Tutorials/SDC/HeatEquation_EX3_C/myfunc_F.H
Tutorials/SDC/HeatEquation_EX3_C/pf_quadrature.f90

commit 5784a293b03ea40adfe1a7bb515803c1ef72e7cd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 22 16:55:58 2018 -0700

    use std::memcpy here instead of reinterpret_cast

Src/Particle/AMReX_ParticleContainerI.H

commit f6b1ebb041503825e26bf3baf86aaeda791648de
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 22 16:15:08 2018 -0700

    simplify timers

Src/Particle/AMReX_ParticleContainerI.H

commit d4bb40e66c98a186fcdbcabe535f9a6d991f6cf2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 22 16:11:40 2018 -0700

    remove code that isn't needed any more

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 0e3e68fcfb487d85c145d1ac0193b0dabb0934d5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 22 16:09:32 2018 -0700

    remove an un-needed copy

Src/Particle/AMReX_ParticleContainerI.H

commit 6f9629d47e78df1afd64d3a73d38d7f2b88f8de6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 22 13:48:20 2018 -0700

    Some systems require flush calls here for the particle io to work correctly. There is a similar work-around in AMReX_FArrayBox.cpp.

Src/Particle/AMReX_ParticleContainerI.H

commit 76b3e77c63bea2b6f70142bcf5648d15c4bdb9e1
Merge: 2aa1ecfdd a66a2676f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 22 13:04:24 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2aa1ecfdd97334d555ecce10b903fbd09cb98d18
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 22 12:01:57 2018 -0700

    try threading only the locate

Src/Particle/AMReX_ParticleContainerI.H

commit 782048a5b102a4be24be363de9db6bf7e00cef73
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 22 11:43:27 2018 -0700

    add some more timers

Src/Particle/AMReX_ParticleContainerI.H

commit 2bd98e48e6ec3d896c832679caafbeb626219137
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 22 11:32:25 2018 -0700

    adding threading to the unpack

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit a66a2676fce13e0062aab9ce18a3836c54f261e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 22 07:15:47 2018 -0700

    need to test the fortran function ptr in interp hook

Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp

commit e10441995db13a801a0c809264d7b1000492ddc7
Merge: bfef39ebf f8ec4d84d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 21 18:13:40 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit bfef39ebf3d201f6b75a5956149153ba7fb1e9b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 21 18:13:28 2018 -0700

    minor

Src/AmrCore/AMReX_FillPatchUtil.H

commit 6d86765ecbe95ea5d01d2b8ce1ba3d25253ff571
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 21 18:06:15 2018 -0700

    show how to use interploation hooks in tutorial

Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90
Tutorials/Amr/Advection_octree_F/Source/fillpatch_mod.F90

commit ac6d7b00245ba7746af8fe9cdda68fb75b80ab96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 21 17:50:41 2018 -0700

    add pre- and post-interp hooks in fillpatch for flash

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90

commit 6eebf3fecf862845345948e8a7628e6b5161b2d3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 21 17:41:50 2018 -0700

    update test

Tests/Particles/test.py

commit 58b37604ab7e3e54fd7498415f5d8836db3ad895
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 21 17:41:36 2018 -0700

    start threading unpacking the particle data in RedistributeMPI

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 95b6697e6f41cb075d20858a811b124d4b660fc0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 21 18:38:16 2018 -0400

    remove duplicate signatures from the list of targets

Tools/F_scripts/write_cuda_headers.py

commit f8ec4d84d6d93aef06815ed55914f6bc1cb59bf5
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jun 21 10:54:39 2018 -0700

    Avoid FillBoundary in recursive step

Src/EB/AMReX_EB_levelset.cpp

commit eb264040b9a59299c3b3cf16cb33be2fcee6c2e3
Merge: ed5173526 0c90ce2bc
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 21 09:57:21 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit ed5173526c190fe8c277e81f796442622fdd8f1e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 21 09:57:12 2018 -0700

    CMake: add NDEBUG only in non-XSDK mode

Tools/CMake/AMReX_Defines.cmake

commit 39de63a406a32cfe3217e7ec367c7f8118ed1ac0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 21 09:36:09 2018 -0700

    Do reductions on host when not offloading

Src/Base/AMReX_BaseFab.cpp

commit 7e13fddd461cb70ac5ce3b5b5ecd531d5da5a146
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 21 08:00:46 2018 -0700

    Add flag to disable device offload

Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_filcc_mod.F90
Src/Base/AMReX_fort_mod.F90
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 0c90ce2bc44433a845655738c4937d80d538dbb6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 20 21:54:44 2018 -0700

    NDEBUG -> AMREX_DEBUG

Src/Amr/AMReX_StateDescriptor.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/Base/AMReX.H
Src/Base/AMReX_BLassert.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_IArrayBox.cpp
Src/Boundary/AMReX_LO_UTIL.F90
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Tests/LinearSolvers/C_TensorMG/testVI.cpp
Tools/C_util/Convergence/Add.cpp
Tools/C_util/Convergence/DiffFab.cpp
Tools/C_util/Convergence/DiffSameDomainRefined.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGrid2.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileNormB.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp
Tools/C_util/Convergence/RichardsonConvergenceTest.cpp
Tools/C_util/Statistics/PltFileFluxAve.cpp
Tools/C_util/Statistics/PltFileList.cpp
Tools/C_util/Statistics/PltFileStat.cpp
Tools/C_util/Statistics/PltFileXAve.cpp
Tools/GNUMake/Make.defs

commit 0911eed7a39394dbd4a45c873c2248934e041784
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 20 17:59:48 2018 -0700

    compiles

Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp

commit d5c9a32aec89834d201f724a39e7e482568630aa
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 20 20:39:05 2018 -0400

    Broken Arena Change

Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BArena.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_CArena.H

commit 0a81f14094d90d5646c300419f70cd724002d770
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Wed Jun 20 17:09:12 2018 -0700

    Ramp written for EB2, with both regular plane arguments and slope-point args. tested with Sod, will test Shock Reflection

Tutorials/EB/CNS/Exec/Sod/inputs
Tutorials/EB/CNS/Source/CNS_init_eb.cpp
Tutorials/EB/CNS/Source/CNS_init_eb2.cpp

commit 25b770c5438993fbc8b5de304f48f52b2eb2c488
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Jun 20 17:02:00 2018 -0700

    change the way `valid` is populated... this should perform better if n_pad is large

Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_levelset_F.F90

commit 303b6319fc67d01dfd25ecb2fabe2bfbcac136d2
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 20 18:41:11 2018 -0400

    Update inputs files.

Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d
Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d

commit 8cf5b25c9060a050e6f95e429b3c0e6ada3e8e34
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 20 17:52:52 2018 -0400

    Addition of Device & CUDA from Max's branch. Devices initialize & finalize added to AMReX.cpp. Arenas adjusted to work with multiple MPI ranks.

Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_BArena.H
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_Managed.H
Src/Base/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp
Tutorials/GPU/HelloWorld_C/main.cpp

commit 79650123e53095383ef0eb381299100e94bcad42
Author: Minion <mlminion@lbl.gov>
Date:   Wed Jun 20 12:34:08 2018 -0700

    moving SDC tutorials into separate directory

Tutorials/SDC/HeatEquation_EX1_C/GNUmakefile
Tutorials/SDC/HeatEquation_EX1_C/Make.package
Tutorials/SDC/HeatEquation_EX1_C/advance.cpp
Tutorials/SDC/HeatEquation_EX1_C/advance_2d.f90
Tutorials/SDC/HeatEquation_EX1_C/advance_3d.f90
Tutorials/SDC/HeatEquation_EX1_C/init_phi_2d.f90
Tutorials/SDC/HeatEquation_EX1_C/init_phi_3d.f90
Tutorials/SDC/HeatEquation_EX1_C/inputs_2d
Tutorials/SDC/HeatEquation_EX1_C/inputs_3d
Tutorials/SDC/HeatEquation_EX1_C/main.cpp
Tutorials/SDC/HeatEquation_EX1_C/myfunc.H
Tutorials/SDC/HeatEquation_EX1_C/myfunc_F.H
Tutorials/SDC/HeatEquation_EX1_C/pf_quadrature.f90

commit 723e167a45164f32ea03a96cf1a51d9415fd52a0
Merge: 7983a86d0 d3a127c70
Author: Minion <mlminion@lbl.gov>
Date:   Wed Jun 20 12:29:11 2018 -0700

    Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC

commit 7983a86d014f5505ffcfcee146a33fb64bc98c9f
Author: Minion <mlminion@lbl.gov>
Date:   Wed Jun 20 12:28:28 2018 -0700

    starting to clean up SDC structures

Tutorials/Basic/SDCHeat_Equation_EX1_C/GNUmakefile
Tutorials/Basic/SDCHeat_Equation_EX1_C/Make.package
Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp
Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_2d.f90
Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_2d
Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp
Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H
Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H
Tutorials/Basic/SDCHeat_Equation_EX1_C/pf_quadrature.f90

commit 3766d6a8bab33c0320e4acaae80edfed0e9994ea
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Jun 20 11:41:51 2018 -0700

    fix naming convention for fortran module

Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset_F.F90

commit a83507a0e26add9ca3248a50a2ce3c833e62d897
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 20 09:52:11 2018 -0700

    add an argument to makeSFC to limit the maximal number of boxes a process can get

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit a86326cc5dda3be186bb756e8da3cfb7036b199c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 20 12:13:01 2018 -0400

    fix the ability to compile normal after CUDA w/o headers getting in the way

Tools/GNUMake/Make.rules

commit 08307bb0c1f8a48573f81eff22aac5a4deceff5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 20 07:59:21 2018 -0700

    update make

Src/EB2/CMakeLists.txt
Src/EB2/Make.package

commit a8421ed87904f2869578e2f2bf8f0a94dd9d8450
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 19 19:53:30 2018 -0700

    Generalize the IBM config so it is not OLCF specific

Tools/GNUMake/comps/ibm.mak
Tools/GNUMake/sites/Make.olcf

commit 2f2acc311d50c8fb9ccb69f1d1140831894267fc
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 19 19:51:16 2018 -0700

    Update LLNL MPI setup

Tools/GNUMake/sites/Make.llnl

commit 34e39cbec74f61bc5d231a19b69fb76ee4ecc131
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 19 18:07:48 2018 -0700

    RotationIF: fix 2d compilation; add std:: to cos and sin for
                portability; fix the sign in rotation matrix because we
                are rotating the object.

Src/EB2/AMReX_EB2_IF_Rotation.H

commit 26f4d00baf6abc2ffc6cf8de3e8138ec6c4c8253
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 19 17:27:45 2018 -0700

    fix typo

Src/AmrCore/AMReX_INTERP_2D.F90

commit 3e180e08588d7faa535834bd3b9e8727f87cc266
Merge: 2f83e472e 954ed5f2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 19 17:15:42 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2f83e472e16903334fa3f7f16084cdf41563a19c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 19 17:15:29 2018 -0700

    xSDK: fix some Fortran print

Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/Base/AMReX_COORDSYS_2D.F90
Src/Base/AMReX_COORDSYS_3D.F90
Src/EB2/AMReX_eb2_3d.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90
Src/Particle/AMReX_Particle_mod_1d.F90
Src/Particle/AMReX_Particle_mod_2d.F90
Src/Particle/AMReX_Particle_mod_3d.F90

commit d3a127c70971be6fbcb82356a1e51be283aa7d9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 19 17:03:47 2018 -0700

    typo

Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H

commit f1bc3faa6eeb6618b5234c2ecc924e7d53e8d7b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 19 16:38:09 2018 -0700

    xSDK: print

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_AmrCore.H
Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_BoxDomain.cpp
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_NFiles.cpp
Src/Base/AMReX_ParmParse.cpp
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_VisMF.cpp
Src/EB2/AMReX_EB2_GeometryShop.H
Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H

commit 4356487b7ccc0ffcb9a54cc432e19937d826885f
Author: sireeveslbl <sireeves@lbl.gov>
Date:   Tue Jun 19 16:24:22 2018 -0700

    Rotation about the origin axes

Src/EB2/AMReX_EB2_IF_Rotation.H

commit 954ed5f2c9368dd088a4f1aeab5c480f7550284c
Merge: 792a904ee bd5477a9c
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jun 19 16:08:45 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 792a904eec1ae9ca2ac55a51a710f5d8f61565ea
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jun 19 16:08:42 2018 -0700

    update EB level-set to reflect recent changes in mfix

Src/EB/AMReX_EB_F.H
Src/EB/AMReX_EB_geometry.F90
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_levelset_F.F90
Src/EB/AMReX_compute_normals.F90

commit bd5477a9c3262d59c2cbd04d78201658a440a8dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 19 15:17:42 2018 -0700

    turn off print unless verbose is true

Src/Base/AMReX_Utility.cpp

commit 19313a92be69c4178ba1023c309e1e741a33021c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 19 15:17:02 2018 -0700

    add amrex::RuntimeError and amrex.throw_exception ParmParse parameter

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_Exception.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 5f6d498fb63cfe2c6fc849f291b81ad6dc77a4de
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 19 12:26:45 2018 -0700

    some clean up / comments

Tutorials/Particles/CellSortedParticles/CellSortedPC.H
Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp

commit 3f569b5497139cca5a1a76a09078df45ab060ffa
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 19 12:20:51 2018 -0700

    store vectors directly instead of unique_ptr to vectors

Tutorials/Particles/CellSortedParticles/CellSortedPC.H
Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp

commit 9f650ea0c0c8a8812b62da95b8f1055657774662
Merge: 4f0d546f2 37afd673f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 19 10:52:02 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4f0d546f221b1f98b5e045f640923d18f641eac7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 19 10:51:45 2018 -0700

    remove another unused variable.

Src/Base/AMReX_NFiles.cpp

commit 67f56724ea1789403ba77ff17f1362add1f22fc0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 19 10:47:31 2018 -0700

    remove unused variables.

Src/Base/AMReX_MultiFabUtil_nd.F90

commit 37afd673f9947b093bab463e59b664a91963abff
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 19 09:50:10 2018 -0700

    adding an additional Timer to RedistributeMPI

Src/Particle/AMReX_ParticleContainerI.H

commit 2a4efea2f1dfd6cfecf75c8386a3c557755e680e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 18 16:33:31 2018 -0700

    remove need to explicitly update the structure of the cell vectors.

Tutorials/Particles/CellSortedParticles/CellSortedPC.H
Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp
Tutorials/Particles/CellSortedParticles/main.cpp

commit cbdbee6b74908a400083ff011a4d9018f1740ea2
Merge: d987660f4 b88cd73a8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 18 15:40:55 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d987660f41e89e832799c3fe2a70efe2242a1f41
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 18 15:40:41 2018 -0700

    starting to track to the ref of the BA and DM that the cell vectors are defined on.

Tutorials/Particles/CellSortedParticles/CellSortedPC.H
Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp

commit ce50a3fa1b0117b9b37c349ccdd912485f9094b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 18 10:21:50 2018 -0400

    have the python preprocessor remove unwanted preprocessor directives

Tools/F_scripts/write_cuda_headers.py
Tools/GNUMake/Make.rules

commit c63f46ff65e7dd1b2067da31dab97d88bf18e608
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 18 10:09:11 2018 -0400

    fix CUDA flags

Tools/GNUMake/Make.rules

commit b88cd73a8e9c0a3efa709baffac6849f1c016816
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jun 17 22:18:47 2018 -0400

    add some macros to sync with what is happening on the gpu branch
    this gives us CPU compatibility

Src/Base/AMReX_ArrayLim.H

commit 7e7c4122c55572d237df83947d6f16548468660a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 17 13:03:24 2018 -0400

    Handle MPICH with CUDA

Tools/GNUMake/Make.defs

commit 3342dbe48c805496e2712811fabbb8c862456662
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jun 17 11:41:01 2018 -0400

    don't pass the MPI preprocessor directives into the CUDA stuff

Tools/GNUMake/Make.rules

commit 3613075489a2a3b2c6023085e5304b8f0d435c21
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Sat Jun 16 19:24:44 2018 -0700

    optimal SDC order for heat equation

Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp
Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_2d.f90
Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_2d
Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp
Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H
Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H
Tutorials/Basic/SDCHeat_Equation_EX1_C/pf_quadrature.f90

commit 4c83d6724037f90c699872662ed7b024d635ed8e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 15 16:52:42 2018 -0700

    enable OpenMP in some loops

Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp

commit ba0a78a0f77d719d523cdc392a1821d9dc1da437
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 15 16:45:54 2018 -0700

    turn on mpi

Tutorials/Particles/CellSortedParticles/GNUmakefile

commit 5d32eb88bc423a85fdf44e43a69198a9c8e50df8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 15 16:44:28 2018 -0700

    keeping track of which particle in which cell as they move around.

Tutorials/Particles/CellSortedParticles/CellSortedPC.H
Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp
Tutorials/Particles/CellSortedParticles/cell_sorted_3d.F90
Tutorials/Particles/CellSortedParticles/cell_sorted_F.H
Tutorials/Particles/CellSortedParticles/main.cpp

commit 94f69a9eb9e523b1560efe4f0a34140f813e5342
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 15 14:57:56 2018 -0700

    use the fortran to link when using intel with a Fortran main.

Tools/GNUMake/comps/intel.mak
Tutorials/Amr/Advection_F/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_F/GNUmakefile
Tutorials/Basic/HelloWorld_F/GNUmakefile
Tutorials/Basic/main_F/GNUmakefile
Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile

commit 482ba98598fd25f612661fd409c2ef82057f854a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 15 12:52:04 2018 -0700

    start working on cell-sorted particles for DSMC

Tutorials/Particles/CellSortedParticles/CellSortedPC.H
Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp
Tutorials/Particles/CellSortedParticles/GNUmakefile
Tutorials/Particles/CellSortedParticles/Make.package
Tutorials/Particles/CellSortedParticles/cell_sorted_3d.F90
Tutorials/Particles/CellSortedParticles/cell_sorted_F.H
Tutorials/Particles/CellSortedParticles/inputs
Tutorials/Particles/CellSortedParticles/main.cpp

commit f34caa7547b10445639b1fa4a78b8993fda93ad4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 15 12:50:58 2018 -0700

    give ParticleContainer a virtual destructor.

Src/Particle/AMReX_Particles.H

commit 2e0797832067d4a2f2bdb2beecf61108e0154ffd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 14 19:47:10 2018 -0400

    add back in the c99 standard

Tools/GNUMake/Make.rules

commit 5dbb67046ca257762b1dd0149bb72c0c81a028f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 14 16:05:24 2018 -0700

    EB MLMG: add interp

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit 075ce237d62f559a2163360235123e7369d6e4db
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Jun 14 18:29:50 2018 -0400

    Redesign GeometryData object and data function to prevent caching.

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit f581cddacbd4871acf13a00b1f847667c0d304f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 14 18:17:16 2018 -0400

    remove the check on the gcc return code for now
    it works for gcc > 6.4.0 but not earlier

Tools/F_scripts/preprocess.py

commit ffedf72ed7165d940840245007d6608e1e8b83a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 14 14:57:39 2018 -0700

    EB MLMG: fix bug

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90

commit b47e76f8c91edfa449a46165e33699765f2e4790
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 14 14:22:43 2018 -0700

    EB MLMG: interp

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_F.H

commit be3e7f91c490e273dd6e9d177125db6d9e9cdea6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 14 17:08:31 2018 -0400

    don't restrict to python3

Tools/F_scripts/write_cuda_headers.py

commit 72b3d2c04a9aca3a0ab2ea8af576c4cdd504bf80
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 14 16:11:05 2018 -0400

    Fix IBM MPI library

Tools/GNUMake/sites/Make.olcf

commit 3223c783811cec73a1c1622b95ebf60115827948
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 14 16:03:22 2018 -0400

    this works

Tools/F_scripts/write_cuda_headers.py

commit 743ca37eb884392a124b7b2a5388dd6e055805b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 14 15:07:55 2018 -0400

    this is mostly right, but somewhat wrong

Tools/F_scripts/write_cuda_headers.py

commit 8a8bc7fa123fa9481ce411c0a549a862508df393
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 14 11:22:02 2018 -0700

    add a new eb_average_down

Src/Base/AMReX_FabArray.H
Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_3d.F90
Src/EB/AMReX_EBMultiFabUtil_F.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 516dc6a0f7032ef8d38d7903b37e3bb7286d98a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 14 13:24:49 2018 -0400

    fix the case where a sig is on a line to itself

Tools/F_scripts/write_cuda_headers.py

commit 268e92831173e3268506c3c7fc0619e04357e080
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 14 10:10:32 2018 -0700

    EB MLMG: normalize

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit 2a4ad73dc5a337bec67c0be0a02c3cc5e27f076d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 14 11:53:48 2018 -0400

    restore file that my script overwrote :(

Src/Base/AMReX_BaseFab_f.H

commit 9e435207d11d7a24ae7a310355b63dc84786ba5c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 14 11:50:25 2018 -0400

    weren't storing preprocessed headers

Src/Base/AMReX_BaseFab_f.H
Tools/F_scripts/write_cuda_headers.py

commit dcf863bc97661b6fd24ed7e0432f816d7f939b16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 14 10:27:18 2018 -0400

    fix the preprocessing

Tools/F_scripts/preprocess.py
Tools/GNUMake/Make.rules

commit 07e5de83cfcf8baa32bf03cb8d284f25cd1f4565
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 13 21:49:08 2018 -0400

    the new preprocess version of the script.  Doesn't work yet

Tools/F_scripts/preprocess.py
Tools/F_scripts/write_cuda_headers.py
Tools/GNUMake/Make.rules

commit aec591bd6001ceca4d6a69e870deedcde9b25cd9
Merge: 50996d279 de5346057
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jun 13 17:32:50 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 50996d2791ce72a7fc2aba01631d88feb3bca788
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jun 13 17:32:38 2018 -0700

    update NeighborList Tutorial

Tutorials/Particles/NeighborList/NeighborListParticleContainer.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp

commit 0e4369c3f8d1f3c67c1577c0fca552eceb47d982
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jun 13 17:32:18 2018 -0700

    use a template rather than a virtual function for checking particle pairs.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 89a5e9ba71a5526d23dbcddba3a1a424eb133084
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 13 17:03:37 2018 -0700

    EB MLMG: gsrb

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit 75a026b586a7c2cbba6e3707d88282a5a136b416
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 13 19:06:56 2018 -0400

    HeatEquation_EX_1 works with USE_CUDA=FALSE in 2D and 3D, with global kernels in C and passing by value.

Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit ceac75dd2739c6df561f507fb24a033adf739d47
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 13 19:02:37 2018 -0400

    Remove unnecessary #ifdefs around GeometryData object.

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp

commit e4edbe75625b99cd96eb61c2e2a2bc459117f1d9
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 13 19:01:34 2018 -0400

    CUDA function wrappers for USE_CUDA=FALSE.

Src/Base/AMReX_Managed.H

commit 5984d25757d21d253d3f9b2a715c64f2c74ecfb1
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 13 19:00:57 2018 -0400

    Creation and implementation of amrex_simpleArray to allow HOST DEVICE function declaration on macros.

Src/Base/AMReX_ArrayLim.H

commit 96ec006c4ef30a083dad04c616f0de9bda0a51e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 13 13:59:01 2018 -0700

    EB MLMG: adotx and factories

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 465eb90970c44b4aa17f59d2ffb7e52b1937ba23
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 13 15:48:06 2018 -0400

    split the preprocessor out for reuse

Tools/F_scripts/dep.py
Tools/F_scripts/preprocess.py

commit de53460570e500b22bc27b85bd5de795294728bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 13 12:20:10 2018 -0700

    eb/cns: more udpates of inputs

Tutorials/EB/CNS/Exec/Pulse/inputs
Tutorials/EB/CNS/Exec/Pulse/inputs.regt
Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs
Tutorials/EB/CNS/Exec/Sod/inputs

commit 2310e83a5d55a6c81e1ac2c23353b6cc7e210424
Merge: 90071dd9a 1b34a9329
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 13 11:21:28 2018 -0700

    Merge branch 'eb2' into weiqun/mlmg

commit 1b34a93290c068d38a8f2f9541a9404c5606bc78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 13 11:20:22 2018 -0700

    eb/cns: update inputs

Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs
Tutorials/EB/CNS/Exec/Combustor/inputs
Tutorials/EB/CNS/Exec/Combustor/inputs.regt
Tutorials/EB/CNS/Exec/Combustor/inputs.testing
Tutorials/EB/CNS/Exec/Combustor/inputs_combustor
Tutorials/EB/CNS/Exec/Pulse/inputs
Tutorials/EB/CNS/Exec/Pulse/inputs.regt
Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs
Tutorials/EB/CNS/Exec/ShockRef/inputs
Tutorials/EB/CNS/Exec/ShockRef/inputs.amr
Tutorials/EB/CNS/Exec/ShockRef/inputs.regt

commit 8c32a704fd0cf6495d4b17065907e4336e6def03
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 13 09:55:26 2018 -0700

    Fortran: add max_coarsening_level

Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_mod.F90
Src/F_Interfaces/LinearSolvers/AMReX_poisson_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90

commit 33e205d0861d2349f2d58792b2f8007a78965ec9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 13 09:45:34 2018 -0700

    Fortran: add multigrid % set_bottom_solver

Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90
Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90

commit 90071dd9ad8bb70214eba4977ac802a16c26f2e3
Merge: ebb6a2e00 07d886939
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 13 08:59:22 2018 -0700

    Merge branch 'eb2' into weiqun/mlmg

commit 07d886939fc07a772ae930d9a7922989993a353a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 13 08:58:49 2018 -0700

    fix typo

Src/AmrTask/tutorials/MiniApps/HeatEquation/myfunc_F.H
Tests/ProfTests/HeatEquation_EX1_C/Source/myfunc_F.H
Tests/ProfTests/ThirdParty/Source/myfunc_F.H
Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc_F.H
Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc_F.H
Tutorials/Basic/HeatEquation_EX3_C/Source/myfunc_F.H
Tutorials/CVODE/EX1/myfunc_F.H
Tutorials/CVODE/EX2/myfunc_F.H

commit 0e82dff8192b475419933ba0bb611a762c7302ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 13 08:54:36 2018 -0700

    add init eb2 in a new file

Tutorials/EB/CNS/Source/CNS_init_eb2.cpp

commit ebb6a2e00a3c7c829469cb78cafb45add563465e
Merge: 8dde62c18 4b47bab38
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 20:49:41 2018 -0700

    Merge branch 'eb2' into weiqun/mlmg

commit 4b47bab38fb1bfbaf6c4369ed00b13ff9f06ba41
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 20:49:09 2018 -0700

    add required coarsening level

Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_IndexSpaceI.H
Tests/EBEB2/MyTest.cpp
Tutorials/EB/CNS/Source/main.cpp

commit 0fa5fd0dc369ed3075bb4997fa418696c9f93693
Merge: 75721da5a 70deacbc5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 12 20:12:43 2018 -0700

    Merge branch 'development' into gpu

commit 75721da5a7ea9cd151bdc57bc4bb014ff4c75b93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 12 22:53:40 2018 -0400

    can't have CPP_sources be a dependency for write_cuda_headers.py
    since it now writes the CPP sources in a new location

Tools/GNUMake/Make.rules

commit e67debb704b4415822b4f9d175fd1f60870ff2f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 12 21:42:26 2018 -0400

    this does the C++ #pragma expansion
    still need to hook it into the vpath

Tools/F_scripts/write_cuda_headers.py
Tools/GNUMake/Make.rules

commit 8dde62c180453857d60a83ad5ff4a8cbc3c0b29d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 17:13:05 2018 -0700

    EBABecLap: start adotx

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H

commit 26ac13a69c08a7dc79738853d87a894d686f9855
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 12 15:41:50 2018 -0700

    Use #pragma gpu

Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_BaseFab.cpp
Tutorials/GPU/HeatEquation_EX1_C/advance.cpp

commit 2419f72a3138ddbfb642fe794e8d0c77279cf430
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 14:56:50 2018 -0700

    EBABecLap: prepare for solve

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 255fe9213e3192990fef4b820dbc09fb6596c024
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 13:58:43 2018 -0700

    stubs

Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp

commit 3da6218309759ae76eaee1c7eb5a94ef63cdd5e3
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jun 12 16:26:54 2018 -0400

    Pass GeometryData by class.

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit bda53b3d0cafacab01b629fbb6a23b107f1f19f5
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jun 12 16:13:19 2018 -0400

    Add Pinned version of memory for passing small constant objects to kernels. Used on GeometryData.

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Managed.H

commit cb48bc55fa1c0011780211f6641b72d4a91fb31f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 13:04:08 2018 -0700

    it's possible to have only one cut

Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90

commit e8f07076a3cc7262a459e459dddaf48c6a96f284
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 13:04:08 2018 -0700

    it's possible to have only one cut

Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90

commit 53bac3ee7e13540326aea905949300cefe00ac74
Merge: 58a5eb84b 3dcf1ce1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 12:27:51 2018 -0700

    Merge branch 'weiqun/eb2' into weiqun/mlmg

commit 58a5eb84b13bf029ddb6929c86959c23739ab822
Merge: f5a88d9f3 70deacbc5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 12:27:35 2018 -0700

    Merge branch 'development' into weiqun/mlmg

commit 6cfb6bcd8386cee33df4ab253d3241b08a7d7ba9
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jun 12 15:20:17 2018 -0400

    Change HeatEquation_EX1 to pass Box by class to C++ based wrapper kernel.

Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.f90
Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.f90
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H

commit b204c08f0fbf58e585b6b6d57e379ec4260ede27
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jun 12 15:18:30 2018 -0400

    Testing passing Box into kernel by class.

Tutorials/GPU/HelloWorld_C/main.cpp

commit 3dcf1ce1ab9c3f5fdab1f7e8db1cdd5b9e4babc6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 12:18:14 2018 -0700

    EB/CNS: set support level before initializing EB2

Tutorials/EB/CNS/Exec/Sod/inputs
Tutorials/EB/CNS/Source/main.cpp

commit aafc649ada86c079bf14caf485bc3ebe6d4aad6a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jun 12 15:17:43 2018 -0400

    Declaring a few more function __host__ __device__.

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_RealBox.H

commit 5fa5a121c7163b2c4602a1d5d42ccd89b397dd19
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 12 14:27:15 2018 -0400

    AMREX_ARLIM_VAL is no longer required

Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_filcc_f.H
Tools/F_scripts/write_cuda_headers.py
Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H

commit 70deacbc592f6bf4ab00da083431674e3e4bdf1d
Merge: ea2f56096 ea6d89f90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 10:42:36 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ea6d89f9052b755fb44bd007d13209c840ae380b
Merge: d4848b6c5 5ffb39150
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 12 10:27:30 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d4848b6c55da179745dfae45bc9b059f111ba3fc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 12 10:27:12 2018 -0700

    just have Make.ccse refer to Make.unknown - should work on both updgraded and non-updated ccse machines.

Tools/GNUMake/sites/Make.ccse

commit ea2f56096c0c808addfaf903cecf73b184b90d5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 10:15:54 2018 -0700

    fix make of the eb levelset test

Tutorials/EB/LevelSet/Exec/GNUmakefile

commit 5812441de9d619762c2e5aee42d3615ce5bffd6c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 09:48:20 2018 -0700

    no need to have USE_EB2

Tools/GNUMake/Make.defs

commit 03ffa38390c0762949ddb4e6fde67934934d8dab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 09:39:38 2018 -0700

    add EB2 to cmake

Src/CMakeLists.txt
Src/EB2/CMakeLists.txt

commit c7f6b57e8fe6587e2526bf59d95783612d196964
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 12 12:24:19 2018 -0400

    Move a device sync to the right place

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H

commit 69033e9a701a8a9db92892181ac166ed8aae3d35
Merge: 32f7dc170 5ffb39150
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 12 09:19:07 2018 -0700

    Merge branch 'development' into weiqun/eb2

commit e366079e90abc501f68f70f62f638890f810a661
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 12 11:57:58 2018 -0400

    Cover some more Box functions, for safety

Src/Base/AMReX_Box.H

commit c7fccf4622043bafd5648935e0dfb618192cead5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 12 11:48:12 2018 -0400

    Use the FA arena

Src/Base/AMReX_FabArrayCommI.H

commit 5ec60a3f65d8f9ea87acfd13c0976fef4c57d414
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 11 20:38:33 2018 -0400

    Fix indexing issue in copyfrommem

Src/Base/AMReX_BaseFab_nd.F90

commit 32f7dc170a53d4536f0de51b7527a39fb23b8471
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 11 17:28:13 2018 -0700

    add all_regular

Src/AmrCore/AMReX_AmrMesh.cpp
Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_IF_AllRegular.H
Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Src/EB2/Make.package
Tutorials/EB/CNS/Exec/Sod/inputs
Tutorials/EB/CNS/Source/CNS_init_eb.cpp
Tutorials/EB/CNS/Source/Make.package
Tutorials/EB/CNS/Source/main.cpp

commit b8af3d7ef1736706438adf49bb9597dbadfc678a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 11 18:28:05 2018 -0400

    Fix offsets in copytomem/copyfrommem

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit 5dc795bb8db6e2522d9e7b3d900986f5d89c5234
Merge: 5cc607a7c 09265f80a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 11 15:47:41 2018 -0700

    Merge branch 'development' into weiqun/eb2

commit 8519ea6b10ce533e90e29af4e37552405b2c501a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 11 17:14:27 2018 -0400

    Use AMREX_ARLIM_3D

Src/Base/AMReX_ArrayLim.H

commit 5ffb39150a7a850a744853a8e6613d240b816cab
Merge: 09265f80a 5132e9b24
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jun 11 13:39:54 2018 -0700

    Merge pull request #274 from jaharris87/development
    
    Add interface for character bcast to F_BaseLib

commit 998114d796ebf08512b511e2f1d72bda51050ff7
Merge: 97bc4282a 1f86292f0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 11 16:26:50 2018 -0400

    Merge branch 'development' into gpu

commit 5cc607a7caa089cd3161bbf482684f8d48f11696
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 11 13:20:41 2018 -0700

    coarsen valid cells only

Src/EB/AMReX_EBCellFlag.H
Src/EB2/AMReX_EB2_Level.cpp
Tests/EBEB2/inputs

commit 09265f80a8469d50490d231792f78a9f8950c061
Merge: 3ec893519 1f86292f0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 11 13:14:03 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 3ec89351911c8e532ed80faf0fb281ff0eb2b1c4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 11 13:13:52 2018 -0700

    clean up CreateGhost and CreateVirtualParticles

Src/Particle/AMReX_ParticleContainerI.H

commit 1a8164e2b2b190a832936c97a9143024f8519c44
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 11 13:11:15 2018 -0700

    remove unused static member of RealVect

Src/Base/AMReX_RealVect.H

commit 5ff8a9bd5049864f7381107fff4f3bd8382f2e5c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 11 13:01:10 2018 -0700

    silence another warning

Src/Particle/AMReX_ParticleContainerI.H

commit aad7b52712d92e1c8f50b4ce3a6643c1848a005f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 11 12:58:14 2018 -0700

    silence unused variable compiler warning

Src/Particle/AMReX_ParticleContainerI.H

commit 5132e9b244089ed2a64a633e9fe03d4c68308f46
Author: Harris, James Austin <harrisja@ornl.gov>
Date:   Mon Jun 11 15:25:22 2018 -0400

    Add interface for character bcast to F_BaseLib

Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit 1f86292f0c372875b3fcd1eb54f2c3d655b2c1ff
Merge: f0cd1e531 0e3370dd4
Author: Daniel Ladiges <drladiges@lbl.gov>
Date:   Mon Jun 11 10:36:05 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit f0cd1e531f065c860e4120196a861726cd82eed8
Author: Daniel Ladiges <drladiges@lbl.gov>
Date:   Mon Jun 11 10:30:45 2018 -0700

    Added bl_random_.f90
    bl_random_c.cpp
    bl_random_c.H
    
    to make package

Src/F_BaseLib/FParallelMG.mak

commit 766ab53894dc6281390d2685ff6b5284cb9f7597
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Jun 11 00:37:42 2018 -0400

    GeomData into all kernels. Requires non-const Geometry in advance.cpp function call in current form.

Src/Base/AMReX_Geometry.H
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H

commit 97bc4282a2cae52ee7b48c5b564fdacb69d108f8
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 10 21:48:45 2018 -0400

    Sync up with the original heat equation example

Tutorials/GPU/HeatEquation_EX1_C/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/physbc.cpp

commit 9ce350b75d245a437b0992a44bec254eeaa97c56
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 10 21:43:27 2018 -0400

    Complete removal of amrex_fort_launch (except PIC)

Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_filcc_f.H
Src/Base/AMReX_filcc_mod.F90
Tutorials/GPU/HeatEquation_EX1_C/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H

commit a1208681c95bcf960e3a02fcc81a4b4ab6d934c5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 10 21:17:19 2018 -0400

    Finish BaseFab

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit 40d5e4486cc37bda433237120ea1788c75614b27
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 10 20:49:33 2018 -0400

    Convert more BaseFab to new launch mechanism

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit 8d8d982bb41fb75da8cf60bd41392a4b6d0a0ec6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 9 13:58:44 2018 -0700

    fix bug in 3d cell flag

Src/EB2/AMReX_eb2_3d.F90
Tests/EBEB2/MyTest.cpp

commit 1925d35f47071c688db39f5d7949b28cffd16268
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 9 13:16:56 2018 -0700

    ignore cells outside domain for cellflagfab type

Src/EB2/AMReX_EB2_Level.cpp
Tests/EBEB2/GNUmakefile

commit 0e3370dd4f32cd3a8611eace966ecac4055d76dc
Merge: de6893069 9f62a0347
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sat Jun 9 12:24:21 2018 -0700

    Merge pull request #266 from AMReX-Codes/f_interfaces_particles
    
    Adding some particle support to the F_Interfaces

commit 8acd7254a9cfaa84681cf6817ceaeb89a81cf627
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 8 22:53:05 2018 -0700

    typo

Tests/EBEB2/GNUmakefile
Tests/EBEB2/initEB.cpp

commit 80ce3d192addd63ce7149f6d3740dff4a530355b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 8 22:10:08 2018 -0700

    set default value fo boundary centroid to -1 for consistence with the old implementation

Tests/EBEB2/MyTest.cpp
Tests/EBEB2/inputs

commit 9f62a03475bf480810256eb18dad83e9e6369ce1
Merge: c230aa78a 986710c5c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 8 21:54:10 2018 -0700

    Merge branch 'f_interfaces_particles' of github.com:AMReX-Codes/amrex into f_interfaces_particles

commit c230aa78a2f2af896091f27e726ceeff055ba156
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 8 21:53:00 2018 -0700

    simplify logic in advection kernels

Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90

commit 8c758e6a979d346c3e1ab1147fe0be24f7821c14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 8 21:49:06 2018 -0700

    zero out neighbors for covered cells

Src/EB/AMReX_EBCellFlag.H

commit 14e1f010bccadae0c2b6babde00a771b9b096720
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Fri Jun 8 17:07:17 2018 -0700

    initial ascent integration

Src/Base/AMReX_Conduit_Blueprint.cpp
Tests/Blueprint/AssignMultiLevelDensity/GNUmakefile
Tests/Blueprint/AssignMultiLevelDensity/main.cpp
Tests/Blueprint/HeatEquation_EX1_C/Exec/GNUmakefile
Tests/Blueprint/HeatEquation_EX1_C/Source/main.cpp

commit 18069131a39cbbf6b982ddd51b30c1a4f868dc4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 8 17:06:28 2018 -0700

    fix the check for multi-cuts

Src/EB2/AMReX_eb2_2d.F90

commit 147c015f35d848a7ac68bfa55b8c0b128130c8b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 8 16:33:45 2018 -0700

    add plane to test

Tests/EBEB2/initEB.cpp
Tests/EBEB2/inputs

commit 59c4ecec293caf43defdca8aab585c595fdeddb0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 8 16:08:44 2018 -0700

    buid cell flags from aperture

Src/EB/AMReX_ebcellflag_mod.F90
Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90
Tests/EBEB2/MyTest.cpp

commit 3dafa8bfe38dcbabcc9f080d96aa6d2dd6d6c56b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 8 14:30:14 2018 -0700

    fix coarsening

Src/EB2/AMReX_eb2_2d.F90

commit 7cb390864011623c8ce615d8d988e53fb30b9bb9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 8 14:20:19 2018 -0700

    bug fix

Src/EB/AMReX_EBTower.cpp
Src/EB2/AMReX_eb2_2d.F90
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Tests/EBEB2/MyTest.H
Tests/EBEB2/MyTest.cpp
Tests/EBEB2/initEB.cpp
Tests/EBEB2/inputs

commit 7f612820518f6a0818e30662eb96aebd7d9c2c1e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 8 12:32:15 2018 -0700

    convert this logical to a c_int

Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90

commit 92947f6cd9f81614bf8b3fbf6b00de6f7e3481c8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 8 12:26:48 2018 -0700

    use nullptr instead of NULL

Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp

commit f5472ac8d38738e03107899775d853c7cb308706
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 8 12:24:34 2018 -0700

    this doesn't need to be a target

Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90

commit 1af7dc1c69080e09d3b78cdc18b852bbc65f528b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 8 12:21:15 2018 -0700

    change name of these variables so as not to clash with Fortran built-ins

Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90

commit 9f5e9061de9d0f39588ac1bc4a6582af6cdad053
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 8 11:13:05 2018 -0700

    avoid comparing domain boundary cells

Src/EB2/AMReX_eb2_2d.F90
Tests/EBEB2/MyTest.cpp

commit 686c3888affebe67d703323809416519a4c800c4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jun 8 11:02:46 2018 -0700

    Start porting BaseFab to use the new launch mechanism

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit 5f69b6949f137b782376e11870d9df081bccfbb8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 8 10:51:03 2018 -0700

    zero out number of vofs for covered cell

Src/EB/AMReX_ebcellflag_mod.F90

commit e1e0393f5712df19eec331b3ba8161843fa31dd9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 8 10:40:04 2018 -0700

    change the default value of EBCellFlag in 2d for comparison

Src/EB/AMReX_EBCellFlag.H

commit 260c9246ab11fdf3e4d4510c15c439dad520fec3
Author: Cyrus Harrison <cyrush@llnl.gov>
Date:   Fri Jun 8 10:34:19 2018 -0700

    initial blueprint support

Src/Base/AMReX_Conduit_Blueprint.H
Src/Base/AMReX_Conduit_Blueprint.cpp
Src/Base/Make.package
Tests/Blueprint/AssignMultiLevelDensity/GNUmakefile
Tests/Blueprint/AssignMultiLevelDensity/Make.package
Tests/Blueprint/AssignMultiLevelDensity/inputs
Tests/Blueprint/AssignMultiLevelDensity/main.cpp
Tests/Blueprint/HeatEquation_EX1_C/Exec/GNUmakefile
Tests/Blueprint/HeatEquation_EX1_C/Exec/inputs_2d
Tests/Blueprint/HeatEquation_EX1_C/Exec/inputs_3d
Tests/Blueprint/HeatEquation_EX1_C/Source/Make.package
Tests/Blueprint/HeatEquation_EX1_C/Source/advance.cpp
Tests/Blueprint/HeatEquation_EX1_C/Source/advance_2d.f90
Tests/Blueprint/HeatEquation_EX1_C/Source/advance_3d.f90
Tests/Blueprint/HeatEquation_EX1_C/Source/init_phi_2d.f90
Tests/Blueprint/HeatEquation_EX1_C/Source/init_phi_3d.f90
Tests/Blueprint/HeatEquation_EX1_C/Source/main.cpp
Tests/Blueprint/HeatEquation_EX1_C/Source/myfunc.H
Tests/Blueprint/HeatEquation_EX1_C/Source/myfunc_F.H
Tests/Blueprint/README.txt
Tools/GNUMake/Make.defs

commit 2179be3f7e4ab8dd9f81ccf71dd6956b8c4f6c0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 8 10:32:39 2018 -0700

    fix bug

Src/EB2/AMReX_EB2_Level.cpp
Src/EB2/AMReX_eb2_2d.F90

commit 6529aa2716309566b4f8f1a5e6359a97261ae41a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jun 8 10:23:05 2018 -0700

    16x16 seems to be better

Src/Base/AMReX_Device.cpp

commit 368569661f28ac073b77f41ecc5acd61baba4a27
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Jun 8 13:21:55 2018 -0400

    Initial GeometryData tests and implementation in HeatEquation_EX_1.

Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp
Tutorials/GPU/HelloWorld_C/GNUmakefile
Tutorials/GPU/HelloWorld_C/inputs_geometry
Tutorials/GPU/HelloWorld_C/main.cpp
Tutorials/GPU/HelloWorld_C/run.script
Tutorials/GPU/run.script

commit 6d8eb3cff52b703e4f006326d9b7df3e12f1e1c8
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Jun 8 13:19:56 2018 -0400

    GeometryData object for CUDA managed memory.

Src/Base/AMReX_Box.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_RealBox.H

commit 9b9283b7d67f2248344cbb6185c547b95bf38aa3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jun 8 09:47:37 2018 -0700

    Switch to 32x8 thread layout

Src/Base/AMReX_Device.cpp

commit 39eafc15440bad0dec60b6308c757b83668a3432
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 8 09:46:08 2018 -0700

    for consistence, set boundary centroid to -1 for regular and cover cells

Src/EB/AMReX_EBTower.cpp
Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90
Tests/EBEB2/MyTest.H
Tests/EBEB2/MyTest.cpp
Tests/EBEB2/initEB.cpp
Tests/EBEB2/inputs

commit 0e8e28b16ebb9bdfb5da2195fdedb2afba4b2fe0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 7 20:33:20 2018 -0400

    Need to pass an int by value

Src/Base/AMReX_BaseFab_nd.F90

commit 091b2e9b5a14e040058e80aaec8294e5dc66ffa1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 7 17:11:06 2018 -0700

    parameter eb2.use_eb2 and function makeEBFabFactory

Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_FabArrayBase.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2.cpp
Tutorials/EB/CNS/Exec/Make.CNS

commit de689306973c625683999b18087ae74c1ce08a52
Merge: bf1e68108 6aaacfeac
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 7 16:27:51 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit bf1e6810819faeac2e97609ff5dfa8a95c353706
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 7 16:27:45 2018 -0700

    Add C++ versions of fcompare and fextract

Tools/Postprocessing/C_Src/fcompare.cpp
Tools/Postprocessing/C_Src/fextract.cpp

commit f571114d6acc9cee1f44fbc859c6fc7a8ebba37a
Author: John Wakefield <JWakefield@lbl.gov>
Date:   Thu Jun 7 16:19:00 2018 -0700

    Changed SWFFT max_sizes to be at least as large as inputs.

Tutorials/SWFFT/inputs.128

commit fce0b488d07ff9117d44790716ff0c936a7ea5fe
Author: John Wakefield <JWakefield@lbl.gov>
Date:   Thu Jun 7 16:18:39 2018 -0700

    Changed SWFFT max_sizes to be at least as large as inputs.

Tools/C_util/AugmentPlotfile/AugFolder.sh
Tools/C_util/AugmentPlotfile/GNUmakefile
Tutorials/SWFFT/inputs.32
Tutorials/SWFFT/inputs.64
Tutorials/SWFFT/swfft_solver.cpp

commit 8c3722f84bebfc6d389e78753fdd5dfc6268a8f5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 7 19:12:31 2018 -0400

    Fix the block/thread override

Src/Base/AMReX_Device.cpp

commit 95a4bf23650aaebd8ef29055d0eb362554fd1720
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 7 15:52:03 2018 -0700

    scale

Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_IF_Scale.H
Src/EB2/Make.package
Tests/EBEB2/MyTest.cpp

commit d76d18d5fdc723b60901d01f00cdafff150b06da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 7 15:09:02 2018 -0700

    add ellipsoid

Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_IF_Ellipsoid.H
Src/EB2/Make.package

commit 6aaacfeac9eb39a383b5468bcead61e9abf90f9e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 7 14:45:11 2018 -0700

    Moved files from amrex/Tools/Postprocessing/F_Src/MAESTRO* into MAESTRO/Diagnostics.

Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/GNUmakefile
Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra.f90
Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90
Tools/Postprocessing/F_Src/MAESTRO_tests/GNUmakefile
Tools/Postprocessing/F_Src/MAESTRO_tests/fgaussianpulse.f90
Tools/Postprocessing/F_Src/MAESTRO_tests/fmlcompare.f90
Tools/Postprocessing/F_Src/MAESTRO_tests/fmlconverge.f90
Tools/Postprocessing/F_Src/MAESTRO_tests/fnorm.f90
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/GNUmakefile
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/feint.f90
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo.f90
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo_driver.py
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fwdconvect.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/GNUmakefile
Tools/Postprocessing/F_Src/MAESTRO_xrb/fad_excess.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/fbuoyancy.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/fconv_slopes.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/frates.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/fspec_total_mass.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/fspeciesmass.f90

commit bf0678e5b06b0a37fcd45b4bc1ae6ccdfa33c138
Merge: cd2b8773f d8b647d08
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 7 14:37:22 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit cd2b8773faa6aa941b144d70315a046e2779fd7a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 7 14:36:49 2018 -0700

    Moved amrex/Tools/Postprocessing/F_Src/CASTRO_radiation files out of amrex and into Castro itself

Tools/Postprocessing/F_Src/CASTRO_radiation/GNUmakefile
Tools/Postprocessing/F_Src/CASTRO_radiation/fgaussianpulse.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/flgt_frnt1d.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/fradshock.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/fradsource.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/fradsphere.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/frhdshocktube.f90

commit 53fad007f43b90672d598063a7eed73457d0304a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 7 14:29:27 2018 -0700

    some modification for comparison of the two implementations

Src/EB/AMReX_EBTower.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp
Tests/EBEB2/inputs

commit e19e5dd3b7fcc345df11b9de1a8f9a74cfd26132
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 7 13:56:00 2018 -0700

    function to covert MultiCutFab to MultiFab

Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp
Tests/EBEB2/MyTest.cpp

commit c0d75ea730364967313e3d0bb11576dc0ad98beb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 7 13:27:45 2018 -0700

    fix return type

Src/EB/AMReX_EBCellFlag.cpp
Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp

commit 13e166fe7593321a6ae27a14175bf9f91209cddd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 7 13:25:40 2018 -0700

    fill boundary centroid, area fraction and face centtroid

Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_WrappedGShop.cpp
Tests/EBEB2/MyTest.cpp

commit 564ab0f5478f83643fdc9f2451fd245bd258efd9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 7 12:48:15 2018 -0700

    Handle the OpenMPI + CUDA case generally, not just for CORAL

Tools/GNUMake/Make.defs
Tools/GNUMake/sites/Make.llnl
Tools/GNUMake/sites/Make.olcf

commit fff2d838c8f38f5866b7caac9ca4da3b605f3156
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 7 12:38:36 2018 -0700

    fix # of components for face centroid

Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90

commit 90a22fe43cc80c2d5efd2903e947f4fec751d855
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 7 12:01:31 2018 -0700

    fix # of components

Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBTower.cpp

commit ad7e7aec4b1b07296d4e9b6f59fe4fc60d3946b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 7 11:59:00 2018 -0700

    fill centroid

Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBTower.cpp
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp
Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Tests/EBEB2/MyTest.H
Tests/EBEB2/MyTest.cpp

commit f4980e5c1d604220f9f0f9964b3539216c55f5bd
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 7 14:07:41 2018 -0400

    Fix capitalization in a macro

Src/Base/AMReX_Device.cpp

commit 628a7836f4addb92c386514c0522d5ae9d0f7ce4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 7 10:35:18 2018 -0700

    fill cell flags

Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBCellFlag.cpp
Src/EB/AMReX_EBDataCollection.cpp
Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Tests/EBEB2/MyTest.cpp

commit d8b647d08e1123b6718163134ffae657aff00403
Merge: 8b532f089 745221393
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Jun 7 11:17:49 2018 -0600

    Merge pull request #271 from AMReX-Codes/corner-fill-update
    
    updated corner fill for non-cross stencil to work in 3D as well as 2D

commit 7452213930935a7595e3ae958fa73de901434c79
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Jun 7 12:08:19 2018 -0500

    updated corner fill for non-cross stencil to work in 3D as well as 2D

Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90

commit af001afecea0d97b30d191711e3912a9e4583d01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 7 09:11:47 2018 -0700

    make EB2:max_grid_size a ParmParse parameter

Src/Base/AMReX.cpp
Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_IndexSpaceI.H
Tests/EBEB2/MyTest.cpp

commit e03f69128fc45031c0b7493eff73aa3979f4f45e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 7 08:52:31 2018 -0700

    Disable calls to memadvise for unsupported GPUs

Src/Base/AMReX_Device.cpp

commit 434362f5eaba5ae90480549be36331438955adbf
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 7 08:52:17 2018 -0700

    Collect the CUDA device properties in C++

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 40b20bb66a30adeef9008bee490765599949397f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 6 23:42:58 2018 -0400

    Remove some more dependences on the tile box

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit 3cfa4c02778039528620c76314af8f0f684f6721
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 6 23:23:23 2018 -0400

    Rewrite fab copy to avoid dependence on lo

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit 49023d75d109bef14dc5b051258d4411d16602b7
Merge: a26f64254 8b532f089
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 6 20:49:19 2018 -0400

    Merge branch 'development' into gpu

commit a26f642548aaacca901ec9bfccabe6884f5378f6
Merge: 2c34d881a 82f7a2c35
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 6 20:40:36 2018 -0400

    Merge commit '82f7a2c35a68e74bc12a7058d5d09d790031973c' into gpu

commit 0a051a46909a72b60fccda30b5e20f0b934736f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 6 17:40:11 2018 -0700

    new EB factory

Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Tests/EBEB2/MyTest.H
Tests/EBEB2/MyTest.cpp
Tests/EBEB2/initEB.cpp
Tests/EBEB2/inputs

commit 6d60470feffd45b28418f6c94042871f1a8ff634
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 6 17:07:26 2018 -0700

    move initEB to a new file

Tests/EBEB2/Make.package
Tests/EBEB2/MyTest.cpp
Tests/EBEB2/initEB.cpp

commit 618980c66537ecd653730e4b65e66914e46db069
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 6 16:15:27 2018 -0700

    2d compiles

Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Src/EB2/AMReX_eb2_2d.F90
Tests/EBEB2/MyTest.H
Tests/EBEB2/MyTest.cpp

commit 9ed72258180c50a1d26bf5ff9325c5db54de874a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 6 15:18:39 2018 -0700

    coarsen geometry

Src/EB/AMReX_ebcellflag_mod.F90
Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_IndexSpaceI.H
Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Src/EB2/AMReX_EB2_MultiGFab.H
Src/EB2/AMReX_EB2_MultiGFab.cpp
Src/EB2/AMReX_eb2_3d.F90
Tests/EBEB2/MyTest.H
Tests/EBEB2/MyTest.cpp
Tests/EBEB2/inputs

commit 4dd1cf4d80babd04cd7c9b5f9755ca2a8e5616db
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 6 17:58:48 2018 -0400

    Turn on advance and change bc vector to HostAllocator.

Tutorials/GPU/HeatEquation_EX2_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX2_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc.H

commit 9a386ab25b2a3d2aa26dbe9f1e423057dc47ac89
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 6 17:58:10 2018 -0400

    Add CudaHostAllocator for cudaMallocHost based Vectors.

Src/Base/AMReX_BCRec.H
Src/Base/AMReX_CudaAllocators.H

commit 2c34d881ae644fd670d4ff973bf9273b4c831dce
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 6 14:47:24 2018 -0700

    Add a registerBox hook for new growntilebox

Src/Base/AMReX_MFIter.cpp

commit fa9866d6c1001beb169b0da1afec36cd53d9c4fc
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 6 17:03:22 2018 -0400

    HeatEquation_EX2_C with BCs and managed vector running with small problem. Also awaiting features for further improvement.

Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCUtil.H
Src/Base/AMReX_BCUtil.cpp
Tutorials/GPU/HeatEquation_EX2_C/Exec/GNUmakefile
Tutorials/GPU/HeatEquation_EX2_C/Exec/inputs_2d
Tutorials/GPU/HeatEquation_EX2_C/Exec/inputs_3d
Tutorials/GPU/HeatEquation_EX2_C/Source/Make.package
Tutorials/GPU/HeatEquation_EX2_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX2_C/Source/advance_2d.f90
Tutorials/GPU/HeatEquation_EX2_C/Source/advance_3d.f90
Tutorials/GPU/HeatEquation_EX2_C/Source/init_phi_2d.f90
Tutorials/GPU/HeatEquation_EX2_C/Source/init_phi_3d.f90
Tutorials/GPU/HeatEquation_EX2_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc.H
Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc_F.H

commit fe056487f92dd48820c3974dac096d1706bed838
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 6 14:01:21 2018 -0700

    Avoid non amrex-prefixed macros

Src/Amr/AMReX_Amr.cpp
Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_FILCC_1D.F90
Tools/F_scripts/write_cuda_headers.py

commit 59b9b5748c43faa969728801b26e7df963e7fa70
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 6 16:59:49 2018 -0400

    CudaAllocators for Vector CUDA memory management.

Src/Base/AMReX_CudaAllocators.H
Src/Base/AMReX_Vector.H
Src/Base/Make.package

commit 32a0c1720bb12b89a104c755deecc0d2a8499588
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 6 16:56:56 2018 -0400

    Improved HeatEquation_EX_1 for larger problem. Awaiting features for further improvement.

Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit 9ce0e74bbf8b7ea241a3742c895cd9f4b0241fd6
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 6 10:36:44 2018 -0700

    Correct summitdev MPI setup in F_mk

Tools/F_mk/GMakeMPI.mak

commit 0301b2d09031bd98597feaa46b8b1f68b18c4081
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 6 10:35:38 2018 -0700

    Update LLNL MPI setup

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.llnl

commit 96ac0345fd3b699cea840d705ce06243f31ac78a
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 6 13:02:07 2018 -0400

    Clean up

Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit b387c1ae3740f9e54ee785993f3c930ecf574850
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 6 08:43:31 2018 -0700

    eb cell flags

Src/EB/AMReX_ebcellflag_mod.F90
Src/EB2/AMReX_EB2_MultiGFab.H
Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90
Tests/EBEB2/MyTest.cpp

commit d9f60b318b6ad0999b59ec5302e715884cbc3672
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Jun 6 11:40:09 2018 -0400

    HeatEquation_EX1 first draft. Running with kernels. Needs threads and blocks setup.

Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.f90
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H

commit 53e170aa0e75ee2cda044bcde2a8e78f0e84ce2b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 5 19:31:57 2018 -0400

    Include amrex_ macros

Tools/F_scripts/write_cuda_headers.py

commit d90a3ad5f4aaa0581bf6d97dccbe38e8fda3daa0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 5 19:31:37 2018 -0400

    Use basename to avoid bug in find_files_vpath

Tools/F_scripts/find_files_vpath.py

commit f980914dd2b09eb22d2c813dd9503f20ffeb7373
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 5 19:00:54 2018 -0400

    Catch amrex_arlim_val too

Tools/F_scripts/write_cuda_headers.py
Tools/GNUMake/Make.rules

commit d4ac06eb75a6a20d47c597a56803a322f2d99e85
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 5 18:57:35 2018 -0400

    Fix the header class for basefab

Src/Base/Make.package

commit 5ba258140121177ff606e6b8c3f488580e1220c1
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 5 18:57:11 2018 -0400

    Add amrex_arlim_rep

Src/Base/AMReX_ArrayLim.H

commit 1d1059682776bacef7ad55773c86e205f4b43add
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Tue Jun 5 18:31:28 2018 -0400

    Pass IFABs by value in write_cuda_headers.py

Tools/F_scripts/write_cuda_headers.py

commit 5cd55908ecb8485b1d0e3003a9e49ac32bbf2f2a
Merge: 4f514f8ce 29f51056c
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Tue Jun 5 18:17:58 2018 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 4f514f8ce708d36472c942f9ea7f04f065a5a6f9
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Tue Jun 5 18:17:53 2018 -0400

    Fix bound subroutine searching in write_cuda_headers.py

Tools/F_scripts/write_cuda_headers.py

commit 8b532f089a284bf01676bdedbd9b74979534aaa2
Merge: b83be4151 dd4b70f4f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 5 15:12:45 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit b83be41512858dfa2598ad02bbb1fa1772e33192
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 5 15:11:36 2018 -0700

    fix a new bug in amrex_pd_bcast

Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ParallelDescriptor_F.F90

commit 1b09bdfb2834058f2e4effbad85bbb0d80cbbfba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 5 15:11:36 2018 -0700

    fix a new bug in amrex_pd_bcast

Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ParallelDescriptor_F.F90

commit 29f51056ccf50beb7b90aec6f192f0ff08f51fce
Merge: 23d70a5ad bba9bef8b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 5 17:58:11 2018 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit bba9bef8b77cf47063c54c8fb2a7af864721d26b
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Tue Jun 5 17:19:38 2018 -0400

    Fix target finding bug in write_cuda_headers.py

Tools/F_scripts/write_cuda_headers.py

commit 14f5fcc708ddfd8466b256af8ebefc2bccf280f4
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Tue Jun 5 17:17:28 2018 -0400

    Make the function signature error verbose for write_cuda_headers.py

Tools/F_scripts/write_cuda_headers.py

commit 23d70a5ad7eb8f9340128106192ed63477d12abf
Merge: be2997909 4a706af6b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 5 15:34:29 2018 -0400

    Merge commit '4a706af6b9899688636480ed77e34b0b8972cea7' into gpu

commit be2997909d328c6755a910273f022c3f906d77e4
Merge: dd8dc11c0 a292478ca
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 5 15:25:04 2018 -0400

    Merge commit 'a292478ca0999bdcf6281e467e77f838ae9750dc' into gpu

commit d766396ed3541f0a0fa294106ae2b23ab0177f7f
Merge: 026f0b3a9 dd4b70f4f
Author: Cy Chan <cychan@lbl.gov>
Date:   Tue Jun 5 12:19:55 2018 -0700

    Merge branch 'development' into forkjoin

commit 026f0b3a9518c668c5c1a1c011c0d829cb71e18d
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon May 14 15:56:40 2018 -0700

    forkjoin: modify Print.H to redirect task output to files
      default behavior unchanged
      added ParallelContext frame ID, IO filename, and ostream pointer

OldTutorials/MultiColor_C/main.cpp
Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp
Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_ParallelContext.cpp
Src/Base/AMReX_Print.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit dd4b70f4f56a647fc569a5713fef48979e5f07c8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 5 11:43:34 2018 -0700

    1) Replace . by --> (gnu allowed this but pgi caught it)
    2) remove unused variable

Src/GeometryShop/AMReX_IFSlicerImplem.H
Src/GeometryShop/AMReX_WrappedGShop.cpp

commit a7fac48147db7ffffa935326fc070d8eba0f92c5
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jun 5 14:26:48 2018 -0400

    HeatEqu cleanup

Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp

commit dd8dc11c07d0202c115ff11980141056c4264737
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 5 13:00:54 2018 -0400

    Temp headers depend on all Fortran sources

Tools/GNUMake/Make.rules

commit ecc933f15f0d948aa0e340435263f3dd5e091dc7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue Jun 5 12:16:48 2018 -0400

    First draft of kernel in HeatConduction

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90
Tools/GNUMake/Make.defs
Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d
Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package
Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.f90
Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.f90
Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.f90
Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.f90
Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H
Tutorials/GPU/HelloWorld_C/main.cpp

commit 47179f6ab6c0324d67382299326d29394a4cac42
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 5 10:59:52 2018 -0400

    Really always re-execute the temp CUDA header rule, and also avoid infinite loops

Tools/GNUMake/Make.rules

commit a7836daaa3a879160f6dc33d116c78c70df3f265
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 5 10:50:44 2018 -0400

    Revert "Always re-execute the temp CUDA header rule"
    
    This reverts commit 0ce010e325c028348bb2c83a750e9f93a1d963ec.

Tools/GNUMake/Make.rules

commit 0ce010e325c028348bb2c83a750e9f93a1d963ec
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 5 10:33:50 2018 -0400

    Always re-execute the temp CUDA header rule

Tools/GNUMake/Make.rules

commit 856ea01ba556d1bb8956e2dd84c85e3268f81843
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 5 00:05:44 2018 -0400

    Fix the device launch macro token concatenation

Src/Base/AMReX_BLFort.H

commit b519ce3a06405be06cba0fe15cbb093eba045ba7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 4 17:08:03 2018 -0700

    combustor

Src/EB2/AMReX_EB2_IF_Intersection.H
Src/EB2/AMReX_EB2_IF_Union.H
Src/EB2/AMReX_eb2_3d.F90
Tests/EBEB2/MyTest.cpp

commit 57647a5cda2aa7ab5bfcc00b2078d79c846f0048
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 4 16:34:18 2018 -0700

    lathe and translate

Src/EB2/AMReX_EB2_IF_Lathe.H
Src/EB2/AMReX_EB2_IF_Translation.H
Src/EB2/Make.package
Tests/EBEB2/MyTest.cpp
Tests/EBEB2/inputs

commit 664041f430966d62ad657d36117d1f96451275d3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 4 18:25:11 2018 -0400

    Fix the macros so CPU code works

Src/Base/AMReX_ArrayLim.H

commit 0958929c12027533686a3dac94bbb8c222b6e5e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 4 15:22:59 2018 -0700

    translation

Src/EB2/AMReX_EB2_IF_Box.H
Src/EB2/AMReX_EB2_IF_Complement.H
Src/EB2/AMReX_EB2_IF_Translation.H
Src/EB2/Make.package
Tests/EBEB2/MyTest.cpp

commit 07de7089d018957569b893c6eb56855a44ce6079
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 4 18:16:03 2018 -0400

    Fix up the CUdA header generation

Tools/F_scripts/find_files_vpath.py
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 68f5d95a057b93ac1dcaeea02b314a4c8d4ed1c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 4 15:10:25 2018 -0700

    add Complement

Src/EB2/AMReX_EB2_IF_Box.H
Src/EB2/AMReX_EB2_IF_Complement.H
Src/EB2/AMReX_EB2_IF_Cylinder.H
Src/EB2/AMReX_EB2_IF_Plane.H
Src/EB2/AMReX_EB2_IF_Sphere.H
Src/EB2/Make.package
Tests/EBEB2/MyTest.cpp

commit f4b99639424f94533910d04b779f8014756a4ea6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 4 13:22:48 2018 -0700

    add two arguments versions of amrex_error

Src/Base/AMReX_error_mod.F90

commit 1a77d25dffb8a0826933e8ed9f84f8f2e3cfb685
Merge: 303523c11 624e31102
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 4 12:22:05 2018 -0700

    Merge branch 'development' into weiqun/eb2

commit 624e3110215692c614628bbc244d357b8bbf9e11
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 4 12:05:33 2018 -0700

    add amrex_io_module

Src/Base/AMReX_io_mod.F90
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 104ce7ffe2134f2a22334fabec12b901fad4d3ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 4 11:59:50 2018 -0700

    add amrex_pd_wtime

Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ParallelDescriptor_F.F90

commit 5a6a455fa7ff496d401bc2979ce62d632ffc5a13
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 4 14:26:18 2018 -0400

    Move CUDA header script over from StarLord

Tools/F_scripts/write_cuda_headers.py
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit a61f1fa46be1a92e9f2def7ca97d143cc179ea88
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 4 13:40:21 2018 -0400

    Add an apparently necessary device synchronize

Src/Base/AMReX_FabArray.H

commit 303523c11e64a901e766cb53b8da45d4f462e577
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 3 16:50:05 2018 -0700

    Union and intersection

Src/Base/AMReX_IndexSequence.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2_GeometryShop.H
Src/EB2/AMReX_EB2_IF_Intersection.H
Src/EB2/AMReX_EB2_IF_Union.H
Src/EB2/AMReX_EB2_IndexSpaceI.H
Src/EB2/Make.package
Tests/EBEB2/MyTest.cpp

commit 14efdc35d03668ceb818bb26dc50663deccd54b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 3 07:35:35 2018 -0700

    clean up

Src/EB2/AMReX_EB2.cpp

commit 1288283430b8b99c08d2cdaa1f6d74eccff5be06
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 3 07:32:46 2018 -0700

    add PlaneIF

Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_IF_Box.H
Src/EB2/AMReX_EB2_IF_Cylinder.H
Src/EB2/AMReX_EB2_IF_Plane.H
Src/EB2/Make.package

commit 709189f3070a70f96ed1e64e7023168c3fea80e7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jun 2 17:53:53 2018 -0700

    Replace dp_t by rt

Tools/F_scripts/write_probin.py

commit 6cd3ed1738a046c2e83ea2288b37c24a6bff0d37
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 2 16:36:47 2018 -0700

    add Box

Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_IF_Box.H
Src/EB2/AMReX_EB2_IF_Cylinder.H
Src/EB2/Make.package

commit 15bfee6dceb5ce4bf82fc78227709364dd6d0a86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 2 15:50:39 2018 -0700

    rename so that all implicit function files start with AMReX_EB2_IF_

Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_IF_Cylinder.H
Src/EB2/AMReX_EB2_IF_Sphere.H
Src/EB2/Make.package

commit 17b8e4fc10366e0128974e55f08b79d0a39ceb08
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 2 15:23:07 2018 -0700

    function to fill volume fraction

Src/EB2/AMReX_EB2_Level.cpp
Tests/EBEB2/MyTest.cpp

commit 986710c5ce8baf16961158726f3489bf7bab0148
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 2 14:05:19 2018 -0700

    fix omp compilation

Tutorials/Amr/Advection_F/Source/evolve_mod.F90

commit 6b93ba7ad8759d24d55b9c4902a69e0e7dd8191c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 2 08:56:19 2018 -0700

    add getLevel

Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_IndexSpaceI.H
Tests/EBEB2/MyTest.cpp

commit 4e3b5a6529e8004c0fdac8e03f7141c7487fbede
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 2 08:38:49 2018 -0700

    cleanup

Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_IndexSpaceI.H

commit 3ddd681d7c598d473a5415292e40dd40f4a84d9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 2 08:03:00 2018 -0700

    add base Level class

Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2_IndexSpaceI.H
Src/EB2/AMReX_EB2_Level.H
Src/EB2/AMReX_EB2_Level.cpp
Src/EB2/Make.package

commit 6af8cf48117cd41b7cb1ffbb82a9ecfd65f750a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 2 07:31:33 2018 -0700

    add a new test

Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2_ISLevel.H
Tests/EBEB2/GNUmakefile
Tests/EBEB2/Make.package
Tests/EBEB2/MyTest.H
Tests/EBEB2/MyTest.cpp
Tests/EBEB2/inputs
Tests/EBEB2/main.cpp

commit 8433e94744e62be608a95b7ba35eaed3dfc9b976
Author: Kevin Gott <kngott@lbl.gov>
Date:   Sat Jun 2 00:01:34 2018 -0400

    BaseFab buildable on GPU with all constructors except copy. Test included.

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_Managed.H
Tutorials/GPU/HelloWorld_C/main.cpp

commit 3831810d8b55412fb0087721e266a8a713a7e470
Merge: 30818a9fe f699c21d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 1 17:06:44 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 30818a9fe888c7c89b57f4cc01ff25ca3909e5d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 1 17:06:15 2018 -0700

    add bast to amrex_paralleldescriptor_module

Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ParallelDescriptor_F.F90

commit 3e2c5e607ce228d1606e43c95bcc3c8e5db64f09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 1 14:47:23 2018 -0700

    finish 2d cells

Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_eb2_2d.F90

commit 246cac80d5d91ab391f9e61ec68b996bc9e10285
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 1 13:13:30 2018 -0700

    assert there are no multiple cuts in 2d

Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_eb2_2d.F90

commit f699c21d1c97e12bafd042d3f12884b8a63f567e
Merge: 774210498 bad02aacf
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 1 10:39:17 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 77421049828386291150be68b3cff98a3330fded
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 1 10:38:53 2018 -0700

    adding an Electromagnetic PIC tutorial to development

Tutorials/Particles/ElectromagneticPIC/Constants.H
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H
Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp
Tutorials/Particles/ElectromagneticPIC/Evolve.H
Tutorials/Particles/ElectromagneticPIC/Evolve.cpp
Tutorials/Particles/ElectromagneticPIC/GNUmakefile
Tutorials/Particles/ElectromagneticPIC/IO.H
Tutorials/Particles/ElectromagneticPIC/IO.cpp
Tutorials/Particles/ElectromagneticPIC/Make.package
Tutorials/Particles/ElectromagneticPIC/NodalFlags.H
Tutorials/Particles/ElectromagneticPIC/NodalFlags.cpp
Tutorials/Particles/ElectromagneticPIC/em_pic_3d.F90
Tutorials/Particles/ElectromagneticPIC/em_pic_F.H
Tutorials/Particles/ElectromagneticPIC/inputs
Tutorials/Particles/ElectromagneticPIC/main.cpp

commit bad02aacf581aff5483552911f81bbe1b3291f74
Merge: 69c7ea2b9 73475491a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jun 1 09:50:17 2018 -0700

    Merge pull request #267 from cgilet/master
    
    Fix --ghost option.  Do not advance farg in case(--ghost) section bec…

commit 73475491a28f0ef6569a92f44d9da5c25d3b15f8
Author: cgilet <cgilet@gmail.com>
Date:   Fri Jun 1 12:40:08 2018 -0400

    Fix --ghost option.  Do not advance farg in case(--ghost) section because --ghost does not take any arguments.

Tools/Postprocessing/F_Src/fcompare.f90

commit 69c7ea2b9ecdff7deba1360bc48ef059ed192276
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 1 09:33:11 2018 -0700

    remove some old Fortran BoxLib tutorials

OldTutorials/AMR_Adv_F/Exec/SingleVortex/GNUmakefile
OldTutorials/AMR_Adv_F/Exec/SingleVortex/GPackage.mak
OldTutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90
OldTutorials/AMR_Adv_F/Exec/SingleVortex/inputs_2d
OldTutorials/AMR_Adv_F/Exec/SingleVortex/inputs_3d
OldTutorials/AMR_Adv_F/Exec/SingleVortex/set_velocity.f90
OldTutorials/AMR_Adv_F/Exec/UniformVelocity/GNUmakefile
OldTutorials/AMR_Adv_F/Exec/UniformVelocity/GPackage.mak
OldTutorials/AMR_Adv_F/Exec/UniformVelocity/init_phi.f90
OldTutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_2d
OldTutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_3d
OldTutorials/AMR_Adv_F/Exec/UniformVelocity/set_velocity.f90
OldTutorials/AMR_Adv_F/Source/GPackage.mak
OldTutorials/AMR_Adv_F/Source/advance.f90
OldTutorials/AMR_Adv_F/Source/compute_flux.f90
OldTutorials/AMR_Adv_F/Source/main.f90
OldTutorials/AMR_Adv_F/Source/slope.f90
OldTutorials/AMR_Adv_F/Source/tag_boxes.f90
OldTutorials/AMR_Adv_F/Source/update_phi.f90
OldTutorials/AMR_Adv_F/Source/write_plotfile.f90
OldTutorials/Exp_CNS_NoSpec_F/CNSEquations.tex
OldTutorials/Exp_CNS_NoSpec_F/GNUmakefile
OldTutorials/Exp_CNS_NoSpec_F/GPackage.mak
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.c
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.h
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/GNUmakefile
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/bench.c
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.h
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.x86.c
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/Make.package
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/timer_c.c
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/Make.package
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/README
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/advance.f90
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/main.f90
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/README
OldTutorials/Exp_CNS_NoSpec_F/README
OldTutorials/Exp_CNS_NoSpec_F/advance.f90
OldTutorials/Exp_CNS_NoSpec_F/init_data.f90
OldTutorials/Exp_CNS_NoSpec_F/inputs.jbb
OldTutorials/Exp_CNS_NoSpec_F/inputs_3d
OldTutorials/Exp_CNS_NoSpec_F/main.f90
OldTutorials/Exp_CNS_NoSpec_F/write_plotfile.f90
OldTutorials/GettingStarted_F/GNUmakefile
OldTutorials/GettingStarted_F/GPackage.mak
OldTutorials/GettingStarted_F/main.f90
OldTutorials/GettingStarted_F/work_on_data.f90
OldTutorials/HeatEquation_EX1_F/GNUmakefile
OldTutorials/HeatEquation_EX1_F/GPackage.mak
OldTutorials/HeatEquation_EX1_F/advance.f90
OldTutorials/HeatEquation_EX1_F/init_phi.f90
OldTutorials/HeatEquation_EX1_F/inputs_2d
OldTutorials/HeatEquation_EX1_F/inputs_3d
OldTutorials/HeatEquation_EX1_F/main.f90
OldTutorials/HeatEquation_EX1_F/write_plotfile.f90
OldTutorials/HeatEquation_EX2_F/GNUmakefile
OldTutorials/HeatEquation_EX2_F/GPackage.mak
OldTutorials/HeatEquation_EX2_F/advance.f90
OldTutorials/HeatEquation_EX2_F/define_bc_tower.f90
OldTutorials/HeatEquation_EX2_F/init_phi.f90
OldTutorials/HeatEquation_EX2_F/inputs_2d
OldTutorials/HeatEquation_EX2_F/inputs_3d
OldTutorials/HeatEquation_EX2_F/main.f90
OldTutorials/HeatEquation_EX2_F/multifab_physbc.f90
OldTutorials/HeatEquation_EX2_F/write_plotfile.f90
OldTutorials/HeatEquation_EX3_F/GNUmakefile
OldTutorials/HeatEquation_EX3_F/GPackage.mak
OldTutorials/HeatEquation_EX3_F/advance.f90
OldTutorials/HeatEquation_EX3_F/define_bc_tower.f90
OldTutorials/HeatEquation_EX3_F/init_phi.f90
OldTutorials/HeatEquation_EX3_F/inputs_2d
OldTutorials/HeatEquation_EX3_F/inputs_3d
OldTutorials/HeatEquation_EX3_F/main.f90
OldTutorials/HeatEquation_EX3_F/multifab_physbc.f90
OldTutorials/HeatEquation_EX3_F/write_plotfile.f90
OldTutorials/HeatEquation_EX4_F/GNUmakefile
OldTutorials/HeatEquation_EX4_F/GPackage.mak
OldTutorials/HeatEquation_EX4_F/advance.f90
OldTutorials/HeatEquation_EX4_F/define_bc_tower.f90
OldTutorials/HeatEquation_EX4_F/init_phi.f90
OldTutorials/HeatEquation_EX4_F/inputs_2d
OldTutorials/HeatEquation_EX4_F/inputs_3d
OldTutorials/HeatEquation_EX4_F/main.f90
OldTutorials/HeatEquation_EX4_F/multifab_physbc.f90
OldTutorials/HeatEquation_EX4_F/write_plotfile.f90
OldTutorials/HeatEquation_EX5_F/GNUmakefile
OldTutorials/HeatEquation_EX5_F/GPackage.mak
OldTutorials/HeatEquation_EX5_F/advance.f90
OldTutorials/HeatEquation_EX5_F/define_bc_tower.f90
OldTutorials/HeatEquation_EX5_F/init_phi.f90
OldTutorials/HeatEquation_EX5_F/inputs-rt
OldTutorials/HeatEquation_EX5_F/inputs-rt-expl
OldTutorials/HeatEquation_EX5_F/inputs-rt-impl
OldTutorials/HeatEquation_EX5_F/inputs_2d
OldTutorials/HeatEquation_EX5_F/inputs_3d
OldTutorials/HeatEquation_EX5_F/main.f90
OldTutorials/HeatEquation_EX5_F/multifab_physbc.f90
OldTutorials/HeatEquation_EX5_F/write_plotfile.f90
OldTutorials/MultiGrid_F/GNUmakefile
OldTutorials/MultiGrid_F/README
OldTutorials/MultiGrid_F/constants.f90
OldTutorials/MultiGrid_F/cycle_tower.f90
OldTutorials/MultiGrid_F/fmg_cycle.f90
OldTutorials/MultiGrid_F/init_coeffs.f90
OldTutorials/MultiGrid_F/init_rhs.f90
OldTutorials/MultiGrid_F/inputs_fmg_lin_2d
OldTutorials/MultiGrid_F/inputs_fmg_lin_3d
OldTutorials/MultiGrid_F/inputs_fmg_pc_2d
OldTutorials/MultiGrid_F/inputs_fmg_pc_3d
OldTutorials/MultiGrid_F/inputs_v_lin_2d
OldTutorials/MultiGrid_F/inputs_v_lin_3d
OldTutorials/MultiGrid_F/inputs_v_pc_2d
OldTutorials/MultiGrid_F/inputs_v_pc_3d
OldTutorials/MultiGrid_F/main.f90
OldTutorials/MultiGrid_F/solve.f90
OldTutorials/MultiGrid_F/traverse.f90
OldTutorials/MultiGrid_F/v_cycle.f90
OldTutorials/Random_F/GNUmakefile
OldTutorials/Random_F/GPackage.mak
OldTutorials/Random_F/main.f90
OldTutorials/Tiling_Heat_F/GNUmakefile
OldTutorials/Tiling_Heat_F/GPackage.mak
OldTutorials/Tiling_Heat_F/advance.f90
OldTutorials/Tiling_Heat_F/init_phi.f90
OldTutorials/Tiling_Heat_F/inputs_3d
OldTutorials/Tiling_Heat_F/main.f90
OldTutorials/Tiling_Heat_F/results.txt
OldTutorials/Tiling_Heat_F/results/babbage_omp.run
OldTutorials/Tiling_Heat_F/results/results.txt
OldTutorials/Tiling_Heat_F/results/t1a.txt
OldTutorials/Tiling_Heat_F/results/t1b.txt
OldTutorials/Tiling_Heat_F/results/t2a.txt
OldTutorials/Tiling_Heat_F/results/t2b.txt
OldTutorials/Tiling_Heat_F/results/t3a.txt
OldTutorials/Tiling_Heat_F/results/t3b.txt
OldTutorials/Tiling_Heat_F/results/t4a.txt
OldTutorials/Tiling_Heat_F/results/t4b.txt
OldTutorials/Tiling_Heat_F/results/t5a.txt
OldTutorials/Tiling_Heat_F/results/t5b.txt
OldTutorials/Tiling_Heat_F/results/t6a.txt
OldTutorials/Tiling_Heat_F/results/t6b.txt
OldTutorials/Tiling_Heat_F/results/t7a.txt
OldTutorials/Tiling_Heat_F/results/t7b.txt
OldTutorials/Tiling_Heat_F/write_plotfile.f90
OldTutorials/WaveEquation_F/GNUmakefile
OldTutorials/WaveEquation_F/GPackage.mak
OldTutorials/WaveEquation_F/advance.f90
OldTutorials/WaveEquation_F/init_data.f90
OldTutorials/WaveEquation_F/inputs_2d
OldTutorials/WaveEquation_F/inputs_3d
OldTutorials/WaveEquation_F/main.f90
OldTutorials/WaveEquation_F/write_plotfile.f90

commit f3a0691f3aee87830c3d76a66a217c11428896db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 1 09:31:23 2018 -0700

    rename

OldMiniApps/FillBoundary/GNUmakefile
OldMiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
OldMiniApps/FillBoundary/README
OldMiniApps/FillBoundary/qsub.ipm.bat
OldMiniApps/MultiGrid_C/COEF_3D.F
OldMiniApps/MultiGrid_C/COEF_F.H
OldMiniApps/MultiGrid_C/GNUmakefile
OldMiniApps/MultiGrid_C/Make.package
OldMiniApps/MultiGrid_C/README
OldMiniApps/MultiGrid_C/RHS_3D.F
OldMiniApps/MultiGrid_C/RHS_F.H
OldMiniApps/MultiGrid_C/main.cpp
OldMiniApps/MultiGrid_C/qsub.ipm.bat
Tools/CompileTesting/compiletesting.py

commit a85f24130fe6e1b4663c5b43813654af0a8d08d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 1 09:21:52 2018 -0700

    remove some old mini apps

MiniApps/PGAS_SMC/GNUmakefile
MiniApps/PGAS_SMC/LiDryer.c
MiniApps/PGAS_SMC/Make.package
MiniApps/PGAS_SMC/SMC.H
MiniApps/PGAS_SMC/SMC.cpp
MiniApps/PGAS_SMC/SMC_F.H
MiniApps/PGAS_SMC/SMC_advance.cpp
MiniApps/PGAS_SMC/SMC_init.cpp
MiniApps/PGAS_SMC/SMC_io.cpp
MiniApps/PGAS_SMC/chemistry_module.f90
MiniApps/PGAS_SMC/derivative_stencil.f90
MiniApps/PGAS_SMC/init_data.f90
MiniApps/PGAS_SMC/kernels.f90
MiniApps/PGAS_SMC/main.cpp
MiniApps/PGAS_SMC/make_plot.f90
MiniApps/PGAS_SMC/transport_properties.f90
MiniApps/PGAS_SMC/variables.f90
MiniApps/SMC/GNUmakefile
MiniApps/SMC/GPackage.mak
MiniApps/SMC/LiDryer.c
MiniApps/SMC/_parameters
MiniApps/SMC/advance.f90
MiniApps/SMC/chemistry_module.f90
MiniApps/SMC/derivative_stencil.f90
MiniApps/SMC/init_data.f90
MiniApps/SMC/initialize.f90
MiniApps/SMC/inputs_SMC
MiniApps/SMC/kernels.f90
MiniApps/SMC/main.f90
MiniApps/SMC/make_plotfile.f90
MiniApps/SMC/probin.template
MiniApps/SMC/smc.f90
MiniApps/SMC/smcdata.f90
MiniApps/SMC/time.f90
MiniApps/SMC/transport_properties.f90
MiniApps/SMC/variables.f90

commit c2da595466d4ff2a4db229aed31730b5e393fdd9
Merge: 2f38bb77a e767cd1a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 1 08:49:25 2018 -0700

    Merge branch 'development' into weiqun/eb1

commit e767cd1a9e7a7ec78bd99da4afa9021c3129a8b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 1 08:47:53 2018 -0700

    update CHANGES

CHANGES

commit 2f38bb77abed4827800c41723739579e9ccf0f43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 31 17:32:11 2018 -0700

    more on 2d

Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_GeometryShop.H
Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_EB2_MultiGFab.H
Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90

commit 738a906cf017c5d4e05ed89707db5dc0f0d54011
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 31 14:44:28 2018 -0700

    add a new EB2::Initialize with simple geometries

Src/Base/AMReX_Array.H
Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2.cpp

commit 9cfae8839c4df3d57120e3905ec4009c503fc2ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 31 14:04:25 2018 -0700

    no need to use least square in 2d

Src/EB2/AMReX_eb2_3d.F90

commit 040c5b71fa80397bcc65130a933e9b80ff33e5c1
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu May 31 15:46:19 2018 -0400

    BaseFab::copy, copyToMem and copyFromMem tested and working. std::min and std::max in IntVect written out to avoid namespace conflict.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90
Src/Base/AMReX_Box.H
Src/Base/AMReX_IntVect.H
Tutorials/GPU/HelloWorld_C/main.cpp

commit 9ab8bc0df885d155c4718724c1c9349cade24199
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 31 11:31:59 2018 -0700

    move the if np == 0 checks to inside the fortran subroutines.

Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/Advection_F/Source/evolve_mod.F90

commit 7a4158984319f06aca4c0a31eff332a2412db5c9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 31 11:19:08 2018 -0700

    make this a bit less hard-coded for tracers

Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90
Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/Advection_F/Source/evolve_mod.F90
Tutorials/Amr/Advection_F/Source/initdata.F90
Tutorials/Amr/Advection_F/Source/my_amr_mod.F90
Tutorials/Amr/Advection_F/Source/plotfile_mod.F90

commit b5b3d966019a8b68ef1cb8e46e81c184b47e7bad
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 31 11:08:53 2018 -0700

    rename particle container module files

Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90
Src/F_Interfaces/Particle/Make.package

commit fa610dcf504865987a6cac9cb1746827384f0d0a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 31 10:57:35 2018 -0700

    implement 3d

Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90

commit 16f0ae1369814d7233afa4674c11a1daaa10c8bd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 31 10:30:42 2018 -0700

    refactor advect_particles into a loop over spacedim

Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90

commit 181a13d1f0754104aeab8592a38940d4a2d4a9f2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 31 10:07:09 2018 -0700

    advection tutorial working with particles

Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90

commit baf2029ea6d69101c8b584e90cb96f50cbc61ed7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 31 09:33:29 2018 -0700

    compute centroid

Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_eb2_3d.F90

commit 12f4422adfa25b5b22e47e04861914579edfa998
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 31 09:28:56 2018 -0700

    some bug fixes

Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/Amr/Advection_F/Source/evolve_mod.F90
Tutorials/Amr/Advection_F/Source/initdata.F90

commit f89b34026b31efe964f829af3758ddd2da74a5a5
Merge: 763c59107 fdb98cac9
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu May 31 08:47:23 2018 -0700

    Merge pull request #265 from jameslehoux/patch-1
    
    Updated SingleVortex GNUmakefile

commit fdb98cac93944b13d1647247738766239c8f1f46
Author: jameslehoux <37665786+jameslehoux@users.noreply.github.com>
Date:   Thu May 31 14:49:27 2018 +0100

    Updated SingleVortex GNUmakefile
    
    Corrected AMREX_HOME to allow it to be built (should be 5 levels up, was 4 levels)

Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile

commit 53a3755e5d561636351f4dd0ad273a42a71bf441
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 30 20:58:10 2018 -0700

    implement advect_particles in 2D

Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/Amr/Advection_F/Source/evolve_mod.F90
Tutorials/Amr/Advection_F/Source/plotfile_mod.F90

commit 9bbbaafc6dd6d38a72abf0ee5ec361735d1ce1e1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 30 18:21:21 2018 -0700

    3D version of advect particles

Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/Advection_F/Source/evolve_mod.F90

commit 3a0b7fb4bbc99a88db15bafb266a319e8c743d10
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 30 18:11:56 2018 -0700

    wrap the call to c_to_f_pointer in amrex_get_particles

Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90
Tutorials/Amr/Advection_F/Source/evolve_mod.F90

commit 460764ff0bb6971aa9a8974271213f341a711b1d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 30 17:51:03 2018 -0700

    also pass the velocity data into advect_particles

Tutorials/Amr/Advection_F/Source/evolve_mod.F90

commit 763c591077dee3f682e5e666d5f8dcea0c568894
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 30 16:26:57 2018 -0700

    MFIter dynamic scheduling: must call barrier before setting the staic variable

Src/Base/AMReX_MFIter.cpp

commit ef0deaf54d2c8d9fe1e1861e8b802fa228930797
Author: John Wakefield <JWakefield@lbl.gov>
Date:   Wed May 30 15:49:12 2018 -0700

    Added skipping of existing components.

Tools/C_util/AugmentPlotfile/AugmentPlotfile.cpp
Tools/C_util/AugmentPlotfile/inputs

commit 5822e63da0b9810bbcd668c64ff5ae1d0b1f4a68
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed May 30 16:23:26 2018 -0400

    Fix fortran bind name.

Src/Base/AMReX_BaseFab_nd.F90

commit ca9ff4e0559b3812d127247a3582021f0d44c320
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed May 30 13:41:30 2018 -0400

    Intermediate commit before working on std::min and std::max.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90
Src/Base/AMReX_Box.H
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H
Tutorials/GPU/HelloWorld_C/main.cpp

commit 81f8f32a4b6f79143728bc5c788225d4fde8916c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 29 20:07:46 2018 -0700

    starting to implement advection kernel for tracer particles in Fortran

Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90
Tutorials/Amr/Advection_F/Source/evolve_mod.F90

commit 010853e190750f6659b1daadf44848a084824fa0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 29 15:52:54 2018 -0700

    compute 2nd moments on faces

Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_eb2_3d.F90

commit e66b015d0275d598cc53fcbd4d2cdaa4d2e4b111
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue May 29 19:26:02 2018 -0400

    BaseFab<int> setval tests. Working fine.

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_CArena.cpp
Tutorials/GPU/HelloWorld_C/main.cpp

commit d575b853e0a00192ab60082282acf12fb51017ba
Author: atmyers <atmyers2@gmail.com>
Date:   Tue May 29 16:14:30 2018 -0700

    add routine to recalculate superparticle size

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit b7fd3d380622ca026b97000fa5188d893aafa628
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue May 29 18:53:55 2018 -0400

    Change macros to have prefix AMREX_CUDA_

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_Managed.H
Tutorials/GPU/HelloWorld_C/main.cpp

commit 46810f576f04947b869bcbcb7503d9805289f72b
Author: John Wakefield <JWakefield@lbl.gov>
Date:   Tue May 29 14:02:22 2018 -0700

    Augmentplotfile working in parallel

Tools/C_util/AugmentPlotfile/AugmentPlotfile.cpp
Tools/C_util/AugmentPlotfile/GNUmakefile

commit deb9a496e3898198cd61b5ef470aaf132e4d8216
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue May 29 16:34:27 2018 -0400

    BaseFab setVal running on both host and device. Small make system tweak for OpenMP.

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90
Tools/GNUMake/sites/Make.olcf
Tutorials/GPU/HelloWorld_C/main.cpp

commit 1ab91232105d9f9323db0b8aa7163f6cb2c3a30d
Author: John Wakefield <JWakefield@lbl.gov>
Date:   Tue May 29 13:29:01 2018 -0700

    Augment plotfile functional in serial.

Tools/C_util/AugmentPlotfile/AugmentPlotfile.cpp
Tools/C_util/AugmentPlotfile/AugmentPlotfile_F.H
Tools/C_util/AugmentPlotfile/AugmentPlotfile_F.f90
Tools/C_util/AugmentPlotfile/GNUmakefile
Tools/C_util/AugmentPlotfile/inputs

commit eb8168b6c52720ab033f2ab6d5a6c38e2b74da35
Author: John Wakefield <JWakefield@lbl.gov>
Date:   Tue May 29 13:26:58 2018 -0700

    Added cell size getter.

Src/Extern/amrdata/AMReX_AmrData.H

commit 0e31e57ffcba528906bcdfe39de63d37cde582d3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 29 11:33:38 2018 -0700

    fix amrex_get_particles and add a function for returning the number of particles in a tile.

Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90
Tutorials/Amr/Advection_F/Source/evolve_mod.F90

commit 5877d820f3506c759cd330da780f40663ffd2d27
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 29 10:51:58 2018 -0700

    initialize the tracer particle velocities to zero instead of the weird thing it was doing before

Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit 038263c0dffd8bde49c27c7a26eb40baf2d10190
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 29 10:47:13 2018 -0700

    add a function for getting the particls on a tile in fortran.

Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90
Tutorials/Amr/Advection_F/Source/evolve_mod.F90

commit 1da64057ab0655fcc9b67c6d0ebc728b1feda647
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 29 10:24:11 2018 -0700

    add cylinder

Src/EB2/AMReX_EB2_CylinderIF.H
Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_EB2_SphereIF.H
Src/EB2/AMReX_eb2_3d.F90
Src/EB2/Make.package

commit e07ee4f0bb5b723c174497417c7cc347e607f3fb
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon May 28 20:17:53 2018 -0400

    First edit of BArena to allocate BaseFab data. Need to edit CArena as well for COALESCE_FABS.

Src/Base/AMReX_Arena.H
Src/Base/AMReX_BArena.H
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_Managed.H
Tools/GNUMake/Make.defs
Tutorials/GPU/HelloWorld_C/main.cpp
Tutorials/GPU/HelloWorld_C/outline.cpp

commit a2649a7ee31498190fa8ea08127e9e1585df9fdb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 26 18:55:44 2018 -0700

    compute volume fraction, and  boundary norm, centrold and area

Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_eb2_3d.F90

commit 7f123f5d5abeff713ed5377b3e3e28aefcff5258
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 26 17:34:07 2018 -0700

    fix small cells and almost regular cells

Src/EB2/AMReX_eb2_3d.F90

commit 55bf91ae14942a1681e9c6d928963d1ba9a406e8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 25 16:46:42 2018 -0700

    some bug fixes.

Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90

commit a6df1f1a5d63e67b718eddc4e52dffa581afed9f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 25 16:46:26 2018 -0700

    put the calls to amrex_particle_redistribute in the right place in the update loop.

Tutorials/Amr/Advection_F/Source/evolve_mod.F90

commit d61fb18cbc9f2c19023d9dc5b64fcc2d9076f2e6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 25 16:01:42 2018 -0700

    wrap Redistribute.

Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90

commit bd870dfcc50acb7a43151ae74236dd95efda1f5b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 25 15:27:18 2018 -0700

    writing plot files.

Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90
Tutorials/Amr/Advection_F/Source/fmain.F90
Tutorials/Amr/Advection_F/Source/initdata.F90
Tutorials/Amr/Advection_F/Source/my_amr_mod.F90
Tutorials/Amr/Advection_F/Source/plotfile_mod.F90

commit 9b4bfe153f691ef5e344cfda9a1b5584ea912bf5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 25 14:07:23 2018 -0700

    also wrap InitOnePerCell

Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90
Tutorials/Amr/Advection_F/Source/fmain.F90

commit 09086ec9eaf8fbf6af263e65bc14e610b9542769
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 25 13:48:23 2018 -0700

    showing that I can initialize a tracer particle container from Fortran

Src/AmrCore/AMReX_AmrCore.cpp
Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90
Tutorials/Amr/Advection_F/Source/fmain.F90

commit 266b4fbf88cc88ca03dd836481d8e6cedebc20e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 25 13:42:31 2018 -0700

    compute area fraction and face centroids for y and z-faces

Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_eb2_3d.F90

commit 9545ed179a5983291cd62af652e89ddb787a3104
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 25 12:42:41 2018 -0700

    compute area fraction and face centroids for x-faces

Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_GeometryShop.H
Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_eb2_3d.F90

commit 15ac433de5ba2800da822e9a37ac27658c41ca4b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 25 11:46:56 2018 -0700

    first attempt at wrapping the AmrTracerParticleContainer for use with the Fortran interfaces.

Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp
Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90
Tutorials/Amr/Advection_F/Exec/Make.Adv
Tutorials/Amr/Advection_F/Exec/SingleVortex/GNUmakefile

commit 2846a0133ec2d7715cbcdd3d85fe291dd25d8f0e
Merge: 7dcf984cc 52de4f292
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 24 11:00:09 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 7dcf984cc92acfa97ddbc776261aa21614073d8f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 24 10:59:51 2018 -0700

    fix timer name

Src/Particle/AMReX_ParticleContainerI.H

commit a8e0523b8a50e2d1d6d3bfabc28d8b3021938a68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 24 10:25:41 2018 -0700

    3d build_types

Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_EB2_MultiGFab.H
Src/EB2/AMReX_EB2_MultiGFab.cpp
Src/EB2/AMReX_eb2_2d.F90
Src/EB2/AMReX_eb2_3d.F90

commit 5ea7c58c387f909c5272dc508ae72f1e55473d46
Merge: 8ac55fed9 52de4f292
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 23 12:38:28 2018 -0700

    Merge branch 'development' into weiqun/eb2

commit 8ac55fed954cf1483e689d51ba82c90633fd59ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 23 12:38:22 2018 -0700

    fix typo and add an alias IntVect::hasher

Src/Base/AMReX_Box.H
Src/Base/AMReX_IntVect.H
Src/EB2/AMReX_EB2_Graph.H

commit 52de4f2921781f0d4ad61b8e2d6aaa7157028154
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 23 10:51:15 2018 -0700

    fix non-mpi build

Src/Base/AMReX_FabArrayCommI.H

commit c28695be42ec42b98a3e01996f7ccc57167d992d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 23 10:38:52 2018 -0700

    non-blocking parallel copy

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H

commit be5059853e42d18f1c8c13eab06331724848ba40
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed May 23 12:53:29 2018 -0400

    Test update.

Tutorials/GPU/HelloWorld_C/GNUmakefile
Tutorials/GPU/HelloWorld_C/main.cpp

commit 8358df65874c44da760f04392b2b6191525edeb4
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue May 22 21:52:47 2018 -0400

    compiler no longer complaining

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab_nd.F90
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tutorials/GPU/HelloWorld_C/main.cpp

commit 149791101ceb74a6e4801fa3891d7f8424f57ee5
Merge: 5afe1ad18 6fa2d2118
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 22 11:15:07 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5afe1ad18c5544169802304a2d396d9f62ee47ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 22 11:15:00 2018 -0700

    rm a profiler

Src/Particle/AMReX_ParticleContainerI.H

commit ba41ec3d12276e5330253beabbf448ff7103f233
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue May 22 10:59:23 2018 -0400

    setVal working.

Src/Base/AMReX_BaseFab.H
Tools/GNUMake/comps/nvcc.mak

commit 6fa2d2118e714bfc03298ba8f8698b36f8b25d73
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon May 21 17:20:22 2018 -0700

    endl -> std::endl so this compiles

Tools/C_util/Convergence/RichardsonConvergenceTest.cpp

commit 7658742c039d2982c8c3e921d7a252c5a98eb7c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 21 17:04:48 2018 -0700

    SumBoundary: use IntVect version of Copy

Src/Base/AMReX_MultiFab.cpp

commit e65dda013f81a471ccb6cda33128e605d4615d07
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon May 21 16:14:02 2018 -0700

    Fix MPI compilation at LLNL

Tools/GNUMake/sites/Make.llnl

commit 39274912b315948f460c45f804c5094a07e61810
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 21 16:11:06 2018 -0700

    fix tiling bug in nodal linear solver

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit d871892461863f8cf0e159ebc3c796d8f83f1925
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon May 21 17:21:24 2018 -0400

    BaseFab::setVal prepped except for 'ForEach'

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_Managed.H
Tutorials/GPU/HelloWorld_C/main.cpp

commit 5104ebe7158e75231f9064c58be4b7247932d89b
Merge: a443a8be0 6c7df835b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 21 13:04:33 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6c7df835bbada0c2d0c1b68b3686f8ee86d3eb94
Merge: a768d074e b44bdba71
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon May 21 11:45:46 2018 -0700

    Merge pull request #263 from knutsvk/development
    
    add pp.query for unstable_criterion

commit b44bdba71da8dec464416c92ed9507cb2e637938
Author: knutsvk <ksk38@cam.ac.uk>
Date:   Mon May 21 13:35:43 2018 +0100

    add pp.query for unstable_criterion

Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp

commit a443a8be0d8e96cc5411e734b946ae7e27c586a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 19 17:20:29 2018 -0700

    fix single precision for 2d too

Src/AmrCore/AMReX_FillPatchUtil_2d.F90

commit a768d074e7d718f96828913124bd11aefc713ad2
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri May 18 16:11:27 2018 -0700

    Fix single precision issue in AmrCore

Src/AmrCore/AMReX_FillPatchUtil_3d.F90

commit c873d381969951d991e2b76e66403ac84c505edf
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri May 18 18:26:53 2018 -0400

    FORT_LAUNCH -> AMREX_FORT_LAUNCH, DEVICE_LAUNCH -> AMREX_DEVICE_LAUNCH

Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_filcc_f.H
Tutorials/GPU/HeatEquation_EX1_C/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H

commit f5e87387312d6f717caeb1e2a32fddecd2fbecd9
Merge: 5d617c468 e9366d8f0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri May 18 17:50:50 2018 -0400

    Merge commit 'e9366d8f02bc9ebab7e1defe4f5cdc0f55fcb67b' into gpu

commit 5d617c46874f3613be8eab5d8534b00b5747bcd9
Merge: 0ffe665fc 9e3ed0489
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 17 22:19:20 2018 -0400

    Merge commit '9e3ed04897fb938e5e474aa870307badc52f71e1' into gpu

commit 0ffe665fc71049445a6194a7a4e9e0f1a57508bf
Merge: 6abff4bc5 652a065d4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 17 21:39:01 2018 -0400

    Merge commit '652a065d4545bb442325f2a8fd2403f809e457cb' into gpu

commit 6abff4bc57e2b039a209593c9a50c8c324525156
Merge: f1bec191a 184fba026
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 17 21:38:44 2018 -0400

    Merge commit '184fba0260e4b067bec73f28d9422e5837bb5ef5' into gpu

commit 52469100477a5b379b4990682f8368578786a4e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 17 14:00:16 2018 -0700

    ignore .nfs* files

.gitignore

commit a29524c51e7e3f7f0e7105e27488511b646d7438
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 17 13:56:49 2018 -0700

    rm .nfs file

Tutorials/GPU/HelloWorld_C/.nfs0000000002226f1d00001727.REMOVED.git-id

commit fcd70e9a1bcc3b426eec0b3bf505c6997cae111b
Merge: 1ad83b522 fc00f4451
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 17 09:52:18 2018 -0700

    Merge branch 'development' into weiqun/eb1

commit f1bec191aa148d928b8889c83d326ef6aef72004
Merge: 70657f5f0 51452f005
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 17 11:50:38 2018 -0400

    Merge commit '51452f005e31fe1479fdc50c2a3deee9e0e262e1' into gpu

commit 70657f5f049ddff15354afe506069c7a44d7ba4b
Merge: 16dc17dcc 84603a9fb
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 17 11:47:30 2018 -0400

    Merge commit '84603a9fbf1a7bfd1ec8da77edae3e9c007fb61f' into gpu

commit 16dc17dcc35bbe03b71cf67e8d551d402d83472a
Merge: 405aaa9f8 8e47f3e29
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 17 11:43:09 2018 -0400

    Merge commit '8e47f3e29251589312e5185c9d3046264de328d6' into gpu

commit 405aaa9f8028b40ac5e24ed663fd78275a5490bf
Merge: b4d34fa47 b033d37ee
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 17 11:42:55 2018 -0400

    Merge commit 'b033d37eec1bf75f2aafe7de98d14a9cab1a4ddf' into gpu

commit b4d34fa4776688a274a52846814f0c0028afbd6a
Merge: 3d4af98db db34ed33d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 17 11:32:11 2018 -0400

    Merge commit 'db34ed33d6fa36e354a89f06aa19866051a8ca55' into gpu

commit 3d4af98dbc001e9f713357d7ffc3e0f3e18ea2d6
Merge: 9ebb799a1 4e8451c56
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 17 11:28:39 2018 -0400

    Merge commit '4e8451c562ea5f04f149552f8aa0b1dcae651b2c' into gpu

commit 9ebb799a1e736ecf12d4ac36a8185ee0d537bc1b
Merge: bcba864c8 52a2e1b04
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 17 11:17:34 2018 -0400

    Merge commit '52a2e1b04801e71b7282069ad26a0997c199b30c' into gpu

commit bcba864c8c4eca59ec8f3d62436060872de696c8
Merge: d025614f8 8cd48768f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 17 11:16:10 2018 -0400

    Merge commit '8cd48768ff841c33e83cefd74a78d14f5abca79e' into gpu

commit d025614f85c2bb6a2407b6353362721d64ac3b8a
Merge: 40bbc9bef 8e103b621
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 17 10:51:27 2018 -0400

    Merge commit '8e103b621daa6f34b4f5cef43b07869f873b7c2c' into gpu

commit 40bbc9befcaa60bb3d55f74c0ea8cdd9e0f79b06
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 16 20:56:23 2018 -0400

    Allow runtime overriding of strided grid/block size

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 5c414492140573da4b90d34f820c36f4c9b53315
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 16 16:09:32 2018 -0400

    sharedmemcarveout is only in 9.1+

Src/Base/AMReX_BLFort.H

commit 6ed070e2ce9003085bd46f64f233f8f81b6e7b69
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 16 11:38:15 2018 -0400

    Set the default register count to 255

Tools/GNUMake/Make.defs

commit b72f93a03f1de8eecf94e8e7922901b81827528f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 16 11:37:45 2018 -0400

    Cap filcc at 128 registers

Src/Base/Make.package

commit 8ceaac49d2c7190aeeb018f4996b5775b698619f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 16 11:36:44 2018 -0400

    Add the ability to do a file-specific register maximum

Tools/GNUMake/Make.rules

commit a38a5646eed0b9ede1875559334318a56da055da
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 16 07:21:13 2018 -0400

    Compare correct y and z dimensions

Src/Base/AMReX_CUDA.F90

commit 7f355cc7c5aaaa054c1ba68af49215b37a6c190d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 16 07:19:37 2018 -0400

    Correct the sanity check on too many threads

Src/Base/AMReX_CUDA.F90

commit 1566090f0b482abdfdd5ce5190fa4e704245f649
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 16 05:27:22 2018 -0400

    Limit to 256 threads per block

Tools/GNUMake/Make.defs

commit f4f509048b2a40a8a6836886636e3741404d4ff7
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue May 15 20:12:26 2018 -0400

    Add more macros for the GPU script

Src/Base/AMReX_ArrayLim.H

commit fc00f4451bd88eb0fcf47f589352a35911b8d7d4
Merge: 77b71f411 df739c5c2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 15 20:06:40 2018 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development

commit 77b71f4113296962339b741f1e6c93586c27182b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 15 20:06:13 2018 -0400

    make this importable

Tools/F_scripts/find_files_vpath.py

commit 4315cfc91a2e92f8297a5fa48e2542f23c8e1a45
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue May 15 17:11:29 2018 -0400

    IntVect managed memory start. Need AMReX_Vector to keep going.

Src/Base/AMReX_IntVect.H

commit c10e1f16b72b9d94e28d5d53bc6556f6c2678ed3
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue May 15 17:10:42 2018 -0400

    First outline of managed memory class and macros.

Src/Base/AMReX_Managed.H
Src/Base/Make.package
Tutorials/GPU/HelloWorld_C/.nfs0000000002226f1d00001727.REMOVED.git-id
Tutorials/GPU/HelloWorld_C/GNUmakefile
Tutorials/GPU/HelloWorld_C/Make.package
Tutorials/GPU/HelloWorld_C/main.cpp
Tutorials/GPU/HelloWorld_C/outline.cpp

commit 19b2cf825523016a62858acbc307b2e5995e70b6
Author: Kevin Gott <kngott@lbl.gov>
Date:   Tue May 15 17:09:57 2018 -0400

    Copy of GPU build system from gpu branch.

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/Linux_pgi.mak
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.local.template
Tools/GNUMake/Make.machines
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/ibm.mak
Tools/GNUMake/comps/nvcc.mak
Tools/GNUMake/comps/pgi.mak
Tools/GNUMake/packages/Make.cvode
Tools/GNUMake/sites/Make.llnl
Tools/GNUMake/sites/Make.olcf
Tools/GNUMake/tools/Make.craypat
Tools/GNUMake/tools/Make.vtune

commit df739c5c275a4226a26835f32ce01170354322a3
Merge: cddc70570 fd2120bde
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 15 13:08:21 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cddc70570b1370ba21e2aec3c4e2567d75895509
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 15 13:08:08 2018 -0700

    add option to interpolate in space when using amrex::get_slice_data

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_MultiFabUtil_nd.F90

commit 1ad83b522ec1d01f779ad2d414f2366cf6841728
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 15 12:23:09 2018 -0700

    find intercept using Brent method

Src/Base/AMReX_Box.H
Src/EB2/AMReX_EB2_GeometryShop.H
Src/EB2/AMReX_EB2_Graph.H
Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_eb2_2d.F90

commit ae0bbda0a85d3f1072e251a8ed6c62869cbe1e6f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 14 10:10:35 2018 -0700

    build types

Src/EB2/AMReX_EB2_GeometryShop.H
Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_EB2_MultiGFab.H
Src/EB2/AMReX_EB2_MultiGFab.cpp
Src/EB2/AMReX_EB2_SphereIF.H
Src/EB2/AMReX_eb2_2d.F90

commit 1f47eda8346d11531a210321fafb66ecbe74c3e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 13 07:29:09 2018 -0700

    add fortran function stub for building types

Src/Base/AMReX_LayoutData.H
Src/EB2/AMReX_EB2_F.H
Src/EB2/AMReX_EB2_GeometryShop.H
Src/EB2/AMReX_EB2_Graph.H
Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_EB2_MultiGFab.H
Src/EB2/AMReX_EB2_MultiGFab.cpp
Src/EB2/AMReX_eb2_2d.F90
Src/EB2/Make.package

commit 7da568f9f6261170a796852cbd9b60eb3aca24a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 12 08:26:04 2018 -0700

    keep cut boxes only

Src/EB2/AMReX_EB2_GeometryShop.H
Src/EB2/AMReX_EB2_Graph.H
Src/EB2/AMReX_EB2_ISLevel.H

commit 279ab03af29c7ba0b556ed251c776f87576b7bcd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 11 18:32:38 2018 -0700

    start EB2:Graph

Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2_GeometryShop.H
Src/EB2/AMReX_EB2_Graph.H
Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_EB2_IndexSpaceI.H
Src/EB2/AMReX_EB2_SphereIF.H
Src/EB2/Make.package

commit fd2120bdefd88564b1863090fbd15b7576ff23e3
Merge: 18787cf7c 2e22862f5
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri May 11 15:07:24 2018 -0700

    Merge branch 'mr/cmake' into development

commit 18787cf7c657bda4ebe6caeba07b47784d8eae82
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri May 11 14:42:52 2018 -0700

    Remove debugging output.

Src/GeometryShop/AMReX_EBISLevel.cpp

commit 4ffd20ff728b9218323691be55f99aac63d5304b
Author: Cy Chan <cychan@lbl.gov>
Date:   Fri May 11 13:46:31 2018 -0700

    ForkJoin:
      remove task_rank_n member field since split_bounds duplicates information
      add forkjoin.verbose input parameter
      make MyTask and NTasks public

OldTutorials/MultiColor_C/inputs
OldTutorials/MultiColor_C/main.cpp
Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp

commit 1bfeffd59271809501005d58e1adc07adf9c0814
Author: Cy Chan <cychan@lbl.gov>
Date:   Fri May 11 13:06:07 2018 -0700

    some clean up

OldTutorials/MultiColor_C/inputs
OldTutorials/MultiColor_C/main.cpp
Src/Base/AMReX_ForkJoin.cpp

commit b115882bbe0d7f34bda546f4d85f86370d49cd66
Merge: 12a046bfd f86b0149e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 11 12:45:04 2018 -0700

    Merge pull request #260 from nataraj2/master
    
    Advection_F generalized to 2d and 3d

commit c83b89e23dcee82225720ec288a5b8ab3a75f972
Author: Cy Chan <cychan@lbl.gov>
Date:   Fri May 11 12:36:45 2018 -0700

    changed MultiFab collectives to use ParallelContext subcommunicator instead of ParallelDescriptor
      added Parallel(All)Reduce Or and And
      added ParallelAllGather and ParallelGather functions
      updates to MultiFab::(min/max)Index()
        remove broadcast, replace with allgather, everyone does reduction

OldTutorials/MultiColor_C/main.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelReduce.H

commit 2e22862f55a19435902a338c6f10a4ef0ed8e466
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri May 11 11:58:40 2018 -0700

    Fix namespace in export file

Tools/CMake/AMReXConfig.cmake.in

commit aad0b8bbaf42909958a88d5d199f70c41aa41e63
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri May 11 11:55:52 2018 -0700

    Disable linear solver legacy components by default

Docs/sphinx_documentation/source/BuildingAMReX.rst
Src/LinearSolvers/CMakeLists.txt
Tools/CMake/AMReX_Options.cmake

commit 12a046bfdb93fcf806150312e327e0f1d41545d9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 11 11:05:12 2018 -0700

    make this link go directly to the issues page.

Docs/sphinx_documentation/source/index.rst

commit 51f3854e879106097d5a932903ed05b68d7c2abc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 11 11:03:49 2018 -0700

    remove duplicated link

Docs/sphinx_documentation/source/Introduction.rst

commit 12344faee0196c521d00dd656b5bca30f6d288ba
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 11 11:02:39 2018 -0700

    remove duplicated information between the introduction and main landing page for the docs.

Docs/sphinx_documentation/source/Introduction.rst
Docs/sphinx_documentation/source/index.rst

commit 43808b82be81ef8fa023ec73c0dd7ea557b67eeb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 11 11:00:49 2018 -0700

    use hyperlink targets instead of including the entire test of links in the text.

Docs/sphinx_documentation/source/index.rst

commit 645cabd979f563cbff56638e668ff5331e7bd30f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 11 10:49:03 2018 -0700

    include a link to the Doxygen API docs on the main page for the long-form documentation.

Docs/sphinx_documentation/source/index.rst

commit 6eea5ddc85a5aa062887e6cb186143d74d68759e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 11 10:47:03 2018 -0700

    some clarifying remarks in the documenation

Docs/sphinx_documentation/source/Introduction.rst
Docs/sphinx_documentation/source/index.rst

commit db48ae55ae984f892f1a3f625d544a45a67bc8f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 10 21:02:35 2018 -0700

    fix MLMG nodal solver in case there is no coarsening at all

Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 755cb02715eaba2b320a7aa9ea64589c6cfb777c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 10 17:28:26 2018 -0700

    start EB2 and set up IndexSpace

Src/Base/AMReX_Array.H
Src/EB2/AMReX_EB2.H
Src/EB2/AMReX_EB2.cpp
Src/EB2/AMReX_EB2_GeometryShop.H
Src/EB2/AMReX_EB2_ISLevel.H
Src/EB2/AMReX_EB2_IndexSpaceI.H
Src/EB2/AMReX_EB2_SphereIF.H
Src/EB2/Make.package
Tools/GNUMake/Make.defs

commit fd8b91f14e2d28ce5a28d4599c77efaa6b5ff69a
Merge: 49a24be88 013c2b562
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 10 16:44:32 2018 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development

commit 49a24be88174c88198ac39ed3e1545b7913f1b92
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 10 16:44:17 2018 -0400

    allow for multiple specific variables to be output

Tools/Postprocessing/F_Src/fextrema.f90

commit ebd458199d1669b317e9a85b4ff808e121fe4688
Author: Cy Chan <cychan@lbl.gov>
Date:   Thu May 10 11:47:48 2018 -0700

    add support for custom MultiFab component split across tasks

OldTutorials/MultiColor_C/inputs
OldTutorials/MultiColor_C/main.cpp
Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp

commit 013c2b5625641fe91c1fcc1be23f02afeabb7978
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 10 11:30:38 2018 -0700

    Remove ifdef from around void setCoarseningStrategy so that we can call it even with EB defined.

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H

commit a570caf8595f571247b5954002d17e10643a6af8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 10 12:28:52 2018 -0400

    GCC 8.x introduces more options for the sanitizers -- enable
    them is we are building with GCC >= 8

Tools/GNUMake/comps/gnu.mak

commit 83a920e397ccf91ee5b2c2538c685f09f08e26ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 10 08:45:14 2018 -0700

    makeFineMask works for any index types as long as they are consistent

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 6df45d6e5b3959e8095c350e0d32139e4ae66f2b
Merge: 29a641163 a4dfe07f3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 9 17:38:42 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 29a6411632701722978d6e38208dcfd07f1a2994
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 9 17:38:27 2018 -0700

    add a function to test for the intersection of two RealBoxes

Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp

commit 9b6e9b86e743bf9e7926d356a4ca59dd356e0756
Author: Cy Chan <cychan@lbl.gov>
Date:   Wed May 9 15:41:40 2018 -0700

    forkjoin: add some error checking

OldTutorials/MultiColor_C/inputs
OldTutorials/MultiColor_C/main.cpp
Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp

commit a4dfe07f39f1b748055d8547a0bad3a04a868ce1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 9 14:46:56 2018 -0700

    makeFineMask function

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 3fe4edb5a96c1a272745d63d5196ae561aa460e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 9 14:45:44 2018 -0700

    enable iMultiFab operator= for rvalue rhs

Src/Base/AMReX_iMultiFab.H

commit f5a88d9f3250796279400e38217fa86ef468e9dc
Merge: 2ec5aadd0 6046ef355
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 9 10:02:26 2018 -0700

    Merge branch 'development' into weiqun/mlmg

commit 6046ef3554d21ed839ca2c0adec06a2fc8540cab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 9 09:24:04 2018 -0700

    ParmParse: support FILE=probin where probin is a Fortran namelist file

Src/Base/AMReX_parmparse_mod.F90

commit b005675fffcff4474b639a44a86f81d3d81372ee
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 8 17:32:05 2018 -0700

    Add AMReX_CoveredSlabs* to CMakeLists.txt

Src/GeometryShop/CMakeLists.txt

commit 3c8230d127dadac9cd8424705078e8207c08a6e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 8 17:24:57 2018 -0700

    amrex namespace and prefix

Src/EB/AMReX_EB_F.H
Src/EB/AMReX_EB_geometry.F90
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_levelset_F.F90
Src/EB/AMReX_compute_normals.F90
Tutorials/EB/LevelSet/Src/main.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp
Tutorials/EB/LevelSet/Src/make_shapes.H

commit 208805189c899d0d6ff1e31de46a1921ca048858
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 8 16:58:54 2018 -0700

    EB levelset: make 2d compile

Src/EB/AMReX_EB_levelset.cpp
Tutorials/EB/LevelSet/Src/main.cpp

commit 7ff11b56b58875b0a12b37fcfc646c12d4d36d8d
Merge: 82bf80056 af18bac57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 8 15:37:13 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 82bf800566ad26007d0e04f247ed424f9d256659
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 8 15:37:04 2018 -0700

    define USE_EB=TRUE and simplify GNUmakefile

Tutorials/EB/LevelSet/Exec/GNUmakefile

commit af18bac57acbfa00f181f3b9390cab330c279d04
Merge: 7a25adc22 900892ef8
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue May 8 15:31:02 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 7a25adc223ce9f33a60d32496523757c36abcb06
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue May 8 15:30:55 2018 -0700

    cleanup

Tutorials/EB/LevelSet/Src/Make.package

commit 900892ef89c6c4d26c8423789c8f13db11ef1077
Merge: 9c7f0aba1 93daf0ebb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 8 15:06:17 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9c7f0aba14f1b29dac50c8bfeec79266764de811
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 8 15:06:13 2018 -0700

    ParmParse now reads Fortran namelist blocks in inputs file and saves them in amrex_namelist in amrex_parmparse_module.  This allows mixing ParmParse parameters and Fortran namelist parameters in a single inputs file.  Note that namelist is not stored in ParmParse database.

Src/Base/AMReX_ParmParse.cpp
Src/Base/AMReX_parmparse_mod.F90

commit f1a954bd0a94533ba9716764407376f6c5c03a4e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue May 8 17:43:28 2018 -0400

    Remove a stray variadic arg

Src/Base/AMReX_BLFort.H

commit 93daf0ebb8c7ff4824daeb6ff8b3310dc8efe221
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue May 8 14:19:32 2018 -0700

    moved level-set source into AMReX Src/EB

Src/EB/AMReX_EB_F.H
Src/EB/AMReX_EB_geometry.F90
Src/EB/AMReX_EB_levelset.H
Src/EB/AMReX_EB_levelset.cpp
Src/EB/AMReX_EB_levelset_F.F90
Src/EB/AMReX_compute_normals.F90
Src/EB/CMakeLists.txt
Src/EB/Make.package
Tutorials/EB/LevelSet/Src/Make.package
Tutorials/EB/LevelSet/Src/make_eb.cpp
Tutorials/EB/LevelSet/Src/make_shapes.H

commit 389bc79f5d9365a5dbfa64465905454502e9ac3f
Merge: 0ffdba5f8 8ba1deff4
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue May 8 13:35:42 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 0ffdba5f897686c171267cd01267c81fbeb6b9c0
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue May 8 13:35:26 2018 -0700

    Fix level-set tutorial

Tutorials/EB/LevelSet/Exec/inputs
Tutorials/EB/LevelSet/Src/main.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp
Tutorials/EB/LevelSet/Src/make_poly.cpp
Tutorials/EB/LevelSet/Src/make_shapes.H

commit 8ba1deff4f04a58fc0c79b0e635deb902df50dd6
Merge: 175f9b823 2fccc5260
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue May 8 13:15:25 2018 -0700

    Merge pull request #259 from AMReX-Codes/dtg_branch
    
    added CoveredSlab geometry generation per Marc's request so we can ha…

commit 10f0ea652380891d438cd13ececa981f99adb019
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Apr 26 15:45:29 2018 -0400

    fix PGI compilation
    PGI complains that with the 'pure' keyword here:
    
    PGF90-S-0074-Illegal number or type of arguments to heapsort_indirect_d - arguments of greater_d and cmp do not agree (/home/zingale/development/AMReX//Src/F_BaseLib/knapsack.f90: 85)

Src/F_BaseLib/knapsack.f90

commit 6679b4500420fbebe030fe80d1fa7ada9e79dee4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue May 8 16:14:06 2018 -0400

    PGI now uses a different variable for the CUDA toolkit

Tools/GNUMake/comps/pgi.mak

commit 2fccc5260d87b302b53c28968d89ba05dae351d2
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue May 8 13:13:22 2018 -0700

    added CoveredSlab geometry generation per Marc's request so we can have geometries with sharp corners.

Src/GeometryShop/AMReX_CoveredSlabs.H
Src/GeometryShop/AMReX_CoveredSlabs.cpp
Src/GeometryShop/Make.package
Tutorials/EB/GeometryGeneration/exec/GNUmakefile
Tutorials/EB/GeometryGeneration/exec/coveredSlabs.cpp
Tutorials/EB/GeometryGeneration/exec/coveredslabs.inputs

commit 175f9b823c1ee095826070693968465b8fe3f291
Merge: 252ab0f93 c9c052edc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 8 10:45:38 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 252ab0f93ccaa8df63c82b13b645e74ac353842c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 8 10:45:30 2018 -0700

    MLMG: refactor grids agglomeration so that it works even if the argument grids is not directly coarsenable.

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit c9c052edc1dd6c250d98c98bc0c8deb239b4be84
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 8 10:37:02 2018 -0700

    Add Tutorials/EB/LevelSet to demonstrate how to generate level set from EB specification.

Tutorials/EB/LevelSet/Exec/GNUmakefile
Tutorials/EB/LevelSet/Exec/inputs
Tutorials/EB/LevelSet/Src/Make.package
Tutorials/EB/LevelSet/Src/compute_normals.f90
Tutorials/EB/LevelSet/Src/eb_F.H
Tutorials/EB/LevelSet/Src/eb_geometry.f90
Tutorials/EB/LevelSet/Src/eb_levelset.H
Tutorials/EB/LevelSet/Src/eb_levelset.cpp
Tutorials/EB/LevelSet/Src/eb_levelset_f.f90
Tutorials/EB/LevelSet/Src/main.cpp
Tutorials/EB/LevelSet/Src/make_cylinder.cpp
Tutorials/EB/LevelSet/Src/make_eb.cpp
Tutorials/EB/LevelSet/Src/make_poly.cpp
Tutorials/EB/LevelSet/Src/make_shapes.H

commit 07cb7e86bd5a51028c56d0657bd55ebba83a19c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 7 17:34:18 2018 -0700

    MLMG: assert grids are coarsenable

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit a7a282dfecb1d607d5398f2a8a2d3c59ed8b15b3
Merge: fac7b019c a245bde43
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon May 7 17:18:43 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit fac7b019ce141ea0d51b57806df8f841dd0f9ad7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon May 7 17:18:37 2018 -0700

    Revert "Allow face-based arrays to coarsen even if the boxes don't quite line up right (eg if a fine"
    
    This reverts commit 4c81fbb2ed12307fb765f124b0c3f38657a481f6.

Src/Base/AMReX_MultiFabUtil.cpp

commit a245bde43a760f7c6d08e4dd2b725026cabea901
Merge: 40e833a9e 4c81fbb2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 7 17:10:40 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 40e833a9e74313024032e6fa352853724f70be07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 7 17:10:36 2018 -0700

    fix print in TinyProfiler

Src/Base/AMReX_TinyProfiler.cpp

commit 4c81fbb2ed12307fb765f124b0c3f38657a481f6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon May 7 16:56:03 2018 -0700

    Allow face-based arrays to coarsen even if the boxes don't quite line up right (eg if a fine
    32x32 domain is broken into boxes 15-wide and 17-wide but the coarse boxes are 8x8)

Src/Base/AMReX_MultiFabUtil.cpp

commit 214757a5ab381090e428c73186850f0e1d128078
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 7 16:49:42 2018 -0700

    avoid using cout and cerr directly

Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_TracerParticles.cpp

commit 2adf9dd7cc46d921021ce3aa62510f35ca3cffa2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 7 15:37:23 2018 -0700

    avoid using cout and cerr directly in Base/

Src/Base/AMReX.cpp
Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_NFiles.cpp
Src/Base/AMReX_ParmParse.cpp
Src/Base/AMReX_RealBox.cpp
Src/Base/AMReX_TinyProfiler.cpp
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_VisMF.cpp

commit afdaca4e920bddcf42db232be358b120595493a8
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon May 7 18:07:45 2018 -0400

    Indent make.olcf for clarity

Tools/GNUMake/sites/Make.olcf

commit f0377862bf479d0aa866f307d668bbd22bcb867f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 7 15:01:05 2018 -0700

    add amrex::ErrorStream and remove cout and cerr from Amr/

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateDescriptor.cpp
Src/Base/AMReX.H
Src/Base/AMReX.cpp

commit f86b0149eda5243a5e731396a31f6dd2e7936911
Author: Mahesh Natarajan <natarajan@dhcp-rhodes-837.redrover.cornell.edu>
Date:   Mon May 7 17:46:46 2018 -0400

    Advection_F generalized to 2d and 3d

Tutorials/Amr/Advection_F/Exec/SingleVortex/movie.visit

commit 9fd6972b0ffab513abee24afb2bc86a11e79b58d
Author: Mahesh Natarajan <natarajan@dhcp-rhodes-837.redrover.cornell.edu>
Date:   Mon May 7 17:44:57 2018 -0400

    Advection_F generalized to 2d and 3d

Tutorials/Amr/Advection_F/Exec/SingleVortex/.GNUmakefile.swp

commit ba1605f5d0ea57e22e0ae51d7b933465eea4c525
Author: Mahesh Natarajan <natarajan@dhcp-rhodes-837.redrover.cornell.edu>
Date:   Mon May 7 17:44:37 2018 -0400

    Advection_F generalized to 2d and 3d

Tutorials/Amr/Advection_F/Exec/SingleVortex/.inputs.swp

commit d9e1683d7ecdd9f3f19fec80935f0eb25022d028
Author: Mahesh Natarajan <natarajan@dhcp-rhodes-837.redrover.cornell.edu>
Date:   Mon May 7 17:43:32 2018 -0400

    Advection_F generalized to 2d and 3d

Tutorials/Amr/Advection_F/Exec/SingleVortex/.GNUmakefile.swp
Tutorials/Amr/Advection_F/Exec/SingleVortex/.inputs.swp
Tutorials/Amr/Advection_F/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_F/Exec/SingleVortex/Make.package
Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_2d.f90
Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_3d.f90
Tutorials/Amr/Advection_F/Exec/SingleVortex/face_velocity_3d.F90
Tutorials/Amr/Advection_F/Exec/SingleVortex/movie.visit
Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/Advection_F/Source/Src_3d/Make.package
Tutorials/Amr/Advection_F/Source/Src_3d/compute_flux_3d.f90
Tutorials/Amr/Advection_F/Source/Src_3d/slope_3d.f90

commit 3b4c41d86d7265402a3b52458cc46de005c4d8e1
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon May 7 16:30:37 2018 -0400

    Fix MPI compilation on summitdev

Tools/GNUMake/sites/Make.olcf

commit 1587672584592402f47dd9877a1e0f4bd37eda6b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon May 7 11:51:17 2018 -0700

    added a bit about using WrappedGShop for generating higher order EB moments.

Docs/sphinx_documentation/source/EB.rst

commit 3c88047259978c0fd5481d1c1ff8fd56910c63bb
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon May 7 10:32:20 2018 -0700

    added derivative functions for Union, Intersection and Complement implicit functions.

Src/GeometryShop/AMReX_ComplementIF.H
Src/GeometryShop/AMReX_ComplementIF.cpp
Src/GeometryShop/AMReX_IntersectionIF.H
Src/GeometryShop/AMReX_IntersectionIF.cpp
Src/GeometryShop/AMReX_UnionIF.H
Src/GeometryShop/AMReX_UnionIF.cpp

commit 3537b101576e21020e25bc20657ed2e759c801e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 7 09:45:25 2018 -0700

    add geom_type box to Tests/EBbcent

Tests/EBbcent/main.cpp

commit 8eda5e5aecafff79f17889316ab183ba0469bd51
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun May 6 17:49:57 2018 -0400

    Use the new shared mem carveout attribute for CUDA 9

Src/Base/AMReX_BLFort.H

commit 50aa4a0f86345d68dac4165b581d4e79c27b1267
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun May 6 17:27:48 2018 -0400

    Always do strided DEVICE_LAUNCH

Src/Base/AMReX_BLFort.H

commit e2c2dfbaea29139d4aa569a4a6f2173813294f3e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun May 6 17:27:38 2018 -0400

    Note minimum number of threads

Src/Base/AMReX_Device.cpp

commit 59e682ed779d4572b13b6aa3c4db8d9d37a0a4a8
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun May 6 16:35:40 2018 -0400

    Update the grid strided loop layout

Src/Base/AMReX_Device.cpp

commit b9ed0f31ef33730dbc36a5608cd7313190cb09b9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun May 6 15:12:43 2018 -0400

    Add a grid-strided device launch macro

Src/Base/AMReX_BLFort.H

commit bcdc08e86ad5080ff4f9d657e6311504355e83c6
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun May 6 07:06:24 2018 -0400

    Add a function for doing a grid-stride kernel

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 7ce13c146c633316fc9fed7677119863b4fd641d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun May 6 07:05:11 2018 -0400

    Add function to return number of device SMs

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H

commit 010142c31722ad00e386afa3e8ca79a6c39238e0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat May 5 20:08:15 2018 -0400

    Add a DEVICE_LAUNCH macro

Src/Base/AMReX_BLFort.H

commit 58cba37c40c961e54b56a0428190d2200244790f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat May 5 19:37:32 2018 -0400

    Move nvcc code to a unique file

Tools/GNUMake/comps/ibm.mak
Tools/GNUMake/comps/nvcc.mak
Tools/GNUMake/comps/pgi.mak

commit ca4684a3a503c903388b356ecf4e290a29119ffe
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat May 5 19:31:13 2018 -0400

    Sync up IBM compile flags with PGI

Tools/GNUMake/comps/ibm.mak

commit 3b0a16b8b6f42cb048750c159534c96a171913e3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat May 5 17:14:42 2018 -0400

    Nullify a function template for CUDA

Src/Base/AMReX_BLFort.H

commit e7208abe149cbe00a046a968bdaecbc2d3211c8f
Merge: fb6c45e05 955e63d37
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat May 5 16:36:30 2018 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit fb6c45e05ac460ebdf36d4f47ab9b58e93be96fd
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat May 5 16:36:25 2018 -0400

    Do not link device code until final link

Src/Base/AMReX_BLFort.H
Tools/GNUMake/comps/pgi.mak

commit 1a05cf9f239be4d9ae3db2a9b05ec0a74efb7bc2
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat May 5 16:36:08 2018 -0400

    get_loop_bounds is a device call

Src/Base/AMReX_Device.H

commit e66fce7c78536057efbd628951982008e4df77e1
Merge: 129c879cd dc3725379
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 4 16:07:08 2018 -0700

    Merge pull request #256 from AMReX-Codes/cg-mulicomponent
    
    updated CG solver for multicomponent solves

commit dc3725379e2b183fbf07bd8b1e57fd75fb7cdb3c
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri May 4 17:04:33 2018 -0600

    updated CG solver for multicomponent solves

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit 129c879cde5c9b4c029128dfdb05496d3e5dc552
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 4 15:37:02 2018 -0700

    add FabArray::Redistribute function that redistributes FabArray data from one to another with the same BoxArray but different DistributionMapping

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayCommI.H

commit 955e63d37eca618391dcb0ef3bc2a6e8d9ca664a
Merge: 0d80eb045 ee42ed839
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri May 4 17:16:21 2018 -0400

    Merge branch 'gpu' of https://github.com/AMReX-Codes/amrex into gpu

commit 0d80eb045e3502837206c9fe03439709a44f72c0
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri May 4 17:15:44 2018 -0400

    pass the allocator template parameter in to all uses of the base class in Vector.

Src/Base/AMReX_Vector.H

commit 0558b5020d440c5c619c98b60753bafd9b6b7410
Author: Andrew Myers <atmyers@lbl.gov>
Date:   Fri May 4 16:17:32 2018 -0400

    make swapBytes a regular, non-template function.

Src/Base/AMReX_IntConv.H
Src/Base/AMReX_IntConv.cpp

commit fc3bf820520e4f6feaff6c72948c711a927cd9f9
Merge: 3e526a4fb 79d17e376
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 4 12:18:38 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 3e526a4fb8f8f6df36dd8fb7f75a476d40bbe9d4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 4 12:18:09 2018 -0700

    merging.

Src/GeometryShop/AMReX_IndexedMoments.H
Src/GeometryShop/AMReX_IrregNode.cpp
Tests/EBbcent/GNUmakefile
Tests/EBbcent/Make.package
Tests/EBbcent/main.cpp

commit 9f899a9015cba1673d27336553c31d3142d74b4b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 4 12:14:00 2018 -0700

    make the swapBytes function templated on size rather than type to make it work on Titan with cce

Src/Base/AMReX_IntConv.H
Src/Base/AMReX_IntConv.cpp

commit 79d17e376e936d4077488e99297e6b62de727bee
Merge: f5e53e40a eef19594d
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri May 4 11:00:15 2018 -0700

    Merge pull request #255 from AMReX-Codes/eb-bcent
    
    bug fix in higher order moments

commit eef19594d717edba31d165236223b52be36fbdee
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri May 4 10:57:53 2018 -0700

    added fix for where EBMoments get the wrong sign

Src/GeometryShop/AMReX_IndexedMoments.H
Src/GeometryShop/AMReX_IrregNode.cpp
Tests/EBbcent/main.cpp

commit f5e53e40ac1f6cbfd2909467ca132aea985eeea6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 4 10:13:34 2018 -0700

    fix loop bounds problem in BndryRegister.

Src/Boundary/AMReX_BndryRegister.cpp

commit 95556263dcf414d9dd3e598d6f4fabd75de9ef7b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 4 10:04:52 2018 -0700

    simplify the logic here a bit.

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit 55ee4050e9bd0da8addb10eee37aa3b810a38d94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 4 09:56:47 2018 -0700

    test for debugging

Tests/EBbcent/GNUmakefile
Tests/EBbcent/Make.package
Tests/EBbcent/main.cpp

commit d0c0dea66053d254b3ab8caf6bcebdd98f18534c
Merge: d01c55c55 ad6834c48
Author: atmyers <atmyers2@gmail.com>
Date:   Thu May 3 21:00:51 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit d01c55c55932ab777a67c24bea6f484d6e2c34c0
Author: atmyers <atmyers2@gmail.com>
Date:   Thu May 3 21:00:28 2018 -0700

    remove the version of amrex::ResetRandomSeed that set all the threads to have the same seed.

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit ad6834c48c7dd369499e42750387d3822bb0b122
Merge: 89bc7f12c 1d4340f60
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 3 15:00:47 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 89bc7f12ccd0543e51cc64d9664dc4d3f2478a3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 3 14:57:36 2018 -0700

    add cg to MLMG

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 4f994875f50d6f07bf40dfdcd4791520ee1d5741
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 3 13:50:28 2018 -0700

    clean up SPMD.H

Src/Base/AMReX_SPMD.H
Src/Base/AMReX_SPMD.cpp
Src/Base/AMReX_SPMDI.H
Src/Base/AMReX_parstream.cpp
Src/GeometryShop/AMReX_FabArrayIO.H
Tests/GeometryShop/regression/levelRedistTest.cpp

commit 1d4340f6037a3b1520814872789d94bbb3dfbf56
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu May 3 13:49:05 2018 -0700

    MultiFab is_nodal test for a single direction

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit ee42ed8398e4adbe0b72ebc202927a446085add6
Author: Max Katz <katz12@llnl.gov>
Date:   Thu May 3 13:34:35 2018 -0700

    Update to new SMPI at LLNL

Tools/GNUMake/sites/Make.llnl

commit ce295fb000c67a8fab8d2fcb33314876095da7fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 3 13:24:00 2018 -0700

    change pout basename to amrex_pout and use ParmParse instead of environment variable for specifying output interval

Src/Base/AMReX_parstream.H
Src/Base/AMReX_parstream.cpp

commit eeacd27936e5a8a5bff9511c70419055789b2aa7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 3 12:47:11 2018 -0700

    amrex::Initialize can now take an std::ostream argument for amrex::Print() to use

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_Print.H

commit 84c26d118f7186013814a068817e9bc68927cb1a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 3 11:59:52 2018 -0700

    Sync up LLNL build system

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.llnl

commit 929d2ca2ef3450995a2ae3c23c42613bfbbcc1de
Merge: 4e4750071 b875ca3c4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 3 11:59:19 2018 -0700

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 9ddcca20bbe8da7bddc7443f07d34736d585ce0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 2 16:14:45 2018 -0700

    rm EBAMRElliptic

Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H
Src/EBAMRElliptic/AMReX_BaseBCFuncEval.H
Src/EBAMRElliptic/AMReX_BiCGStabSolver.H
Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H
Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp
Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOp.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp
Src/EBAMRElliptic/AMReX_EBEllipticFort.F90
Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H
Src/EBAMRElliptic/AMReX_EBMultiGrid.H
Src/EBAMRElliptic/AMReX_EBSimpleSolver.H
Src/EBAMRElliptic/AMReX_EBSimpleSolver.cpp
Src/EBAMRElliptic/AMReX_LinearSolver.H
Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.H
Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp
Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H
Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp
Src/EBAMRElliptic/AMReX_NoOpSolver.H
Src/EBAMRElliptic/AMReX_VCAggStencil.H
Src/EBAMRElliptic/AMReX_VCAggStencil.cpp
Src/EBAMRElliptic/Make.package
Tests/EBAMRElliptic/exec/GNUmakefile
Tests/EBAMRElliptic/exec/cond.inputs
Tests/EBAMRElliptic/exec/conductivitySolve.cpp

commit 54debc4c8152b02e0c6170077c21a1d6c4ae567e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 1 11:23:39 2018 -0700

    minor update

INSTALL

commit 82f7a2c35a68e74bc12a7058d5d09d790031973c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 1 09:32:44 2018 -0700

    update CHANGES

CHANGES

commit 3ce7d61f3844f72e9fc6b61e6ed87ec3d252dde7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Apr 27 17:39:20 2018 -0700

    MemCheck versions of flush for testing after timeSteps.

Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BLProfiler.cpp

commit 7d6cfcfed083736e726c3c18992f1896b9bc8d70
Author: Kevin Gott <kngott@lbl.gov>
Date:   Fri Apr 27 14:45:35 2018 -0700

    BL_PROFILE_FLUSH() allows user-specified profiling database writes. input flag 'blprofiler.prof_flushprint' can be set to false to remove intermediate std::cout outputs.

Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BLProfiler.cpp
Tests/ProfTests/HeatEquation_EX1_C/Exec/GNUmakefile
Tests/ProfTests/HeatEquation_EX1_C/Exec/inputs_2d
Tests/ProfTests/HeatEquation_EX1_C/Exec/inputs_3d
Tests/ProfTests/HeatEquation_EX1_C/Source/Make.package
Tests/ProfTests/HeatEquation_EX1_C/Source/advance.cpp
Tests/ProfTests/HeatEquation_EX1_C/Source/advance_2d.f90
Tests/ProfTests/HeatEquation_EX1_C/Source/advance_3d.f90
Tests/ProfTests/HeatEquation_EX1_C/Source/init_phi_2d.f90
Tests/ProfTests/HeatEquation_EX1_C/Source/init_phi_3d.f90
Tests/ProfTests/HeatEquation_EX1_C/Source/main.cpp
Tests/ProfTests/HeatEquation_EX1_C/Source/myfunc.H
Tests/ProfTests/HeatEquation_EX1_C/Source/myfunc_F.H

commit 755a2637590dd5d0b2611d49e26334373d424143
Merge: ab5bad3e6 3bb9120db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Apr 27 08:39:20 2018 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ab5bad3e69ec6ef5a91cfda217df77c448e633db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Apr 27 08:38:45 2018 -0400

    only warn if not all variables are present
    still send a success code so tests pass when we add new variables

Tools/Postprocessing/F_Src/fcompare.f90

commit 3bb9120dbab77e93383b1762721a0f3049fa2bd6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 26 22:33:15 2018 -0700

    get aroung a compiler bug?

Src/Base/AMReX_Box.H

commit 883cab78c619664885888cd00eaedea433166691
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 26 15:57:04 2018 -0700

    remove a number of function level static variables that may not be thread safe

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IndexType.cpp
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp

commit 0ca446f913b0c6e725f8998accc894248e40a533
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 26 15:33:13 2018 -0700

    tidy

Src/Base/AMReX_Box.H

commit 01bfe7fee7e04e7861e37ed43314b02fd8e02ba6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 26 13:36:27 2018 -0700

    fix new Box bug and revert my revert

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp

commit 6e621c09f11242996d0abfe18f27dd77c3f63694
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 26 13:31:26 2018 -0700

    fix omp compilation

Src/Boundary/AMReX_YAFluxRegister.cpp

commit 410e0180ef09703129f798f42bc3ecdd9f2e1742
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 26 13:22:36 2018 -0700

    revert my change in Box due to a bug

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp

commit 11ea492c399264c45c31dc0bd20b302c9dc3ad9e
Merge: 241477379 84c26c314
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 26 13:00:46 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 24147737936fe8a1ebb24dbf43d69d47c0c17b37
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 26 13:00:43 2018 -0700

    omp in in YAFluxRegister::define

Src/Boundary/AMReX_YAFluxRegister.cpp

commit 84c26c3146fbf38b19b0546c0660505823f99f81
Merge: 8f33aaeb1 4e284a627
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Apr 26 12:54:12 2018 -0700

    Merge pull request #252 from AMReX-Codes/pgi
    
    fix PGI compilation

commit 4e284a6272eabb85b7f3d67f20b4ba6eeeda0fa1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Apr 26 15:45:29 2018 -0400

    fix PGI compilation
    PGI complains that with the 'pure' keyword here:
    
    PGF90-S-0074-Illegal number or type of arguments to heapsort_indirect_d - arguments of greater_d and cmp do not agree (/home/zingale/development/AMReX//Src/F_BaseLib/knapsack.f90: 85)

Src/F_BaseLib/knapsack.f90

commit 8f33aaeb1c01bcb33e4c95065cc84a0b16f66955
Merge: c593af9bc 4a706af6b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Apr 26 12:16:23 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit c593af9bc91ebe072c50b87f7fa9f6d72fd317e5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Apr 26 12:14:48 2018 -0700

    Remove unused variables

Src/GeometryShop/AMReX_GeometryShop.cpp

commit 0f00c9297ba46a38ed5279281142c6198d7b31f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 26 11:12:28 2018 -0700

    optimization in YAFluxRegister::define

Src/Boundary/AMReX_YAFluxRegister.cpp

commit 55ffef4deec4abdbece86282e488d2060fc1c7c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 26 11:10:04 2018 -0700

    inline most of IntVect and Box functions

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IndexType.cpp
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp

commit 4a706af6b9899688636480ed77e34b0b8972cea7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 25 22:13:20 2018 -0700

    when BoxArray is cell-centered and its coarse ratio is 1, use the internal Box data directly

Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.H

commit 6e49518b33a37173710dc20673a2b4b5ba08014a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 25 16:41:46 2018 -0700

    add Tests/complementIn

Src/Base/AMReX_VisMF.cpp
Tests/complementIn/GNUmakefile
Tests/complementIn/Make.package
Tests/complementIn/grids/grids_1
Tests/complementIn/grids/grids_10.REMOVED.git-id
Tests/complementIn/grids/grids_2
Tests/complementIn/grids/grids_3.REMOVED.git-id
Tests/complementIn/grids/grids_4.REMOVED.git-id
Tests/complementIn/grids/grids_5.REMOVED.git-id
Tests/complementIn/grids/grids_6
Tests/complementIn/grids/grids_7
Tests/complementIn/grids/grids_8.REMOVED.git-id
Tests/complementIn/grids/grids_9.REMOVED.git-id
Tests/complementIn/main.cpp

commit 1f0eaa1e02265c7de5c81e3ea450e845c838408e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 25 16:09:07 2018 -0700

    replace sed with perl here.

Tools/GNUMake/Make.rules

commit be745eae5ad103f0962d994f61fae1298af791f8
Merge: 5c480e9bf 24172ad26
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Apr 25 15:40:19 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 5c480e9bfc838413f349ecd95730d084acc264a3
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Apr 25 15:40:08 2018 -0700

    add this newline in a way that works with OS X sed.

Tools/GNUMake/Make.rules

commit 24172ad260b8507804d0ab7f38f4fb8160f39087
Merge: 5c4dd86bc 2be6da208
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 25 15:13:08 2018 -0700

    Merge branch 'development' into weiqun/complementIn

commit 5c4dd86bcf16d6d438b376ea12822abb4238615a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 25 13:53:42 2018 -0700

    fix assertion

Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.cpp

commit e72d4948e6c8c6142551a24b599dc70bf0f83589
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 25 13:37:22 2018 -0700

    more optimization on using complementIn

Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxDomain.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit 2249ef43881df679098a6170fc8ecbc9eb810b26
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 25 13:03:30 2018 -0700

    optimization of BoxList::complementIn

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.cpp

commit 2be6da2084ffdbd57bdb92b367a87025a1a4e2bf
Merge: 3f165e315 51b00bfce
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Apr 25 11:23:47 2018 -0700

    Merge branch 'mr/cmake' into development

commit 3f165e3155585a9ca0e766f0a7546f536eccc9b2
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Apr 25 10:39:51 2018 -0700

    remove the newline here, as Mac's sed doesn't like it.

Tools/GNUMake/Make.rules

commit 46bec5fdc3bcdcb844e73ff493fb68ab15c59887
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Apr 25 10:22:48 2018 -0700

    include missing header in AMReX_IntVect.H

Src/Base/AMReX_IntVect.H

commit 4f057ac5e202c8474400f95feb6749d7cb8346a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 24 14:57:10 2018 -0700

    profiling BoxList::complementIn

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_BoxList.cpp

commit 51b00bfcec6a3c75d43ae65a735f060f2419c057
Merge: d7d43c81b 84cf40057
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Apr 24 11:35:28 2018 -0700

    Merge branch 'development' into mr/cmake

commit d7d43c81bdc4a0471c8b8e6a83fd590e01761611
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Apr 24 11:30:27 2018 -0700

    CMake:update docs

Docs/sphinx_documentation/source/BuildingAMReX.rst
Tools/CMake/AMReX_Config.cmake

commit f3a40411c6b22891c8505f769ca44ea2e758dad9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 24 11:06:51 2018 -0700

    BoxList::complementIn calls BoxArray::complementIn

Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp

commit 84cf40057d4823790728b61067f78e5714038194
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 24 07:46:49 2018 -0700

    fix typos

Src/Base/AMReX_MultiFab.cpp

commit cbd493790f09f43482a7809d33220528ecd779c0
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Apr 23 22:04:56 2018 -0700

    Initialize fab ptr array with nullptr, allowing safe call to delete whether or not data allocated, then remove FabArray::ok() test in AmrData::FlushGrids, allowing FlushGrids to clear fabs even if not allocated. Add AmrData::FlushGrids() function to clear all variables.

Src/Base/AMReX_FabArray.H
Src/Extern/amrdata/AMReX_AmrData.H
Src/Extern/amrdata/AMReX_AmrData.cpp

commit c4acf5c4eaeb68266e84716c17c93821a39784f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 23 17:08:30 2018 -0700

    add some functions in MultiFab to deal with IntVect ghost cells

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit b37309aa6c4f7e1a16029ca83c2ce2260407ebf9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 23 13:24:23 2018 -0700

    add some profilers

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit 91c2de675846b5c07d1a73936f04bce76f15538e
Merge: 7dceef395 cc8ff1541
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 23 13:21:14 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 7dceef395e96001d4041a882cc354a2ac9b7c7b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 23 13:20:50 2018 -0700

    BoxList::reserve is bad if it is used in a loop!

Src/Base/AMReX_BoxList.cpp

commit cc8ff1541f7c1db41f2ce99c9ad2bc3d8c959d68
Merge: bfb64b22d b6152ed6e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 23 11:27:39 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit bfb64b22d5bb4abf1a6d98b22f3ad79011eb9f58
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 23 11:23:16 2018 -0700

    refactor the CreateVirtualParticles code so that we don't create the buffer if we're not doing Cell aggregation.

Src/Particle/AMReX_ParticleContainerI.H

commit 20cf608bdf77d92b01e6c7d0daf8dabf494dd5c9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 23 10:53:52 2018 -0700

    use a C++-style cast here.

Src/Particle/AMReX_ParticleContainerI.H

commit b6152ed6ec2fcfbce1f7b20b7b09a035f6fe793b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 21 18:38:47 2018 -0700

    add --enable-xsdk-defaults to configure

Tools/GNUMake/Make.defs
Tools/libamrex/configure.py

commit cca6e695d7e8da8da0eb2242bfdd051cbce7362e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 21 18:02:08 2018 -0700

    some amrex prefix in EB

Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_IrregNode.cpp
Src/GeometryShop/AMReX_NormalDerivative.cpp
Src/GeometryShop/AMReX_SmoothIntersection.cpp
Src/GeometryShop/AMReX_TransformIF.cpp
Tutorials/EB/CNS/Exec/Combustor/bc_fill_nd.F90
Tutorials/EB/CNS/Source/CNS_setup.cpp
Tutorials/EB/CNS/Source/fortran/bc_fill_nd.F90

commit e5612a8b5b78580d87c92f7b857b4c3ba3d3735e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 21 17:37:13 2018 -0700

    do not build with unused old particles fortran routines

Src/Particle/AMReX_Particles_1D.F
Src/Particle/AMReX_Particles_2D.F
Src/Particle/AMReX_Particles_3D.F
Src/Particle/AMReX_Particles_F.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 0dca11b1eaec148a7360fd5635638590b3930abc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 21 17:25:59 2018 -0700

    AMREX_XSDK: Particle/

Src/Particle/AMReX_LoadBalanceKD.H
Src/Particle/AMReX_LoadBalanceKD.cpp
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_Particles_F.H

commit aec8f767eccdcb41402fafbe9a18ef04ce1be6f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 21 15:55:03 2018 -0700

    AMREX_XSDK: C_CellMG/

Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp

commit 3426ac8a55aa09f6eea912d879c5fef251e34f41
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 21 15:31:29 2018 -0700

    some amrex_ in LinearSovlers/

Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp

commit d60e747c946a165524eb2e32567d3499d999e012
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 21 14:34:52 2018 -0700

    AMREX_XSDK: Boundary/

Src/Base/AMReX_BaseFab.H
Src/Boundary/AMReX_INTERPBNDRYDATA_F.H
Src/Boundary/AMReX_LO_BCTYPES.H
Src/Boundary/AMReX_MacBndry.cpp
Src/Boundary/AMReX_Mask.cpp
Src/Boundary/AMReX_YAFluxRegister.H

commit 5aa658395d43cebd624b9f5a3a902920de9dca01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 21 14:04:54 2018 -0700

    amrex prefix in Amr/

Src/Amr/AMReX_Extrapolater.cpp
Src/Amr/AMReX_extrapolater_1d.f90
Src/Amr/AMReX_extrapolater_2d.f90
Src/Amr/AMReX_extrapolater_3d.f90

commit 50d17203ec9f3ac59125862d5fab3b6af985af24
Merge: a292478ca 998fa4b8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 21 10:48:48 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a292478ca0999bdcf6281e467e77f838ae9750dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 21 10:47:09 2018 -0700

    Merge branch 'weiqun/ng' into development

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/AmrTask/AMFIter/AMReX_AmrTask.H
Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H
Src/AmrTask/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp
Src/Base/AMReX_iMultiFab.cpp
Tools/CompileTesting/compiletesting.py

commit d5941f43735ff34105493a1177171c4baf3f643e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 20 17:37:41 2018 -0700

    CMake:generate AMReX_BuildInfo.cpp and include it in the build

Src/CMakeLists.txt
Tools/CMake/AMReX_CMakeVariables.cmake

commit b9fe4044cf2f5dd37bedb19bc5aab28f7daf2fbc
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 20 15:56:04 2018 -0700

    CMake:fix CMakeLists bugs

Src/LinearSolvers/CMakeLists.txt

commit b875ca3c4e1e2ec6167d7b1ec0d71d351d55188e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Apr 20 18:46:10 2018 -0400

    Sync up Titan build properties for CUDA

Tools/GNUMake/sites/Make.olcf

commit 684a5c976a1cc2335df457c590f04287f4aa495e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Apr 20 18:45:52 2018 -0400

    Guard against using CUDA 8 when unavailable

Src/Base/AMReX_Device.cpp

commit 998fa4b8fe7af1e19cf907e0694d27c47613b954
Merge: 278372d20 be65e9bca
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Apr 20 15:27:17 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 278372d204fe28309c873f9444466a2338e12e18
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Apr 20 15:09:47 2018 -0700

    be more conservative with writing output files in this tutorial by default.

Tutorials/Particles/ElectrostaticPIC/inputs
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit be65e9bcab84d79bbe90fe5cbd1440772230e258
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 20 14:53:46 2018 -0700

    for typecheck

Src/Boundary/AMReX_INTERPBNDRYDATA_F.H

commit 0c23a180e0bbeca75e7efada8be885fb38c33303
Merge: b74bf24b5 d06d4d5d8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Apr 20 14:00:41 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit b74bf24b5eef19b2168420b588c17706b3b11b93
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Apr 20 14:00:12 2018 -0700

    Move distribution.h to distribution_c.h

Src/Extern/SWFFT/Distribution.H
Src/Extern/SWFFT/Make.package
Src/Extern/SWFFT/distribution.c
Src/Extern/SWFFT/distribution_c.h

commit 2ec5aadd06d0e05b09b11dd33e5ed9d3dc1d2881
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 20 11:14:43 2018 -0700

    fix makefile

Src/LinearSolvers/MLMG/Make.package

commit eed135499fca90721a8fa016b46b419ad37084ed
Merge: cb4eefd2b d06d4d5d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 20 11:11:22 2018 -0700

    Merge branch 'development' into weiqun/mlmg

commit d06d4d5d8ac92626d122f75ee1a52986be5942d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 20 11:04:03 2018 -0700

    AMREX_CRSEGRNDOMP

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.cpp
Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp
Tutorials/EB/CNS/Exec/Make.CNS

commit 06d1947aa2736d08be7bf43319eb0a347be0c18b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 20 10:54:11 2018 -0700

    minor

Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_StateData.cpp

commit 6a74d10946aa6f6e694d436f56b6f3f7109b9509
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Apr 20 10:44:39 2018 -0700

    CMake:more xSDK stuff

Src/CMakeLists.txt
Src/F_BaseLib/CMakeLists.txt
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake

commit 75f3354c4eacbd313970d272c1f163f2ca1efb09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 20 10:30:34 2018 -0700

    add anonymous namespace to some file scope classes

Src/AmrCore/AMReX_Cluster.cpp

commit 3462a70a2079f6eacfabe38066b2bae6afee365d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 20 09:57:53 2018 -0700

    use amrex_bc_types_module instead of AMReX_bc_types.fi

Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90

commit bbc2443ec55722d9498e32d5ea6a2f8281efbfdc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 20 09:35:51 2018 -0700

    remove some old tutorials

OldTutorials/GettingStarted_C/GNUmakefile
OldTutorials/GettingStarted_C/Make.package
OldTutorials/GettingStarted_C/main.cpp
OldTutorials/GettingStarted_C/work_on_data_2d.f90
OldTutorials/GettingStarted_C/work_on_data_3d.f90
OldTutorials/HeatEquation_EX2_C/FILCC_2D.F
OldTutorials/HeatEquation_EX2_C/FILCC_3D.F
OldTutorials/HeatEquation_EX2_C/GNUmakefile
OldTutorials/HeatEquation_EX2_C/Make.package
OldTutorials/HeatEquation_EX2_C/advance_2d.f90
OldTutorials/HeatEquation_EX2_C/advance_3d.f90
OldTutorials/HeatEquation_EX2_C/bc_fill_nd.F90
OldTutorials/HeatEquation_EX2_C/init_phi_2d.f90
OldTutorials/HeatEquation_EX2_C/init_phi_3d.f90
OldTutorials/HeatEquation_EX2_C/inputs_2d
OldTutorials/HeatEquation_EX2_C/inputs_3d
OldTutorials/HeatEquation_EX2_C/main.cpp
OldTutorials/HeatEquation_EX2_C/myfunc_F.H
OldTutorials/HeatEquation_EX2_C/writePlotFile.H
OldTutorials/HeatEquation_EX2_C/writePlotFile.cpp

commit 3b36d61676bab94bdaa9a7959479377b4c5f2d49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 20 09:30:42 2018 -0700

    add AMREX_

Src/Extern/ProfParser/AMReX_AVGDOWN_2D.F
Src/Extern/ProfParser/AMReX_AVGDOWN_3D.F
Src/Extern/amrdata/AMReX_FABUTIL_1D.F
Src/Extern/amrdata/AMReX_FABUTIL_2D.F
Src/Extern/amrdata/AMReX_FABUTIL_3D.F
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit cb4eefd2b2e52a2104bbc0013999e07e2d0dbacc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 20 09:04:17 2018 -0700

    start MLEBABecLap

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H
Src/LinearSolvers/MLMG/Make.package

commit e3fce29b7f13caad9bbb4999ae0210de360d6575
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Apr 19 18:00:42 2018 -0700

    Add a simple AmrData-based function to computer (weighted) horizontal averages of plotfile variables.

Tools/Postprocessing/C_Src/HorizontalAvg.cpp

commit fec4515b9c3babfa149f3978b02193c656701e75
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 19 15:03:14 2018 -0700

    CMake:one step closer to xSDK compliance

Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_CompilersFlags.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake

commit e247eeeec946b305dcd6cd98131c0a71c4d0db1e
Merge: 798053448 ec82972ee
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Apr 19 12:40:49 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 79805344862e09165aafe965d9c9caf0a0fe75f0
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Apr 19 12:40:37 2018 -0700

    move these function out of an anonymous namepsace and into a separate file to avoid compiler warnings.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleMPIUtil.H
Src/Particle/AMReX_ParticleMPIUtil.cpp
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 9871bc976c10640cb3a493d421e7482cd9296748
Merge: 50370618e ec82972ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 19 11:36:23 2018 -0700

    Merge branch 'development' into weiqun/mlmg

commit e40b77fd8758312dcf685244079e5ccb86562c97
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Apr 19 11:23:06 2018 -0700

    remove some unused variables from the ElectrostaticPIC particle container

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit ec82972ee8637038d4363088726b2c0f2cdc7f0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 19 11:08:07 2018 -0700

    amrex prefix in LinearSolver/

Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H
Src/LinearSolvers/C_CellMG/AMReX_LO_F.H
Src/LinearSolvers/C_CellMG/AMReX_LP_F.H
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG/AMReX_MG_F.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp
Tests/LinearSolvers/C_CellMG/COEF_F.H
Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit dbe0a8054b7ca2ec561af7d81e5c3999a17f384c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 19 10:49:44 2018 -0700

    amrex prefix in Amr/ and Particle/ etc.

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_Derive.H
Src/Amr/AMReX_StateDescriptor.cpp
Src/Extern/ProfParser/AMReX_AVGDOWN_F.H
Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp
Src/Extern/ProfParser/BLProfParser.y
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp
Src/Particle/AMReX_ParticleContainerI.H
Tests/C_BaseLib/tUMap.cpp
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit f6305f00de331a7f20df05244e721c716bb84767
Merge: efed842b8 e757418ce
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Apr 19 10:42:31 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit efed842b845a5a6cceeed66cc16c8e290b0fbff8
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Apr 19 10:42:19 2018 -0700

    remove the ShortRangeParticles tutorial, as that stuff is all included in the NeighborList tutorial now.

Tutorials/Particles/ShortRangeParticles/GNUmakefile
Tutorials/Particles/ShortRangeParticles/Make.package
Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H
Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp
Tutorials/Particles/ShortRangeParticles/inputs
Tutorials/Particles/ShortRangeParticles/main.cpp
Tutorials/Particles/ShortRangeParticles/short_range_2d.f90
Tutorials/Particles/ShortRangeParticles/short_range_3d.f90
Tutorials/Particles/ShortRangeParticles/short_range_F.H

commit 642918e862c6db52b6fca298d7e6235fdc6e69be
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Apr 19 10:40:46 2018 -0700

    some minor tweaks to the particle documentation.

Docs/sphinx_documentation/source/Chapter8.rst
Docs/sphinx_documentation/source/Particle.rst

commit 3b27adfa731e33e72810a83b7d477dae8369aa9f
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Apr 19 10:40:11 2018 -0700

    add some info about the particle tutorials

Docs/sphinx_tutorials/source/Particles_Tutorial.rst

commit 5b1f39705c11388d3e1d676b59447945bc5fd1ed
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Apr 19 10:39:44 2018 -0700

    fix typo

Docs/sphinx_tutorials/source/Basic_Tutorial.rst

commit 50370618ea1d6eed1bd5dfb6822298ad8d31750a
Merge: 15ef44292 e757418ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 19 10:15:27 2018 -0700

    Merge branch 'development' into weiqun/mlmg

commit e757418cef312638abde00af6d57a82f20eadc12
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 19 09:05:20 2018 -0700

    fix the conflict between macro and enum type

Src/Base/AMReX_BC_TYPES.H
Src/Boundary/AMReX_MacBndry.cpp

commit f09f08278b8be9b6e8715084746c3768a786c437
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 19 08:56:19 2018 -0700

    remove preprocessor directive form AMReX_bc_types.fi

Src/Base/AMReX_bc_types.fi

commit a3864b1c8fdd4fe035318cf0f01e45ed6fb8174c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 18 22:03:50 2018 -0700

    amrex prefix in AmrCore and Boundary

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_ErrorList.H
Src/AmrCore/AMReX_ErrorList.cpp
Src/AmrCore/AMReX_FLUXREG_F.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_INTERP_F.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/Boundary/AMReX_INTERPBNDRYDATA_F.H
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_MacBndry.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrCore/Source/bc_fill_nd.F90

commit 41a963791bf27fa6307eb24259d4cbf4a004dcda
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 18 17:02:23 2018 -0700

    D_DECL --> AMREX_D_DECL

Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp

commit 1fb41c58b5dea58bb122a01e4dd653eb9a401d13
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 18 16:57:23 2018 -0700

    AMREX_XSDK: bc types and filcc

Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BCRec.cpp
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90
Src/Base/AMReX_filcc_mod.F90

commit 36a726cd6e9d367431db17e871d52af32f136bc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 18 14:56:52 2018 -0700

    make sure enum base type is int in BC_TYPES.H

Src/Base/AMReX_BC_TYPES.H

commit 7e0630d3996de76c6bedd4cf231dbec4c60eda15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 18 14:31:30 2018 -0700

    AMREX_XSDK: BC_TYPES.H

Src/Base/AMReX_BCRec.cpp
Src/Base/AMReX_BC_TYPES.H
Src/Base/AMReX_bc_types_mod.F90

commit 7d9cdcc1617d420264693f9826aa029f4a9eb92a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 18 14:06:10 2018 -0700

    add amrex_random and amrex_random_int and AMREX_XSDK old fortran interface to amrex::Random

Src/Base/AMReX_RealVect.cpp
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_fort_mod.F90

commit 6b3ee0ea7cc5bdc0cb839f9c8b2a02fdce40c515
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Apr 18 15:31:52 2018 -0700

    CMake:fix tutorials link issue

Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt

commit f5825a8301498230824012f366cca12bf28ec3bf
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Apr 18 13:05:17 2018 -0700

    CMake:forgot to include Fortran-only defines

Tools/CMake/AMReX_CompilersFlags.cmake

commit 89ab5c57da2594458bf1164b5deed4a483cc38ba
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Apr 18 11:33:05 2018 -0700

    added some const_cast calls so that ParallelContext will continue to compile with old versions of MPI.

Src/Base/AMReX_ParallelContext.cpp

commit 2e4e2f35c23dbdfd24e95ea8c89fa75de501d5e8
Merge: 1e38ab0d4 fe83b6596
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Apr 18 11:16:16 2018 -0700

    Merge pull request #249 from AMReX-Codes/dtg_branch
    
    moment convergence test good to go.

commit fe83b6596b372a752674409632959abe926cc7bb
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Apr 18 11:14:56 2018 -0700

    fixed another test that got broken by an interface change.  Moment convergence test works fine.

Tests/GeometryShop/regression/fabfromif.cpp
Tests/GeometryShop/regression/simplemomentexample.inputs

commit af265ab15b2aa1c4c8e97849348278d8fed6f5d2
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Apr 18 11:11:41 2018 -0700

    CMake: modify how compiler flags are handled

Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_CompilersFlags.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake

commit 1e38ab0d4245b33f4734e953675654923dae58d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 18 11:03:41 2018 -0700

    fix a test

Tests/C_BaseLib/tUMap.cpp

commit 71bed02cf854d6b3a75de1ff49d302bd0212151f
Merge: f505226e8 41ec5f363
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Apr 18 10:54:49 2018 -0700

    Merge branch 'development' into dtg_branch

commit 41ec5f3634ebe7f849077b723f4785d5158fd307
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 18 10:27:17 2018 -0700

    mempool_module --> amrex_mempool_module

Docs/sphinx_documentation/source/Basics.rst
Src/AmrCore/AMReX_FillPatchUtil_2d.F90
Src/AmrCore/AMReX_FillPatchUtil_3d.F90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/slope_2d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/slope_3d.f90
Src/Base/AMReX_mempool_f.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/vector_i.f90
Src/F_Interfaces/Base/AMReX_base_mod.F90
Src/F_Interfaces/Base/AMReX_fab_mod.F90
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_2d/slope_2d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/slope_3d.f90
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/slope_2d.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/slope_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/slope_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/slope_3d.f90
Tutorials/EB/CNS/Source/fortran/CNS_divop.F90
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90

commit 5e61d7726d5a3138778cb7f27d031db1086a83c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 18 10:00:24 2018 -0700

    AMREX_XSDK: filcc

Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90
Tutorials/Basic/HeatEquation_EX2_C/Source/AMReX_FILCC_2D.F
Tutorials/Basic/HeatEquation_EX2_C/Source/AMReX_FILCC_3D.F

commit e9366d8f02bc9ebab7e1defe4f5cdc0f55fcb67b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 17 14:48:01 2018 -0700

    use new ArrayLim macros in Base

Src/Amr/AMReX_AmrLevel.cpp
Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp
Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_COORDSYS_F.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp

commit 9e3ed04897fb938e5e474aa870307badc52f71e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 17 14:34:55 2018 -0700

    FORTRAN_BOXLIB --> AMREX_FORTRAN_BOXLIB; add amrex prefix a BaseFab Fortran functions; add amrex prefix to macros in AMReX_ArrayLim.H.

Src/Base/AMReX_Array.H
Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BLassert.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.f90
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_MemPool.cpp
Src/F_BaseLib/backtrace_c.cpp
Tools/F_mk/GMakedefs.mak

commit 520cdbb549e69a683a5cd6a2cf7a45cf3e33d235
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 17 17:28:26 2018 -0700

    put subroutine filcc inside #ifndef AMREX_XSDK

Src/Base/AMReX_BLBoxLib_F.F90
Src/Base/AMReX_BLProfiler_F.F90
Src/Base/AMReX_BLutil_F.F90
Src/Base/AMReX_BaseUmap_f.H
Src/Base/AMReX_BaseUmap_nd.f90
Src/Base/AMReX_FILCC_1D.F90

commit 07cacb033b6be749d5e5a33d8c18ff11a4d6e9aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 17 17:08:19 2018 -0700

    add missing std::

Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit 64e3f3a858a3935f0ed236dafb3c555acfa8e26b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 17 16:23:10 2018 -0700

    D_* -> AMREX_D_* macros in Base/

Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_SPACE.H
Src/Base/AMReX_SPMD.H
Src/Base/AMReX_SPMDI.H
Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp

commit 663add137c7d93aee146020cb9262dd38d8a9331
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 17 15:54:43 2018 -0700

    put some variables inside #ifndef AMREX_XSDK

Src/Base/AMReX_CONSTANTS.H
Src/Base/AMReX_REAL.H
Src/Base/AMReX_bc_types.fi
Src/Base/AMReX_bc_types_mod.F90

commit e5ae46f10b158f9b2ebcbcbbf43509fea25fb287
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 17 15:43:12 2018 -0700

    more namespace/prefix changes in Base/

Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BaseUmap_f.H
Src/Base/AMReX_PhysBCFunct.H
Tests/ProfTests/ThirdParty/Source/main.cpp

commit 7b23a2b540e1ebf563fd74cef785189974a0e3dd
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Apr 17 17:13:41 2018 -0700

    fillNodalMultifab: allignment factor could be ratio => int -> Real

Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp

commit f505226e86d597891c25998672077c2a05f02a03
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Apr 17 17:04:03 2018 -0700

    added moment convergence test.

Tests/GeometryShop/regression/GNUmakefile
Tests/GeometryShop/regression/momentConvTest.cpp
Tests/GeometryShop/regression/momentconvtest.inputs

commit 45b42236b2713e8baef0dde9f4d5d24e6ee65777
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 17 11:09:47 2018 -0700

    amrex prefix for include guards

Src/AmrCore/AMReX_AmrParGDB.H
Src/Boundary/AMReX_InterpBndryData.H
Src/GeometryShop/AMReX_AggStencil.H
Src/GeometryShop/AMReX_AggStencilI.H
Src/GeometryShop/AMReX_AllRegularService.H
Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H
Src/GeometryShop/AMReX_AnisotropicIF.H
Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_BaseEBCellFABI.H
Src/GeometryShop/AMReX_BaseEBCellFactory.H
Src/GeometryShop/AMReX_BaseEBFaceFAB.H
Src/GeometryShop/AMReX_BaseEBFaceFABI.H
Src/GeometryShop/AMReX_BaseIF.H
Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/AMReX_CH_EBIS_ORDER.H
Src/GeometryShop/AMReX_CellEdge.H
Src/GeometryShop/AMReX_ComplementIF.H
Src/GeometryShop/AMReX_ConstrainedLS.H
Src/GeometryShop/AMReX_CoordinateSystem.H
Src/GeometryShop/AMReX_CoordinateSystemImplem.H
Src/GeometryShop/AMReX_CutCellMoments.H
Src/GeometryShop/AMReX_CutCellMomentsImplem.H
Src/GeometryShop/AMReX_DivNormalRefinement.H
Src/GeometryShop/AMReX_DivNormalRefinementImplem.H
Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBCellFAB.H
Src/GeometryShop/AMReX_EBCellFactory.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBDataVarMacros.H
Src/GeometryShop/AMReX_EBDebugDump.H
Src/GeometryShop/AMReX_EBDebugOut.H
Src/GeometryShop/AMReX_EBFaceFAB.H
Src/GeometryShop/AMReX_EBFluxFAB.H
Src/GeometryShop/AMReX_EBFluxFactory.H
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBISBox.H
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBLevelGrid.H
Src/GeometryShop/AMReX_EBLevelRedist.H
Src/GeometryShop/AMReX_EBLoHiCenter.H
Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H
Src/GeometryShop/AMReX_EB_TYPEDEFS.H
Src/GeometryShop/AMReX_EllipsoidIF.H
Src/GeometryShop/AMReX_ExtrudeIF.H
Src/GeometryShop/AMReX_FabArrayIO.H
Src/GeometryShop/AMReX_FaceIndex.H
Src/GeometryShop/AMReX_FaceIterator.H
Src/GeometryShop/AMReX_Factorial.H
Src/GeometryShop/AMReX_FixedRefinement.H
Src/GeometryShop/AMReX_FixedRefinementImplem.H
Src/GeometryShop/AMReX_FlatPlateGeom.H
Src/GeometryShop/AMReX_GenericArithmetic.H
Src/GeometryShop/AMReX_GenericArithmeticI.H
Src/GeometryShop/AMReX_GeomIntersectUtils.H
Src/GeometryShop/AMReX_GeometryService.H
Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GraphNode.H
Src/GeometryShop/AMReX_IFData.H
Src/GeometryShop/AMReX_IFDataImplem.H
Src/GeometryShop/AMReX_IFSlicer.H
Src/GeometryShop/AMReX_IFSlicerImplem.H
Src/GeometryShop/AMReX_IndexTM.H
Src/GeometryShop/AMReX_IndexTMI.H
Src/GeometryShop/AMReX_IndexedMoments.H
Src/GeometryShop/AMReX_IntVectSet.H
Src/GeometryShop/AMReX_IntersectionIF.H
Src/GeometryShop/AMReX_IrregFAB.H
Src/GeometryShop/AMReX_IrregFABFactory.H
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_KDStruct.H
Src/GeometryShop/AMReX_KDTree.H
Src/GeometryShop/AMReX_LSProblem.H
Src/GeometryShop/AMReX_LSProblemImplem.H
Src/GeometryShop/AMReX_LSquares.H
Src/GeometryShop/AMReX_LatheIF.H
Src/GeometryShop/AMReX_LoHiSide.H
Src/GeometryShop/AMReX_MetaPrograms.H
Src/GeometryShop/AMReX_MinimalCCCM.H
Src/GeometryShop/AMReX_MinimalCCCMImplem.H
Src/GeometryShop/AMReX_MomentIterator.H
Src/GeometryShop/AMReX_MomentIteratorImplem.H
Src/GeometryShop/AMReX_Moments.H
Src/GeometryShop/AMReX_MonomialPowers.H
Src/GeometryShop/AMReX_MultiIndex.H
Src/GeometryShop/AMReX_MultiIndexImplem.H
Src/GeometryShop/AMReX_NoRefinement.H
Src/GeometryShop/AMReX_NoRefinementImplem.H
Src/GeometryShop/AMReX_NormalDerivative.H
Src/GeometryShop/AMReX_NormalDerivativeNew.H
Src/GeometryShop/AMReX_Notation.H
Src/GeometryShop/AMReX_PXStuff.H
Src/GeometryShop/AMReX_PlaneIF.H
Src/GeometryShop/AMReX_PolyGeom.H
Src/GeometryShop/AMReX_PolynomialIF.H
Src/GeometryShop/AMReX_RedistStencil.H
Src/GeometryShop/AMReX_RefinementCriterion.H
Src/GeometryShop/AMReX_STLAsciiReader.H
Src/GeometryShop/AMReX_STLBox.H
Src/GeometryShop/AMReX_STLExplorer.H
Src/GeometryShop/AMReX_STLIF.H
Src/GeometryShop/AMReX_STLMesh.H
Src/GeometryShop/AMReX_STLReader.H
Src/GeometryShop/AMReX_STLUtil.H
Src/GeometryShop/AMReX_SmoothAbsoluteValue.H
Src/GeometryShop/AMReX_SmoothIntersection.H
Src/GeometryShop/AMReX_SmoothUnion.H
Src/GeometryShop/AMReX_SphereIF.H
Src/GeometryShop/AMReX_Stencils.H
Src/GeometryShop/AMReX_TransformIF.H
Src/GeometryShop/AMReX_UnionIF.H
Src/GeometryShop/AMReX_VoFIterator.H
Src/GeometryShop/AMReX_VolIndex.H
Src/GeometryShop/AMReX_WrappedGShop.H
Src/GeometryShop/AMReX_ZCylinder.H
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H
Src/LinearSolvers/C_CellMG/AMReX_LO_F.H
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_MG_F.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H
Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H
Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/AMReX_stencil_types.H
Tools/GNUMake/Make.defs

commit 04a5ec117c6d019c97a86ed5149b424576b17a58
Merge: 58007fb15 bdd541481
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Apr 17 12:36:51 2018 -0700

    Merge pull request #248 from AMReX-Codes/dtg_branch
    
    adding simple higher order moments example

commit bdd541481d2fddfaecdb0cb81fb19e0b124dba83
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Apr 17 12:34:43 2018 -0700

    added simple example that illustrates moment stuff.  I also fixed a test whose interface had moved out from under it.

Tests/GeometryShop/regression/GNUmakefile
Tests/GeometryShop/regression/fabfromif.cpp
Tests/GeometryShop/regression/momentConvTest.cpp
Tests/GeometryShop/regression/simpleMomentExample.cpp
Tests/GeometryShop/regression/simplemomentexample.inputs
Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp

commit 383e49af11616262120f7c8b9d459e207c73a1cb
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Apr 17 11:48:06 2018 -0700

    CMake:start implementation of xSDK guidelines

Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake

commit 58007fb1590a4607d25a911890145a3d655f44a3
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Apr 17 11:40:52 2018 -0700

    allow the passing of a number of ghost cells when constructing the redistribute mask

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 652a065d4545bb442325f2a8fd2403f809e457cb
Merge: 8ff0aa628 bc6f821d1
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Apr 16 18:03:48 2018 -0700

    Merge remote-tracking branch 'origin/development' into jpb/fill-nodal

commit 8ff0aa628c7ac6441ca2e96eec5441890643a459
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Apr 16 18:03:14 2018 -0700

    allow filling nodal MF with different refinement than EBIndexSpace's dx

Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp

commit 75d157ac30833ef9719105cc668abd6477f875e8
Author: shashankNREL <shashank.yellapantula@nrel.gov>
Date:   Mon Apr 16 14:05:12 2018 -0600

    Modification of MLMG to use IJ matrix interface

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/GNUmakefile
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit bc6f821d1e7d89e324cfcc965a85d7b514930ab8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 16 10:25:01 2018 -0700

    restore previous exception trap status in amrex::Finalize

Src/Base/AMReX.cpp

commit 8cbe08bcc99b67b5bfad0004c4ffe56381556e93
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 16 09:51:09 2018 -0700

    add amrex.call_addr2line parameter so that the call to add2rline can be skipped

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_BLBackTrace.cpp

commit 71f9c712640e142d1eba2559f7b05d8ae4ed851a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 16 09:15:07 2018 -0700

    move SIG_DFL to the beginning of handler

Src/Base/AMReX_BLBackTrace.cpp

commit 184fba0260e4b067bec73f28d9422e5837bb5ef5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 15 13:31:41 2018 -0700

    add a Fortran module for ParallelDescriptor

Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ParallelDescriptor_F.F90
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 6a3d6c1a211ea794b777b681e9723c1225539d33
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Apr 14 13:15:23 2018 -0400

    simple script to report git describe/hashes

Tools/C_scripts/describe_sources.py

commit 51452f005e31fe1479fdc50c2a3deee9e0e262e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 12 17:58:13 2018 -0700

    This is weird.  GCC 7 with certain combination of flags requires explicitly defining these std::allocator's otherwise it fails at link time.  Note that we have seen this before.

Src/Base/AMReX.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_ParallelReduce.H
Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp

commit 28579a4768cfc6c7eb4bd9f0d0d49023b7a21d83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 12 17:38:01 2018 -0700

    Comment out everything in Make.local.template.  It was meant just to show things that can be done in Make.local, not meant for people to simply copy it to Make.local

Tools/GNUMake/Make.local.template

commit 71d0fcd2cde8d32e3e731b0fc5e2754c26cdaf54
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 12 17:06:21 2018 -0700

    CMake: fix bug in site recognition

Tools/CMake/AMReX_Machines.cmake
Tools/CMake/AMReX_ThirdPartyProfilers.cmake

commit 500da205bde2914564c0b359b543acf797074b65
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 12 15:41:10 2018 -0700

    CMake: add support for third party profiler tools

Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Machines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_ThirdPartyProfilers.cmake

commit 0e9e805bf66f1be4222c242a1ae110afddfe5211
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 12 14:22:23 2018 -0700

    CMake: add host infos and third party profiling options

Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Machines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_Utils.cmake

commit 4e750b6e89620f34ca96206fe88b1cd95381d321
Merge: 1f1f3033a b3569b6ca
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 12 10:41:56 2018 -0700

    Merge branch 'development' into mr-cmake

commit 1f1f3033aa1a217a4d164491e81f79460bdac02f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 12 10:40:10 2018 -0700

    CMake: turn off verbosity by default

CMakeLists.txt

commit 61b2b7ef745645f642342c0c0254a0a1983fdaef
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Apr 12 10:30:37 2018 -0700

    CMake: slightly modify setup

CMakeLists.txt
Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Compilers.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_Utils.cmake
Tools/CMake/AMReX_Version.cmake

commit 4d494f132f175e23434692118778cdb916ea8a69
Author: shashankNREL <shashank.yellapantula@nrel.gov>
Date:   Thu Apr 12 10:44:23 2018 -0600

    Removed some additional unused variables

Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp

commit 93c38f58cc43736d8fec7331edae99e6acb326fd
Author: shashankNREL <shashank.yellapantula@nrel.gov>
Date:   Thu Apr 12 10:39:48 2018 -0600

    Optimized the IJ matrix interface

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H

commit b3569b6ca8c956562bfc94cf154c6badb545a685
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 12 08:36:26 2018 -0700

    fix AMREX_DIMENSION_AGNOSTIC

Tools/GNUMake/Make.defs

commit e655c8853aaa3ee890a3a90b3bc8f8807d52c8e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 11 16:53:23 2018 -0700

    add AMREX_NO_STRICT_PREFIX

Tools/CMake/AMReX_Defines.cmake
Tools/GNUMake/Make.defs

commit 84603a9fbf1a7bfd1ec8da77edae3e9c007fb61f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 11 16:05:27 2018 -0700

    update cmake for AMREX_DEBUG and AMREX_PARTICLES

Tools/CMake/AMReX_Defines.cmake

commit 2ea89c5fad5110be8c52f17b3e6828fb1240bd72
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 11 15:41:07 2018 -0700

    DEBUG --> AMREX_DEBUG

Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabArrayCommI.H
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_NFiles.cpp
Src/Extern/ProfParser/AMReX_BLProfStats.cpp
Tools/GNUMake/Make.defs

commit c4657f5c16db2baf4d430a704d691fe52a003b15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 11 13:37:03 2018 -0700

    DIMENSION_AGNOSTIC --> AMREX_DIMENSION_AGNOSTIC

Src/Amr/AMReX_Amr.cpp
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Tools/GNUMake/Make.defs

commit fda52fd558d9057946c05662cbf8df7cb52590c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 11 13:32:27 2018 -0700

    add AMREX_ version of BL_* definitions

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 7bb879c66325d7587a0543c10865bddd7f1bc6d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 11 12:59:39 2018 -0700

    USE_CVODE --> AMREX_USE_CVODE

Tools/GNUMake/packages/Make.cvode

commit 2a07007b783479e7eb667e020eb446b85bd6ef2b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 11 11:38:29 2018 -0700

    PARTICLES and USE_PARTICLES --> AMREX_PARTICLES

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.H
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Src/Particle/AMReX_NeighborParticles.H
Tools/GNUMake/Make.defs
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit e998f2c3335072c70b97d703b5d8278e9c71ea5a
Author: kngott <kngott@lbl.gov>
Date:   Wed Apr 11 14:23:15 2018 -0700

    Adjust third party profiling macros to 'AMREX_name'.

Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_ThirdPartyProfiling.H
Tools/GNUMake/Make.defs
Tools/GNUMake/tools/Make.craypat
Tools/GNUMake/tools/Make.forge
Tools/GNUMake/tools/Make.vtune

commit 75a2ed4332947a199c40c4a0719d09455ca27d53
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Apr 9 17:54:33 2018 -0700

    Add link to original SWFFT source code

Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst

commit 4c2aee4f01bf9f1010dbcdd967ceef902fa29f9c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Apr 9 17:50:44 2018 -0700

    Update the sample inputs files in Tutorials/SWFFT.

Tutorials/SWFFT/inputs.128
Tutorials/SWFFT/inputs.32
Tutorials/SWFFT/inputs.64
Tutorials/SWFFT/run_me
Tutorials/SWFFT/swfft_solver.cpp

commit 711267d4fd57e5dc420a4aff3cb9efc39a64fbe9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Apr 9 17:19:04 2018 -0700

    Adding source code for SWFFT so that the Tutorial can run.

Src/Extern/SWFFT/AlignedAllocator.h
Src/Extern/SWFFT/COPYING
Src/Extern/SWFFT/CheckDecomposition.c
Src/Extern/SWFFT/Dfft.H
Src/Extern/SWFFT/DfftC.cpp
Src/Extern/SWFFT/Distribution.H
Src/Extern/SWFFT/DistributionC.cpp
Src/Extern/SWFFT/Error.h
Src/Extern/SWFFT/Make.package
Src/Extern/SWFFT/README
Src/Extern/SWFFT/TimingStats.h
Src/Extern/SWFFT/complex-type.h
Src/Extern/SWFFT/distribution.c
Src/Extern/SWFFT/distribution.h

commit 9bfb66072250f7d4437f1837c802c1d6b2a5a86c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Apr 9 16:54:21 2018 -0700

    Update SWFFT Tutorial.

Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst

commit d67d9b553e9a58c4ba97856fce051fef00704fe1
Merge: ad727db71 9aa110e60
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Apr 9 16:16:30 2018 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit ad727db71dc2ad40b587fb93401c2f3594e3421e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Apr 9 16:16:03 2018 -0400

    fextrema was a little misleading, since it was not giving the
    extrema over the whole domain.  Now it does by looping over all
    levels

Tools/Postprocessing/F_Src/fextrema.f90

commit d86b7cda29ac456b6fc9c3a7a8489cff490c4f26
Merge: 2760c709c 8ad6f6d2b
Author: shashankNREL <shashank.yellapantula@nrel.gov>
Date:   Mon Apr 9 12:52:08 2018 -0600

    Added the IJ solver call to amrex_hypre.cpp

commit 9aa110e601dc8c801467eb666f497013a4554ed7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 9 11:33:43 2018 -0700

    Remove FORTH from AMReX_CONSTANTS.H as well.

Src/Base/AMReX_CONSTANTS.H

commit 2760c709ce4fc13158dbb157f548efe2b8539349
Author: shashankNREL <shashank.yellapantula@nrel.gov>
Date:   Mon Apr 9 12:02:02 2018 -0600

    Moved the HYPRE IJ calls to Fortran; Works well on the HYPRE tutorial case and compares well against the SStruct interface

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_Hypre.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H
Src/Extern/HYPRE/Make.package

commit 980bd79270be24ecfbc8afb1083a8e42ef15aef8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 9 10:33:48 2018 -0700

    replace 'forth' with 'fourth'

Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90

commit 18a4daea42fc1e2e8bca80dffd770ea5e1d64152
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 9 10:25:27 2018 -0700

    remove redundant definition of 1/4 in AMReX_constants_mod.f90

Src/Base/AMReX_constants_mod.f90

commit 1e4671e2d8df61a4fbb1a8ad65e18cdcda2fc1da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 8 18:29:20 2018 -0700

    add Fortran interface to FluxRegister::OverwriteFlux

Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90

commit 4c7886bca1bc998858068c57f90cae279b9ada3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 8 18:00:20 2018 -0700

    add FluxRegister::OverwriteFlux

Src/AmrCore/AMReX_FLUXREG_F.H
Src/AmrCore/AMReX_FLUXREG_nd.F90
Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/CMakeLists.txt
Src/AmrCore/Make.package

commit ef7d5306e4f401345e6d24fb6e967e0e12544506
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 8 09:00:37 2018 -0700

    Link back to documentation

Docs/sphinx_tutorials/source/CVODE_Tutorial.rst

commit 09c908cf7cd511d65e0c7e3a4d73224d9ef629c0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 8 08:42:05 2018 -0700

    Try to fix link.

Docs/sphinx_documentation/source/CVODE.rst

commit 567f6224a46834805ec3ec6e156f29c77f3175a6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 8 08:14:17 2018 -0700

    update link

Docs/sphinx_documentation/source/CVODE.rst

commit ed9d3c6b3e0c22277f681af2e3cb2f70518a8771
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 8 08:06:27 2018 -0700

    Move the CVODE Tutorial description into the Tutorials section

Docs/sphinx_documentation/source/CVODE.rst
Docs/sphinx_tutorials/source/CVODE_Tutorial.rst

commit 5e0903d1e97968c5f9b6aa3d6356b4074d43d5e7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 8 07:54:56 2018 -0700

    Update Basics_Tutorials page

Docs/sphinx_tutorials/source/Basic_Tutorial.rst

commit 53f1cba2d3ebd75842e7705befc3ea8fadbddeb8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Apr 7 18:05:15 2018 -0700

    Start to fill in the Tutorials documentation.

Docs/sphinx_tutorials/source/Basic_Tutorial.rst
Docs/sphinx_tutorials/source/index.rst

commit 52a0e790ef2b65a6e6cdafdad95a4da0e6d907da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 7 16:55:03 2018 -0700

    add mising conf.py

Docs/sphinx_tutorials/source/conf.py

commit 8918e33b1c160de4473e4836477324e7ae75be8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 7 16:38:20 2018 -0700

    rm old ParmParse Fortran

Src/Base/AMReX_BLParmParse_F.F90
Src/Base/AMReX_ParmParse.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 868637034f053480144e04c424fbf88f330db3d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 7 16:32:58 2018 -0700

    rm AMReX_bl_flush.f

Src/Base/AMReX_bl_flush.f

commit 6c26cbcb3e007ab3c29db805bb7bedba2f43be57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 7 16:29:38 2018 -0700

    rm AMReX_SPACE_F.H

Src/Base/AMReX_SPACE_F.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 8a2f08ae5e1bb82a232f5bc5686c7c5978ea9d24
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 7 16:20:35 2018 -0700

    add a wrapper to polyintercoeff for tensormg

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_2D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_3D.F
Src/LinearSolvers/C_TensorMG/Make.package
Src/LinearSolvers/C_TensorMG/amrex_tmg_util.F90

commit 479b9ec61988ece342f93ccf07d817b933df0817
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 7 14:11:21 2018 -0700

    C_CellMG4: .F files to .F90 files

OldTutorials/MultiGrid_C/GNUmakefile
Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F90
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F90
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F90
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F90
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H
Src/LinearSolvers/C_CellMG4/Make.package

commit 873b3c8981fcc68313e4bbe723b15169f1145a3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 7 10:44:46 2018 -0700

    remove AMREX_REAL.H from Fortran 90 files

Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90
Src/Boundary/AMReX_LO_UTIL.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F
Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_2D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_3D.F
Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90

commit 61d5e2762ace8a40821696b3f6b8faf1864129a9
Merge: 76fcd0ec6 bc2e80885
Author: Marc Day <MSDay@lbl.gov>
Date:   Sat Apr 7 15:40:37 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 76fcd0ec64e045f006063e6ac71414ea924d1c83
Author: Marc Day <MSDay@lbl.gov>
Date:   Sat Apr 7 15:40:25 2018 -0700

    Fix bugs in postprocessing codes, add matlab .m script files that can read the output generated by PlotfileToMatLab.cpp

Tools/C_util/WritePlotFile.cpp
Tools/Postprocessing/C_Src/GNUmakefile
Tools/Postprocessing/C_Src/PtwisePltTransform.cpp
Tools/Postprocessing/C_Src/binread.m
Tools/Postprocessing/C_Src/mk2d.m

commit bc2e808856eade1af6c0fb8610441bb4c8bc8c14
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Apr 7 15:18:47 2018 -0700

    Move tutorials.rst to index.rst

Docs/sphinx_tutorials/source/index.rst

commit ecd1c0df870a8c4cd5a35d81a34ce3a3e7e90e6a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Apr 7 15:09:13 2018 -0700

    Try to build tutorials_html separately from docs_html

Docs/sphinx_documentation/Makefile
Docs/sphinx_documentation/source/AMReX_Profiling_Tools.rst
Docs/sphinx_documentation/source/AmrCore.rst
Docs/sphinx_documentation/source/AmrCore/figs/Adv1.pdf
Docs/sphinx_documentation/source/AmrCore/figs/Adv1.png
Docs/sphinx_documentation/source/AmrCore/figs/Adv2.pdf
Docs/sphinx_documentation/source/AmrCore/figs/Adv2.png
Docs/sphinx_documentation/source/AmrCore/figs/Adv3.pdf
Docs/sphinx_documentation/source/AmrCore/figs/Adv3.png
Docs/sphinx_documentation/source/AmrCore/figs/Adv4.pdf
Docs/sphinx_documentation/source/AmrCore/figs/Adv4.png
Docs/sphinx_documentation/source/AmrCore/figs/Adv5.pdf
Docs/sphinx_documentation/source/AmrCore/figs/Adv5.png
Docs/sphinx_documentation/source/AmrCore/figs/flowchart.odg
Docs/sphinx_documentation/source/AmrCore/figs/flowchart.pdf
Docs/sphinx_documentation/source/AmrCore/figs/flowchart.png
Docs/sphinx_documentation/source/AmrCore/figs/subcycling.pdf
Docs/sphinx_documentation/source/AmrCore/figs/subcycling.png
Docs/sphinx_documentation/source/AmrCore/figs/subcycling.tex
Docs/sphinx_documentation/source/AmrLevel.rst
Docs/sphinx_documentation/source/AmrLevel/figs/flowchart.odg
Docs/sphinx_documentation/source/AmrLevel/figs/flowchart.pdf
Docs/sphinx_documentation/source/AmrLevel/figs/flowchart.png
Docs/sphinx_documentation/source/Basics.rst
Docs/sphinx_documentation/source/Basics/amrgrids.pdf
Docs/sphinx_documentation/source/Basics/amrgrids.png
Docs/sphinx_documentation/source/Basics/cc_growbox.pdf
Docs/sphinx_documentation/source/Basics/cc_growbox.png
Docs/sphinx_documentation/source/Basics/cc_tilebox.pdf
Docs/sphinx_documentation/source/Basics/cc_tilebox.png
Docs/sphinx_documentation/source/Basics/cc_validbox.pdf
Docs/sphinx_documentation/source/Basics/cc_validbox.png
Docs/sphinx_documentation/source/Basics/ec_growbox.pdf
Docs/sphinx_documentation/source/Basics/ec_growbox.png
Docs/sphinx_documentation/source/Basics/ec_tilebox.pdf
Docs/sphinx_documentation/source/Basics/ec_tilebox.png
Docs/sphinx_documentation/source/Basics/ec_validbox.pdf
Docs/sphinx_documentation/source/Basics/ec_validbox.png
Docs/sphinx_documentation/source/Basics/figs/flowchart.odg
Docs/sphinx_documentation/source/Basics/figs/flowchart.pdf
Docs/sphinx_documentation/source/Basics/figs/flowchart.png
Docs/sphinx_documentation/source/Basics/indextypes.pdf
Docs/sphinx_documentation/source/Basics/indextypes.png
Docs/sphinx_documentation/source/BuildingAMReX.rst
Docs/sphinx_documentation/source/CVODE.rst
Docs/sphinx_documentation/source/Chapter10.rst
Docs/sphinx_documentation/source/Chapter11.rst
Docs/sphinx_documentation/source/Chapter12.rst
Docs/sphinx_documentation/source/Chapter13.rst
Docs/sphinx_documentation/source/Chapter14.rst
Docs/sphinx_documentation/source/Chapter2.rst
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build_and_deploy.sh

commit 8e47f3e29251589312e5185c9d3046264de328d6
Merge: 8139e2091 1812a7fea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 18:07:00 2018 -0700

    Merge branch 'weiqun/macros' into development

commit 1812a7fea73f4f58b3338c6c22ff89e9810ac747
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 18:00:36 2018 -0700

    expand typedef for typecheck and fix type problems

Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_F.H

commit 0577bc9d03bb44bfafa9d31c730b1e5c475bc58a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 17:56:35 2018 -0700

    rename for typecheck

Src/AmrCore/AMReX_FLUXREG_1D.F90
Src/AmrCore/AMReX_FLUXREG_2D.F90
Src/AmrCore/AMReX_FLUXREG_3D.F90
Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/Base/AMReX_COORDSYS_1D.F90
Src/Base/AMReX_COORDSYS_2D.F90
Src/Base/AMReX_COORDSYS_3D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90

commit 94a8064e3d74fe5df78254016c0c44bdac2debce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 17:38:59 2018 -0700

    break up some really long lines

Src/AmrCore/AMReX_FLUXREG_2D.F90
Src/AmrCore/AMReX_FLUXREG_3D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/Base/AMReX_COORDSYS_3D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90

commit 66ade5775fbb04aa959a213b2f5058e2da671033
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 17:19:01 2018 -0700

    filcc: remove AMReX_REAL.H

Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90

commit d2199e44b782787e5ab6da9bc8076bd30bd635d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 17:03:46 2018 -0700

    linear solver routines: module and c binding

Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H
Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_F.H
Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_F.H
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_F.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp
Src/LinearSolvers/C_CellMG/AMReX_lo_bctypes.fi
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit 8139e209124dbd44355ac65711a20ce2a1ec097c
Merge: 42aa36b7a 79991da77
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Apr 6 16:44:57 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 42aa36b7a592c48e7c9100a786590706c01bb61a
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Apr 6 16:44:49 2018 -0700

    Add a simple AmrData-based post-processing function

Tools/C_util/WritePlotFile.H
Tools/C_util/WritePlotFile.cpp
Tools/Postprocessing/C_Src/GNUmakefile
Tools/Postprocessing/C_Src/Make.package
Tools/Postprocessing/C_Src/PtwisePltTransform.cpp
Tools/Postprocessing/C_Src/PtwisePltTransform_nd.f90

commit 0a26f4eb1457bc19ca9de9c2ad1b5c35a5481541
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 16:02:03 2018 -0700

    put interpbndrydata routine into module and add c binding

Src/Base/AMReX_constants_mod.f90
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_F.H
Src/Boundary/AMReX_InterpBndryData.cpp

commit d96918b892e552e584ee11c8d899d80bba8c4cfa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 14:44:23 2018 -0700

    put coordsys routines into module

Src/Base/AMReX_COORDSYS_1D.F90
Src/Base/AMReX_COORDSYS_2D.F90
Src/Base/AMReX_COORDSYS_3D.F90
Src/Base/AMReX_COORDSYS_F.H
Src/Base/AMReX_CoordSys.cpp

commit af412264f1b6693b1d7fae3ba93429bd25fa2c39
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 14:25:20 2018 -0700

    put interpolation routines into module

Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/AmrCore/AMReX_INTERP_F.H
Src/AmrCore/AMReX_Interpolater.cpp

commit 79991da772b94b7b98ab61c9597fa1708163d826
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 6 14:13:16 2018 -0700

    fix the ParticleContainer::Restart routine to work when levels are lost on restart.'

Src/Particle/AMReX_ParticleContainerI.H

commit b94c0a0b42e6620b6f56b8008bea93c019df8b83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 13:37:17 2018 -0700

    put flux register fortran code into module

Src/AmrCore/AMReX_FLUXREG_1D.F90
Src/AmrCore/AMReX_FLUXREG_2D.F90
Src/AmrCore/AMReX_FLUXREG_3D.F90
Src/AmrCore/AMReX_FLUXREG_F.H
Src/AmrCore/AMReX_FluxRegister.cpp

commit 813e23da8c13d02ec9418dfd4538562910d9ad81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 12:50:42 2018 -0700

    replace DIM[123]

Src/AmrCore/AMReX_INTERP_3D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90

commit f6f9ed6e439b4b3d9c548bcbce660e23e68576d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 12:48:00 2018 -0700

    move ARRAYLIM_?D.F90 to IAMR

Src/Amr/AMReX_ARRAYLIM_1D.F90
Src/Amr/AMReX_ARRAYLIM_2D.F90
Src/Amr/AMReX_ARRAYLIM_3D.F90
Src/Amr/CMakeLists.txt
Src/Amr/Make.package

commit ed14f486efd4126b8c76ce13b1f2bf4809e5cfa7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 11:17:44 2018 -0700

    remove AMReX_ArrayLim.H from F90 files

Src/Amr/AMReX_ARRAYLIM_1D.F90
Src/Amr/AMReX_ARRAYLIM_2D.F90
Src/Amr/AMReX_ARRAYLIM_3D.F90
Src/AmrCore/AMReX_FLUXREG_1D.F90
Src/AmrCore/AMReX_FLUXREG_2D.F90
Src/AmrCore/AMReX_FLUXREG_3D.F90
Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/Base/AMReX_COORDSYS_1D.F90
Src/Base/AMReX_COORDSYS_2D.F90
Src/Base/AMReX_COORDSYS_3D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90

commit e6b6ef5fd918f6ec1da00017a48c469abd2dbe06
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 11:10:21 2018 -0700

    replace ARG_L1, ARG_L2, ... etc.

Src/Amr/AMReX_ARRAYLIM_1D.F90
Src/Amr/AMReX_ARRAYLIM_2D.F90
Src/Amr/AMReX_ARRAYLIM_3D.F90
Src/AmrCore/AMReX_FLUXREG_1D.F90
Src/AmrCore/AMReX_FLUXREG_2D.F90
Src/AmrCore/AMReX_FLUXREG_3D.F90
Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/Base/AMReX_COORDSYS_1D.F90
Src/Base/AMReX_COORDSYS_2D.F90
Src/Base/AMReX_COORDSYS_3D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90

commit 05d0e691479316e3c1bd33a511373d41d9b2911b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 11:04:39 2018 -0700

    replace DIM1, DIM2 and DIM3

Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90

commit c32a81f00ead4d405fde7d1b577dcccfb152f5a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 11:00:10 2018 -0700

    replace DIMV

Src/AmrCore/AMReX_FLUXREG_1D.F90
Src/AmrCore/AMReX_FLUXREG_2D.F90
Src/AmrCore/AMReX_FLUXREG_3D.F90
Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/Base/AMReX_COORDSYS_1D.F90
Src/Base/AMReX_COORDSYS_2D.F90
Src/Base/AMReX_COORDSYS_3D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90

commit e98d6972faf07cfed70bbfd1701ce3362861b299
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 10:55:55 2018 -0700

    replace DIMDEC in F90 files

Src/Amr/AMReX_ARRAYLIM_1D.F90
Src/Amr/AMReX_ARRAYLIM_2D.F90
Src/Amr/AMReX_ARRAYLIM_3D.F90
Src/AmrCore/AMReX_FLUXREG_1D.F90
Src/AmrCore/AMReX_FLUXREG_2D.F90
Src/AmrCore/AMReX_FLUXREG_3D.F90
Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/Base/AMReX_COORDSYS_1D.F90
Src/Base/AMReX_COORDSYS_2D.F90
Src/Base/AMReX_COORDSYS_3D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90

commit 92fa0eddca9fed3901354eb41b7ed28a6d48d461
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 6 10:53:39 2018 -0700

    replace DIMS in F90 files

Src/Amr/AMReX_ARRAYLIM_1D.F90
Src/Amr/AMReX_ARRAYLIM_2D.F90
Src/Amr/AMReX_ARRAYLIM_3D.F90
Src/AmrCore/AMReX_FLUXREG_1D.F90
Src/AmrCore/AMReX_FLUXREG_2D.F90
Src/AmrCore/AMReX_FLUXREG_3D.F90
Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/Base/AMReX_COORDSYS_1D.F90
Src/Base/AMReX_COORDSYS_2D.F90
Src/Base/AMReX_COORDSYS_3D.F90
Src/Base/AMReX_FILCC_3D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90
Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90

commit 87388019d5d85eccaa83accf6150a7fa80fb26e6
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Apr 6 10:52:19 2018 -0700

    Remove commented out code, clean up slightly.

Tools/Postprocessing/C_Src/PlotfileToMatLab.cpp

commit b033d37eec1bf75f2aafe7de98d14a9cab1a4ddf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 5 14:18:25 2018 -0700

    add AMREX prefix to some include guards

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AuxBoundaryData.H
Src/Amr/AMReX_Derive.H
Src/Amr/AMReX_Extrapolater.H
Src/Amr/AMReX_LevelBld.H
Src/Amr/AMReX_PROB_AMR_F.H
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateDescriptor.H
Src/AmrCore/AMReX_Cluster.H
Src/AmrCore/AMReX_ErrorList.H
Src/AmrCore/AMReX_FLUXREG_F.H
Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_INTERP_F.H
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_TagBox.H
Src/AmrTask/AMFIter/AMReX_AmrTask.H
Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H
Src/AmrTask/Amr/AMReX_AmrLevelTask.H
Src/AmrTask/AmrCore/AMReX_FillPatchUtil.H
Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BC_TYPES.H
Src/Base/AMReX_BLBackTrace.H
Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseIndex.H
Src/Base/AMReX_BaseUmap_f.H
Src/Base/AMReX_COORDSYS_F.H
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_Periodicity.H
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_SPMD.H
Src/Base/AMReX_SPMDI.H
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_parstream.H
Src/Boundary/AMReX_BndryData.H
Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BoundCond.H
Src/Boundary/AMReX_FabSet.H
Src/Boundary/AMReX_INTERPBNDRYDATA_F.H
Src/Boundary/AMReX_LO_BCTYPES.H
Src/Boundary/AMReX_MacBndry.H
Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_MultiMask.H
Src/Extern/HYPRE/AMReX_HypreABecLap.H
Src/Extern/HYPRE/AMReX_HypreABec_F.H
Src/Particle/AMReX_ParGDB.H
Src/Particle/AMReX_Particles.H

commit d73c54f48e0b20ff7ae56c7733bb00b3dbbcbcc8
Merge: 521912070 f4043b49e
Author: asalmgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 14:21:27 2018 -0700

    Merge pull request #240 from AMReX-Codes/add_matlab_conv
    
    Add plotfile-to-Matlab converter.

commit 521912070ce405e331f1e4c7820e4393624e55c3
Author: kngott <kngott@lbl.gov>
Date:   Wed Apr 4 12:06:13 2018 -0700

    Adjustment to RStartStop profiling object to reomve padding and eliminate valgrind warning message.

Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BLProfiler.cpp

commit 8ad6f6d2bcdd6db43c2d1b7bcf9584fe6216ef3e
Author: shashankNREL <shashank.yellapantula@nrel.gov>
Date:   Wed Apr 4 12:56:17 2018 -0600

    Added call to the IJ solver in the hypre solver constructor

Src/Extern/HYPRE/AMReX_Hypre.cpp

commit 15ef4429275075c1baf93dca131e434101745583
Merge: e5a862513 9c021357a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 4 09:24:03 2018 -0700

    Merge branch 'development' into weiqun/mlmg

commit f4043b49e564891ac32c60f64b0613579b8335cb
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Apr 3 11:25:43 2018 -0700

    Add plotfile-to-Matlab converter.

Tools/Postprocessing/C_Src/GNUmakefile
Tools/Postprocessing/C_Src/Make.package
Tools/Postprocessing/C_Src/PlotfileToMatLab.cpp

commit 9c021357ab2b68d0646325f66452d049c9cb7c43
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Apr 3 11:19:21 2018 -0700

    just to be _really_ clear about how to open flow fields with paraview

Docs/sphinx/source/Visualization.rst

commit f04a8b1668c8d1e360d58352b02f913853038ccb
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Apr 3 11:16:50 2018 -0700

    Fix some small problems with the documentation

Docs/sphinx/source/Basics.rst
Docs/sphinx/source/Visualization.rst

commit db34ed33d6fa36e354a89f06aa19866051a8ca55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 3 10:56:19 2018 -0700

    fix a typo

Src/Base/AMReX_ParallelContext.H

commit 9831a9b2d9edf9edf5cccd653cb09fa1cd314919
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 3 10:06:57 2018 -0700

    Make amrex::Array an alias of std::array instead of amrex::Vector.  This may break some codes.  But warning was given 4 months ago.

Src/Base/AMReX_Array.H

commit cc3afa8a49377c6ff8a5d31c32e23c40f17636d0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 3 09:40:35 2018 -0700

    remove a debug print statement from ParticleContainer::Checkpoint

Src/Particle/AMReX_ParticleContainerI.H

commit d6f6adb5e4f690c3d1d627d67117a03359185032
Merge: 6bb31258b 834553d7f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 2 18:57:56 2018 -0700

    Merge branch 'forkjoin' into development

commit 834553d7f03391d78c69a1ce6279f281585c4d30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 2 18:40:45 2018 -0700

    Merge branch 'development' into forkjoin

Docs/sphinx/source/EB.rst
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ThirdPartyProfiling.H
Src/Base/Make.package
Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Tests/ProfTests/ThirdParty/Exec/GNUmakefile
Tests/ProfTests/ThirdParty/Exec/inputs_2d
Tests/ProfTests/ThirdParty/Exec/inputs_3d
Tests/ProfTests/ThirdParty/Source/Make.package
Tests/ProfTests/ThirdParty/Source/advance.cpp
Tests/ProfTests/ThirdParty/Source/advance_2d.f90
Tests/ProfTests/ThirdParty/Source/advance_3d.f90
Tests/ProfTests/ThirdParty/Source/init_phi_2d.f90
Tests/ProfTests/ThirdParty/Source/init_phi_3d.f90
Tests/ProfTests/ThirdParty/Source/main.cpp
Tests/ProfTests/ThirdParty/Source/myfunc.H
Tests/ProfTests/ThirdParty/Source/myfunc_F.H
Tools/GNUMake/Make.defs
Tools/GNUMake/tools/Make.forge
Tools/GNUMake/tools/Make.vtune

commit 6bb31258b0ceb06d23ed267828de99e450ce4687
Merge: 0e1a31b9b b94ed2b6a
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Apr 2 17:30:05 2018 -0700

    Merge branch 'development' into jpb/fill-nodal

commit 0e1a31b9b48c430155caf5a887ddac2acebb9096
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Apr 2 17:21:10 2018 -0700

    fix double-scaling if fillNodalArrays from AnisotropicIF

Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp

commit b94ed2b6af36141e6334a324168347ae720fc1f3
Merge: 22331f5a1 e38db4fcb
Author: kngott <kngott@lbl.gov>
Date:   Mon Apr 2 16:07:07 2018 -0700

    Merge branch 'kngott_tpp' into development

commit e38db4fcbeef6b83f30e2930171373a6649b599d
Merge: a3616cd09 212af5064
Author: kngott <kngott@lbl.gov>
Date:   Mon Apr 2 16:03:46 2018 -0700

    Merge branch 'development' into kngott_tpp

commit a3616cd091dda8b8b8e5a4efc9c661b620252712
Author: kngott <kngott@lbl.gov>
Date:   Mon Apr 2 15:56:06 2018 -0700

    Final Third Party Version

Src/Base/AMReX_BLProfiler.H
Tests/ProfTests/ThirdParty/Exec/GNUmakefile
Tests/ProfTests/ThirdParty/Exec/inputs_2d
Tests/ProfTests/ThirdParty/Exec/inputs_3d
Tests/ProfTests/ThirdParty/Source/Make.package
Tests/ProfTests/ThirdParty/Source/advance.cpp
Tests/ProfTests/ThirdParty/Source/advance_2d.f90
Tests/ProfTests/ThirdParty/Source/advance_3d.f90
Tests/ProfTests/ThirdParty/Source/init_phi_2d.f90
Tests/ProfTests/ThirdParty/Source/init_phi_3d.f90
Tests/ProfTests/ThirdParty/Source/main.cpp
Tests/ProfTests/ThirdParty/Source/myfunc.H
Tests/ProfTests/ThirdParty/Source/myfunc_F.H
Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp

commit 22331f5a12eec954ce27b862443e3d35d1465cd6
Merge: 4cc12b30a 212af5064
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Apr 2 15:14:15 2018 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 4cc12b30a9bc76004c519cc6d98401a89048b55d
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Apr 2 15:13:55 2018 -0700

    added a bit about EBIndexSpace::read and EBIndexSpace::write into the User's guide.

Docs/sphinx/source/EB.rst

commit 212af506478499fed116751ac1083f0515c51fd9
Author: kngott <kngott@lbl.gov>
Date:   Mon Apr 2 15:13:19 2018 -0700

    Eliminate extra padding in ReadAndBcastFile.

Src/Base/AMReX_ParallelDescriptor.cpp

commit 41456520f67b46effb9e06dba3abe1fa441372ef
Author: shashankNREL <shashank.yellapantula@nrel.gov>
Date:   Mon Apr 2 13:44:01 2018 -0600

    Added HYPRE Matrix IJ Interface

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.H
Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H

commit c0fa861fdd9f9bb24666568eeac0a1ae1901f23b
Merge: 4e8451c56 9f1d24e84
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 2 09:40:32 2018 -0700

    Merge branch 'development' into forkjoin

commit 9f1d24e84a4263bb74abe7f12703715de3dd54f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 2 09:38:03 2018 -0700

    update changes

CHANGES

commit 35ec89c33c3f78054d970e191a2cacfe2f8767c9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 1 09:32:02 2018 -0700

    Add pointers to individual files

Docs/sphinx/source/tutorials.rst

commit 2488c06213511d4354ea6a0b8de7668233f8ce24
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 1 09:31:47 2018 -0700

    Add file for each Tutorial directory

Docs/sphinx/source/AMR_Tutorial.rst
Docs/sphinx/source/Basic_Tutorial.rst
Docs/sphinx/source/CVODE_Tutorial.rst
Docs/sphinx/source/EB_Tutorial.rst
Docs/sphinx/source/HYPRE_Tutorial.rst
Docs/sphinx/source/LinearSolvers_Tutorial.rst
Docs/sphinx/source/Particles_Tutorial.rst
Docs/sphinx/source/SWFFT_Tutorial.rst

commit 514ed9eb6a17737c36552fe96c4a115510d52e72
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 1 09:18:49 2018 -0700

    Trying to set up tutorals link

Docs/sphinx/source/tutorials.rst

commit e1f90415471db1586c7718047a3633ce75ed7d05
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Apr 1 09:09:32 2018 -0700

    Add Tutorials.rst for first start at Tutorials link from amrex io page.

Docs/sphinx/source/Tutorials/Tutorials.rst

commit fcdb2bba62412c87a35d5c31aab803d59e4522c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 31 14:32:00 2018 -0700

    replace HUGE with numeric_limits constexpr functions

Src/GeometryShop/AMReX_ConstrainedLS.cpp
Src/GeometryShop/AMReX_LSProblemImplem.H

commit c19a9dfe9267da884c36ef0a7cb9edfc51f5da04
Merge: 424b25bff 0846a94e6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 30 16:32:07 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 424b25bffa218566ba9f13abcf1787c2cf1ad447
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 30 16:31:57 2018 -0700

    add some parentheses here to silence compiler warnings.

Src/Base/AMReX_MultiFabUtil.cpp

commit 0846a94e604b9137a255f6d0d6c19f35c24712f3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 30 14:51:37 2018 -0700

    Modify the AssignDensity routine here (and the interfaces and calling routines in Nyx) so that we can pass in the number of grow cells used to define the array that will hold the particle deposition.  Some previous calls defaulted to 1 ghost cell which is not big enough if valid particles live in ghost cells themselves (eg if starting the second level 1 solve of a subcycled level 0-1-2 simulation.)

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit ac4333e1ba7cba11a30083840833287c95930531
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 30 14:18:17 2018 -0700

    Removing RegressionTesting from the amrex repo. These live at https://github.com/AMReX-Codes/regression_testing now.

Tools/RegressionTesting/AMReX-tests.ini
Tools/RegressionTesting/README
Tools/RegressionTesting/example-tests.ini
Tools/RegressionTesting/gen_compile_test.sh
Tools/RegressionTesting/params.py
Tools/RegressionTesting/reg_test_gc.py
Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/repo.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_report.py
Tools/RegressionTesting/test_util.py

commit a8745d4785328e6457021dcd19602ed4ea683ccf
Merge: d7c93cbc8 79666bdee
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 29 16:43:14 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d7c93cbc861e4c203b952dfdf2551342adc1a885
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 29 16:42:22 2018 -0700

    improve omp scaling of CacheNeighborInfo

Src/Particle/AMReX_NeighborParticlesI.H

commit 79666bdee0bde8ca86895c28b35340f2366b4a18
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 29 16:06:09 2018 -0700

    Fix typo in init_rhs and make sure the rhs sums to 0

Tutorials/SWFFT/SWFFT_Test.cpp
Tutorials/SWFFT/SWFFT_Test_F.F90
Tutorials/SWFFT/swfft_solver.cpp

commit 4e8451c562ea5f04f149552f8aa0b1dcae651b2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 29 14:42:11 2018 -0700

    split some FabArray communciation functions into a separate file

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayCommI.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 52a2e1b04801e71b7282069ad26a0997c199b30c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 29 13:53:40 2018 -0700

    use move when possible

OldTutorials/MultiFabTests_C/MultiFabFillBoundary.cpp
OldTutorials/MultiFabTests_C/MultiFabReadWrite.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_ForkJoin.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_VisMF.cpp
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/F_Interfaces/Base/AMReX_distromap_fi.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 9a24f1571826b562692d149eb152ddc50c5ee985
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 29 13:05:48 2018 -0700

    add new constructor that moves

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_ParallelContext.cpp

commit b6af6fd0c87ff1ec0d66749399532b078dd3b92c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 29 12:56:06 2018 -0700

    MLMG: fix subcommunicator

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit e0cab03fa249839ae16ed46bfb384977f22a798c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 29 12:34:01 2018 -0700

    MLMG: update for fork/join

Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_ParallelContext.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 8cd48768ff841c33e83cefd74a78d14f5abca79e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 29 11:23:59 2018 -0700

    add ParallelReduce, rename some functions and use MLMG in MultiColor_C

OldTutorials/MultiColor_C/GNUmakefile
OldTutorials/MultiColor_C/main.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_ForkJoin.cpp
Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_ParallelContext.cpp
Src/Base/AMReX_ParallelReduce.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 81e1b5c20f5e07b4688bf1629b62352469a7d210
Merge: 316504ac4 9d84a39a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 29 10:09:20 2018 -0700

    Merge branch 'development' into forkjoin
    
    Conflicts:
            Src/Amr/AMReX_AmrLevel.cpp

commit 316504ac4afca41b1cbf20dfbc6b67dabe1c6c46
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 29 10:07:21 2018 -0700

    store groups to avoid repeatedly creating groups in rank translation

Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_ParallelContext.cpp

commit b6abe60314b0f04de317d85a8ee553df46f284cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 29 09:34:29 2018 -0700

    fix MultiColor_C

Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp
Src/Base/AMReX_ParallelContext.cpp

commit 01f1c89d4e8fab674e7f836c493183ad5fe18666
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 29 08:52:19 2018 -0700

    rename

Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_ForkJoin.cpp
Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_ParallelContext.cpp

commit 9d84a39a4dacaab3aec2a357c4e30b84b08e7ce6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 29 08:28:33 2018 -0700

    Change name from solver_itself to swfft_solver

Tutorials/SWFFT/SWFFT_Test.cpp
Tutorials/SWFFT/swfft_solver.cpp

commit c1adb53c4dbe8ef86f35af383ce8f4475378eb64
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 29 08:02:44 2018 -0700

    Modify so that the interface to the solver isn't part of the testing
    class, but a stand alone routine that takes the rhs multifab and geometry and
    returns the soln multifab.

Tutorials/SWFFT/Make.package
Tutorials/SWFFT/SWFFT_Test.H
Tutorials/SWFFT/SWFFT_Test.cpp
Tutorials/SWFFT/SWFFT_Test_F.F90
Tutorials/SWFFT/SWFFT_Test_F.H
Tutorials/SWFFT/main.cpp
Tutorials/SWFFT/swfft_solver.cpp

commit 0473face11f676988a65d1234a18756cefa4c974
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 28 21:22:21 2018 -0700

    Update the call to the solver so it correctly handles the case
    where we decompose a cubic grid into different numbers of grids
    in each direction, eg a 32^3 grid decomposed into 32x16x16 boxes.

Tutorials/SWFFT/SWFFT_Solver.cpp
Tutorials/SWFFT/SWFFT_Solver_F.F90
Tutorials/SWFFT/SWFFT_Solver_F.H
Tutorials/SWFFT/inputs.32

commit 622003b1e361fb8954538962b34911704aec7642
Merge: 06fb8a43d 0591e30b8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 28 20:36:15 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit 06fb8a43d378833e6383ebde58fa239b40fe23e6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 28 20:35:23 2018 -0700

    Change the user interface so that for both max_grid_size and n_cell
    you can enter one value, which would set the values in all directions
    to that value, or it can take in 3 values, one for each direction (in 3d)

Tutorials/SWFFT/SWFFT_Solver.H
Tutorials/SWFFT/SWFFT_Solver.cpp

commit 0591e30b836fe8451c1b2462d7e610dc365f62b7
Merge: 5b2f40d9c 0b5a226e5
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Mar 28 17:39:56 2018 -0700

    Merge pull request #235 from AMReX-Codes/MLLinOp_Fix
    
    MLLinop Corner Fix

commit 0b5a226e580c25dd711273be6658133c5a4009a4
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Mar 28 19:27:39 2018 -0500

    removed mask condition and added support for mixed bcs

Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90

commit 5b7594f32901603a3ab78df50db9a76a0b219ed3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 28 17:00:06 2018 -0700

    update DistributionMapping for fork/join

Src/Base/AMReX_DistributionMapping.cpp

commit dcbc97f351559175c70c53c3eb3a33038188dc88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 28 12:41:42 2018 -0700

    update FabArray communication for fork/join

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_ParallelReduce.H

commit 5b2f40d9cefe97e31102d1f0a2b7f99028527659
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 28 10:58:52 2018 -0700

    add Sod test to EB/CNS

Tutorials/EB/CNS/Exec/Sod/GNUmakefile
Tutorials/EB/CNS/Exec/Sod/Make.package
Tutorials/EB/CNS/Exec/Sod/cns_prob.F90
Tutorials/EB/CNS/Exec/Sod/inputs

commit e640bfff93483ae61bca8a9c5fca529def5ac248
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 28 09:32:36 2018 -0700

    use the global communicator in ParallelDescriptor

Src/AmrTask/AMFIter/AMReX_AmrTask.H
Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H
Src/Base/AMReX.cpp
Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_Print.H

commit ffd031139a5a74ebd97fee8c978a02bde151607e
Merge: a6e0d6bf7 58f493f91
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 28 09:51:38 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a6e0d6bf7d3b5f1374cc2fe13c0769db99929b15
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 28 09:51:22 2018 -0700

    remove AllReduce from RedistributeMPI

Src/Particle/AMReX_ParticleContainerI.H

commit cbb769576554242a08b33346c9035279b92ac23d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 28 09:21:38 2018 -0700

    MLMG bottom: use ParallelContext

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 58f493f9186b1725bf07050238e0c8bbe73bf7fd
Merge: 394d6d9f2 566a30e5d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Mar 28 08:59:23 2018 -0700

    Merge pull request #234 from AMReX-Codes/MLCellLinOp_NCompFix
    
    Enable multicomponent flux registers

commit 566a30e5d3e06813398a9e338e7de3ec19ec89db
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Mar 28 11:28:40 2018 -0400

    removed extra comment

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit 52fefb47153e7712f08eccd86b59cfff40a403ce
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Mar 28 11:27:23 2018 -0400

    fixed bug caused by assuming single component flux registers

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit d2d7cce46327f962287908d06921d422896863d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 27 16:27:29 2018 -0700

    simplify SeqNum()

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit 0f924fda42acc39d479fcf6c064fb6936666b92c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 27 14:48:38 2018 -0700

    fix a new bug

Src/Base/AMReX_ParallelDescriptor.cpp

commit f39b46c9b8e561c7add10234e37069256fff5ea7
Merge: 094db81a2 394d6d9f2
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Mar 27 16:54:25 2018 -0400

    Merge branch 'development' into gpu

commit 4333b017fe7c7b14dd0bf63f114c0df1fbe25895
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 27 13:54:01 2018 -0700

    fix non-MPI

Src/Base/AMReX_ParallelDescriptor.cpp

commit 394d6d9f2187dd5335968071d4bc83ec1e01fadd
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Mar 27 16:29:45 2018 -0400

    Add IBM MPI lib for Fortran on Summit

Tools/GNUMake/sites/Make.olcf

commit 515a5b0b10a35f3a063ceb3e63581d070c8cfb3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 27 11:56:38 2018 -0700

    rm BroadCast DistributionMapping and BoxArray

Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit 2baeac6e02b02b85e60de1b5b4b33d4e4a0f93ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 27 11:51:52 2018 -0700

    rm PFC

Src/Amr/AMReX_Amr.cpp
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit 8e103b621daa6f34b4f5cef43b07869f873b7c2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 27 11:36:51 2018 -0700

    rm FAPId

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 1aab47864030a14164f416202a5392362b41ece2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 27 11:25:27 2018 -0700

    rm FAPointers

Src/Base/AMReX_FabArray.H

commit 03216dad6667eebf0194e11ce8b71bb6671d9dda
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 27 11:16:32 2018 -0700

    rm MoveFabs

OldTutorials/MultiFabTests_C/GNUmakefile
OldTutorials/MultiFabTests_C/GridMoveTest.cpp
OldTutorials/MultiFabTests_C/Make.package
OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp
Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.H

commit 2616290db559025e871c4ad7863f1437d1a9a191
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 27 11:05:43 2018 -0700

    rm AddProcsToComp

Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_FabSet.H

commit dfe15ac19c592ff10d1831a074703be39b057ba0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 27 10:57:48 2018 -0700

    rm more sidecar stuff

OldTutorials/DataServicesTest0/GNUmakefile
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_MemProfiler.H
Src/Base/AMReX_MemProfiler.cpp
Tests/IOBenchmark/GNUmakefile

commit 70b098c021b0b90de6d727e540182552da801445
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 27 10:29:23 2018 -0700

    first pass of removing sidecar

Docs/Readme.sidecars
OldTutorials/Sidecar_EX1/DestMFTest.cpp
OldTutorials/Sidecar_EX1/GNUmakefile
OldTutorials/Sidecar_EX1/GridMoveTest.cpp
OldTutorials/Sidecar_EX1/InTransitAnalysis.H
OldTutorials/Sidecar_EX1/InTransitAnalysis.cpp
OldTutorials/Sidecar_EX1/Make.package
OldTutorials/Sidecar_EX1/NSidecarsTest.cpp
OldTutorials/Sidecar_EX1/SidecarResizeTest.cpp
OldTutorials/Sidecar_EX1/TestRankSets.cpp
OldTutorials/Sidecar_EX1/inputs_3d
OldTutorials/Sidecar_EX1/inputs_sc
OldTutorials/Sidecar_EX1/run.sh
Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/AmrTask/AMFIter/AMReX_AmrTask.H
Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H
Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Src/Base/AMReX.cpp
Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_ParallelContext.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_Print.H
Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90
Tests/C_BaseLib/BcastClasses/BcastClasses.cpp
Tests/C_BaseLib/BcastClasses/GNUmakefile
Tools/CompileTesting/compiletesting.py

commit ee95e75e97f2fec1cece588871dce76d479f6d50
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Mar 27 09:16:25 2018 -0700

    Get rid of more IOIOIO:CD writes

Src/Amr/AMReX_AmrLevel.cpp

commit d3010f90a8b6fdbc1729d5e42170579ad2f9d801
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Mar 27 09:15:19 2018 -0700

    Get rid of all those IOIOIOI write statements

Src/Amr/AMReX_Amr.cpp

commit e5dd1086dcdbc309a16ebc541af0d7737ee87a72
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 26 15:52:44 2018 -0700

    c bind for hoextraptocc

Src/Base/AMReX_filcc_f.H
Src/Base/AMReX_filcc_mod.F90

commit 5b989f4be165ae6f8caaac0c5afa482a819fde93
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 26 13:22:40 2018 -0700

    Remove the IOIOIOIO print statements

Src/Particle/AMReX_ParticleContainerI.H

commit 40c4dd225bc6fdf0333586d3bd87e41fe34a3cf4
Merge: 099a99897 e608757a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 26 12:26:38 2018 -0700

    Merge branch 'development' into forkjoin
    
    Conflicts:
            Src/Base/AMReX.cpp
            Src/Base/AMReX_ParallelDescriptor.cpp

commit e608757a0716994636bc2001a5a4607d731cc798
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Mar 26 10:53:44 2018 -0700

    removed slabservice-- an unused geometry service.

Src/GeometryShop/AMReX_SlabService.H
Src/GeometryShop/AMReX_SlabService.cpp
Src/GeometryShop/CMakeLists.txt

commit ffb6a9eb20819d2ad0ea2eee9bc51ddea50b9689
Merge: a4044a7ec 4d324a835
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Mar 26 10:43:35 2018 -0700

    merging stuff

commit 4d324a835733f996c9311905d2845e08c58273a0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Mar 26 10:36:59 2018 -0700

    updated CMakeLists.txt

Src/GeometryShop/CMakeLists.txt

commit a4044a7ec6da04488c6b3752f606825ab2556de9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 26 10:24:39 2018 -0700

    nodal solvability: fix a bug

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit fd3833b2cb6ac947f1defed7bcb76ac2292c9a3a
Merge: d66cdbc1c 0362f0600
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 26 09:05:27 2018 -0700

    Merge branch 'development' into nd_solvability

commit 0362f0600d969afdfabccbd4f1d75b9b814f79e5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 26 07:26:43 2018 -0700

    Missed another one

Src/GeometryShop/CMakeLists.txt

commit ccef59b93960ab0efdc32995042b421cadffdf8d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 26 07:22:43 2018 -0700

    Fix typo

Src/GeometryShop/CMakeLists.txt

commit bbbd4b30c78ff5f0b1f9ab327e363cd1e56c3958
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 26 07:18:21 2018 -0700

    Missed another one...

Src/GeometryShop/CMakeLists.txt

commit 084bda0ba8c58483fca7b8c6c864c7dd3f6a1daa
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 26 07:14:52 2018 -0700

    Fix typo

Src/GeometryShop/CMakeLists.txt

commit a947fa0a3aa38052fc5b56a963dea83bca38f69b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 26 07:12:26 2018 -0700

    I think I got the rest of them...

Src/GeometryShop/CMakeLists.txt

commit 0aa9f24e0cd31ad35f165052ada18a8af8a6fe2d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 26 07:04:02 2018 -0700

    Add AMReX_IndexedMoments.H to CMakeLists.txt

Src/GeometryShop/CMakeLists.txt

commit 65edfc2d8dd551a6844d90a16e00b0adddcf9406
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 25 16:19:47 2018 -0700

    some minor additions to Finalize

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_Geometry.cpp

commit 068d07bb5a9364ad0713471a1955c42d1b993366
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 25 15:09:14 2018 -0700

    Tests/ThirdPartiLib: solve Poisson

GNUmakefile.in
Src/Base/AMReX_ParallelDescriptor.cpp
Tests/ThirdPartyLib/bar.F90
Tests/ThirdPartyLib/foo.cpp

commit af08aeb5facd74c9873e930497a574f23a3a08fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 24 23:57:38 2018 -0700

    reentrant: AMReX.cpp

Src/Base/AMReX.cpp
Src/Base/AMReX_MemPool.H
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_MemProfiler.H
Src/Base/AMReX_MemProfiler.cpp
Src/Base/AMReX_ParmParse.cpp

commit 7c301e84e30d20f63a42ed09861208a80e09e419
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 24 21:38:34 2018 -0700

    add a test for using amrex as a third-party library

Tests/ThirdPartyLib/GNUmakefile
Tests/ThirdPartyLib/Readme
Tests/ThirdPartyLib/bar.F90
Tests/ThirdPartyLib/foo.cpp
Tests/ThirdPartyLib/main.c

commit 2ac7f2a03bc153aee6cdd3492e6ad1ff2ba66913
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 24 19:58:30 2018 -0700

    no longer print # of MPI processes and OMP threads if verbose is not on

Src/Base/AMReX.cpp

commit a19a8fad9763875f727a4b00de0f2fdf9e3b09d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 24 19:43:51 2018 -0700

    MPI_Comm is now safe if AMReX is initialized and then finalized repeated

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_ParallelDescriptor.cpp
Src/F_Interfaces/Base/AMReX_init_fi.cpp
Src/F_Interfaces/Base/AMReX_parallel_mod.F90

commit d3271447c9da0667b891c4aaa36704d73c99c784
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 24 19:36:00 2018 -0700

    rm F_BaseLib and F_MG from libamrex

GNUmakefile.in

commit bbb54fbe8a925bdda4c97249af44eb32b1183275
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 24 14:52:29 2018 -0700

    amrex::Initialize is now OK with argc=0.  do not stop if get_command fails

Src/Base/AMReX.cpp
Src/F_Interfaces/Base/AMReX_init_mod.F90

commit 449d64649f5f0164c678d770cccfffc55be26d35
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 24 13:09:20 2018 -0700

    if the communicator given is MPI_COMM_WORLD, we should go ahead calling MPI_Init

Src/F_Interfaces/Base/AMReX_parallel_mod.F90

commit 094db81a263ed2de59303bae406f847282a89479
Merge: 1558c461d 05b79343e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Mar 25 13:17:36 2018 -0400

    Merge branch 'development' into gpu

commit 1558c461d233d728143a11b9ab9eca3ddf3a3c2c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Mar 25 12:57:33 2018 -0400

    Use built-in F90 link when compiling with CUDA

Tools/GNUMake/Make.rules
Tools/GNUMake/comps/pgi.mak

commit 05b79343e77c7a79f1a9213ea18a892ab4169f87
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Mar 24 11:21:10 2018 -0700

    Updated the SWFFT Tutorial so 1) It correctly solves the Poisson equation
    on a single grid, 2) it creates a version of the DistributionMapping to
    pass to dfft.

Tutorials/SWFFT/README
Tutorials/SWFFT/SWFFT_Solver.H
Tutorials/SWFFT/SWFFT_Solver.cpp
Tutorials/SWFFT/SWFFT_Solver_F.F90
Tutorials/SWFFT/SWFFT_Solver_F.H
Tutorials/SWFFT/inputs.128
Tutorials/SWFFT/inputs.32
Tutorials/SWFFT/inputs.64

commit d66cdbc1ca0067206ede589732d45e51559b1ce0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 23 20:36:59 2018 -0700

    merge two mfiter loops

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 60b02681b583a3ca2e4238f7891b59244d35c19b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 23 18:05:16 2018 -0700

    solve nodal solvability

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/Make.package

commit 16ddf9bd30d61e1795b126c6ee9a6867cb9058b9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 23 16:44:42 2018 -0700

    This version seems to work.

Tutorials/SWFFT/SWFFT_Solver.H
Tutorials/SWFFT/SWFFT_Solver.cpp

commit 7dad5979ca9567ce8a7c7d71ad4c01434688aded
Merge: e92ed6fc1 0ef49dabe
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 23 15:49:51 2018 -0700

    Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development

commit e92ed6fc15da735bd8c30315db742ef9e215289f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 23 15:49:40 2018 -0700

    Save this before I accidentally delete it

Tutorials/SWFFT/SWFFT_Solver.cpp

commit 0ef49dabe81a476b9e01124934684a04f108e341
Merge: e7a1e67f4 6ef68a97d
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Mar 23 13:54:12 2018 -0700

    Merge pull request #232 from AMReX-Codes/dtg/high_order_moments
    
    added higher order moment infrastructure

commit 6ef68a97db813cce11772c76854745addc2f9bff
Merge: 3b9fcc260 e7a1e67f4
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Mar 23 13:51:48 2018 -0700

    Merge branch 'development' into dtg/high_order_moments

commit 3b9fcc26078c99d65068bd55af2f78f8cc1c8caf
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Mar 23 13:50:42 2018 -0700

    geometry generation with higher order moments now passes all the regression tests.

Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBLevelGrid.cpp
Tests/GeometryShop/regression/ebio.cpp

commit 43395ead1570c9e32525cac83e5c7c73988fb4f4
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Mar 23 10:38:36 2018 -0700

    fixed eb data serialization.  all serial regression tests pass now.  on to mpi testing

Src/GeometryShop/AMReX_BaseEBCellFABI.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_FabArrayIO.H
Tests/GeometryShop/regression/serialization.cpp

commit e7a1e67f44a14365956070d0c3442b279e1853dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 23 09:01:19 2018 -0700

    fix non-mpi build

Src/Base/AMReX_ParallelDescriptor.cpp

commit 099a99897456895a914964627852f015e61bbdaa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 23 08:55:41 2018 -0700

    array version of rank translation

Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_ParallelContext.cpp

commit 7287e8113025ed99c789b58b963780192abe95ab
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Mar 22 16:27:25 2018 -0700

    Fix ParallelDescriptor::Waitany and update all other MPI_Wait calls to use the ParallelDescriptor versions.

Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Tools/AMRProfParser/TestCodes/ProfWaitTest.cpp

commit a5a11964a968901ea360e1be76a04717d8b33726
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 22 15:56:22 2018 -0700

    use the ParallelDescriptor version of Waitall in the particle communication routines.

Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleContainerI.H

commit 47f8837fd99aef576ebcff4a552ed796316099c0
Merge: 6a679202f 6caf213d8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 22 14:49:04 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6a679202f2fed46acc7f08c506d364835e162fe9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 22 14:48:55 2018 -0700

    fix omp shared variable list in plt_compare_diff_grids

Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90

commit ecc33e176607fe0b25eb58fdcfa9a76be88df86b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 22 14:44:58 2018 -0700

    use MyProcAll instead of MyProc in some places; if the current context is the global communicator, no need to call translate

Src/Amr/AMReX_AmrLevel.cpp
Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_ParallelContext.cpp
Src/Base/AMReX_Print.H

commit 6caf213d835da64f482510a30955a5db3d669dbd
Author: Kevin Gott <kngott@lbl.gov>
Date:   Thu Mar 22 14:21:47 2018 -0700

    Profiling added to the MPI Wait call wrappers. Simple test case also included.

Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_ParallelDescriptor.cpp
Tools/AMRProfParser/TestCodes/GNUmakefile
Tools/AMRProfParser/TestCodes/ProfWaitTest.cpp

commit fd30f89e03d7712ffe2a0685c2a65ce19c6f19fd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 22 13:28:04 2018 -0700

    add extra newline

Tools/RegressionTesting/test_report.py

commit 66f30833ac52b0cfa369c88a8e47229c97d1df06
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 22 12:50:16 2018 -0700

    protect against pcomp_line being None.

Tools/RegressionTesting/test_report.py

commit acf4a415149d96c894f633e270cb0d7837688a51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 22 12:44:41 2018 -0700

    use ParallelContext in ParallelDescriptor

Src/Base/AMReX.cpp
Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_ParallelContext.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit 88ef1f83bf0e041df00d346637b68a9b402912c2
Merge: 94aea4f56 ccc6f02fb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 22 12:09:55 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 94aea4f568352b11b374766cef99be7aab7d0e4d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 22 12:09:44 2018 -0700

    hack the test suite to print out the particle comparison command.

Tools/RegressionTesting/test_report.py

commit 8f275717dfbd8056bb692f95f6c6620c0fdc0c2e
Merge: be0dcd1d8 ccc6f02fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 22 09:43:34 2018 -0700

    Merge branch 'development' into forkjoin

commit ccc6f02fbac7e01ed15d40488565d7f012e04ccd
Author: Kevin Gott <kngott@lbl.gov>
Date:   Wed Mar 21 19:41:07 2018 -0700

    Add empty Wait wrappers for cases without MPI.

Src/Base/AMReX_ParallelDescriptor.cpp

commit b691dc884247abe94608f9357732a42523822e3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 21 17:18:35 2018 -0700

    need to call MPI_Comm_free even wehn bl_fortran_mpi_comm_free has been called because the one in Fortran is a duplicate

Src/Base/AMReX_ParallelDescriptor.cpp

commit 03b96602c66c751421fa457d29ff7de2aac05eea
Author: kngott <kngott@lbl.gov>
Date:   Wed Mar 21 16:21:48 2018 -0700

    AMReX wrappers for all MPI Wait functions. Profiling to be added and tested.

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Tools/AMRProfParser/TestCodes/GNUmakefile
Tools/AMRProfParser/TestCodes/ProfWaitTest.cpp

commit c6372a1b3caf15efa6f3329fbbff3aaff42a7fd9
Author: kngott <kngott@lbl.gov>
Date:   Wed Mar 21 16:10:13 2018 -0700

    Make.allinea file rename to Make.forge

Tools/GNUMake/tools/Make.forge

commit 2ec36bac92175513e787baf6915a5b239115c9b5
Author: kngott <kngott@lbl.gov>
Date:   Wed Mar 21 16:08:33 2018 -0700

    TPP header file

Src/Base/AMReX_ThirdPartyProfiling.H

commit cf0c8e6e72ac600d72d760180d320b1ae3b46d49
Author: kngott <kngott@lbl.gov>
Date:   Wed Mar 21 16:05:51 2018 -0700

    Third Party Profiling First Attempt

Src/Base/AMReX_BLProfiler.H
Src/Base/Make.package
Tools/GNUMake/Make.defs
Tools/GNUMake/tools/Make.vtune
Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp

commit bc57cfce59a1115c878d955b253d7c8bf8868b47
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Mar 21 14:51:46 2018 -0700

    serialization still broken for higher order but all the other tests pass

Src/GeometryShop/AMReX_EllipsoidIF.H
Src/GeometryShop/AMReX_EllipsoidIF.cpp
Src/GeometryShop/AMReX_PlaneIF.cpp
Tests/GeometryShop/regression/fabio.cpp
Tests/GeometryShop/regression/levelRedistTest.cpp
Tests/GeometryShop/regression/multicelllev.cpp
Tests/GeometryShop/regression/multicelllev.inputs
Tests/GeometryShop/regression/runalltests.serial.sh

commit c17687132baf4da0c7f058d080fa2347de11dc52
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Mar 21 13:30:48 2018 -0700

    fix over-zealous deletions

build_and_deploy.sh

commit e5f901fa4d28168dde8362fcf32549742821cf25
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Mar 21 11:57:53 2018 -0700

    fixed more tests so they also run with WrappedGShop.

Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp
Tests/GeometryShop/regression/dataArith.cpp
Tests/GeometryShop/regression/ebio.cpp
Tests/GeometryShop/regression/ebnormalizeTest.cpp
Tests/GeometryShop/regression/fabfromif.cpp
Tests/GeometryShop/regression/serialization.cpp

commit b4f9fc4f0692f77597f375f975419eb3bfa26f45
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Mar 21 11:48:41 2018 -0700

    fix broken link in the docs (to Amrvis profiling)

Docs/sphinx/source/AMReX_Profiling_Tools.rst
Docs/sphinx/source/GettingStarted.rst

commit 394bb421e50420a6a5e81b58e4904ac4291b8d53
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Mar 21 11:06:26 2018 -0700

    debugging travis script

build_and_deploy.sh

commit e6ca34ca9ab76a4d2758e47d5cbc94c38f953e48
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Wed Mar 21 10:52:32 2018 -0700

    update travis to reflect new web root for docs

build_and_deploy.sh

commit 6274575ebceb4f979f76c94ee08dbc161053e44c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Mar 20 16:28:40 2018 -0700

    More tests are passing.  Higher order stuff coming along.

Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_IrregNode.cpp
Src/GeometryShop/AMReX_PlaneIF.H
Src/GeometryShop/AMReX_PlaneIF.cpp
Src/GeometryShop/AMReX_WrappedGShop.H
Src/GeometryShop/AMReX_WrappedGShop.cpp
Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp
Tests/GeometryShop/ramp/main.cpp

commit d9583b50c4f9cf00dfaf1e52f6e19d19ee4bfa87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 20 13:32:38 2018 -0700

    EBFluxRegister: fix a bug when tile size is odd

Src/EB/AMReX_EBFluxRegister.cpp

commit cc3118699a0c94f244a56690632c435a70c7ddd9
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Mar 20 10:58:21 2018 -0700

    first higher order test passed.   I still have to put in the new bits that fix regular next to covered and add more derivative methods to the implicit function classes.

Src/Base/AMReX_IntVect.H
Src/GeometryShop/AMReX_SphereIF.H
Src/GeometryShop/AMReX_SphereIF.cpp
Src/GeometryShop/AMReX_WrappedGShop.cpp

commit 92863545c869bc88716ef6cf882b9bc87c899466
Merge: 67c324137 418931cd4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Mar 20 10:20:34 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 67c32413744ec0b9c6fe0ced52381a5e24b72f66
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Mar 20 10:20:22 2018 -0700

    wrap this variable in a BL_USE_MPI ifdef

Src/Base/AMReX_ParallelDescriptor.cpp

commit 418931cd4b41a1c31ec83aeb7f13d30a003a50cc
Merge: 7f7b39be9 b1c768804
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Mar 20 09:20:22 2018 -0700

    Merge pull request #229 from JBlaschke/development
    
    GNUMake used by Tools/F_mk and Tools/Postprocessing/C_Src should respect settings in Make.local

commit 42a34e8d0586271f2787916abdc8b757ec709ebe
Merge: b6088f279 7f7b39be9
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Mar 19 15:46:24 2018 -0700

    merging with dev branch

commit b6088f27927d498f9045d49fedc407f1b6dac392
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Mar 19 15:44:03 2018 -0700

    more fixes.  I am not sure how to get Marc's intersection information in the new context.   Still need to fix a bunch of implicit function so they produce their derivatives.

Src/GeometryShop/AMReX_BaseIF.H
Src/GeometryShop/AMReX_WrappedGShop.H
Src/GeometryShop/AMReX_WrappedGShop.cpp
Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp

commit 7f7b39be9a529ff390532872625bb61828554c7a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 19 15:39:26 2018 -0700

    move amrex_malloc and amrex_free to cpp file so that linker can find them for Fortran code

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit a6fd1c3c31984f8dc0c02bfa7c22145b6a1b437e
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Mar 19 15:01:39 2018 -0700

    Serialization of higher order moments is written and compiles.  On to testing.

Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFAB.cpp
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_EBData.cpp

commit c248b8802de3febe60064606d914fc6458f86245
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Mar 19 11:33:35 2018 -0700

    put Weiqun's isnan code into a template specialization so BaseIFFAB can work with other data types

Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFAB.cpp
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_EBISBox.H
Src/GeometryShop/Make.package

commit b1c768804c23d5c7bd69e39416ce793d87a408ab
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Mar 18 21:39:25 2018 -0700

    fix typo in docs

Docs/sphinx/source/BuildingAMReX.rst

commit 6cf86e038a69deb511314627db26da86cd3dcf00
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Mar 18 21:30:45 2018 -0700

    GNUMake used by Tools/F_mk and Tools/Postprocessing/C_Src now respects compiler options in Make.local

Tools/F_mk/comps/gfortran.mak
Tools/Postprocessing/C_Src/GNUmakefile

commit a21e66edfbcf2f3b3d759c0756f510a73e4afb9e
Merge: 95a61482a 0bb22d0a5
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Mar 16 17:25:42 2018 -0700

    Merge pull request #227 from AMReX-Codes/MultiComponentMLMG
    
    Multi component mlmg

commit 0bb22d0a5d515e539fa3b1e52f2ea1bcf91f6dc2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 16 16:38:07 2018 -0700

    multi-component solvability fix for cell-centered solve

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit f50b256481629e2660afafa8808cc93859862315
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Mar 16 16:15:55 2018 -0700

    integration with EBIS is complete except for the serialization stuff.  This is very much like saying that except for the hundred year war, it was a heck of a century.

Src/GeometryShop/AMReX_BaseIF.H
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBDataFactory.H
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_FlatPlateGeom.cpp
Src/GeometryShop/AMReX_GeometryService.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_WrappedGShop.H
Src/GeometryShop/AMReX_WrappedGShop.cpp

commit 70b6feaca9d199a5298d9a348436a96c841dbc61
Merge: 23ae3f7de 23eddc916
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Fri Mar 16 15:47:15 2018 -0700

    Merge pull request #228 from AMReX-Codes/MCMLMG_bc
    
    Add isCrossStencil virtual function to MLCellLinOp.  For non-cross st…

commit 95a61482af81aad71b33587835431c3a9e90eecc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 16 14:28:17 2018 -0700

    grow by an additional cell here (can be needed even if all particles are in the right place due to roundoff errors).

Src/Particle/AMReX_NeighborParticlesI.H

commit 7a11bb16fa68472e431fb4a6310447556a602471
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 16 14:26:50 2018 -0700

    add some debug-mode asserts to help catch problems earlier.

Src/Particle/AMReX_NeighborParticlesI.H

commit ac153521567b6ab07b381404a766dd3469d70d37
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 16 14:06:15 2018 -0700

    use an explicit cast here to shut up compiler warnings.

Src/Particle/AMReX_ParticleContainerI.H

commit 23eddc91615b135a6c02b60aba6f2feb28ae52eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 16 12:23:58 2018 -0700

    Add isCrossStencil virtual function to MLCellLinOp.  For non-cross stencil, extend mask to corners and extrpolation is done only for non-covered corner cells.

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90

commit 23ae3f7de65d7962199b134ccec4ebab59b76cbd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 16 11:03:38 2018 -0700

    use double precision

Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90

commit 754aa6c9064c98d23796f56a3852cd351202e3d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 16 10:26:58 2018 -0700

    no need to have overriding virtual function getNComp in MLCellLinop because a default implementation already exists in its base class MLLinOp

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit 1d82268888a15d958e36d8522d1b58a470cce6b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 16 10:16:11 2018 -0700

    minor

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit 2f6fed098efcca599d7e5d7a52fcf85aca4ca674
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 16 10:05:24 2018 -0700

    no need to call linop.prepareForSolve in cases it has been called

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 7817506a6c9affd2aa9744009342e77b54a97001
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 16 09:37:34 2018 -0700

    fix type mismatch

Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90

commit 48cba9f1cb5fe0899061e458f3578abb1e3fcaf6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 16 09:30:14 2018 -0700

    fix typos in 1d

Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90

commit 3a1ce445ea98b04416b33c0bb69969036349e3c6
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Mar 15 17:59:24 2018 -0600

    reverted bndrydata

Src/Boundary/AMReX_BndryData.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90

commit f6ae7f8e7e83f5db37367da4407a67fd99630290
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Mar 15 17:49:01 2018 -0600

    reverted ncomp changes

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit fa972fadf50ec4905f8b93309006815df38996d5
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Mar 15 16:39:37 2018 -0600

    fixed 3d error

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90

commit 96d2bc45678e39268868187c80c5c87e397b465b
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Mar 15 16:14:09 2018 -0600

    minor fixes to MLCG norm and to the number of components for masks in MLCellLinOp

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit f75c4a7c483b07ce01aa1ce4c092b0465c17b8a4
Merge: 099cdaa96 06fbde903
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Mar 15 15:55:57 2018 -0600

    Merge branch 'development' into MultiComponentMLMG

commit 099cdaa965dd2c5f8448bdb7b0fd4c9355e877a8
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Mar 15 15:47:19 2018 -0600

    removed printout statement

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit be0dcd1d8912e85d1901a575786ea855734ecbdc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 15 14:22:37 2018 -0700

    move task splitting stuff from ParallelContext into ForkJoin

Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp
Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_ParallelContext.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ccse-mpi.H

commit 50cbb3cd3354842a92aafefbc1ead8a03efb63c8
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Mar 15 11:10:16 2018 -0700

    port of higher order moment infrastructure is complete.   Now I need to integrate it into EBIndexSpace and all that.

Src/GeometryShop/AMReX_IFData.cpp
Src/GeometryShop/AMReX_IndexedMoments.H
Src/GeometryShop/AMReX_MetaPrograms.H
Src/GeometryShop/AMReX_MonomialPowers.H
Src/GeometryShop/Make.package

commit c9ef4a2913e4830e88cef21d083d76826150825f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 15 10:24:57 2018 -0700

    include ParallelContext in ParallelDescriptor header

Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ccse-mpi.H

commit 3942512a6a2d3851f1f90fad8880c089891c2807
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 15 09:00:46 2018 -0700

    more to private of ForkJoin

Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp

commit 06fbde90310426eaec0f65217d86a16bcc926b3b
Merge: 1e2b733d8 4851bf754
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 14 23:15:12 2018 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 1e2b733d800c6f3a31cecc7c092a22ce288664c1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 14 23:14:48 2018 -0700

    some changes needed in the test suite for SedonaBox

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_report.py

commit 63c84f95fa27499ec59817c4aec88b97f9776a38
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Mar 14 15:58:42 2018 -0700

    lots of progress made in the big slog.

Src/GeometryShop/AMReX_IFSlicer.H
Src/GeometryShop/AMReX_IndexedMoments.H
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_IrregNode.cpp
Src/GeometryShop/AMReX_MinimalCCCMImplem.H
Src/GeometryShop/AMReX_NormalDerivativeNew.H
Src/GeometryShop/AMReX_WrappedGShop.cpp

commit 17d1a391bbdc5fd3a6e766e42b0bb094702c1e70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 14 14:42:10 2018 -0700

    move MFFork to private and other minor changes

Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp

commit c6e0eba32eeea98e201fb16d34712fe28f037b68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 14 14:00:50 2018 -0700

    make MultiColor_C compile again

OldTutorials/MultiColor_C/GNUmakefile
OldTutorials/MultiColor_C/inputs
OldTutorials/MultiColor_C/main.cpp

commit ff460b4e442904e1b67027a68394428da9b64177
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 14 12:36:23 2018 -0700

    remove Color

Src/Base/AMReX.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_ForkJoin.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_ParallelContext.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_iMultiFab.cpp
Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_FabSet.H
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 23b16f48a0e2c438f1161e16afa816928f5d13d0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Mar 14 11:53:24 2018 -0700

    waist deep in the big muddy

Src/GeometryShop/AMReX_EB_TYPEDEFS.H
Src/GeometryShop/AMReX_IndexTM.H
Src/GeometryShop/AMReX_IndexedMoments.H
Src/GeometryShop/AMReX_IndexedMomentsImplem.H
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_MomentIterator.H
Src/GeometryShop/AMReX_MomentIteratorImplem.H
Src/GeometryShop/AMReX_MonomialPowers.H
Src/GeometryShop/Make.package

commit e4fc09febed54534243c8d4a41c771dbc92534c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 14 09:42:51 2018 -0700

    add ParallelContex::init and finalize to amrex::Initialize and Finalize

OldTutorials/MultiColor_C/main.cpp
Src/Base/AMReX.cpp

commit 8c9d43820ed88b2b3a0b2a4a92652f0f3b3df49e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 14 09:35:00 2018 -0700

    move AMReX_ForkJoin and AMReX_ParallelContext to Base/

OldTutorials/MultiColor_C/GNUmakefile
Src/Base/AMReX_ForkJoin.H
Src/Base/AMReX_ForkJoin.cpp
Src/Base/AMReX_ParallelContext.H
Src/Base/AMReX_ParallelContext.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 4851bf7543950f4acc4136f011742f0387dd5dc0
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Mar 13 16:27:56 2018 -0700

    CMake:start setup for profiling improvements

Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake

commit a3e1be703d47860da329bf488c02719b2344b2eb
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Mar 13 15:34:16 2018 -0700

    templates and namespaces are really not fond of one another

Src/Base/AMReX_IntVect.H
Src/GeometryShop/AMReX_ConstrainedLS.H
Src/GeometryShop/AMReX_ConstrainedLS.cpp
Src/GeometryShop/AMReX_CoordinateSystem.H
Src/GeometryShop/AMReX_CoordinateSystemImplem.H
Src/GeometryShop/AMReX_CutCellMoments.H
Src/GeometryShop/AMReX_CutCellMoments.cpp
Src/GeometryShop/AMReX_CutCellMomentsImplem.H
Src/GeometryShop/AMReX_DivNormalRefinement.H
Src/GeometryShop/AMReX_DivNormalRefinementImplem.H
Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBArith.cpp
Src/GeometryShop/AMReX_EBGeomDebugDump.H
Src/GeometryShop/AMReX_EBGeomDebugOut.H
Src/GeometryShop/AMReX_EBGeomDebugOut.cpp
Src/GeometryShop/AMReX_EB_TYPEDEFS.H
Src/GeometryShop/AMReX_Factorial.H
Src/GeometryShop/AMReX_GenericArithmetic.H
Src/GeometryShop/AMReX_GenericArithmeticI.H
Src/GeometryShop/AMReX_IFData.H
Src/GeometryShop/AMReX_IFData.cpp
Src/GeometryShop/AMReX_IFDataImplem.H
Src/GeometryShop/AMReX_IFSlicer.H
Src/GeometryShop/AMReX_IFSlicer.cpp
Src/GeometryShop/AMReX_IFSlicerImplem.H
Src/GeometryShop/AMReX_IndexTM.H
Src/GeometryShop/AMReX_IndexTMI.H
Src/GeometryShop/AMReX_IndexedMoments.H
Src/GeometryShop/AMReX_IndexedMomentsImplem.H
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_LSProblem.H
Src/GeometryShop/AMReX_LSProblem.cpp
Src/GeometryShop/AMReX_LSProblemImplem.H
Src/GeometryShop/AMReX_LSquares.H
Src/GeometryShop/AMReX_LSquares.cpp
Src/GeometryShop/AMReX_MinimalCCCM.H
Src/GeometryShop/AMReX_MinimalCCCM.cpp
Src/GeometryShop/AMReX_MinimalCCCMImplem.H
Src/GeometryShop/AMReX_MomentIterator.H
Src/GeometryShop/AMReX_MultiIndex.H
Src/GeometryShop/AMReX_MultiIndexImplem.H
Src/GeometryShop/AMReX_NoRefinement.H
Src/GeometryShop/AMReX_NoRefinementImplem.H
Src/GeometryShop/AMReX_NormalDerivative.H
Src/GeometryShop/AMReX_NormalDerivative.cpp
Src/GeometryShop/AMReX_NormalDerivativeImplem.H
Src/GeometryShop/AMReX_NormalDerivativeNew.H
Src/GeometryShop/AMReX_NormalDerivativeNewImplem.H
Src/GeometryShop/AMReX_Notation.H
Src/GeometryShop/AMReX_RefinementCriterion.H
Src/GeometryShop/AMReX_SmoothAbsoluteValue.cpp
Src/GeometryShop/AMReX_SmoothIntersection.cpp
Src/GeometryShop/AMReX_WrappedGShop.H
Src/GeometryShop/AMReX_WrappedGShop.cpp
Src/GeometryShop/Make.package

commit 09005870ec480b3fe785b2362d2f3013e240e3a6
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Mar 12 16:34:47 2018 -0700

    more slogging through the vast amount of code needed to get higher order geometric information.

Src/GeometryShop/AMReX_ConstrainedLS.cpp
Src/GeometryShop/AMReX_CutCellMoments.cpp
Src/GeometryShop/AMReX_CutCellMomentsImplem.H
Src/GeometryShop/AMReX_DivNormalRefinementImplem.H
Src/GeometryShop/AMReX_EBGeomDebugOut.H
Src/GeometryShop/AMReX_EBGeomDebugOut.cpp
Src/GeometryShop/AMReX_EB_TYPEDEFS.H
Src/GeometryShop/AMReX_IFDataImplem.H
Src/GeometryShop/AMReX_IndexedMoments.H
Src/GeometryShop/AMReX_IndexedMomentsImplem.H
Src/GeometryShop/AMReX_LSProblemImplem.H
Src/GeometryShop/AMReX_MinimalCCCM.cpp
Src/GeometryShop/AMReX_MinimalCCCMImplem.H
Src/GeometryShop/AMReX_MomentIterator.H
Src/GeometryShop/AMReX_NormalDerivative.cpp
Src/GeometryShop/AMReX_NormalDerivativeNew.H
Src/GeometryShop/AMReX_RefinementCriterion.H
Src/GeometryShop/AMReX_SmoothIntersection.cpp
Src/GeometryShop/AMReX_WrappedGShop.H
Src/GeometryShop/AMReX_WrappedGShop.cpp
Src/GeometryShop/Make.package

commit 41306e00d9a46d6abd85a58836a187377ba0cdcf
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Mar 12 12:31:43 2018 -0700

    the slog continues

Src/Base/AMReX_IntVect.H
Src/GeometryShop/AMReX_BaseIF.H
Src/GeometryShop/AMReX_ConstrainedLS.cpp
Src/GeometryShop/AMReX_CoordinateSystemImplem.H
Src/GeometryShop/AMReX_CutCellMoments.cpp
Src/GeometryShop/AMReX_Factorial.H
Src/GeometryShop/AMReX_IFSlicer.H
Src/GeometryShop/AMReX_IFSlicer.cpp
Src/GeometryShop/AMReX_IndexTM.H
Src/GeometryShop/AMReX_IndexTMI.H
Src/GeometryShop/AMReX_IndexedMomentsImplem.H
Src/GeometryShop/AMReX_LSProblem.cpp
Src/GeometryShop/AMReX_NormalDerivative.H
Src/GeometryShop/AMReX_NormalDerivative.cpp
Src/GeometryShop/AMReX_SmoothAbsoluteValue.H
Src/GeometryShop/AMReX_SmoothIntersection.H
Src/GeometryShop/AMReX_SmoothUnion.H
Src/GeometryShop/AMReX_SmoothUnion.cpp

commit 9f0695b565ffa011a535b949c73e5efdcde31b02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 11 18:27:34 2018 -0700

    move public apply from MLLinOp to MLMG

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit efe9926c8a6397ae1a1fa153e8ce11bb664f9119
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 11 16:18:28 2018 -0700

    add public apply function to MLLinOp

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 71436fbe29f1c28ac08e55e4375510694f0fad87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 11 14:07:09 2018 -0700

    MLMG: option to set max coarsening level

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp

commit 0b4cdc82ee82148b5d58d41eb617b5e0e92fd8cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 9 17:12:49 2018 -0800

    add amrex_malloc and amrex_free to Fortran module amrex_fort_module

Src/Base/AMReX_Utility.H
Src/Base/AMReX_fort_mod.F90

commit d5f6ad1b2819519758075c2e9fd44a0d352085c4
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Mar 9 15:57:30 2018 -0800

    slogging through the vast amount of code needed to get higher order geometric information.

Src/GeometryShop/AMReX_CH_EBIS_ORDER.H
Src/GeometryShop/AMReX_ConstrainedLS.H
Src/GeometryShop/AMReX_ConstrainedLS.cpp
Src/GeometryShop/AMReX_CoordinateSystem.H
Src/GeometryShop/AMReX_CoordinateSystemImplem.H
Src/GeometryShop/AMReX_CutCellMoments.H
Src/GeometryShop/AMReX_CutCellMoments.cpp
Src/GeometryShop/AMReX_CutCellMomentsImplem.H
Src/GeometryShop/AMReX_DivNormalRefinement.H
Src/GeometryShop/AMReX_DivNormalRefinementImplem.H
Src/GeometryShop/AMReX_EBGeomDebugDump.H
Src/GeometryShop/AMReX_EBGeomDebugOut.H
Src/GeometryShop/AMReX_EBGeomDebugOut.cpp
Src/GeometryShop/AMReX_EB_TYPEDEFS.H
Src/GeometryShop/AMReX_Factorial.H
Src/GeometryShop/AMReX_FixedRefinement.H
Src/GeometryShop/AMReX_FixedRefinementImplem.H
Src/GeometryShop/AMReX_GenericArithmetic.H
Src/GeometryShop/AMReX_GenericArithmeticI.H
Src/GeometryShop/AMReX_IFData.H
Src/GeometryShop/AMReX_IFData.cpp
Src/GeometryShop/AMReX_IFDataImplem.H
Src/GeometryShop/AMReX_IFSlicer.H
Src/GeometryShop/AMReX_IFSlicer.cpp
Src/GeometryShop/AMReX_IFSlicerImplem.H
Src/GeometryShop/AMReX_IndexTM.H
Src/GeometryShop/AMReX_IndexTMI.H
Src/GeometryShop/AMReX_IndexedMoments.H
Src/GeometryShop/AMReX_IndexedMomentsImplem.H
Src/GeometryShop/AMReX_LSProblem.H
Src/GeometryShop/AMReX_LSProblem.cpp
Src/GeometryShop/AMReX_LSProblemImplem.H
Src/GeometryShop/AMReX_MetaPrograms.H
Src/GeometryShop/AMReX_MinimalCCCM.H
Src/GeometryShop/AMReX_MinimalCCCM.cpp
Src/GeometryShop/AMReX_MinimalCCCMImplem.H
Src/GeometryShop/AMReX_MomentIterator.H
Src/GeometryShop/AMReX_MultiIndex.H
Src/GeometryShop/AMReX_MultiIndexImplem.H
Src/GeometryShop/AMReX_NoRefinement.H
Src/GeometryShop/AMReX_NoRefinementImplem.H
Src/GeometryShop/AMReX_NormalDerivative.H
Src/GeometryShop/AMReX_NormalDerivative.cpp
Src/GeometryShop/AMReX_NormalDerivativeImplem.H
Src/GeometryShop/AMReX_NormalDerivativeNew.H
Src/GeometryShop/AMReX_NormalDerivativeNewImplem.H
Src/GeometryShop/AMReX_Notation.H
Src/GeometryShop/AMReX_RefinementCriterion.H
Src/GeometryShop/AMReX_SmoothAbsoluteValue.H
Src/GeometryShop/AMReX_SmoothAbsoluteValue.cpp
Src/GeometryShop/AMReX_SmoothIntersection.H
Src/GeometryShop/AMReX_SmoothIntersection.cpp
Src/GeometryShop/AMReX_SmoothUnion.H
Src/GeometryShop/AMReX_SmoothUnion.cpp
Src/GeometryShop/AMReX_WrappedGShop.H
Src/GeometryShop/AMReX_WrappedGShop.cpp
Src/GeometryShop/Make.package

commit b70c2fa2edc7a8184cd67d7ab4dd6942cd9d7da6
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Mar 9 15:56:28 2018 -0800

    slogging through the vast amount of code needed to get higher order geometric information.

Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp

commit 0833f02f7ebad6191f8084e7c9d70485e7d9a10d
Author: Cy Chan <cychan@lbl.gov>
Date:   Thu Mar 8 20:35:20 2018 -0800

    bunch of small updates to fork-join
      follow some of weiqun's suggestions
      trying to follow existing AMReX conventions
      put mpi_tag back as frame member so each frame has its own copy

OldTutorials/MultiColor_C/AMReX_ForkJoin.H
OldTutorials/MultiColor_C/AMReX_ForkJoin.cpp
OldTutorials/MultiColor_C/AMReX_ParallelContext.H
OldTutorials/MultiColor_C/AMReX_ParallelContext.cpp
OldTutorials/MultiColor_C/main.cpp

commit 9a4b88f89a8ce8547966bcbbd826325dec5b2ce3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 8 16:04:00 2018 -0800

    don't use MPI_COMM_WORLD directly

Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp

commit 7896ed75bfae2392b09ad1bda36b06557b520098
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 8 14:14:47 2018 -0800

    improve profiling in Neighbor Particles.

Src/Particle/AMReX_NeighborParticlesI.H

commit dadca42e369721f3d3c3309823cfcdf420343fe3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 8 11:32:01 2018 -0800

    a bunch of small changes

OldTutorials/MultiColor_C/AMReX_ForkJoin.H
OldTutorials/MultiColor_C/AMReX_ForkJoin.cpp
OldTutorials/MultiColor_C/AMReX_ParallelContext.H
OldTutorials/MultiColor_C/AMReX_ParallelContext.cpp
OldTutorials/MultiColor_C/main.cpp

commit b333e5107963aab01339cfc84bc04bc335588ad1
Merge: 91e93a1c7 eef719e51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 8 08:56:09 2018 -0800

    Merge branch 'development' into forkjoin

commit e5a862513ca7ebf3f9ade5c3e7c2ab25bcf63d98
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 7 17:13:03 2018 -0800

    nodal projection: bug fix in restriction

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 91e93a1c75c2c1fdfd5f5e027d3c73b576eb6e02
Author: Cy Chan <cychan@lbl.gov>
Date:   Wed Mar 7 16:14:01 2018 -0800

    moved ParallelContext and ForkJoin into separate files

OldTutorials/MultiColor_C/AMReX_ForkJoin.H
OldTutorials/MultiColor_C/AMReX_ForkJoin.cpp
OldTutorials/MultiColor_C/AMReX_ParallelContext.H
OldTutorials/MultiColor_C/AMReX_ParallelContext.cpp
OldTutorials/MultiColor_C/GNUmakefile
OldTutorials/MultiColor_C/main.cpp

commit 3b4aa8d220e385d9873c13ed918d930c721a0e52
Author: Cy Chan <cychan@lbl.gov>
Date:   Wed Mar 7 15:37:56 2018 -0800

    fork join can be invoked multiple times using same ForkJoin object
      reuses forked multifabs and distribution maps across invocations
      added distribution map cache member
      added verbose debugging information

OldTutorials/MultiColor_C/main.cpp

commit 9eb5075c0c4f7aff6ad6f42ea2654000487c6138
Merge: 5d5fb8472 eef719e51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 7 14:47:16 2018 -0800

    Merge branch 'development' into weiqun/mlmg

commit eef719e51d051f567f881d40a3b0a65e050a61bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 7 14:44:09 2018 -0800

    mlmg: print the correct residual for vebose>=4

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 5d5fb8472069c4ad73a87d37a799acb9d8d634dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 7 13:52:57 2018 -0800

    nodal projection: allow coarsening strategy be sigma for all regular eb

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H

commit 50277b148f35658256da1561ebe7481331b5bf57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 7 13:34:16 2018 -0800

    nodal projection: in restriction and interpolation, if both weights are zero, take average

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit d3b77e1b17d62c0fbef20ab0cdeb06de07049c77
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 7 12:58:44 2018 -0800

    nodal projection: fix bug

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 697fa1c51152add37a57c27eb09fb1f85cb157a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 7 12:52:30 2018 -0800

    nodal projection: fix array bound and index bug

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 0b2beeaf21d0201146ccf353582bbb4413e7119f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 7 12:50:55 2018 -0800

    nodal projection: fix array bound

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 95805cbf7cf80bfe7160a21d9a9b742efe84c09e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 7 12:49:22 2018 -0800

    nodal projection: fix divide by zero and change some parameters back to default

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit b813065eee6ef8c199793727446577dc7777c10c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 7 09:57:03 2018 -0800

    WIP: RAP stencil for testing constant sigma

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 39949bac97468583f2dbefcdd1cd5a831a08990f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 7 09:50:44 2018 -0800

    3d nodal projection: RAP version of restriction

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 94719de7b9dddfef01594c0c791127d2be32a9f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 6 17:32:04 2018 -0800

    remove _images/ from top directory because the only figure there has a copy already in Docs/ as it should be

_images/ParaView_filegroup.png

commit 0778227cf9bbfab34a7aac0fba479a34aa81d09f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 6 17:07:21 2018 -0800

    WIP: RAP version of restriction

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit e633e791b3e2394abe3127c0cc17d2377b07f7ba
Author: Cy Chan <cychan@lbl.gov>
Date:   Tue Mar 6 16:26:46 2018 -0800

    only create distribution mapping object once per (box array, task) pair
      multiple multifabs accessed by each task may share the same boxarray
      they need to have same distribution mapping

OldTutorials/MultiColor_C/main.cpp

commit dca5d8d1ad137dbfb5000ed0038d5c92180b09c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 6 14:33:44 2018 -0800

    3d nodal projection: RAP version of interpolation

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 3d03bedf29b8e5a2c74b309ffa6d3e2087676ed9
Author: Cy Chan <cychan@lbl.gov>
Date:   Tue Mar 6 14:14:39 2018 -0800

    more work on fork join and parallel context frames:
      updated local/global rank translation
      added mpi tag getter/incrementer with wrap-around
      init first frame to ParallelDescriptor::Communicator
      update asserts to AMREX_ style
      update enum to enum class

OldTutorials/MultiColor_C/main.cpp
Src/Base/AMReX_ParallelDescriptor.H

commit b51d4969607f8cd40400d362651bd411f5a1efad
Merge: e3285d7fe e9746fd49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 6 13:14:52 2018 -0800

    Merge branch 'development' into weiqun/mlmg

commit 346dd5ecb000d0f922293f3c75b417d225e7d74b
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Tue Mar 6 10:21:08 2018 -0700

    added update for ghost corners (2D only)

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90

commit e9746fd49dcebd96886e07c39902483c6847e0bf
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Mar 6 09:04:50 2018 -0800

    put this preprocessor macro back.

Src/GeometryShop/AMReX_EBFluxFAB.H

commit c342b9780da37b12754f73c7658bb85cb7406d7a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 5 16:29:42 2018 -0800

    Update the multifab norms to use versions in Src/Base instead of local definitions.

Tests/LinearSolvers/C_CellMG/macprojTest.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit e3285d7fee0e51fa840fe2de9a473fe4c3206b4b
Merge: 736ea1c12 d38afdc30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 5 16:17:11 2018 -0800

    Merge branch 'development' into weiqun/mlmg

commit d38afdc30c809a0b24673420a90c3900b56bbfaf
Merge: 5a32e6056 14618f725
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 5 16:16:15 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5a32e605658428987b7ba55399e172c7b14ce5f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 5 16:08:19 2018 -0800

    update CHANGES

CHANGES

commit 223639fc5f63fae860dbfa5b0837a2e1771015ad
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Mon Mar 5 17:00:10 2018 -0700

    removed comment

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 5e481b2f3719fb0822334db94328457404486331
Author: Cy Chan <cychan@lbl.gov>
Date:   Mon Mar 5 12:13:21 2018 -0800

    added single mode for MF access in fork-join
    added task bound split calculation
    misc. clean up

OldTutorials/MultiColor_C/main.cpp

commit 14618f7253b7dcec48b2916f7505784be367b832
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 5 09:36:45 2018 -0800

    Cleaning out more headings for consistency

Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H
Src/EBAMRElliptic/AMReX_BaseBCFuncEval.H
Src/EBAMRElliptic/AMReX_BiCGStabSolver.H
Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H
Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp
Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOp.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp
Src/EBAMRElliptic/AMReX_EBMultiGrid.H
Src/EBAMRElliptic/AMReX_EBSimpleSolver.H
Src/EBAMRElliptic/AMReX_EBSimpleSolver.cpp
Src/EBAMRElliptic/AMReX_LinearSolver.H
Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.H
Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp
Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H
Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp
Src/EBAMRElliptic/AMReX_NoOpSolver.H
Src/EBAMRElliptic/AMReX_VCAggStencil.H
Src/EBAMRElliptic/AMReX_VCAggStencil.cpp
Src/EBAMRTools/AMReX_EBCoarseAverage.cpp

commit bd1ffca734663cca65becd2800f8284a35f22429
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 5 09:30:43 2018 -0800

    More consistency fixes.

Src/GeometryShop/AMReX_ZCylinder.H
Src/GeometryShop/AMReX_ZCylinder.cpp

commit be1b3293546291d67b9be72d46ea954adb0c9d40
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 5 09:28:45 2018 -0800

    For consistency, remove logo at top of files.  If we decide on a common header later we can then
    add it to all files uniformly

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseIndex.H
Src/Base/AMReX_BoxIterator.H
Src/Base/AMReX_BoxIterator.cpp
Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp
Src/Base/AMReX_SPMD.H
Src/Base/AMReX_SPMD.cpp
Src/Base/AMReX_SPMDI.H
Src/Base/AMReX_parstream.H
Src/Base/AMReX_parstream.cpp
Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H
Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp
Src/EBAMRTools/AMReX_DivergenceOp.H
Src/EBAMRTools/AMReX_DivergenceOp.cpp
Src/EBAMRTools/AMReX_EBCFInterp.H
Src/EBAMRTools/AMReX_EBCFInterp.cpp
Src/EBAMRTools/AMReX_EBCoarseAverage.H
Src/EBAMRTools/AMReX_EBFastFR.H
Src/EBAMRTools/AMReX_EBFastFR.cpp
Src/EBAMRTools/AMReX_EBFineInterp.H
Src/EBAMRTools/AMReX_EBFineInterp.cpp
Src/EBAMRTools/AMReX_EBLevelDataOps.H
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Src/EBAMRTools/AMReX_GradientOp.H
Src/EBAMRTools/AMReX_GradientOp.cpp
Src/EBAMRTools/AMReX_MeshRefine.H
Src/EBAMRTools/AMReX_MeshRefine.cpp
Src/GeometryShop/AMReX_AggStencil.H
Src/GeometryShop/AMReX_AggStencilI.H
Src/GeometryShop/AMReX_AllRegularService.H
Src/GeometryShop/AMReX_AllRegularService.cpp
Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H
Src/GeometryShop/AMReX_AnisotropicIF.H
Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_BaseEBCellFABI.H
Src/GeometryShop/AMReX_BaseEBCellFactory.H
Src/GeometryShop/AMReX_BaseEBFaceFAB.H
Src/GeometryShop/AMReX_BaseEBFaceFABI.H
Src/GeometryShop/AMReX_BaseIF.H
Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_BaseIFFactory.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/AMReX_BaseIVFactory.H
Src/GeometryShop/AMReX_CellEdge.H
Src/GeometryShop/AMReX_CellEdge.cpp
Src/GeometryShop/AMReX_ComplementIF.H
Src/GeometryShop/AMReX_ComplementIF.cpp
Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBArith.cpp
Src/GeometryShop/AMReX_EBCellFAB.H
Src/GeometryShop/AMReX_EBCellFAB.cpp
Src/GeometryShop/AMReX_EBCellFactory.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBDataFactory.H
Src/GeometryShop/AMReX_EBDataVarMacros.H
Src/GeometryShop/AMReX_EBDebugDump.H
Src/GeometryShop/AMReX_EBDebugOut.H
Src/GeometryShop/AMReX_EBDebugOut.cpp
Src/GeometryShop/AMReX_EBFaceFAB.H
Src/GeometryShop/AMReX_EBFaceFAB.cpp
Src/GeometryShop/AMReX_EBFluxFAB.H
Src/GeometryShop/AMReX_EBFluxFAB.cpp
Src/GeometryShop/AMReX_EBFluxFactory.H
Src/GeometryShop/AMReX_EBFluxFactory.cpp
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISBox.H
Src/GeometryShop/AMReX_EBISBox.cpp
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Src/GeometryShop/AMReX_EBLevelGrid.H
Src/GeometryShop/AMReX_EBLevelGrid.cpp
Src/GeometryShop/AMReX_EBLevelRedist.H
Src/GeometryShop/AMReX_EBLevelRedist.cpp
Src/GeometryShop/AMReX_EBLoHiCenter.H
Src/GeometryShop/AMReX_EBLoHiCenter.cpp
Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H
Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp
Src/GeometryShop/AMReX_Ellipsoid.cpp
Src/GeometryShop/AMReX_EllipsoidIF.H
Src/GeometryShop/AMReX_EllipsoidIF.cpp
Src/GeometryShop/AMReX_ExtrudeIF.H
Src/GeometryShop/AMReX_ExtrudeIF.cpp
Src/GeometryShop/AMReX_FabArrayIO.H
Src/GeometryShop/AMReX_FabArrayIO.cpp
Src/GeometryShop/AMReX_FaceIndex.H
Src/GeometryShop/AMReX_FaceIndex.cpp
Src/GeometryShop/AMReX_FaceIterator.H
Src/GeometryShop/AMReX_FaceIterator.cpp
Src/GeometryShop/AMReX_FlatPlateGeom.H
Src/GeometryShop/AMReX_FlatPlateGeom.cpp
Src/GeometryShop/AMReX_GeometryService.H
Src/GeometryShop/AMReX_GeometryService.cpp
Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_GraphNode.H
Src/GeometryShop/AMReX_GraphNode.cpp
Src/GeometryShop/AMReX_IntVectSet.H
Src/GeometryShop/AMReX_IntVectSet.cpp
Src/GeometryShop/AMReX_IntersectionIF.H
Src/GeometryShop/AMReX_IntersectionIF.cpp
Src/GeometryShop/AMReX_IrregFAB.H
Src/GeometryShop/AMReX_IrregFAB.cpp
Src/GeometryShop/AMReX_IrregFABFactory.H
Src/GeometryShop/AMReX_IrregFABFactory.cpp
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_IrregNode.cpp
Src/GeometryShop/AMReX_KDStruct.H
Src/GeometryShop/AMReX_LSquares.H
Src/GeometryShop/AMReX_LSquares.cpp
Src/GeometryShop/AMReX_LatheIF.H
Src/GeometryShop/AMReX_LatheIF.cpp
Src/GeometryShop/AMReX_LoHiSide.H
Src/GeometryShop/AMReX_LoHiSide.cpp
Src/GeometryShop/AMReX_Moments.H
Src/GeometryShop/AMReX_Moments.cpp
Src/GeometryShop/AMReX_PXStuff.H
Src/GeometryShop/AMReX_PXStuff.cpp
Src/GeometryShop/AMReX_PlaneIF.H
Src/GeometryShop/AMReX_PlaneIF.cpp
Src/GeometryShop/AMReX_PolyGeom.H
Src/GeometryShop/AMReX_PolyGeom.cpp
Src/GeometryShop/AMReX_PolynomialIF.H
Src/GeometryShop/AMReX_PolynomialIF.cpp
Src/GeometryShop/AMReX_RedistStencil.H
Src/GeometryShop/AMReX_RedistStencil.cpp
Src/GeometryShop/AMReX_STLAsciiReader.H
Src/GeometryShop/AMReX_STLAsciiReader.cpp
Src/GeometryShop/AMReX_STLBox.H
Src/GeometryShop/AMReX_STLBox.cpp
Src/GeometryShop/AMReX_STLExplorer.H
Src/GeometryShop/AMReX_STLExplorer.cpp
Src/GeometryShop/AMReX_STLIF.H
Src/GeometryShop/AMReX_STLIF.cpp
Src/GeometryShop/AMReX_STLMesh.H
Src/GeometryShop/AMReX_STLMesh.cpp
Src/GeometryShop/AMReX_STLReader.H
Src/GeometryShop/AMReX_STLUtil.H
Src/GeometryShop/AMReX_STLUtil.cpp
Src/GeometryShop/AMReX_SlabService.H
Src/GeometryShop/AMReX_SlabService.cpp
Src/GeometryShop/AMReX_SphereIF.H
Src/GeometryShop/AMReX_SphereIF.cpp
Src/GeometryShop/AMReX_Stencils.H
Src/GeometryShop/AMReX_Stencils.cpp
Src/GeometryShop/AMReX_TransformIF.H
Src/GeometryShop/AMReX_TransformIF.cpp
Src/GeometryShop/AMReX_UnionIF.H
Src/GeometryShop/AMReX_UnionIF.cpp
Src/GeometryShop/AMReX_VoFIterator.H
Src/GeometryShop/AMReX_VoFIterator.cpp
Src/GeometryShop/AMReX_VolIndex.H
Src/GeometryShop/AMReX_VolIndex.cpp

commit c884ae8b39ffe062ac7951c06edfa43cfb4942cc
Merge: b1141c379 77b41c8c0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Mar 5 08:55:37 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit b1141c37903dea1e54c6bcd7f12032aaf9226254
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Mar 5 08:55:21 2018 -0800

    fixed a bug in ZCylinder

Src/GeometryShop/AMReX_ZCylinder.cpp

commit 77b41c8c0b2dd35c7cb4b30614cd4504f7b39641
Merge: 9be5d5c21 ec28cce9f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Mar 3 22:32:28 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9be5d5c21598baacc3d1d014ce02f8196fc8e7cd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Mar 3 22:30:23 2018 -0800

    improving the scaling of particle redistribute when the changes are known to be local.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit ec28cce9f3cf297f400e46908c29a37c4b39a017
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Mar 2 16:13:53 2018 -0800

    added simple cylinder geometry

Src/GeometryShop/AMReX_ZCylinder.H
Src/GeometryShop/AMReX_ZCylinder.cpp
Src/GeometryShop/Make.package

commit e847daf41defdca24ff68f4b54efd925a65e4922
Author: Cy Chan <cychan@lbl.gov>
Date:   Fri Mar 2 15:41:42 2018 -0800

    working on test implementation of fork-join

OldTutorials/MultiColor_C/inputs
OldTutorials/MultiColor_C/main.cpp

commit 65365bfc2c01814adcc98d84cc2be28d068368a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 2 10:48:16 2018 -0800

    new BoxList constructor making n Boxes by chopping a given Box in a given direction

Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp

commit 50fff4d78925e696f447695b401b09bd3c8eab7d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 2 10:46:42 2018 -0800

    add enum class Direction

Src/Base/AMReX_Orientation.H

commit b23830bf83ba1195c17a1d75e125c038b2c3f28c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 2 10:04:19 2018 -0800

    more flush fixed

MiniApps/SMC/main.f90
MiniApps/SMC/smc.f90
OldTutorials/AMR_Adv_F/Source/main.f90
OldTutorials/Random_F/main.f90

commit ad7612d53c6127b6b24341cf49ab46afaf15976d
Merge: edc840b8b 657ea8953
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Mar 2 09:56:12 2018 -0800

    Merge pull request #219 from AMReX-Codes/flush
    
    Use Fortran intrinsic flush instead of call flush

commit edc840b8bba48d1194a1f7b6dc217f3be4b11a7c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 2 09:53:08 2018 -0800

    new BoxList constructor that makes n Boxes from a single Box where n is an argument to the constructor

Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp

commit 0aa64f454154462dbb4bc2575ac2606a13632645
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 1 19:10:31 2018 -0800

    Add README for Tutorials/SWFFT

Tutorials/SWFFT/README

commit 38aac2164fbb7c62f9f24fc3413602220294169a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 1 19:04:39 2018 -0800

    Change in comment only.

Src/Base/AMReX_parstream.H
Src/Base/AMReX_parstream.cpp

commit 736ea1c12a6671898b59f0f5fca47ad21d92297e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 1 17:17:33 2018 -0800

    WIP nodal projection

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H

commit b3f5199f311950c2cf15100f7118f9fa4776099d
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Thu Mar 1 17:45:47 2018 -0700

    Basic multicomponent MLMG solves working in 2D.

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_F.H

commit ed3caea3dd6e09931f9a07ba75839fb643196ec4
Merge: 1c96a5dc8 5dead2f82
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 1 15:36:41 2018 -0800

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 1c96a5dc890fee30353fac07c6c5e93aaab01c9a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 1 15:36:30 2018 -0800

    update AMReX_BCUtil.cpp to reflect recent API change to the wrapper around cudaMemcpyAsync.

Src/Base/AMReX_BCUtil.cpp

commit efd18d378bf41a6ebe6d11847ab8c0af878b6aef
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 1 15:34:50 2018 -0800

    remove use of 'ParticleVector', which doesn't exist on the gpu branch anymore

Src/Particle/AMReX_Particles.H

commit 17695c10fed47f2b7049ef73aba32fa7984c87a8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 1 13:18:22 2018 -0800

    Remove unused MyProc and quiet some gnu compiler warnings.

Src/Particle/AMReX_ParticleContainerI.H

commit 66b35f1562bbd67e1e5e0bce0fcfe3046759f548
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Mar 1 13:01:50 2018 -0500

    add an option to specific the height (in 2-d) for a slice

Tools/Postprocessing/F_Src/fextract.f90

commit 36a225792114c7b424a7a72a2bed10d004988a94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 1 08:47:24 2018 -0800

    update CHANGES

CHANGES

commit 7ac4a5f608e33cd5301df1d14a6825cc12f88119
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 1 08:45:32 2018 -0800

    update CHNAGES

CHANGES

commit 87c7fe6daf22076c2321921911858ad340706cc0
Author: Brandon Runnels <brunnels@uccs.edu>
Date:   Wed Feb 28 16:46:27 2018 -0700

    Began update for MLMG, MLCG, MLLinop, MLCellLinop for multicomponent.

Src/Base/AMReX_DistributionMapping.cpp
Src/Boundary/AMReX_BndryData.cpp
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 5180b0d7e21a21f08341c5361b88a5373fca57e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 28 15:12:25 2018 -0800

    nodal projection: allow rhnd for rap if it's zero

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit b75aef02f7ac9770033bb991a2e78cdbfe700961
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 28 14:45:51 2018 -0800

    nodal projection: clean up the simple rap

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit b34a4d2c36f44731132a1895929f385bf3a265ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 28 14:36:25 2018 -0800

    3d eb nodal projection: smoothers

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 7591f704a9f63b6a6f66428aaa89ec2c5eaf8fe9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 28 14:08:46 2018 -0800

    3d eb nodal projection: stencil verion of A dot x

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 4e4750071a51c6ed288513101f75eaec73c26a18
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Feb 28 12:43:45 2018 -0800

    Fix comments

Tools/GNUMake/sites/Make.olcf

commit 957bb4799f1b94bf74c6655a707349bdd28632ef
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Feb 28 11:54:23 2018 -0800

    Add README and clean up GNUmakefile

Tutorials/SWFFT/GNUmakefile
Tutorials/SWFFT/inputs

commit 8906e0b6edc4bc84767e8e532829f2e29660f071
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Feb 28 11:35:24 2018 -0800

    Slight tweaks

Tutorials/SWFFT/SWFFT_Solver.cpp
Tutorials/SWFFT/main.cpp

commit ccc5b95fda7c08777b1a400e9936b9b1c78a7298
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Feb 28 11:18:51 2018 -0800

    Add Tutorial demonstrating how to call the SWFFT wrapper for the fftw3 solver.

Tutorials/SWFFT/GNUmakefile
Tutorials/SWFFT/Make.package
Tutorials/SWFFT/SWFFT_Solver.H
Tutorials/SWFFT/SWFFT_Solver.cpp
Tutorials/SWFFT/SWFFT_Solver_F.F90
Tutorials/SWFFT/SWFFT_Solver_F.H
Tutorials/SWFFT/inputs
Tutorials/SWFFT/main.cpp

commit 0d77ae144421eb461bf42ade2ed6cf0557248a11
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 28 09:07:01 2018 -0500

    fix typo to make things compile

Src/Amr/AMReX_extrapolater_2d.f90

commit dea01be4a4c2ade864a347028f7ecdd6199a98ff
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 27 17:27:54 2018 -0800

    BL_SPACEDIM --> AMREX_SPACEDIM

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AuxBoundaryData.cpp
Src/Amr/AMReX_Derive.cpp
Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StateDescriptor.cpp
Src/Amr/AMReX_extrapolater_2d.f90

commit 82f31414e847bce472f92d27a6d317ab93a427ef
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 27 17:25:41 2018 -0800

    BL_SPACEDIM --> AMREX_SPACEDIM

Src/Boundary/AMReX_BndryData.H
Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_INTERPBNDRYDATA_F.H
Src/Boundary/AMReX_InterpBndryData.cpp

commit d53ae887137cc7fdd765dbe2d66e5e65acea2730
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 27 17:23:08 2018 -0800

    BL_SPACEDIM --> AMREX_SPACEDIM

Src/GeometryShop/AMReX_EBArith.cpp
Src/GeometryShop/AMReX_EBDataVarMacros.H
Src/GeometryShop/AMReX_EBFluxFAB.H
Src/GeometryShop/AMReX_EBLoHiCenter.H
Src/GeometryShop/AMReX_EBLoHiCenter.cpp
Src/GeometryShop/AMReX_ExtrudeIF.cpp
Src/GeometryShop/AMReX_GeometryService.cpp
Src/GeometryShop/AMReX_LatheIF.cpp
Src/GeometryShop/AMReX_PolyGeom.H
Src/GeometryShop/AMReX_PolyGeom.cpp
Src/GeometryShop/AMReX_STLExplorer.cpp
Src/GeometryShop/AMReX_TransformIF.cpp
Src/GeometryShop/AMReX_VolIndex.cpp

commit a0acf94ef5e1294aca268e395c69809e97522299
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 27 17:17:24 2018 -0800

    Change BL_SPACEDIM --> AMREX_SPACEDIM

Src/Particle/AMReX_LoadBalanceKD.cpp
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_Particles_F.H
Src/Particle/AMReX_TracerParticles.H
Src/Particle/AMReX_TracerParticles.cpp

commit 2ab1c6c5bdaca7c6a473f9f41bef8d2e4f8c9683
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 27 17:02:24 2018 -0800

    3d eb nodal projection: set integral and connection

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 028c3da1b7b7d7e281a5195418fe39ac877651f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 27 20:00:34 2018 -0500

    fix spelling of AMREX_SPACEDIM

Src/Base/AMReX_DistributionMapping.cpp

commit cc7fadc99473554106605c998dbd9dd22b5c2c66
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 27 16:01:06 2018 -0800

    Replace BL_SPACEDIM by AMREX_SPACEDIM

Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FillPatchUtil_F.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_F.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrCore/AMReX_TagBox.cpp

commit 38229c41f84d353e20a88c88c1528877a9da4693
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 27 15:57:43 2018 -0800

    Replace BL_SPACEDIM by AMREX_SPACEDIM.

Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCRec.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxIterator.H
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_Orientation.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_Periodicity.cpp
Src/Base/AMReX_PhysBCFunct.cpp
Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp
Src/Base/AMReX_RealVect.H
Src/Base/AMReX_SPACE_F.H
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_filcc_mod.F90
Src/Base/AMReX_iMultiFab.cpp

commit 57309720ba4d406024b2250334192d63d6a99fc0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Feb 27 14:55:17 2018 -0800

    Update with 3rd and 4th slide decks

Docs/sphinx/source/Chapter12.rst

commit 5dead2f8232fd2abf3190de102e54fbf3ab3bc1d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Feb 26 13:11:05 2018 -0500

    Hook in register capping to IBM compiler

Tools/GNUMake/comps/ibm.mak

commit ab9529cd42f6fde3106f82dfa49c304c05b9dc86
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 24 20:55:46 2018 -0500

    Do cudaMemcpyAsync in C++, not Fortran

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_MFIter.cpp

commit 43f46d9a3941630f5c69266cf00f888b658f564c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 24 19:52:11 2018 -0500

    Handle maximum register counts

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/pgi.mak

commit 7e364b327c650139c1a6da03e9c4aec67e571e2f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 24 19:14:59 2018 -0500

    Avoid unnecessary MPI linking for non-MPI code with IBM

Tools/GNUMake/comps/ibm.mak

commit b96bc6bab0f0fd99c62f8fa4947077bb35bf4030
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 24 16:49:36 2018 -0500

    Generalize CUDA version/compute capabilities

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/Linux_pgi.mak

commit 3573919681cf6a85759b521341b4dfb239b7c6a4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Feb 24 16:33:06 2018 -0500

    Fix preprocessing issues on summit

Tools/F_mk/GMakedefs.mak

commit f195760b543870c32f7aae0ac44d6b62058722c0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Feb 23 20:45:45 2018 -0500

    Specify a default maximum of 512 threads per CUDA threadblock
    
    This is because we usually need 8 threads to handle ghost zones
    in a FillPatch, and in a corner this could require 8x8x8 = 512
    threads, so the default maximum should allowe for this case.

Tools/GNUMake/Make.defs

commit 8788b19401638e9b843859b8ae5278019875ae68
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Feb 23 20:45:36 2018 -0500

    Specify CUDA/compute capabilities for summit/summitdev

Tools/GNUMake/sites/Make.olcf

commit ed75545e90a25f820c90a4ebef2e51c3a040d301
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Feb 23 20:45:09 2018 -0500

    Allow for a more general selection of CUDA version

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/pgi.mak

commit 5f016bff214b2990f877078a180c2d5fd5447d00
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Feb 23 18:42:08 2018 -0500

    Remove unnecessary CUDA specification

Tools/GNUMake/comps/pgi.mak

commit 32728af90fd47324cbaf76fe0ed1a9f789bcc4f0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Feb 23 18:33:42 2018 -0500

    Disable NVML on Summit since it's not working right now

Tools/GNUMake/sites/Make.olcf

commit bf193fbca005bc85e84e1546c7db46590014df19
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Feb 23 18:32:50 2018 -0500

    Only do immediate gcc_version expansion for CUDA

Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/pgi.mak

commit f57c584067a2048258c808378dbc49a016530ee3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 23 14:06:02 2018 -0800

    mlmg: add assertions to some untested functions

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit ca336b11febce1ec122815c5cae6cd05d64e52e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 23 13:56:42 2018 -0800

    mlmg: MLALaplacian

Src/LinearSolvers/MLMG/AMReX_MLALap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLALap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLALap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLALap_F.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp

commit bcf9afa014a4314ce080223a91a384ea1a0a895a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 23 13:43:45 2018 -0800

    mlmg: rescale 1d & 2d MLPoisson for bicgstab

Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H

commit 12c0d85eed3d9ff9c386d65fed55d07355ac0034
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 23 13:03:25 2018 -0800

    mlmg: rescale MLABecLaplacian for bicgstab

Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp

commit 4c4f445125fa31f891c0ea901ef8ca0af58716a2
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Feb 23 10:24:19 2018 -0800

    CMake: update source list for C_CellMG folder

Src/LinearSolvers/CMakeLists.txt

commit b61d124098cac6c9d38a77122d81ee2b7d7fd482
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Feb 22 22:52:27 2018 -0800

    Update XL flags (#186)
    
    * Tools: move common XL Fortran compiler flags to GENERIC_IBM_FLAGS
    
    * Tools: add flag to enforce fixed form format in XL FORTRAN 77 compiler
    
    This compiler makes assumptions about the source code format based on
    file suffixes, which leads to errors when compiling some AMReX files.
    Fix this by explicitly stating the source code style with this flag.
    
    * Tools: change XL MPI compiler wrappers on summitdev to "mpifort"
    
    The OpenMPI man page for "mpif90" and "mpif77" notes that these wrappers
    are deprecated, and that one should instead use "mpifort" for all
    Fortran files, both free and fixed format. The observant user will note
    also that all three wrappers point to the same file ("opal_wrapper").
    
    This change is currently in contradiction with the documentation on the
    OLCF summitdev website, which recommends continued use of "mpif77" and
    "mpif90".

Tools/GNUMake/comps/ibm.mak
Tools/GNUMake/sites/Make.olcf

commit 67e8009776db0db6ebd53cb6b51a9d3de195b473
Merge: bfc22c0d5 946016376
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 22 17:12:15 2018 -0800

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 167afe92688b906ed4af26321033276b75bf60d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 22 16:30:09 2018 -0800

    nd mlmg: rescale the problem in bicgstab

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 272f98b948cef9c413bd72e1d1796bb957091433
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 22 14:01:45 2018 -0800

    use local parameter

Src/Base/AMReX_constants_mod.f90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit d255390457da0848e3f2a8807687f8e60ef7c013
Merge: 25eee949b 54ad68433
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 22 13:56:48 2018 -0800

    Merge branch 'development' into weiqun/mlmg

commit 25eee949b3ec32d9d99d49b3dacc6af38ac9ad11
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 22 13:40:35 2018 -0800

    rm centroid from EBTower

Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp

commit 54b2d16dc8517843d24a95399033b0635edf478d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 22 13:34:56 2018 -0800

    nodal projection: stub for 1d and 3d

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit aaeeed173412ec122d1804e2c4df8f967628603f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 22 11:57:01 2018 -0800

    nodal projection: clean up

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 946016376c16d231cd85fdd8a161075d852391f8
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Feb 22 03:35:44 2018 -0500

    Switch to C++ for UM hints

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit fd727ab3094711fd60cee1d2c7e5560902e702dc
Author: Donald E. Willcox <dwillcox@users.noreply.github.com>
Date:   Thu Feb 22 01:12:30 2018 -0500

    Change default CUDA_VERSION to 9.0 in Fortran build system. (#220)
    
    This changes the default CUDA version in the Fortran build system back to 9.0 instead of 8.0.
    
    CUDA 9.0 was formerly (cf. commit 23486c8) the default version of CUDA in the Fortran build system.

Tools/F_mk/GMakedefs.mak

commit ae42480af6c257c4a7bb9aeda3159ae2501387f7
Merge: 9369c0212 54ad68433
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Feb 22 00:18:39 2018 -0500

    Merge branch 'development' into gpu

commit 54ad684337aa3de8e5e967e172582338eb66fe91
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Feb 22 00:05:38 2018 -0500

    Use the correct flag for enabling OpenMP in XL

Tools/GNUMake/comps/ibm.mak

commit 657ea89535450161bf706d421524f71e40d9b4b0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Feb 21 23:30:51 2018 -0500

    call flush -> flush

Src/F_BaseLib/multifab_physbc_edgevel.f90

commit ccb5e0f20ef2f270b076a3cd7248d9a8681a1861
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Feb 21 23:29:57 2018 -0500

    call flush -> flush

Src/LinearSolvers/F_MG/cc_mg_cpp.f90

commit f69591db1fcf9f138a6740632fcd62f585e1b918
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Feb 21 23:24:31 2018 -0500

    Move more F77 to F90 to please XL

Src/Amr/AMReX_ARRAYLIM_1D.F
Src/Amr/AMReX_ARRAYLIM_1D.F90
Src/Amr/AMReX_ARRAYLIM_2D.F
Src/Amr/AMReX_ARRAYLIM_2D.F90
Src/Amr/AMReX_ARRAYLIM_3D.F
Src/Amr/AMReX_ARRAYLIM_3D.F90
Src/Amr/CMakeLists.txt
Src/Amr/Make.package
Src/AmrCore/AMReX_FLUXREG_1D.F90
Src/AmrCore/AMReX_FLUXREG_2D.F90
Src/AmrCore/AMReX_FLUXREG_3D.F90
Src/AmrCore/AMReX_INTERP_1D.F90
Src/AmrCore/AMReX_INTERP_2D.F90
Src/AmrCore/AMReX_INTERP_3D.F90
Src/AmrCore/CMakeLists.txt
Src/AmrCore/Make.package
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90
Src/Boundary/AMReX_LO_UTIL.F90
Src/Boundary/CMakeLists.txt
Src/Boundary/Make.package
Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F
Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F
Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F
Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F
Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F
Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90
Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90
Src/LinearSolvers/C_CellMG/Make.package

commit 9369c0212d0138749fd677da16ad350ae94ab8f4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 21 18:45:38 2018 -0800

    enforce max thread count in each direction (#218)
    
    Sometimes the current code create blocks that have too many threads in the z-direction.

Src/Base/AMReX_CUDA.F90

commit bfc22c0d510041bad5f862e5b9314d7266e13fe9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 21 17:01:01 2018 -0800

    enforce max thread count in each direction

Src/Base/AMReX_CUDA.F90

commit ecab00c52f1c3b75007a8efc5f91f56f0b394f88
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 21 16:03:41 2018 -0800

    re-add this figure.

Docs/sphinx/source/Visualization/ParaView_filegroup.png

commit 02f8955f8834e0fed3e60ca0102aed5d12d1a0e6
Author: Utkarsh Ayachit <utkarsh.ayachit@kitware.com>
Date:   Wed Feb 21 15:22:19 2018 -0500

    update docs for ParaView viz.
    
    Updated docs to reflect the new workflow for reading particles in
    ParaView 5.5.

Docs/sphinx/source/Visualization.rst
_images/ParaView_filegroup.png

commit 795968f9dc65738d32bcf30d5960af60b5d86684
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Feb 21 15:16:56 2018 -0800

    Have the default be to build the optimized version

Tests/GeometryShop/STLGeom/GNUmakefile

commit 564bc61f6b285d929215fbf940a4ddb438c6498b
Merge: 222a163a6 14c34c32a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Feb 21 17:19:56 2018 -0500

    Merge branch 'development' into gpu

commit 14c34c32aa1ef18f262b4982533c66e88ddbd523
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Feb 21 17:19:19 2018 -0500

    Restore coalesced fabs option

Src/Base/AMReX_BaseFab.cpp

commit 222a163a6e885e12632caec7cc3de5aeac25f8d2
Merge: 67786385f 0b0b1a192
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Feb 21 15:42:33 2018 -0500

    Merge branch 'development' into gpu

commit 0b0b1a1922eba589ed7f6714c578d8703dc1a521
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Feb 21 14:55:22 2018 -0500

    Make XLF compiler accept C-style comments

Tools/GNUMake/comps/ibm.mak

commit 9fa9ae65b89afe66ffc629e209db004ecdca78cc
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Feb 21 14:32:20 2018 -0500

    Convert some F77 files to F90
    
    This is mainly done to make the IBM compiler happy

Src/Base/AMReX_BLBoxLib_F.F90
Src/Base/AMReX_BLBoxLib_F.f
Src/Base/AMReX_BLParmParse_F.F90
Src/Base/AMReX_BLParmParse_F.f
Src/Base/AMReX_BLProfiler_F.F90
Src/Base/AMReX_BLProfiler_F.f
Src/Base/AMReX_BLutil_F.F90
Src/Base/AMReX_BLutil_F.f
Src/Base/AMReX_COORDSYS_1D.F
Src/Base/AMReX_COORDSYS_1D.F90
Src/Base/AMReX_COORDSYS_2D.F
Src/Base/AMReX_COORDSYS_2D.F90
Src/Base/AMReX_COORDSYS_3D.F
Src/Base/AMReX_COORDSYS_3D.F90
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 5e21d7f1c163675f50ed58c7af7fbf8ac080124d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 21 10:55:09 2018 -0800

    nodal projection: flag to use simple interpolation

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 27646d6fd8a4950f975c6f4eefc843ddece9a72b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 20 16:58:27 2018 -0800

    nodal projection: 2d rap for eb

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit a82a2f97c423ed264ffdfd6dca3b550e07c72648
Merge: 4585db76f 4dac05918
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Feb 20 14:57:02 2018 -0800

    Merge pull request #215 from bcfriesen/update_CCE_flags
    
    Tools: update Cray compiler flags

commit 4dac05918d02d6ebc775f1ee05dcc34f38b4556f
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Feb 20 14:11:25 2018 -0800

    Tools: make Cray compiler trap floating point exceptions when DEBUG=TRUE

Tools/GNUMake/comps/cray.mak

commit a068bd8b16788a49f6507d68a610554540918207
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Feb 20 14:10:31 2018 -0800

    Tools: make Cray compiler print opt report only if building optimized code
    
    There is no reason to save the opt report for debug (non-optimized) code.

Tools/GNUMake/comps/cray.mak

commit 1a5e2a5b92dd6eccc92e9acdf4aa54aae976bd75
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 20 12:59:32 2018 -0800

    nodal projection: rap works in 2d now

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 86fd12409c5b8abc430c5f4d2967ce9335834450
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 20 12:24:05 2018 -0800

    comment out print in VisMF

Src/Base/AMReX_VisMF.cpp

commit ac6dc358a56ff5a7c2e2ec59c3837f252ace43b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 19 14:23:23 2018 -0800

    nodal projection: remove scaling at Neumann boundary for RAP

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 4585db76f21f75e1f2afe4914a35a0e660dd557f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Feb 19 12:18:08 2018 -0800

    Add AMReX_KDStruct.H to Make.package and CMakeLists.txt

Src/GeometryShop/CMakeLists.txt
Src/GeometryShop/Make.package

commit 1075f3071fdd9747d844dfecd966927435a7771b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Feb 19 12:09:08 2018 -0800

    Add the same files to CMakeLists.txt that we add to Make.package

Src/GeometryShop/CMakeLists.txt

commit 2f916454332b9df8df1035db2f2673958968707f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 18 18:29:08 2018 -0800

    nodal projection: first pass of RAP Fortran routines; still need work at boundaries

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit 19af9662a350c61b404549a47361daa9c47dfb8b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 18 12:00:55 2018 -0800

    nodal projection: R in RAP

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit d5aefc2a770c6bba0e837e47e09b98a3e8ef32c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 18 08:22:19 2018 -0800

    nodal projection: p in rap

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit 0c2b985b7b6e82e5eb9a8dc812655d88a06398e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 18 07:45:39 2018 -0800

    mlmg nodal: start RAP

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit fb39c721835af9a38716f0cd1c080c34fb891e07
Merge: 449a8a9ae 2b6f03afe
Author: Marc Day <MSDay@lbl.gov>
Date:   Sat Feb 17 11:26:19 2018 -0800

    Merge pull request #212 from JBlaschke/development
    
    Overlooked this in GNUMake. AMReX should build fine now...

commit 2b6f03afe83949422fc8a56c3fa3ab4c2d18ce6b
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Feb 17 11:16:51 2018 -0800

    Overlooked this in GNUMake. AMReX should build fine now...

Tools/GNUMake/Make.defs

commit 449a8a9ae10be5b753b9d664de41719b897b220a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Feb 16 15:07:00 2018 -0800

    added some files that had been neglected.

Tests/GeometryShop/STLGeom/GNUmakefile
Tests/GeometryShop/STLGeom/stlgeom.cpp

commit fefef566282e312be4af2fd1cdc720afb27dad31
Merge: d74f5089c b87802084
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Feb 16 13:26:04 2018 -0800

    Merge pull request #211 from AMReX-Codes/dtg_branch
    
    merging STL capability into GeometryShop

commit b878020842eae5ed09f533903ad1d791c400e82d
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Feb 16 13:21:14 2018 -0800

    finished integrating STL geometry capability.  Caveat emptor.   If you can manage it, you are far better off using analytic geometric descriptions.

Src/GeometryShop/AMReX_STLAsciiReader.cpp
Src/GeometryShop/AMReX_STLExplorer.cpp
Tests/GeometryShop/STLGeom/bad.cylinder.inputs
Tests/GeometryShop/STLGeom/bad.reactor.inputs
Tests/GeometryShop/STLGeom/good.cylinder.inputs
Tests/GeometryShop/STLGeom/good.reactor.inputs
Tests/GeometryShop/STLGeom/good.sphere.inputs
Tests/GeometryShop/STLGeom/stl.inputs

commit d74f5089caeef87f48a310d89265daf66387fc05
Merge: a197e15a2 927f38104
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Feb 16 09:02:34 2018 -0800

    Merge pull request #210 from JBlaschke/development
    
    GNUMake respects Make.local's compile commands

commit 927f38104a8d219be1e9f051152c13707109f761
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Feb 16 08:52:01 2018 -0800

    gnu.mak warns user if system's default gcc is outdated (<4.8), and reminds the user to specify a Make.local.

Tools/GNUMake/comps/gnu.mak

commit 3dc191e052c0a2d366761bd955d21f06a8020f12
Merge: a914868de a197e15a2
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Feb 15 22:28:14 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit a914868de76d038288da000f6e07d80d29969cf8
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Feb 15 22:27:43 2018 -0800

    WIP clean up documentation formatting

Docs/sphinx/source/Chapter5.rst

commit e5775454991e9b0cbc6674d67944cf21b35fefe7
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Feb 15 22:24:54 2018 -0800

    WIP: clean up formatting (including table captions)

Docs/sphinx/source/Basics.rst
Docs/sphinx/source/Chapter4.rst

commit c03f5724642ce0fecce83b7c796ff43e28493afa
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Feb 15 20:57:40 2018 -0800

    WIP: clean up formatting of docs

Docs/sphinx/source/BuildingAMReX.rst
Docs/sphinx/source/Chapter2.rst
Docs/sphinx/source/Chapter3.rst
Docs/sphinx/source/GettingStarted.rst
Docs/sphinx/source/Introduction.rst
Docs/sphinx/source/index.rst

commit a1cdf60a692b627f5cfc86639816d24c5b0a9803
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Feb 15 20:38:14 2018 -0800

    Document new Make.local behaviour

Docs/sphinx/source/BuildingAMReX.rst

commit 1c8c8c4c65d8ff1a0cbfbb598072e968cef8a4b2
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Feb 15 20:10:40 2018 -0800

    GNUMake compiler settings can be overwritten by Make.local (ie. introduce lazy
    evaluation to `comps/*.mak`). In order to work, compiler version checking for
    gnu had to be disabled (it makes little sense nowdays anyway).

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/cray.mak
Tools/GNUMake/comps/gnu-7.mak
Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/ibm.mak
Tools/GNUMake/comps/intel.mak
Tools/GNUMake/comps/llvm.mak
Tools/GNUMake/comps/nag.mak
Tools/GNUMake/comps/pgi.mak

commit 0420f943e56d5f7e2bb9cd62a84f47aa688a9a9c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Feb 15 16:20:32 2018 -0800

    all the stl code is in geometryshop and it compiles.   not tested yet.

Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp

commit a197e15a2ea1aaa53325b0d457944bf7deb862e9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Feb 15 19:09:40 2018 -0500

    Add Summit to machine list

Tools/GNUMake/Make.machines
Tools/GNUMake/comps/pgi.mak
Tools/GNUMake/sites/Make.olcf

commit 8ea1cb59fc2dc235fb778ca2953d51c050326298
Merge: f6edc51a2 8fa37b8c0
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Feb 15 15:57:29 2018 -0800

    Merge pull request #209 from JBlaschke/development
    
    Forgot to add this file

commit 8fa37b8c0f0786abc99159a2061264da531ff583
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Feb 15 15:52:18 2018 -0800

    Forgot to add this file

Tools/GNUMake/comps/gnu-7.mak

commit f6edc51a27eab70d8bfbf7e0797a8cd09e3e7bff
Merge: 908570755 94b360fea
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Feb 15 15:37:21 2018 -0800

    Merge pull request #208 from JBlaschke/development
    
    Development, added gnu-7 compiler definition

commit 94b360fea9f10f506d8ddafb76aeff0ae05d63d2
Merge: 494af9acc 908570755
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Feb 15 15:33:31 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 494af9acc0b8727ce391370c2a27ead84d79bee5
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Feb 15 15:32:19 2018 -0800

    added gnu-7 build target for gcc-7.x.x compilers.
    Needed, for example, for macOS where gcc links to gcc 4.2

Tools/GNUMake/Make.defs

commit 1fcf31367bd2a5bb9564d0080e5d40755b7b99ce
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Feb 15 15:04:09 2018 -0800

    note to self: never volunteer to port code before looking it over first.

Src/GeometryShop/#AMReX_STLExplorer.H#
Src/GeometryShop/AMReX_CellEdge.cpp
Src/GeometryShop/AMReX_KDStruct.H
Src/GeometryShop/AMReX_KDTree.H
Src/GeometryShop/AMReX_KDTree.cpp
Src/GeometryShop/AMReX_PXStuff.H
Src/GeometryShop/AMReX_PXStuff.cpp
Src/GeometryShop/AMReX_STLAsciiReader.H
Src/GeometryShop/AMReX_STLAsciiReader.cpp
Src/GeometryShop/AMReX_STLBox.H
Src/GeometryShop/AMReX_STLBox.cpp
Src/GeometryShop/AMReX_STLExplorer.H
Src/GeometryShop/AMReX_STLExplorer.cpp
Src/GeometryShop/AMReX_STLIF.H
Src/GeometryShop/AMReX_STLIF.cpp
Src/GeometryShop/AMReX_STLMesh.H
Src/GeometryShop/AMReX_STLMesh.cpp
Src/GeometryShop/AMReX_STLReader.H
Src/GeometryShop/AMReX_STLUtil.H
Src/GeometryShop/AMReX_STLUtil.cpp
Src/GeometryShop/Make.package
Tests/GeometryShop/STLGeom/cylinder.stl
Tests/GeometryShop/STLGeom/reactor.stl
Tests/GeometryShop/STLGeom/sphere.stl

commit 908570755bafa00fa86b5b1d11e97e8504ed6a77
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 15 14:47:30 2018 -0800

    Add additional print statements for the MultiGrid Vcycle when verbose > 1

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 2f459c323b5b09dcd0d329a2e73f70dc105d6c3a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Feb 14 16:24:43 2018 -0800

    slogging through Issac Asher's code to get STL files into EBIndexSpace.

Src/GeometryShop/#AMReX_STLExplorer.H#
Src/GeometryShop/AMReX_CellEdge.H
Src/GeometryShop/AMReX_CellEdge.cpp
Src/GeometryShop/AMReX_Ellipsoid.cpp
Src/GeometryShop/AMReX_KDStruct.H
Src/GeometryShop/AMReX_KDTree.H
Src/GeometryShop/AMReX_KDTree.cpp
Src/GeometryShop/AMReX_STLAsciiReader.H
Src/GeometryShop/AMReX_STLAsciiReader.cpp
Src/GeometryShop/AMReX_STLBox.H
Src/GeometryShop/AMReX_STLBox.cpp
Src/GeometryShop/AMReX_STLExplorer.H
Src/GeometryShop/AMReX_STLExplorer.cpp
Src/GeometryShop/AMReX_STLIF.H
Src/GeometryShop/AMReX_STLIF.cpp
Src/GeometryShop/AMReX_STLMesh.H
Src/GeometryShop/AMReX_STLMesh.cpp
Src/GeometryShop/AMReX_STLReader.H
Src/GeometryShop/AMReX_STLUtil.H
Src/GeometryShop/AMReX_STLUtil.cpp

commit 627ed5272d465165da9440bcd35e6b8657102b4f
Merge: 212ed7da4 eeb8a5eb2
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Feb 14 12:58:56 2018 -0800

    merging with dev branch

commit 57e72351a876c201ffe9d253591c4813d4a15c8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 13 17:09:25 2018 -0800

    eb nodal projection: gauss seidel

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 08df0969bff13623e38fb2a550d74fdb24069afa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 13 16:37:57 2018 -0800

    mlmg: harmonic average for jacobi

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 15bd63570e1e4f0068579b15d8e03a29437d5e8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 13 16:06:26 2018 -0800

    mlmg: enable eb on coarse mg levels

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 36741fb1d6eb15f158593f56b56a00ddc863a55c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 13 15:58:14 2018 -0800

    EBTower: add function testing if the domain is valid

Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp

commit 7a4d8e89a3d600feaf94c846c8bb5922ca851a5f
Merge: 232066016 eeb8a5eb2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 13 15:18:56 2018 -0800

    Merge branch 'development' into weiqun/mlmg

commit 232066016877196d083029fd9018062580b36396
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 13 14:52:01 2018 -0800

    mlmg: store factory as base class pointers

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit eeb8a5eb2d5ef2ec7222366b7492bfcb04469ae7
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Feb 13 12:53:42 2018 -0800

    in the F_MG cell-centered solver, if the user tries to use the fancy bottom solver and the grid structure can't be re-arranged for further coarsening, use fancy_bottom_type in (if it was passed in) before resorting to the default BiCGStab

Src/LinearSolvers/F_MG/mg.f90

commit b2a13fff595765541476779df7db71e4c7d3f433
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 13 09:58:27 2018 -0800

    wip: eb nodal projection: fix rhs

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 9d42a576b48488962750ca6bda04981d8da185e1
Merge: 91a4156d3 898e4fdfb
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Feb 12 12:56:06 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 91a4156d31f82e41c6942f1ba45ae460f396bde9
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Feb 12 12:55:14 2018 -0800

    Fix code to predict data filename

Tools/EBSurfaceTools/ConvertEBSurface.cpp

commit 212ed7da4744cc2ea98d4b52166c957927dbeb31
Merge: 90938a5d5 898e4fdfb
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Feb 12 09:32:34 2018 -0800

    merging with dev branch

commit 898e4fdfbc77f83a3a92fa13152adf3b229eceed
Merge: db406968d a98bd95be
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Feb 12 09:31:28 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit db406968dbfb543673639d0052ade60a54a4152e
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Feb 12 09:31:09 2018 -0800

    added destructor fix that was found by Johannes

Src/EB/AMReX_EBTower.cpp

commit 90938a5d52f12a45e3b565621c27f5093eaf552f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Feb 12 09:26:42 2018 -0800

    tweaked inputs

Tests/GeometryShop/regression/multicelllev.inputs

commit a98bd95be97e30c7e807e491ed2287c34e30bb26
Merge: ada2cde0f 2c5ad4656
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Feb 11 09:11:17 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit ada2cde0f7a5a08d92777025f4b871a99fe3d759
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Feb 11 09:10:58 2018 -0800

    Updated default DATA_Digits_Read from 4 to 5.

Tools/Postprocessing/C_Src/particle_compare.cpp

commit 42d4a3654f03967ff007b32185ab67fe1593e043
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 8 13:24:31 2018 -0800

    wip: eb nodal projection: update velocity at centroids

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit e26ae8fc7bf2a78f077844199bf9aff68e680e71
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 8 11:23:26 2018 -0800

    wip: eb nodal projection jacobi smoother

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 39e76dde9bc12c9f1af57c4d83bb100dc45892d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 8 09:46:47 2018 -0800

    wip: eb node projection: a dot x

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 6825c5b2e55b64ef620c63b80d72192e2da29968
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Feb 8 10:24:09 2018 -0500

    Updated build instructions for source (sphinx -> latex)

Docs/Readme.sphinx

commit dce8c45ae43082923e50b3f7a4fd916e4e6c54ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 7 17:00:41 2018 -0800

    wip: compute the connections

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 16f4848c7b7e9713fe77ec1cafe087c36d396381
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 7 15:04:53 2018 -0800

    wip: add stencil connection

Src/Base/AMReX_constants_mod.f90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit a9036a0bbf088bed3ae563f63e7823fee5a7a483
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 6 15:24:37 2018 -0800

    2d mlmg: another way of interpolation

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit 7137530e7e60c237be28a20d69f4768e9d152ef1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 6 15:08:18 2018 -0800

    2d mlmg: interpolate velocity from cell centers to centroids

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 2c5ad4656e9b89f9d0150008d1208649680dc13a
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Feb 6 14:39:52 2018 -0800

    put IO in its own chapter

Docs/sphinx/source/Basics.rst
Docs/sphinx/source/Chapter6a.rst
Docs/sphinx/source/IO.rst
Docs/sphinx/source/index.rst

commit abd91d4b90fd3981af2e732cc8fe5e06ee894302
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Feb 6 14:33:28 2018 -0800

    wrote documentation for how to do checkpoint/restart

Docs/sphinx/source/Basics.rst
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 7a6d1644faf3ccb562e3f55dfc66631546c06cc1
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Feb 6 14:02:56 2018 -0800

    implemented checkpoint-restart in Tutorials/Amr/Advection_AmrCore

Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrCore/Source/main.cpp

commit 4ff2747ceed26a2985336101a173e4e02f457a89
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 6 13:31:03 2018 -0800

    add centroid to EBTower

Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp

commit 2f7db7cf2e8a1a02f5af6d057081e6e96653ee82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 6 11:17:36 2018 -0800

    mlmg: refactor

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit b70560fc75002568004211eb9901f481a6e4ef11
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 6 09:52:32 2018 -0800

    mlmg: using FactoryType

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit e9fd98e1e504f6e230782c02fd26f9fd72bde6d6
Merge: 005945c38 8e8d4e6a3
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Feb 5 15:39:43 2018 -0800

    Merge pull request #207 from AMReX-Codes/dtg_branch
    
    ebindexspace now can tell you where multi-valued cells start

commit 8e8d4e6a38e7ed804a9c8481317e8d5765834cf6
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Feb 5 15:37:34 2018 -0800

    added functionality to EBIndexSpace which allows the user to find out the finest level where the graph is multivalued in a cell.  The test works in serial and in parallel.   Also I added an ellipsoid implicit function.

Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Src/GeometryShop/AMReX_EllipsoidIF.H
Src/GeometryShop/AMReX_EllipsoidIF.cpp
Src/GeometryShop/Make.package
Tests/GeometryShop/regression/GNUmakefile
Tests/GeometryShop/regression/fabfromif.cpp
Tests/GeometryShop/regression/multicelllev.cpp
Tests/GeometryShop/regression/multicelllev.inputs

commit 30e88d1e691b39c590e6c4ee21e90f00262c2d2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 5 15:31:55 2018 -0800

    mlmg: turn off harmonic average for now because there seems to be a bug; set velocity in covered cells to zero before computing rhs

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 44edec51352ca45bbfa3d5fa28fb6f7e0ac1b5d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 5 13:41:09 2018 -0800

    mlmg: always use harmonic average for eb and make sure no divided-by-zero

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 5c38e6d61c149e7c0d306a8859da631c69a3c675
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 5 12:29:02 2018 -0800

    mlmg: make factory argument to be vector of ptrs

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit ca0ea4278696ed554e49ed1f2ba35c81ad2b19f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 5 11:20:52 2018 -0800

    rm EBNodalProjection tutorial

Tutorials/LinearSolvers/EBNodalProjection/GNUmakefile
Tutorials/LinearSolvers/EBNodalProjection/Make.package
Tutorials/LinearSolvers/EBNodalProjection/MyTest.H
Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp
Tutorials/LinearSolvers/EBNodalProjection/initEB.cpp
Tutorials/LinearSolvers/EBNodalProjection/main.cpp

commit a015d7b34702ef648b97bebdadc3afdbd87849e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 5 11:18:43 2018 -0800

    minor

Tools/GNUMake/comps/gnu.mak

commit 005945c38173d9486a30da4b57747bfa9d1bc4ff
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Feb 3 11:19:16 2018 -0800

    Remove unused variable

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit ddc22772debc4cef821cb08efbd543b59592ab83
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 2 20:10:37 2018 -0800

    Add line break between Lecture1 and Lecture2

Docs/sphinx/source/Chapter12.rst

commit e968523f9bb06669da071ec5fe9e5c17ee35311e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 2 19:17:13 2018 -0800

    Add link to 2nd week of profiling tutorial

Docs/sphinx/source/Chapter12.rst

commit a87c5ef08e0f7769bb44d05cee04b6fbfd278edd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 2 16:09:07 2018 -0800

    Add pointer to Amrvis/Docs/Amrvis.tex

Docs/sphinx/source/Visualization.rst

commit 60c8d493ddb74de5e2985932f5f988b8487ae1e5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 2 15:48:43 2018 -0800

    Update link to amrvis

Docs/sphinx/source/Visualization.rst

commit fbb4c43079d76ed45a3b2a84bf6a69548c326050
Author: Minion <mlminion@lbl.gov>
Date:   Fri Feb 2 15:48:40 2018 -0800

    adding quadrature terms in sweeper

Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp
Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp
Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H

commit 7775775abcc3d9da93267e17cf9ff7a97d089e14
Merge: 269580f68 659770f35
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Feb 2 15:38:50 2018 -0800

    Merge pull request #205 from AMReX-Codes/dtg_branch
    
    fixing a bunch of small stuff with EB

commit 659770f35be8478214263663333152d9f5d9d036
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Feb 2 15:28:53 2018 -0800

    fixed a bunch of tests that were broken because of interface changes.

Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp
Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp
Tests/GeometryShop/flatPlate/flatPlateTest.cpp
Tests/GeometryShop/ramp/main.cpp
Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp
Tests/GeometryShop/sphere/GNUmakefile
Tests/GeometryShop/sphereEBISBox/GNUmakefile

commit 3f51924544ea0a1d6d610a19495e14142e04dcab
Author: Minion <mlminion@lbl.gov>
Date:   Thu Feb 1 17:42:40 2018 -0800

    Using Vector correctly for SDC arrays and saxpy in C++

Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp
Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_2d.f90
Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_2d.f90
Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_2d
Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp
Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H

commit db1b6289e363d73a31ef60a9d2db6d49dddc0e64
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 1 17:05:10 2018 -0800

    MLMG: add factory as optional argument

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 1e337c92ea92bd824718c4681504ac9669c6c6a3
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Feb 1 16:52:44 2018 -0800

    think I have the serialization issue beat but I need to test it more before I put it into dev branch.

Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Tests/GeometryShop/regression/ebio.cpp
Tests/GeometryShop/regression/ebio.inputs
Tests/GeometryShop/regression/serialization.cpp

commit 55fc6b8540a0de40648cedca2bb1f7326b5b9ba1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 1 15:09:21 2018 -0800

    EBNodalProjection test: build factories

Tutorials/LinearSolvers/EBNodalProjection/Make.package
Tutorials/LinearSolvers/EBNodalProjection/MyTest.H
Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp
Tutorials/LinearSolvers/EBNodalProjection/initEB.cpp

commit 56a6a2186c87a90d2a8f136b97dafc7ef45657c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 1 13:33:19 2018 -0800

    mlmg: make sure the corners do not trigger floating point exception and remove fillSolutionBC function because we always fill bc to compute residuals

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit b82e24bf798073529910e96b03d3fd3bf07a37d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 1 10:32:10 2018 -0800

    EBNodalProjection test: setup with eb is done

Tutorials/LinearSolvers/EBNodalProjection/MyTest.H
Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp

commit 269580f688eaaf15d062ed47ac1d5ffd6b33c5ad
Merge: 69797e5c4 f0528bad8
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Feb 1 10:15:28 2018 -0800

    Merge pull request #203 from hsitaram/haribranch
    
    Extrude IF utility

commit 6e21d139351a0f15cfb4f00bf6638e11cc273f8b
Merge: 49acc1d95 69797e5c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 1 08:52:20 2018 -0800

    Merge branch 'development' into weiqun/dev

commit fcc6ab09c3b5501661b900cf04fa078517bf5441
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jan 31 16:24:50 2018 -0800

    took out some directory thrashing.

Src/GeometryShop/AMReX_EBISLevel.cpp
Tests/GeometryShop/regression/ebio.cpp
Tests/GeometryShop/regression/ebio.inputs

commit 30b2c206eaa3b03697a200dddf6f62e4ef53250c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jan 31 16:00:26 2018 -0800

    made ebgraph serialization a bit more consistent.

Src/GeometryShop/AMReX_EBGraph.cpp

commit 0577d411d6637cc899cd91f3eeffdf582ba4781b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jan 31 15:58:01 2018 -0800

    some bugs had crept into EBIndexSpace linearization.   this fixes some of them

Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Src/GeometryShop/AMReX_FabArrayIO.H
Tests/GeometryShop/regression/ebio.cpp

commit f0528bad8efb622c3bfb70c327b526e0b483dd57
Author: hari <hariswaran.sitaraman@nrel.gov>
Date:   Wed Jan 31 14:58:27 2018 -0700

    leaving 2D extruded surface as is

Src/GeometryShop/AMReX_ExtrudeIF.H
Src/GeometryShop/AMReX_ExtrudeIF.cpp
Src/GeometryShop/CMakeLists.txt
Src/GeometryShop/Make.package

commit 69797e5c4b0af436fe29a42b5e10971d1eac2aea
Merge: 75a0263a3 a7c9e7532
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jan 31 12:01:01 2018 -0800

    Merge pull request #201 from AMReX-Codes/dtg_branch
    
    added ability to fill Node-centered FArrayBox from implicit function …

commit a7c9e7532dfbbbde4f1ca8b369452e7579eda9a0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jan 31 11:59:57 2018 -0800

    added ability to fill Node-centered FArrayBox from implicit function values.  Test lives in Tests/GeometryShop/regression

Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Src/GeometryShop/AMReX_GeometryService.H
Src/GeometryShop/AMReX_GeometryShop.H
Tests/GeometryShop/regression/GNUmakefile
Tests/GeometryShop/regression/fabfromif.cpp

commit 49acc1d9509fe01e342987a0178d7ed61613d865
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 31 10:45:06 2018 -0800

    add a profiler to GeometryShop::fillGraph

Src/GeometryShop/AMReX_GeometryShop.cpp

commit bf342f25ab7b873858c6ca338967823445da8046
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 31 10:02:34 2018 -0800

    mlmg: if the solution multifab argument does not have exactly one ghost cell, make a local copy

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 75a0263a38ee6778367b46c8c0d104b629bf4fc9
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 30 17:37:40 2018 -0800

    expanded on the Basics of the HeatEquation_EX1_C tutorial

Docs/sphinx/source/Basics.rst
Docs/sphinx/source/Basics/figs/flowchart.odg
Docs/sphinx/source/Basics/figs/flowchart.pdf
Docs/sphinx/source/Basics/figs/flowchart.png
Docs/sphinx/source/GettingStarted.rst
Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp

commit 651ea123bd6e022722508685b20059de7048329e
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 30 17:01:23 2018 -0800

    re-org tutorials

Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs_2d
Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs_3d
Tutorials/Basic/HeatEquation_EX1_C/Source/Make.package
Tutorials/Basic/HeatEquation_EX1_C/Source/advance.cpp
Tutorials/Basic/HeatEquation_EX1_C/Source/advance_2d.f90
Tutorials/Basic/HeatEquation_EX1_C/Source/advance_3d.f90
Tutorials/Basic/HeatEquation_EX1_C/Source/init_phi_2d.f90
Tutorials/Basic/HeatEquation_EX1_C/Source/init_phi_3d.f90
Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.H
Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc_F.H
Tutorials/Basic/HeatEquation_EX2_C/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs_2d
Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs_3d
Tutorials/Basic/HeatEquation_EX2_C/Source/AMReX_FILCC_2D.F
Tutorials/Basic/HeatEquation_EX2_C/Source/AMReX_FILCC_3D.F
Tutorials/Basic/HeatEquation_EX2_C/Source/Make.package
Tutorials/Basic/HeatEquation_EX2_C/Source/advance.cpp
Tutorials/Basic/HeatEquation_EX2_C/Source/advance_2d.f90
Tutorials/Basic/HeatEquation_EX2_C/Source/advance_3d.f90
Tutorials/Basic/HeatEquation_EX2_C/Source/init_phi_2d.f90
Tutorials/Basic/HeatEquation_EX2_C/Source/init_phi_3d.f90
Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc.H
Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc_F.H
Tutorials/Basic/HeatEquation_EX3_C/Exec/GNUmakefile
Tutorials/Basic/HeatEquation_EX3_C/Exec/inputs_2d
Tutorials/Basic/HeatEquation_EX3_C/Source/Make.package
Tutorials/Basic/HeatEquation_EX3_C/Source/advance.cpp
Tutorials/Basic/HeatEquation_EX3_C/Source/init_phi_2d.f90
Tutorials/Basic/HeatEquation_EX3_C/Source/init_phi_3d.f90
Tutorials/Basic/HeatEquation_EX3_C/Source/inputs_3d
Tutorials/Basic/HeatEquation_EX3_C/Source/main.cpp
Tutorials/Basic/HeatEquation_EX3_C/Source/myfunc.H
Tutorials/Basic/HeatEquation_EX3_C/Source/myfunc_F.H

commit b4548c4d6b4a31fb012d9668887cbb6bf4b5633f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 30 16:29:17 2018 -0800

    added amrex_multifab_build_alias and amrex_imultifab_build_alias to Fortran interface

CHANGES
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 75bd0b7e39d2109cc4b3bb524957fde27b373b7b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 30 15:42:22 2018 -0800

    WIP: nodal projection tutorial

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Tutorials/LinearSolvers/EBNodalProjection/MyTest.H
Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp

commit 42526dd45f0c3dbe716310a94965495bc4734d77
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 30 15:08:32 2018 -0800

    writeFabs function that writes out each individual fab

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit d656c4548677e548c181aebac3402d7fa83f7170
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 30 14:20:58 2018 -0800

    add non-const version of BaseFab::ForEachIV

Src/Base/AMReX_BaseFab.H

commit acf94542b423d5fe35c3337a1e0d1f11212783c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 30 14:20:22 2018 -0800

    start eb nodal projection test

Tutorials/LinearSolvers/EBNodalProjection/GNUmakefile
Tutorials/LinearSolvers/EBNodalProjection/Make.package
Tutorials/LinearSolvers/EBNodalProjection/MyTest.H
Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp
Tutorials/LinearSolvers/EBNodalProjection/main.cpp

commit 33281777d045992f2406d37dae79aa855a2c4135
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 30 15:29:40 2018 -0800

    pass in basic data types (int, real) into fortran using pointers, not pass-by-reference

Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/Amr/Advection_AmrLevel/Source/Adv_F.H
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Basic/HeatEquation_EX1_C/advance.cpp
Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90
Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90
Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H
Tutorials/Basic/HeatEquation_EX2_C/advance.cpp
Tutorials/Basic/HeatEquation_EX2_C/advance_2d.f90
Tutorials/Basic/HeatEquation_EX2_C/advance_3d.f90
Tutorials/Basic/HeatEquation_EX2_C/myfunc_F.H

commit d81a349d56f563cd9a57d341be11081a3fc40542
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Tue Jan 30 14:29:28 2018 -0800

    adding quadrature routines and SDC arrays

Tutorials/Basic/SDCHeat_Equation_EX1_C/Make.package
Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp
Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_2d.f90
Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_3d.f90
Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp
Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H
Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H
Tutorials/Basic/SDCHeat_Equation_EX1_C/pf_quadrature.f90

commit 79488d511f0210a0e4078caf0ea23895d0019b90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 30 10:12:51 2018 -0800

    EB: make sure the BoxArray is cell-centered

Src/EB/AMReX_EBDataCollection.cpp

commit 21051ed97549c5539d45679c93dc16ff090b72b7
Merge: 1d1067abf 2497b19df
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 30 09:53:43 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 1d1067abfdc112d3d8c479eed4c320b29d3a09db
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 30 09:53:33 2018 -0800

    wrap these MPI helper functions in #ifdef BL_USE_MPI

Src/Particle/AMReX_ParticleContainerI.H

commit 2497b19dfdec11d6de0491a1a1ebe9e5f2a4d2be
Merge: 52a8d0718 f574cd5af
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jan 29 14:09:38 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 52a8d0718a15b48a011eef2bab28c64bab12934d
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jan 29 14:09:18 2018 -0800

    profiling lecture notes

Docs/sphinx/source/Chapter12.rst

commit f574cd5afa62db7e78b7e2395593f17cda1a13e0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 29 12:14:04 2018 -0800

    fix a couple of bugs in assert statements that broke compilation in DEBUG.

Src/Particle/AMReX_ParticleContainerI.H

commit 9c9506614eb42ab4044cb092940918dcd1e2505a
Merge: 4ece270d7 39f89a3de
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 29 12:04:54 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4ece270d770ad8c8fd15a7b919f40b62f15d4740
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 29 12:04:10 2018 -0800

    FabArray<BaseFab<int> > -> iMultiFab

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 53ec6356fdda9f8cdc8a10499cfe3a75a811ad66
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 29 11:59:49 2018 -0800

    A version of Redistribute for particles that have only moved a certain amount (typically one cell) since the last Redistibute() call. This version does not need to do All-to-all communication.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 39f89a3de70a1da19e4489c505a2f182f91a61f7
Author: Kevin Gott <kngott@lbl.gov>
Date:   Mon Jan 29 11:18:53 2018 -0800

    Docs update: BL_PROFILE_TINY_FLUSH

Docs/sphinx/source/AMReX_Profiling_Tools.rst

commit 5f31e89dba38d9f492a7ac72f73f28add6335f23
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 29 10:42:21 2018 -0800

    move Redistribute handshake stuff into helper function.

Src/Particle/AMReX_ParticleContainerI.H

commit 3b4d10a0847e7bdf487f6710cbfd018bc905c418
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 26 21:10:30 2018 -0800

    remove now unused template parameter

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp
Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H
Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp

commit 0f3f8bfe21f0a569da35e10b4e1650ea5f45024f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 26 20:53:06 2018 -0800

    Don't require users to call BuildLevelMask - just build it the first time it's needed.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 581bfd935bfe4de8a53c0e1b1096f65ce10dce8b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 26 19:45:09 2018 -0800

    fix a bug recently introduced by me

Src/Base/AMReX_BaseFab.H

commit 105cec5b028e2ea77b9878dcdb40c8229cfdd0d5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 26 17:12:22 2018 -0800

    Add link to sample output

Docs/sphinx/source/AMReX_Profiling_Tools.rst

commit d12ab9626692a42d5bc38c185d60e8126db37c99
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 26 17:05:40 2018 -0800

    Update to include cmake flags as well as GNU make flags

Docs/sphinx/source/AMReX_Profiling_Tools.rst

commit 5430e758d0f10782bc2ff3faab1168a3f3c4fc9c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 26 16:59:01 2018 -0800

    Update sample output

Docs/sphinx/source/AMReX_Profiling_Tools.rst

commit 0e4967661c52b706d9ef39a47570ba65ebe571f9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 26 16:53:03 2018 -0800

    This copy of Readme.profiling only contains information that has not been
    migrated to the online documentation.

Docs/Readme.profiling

commit a46ba7267e7c0453d27f75dc59b14555e53e34fb
Merge: 675b65634 dcd526cce
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 26 16:45:37 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 675b65634aab924fb98cf867525671b084243c39
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 26 16:45:15 2018 -0800

    Break profiling into two parts

Docs/sphinx/source/AMReX_Profiling_Tools.rst
Docs/sphinx/source/Chapter12.rst
Docs/sphinx/source/Chapter13.rst
Docs/sphinx/source/Chapter14.rst
Docs/sphinx/source/External_Profiling_Tools.rst
Docs/sphinx/source/index.rst

commit dcd526ccec39fff970660fc29c5a11c23f6ec2d9
Merge: d607ea0ac 345515a09
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 26 16:25:10 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d607ea0acd84395bdfd4c49e7d85692866b8f2e4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 26 16:25:01 2018 -0800

    use BL_PROFILE_VAR instead of BL_PROFILE here

Src/Particle/AMReX_ParticleContainerI.H

commit 345515a098c8316cf38abff4d10b09ce05068532
Author: kngott <kngott@lbl.gov>
Date:   Fri Jan 26 15:54:01 2018 -0800

    Addition of BL_PROFILE_TINY_FLUSH() to allow the user to flush the TINYPROFILER results to stdout whenever they like.

Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp

commit 72807d73ecbc7bd4c7a62e9cbb625ff0be71b1dc
Merge: 079d67237 9b34e0efa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 26 12:42:34 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 079d672379c57cea7daaed693bc215714211877c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 26 12:41:24 2018 -0800

    hypre add amrex_ prefix to some fortran functions

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H

commit 9b34e0efabc11ef269ae133a6a00eda666127a82
Merge: 4b44036c4 94931b014
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 26 11:16:07 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4b44036c49ec0d725893fc06e7dbe854d648a191
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 26 11:15:57 2018 -0800

    Real -> ParticleType::Real

Src/Particle/AMReX_NeighborParticlesI.H

commit 94931b0146bc00997ee80505ffcd33e4b71ab4a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 26 10:33:27 2018 -0800

    hypre: rm duplicated calls to assemble vectors

Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp

commit a6c852bb1507772ac1937d35883518af62fb38b1
Merge: 94f7fb421 71fccde16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 26 09:01:40 2018 -0800

    Merge branch 'hypre' into development

commit 94f7fb42188a230dbd6698f43950c6ee88d186b4
Merge: 9d53b14e7 fb93d0ba8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 25 18:07:24 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9d53b14e7e7d7aa92f495643b96bf6a74987bccc
Merge: 9ea7ef0c6 b1439903f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 25 18:07:18 2018 -0800

    Merge branch 'weiqun/looping' into development

commit 71fccde16be0fce137782e3cd0d0e2784e060a4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 25 16:08:08 2018 -0800

    mlmg: set hypre verbosity

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit e3345fc9ee7a1d73e9fe02d74d3f7e128e61d6a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 25 15:40:58 2018 -0800

    MLMG: use hypre as bottom solver for cell-centered solve

Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.H
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp

commit fb93d0ba84c5f05f6a0ae82e660c1b7d92fae7fb
Merge: 779e00524 9ea7ef0c6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 25 13:05:46 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 779e005245934372a4f52f83814ae3f58106d55a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 25 12:10:25 2018 -0800

    Change the default for probin_natonce from 32 to 512 since 32 reads at a time is
    way too few when running with many ranks.

Src/Amr/AMReX_Amr.cpp

commit b1439903f23cd1429fdd917b06e3e4cc1029558c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 25 10:28:47 2018 -0800

    add BaseFab::Transform

Src/Base/AMReX_BaseFab.H

commit 02330497517485a0b91d5a6dec2368154369ec88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 25 10:06:05 2018 -0800

    make sure box passed to setVal is ok

Src/Base/AMReX_BaseFab.H
Src/Boundary/AMReX_MultiMask.cpp

commit 9ea7ef0c6fb6c7d9686bff13e50241acf1a9a594
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 25 09:17:52 2018 -0800

    updates

Docs/sphinx/source/Introduction.rst
Docs/sphinx/source/index.rst

commit 48c0145ee0c23efcbf13379836cd5e876b5cc260
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 24 17:20:24 2018 -0800

    bug fixes

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Boundary/AMReX_Mask.cpp

commit e3b6f8175b88ad203724f03926079e1e43c5ddab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 24 15:49:09 2018 -0800

    rm AMReX_Looping.H

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseUmap.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_IArrayBox.cpp
Src/Base/AMReX_Looping.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/Boundary/AMReX_Mask.cpp

commit d69165d1fa0809437030d4110216c4b11dae0ca7
Merge: 74870d51a 829e68df6
Author: Lawrence Minion <mlminion@lbl.gov>
Date:   Wed Jan 24 13:50:51 2018 -0800

    Fixing double naming.
    Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC

commit 74870d51abb00c4e99e5eb9c8a4e16e06d7483b5
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jan 24 11:22:04 2018 -0800

    User's Guide -> Documentation

Docs/sphinx/source/Chapter9.rst
Docs/sphinx/source/Introduction.rst
Docs/sphinx/source/index.rst

commit 68114f84eb556cc3be9c880afb8c72e1b32949ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 24 10:34:00 2018 -0800

    rm ForAllThisBNNXC

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Looping.H
Src/Boundary/AMReX_Mask.cpp

commit c71b0abe3cdaeb9c8d32eb8c6a7e0e673ef608fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 24 10:14:48 2018 -0800

    rm ForAllThisBNNXCBN

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Looping.H
Src/Boundary/AMReX_Mask.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 9b4ea8a14462c5e77a0b24a0d015b2b261440484
Merge: d76c7a650 4e2f7fa24
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 23 19:00:37 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit d76c7a65013ebab5e8a07b491e3ba6a9b4a0530a
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 23 19:00:24 2018 -0800

    update intro

Docs/sphinx/source/Introduction.rst

commit 4e2f7fa2452fc38776841e9790747eb26061c86b
Merge: daf6c6c87 81529a663
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 23 18:02:21 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit daf6c6c87a2d865d088973c1a2ad150137278243
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 23 18:02:03 2018 -0800

    add note about minimum version of yt needed for AMReX Datasets

Docs/sphinx/source/Visualization.rst

commit 80cb4968c2bb9986aea967ee69f18dd648277a2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 23 17:15:16 2018 -0800

    ForAllThisBNNXCBNYCBN is gone

Src/Base/AMReX_Looping.H

commit 81529a66387fd8e45dd6d784f322456e3d5e1078
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 23 17:13:35 2018 -0800

    switch chapters

Docs/sphinx/source/Chapter6.rst
Docs/sphinx/source/Chapter7.rst

commit 04434a199b854e131d50a2dc9aaccf0e6e69465d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 23 17:13:31 2018 -0800

    rm linComb for non-Real type

Src/Base/AMReX_BaseFab.H

commit 49b15aeec17699a2c0db287b5f304a073d99ccdd
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 23 17:11:13 2018 -0800

    linear solver placeholder

Docs/sphinx/source/Basics.rst
Docs/sphinx/source/Chapter5.rst
Docs/sphinx/source/Chapter6.rst
Docs/sphinx/source/LinearSolvers.rst
Docs/sphinx/source/index.rst

commit 2bb0c0a12adf10724c4c91de9e987002f2a5b48b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 23 16:58:14 2018 -0800

    use Accumulate; rm ForAllRevXBNYCBNNN and BaseFab::copyRev

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Looping.H

commit f033f6ca8a705d5a247ca0d00dd5fdd5f4fefd72
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 23 16:47:53 2018 -0800

    ForAllThisBNN is gone

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Looping.H

commit 7e3e27d4f0320dc0ac70c6a82a13e8c8ec2cde29
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 23 16:31:55 2018 -0800

    BaseFab: add ForEach and Accumulate

Src/Base/AMReX_BaseFab.H

commit 58cda74a7c64fe8939c4fea6f74ee10ecec65c23
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 23 16:00:04 2018 -0800

    teaching myself sphinx.  cleaning up user's guide

Docs/sphinx/source/AmrCore.rst
Docs/sphinx/source/AmrLevel.rst
Docs/sphinx/source/Basics.rst
Docs/sphinx/source/Boundary.rst
Docs/sphinx/source/GettingStarted.rst
Docs/sphinx/source/index.rst

commit 829e68df6d3e313057ccf9831274f4087efeaa96
Author: Minion <mlminion@lbl.gov>
Date:   Tue Jan 23 15:37:21 2018 -0800

    Framework for SDC Heat Example

Tutorials/Basic/SDCHeat_Equation_EX1_C/GNUmakefile
Tutorials/Basic/SDCHeat_Equation_EX1_C/Make.package
Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp
Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_2d.f90
Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_3d.f90
Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_2d.f90
Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_3d.f90
Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_2d
Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_3d
Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp
Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H
Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H

commit 1d218918d4663d17c3efd962bbddaf401c68ce7d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 23 14:41:11 2018 -0800

    ForAllThisCPencil is gone

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_IArrayBox.cpp
Src/Base/AMReX_Looping.H

commit e237e4982c5300dab5a37d04c5d60283fd87eea4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 23 14:12:01 2018 -0800

    add some functions to BaseFab in order to eliminate looping macros

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H

commit 416db144ca58a9dad9b0727b25c593739e9dbcce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 23 12:29:29 2018 -0800

    rm unused macros for looping over BaseFabs

Src/Base/AMReX_Looping.H

commit b4a1235934b609fd5b018cb241e01a9cd79dd6b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 23 12:04:53 2018 -0800

    update CHANGES

CHANGES

commit 906e31c02b2d9fa84240ab709defc2e69e2c5f48
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 23 10:33:47 2018 -0800

    Remove the latex source for the users guide -- we now use the .rst files
    in sphinx as the primary source for the documentation.

Docs/AMReXUsersGuide/.gitignore
Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Docs/AMReXUsersGuide/AmrCore/figs/Adv1.pdf
Docs/AMReXUsersGuide/AmrCore/figs/Adv2.pdf
Docs/AMReXUsersGuide/AmrCore/figs/Adv3.pdf
Docs/AMReXUsersGuide/AmrCore/figs/Adv4.pdf
Docs/AMReXUsersGuide/AmrCore/figs/Adv5.pdf
Docs/AMReXUsersGuide/AmrCore/figs/flowchart.odg
Docs/AMReXUsersGuide/AmrCore/figs/flowchart.pdf
Docs/AMReXUsersGuide/AmrCore/figs/subcycling.pdf
Docs/AMReXUsersGuide/AmrCore/figs/subcycling.tex
Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex
Docs/AMReXUsersGuide/AmrLevel/figs/flowchart.odg
Docs/AMReXUsersGuide/AmrLevel/figs/flowchart.pdf
Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/Basics/amrgrids.pdf
Docs/AMReXUsersGuide/Basics/cc_growbox.pdf
Docs/AMReXUsersGuide/Basics/cc_tilebox.pdf
Docs/AMReXUsersGuide/Basics/cc_validbox.pdf
Docs/AMReXUsersGuide/Basics/ec_growbox.pdf
Docs/AMReXUsersGuide/Basics/ec_tilebox.pdf
Docs/AMReXUsersGuide/Basics/ec_validbox.pdf
Docs/AMReXUsersGuide/Basics/figs/flowchart.odg
Docs/AMReXUsersGuide/Basics/figs/flowchart.pdf
Docs/AMReXUsersGuide/Basics/indextypes.pdf
Docs/AMReXUsersGuide/Boundary/Boundary.tex
Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex
Docs/AMReXUsersGuide/CVODE/CVODE.tex
Docs/AMReXUsersGuide/Debugging/Debugging.tex
Docs/AMReXUsersGuide/EB/EB.tex
Docs/AMReXUsersGuide/EB/EB_example.eps
Docs/AMReXUsersGuide/EB/EB_example.fig
Docs/AMReXUsersGuide/EB/EB_example.fig.bak
Docs/AMReXUsersGuide/EB/EB_example.pdf
Docs/AMReXUsersGuide/EB/areas_and_volumes.eps
Docs/AMReXUsersGuide/EB/areas_and_volumes.fig
Docs/AMReXUsersGuide/EB/areas_and_volumes.pdf
Docs/AMReXUsersGuide/EB/eb_fluxes.eps
Docs/AMReXUsersGuide/EB/eb_fluxes.fig
Docs/AMReXUsersGuide/EB/eb_fluxes.fig.bak
Docs/AMReXUsersGuide/EB/eb_fluxes.pdf
Docs/AMReXUsersGuide/EB/graph.pdf
Docs/AMReXUsersGuide/EB/multidivide.pdf
Docs/AMReXUsersGuide/EB/parabsphere.pdf
Docs/AMReXUsersGuide/EB/parabsphere.ps.REMOVED.git-id
Docs/AMReXUsersGuide/EB/redist.eps
Docs/AMReXUsersGuide/EB/redist.fig
Docs/AMReXUsersGuide/EB/redist.pdf
Docs/AMReXUsersGuide/EB/revolution.pdf
Docs/AMReXUsersGuide/EB/revolution.ps.REMOVED.git-id
Docs/AMReXUsersGuide/EB/volume.pdf
Docs/AMReXUsersGuide/Fortran/Fortran.tex
Docs/AMReXUsersGuide/GNUmakefile
Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex
Docs/AMReXUsersGuide/Introduction/Introduction.tex
Docs/AMReXUsersGuide/Particle/Particle.tex
Docs/AMReXUsersGuide/Particle/neighbor_list.pdf
Docs/AMReXUsersGuide/Particle/neighbor_list.tex
Docs/AMReXUsersGuide/Particle/neighbor_particles.pdf
Docs/AMReXUsersGuide/Particle/neighbor_particles.tex
Docs/AMReXUsersGuide/Particle/particle_arrays.pdf
Docs/AMReXUsersGuide/Particle/particle_arrays.tex
Docs/AMReXUsersGuide/Preface/Preface.tex
Docs/AMReXUsersGuide/Profiling/Profiling.tex
Docs/AMReXUsersGuide/Profiling/figs/commtopo.png
Docs/AMReXUsersGuide/Profiling/figs/mpi.png
Docs/AMReXUsersGuide/Profiling/figs/msgsizes.png
Docs/AMReXUsersGuide/Profiling/figs/papi.png
Docs/AMReXUsersGuide/Profiling/figs/summary.png
Docs/AMReXUsersGuide/Profiling/figs/timings.png
Docs/AMReXUsersGuide/README.md
Docs/AMReXUsersGuide/Visualization/Amrvis_2d.eps
Docs/AMReXUsersGuide/Visualization/Amrvis_3d.eps
Docs/AMReXUsersGuide/Visualization/ParaView.eps
Docs/AMReXUsersGuide/Visualization/ParaView_particles.eps.REMOVED.git-id
Docs/AMReXUsersGuide/Visualization/VisIt_2D.eps
Docs/AMReXUsersGuide/Visualization/VisIt_3D.eps
Docs/AMReXUsersGuide/Visualization/Visualization.tex
Docs/AMReXUsersGuide/Visualization/yt_Nyx_density_slice.png
Docs/AMReXUsersGuide/Visualization/yt_Nyx_density_vol_rend.png
Docs/AMReXUsersGuide/amrexsymbols.tex

commit 5ceace152c091d701cf0063d5b80275942e6cdca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 23 09:25:43 2018 -0800

    rm oboslete macros

Src/Amr/AMReX_Amr.cpp
Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Src/Base/AMReX_BLPgas.cpp
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_ccse-mpi.H
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F
Src/Boundary/AMReX_LO_UTIL.F
Src/LinearSolvers/F_MG/FParallelMG.mak

commit 402dd7538865b50b21f16a8f0766de99455828a1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 23 09:54:32 2018 -0800

    Fixed the centering commands.

Docs/sphinx/source/CVODE.rst
Docs/sphinx/source/EB.rst
Docs/sphinx/source/Particle.rst
Docs/sphinx/source/Visualization.rst

commit cac220b5cbed24c2adfffa6e2805c639bc03a473
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 23 09:20:53 2018 -0800

    finally fixed 1d node based bilinear interpolation

Src/AmrCore/AMReX_INTERP_1D.F

commit 4acbf3c064e4f7381629fa38021cd194f4cab5ad
Merge: 1f066afcb 3ba8fd87a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 17:15:31 2018 -0800

    merging.

commit 1f066afcb0f4e64bde706f44bbb2b6c08f1556d0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 17:13:49 2018 -0800

    clarify doc building instructions slightly

Docs/Readme.sphinx

commit 3ba8fd87ad0a17befab11ecfb317c30431672008
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 16:37:19 2018 -0800

    Add details about "make latexpdf"

Docs/Readme.sphinx

commit 5b371b915ae371e57bcee46925f43d25e03bfafb
Merge: 4af3e755c b41660a9a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 16:36:08 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 4af3e755cce1d65d15f9a9bf3656843b9431726d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 16:35:48 2018 -0800

    Replace some centering commands so they work correctly for make latexpdf

Docs/sphinx/source/AmrCore.rst
Docs/sphinx/source/Basics.rst
Docs/sphinx/source/Profiling.rst

commit b41660a9aff1578dee49f2bdff5e79d48e23cfd4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jan 22 16:27:24 2018 -0800

    CMake:do not retrieve git hash if git not installed or .git not present

Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Utils.cmake

commit c465ead19d1da1b7eec3467f6d49912bf815de73
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 15:59:31 2018 -0800

    fix the centering of the tables when building using latexpdf

Docs/sphinx/source/BuildingAMReX.rst

commit 140ac5b4287841db4c226ef9431fdd4a3a3f063f
Merge: e797758f6 3df686d34
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 15:23:54 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit e797758f68fdcf786064d149b2f0551795b0606b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 15:23:47 2018 -0800

    Update rst files

Docs/sphinx/source/Basics.rst
Docs/sphinx/source/BuildingAMReX.rst
Docs/sphinx/source/Particle.rst
Docs/sphinx/source/Visualization.rst

commit 3df686d34b23cfa876305ad0b038fae896e33ba0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 15:03:22 2018 -0800

    add a few comments.

build_and_deploy.sh

commit 5c79bcb9fc9d545f3cb20aee00a83885191eb6fe
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 14:58:24 2018 -0800

    minor

Docs/sphinx/source/BuildingAMReX.rst

commit 6fdeffd34911b7c1e19de0cde6c79f59ca45f749
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 14:54:41 2018 -0800

    update deploy script to compile libamrex before exiting early if not on development

build_and_deploy.sh

commit 2fc8c6b4474282e643964b7e751e7e4492570ce6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 14:37:38 2018 -0800

    override the default page width for the read the docs theme, which is optimized for mobile.

Docs/sphinx/source/conf.py

commit 2ef04933c7f7071a62bc2caaa6f92eecc9854b47
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 14:31:03 2018 -0800

    update the AMReX version every time the docs are built.

Docs/sphinx/source/conf.py

commit 8a0e6ec1d4073f24ad2663be67bb3fe97f924f6b
Merge: 389b0c586 787af403a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 13:44:51 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 389b0c5861cbb61a4448dc014b8c63c3274ba508
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 13:44:41 2018 -0800

    updates to the sphinx installation instructions.

Docs/Readme.sphinx

commit 787af403a7acd0b1bb6c4e0597a9869fcfdd71d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 22 13:28:27 2018 -0800

    Array --> Vector

Src/AmrTask/AMFIter/AMReX_AmrTask.H
Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H
Src/AmrTask/Amr/AMReX_AmrLevelTask.H
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 32dc2019bd1bd8a84936bbd70638d64d1a903454
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 13:00:15 2018 -0800

    More path highlighting

Docs/sphinx/source/AmrCore.rst
Docs/sphinx/source/AmrLevel.rst
Docs/sphinx/source/Basics.rst
Docs/sphinx/source/Boundary.rst
Docs/sphinx/source/Chapter4.rst
Docs/sphinx/source/Chapter6.rst
Docs/sphinx/source/Chapter7.rst
Docs/sphinx/source/Fortran.rst
Docs/sphinx/source/Particle.rst

commit c2866e949581d93aca01be309804d01e89382f5e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 12:54:17 2018 -0800

    More path names

Docs/sphinx/source/BuildingAMReX.rst
Docs/sphinx/source/CVODE.rst
Docs/sphinx/source/Chapter4.rst
Docs/sphinx/source/Chapter6.rst
Docs/sphinx/source/Chapter7.rst
Docs/sphinx/source/GettingStarted.rst
Docs/sphinx/source/Particle.rst
Docs/sphinx/source/Visualization.rst

commit 7754851b06168692f9402a17525b01512b8a8ea2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 12:49:50 2018 -0800

    All path names should be highlighted

Docs/sphinx/source/Boundary.rst
Docs/sphinx/source/BuildingAMReX.rst
Docs/sphinx/source/EB.rst
Docs/sphinx/source/Fortran.rst

commit 7e4f13fe2d671429f2d8143bd65f73d85c8dd655
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 12:46:42 2018 -0800

    formatting

Docs/sphinx/source/Chapter6.rst

commit 61a6f693b83c48c259de6dac458bb7d5443af4ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 22 10:39:09 2018 -0800

    MLMG N-Solve: refactor making grids

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp

commit b075130f36ea330260f077112512ddac862e5a8a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 22 09:23:36 2018 -0800

    MLMG N-Solve: add paramter controlling grid size

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 8b46b285e104d895746d4aeadaa194cfced10d7d
Merge: d2f932189 7292d5db0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 12:09:38 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d2f9321890bccade2821de70fc7afe460192332f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 12:09:28 2018 -0800

    update sphinx instructions.

Docs/Readme.sphinx

commit 7292d5db082fb9cd1509ee7028a633d42113fe23
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 12:07:48 2018 -0800

    Update highlighting

Docs/sphinx/source/AmrCore.rst

commit 431c7bee83ec4035b27fc194374d19e7c6e37c68
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 12:05:11 2018 -0800

    Highlight path names

Docs/sphinx/source/AmrCore.rst

commit f3f5c417df84dc1293e7864d515c6a31c56a6fba
Merge: 9c053344e 3402c4c4c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 12:01:18 2018 -0800

    Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development

commit 3402c4c4c127ff6e3ae03d8032c5bd01663c4514
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 11:56:27 2018 -0800

    fix c++ syntax highlighting for this snippet.

Docs/sphinx/source/Particle.rst

commit 9c053344edbc6f2e3825eded303e3d9655114560
Merge: be53d6b19 953fd4360
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 11:50:53 2018 -0800

    Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development

commit be53d6b199bee6d788fb597703b017372302650b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 11:44:01 2018 -0800

    1) updated BuildingAMReX.rst
    2) Added notes for how to update AMReX documentation in Readme.sphinx

Docs/Readme.sphinx
Docs/sphinx/source/BuildingAMReX.rst

commit 953fd4360f70fc9f03738c55ce8b5d82f66ee3da
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 11:39:07 2018 -0800

    minor docs typo fix

Docs/sphinx/source/Particle.rst

commit dc77f1f55578454db00fd10fd418b047ce62620e
Merge: ed48539bc f5471062e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 11:26:17 2018 -0800

    Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development

commit f5471062e7a98a0525f0b95b0ae7b35aaec5fe61
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 11:21:47 2018 -0800

    remove reference to non-existent section.

Docs/sphinx/source/EB.rst

commit d6cfc45486f4c4bcc0b29ef6d726f5a49494cb18
Merge: aaf35f97e c3b727505
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 22 11:16:28 2018 -0800

    Merge pull request #199 from JBlaschke/development
    
    Fix figure in EB section

commit c3b7275054f0bd53dc87ca7d14ec640c66ee2330
Merge: 86ac72df8 aaf35f97e
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jan 22 11:10:09 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 86ac72df88af63981c80a4545ceee39d458ecac4
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jan 22 11:09:30 2018 -0800

    fix .pdf->.png for figure

Docs/sphinx/source/EB.rst
Docs/sphinx/source/EB/areas_and_volumes.png
Docs/sphinx/source/EB/eb_fluxes.png

commit aaf35f97e2f6c5e542230ad02552b5510ab2cd10
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 22 10:37:40 2018 -0800

    comparison operators for Box

Src/Base/AMReX_Box.H
Src/Base/AMReX_IndexType.H

commit ed48539bcf16e829590e5853eb1057cf79b5b858
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 10:33:24 2018 -0800

    Update several rst files

Docs/sphinx/source/BuildingAMReX.rst
Docs/sphinx/source/Chapter3.rst
Docs/sphinx/source/GettingStarted.rst

commit 93704c83f077818047fa039d3481f5049139fe0d
Merge: 7b1a7ef07 c65b2f4e2
Author: asalmgren <asalmgren@lbl.gov>
Date:   Mon Jan 22 08:00:36 2018 -0800

    Merge pull request #198 from JBlaschke/development
    
    Update Docs

commit c65b2f4e2c829f95a05cc34dcc4b93ba349ac474
Merge: c184500f1 7b1a7ef07
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 21 22:52:45 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit c184500f1cd78f62b45d8d91761318fc3796b60c
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 21 22:51:57 2018 -0800

    fix label issue

Docs/sphinx/source/Basics.rst

commit aeb96cd15fd4c3a14d99ac1412ee9e2bb000f8fd
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 21 22:47:39 2018 -0800

    clean up some rst errors

Docs/sphinx/source/Basics.rst
Docs/sphinx/source/BuildingAMReX.rst
Docs/sphinx/source/CVODE.rst
Docs/sphinx/source/Chapter3.rst
Docs/sphinx/source/GettingStarted.rst
Docs/sphinx/source/Particle.rst
Docs/sphinx/source/intro.rst

commit 17dc1485ebe1513f89673ac8e9640cbddefbb701
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 21 22:32:15 2018 -0800

    Finished formatting CVODE section

Docs/sphinx/source/CVODE.rst
Docs/sphinx/source/Chapter13.rst
Docs/sphinx/source/index.rst

commit 586c244a825b3863c89dd688c197b08d16167ab4
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 21 22:09:22 2018 -0800

    Finished converting Profiling section

Docs/sphinx/source/Profiling.rst

commit dd25d511b6a0f88c5f57b4e4a31d012c84fb806a
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 21 21:37:16 2018 -0800

    Begin converting section on profiling

Docs/sphinx/source/Chapter12.rst
Docs/sphinx/source/Profiling.rst
Docs/sphinx/source/Profiling/figs/commtopo.png
Docs/sphinx/source/Profiling/figs/mpi.png
Docs/sphinx/source/Profiling/figs/msgsizes.png
Docs/sphinx/source/Profiling/figs/papi.png
Docs/sphinx/source/Profiling/figs/summary.png
Docs/sphinx/source/Profiling/figs/timings.png

commit adb04523ae488747d0d71414352e278b29e788fb
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 21 21:31:23 2018 -0800

    finished reformatting visualization section

Docs/sphinx/source/Chapter11.rst
Docs/sphinx/source/Visualization.rst
Docs/sphinx/source/Visualization/Amrvis_2d.png
Docs/sphinx/source/Visualization/Amrvis_3d.png
Docs/sphinx/source/Visualization/ParaView.png.REMOVED.git-id
Docs/sphinx/source/Visualization/ParaView_particles.png.REMOVED.git-id
Docs/sphinx/source/Visualization/VisIt_2D.png
Docs/sphinx/source/Visualization/VisIt_3D.png
Docs/sphinx/source/index.rst

commit 06e19d936b32f7fe062d2112175ac1c5c9d688c7
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 21 20:05:29 2018 -0800

    Finished converting EB chapter

Docs/sphinx/source/Chapter10.rst
Docs/sphinx/source/Chapter11.rst
Docs/sphinx/source/EB.rst
Docs/sphinx/source/EB/EB_example.eps
Docs/sphinx/source/EB/EB_example.fig
Docs/sphinx/source/EB/EB_example.fig.bak
Docs/sphinx/source/EB/EB_example.pdf
Docs/sphinx/source/EB/EB_example.png
Docs/sphinx/source/EB/areas_and_volumes.eps
Docs/sphinx/source/EB/areas_and_volumes.fig
Docs/sphinx/source/EB/areas_and_volumes.pdf
Docs/sphinx/source/EB/eb_fluxes.eps
Docs/sphinx/source/EB/eb_fluxes.fig
Docs/sphinx/source/EB/eb_fluxes.fig.bak
Docs/sphinx/source/EB/eb_fluxes.pdf
Docs/sphinx/source/EB/graph.pdf
Docs/sphinx/source/EB/multidivide.pdf
Docs/sphinx/source/EB/parabsphere.pdf
Docs/sphinx/source/EB/parabsphere.png
Docs/sphinx/source/EB/parabsphere.ps.REMOVED.git-id
Docs/sphinx/source/EB/redist.eps
Docs/sphinx/source/EB/redist.fig
Docs/sphinx/source/EB/redist.pdf
Docs/sphinx/source/EB/redist.png
Docs/sphinx/source/EB/revolution.pdf
Docs/sphinx/source/EB/revolution.png
Docs/sphinx/source/EB/revolution.ps.REMOVED.git-id
Docs/sphinx/source/EB/volume.pdf
Docs/sphinx/source/Visualization/Amrvis_2d.eps
Docs/sphinx/source/Visualization/Amrvis_2d.pdf
Docs/sphinx/source/Visualization/Amrvis_3d.eps
Docs/sphinx/source/Visualization/Amrvis_3d.pdf
Docs/sphinx/source/Visualization/ParaView.eps
Docs/sphinx/source/Visualization/ParaView.pdf
Docs/sphinx/source/Visualization/ParaView_particles.eps.REMOVED.git-id
Docs/sphinx/source/Visualization/ParaView_particles.pdf
Docs/sphinx/source/Visualization/VisIt_2D.eps
Docs/sphinx/source/Visualization/VisIt_2D.pdf
Docs/sphinx/source/Visualization/VisIt_3D.eps
Docs/sphinx/source/Visualization/VisIt_3D.pdf
Docs/sphinx/source/Visualization/yt_Nyx_density_slice.png
Docs/sphinx/source/Visualization/yt_Nyx_density_vol_rend.png
Docs/sphinx/source/index.rst

commit 7b1a7ef07033e95f2f75eaece69a1d55f63a58df
Merge: 309bdcaf9 c4873c7dc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Jan 21 11:41:27 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit fc6e547602936e541455a66ed3d07d424bb63318
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 20 23:49:16 2018 -0800

    Finished converting the Fortran Interface Section

Docs/sphinx/source/Chapter4.rst
Docs/sphinx/source/Chapter9.rst
Docs/sphinx/source/Fortran.rst
Docs/sphinx/source/GettingStarted.rst
Docs/sphinx/source/index.rst

commit 03a9a115c0cbc4c607b263061549800255ecd9c5
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 20 14:04:28 2018 -0800

    Add particle figures to docs

Docs/sphinx/source/Particle/neighbor_list.pdf
Docs/sphinx/source/Particle/neighbor_list.png
Docs/sphinx/source/Particle/neighbor_list.tex
Docs/sphinx/source/Particle/neighbor_particles.pdf
Docs/sphinx/source/Particle/neighbor_particles.png
Docs/sphinx/source/Particle/neighbor_particles.tex
Docs/sphinx/source/Particle/particle_arrays.pdf
Docs/sphinx/source/Particle/particle_arrays.png
Docs/sphinx/source/Particle/particle_arrays.tex

commit 338e6be3c8f86a4c3d4cdffbe181252f2993b26c
Merge: fd6a402cc c4873c7dc
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 20 14:00:36 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit fd6a402cc90c41bb33c321c17787272da719009d
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 20 13:59:47 2018 -0800

    Finished fromatting particles section

Docs/sphinx/source/Amr.rst
Docs/sphinx/source/Particle.rst
Docs/sphinx/source/Particles.rst
Docs/sphinx/source/conf.py

commit c4873c7dc336f5d85e7bc9812a0e3df0258d656f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 19 16:36:52 2018 -0800

    less verbose

Src/Amr/AMReX_Amr.cpp

commit 6e84e5cf7c88519ce39ada659ce257ee8b4e25cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 19 16:33:31 2018 -0800

    MLMG: clean up M-Solve because it has been replaced by nsolve

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 4738a00352c1cc001ac19e8382cd15cbd34ed2f6
Author: kngott <kngott@lbl.gov>
Date:   Fri Jan 19 15:57:16 2018 -0800

    Fix for SparseIO file number calculations.

Src/Base/AMReX_VisMF.cpp

commit 5c1b898f4cd139103bb328318b96b4354c4aa681
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 19 13:30:39 2018 -0800

    MLMG: use SFC in N-Solve

Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 4b4840b01397a904bcdd9c2f5438d60897b85c22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 19 13:15:29 2018 -0800

    MLMG: N-Solve

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 309bdcaf938df5f67dfb91b6c4554cda523b0256
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 19 12:59:36 2018 -0800

    Fix to formatting

Docs/sphinx/source/GettingStarted.rst

commit 069a4ae794db621c3f897e903b6c2d411b36b1e3
Merge: 8cc17ae6c 2fd6ed138
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jan 19 09:09:45 2018 -0800

    Merge pull request #195 from AMReX-Codes/dtg_branch
    
    bug fix push

commit 2fd6ed1383f447a290ab1dd224d41bcce6c3993f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jan 19 09:08:39 2018 -0800

    fixed issue with regression test.  The ghost routine was being called where there were no ghost cells.

Src/EB/AMReX_EBTower.cpp

commit 8cc17ae6ce3938a66c6597dda82edcb7c2ec599b
Merge: 18992267d 72a627886
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jan 19 08:43:40 2018 -0800

    Merge pull request #168 from bcfriesen/IOBenchmark_OpenMP
    
    IOBenchmark: make only master thread flush and close file in thread-shared IO

commit c500710168c0c25d8ca9afaf69789ece8c516143
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 19 00:21:07 2018 -0800

    Fix some typos

Docs/sphinx/source/AmrCore.rst
Docs/sphinx/source/Basics.rst

commit 0491a64c30a00124cda96a65055a13063b4de415
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 19 00:13:36 2018 -0800

    reformatted Amr Source Code section

Docs/sphinx/source/AmrCore/figs/Adv1.pdf
Docs/sphinx/source/AmrCore/figs/Adv1.png
Docs/sphinx/source/AmrCore/figs/Adv2.pdf
Docs/sphinx/source/AmrCore/figs/Adv2.png
Docs/sphinx/source/AmrCore/figs/Adv3.pdf
Docs/sphinx/source/AmrCore/figs/Adv3.png
Docs/sphinx/source/AmrCore/figs/Adv4.pdf
Docs/sphinx/source/AmrCore/figs/Adv4.png
Docs/sphinx/source/AmrCore/figs/Adv5.pdf
Docs/sphinx/source/AmrCore/figs/Adv5.png
Docs/sphinx/source/AmrCore/figs/flowchart.odg
Docs/sphinx/source/AmrCore/figs/flowchart.pdf
Docs/sphinx/source/AmrCore/figs/flowchart.png
Docs/sphinx/source/AmrCore/figs/subcycling.pdf
Docs/sphinx/source/AmrCore/figs/subcycling.png
Docs/sphinx/source/AmrCore/figs/subcycling.tex
Docs/sphinx/source/AmrLevel.rst
Docs/sphinx/source/AmrLevel/figs/flowchart.odg
Docs/sphinx/source/AmrLevel/figs/flowchart.pdf
Docs/sphinx/source/AmrLevel/figs/flowchart.png
Docs/sphinx/source/Chapter7.rst
Docs/sphinx/source/Chapter8.rst

commit 18992267d33d06cd05e6a932afdc612a17d8b9f4
Merge: ce91cce95 2d5c1fc11
Author: asalmgren <asalmgren@lbl.gov>
Date:   Thu Jan 18 19:32:26 2018 -0800

    Merge pull request #193 from JBlaschke/development
    
    Development

commit 2d5c1fc11148a410ddf3b0065ffc76f2231b5b98
Merge: 35aca3c6e ce91cce95
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 18 18:10:57 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 35aca3c6e80cf92c7775dafcec0b7f132a970bd2
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 18 18:05:37 2018 -0800

    finished converting AmrCore

Docs/sphinx/source/AmrCore.rst
Docs/sphinx/source/Chapter6.rst

commit ce91cce95175b59176c28b3f8815d4afb5f2b5f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 18 14:59:27 2018 -0800

    msolve: a different approach to make new BoxArray

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 12cab9e90723184dd11670d3d6c6a227ac142235
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jan 18 14:48:38 2018 -0800

    took print statements out of CNS.cpp

Tutorials/EB/CNS/Source/CNS.cpp

commit ff0f63f0c0d739ae585c5eaf7dc88b558eebc376
Merge: 509e51bfd be79f1526
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jan 18 13:48:02 2018 -0800

    Merge pull request #192 from AMReX-Codes/dtg_branch
    
    bug fixes to the bug fixes to the ...

commit be79f1526a0dc3f7fa60cc96a6869f41c00510d4
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jan 18 13:46:05 2018 -0800

    more bug fixes for periodic stuff.  now the corner cells seem to be correct

Src/EB/AMReX_EBTower.cpp
Tutorials/EB/CNS/Source/CNS.cpp

commit 509e51bfd7f85d6890dc25d03c5d5eacb5426d67
Merge: 5a7d6217e abc8a75bd
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 18 13:31:30 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 5a7d6217e56725072fe42fd09d48b60863d67621
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 18 13:31:20 2018 -0800

    comments only

Tutorials/Basic/HeatEquation_EX3_C/advance.cpp

commit abc8a75bde7506ea319f442e618427d526793d4d
Merge: 27f8c1bc8 baf2125a8
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jan 18 11:48:14 2018 -0800

    Merge pull request #191 from AMReX-Codes/dtg_branch
    
    bug fixes to periodic EBTower

commit baf2125a87a5fa22beec89031cf819842d4d0090
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jan 18 11:46:14 2018 -0800

    bug fixes for periodic stuff.  seems to do the right thing for Ann's case now.

Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_init_eb.cpp

commit 9c1249192644233c8f6add69ec267ea1576d14fb
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 18 11:18:51 2018 -0800

    finished formatting Boundary.rst

Docs/sphinx/source/AmrLevel.rst
Docs/sphinx/source/Basics/amrgrids.pdf
Docs/sphinx/source/Basics/amrgrids.png
Docs/sphinx/source/Basics/cc_growbox.pdf
Docs/sphinx/source/Basics/cc_growbox.png
Docs/sphinx/source/Basics/cc_tilebox.pdf
Docs/sphinx/source/Basics/cc_tilebox.png
Docs/sphinx/source/Basics/cc_validbox.pdf
Docs/sphinx/source/Basics/cc_validbox.png
Docs/sphinx/source/Basics/ec_growbox.pdf
Docs/sphinx/source/Basics/ec_growbox.png
Docs/sphinx/source/Basics/ec_tilebox.pdf
Docs/sphinx/source/Basics/ec_tilebox.png
Docs/sphinx/source/Basics/ec_validbox.pdf
Docs/sphinx/source/Basics/ec_validbox.png
Docs/sphinx/source/Basics/figs/flowchart.odg
Docs/sphinx/source/Basics/figs/flowchart.pdf
Docs/sphinx/source/Basics/figs/flowchart.png
Docs/sphinx/source/Basics/indextypes.pdf
Docs/sphinx/source/Basics/indextypes.png
Docs/sphinx/source/Boundary.rst
Docs/sphinx/source/Chapter6.rst
Docs/sphinx/source/Chapter7.rst
Docs/sphinx/source/Chapter8.rst
Docs/sphinx/source/Particle.rst

commit 38558a4449b1638c4f15397a131835fd94730fa3
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Thu Jan 18 11:03:21 2018 -0800

    finished Basics.rst, added relevant links

Docs/sphinx/source/AmrCore.rst
Docs/sphinx/source/Basics.rst
Docs/sphinx/source/Boundary.rst
Docs/sphinx/source/GettingStarted.rst
Docs/sphinx/source/Visualization.rst
Docs/sphinx/source/index.rst

commit 27f8c1bc82af91f24d43b943be6d532eee974e2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 18 10:50:22 2018 -0800

    To placate gcc-7

Src/Base/AMReX_ParallelReduce.H
Src/Base/AMReX_Vector.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit 67786385fd48690f5b571ff8b2afa9ae904199dd
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jan 18 13:27:20 2018 -0500

    Update to CUDA 9.0 by default

Tools/GNUMake/Make.defs

commit 54f6ed221f7c680e54275433f9463318a5fd5d90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 18 10:00:12 2018 -0800

    msolve: add parameter for grid size

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H

commit 692c48902cc640ef82a0070cd78c1d938a1a44e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 18 09:36:33 2018 -0800

    msolve: minor optimization

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 4af1a7363dec22bb33260907d1f83f432c920a9c
Merge: 1e19e4152 da215a32f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jan 17 16:06:16 2018 -0800

    Merge pull request #189 from AMReX-Codes/dtg_branch
    
    merging support for periodic EBTower into dev branch

commit da215a32f70987459c0a2b3149e77d8ef25b1206
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jan 17 16:04:45 2018 -0800

    added support for periodic to EBTower.  For the tests that I ran, it does the right thing.   I offer no guarantees for implicit functions which are not periodic.

Src/EB/AMReX_EBTower.cpp
Tutorials/EB/CNS/Exec/Pulse/GNUmakefile
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_init_eb.cpp

commit 1e19e415224fba014d712b2d7fe2c40329cf3213
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 17 15:00:30 2018 -0800

    remove mlcg

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 54e0873637bed67e9435db5b4fe3aca8ad85690e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 17 10:42:39 2018 -0800

    use MLALaplacian for M-Solve

Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 2da11d45606d01400a445c4884bef00fd5383fe4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 17 10:41:47 2018 -0800

    mlmg: add MLALaplacian

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLALap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLALap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLALap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLALap_F.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp
Src/LinearSolvers/MLMG/Make.package

commit 682aca8d9320d5df54dd7c38112d2cc35b2f313c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 17 09:35:31 2018 -0800

    M-Solve: support for ref ratio of 4

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 754f023d34ba3ff15ca37aa077a1fef4ec71ec2c
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jan 16 23:20:53 2018 -0800

    finished convering section on MFIter and Tiling

Docs/sphinx/source/Basics.rst

commit 857033dc7744edb988e2a19c1a33e8063167c4de
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jan 16 18:09:02 2018 -0800

    finished FABs documentation

Docs/sphinx/source/Basics.rst

commit 91ed36efa41cea683d694382eb19720537a69c01
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jan 16 20:40:19 2018 -0500

    Add Summit

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.olcf

commit e163bb342adab9a464d9c52cdb5584a8d6035f15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 16 16:59:17 2018 -0800

    msolve: clean up

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 5ae9f1b3a3411d207761d7c06858921da71f85f2
Author: Doreen Fan <dfan@lbl.gov>
Date:   Tue Jan 16 16:27:08 2018 -0800

    Added implicit heat equation solver in Tutorials/Basic/HeatEquation_EX3_C/

Tutorials/Basic/HeatEquation_EX3_C/GNUmakefile
Tutorials/Basic/HeatEquation_EX3_C/Make.package
Tutorials/Basic/HeatEquation_EX3_C/advance.cpp
Tutorials/Basic/HeatEquation_EX3_C/init_phi_2d.f90
Tutorials/Basic/HeatEquation_EX3_C/init_phi_3d.f90
Tutorials/Basic/HeatEquation_EX3_C/inputs_2d
Tutorials/Basic/HeatEquation_EX3_C/inputs_3d
Tutorials/Basic/HeatEquation_EX3_C/main.cpp
Tutorials/Basic/HeatEquation_EX3_C/myfunc.H
Tutorials/Basic/HeatEquation_EX3_C/myfunc_F.H

commit beca7fdff05932235bbb7f9448c8e2c4cac14e00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 16 16:00:57 2018 -0800

    msolve works for at least one example

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 6646c823ddcf55415152a063bd25a5e76ea474ba
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Tue Jan 16 16:12:08 2018 -0800

    work on basics

Docs/sphinx/source/Basics.rst
Docs/sphinx/source/BuildingAMReX.rst
Docs/sphinx/source/Chapter4.rst
Docs/sphinx/source/GettingStarted.rst

commit aaa63601c8a38aae93e72802c319cde30cb29fb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 16 13:37:40 2018 -0800

    firs pass of msolve

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit bce55e63d6c06d0263efc6631ea09b2a48619d21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 16 09:12:51 2018 -0800

    make this regression test much smaller

Tutorials/LinearSolvers/ABecLaplacian_F/inputs-rt-poisson-com

commit 15283e1301836903e16f336bf65040e2d68f2a3b
Merge: 7043a286f 5b6586c92
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jan 15 10:53:11 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 7043a286fb1d65ebf72424b429bb5bb66d53cc9f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Jan 15 10:52:46 2018 -0800

    completed the Building AMReX section

Docs/sphinx/source/BuildingAMReX.rst
Docs/sphinx/source/Chapter3.rst

commit 82984b07953403124e20880ebae31db7209231a3
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 14 12:54:56 2018 -0800

    finished GettingStarted section

Docs/sphinx/source/GettingStarted.rst
Docs/sphinx/source/Visualization.rst

commit d8f7a43158b5c48eddf6dfdabd0056a6a31f475f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 14 12:45:00 2018 -0800

    almost done with GettingStarted

Docs/sphinx/source/Basics.rst
Docs/sphinx/source/Chapter4.rst
Docs/sphinx/source/GettingStarted.rst

commit 4937591baba2f347e0f020eb30b85c2e9ff3c340
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 14 12:21:15 2018 -0800

    find a good comprimize solution for typesetting small fraction

Docs/sphinx/source/GettingStarted.rst

commit 1ae4b8951ab2e592170221d5345b76a7bf7a0e65
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 14 11:53:39 2018 -0800

    working on `GettingStarted` section of the sphinx docs. Note: changing LaTeX references to sphinx rst references for cross-referencing different sections

Docs/sphinx/source/BuildingAMReX.rst
Docs/sphinx/source/Chapter2.rst
Docs/sphinx/source/Chapter3.rst
Docs/sphinx/source/GettingStarted.rst

commit 93f3939bc7ae85771fede43634d3b6fc9a03ee64
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sun Jan 14 11:12:32 2018 -0800

    added preamble to doc index

Docs/sphinx/source/index.rst

commit 5b6586c92c11360608aad835260a14217694af2c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Jan 14 09:52:55 2018 -0800

    Replace FillBoundary by EnforcePeriodicity since the interior ghost cells
    are filled by the loop above

Src/EB/AMReX_EBTower.cpp

commit a28ebf5a4f0cb4f1ad62b71668212a53ad8cd194
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jan 13 18:17:58 2018 -0800

    No longer have a FillBoundary call for MultiCutFabs

Src/EB/AMReX_EBTower.cpp
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp

commit de67b5c3e6520f9867ccd5bdac2f740d05b6f24a
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 13 17:27:07 2018 -0800

    ingore sphinx build dir

.gitignore

commit 19925b583ea9113d455d2227494564d72a4d4f8c
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 13 17:25:45 2018 -0800

    LaTeX Introduction -> rst

Docs/sphinx/source/Introduction.rst

commit 4cdf808fbf96d86755ea71cb1dc05821f5ac9529
Merge: 9eeb1d676 d84491612
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 13 16:49:44 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 9eeb1d6763e7ec105c22d452e6cda4ffb8977c29
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Jan 13 16:49:10 2018 -0800

    tweak: avoid picking up on temporary files generated when making docs

.gitignore

commit d8449161266d64ec2186a6a5c2e6cb7988bb4a98
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jan 13 15:23:46 2018 -0800

    Add FillBoundary call when filling flag and other geometric info so that we can
    correctly fill periodic ghost cells.  (Had to add interface for MultiCutFab)

Src/EB/AMReX_EBTower.cpp
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp

commit b6f792be861030a06b48c93959104c7316eafec8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jan 13 10:14:27 2018 -0800

    Modify parallel copy in the EBTower stuff to include the periodicity flag so
    it will fill periodic ghost cells correctly.  Had to modify an interface
    for MultiCutFabs.

Src/EB/AMReX_EBTower.cpp
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp

commit d1e0b99872133ce46df52de32c963d42a0325d87
Merge: 3fc53c191 da997167f
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jan 12 12:47:40 2018 -0800

    Merge pull request #188 from JBlaschke/development
    
    Documentation

commit 3fc53c191218daead6fb573420f14cf85d872723
Merge: d65705cec cebb5ee84
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jan 12 12:44:27 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d65705cecf93a25dc0d0708e2979180e47e0b8d2
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jan 12 12:44:19 2018 -0800

    Fix typ

Docs/AMReXUsersGuide/Particle/Particle.tex

commit da997167fc10afb7bf37680fe29decdaf086448a
Merge: cebb5ee84 c8271c7b8
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Fri Jan 12 12:39:31 2018 -0800

    Merge branch 'jpb/ug/fix-typos' into development

commit cebb5ee8457037731ba2273432e0d0b3981aa7de
Author: jbb <jbbell@lbl.gov>
Date:   Fri Jan 12 12:24:07 2018 -0800

    added more infomration

Tools/Postprocessing/F_Src/faverplot.f90

commit 1c3c3c244a70dc8694a2d832704fb3d47dcc3ea5
Author: jbb <jbbell@lbl.gov>
Date:   Fri Jan 12 11:59:22 2018 -0800

    cleanup

Tools/Postprocessing/F_Src/faverplot.f90

commit 92a5d491fd1682b86969f20e645409e0178fa396
Author: jbb <jbbell@lbl.gov>
Date:   Fri Jan 12 11:54:59 2018 -0800

    added build to makefile

Tools/Postprocessing/F_Src/GNUmakefile

commit 2b05b75d0a442330d38c89fd5972571c83b0b50c
Merge: 99034427f 85f83e705
Author: jbb <jbbell@lbl.gov>
Date:   Fri Jan 12 11:52:23 2018 -0800

    Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development

commit 99034427fc6b6452a7727a2813c17ee4d2e724b8
Author: jbb <jbbell@lbl.gov>
Date:   Fri Jan 12 11:51:42 2018 -0800

    added code to average a collection of plotfiles

Tools/Postprocessing/F_Src/faverplot.f90

commit 85f83e70568e97ec4e712f5820decf5b98b43853
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 12 09:28:07 2018 -0800

    add some profilers

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 17746a7e06901700c643af8c76e59da0e434757b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 12 09:14:51 2018 -0800

    nodal projection in 2d rz: turn on correction by default

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 3b0266274538e32866536f5e5cc2f9c089264237
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 11 17:34:06 2018 -0800

    nodal projection: fix rz

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit fe08cb9a41ce71447e940a77b07ef989787d8a65
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 11 16:42:04 2018 -0800

    Fix bug affecting the particle container when tiling is off but non-zero tile size is set.

Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParticleContainerI.H

commit 93e9719e9238b3a350c85368077654824ddb2843
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 11 13:42:02 2018 -0800

    nodal projection: some support for rz correction

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 94681e4166f21bdb7a064d47cd0ba8841fafbfaa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 11 12:56:11 2018 -0800

    remove some const so that MPI 2 is happy

Src/Base/AMReX_ParallelReduce.H

commit 22d7b68de64c2d8168273854c11d889f616fe218
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 11 10:19:54 2018 -0800

    fix a bug in my last commit

Src/F_Interfaces/Base/AMReX_FPhysBC.cpp

commit de00a420dfa1e399e23ac3c29afb741220bf96db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 11 09:02:30 2018 -0800

    Fortran module AMReX_fillpatch_module takes a user provided callback
    function for filling physical boundary conditions.  That function used
    to use 0-based index for component (i.e., the last index).  For
    consistence with 1-based index for component in other Fortran modules,
    this has been changed to 1-based index for component.

CHANGES
Src/F_Interfaces/Base/AMReX_FPhysBC.cpp

commit f02d850a0ffac7e3eab3e9112d568d89ea701771
Merge: 56a073bb5 bbd507e5e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 10 17:37:56 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 56a073bb5a7beaee46029fd0b2dfc2a7934ba9d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 10 17:15:26 2018 -0800

    nodal projection: no neumann bc doubling for fine sync residual because how SyncRegister works

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit bbd507e5ede1656bc2c85d50ac7c2d98b291986e
Merge: 2712df36f 902840d23
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 10 16:03:05 2018 -0800

    Merge branch 'profvis' into development

commit 2712df36f9f2e870f5a965f762b09705a3d8c544
Merge: 237debfff 75c1004f9
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 10 16:02:57 2018 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 75c1004f915e74104486de3534c54b68033c77fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 10 14:51:04 2018 -0800

    nodal projection: add support for cc rhs

Src/Base/AMReX_ArrayLim.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 902840d235f1f5e12d3ba1a29452698beb45e3be
Author: kngott <kngott@lbl.gov>
Date:   Wed Jan 10 12:44:12 2018 -0800

    Addition of sends plotfile dispatch feature. Also includes filtering if using serial amrvis.

Src/Extern/amrdata/AMReX_DataServices.cpp

commit c21ce86c1fbcd80da04faad6ebdb16b1fe44285f
Merge: 8d71bff61 237debfff
Author: kngott <kngott@lbl.gov>
Date:   Wed Jan 10 12:40:59 2018 -0800

    Merge branch 'profvis' of https://github.com/AMReX-Codes/amrex into profvis

commit 8d71bff614f900dd78f1906b0a5881610a486097
Author: kngott <kngott@lbl.gov>
Date:   Wed Jan 10 12:40:23 2018 -0800

    Addition of a BroadcastBool class and appropriate test code.

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Tests/C_BaseLib/BcastClasses/BcastClasses.cpp

commit 237debfff6289fcd1f9239e349bfce6a39473b34
Merge: dcd62d278 02da3a220
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 10 11:57:46 2018 -0800

    Merge branch 'development' into profvis

commit dcd62d278fff1e04fa3f80aa015c29f65791c37e
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 10 11:56:55 2018 -0800

    add time range file for timelines.

Src/Extern/amrdata/AMReX_DataServices.cpp

commit 02da3a2200985913f73674003c4bbf5d86fd2d5e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 9 15:40:18 2018 -0800

    fix a bug in 3d nodal projection

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit dc72f408acd68255d4d6abc46894e592dc177132
Merge: 68f69effc 815093d2c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 9 12:45:37 2018 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 68f69effcb6e6c0d8cefc830f8cd934286955c85
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 9 12:45:18 2018 -0800

    bugfix for neighbor particle container when tiling is turned off.

Src/Particle/AMReX_NeighborParticlesI.H

commit 815093d2c3d945135ac901eaae25a7d9efea36ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 9 10:03:18 2018 -0800

    fix fmg for nodal solver

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 3a0278ce0e4b2b5230f2a8a6b79a6e5adbdeeaa2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 9 09:43:54 2018 -0800

    nodal projection: finish inflow

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit e4d9d7783afba2ed742f1f030e4e44d7372c5400
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 8 15:50:57 2018 -0800

    Fortran: add function for testing boxarray box intersection

Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90

commit 38dfbd0a3ab25007dcfee805b19cd3dd3f92c086
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 8 11:10:53 2018 -0800

    minor optimization

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 12c2c575cb8609a639f9ceeb03bf06c3f1c27f5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 8 11:06:32 2018 -0800

    nodal projection: fix sync residual mask

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 248b313f6afb54eea8ba3a4cff85542548179f42
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 8 10:17:30 2018 -0800

    nodal projection: when fine boxes touch the symmetry axis

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit e1027f7c73eaee860d3d92e78407307674ea2cb2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 8 09:14:55 2018 -0800

    no need to apply metric term to coarse mg levels because they get coefficients from average down

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp

commit 5b0978c49ab630551d6ed883e975c58ec6bfa023
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 6 13:28:10 2018 -0800

    fix crse/fine residual at Neumann boundary

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit ad14218ca90719843926a4f982123b0b65fa15f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 5 17:46:44 2018 -0800

    when fine boxes touch Neumann boundary

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 0d3c61785ac2ef0fad9fb7d22e37c4b3b208df10
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 5 10:46:15 2018 -0800

    nodal projection: be explicit on the number of components when calling FillBoundary on velocity because IAMR may pass a MulitFab with more components

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit eec6f91b9f1f99d896d2157f7327ddc792a7220b
Merge: d8efb00a1 f0879f59a
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 4 14:34:34 2018 -0800

    merge fix
    Merge branch 'development' into profvis

commit f0879f59af2838114a31a57f1d0c9b485c0b19d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 3 13:40:30 2018 -0800

    nodal projection: start support for inflow

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit e9e8cb3bdad9cf3debffbbaa0359a9ff3a7c0ffa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 3 12:47:12 2018 -0800

    nodal projection: clean up

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H

commit 596820b5d5016f67ddaa257b335de07f9594fdfb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 3 12:44:15 2018 -0800

    nodal projection: sync solutions after each iteration

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H

commit c5689483572128598d7920942b6a2560d3422443
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 3 10:45:59 2018 -0800

    fix mask in fine sync residual

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 151ee89ac63f5f43cd8fe15e6e4c084ff76bb588
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 3 09:25:24 2018 -0800

    3d nodal projection: fix a bug in crse/fine residual

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit e7fcd9b7d8ab65264567192dbc4a715829b0a087
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 2 14:52:02 2018 -0800

    fix cmake

Src/LinearSolvers/CMakeLists.txt

commit a46ea95241de25c2ee196839c42b280a7873dc83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 2 13:29:13 2018 -0800

    nodal projection: fix tiling bug

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit e554c64f26e20c7e789971c2db5f9b873ecf118e
Merge: fc2a247a6 f295bc8fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 2 09:59:06 2018 -0800

    Merge branch 'development' into weiqun/mlmg

commit fc2a247a6ec966b62f5a601401a605e841e7d89a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 2 09:44:07 2018 -0800

    nodal projection: fix solvability for bottom solver

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H

commit f295bc8fa660d2851b8ee212df3bd9e34eb30fc8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 2 08:30:37 2018 -0800

    update CHANGES

CHANGES

commit dad37957e87ea8e53f432b45879a0fcac185d9df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 30 21:11:59 2017 -0800

    3d nodal projection: bug fixes

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 6976f0d400946cca2c6c69e93fe9fabbc211fdd9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 30 13:29:39 2017 -0800

    3d nodal projection: bug fix

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 89db38650d317105d9755c8ae45700a7b56ee7b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 30 13:13:38 2017 -0800

    3d nodal projection: bug fixes

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 304df1dfd8841027c92a0e47b3c5c72a8cb6c735
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 30 12:32:07 2017 -0800

    3d nodal projection: bug fix

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 3ef0c9e9500bac1aca9df8ebe8cd0d0845f74d00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 30 12:26:44 2017 -0800

    3d nodal projection: bug fix

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit b8ab950671bb6d97c1c5f2996adaaa5b9d8263ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 30 11:49:55 2017 -0800

    3d nodal projection: bug fix

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 6ad0d39e84a11df0906ac65c06fbaca24ecfd2d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 30 11:14:32 2017 -0800

    3d nodal projection: bug fixes

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 8d4339e0d86e20d51167e2d9d0826b7fccc4fd34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 29 21:38:27 2017 -0800

    3d nodal projection: first pass

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 48a947145ee6da3ad248ffbf8700082b44e9cc24
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 29 18:01:58 2017 -0800

    3d nodal projection: fine contribution of residual

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 3e0f0bc186df5efc5a556e49b7483d3dc90fa160
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 29 17:29:07 2017 -0800

    nodal projection: refactor crse/fine residual

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 05905c0f3dca4ed2f7874da1fb147f49a32c4144
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 29 15:44:45 2017 -0800

    3d nodal projection: crse/fine divu

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit ec293c45f75d3102c38d6e9a281458215d5bb920
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 29 15:28:15 2017 -0800

    nodal projection: refactor fine contribution of divu

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 01adc278398cc66a2c6c2705e2f43e3b365b6439
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 28 19:20:29 2017 -0800

    3d nodal projection: fine contribution of divu WIP

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 9c7840effa975b337b71cf41463a8d885418f7c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 26 16:20:28 2017 -0800

    3d nodal projetion: add cell-centered rhs and make new u

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 7f1b15ea277a5207e1b9233ec1c82234791bc7c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 26 13:21:42 2017 -0800

    3d nodal projection: divu

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 575b961316bbc27f2a4ab4b3b41a060f6fb38149
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 26 13:07:49 2017 -0800

    3d nodal projection: arithmetic average version of interpolation

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit e9ec2a2e547622063a5e1c71ca0ba1ba0979d96f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 26 11:45:29 2017 -0800

    3d nodal projection: harmonic average version of interpolation

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 99cf609df32578c35887fe4006867407de85593e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 26 10:20:17 2017 -0800

    3d nodal projection: restriction

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 7a4b4d56f5f3b74c6ee0e82f5f374db020ee8e12
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 25 17:18:37 2017 -0800

    nodal projectoin: minor

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit 5263ee231923765cbda4ed380ed585e834734cbb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 25 17:16:15 2017 -0800

    3d nodal projectoin: Gauss-Seidel smoother

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit d057608cb8e49c2ee6f3df58f422272df7bad23f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 25 16:49:53 2017 -0800

    3d nodal projectoin: Jacobi smoother

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit eefc50e3336bf011a013561dbe833bda4805da2a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 25 16:22:27 2017 -0800

    3d nodal projectoin: arithmetic average version of A dot x

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 87e834943a182ba50aee6dc633fe080793a6ef16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 25 11:16:19 2017 -0800

    3d nodal projection: refactor harmonic average version of A dot x

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 21a1157fe59b8e4b2a6c68d2c01e73ba7fe3a6a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 24 16:48:53 2017 -0800

    nodal projection: optimization of smoother

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit 10e841e4f91b21d4700d804c067284d46204c6e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 24 16:33:22 2017 -0800

    nodal projection: optimization of A dot x

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 2d02b16be177dbd39a5d57ba54903114503c1043
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 24 14:22:01 2017 -0800

    3d nodal projection: harmonic average version of A dot x

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 610e839535d3125383914f47a2951e849ae3eb9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 24 12:51:04 2017 -0800

    3d nodal projection: bc

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit c8271c7b86a28fda26583ea6d061f14876640b0f
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Sat Dec 23 09:50:10 2017 -0800

    Typo in description of ghost cells (in MultiFab). This way makes more sense now

Docs/AMReXUsersGuide/Basics/Basics.tex

commit fc55407de2686edb8805a8114375d89390c2eac4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 22 21:32:30 2017 -0800

    3d nodal projection: average down coefficients

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit eb97d86f5731fd1db9f19fb0be36901e4483d95e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 22 21:20:40 2017 -0800

    3d nodal projection: masks

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit 7d2c4922375191c4ee56a2117b568cd2409e3ee4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 22 21:00:11 2017 -0800

    3d nodal projection: linear interpolation

Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90

commit 24312396987fc2b0651bcefa021a25be3f1addee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 22 18:05:49 2017 -0800

    nodal projection: add stub functions so that 1d and 3d can compile

Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90

commit ff56827d4e82355a99fbc38d8d16398ff8bde0c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 22 17:34:06 2017 -0800

    nodal projection: organization

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H

commit 7e8c436b5a4b737a36fbbed39c3e81afefd23d18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 22 17:03:54 2017 -0800

    nodal projection: clean up

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 9636dcf14be5c9bb40d2efd2934d71bf021e767e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 22 17:01:11 2017 -0800

    nodal projection: cleanup

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit fbb074ed0bacdbef9a996e0cbd6674b3782dbc91
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 22 16:44:42 2017 -0800

    nodal projection: add nodal mask in addition to cell mask

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 00881ad8389c1c417b300ff9eba35da2f26a84be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 22 16:17:07 2017 -0800

    nodal projection: use parameter instead of hardwired number for dirichlet mask

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit c7063a996668b7de35465491c8df5ed4b9d47392
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 22 15:40:16 2017 -0800

    nodal projection: clean up overlap mask

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 5b2e01c5426b43702478c1bda1dce3759379c154
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 22 15:36:59 2017 -0800

    nodal projection: clean up weight

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit eb35e3f3a2608d5dc68f1614c87bbb9d00f3c050
Merge: 5dde12800 2751b4199
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Dec 22 13:37:52 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5dde12800102c597d44ef2911ecb2a765cdf55d2
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Dec 22 13:37:39 2017 -0800

    transform recursive timesteps into iterative tasks

Src/AmrTask/AMFIter/AMReX_AmrTask.H
Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H
Src/AmrTask/graph/AMReX_AbstractTask.H
Src/Base/AMReX_FabArray.H

commit b3d602d720bf254f2adb6214b2032fb17480f90b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Dec 22 14:54:02 2017 -0500

    Remove -lcudart for OpenACC

Tools/GNUMake/comps/pgi.mak

commit 31b5c63bc22fddceccfea977dfe2bac6b79830b9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Dec 22 14:45:51 2017 -0500

    Add .ACC to exe name when USE_ACC=TRUE

Tools/GNUMake/Make.defs

commit b729a7978d9f7d575ef3990a66bd2063b5e172c5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Dec 22 10:53:50 2017 -0800

    Some fixes to the dot, sum, and norm routines of BaseFab. (#184)
    
    These routines were not correctly accessing device data on the return value, and were also inadvertently having each thread zero out the stored sum.

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_nd.F90

commit 409e7a4734380890e3cd7d73cc04ac3640bcc275
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 21 16:21:36 2017 -0800

    f90 nodal solver: the initial residual is now computed as composite residual

Src/LinearSolvers/F_MG/ml_nd.f90

commit ab03f83dd4172ffd09525d073501e6234cfb3e1b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 21 15:55:32 2017 -0800

    fix up residual mask

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 2751b41992829567f4dbebb03993bc6ace474aec
Merge: 69c5a4066 5a9912051
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Dec 21 15:21:42 2017 -0800

    Merge pull request #185 from AMReX-Codes/dtg_branch
    
    moving document and bug fixes to dev branch.

commit 5a9912051bffdf6b0e04f82e1228f8022c2e63b0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Dec 21 15:20:21 2017 -0800

    added section to tutorial document explaining derivation of time interpolation formulae

Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs

commit 11c41cb874f67b9c611dc76599dcd2f253ee3517
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Dec 21 15:19:52 2017 -0800

    bug fix and took out unused functions

Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit bd964211a636ebac49b74d40a793a1d575d5f4f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 21 15:19:13 2017 -0800

    fix a bug

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit d8efb00a174f349acd74ac1c74992c7acd5b05be
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 21 15:06:48 2017 -0800

    precreate update for nyx support.

Src/Amr/AMReX_Amr.cpp

commit 7650a500cd6dafdbd9c7c653a6965d1b39b951b7
Merge: 9d2100e3e d7872c272
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 21 15:05:22 2017 -0800

    merge fix.

commit 980ef629cb150358a5170e9dfdfe483b792ba45e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 21 13:46:41 2017 -0800

    use the restricted rhs for reflux

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 7a4b6519f988c465585c7a9fcb340c2918f26877
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 21 12:39:59 2017 -0800

    nodal project: full weight restriction of rhs

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 69c5a4066ecdec61317c34635c12f2beb2f90f07
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 21 12:16:26 2017 -0800

    patch fcompare to not choke on plotfiles that only have particle data.

Tools/Postprocessing/F_Src/fcompare.f90

commit c9ae9f5b4cba68b76084b8046723d818a0b1ab88
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 21 12:15:30 2017 -0800

    initialize these pointers to Null()

Src/F_BaseLib/plotfile.f90

commit d3bcd85458a1d08b1b9f518b38c112a678c52c39
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Dec 20 23:32:40 2017 -0500

    Do not compile in the old filcc when using CUDA

Src/Base/AMReX_FILCC_3D.F90
Src/Base/AMReX_filcc_mod.F90
Src/Base/Make.package

commit 646442b86bdc766b9b1e0c39deadb990232d6549
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 20 17:55:50 2017 -0800

    Removing the particle stuff from the GPU branch (will add again on a separate branch) (#158)

Src/Particle/AMReX_CudaManagedAllocator.H
Src/Particle/AMReX_Particles.H
Src/Particle/Make.package
Tests/Particles/CUDADeposition/GNUmakefile
Tests/Particles/CUDADeposition/Make.package
Tests/Particles/CUDADeposition/MyParticleContainer.H
Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/cuda_deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_F.H
Tests/Particles/CUDADeposition/inputs
Tests/Particles/CUDADeposition/main.cpp
Tests/Particles/CUDADeposition/solve_for_accel.cpp
Tests/Particles/CUDADeposition/solve_with_f90.cpp
Tests/Particles/ManagedCUDADeposition/GNUmakefile
Tests/Particles/ManagedCUDADeposition/Make.package
Tests/Particles/ManagedCUDADeposition/MyParticleContainer.H
Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp
Tests/Particles/ManagedCUDADeposition/cuda_deposit_3d.f90
Tests/Particles/ManagedCUDADeposition/deposit_3d.f90
Tests/Particles/ManagedCUDADeposition/deposit_F.H
Tests/Particles/ManagedCUDADeposition/inputs
Tests/Particles/ManagedCUDADeposition/main.cpp
Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp
Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp

commit d7872c2723eb52fee85de7d292ba3453e083301e
Merge: 38629f10c b03bb7969
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Dec 20 17:07:53 2017 -0800

    Merge pull request #183 from AMReX-Codes/marc/allow_strict_mode
    
    Marc/allow strict mode

commit 10b55525de429a19fe70b006e746d91b901320e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 20 16:58:05 2017 -0800

    fix weight

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit 77f3bc0f7e8a492bd68e74d415ce5c77cd5fa06d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Dec 20 19:10:19 2017 -0500

    Make NVML support be opt-in

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Tools/GNUMake/Make.defs

commit a7c3fe92f0022a12ecbdd8434666a987089af078
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 20 15:38:46 2017 -0800

    average down nodal rhs and solution

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit ba6265fe670f2f42ffe77a2e4849059cfd07f315
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Dec 20 15:14:57 2017 -0800

    finished the parts ScalarAdvection Tutorial that anyone ought to care about.   I will also add an appendix explaining where the formulae come from.

Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex

commit 7f5cbe0c4ea05caf11f523a9be49bbd4f743eccd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 20 14:42:53 2017 -0800

    fix assertion

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 996847863e8b079e135c276b9606145d08860452
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 20 14:36:56 2017 -0800

    minor optimization

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit b03bb796936a255f1db1a60d5ed8cfb764e4c1a2
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Dec 20 14:23:46 2017 -0800

    Minor changes to satisfy compilation under AMREX_STRICT_MODE

Src/Amr/AMReX_Amr.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBTower.cpp
Src/EB/AMReX_MultiCutFab.cpp
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp

commit 0b4412dae4a45c986c5a92acdffdb92c3127bec3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 20 14:09:13 2017 -0800

    average down of solution is only needed for cell-centered solve

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit a841ab9f2b836811c4c78e29bb0ae3b3b3d3db9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 20 14:03:19 2017 -0800

    nodal interpolation of correction between amr levels

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_F.H

commit 38629f10c640b177cce6b8327bfa61ee06c24cd9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 20 13:54:52 2017 -0800

    allow fcompare to work with plotfiles that only have particle data (for the regression testing suite)

Src/F_BaseLib/plotfile.f90

commit 9b5e524db11f4b27604fcede811d0f82b3803634
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 20 11:10:37 2017 -0800

    use the correct rhs

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 20a281dc65dcc57199cd86f928444ac409b9fc98
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Dec 19 18:29:05 2017 -0800

    added a bunch to document for this tutorial

Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit 6759b6dae2531cb0cbb1bd6e8956f8eae83e7e45
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 19 17:27:23 2017 -0800

    restriction of residual

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 53624ebdf5f438f084c86499faea64b2846a9220
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 19 12:44:21 2017 -0800

    pass fine residual to reflux too

Src/Base/AMReX_MultiFabUtil.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit aef7b501d2d53addfa6e8047680ab59312f1674f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 19 12:03:03 2017 -0800

    make average_down work for nodal too

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit c6632bbfb5493ffb3e593e22833efc00ef2888f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 19 12:01:22 2017 -0800

    add MultiFab::is_cell_centered function

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit b4550409be044543ccde044a1b5b53969d921566
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 19 10:25:05 2017 -0800

    fine contribution of A dot x

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 5817701afd93ab5c94ad62b07f0e0f9c5ff79129
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 18 17:41:28 2017 -0800

    WIP: fine contribution of A dot x

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 8174d57b7d18b1a7ae4b72c675d97cc91e65a67a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 18 17:18:05 2017 -0800

    pass the pld by value instead of by reference.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 474039c9769b01cf5fee43637ae5559f277c9b46
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 18 17:12:33 2017 -0800

    allow caching of the particle location between calls to Reset()

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 19d9fac628db4821a2292e092324b5966e59273b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 18 15:24:02 2017 -0800

    rework the weight

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 19f519feadaa61a96b8051b3ed7e8fbe9c38ff0b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 18 12:39:36 2017 -0800

    fix bad merge.

Src/Particle/AMReX_ParticleContainerI.H

commit 7ec8d63b730dfa6177d3207b988427a4e5c4ce03
Merge: e94a9ab28 8eb0af9be
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 18 12:36:58 2017 -0800

    merging.

commit e94a9ab28f0b9f11c87a74c9fe1deae83357afbf
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 18 12:34:35 2017 -0800

    don't profile this funtion - it gets called too many times and skews results.

Src/Particle/AMReX_ParticleContainerI.H

commit 900328db4d36e8a69abe389921374675745eb03e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 16 14:56:19 2017 -0800

    nodal projection: fix fine contribution

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit 647d5034d314edcbbaa2d0c6408bc5427dce070c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 15 14:53:59 2017 -0800

    add FabArray::ParallelAdd; coarse contribution in nodal projection

Src/Base/AMReX_FabArray.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 9d2100e3e1033f20bd907c016b366a509d0a2906
Author: kngott <kngott@lbl.gov>
Date:   Fri Dec 15 17:35:30 2017 -0800

    BroadcastString and BroadcastStringArray functions, plus corresponding test.

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Tests/C_BaseLib/BcastClasses/BcastClasses.cpp

commit e9919bb4d848003123b088e05eb787cf5cfe050c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 15 13:10:23 2017 -0800

    WIP: compute fine contribution

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 071d8292b164dc65ee1838d9e827f1a05db47b5b
Author: kngott <kngott@lbl.gov>
Date:   Fri Dec 15 12:05:18 2017 -0800

    Improved RemovePiece fix.

Src/Extern/ProfParser/AMReX_BLProfStats.cpp

commit 4f76a92c7b5206188a0df38e8dae9466dcb3d558
Author: kngott <kngott@lbl.gov>
Date:   Fri Dec 15 12:02:02 2017 -0800

    BLProfStats::RemovePiece now successfully removes equal TimeRanges.

Src/Extern/ProfParser/AMReX_BLProfStats.cpp

commit 5e40c6f617da6d319b922060fc6d0cac17690e96
Merge: 001693af5 8eb0af9be
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Thu Dec 14 19:24:08 2017 -0600

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8eb0af9be2098fdeb85f7abe5c685e5e60ef97ea
Author: kngott <kngott@lbl.gov>
Date:   Thu Dec 14 16:52:25 2017 -0800

    Additional profiler flags.

Src/Amr/AMReX_AmrLevel.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp

commit c4faaa8504cf867eafcc2249a5743c14a8b0e547
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 14 14:47:32 2017 -0800

    add rhcc

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 62bf092e5727e1a5c809ba51ac6a4f73098d78f6
Merge: 8a2dc84ce ec1dce22e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Dec 14 13:02:52 2017 -0800

    Merge pull request #178 from bcfriesen/update_CVODE_build
    
    CVODE, Tools: use Cray version of SUNDIALS if module is loaded

commit 8a2dc84ce91973aefe5b9b5f3a3553fa37dea176
Merge: c9a4973de e4a611ee4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Dec 14 13:01:58 2017 -0800

    Merge pull request #179 from AMReX-Codes/fextract
    
    Enable coarse and fine level selection in fextract

commit c9a4973defaeae11d812a96a7f658da6d2a677b9
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Dec 14 12:43:03 2017 -0800

    note about PhysBCFunct class

Docs/AMReXUsersGuide/Boundary/Boundary.tex
Src/Base/AMReX_PhysBCFunct.H

commit d2de2978b7cbe354d7b8cac34f98ab5fa6b39ec7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 13 21:23:48 2017 -0800

    save the number of iterations

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 3d905dbab2f464c044b73cd1ffaeb73f5505deca
Merge: d5d9677d5 bc0c9b817
Author: vince <vebeckner@lbl.gov>
Date:   Wed Dec 13 18:13:46 2017 -0800

    merge fixes.

commit bc0c9b817a0cbbc12aa72b527febdad9b6c927ab
Author: vince <vebeckner@lbl.gov>
Date:   Wed Dec 13 17:56:49 2017 -0800

    added option to set size of DATA_nnnnn digits.

Src/Particle/AMReX_ParticleContainerI.H

commit 6517e242901c5fc291ecde40ad1d87d7364b0b2c
Author: kngott <kngott@lbl.gov>
Date:   Wed Dec 13 17:40:42 2017 -0800

    Timeline in GUI now runs in parallel.

Src/Extern/amrdata/AMReX_DataServices.cpp

commit d5d9677d578628ca85146f8c31e8043f0ef87b8b
Merge: 7ed9c9319 6d7f34542
Author: vince <vebeckner@lbl.gov>
Date:   Wed Dec 13 16:29:14 2017 -0800

    Merge branch 'development' into partio

commit 6d7f345426c2eb1c040eb024ec14084cbd514d11
Merge: ad9129a0d 91aa886f4
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Dec 13 14:52:46 2017 -0800

    Merge pull request #180 from AMReX-Codes/dtg_branch
    
    merging in some small bug fixes and other sundries

commit ec1dce22e2765392660d7f0753647e6d37be8513
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Dec 13 14:10:38 2017 -0800

    CVODE: Update user guide with instructions for linking SUNDIALS on Crays

Docs/AMReXUsersGuide/CVODE/CVODE.tex

commit 47719094f89bcfe344974cef453a0356306b756f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 13 14:05:10 2017 -0800

    compute fine sync residual

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 91aa886f47e476c08883e363c6954da129cf0b31
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Dec 13 14:01:07 2017 -0800

    scalar advection tests passing showing correct covergence 2d/3d, with and without limiting.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_mpi_driver.py

commit e4a611ee4cd42795b878c2515e086b5364682b9a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Dec 13 16:44:06 2017 -0500

    Enable coarse and fine level selection in fextract
    
    fextract previously would extract data on all levels by default. This adds
    options to select a different set of levels; for example, a use case might
    be to only see the data on the finest level so you can examine where the
    refined regions are. The new options are -c/--coarse_level and -f/--fine_level.

Tools/Postprocessing/F_Src/fextract.f90

commit f27f0e96b41330e02178092398bad6b8d4fdb8cb
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Dec 13 12:52:19 2017 -0800

    CVODE, Tools: use Cray version of SUNDIALS if module is loaded
    
    Cray includes SUNDIALS in the "cray-tpsl" module. Use that if the module is
    loaded. If the module is not loaded, then look for the home-cooked version.

Tools/GNUMake/packages/Make.cvode

commit 7ed9c9319bb1a2d5c70d9c5395ef47c55c02d325
Merge: ce513d046 ad9129a0d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Dec 13 12:22:36 2017 -0800

    Merge branch 'development' into partio

commit 5184ded536405a0a97334afbe190a483ceda7b24
Merge: 7b7d3baf8 ad9129a0d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Dec 13 12:20:29 2017 -0800

    merge fixes.

commit 601ba2e72aabb8fe666c4e84cdf02bda7e9334b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 13 12:12:51 2017 -0800

    do not touch dirichlet boundary cells in applybc

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit e5ecf02a73d0a1ff433e837ff0a1f903cf34cb8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 13 10:55:48 2017 -0800

    build dirichlet mask if it hasn't been built when compRHS is called

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 85070fe8ff35877ddd619b65c61bafdc35dfa1ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 12 17:12:47 2017 -0800

    WIP: add nodal mask for inhomogeneous Dirichlet

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 0dec7cb3d74937065c4bfdcfcffb123eac053346
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Dec 12 15:48:56 2017 -0800

    added mpi-driven convergence utility

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_mpi_driver.py

commit 3dcd25b0574aa41bf5b20573018eec4934e8c224
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Dec 12 15:14:11 2017 -0800

    found declaration bug that was causing code to act differently with chopped-up boxes

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit ad9129a0db96754f41c050a707d1518e6417d634
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 12 15:10:57 2017 -0800

    fix FillCoarsePatch as well

Src/Amr/AMReX_AmrLevel.cpp

commit b5a548664c806b30049b42b14fdb3d11453b3d78
Merge: 77807cbe3 1e51a0729
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 12 15:07:12 2017 -0800

    Merge branch 'development' into weiqun/mlmg

commit 1e51a07292b94e0e030fae880b21693c53592f63
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 12 15:02:44 2017 -0800

    fix the old fillpath too

Src/Amr/AMReX_AmrLevel.cpp

commit 8f238dfeee507263fdf8e6cf7f08e8f1855068f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 12 14:53:57 2017 -0800

    need to set ghost cells for temp mfs in FillPatch too

Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_FabArray.H

commit 77807cbe341b221279c73f3e17171510c17b0538
Merge: 2635b1a7d 4745e153b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 12 14:10:45 2017 -0800

    Merge branch 'development' into weiqun/mlmg

commit 4745e153b535c3837b8282f4558c774dcccaa3f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 12 13:20:19 2017 -0800

    FillPatch: initialize the initial data outside physical domain to quiet nan otherwise in some corner cases floating point exception could happen

Src/Amr/AMReX_AmrLevel.cpp

commit af55c38a01f4983db700805b482a83d51b7c4c21
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Dec 12 12:44:16 2017 -0800

    Quiet the compiler in DEBUG mode by avoiding shadowed and unused variables.

Src/F_BaseLib/box_f.f90
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp

commit 86b01a7a70591c7e6e1a04701b427afb92c5a3a9
Merge: 488a65162 2b722ac77
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Dec 12 11:12:26 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2b722ac774f7c5a31a52bb07d77d6a522afcdae2
Merge: c33dfb008 744341ecb
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Dec 12 10:41:24 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c33dfb0086152c82fa196d9303cc9673a47a4195
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Dec 12 10:41:07 2017 -0800

    use the VectorIO stuff in particel checkpoint / restart (again)

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 744341ecb14ef4292ecf6bbbda740b45bf647b3d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Dec 12 10:25:06 2017 -0800

    CMake: add new sources

Src/GeometryShop/CMakeLists.txt

commit 808abbc3b011a757033d8dfe26bd7733e7becd59
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Dec 12 09:37:33 2017 -0800

    add functions to write Vectors of float data when Real is double precision and vice versa.

Src/Base/AMReX_FabConv.H
Src/Base/AMReX_FabConv.cpp
Src/Base/AMReX_VectorIO.H
Src/Base/AMReX_VectorIO.cpp
Tests/Particles/TypeDescriptor/main.cpp

commit 2635b1a7da87ac4f433fe7669f442b7a3dbb1dc2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 12 09:32:54 2017 -0800

    nodal projection: make sync residual consistent with F90 solver

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 5d6e3a053a0dec5db4e8594107595cc4d5b40ab2
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Dec 11 16:17:45 2017 -0800

    4th order with limiting has good convergence in the simplest case.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/debug.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90

commit c2db3b4e79169ea2d6964e8c167aba0f926ba663
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Dec 11 16:12:11 2017 -0800

    Remove assertion from norm1()

Src/Base/AMReX_MultiFab.cpp

commit ce513d046e2a8659e6cc789405e4a689f01d6799
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 11 13:52:20 2017 -0800

    remove diagnostics.

Src/Amr/AMReX_AmrLevel.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit 70bcf5f94cb0942ced4fc29e1073fb50a49c1da1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 11 13:34:56 2017 -0800

    nodal projection: coarse sync residual

Src/Base/AMReX_MultiFab.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit f841eb9209a04bc5e7e8eae99e389a9b9214d184
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 11 09:04:26 2017 -0800

    mlmg: assertions for periodic boundary

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit e208e7a725e092a7168d7f1969cdd443bbe636ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 10 21:06:47 2017 -0800

    fix a compiler warning

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit f9fffaf963495bfc42fa7f1189ba3fc9428ddb0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 10 21:03:04 2017 -0800

    nodal projection: use arithmetic average

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H

commit e4853ed87076ad5b2ba5b83e7fc046b7eb5e2f20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 10 20:48:24 2017 -0800

    nodal projection: fix coefficent at periodic boundary

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit bc84f146a1e571849cbb69b5b8037b9e2670740f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 10 11:35:21 2017 -0800

    add MLNodeLinOp::nodalSync function

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit cb29b071413a9bdf11400690dda5334e16f78351
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 9 22:20:17 2017 -0800

    nodal projection: add arithemic average in addition to harmonic average

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 959ec49a385a049251ab2ed43747453fc85ade88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 8 23:11:57 2017 -0800

    nodal projection: fix periodici boundary

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit a6c5f2da8dc0ca31e618a8236af10727076aa5a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 8 17:52:05 2017 -0800

    For Gauss Seidel, we need to sync

Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H

commit addabf461b2c4a358270ed36c2667cb851266cc9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 8 15:57:03 2017 -0800

    mlmg: print more information

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 1b9ad44fbb67bd407651fa28b14d44f99ee1f2f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 8 15:33:34 2017 -0800

    nodal projection: make new u

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit ca25ccf1932b8e614a0e60b568fb6641436e4fe2
Merge: 9139a01b7 1074e82d7
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Dec 8 14:10:16 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9139a01b7a65d722ff14433d814f9451f16e90de
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Dec 8 14:09:25 2017 -0800

    have AmrMesh abort if it gets a problem domain with zero volume.

Src/AmrCore/AMReX_AmrMesh.cpp

commit 9ed12f8f82f184c4ad5e2052c79d3553504b9efe
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Dec 8 14:04:38 2017 -0800

    add function returning the volume of the RealBox.

Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp

commit 66c7edf032ea30d6df5856637c3d57b5f63d50df
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Dec 8 14:00:22 2017 -0800

    make the RealBox documentation consistent with its actual behavior.

Src/Base/AMReX_RealBox.H

commit 1074e82d7146685b3a6a975019f1b7c07b18828e
Merge: 8a13188cb 010a0f21d
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Dec 8 12:45:19 2017 -0800

    Merge pull request #177 from AMReX-Codes/dtg_branch
    
    merging in corrected rk time interpolators and geometry generation examples

commit 010a0f21d57e754b7a697bf454d669c5c86f9d52
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Dec 8 12:43:25 2017 -0800

    fixed the same bugs in the pwm versions, even though they are not called.

Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit 2f90476afe8295d617fc3baa26b2de7db1c6c252
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 8 12:40:56 2017 -0800

    more precreate directory support.

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp

commit e6795a9db69a66fd0ac2dc5d49010df44828278b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Dec 8 12:35:49 2017 -0800

    fixed bug in time interpolation (you have to be very careful which dt you use).  both rk3 and rk4 get good convergence numbers. and there was much rejoicing.

Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit 7b7d3baf80ee8c7e96489ab09ddb35acd58810e7
Author: kngott <kngott@lbl.gov>
Date:   Fri Dec 8 12:10:22 2017 -0800

    RunTimeline error with va when using multiple procs in GUI.

Src/Extern/ProfParser/AMReX_BLProfStats.H
Src/Extern/ProfParser/AMReX_BLProfStats.cpp
Src/Extern/ProfParser/AMReX_CommProfStats.H
Src/Extern/ProfParser/AMReX_CommProfStats.cpp
Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp
Src/Extern/amrdata/AMReX_DataServices.H
Src/Extern/amrdata/AMReX_DataServices.cpp

commit 7e188c6065d76d4eff0969e9bc63631916cad960
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 8 11:08:41 2017 -0800

    nodal projection: fixed jacobi and added gauss seidel

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 488a651620f0b37f3c784c75b49da8c285edef43
Merge: a82870e14 8a13188cb
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 8 11:01:21 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 8a13188cb643775cbff88f0a94c7d001df5570cb
Merge: 746e975ff e31cc27cf
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 8 10:26:55 2017 -0800

    Merge branch 'marc/geom_surface' into development
    
    This commit adds a capability to write out the intersection
    points between the fine mesh and the embedded boundary geometry,
    and is triggered if the ParmParse option ebis.eb_surface_filename
    is set.  By default it is not set.
    
    Since a surface is not a standard AMReX data structure (yet),
    a custom IO format was created for it.  The surface is created
    and written in parallel, and written in a binary format.  The
    amrex folder, Tools/EBSurfaceTools, contains some code to interact
    with this format.  In particular, the files can be read and the
    surface merged to a single surface on a single processor, and
    written to a simple text file of node and element data (polylines
    in 2D, triangles in 3D). A Python script is provided there to
    convert the output to a VTK format that can be read natively in
    Paraview.
    
    The format of the surface files will be documented elsewhere, but
    can be used, e.g., to store isosurfaces/contours. It may also become
    useful for interacting with computed/fixed boundary data at the eb.

commit e31cc27cfe028a22f9da6fa2000468a301d9f531
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Dec 7 19:48:30 2017 -0800

    Make compiler happier.

Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_GeometryService.cpp
Tools/EBSurfaceTools/ConvertEBSurface.cpp

commit 45e0cebcc66a2153c600527fb0855cee3e1fc6d5
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Dec 7 19:38:09 2017 -0800

    Make 2D version of eb surface stuff compatible with the 3D approach.

Src/GeometryShop/AMReX_EBISLevel.cpp
Tools/EBSurfaceTools/ConvertEBSurface.cpp

commit 7ed5428fb25ca40fac099bf9741daf8ec70878ec
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Dec 7 18:11:49 2017 -0800

    whoops!  Gotta make the dir before writing to it.

Src/GeometryShop/AMReX_EBISLevel.cpp

commit a5f0446e8b50df68afbf6db6cbc9664e2ca205f0
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Dec 7 18:00:55 2017 -0800

    Move some code around.

Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_GeomIntersectUtils.H
Src/GeometryShop/AMReX_GeomIntersectUtils.cpp

commit bbcf653f9f31c7374509553ddb91e0c30852f12a
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Dec 7 17:40:20 2017 -0800

    Make 3D output write to a folder+header and use binary IO.  Add EBSurfaceTools folder with code to read surface out, and reduce the surface across boxes and write a simple ASCII text file.  Include a python script to convert this to VTK-compatible format for viewing in Paraview.

Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_GeomIntersectUtils.H
Src/GeometryShop/AMReX_GeomIntersectUtils.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp
Tools/EBSurfaceTools/ConvertEBSurface.cpp
Tools/EBSurfaceTools/GNUmakefile
Tools/EBSurfaceTools/isoToVTK.py

commit ea18c12d9a16eba76a3bce359692ed8bb97c42b8
Merge: b421f22f3 746e975ff
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 7 17:12:55 2017 -0800

    merge fix.

commit bcce7915bbcc7250bbc8902064ebfccfdf755f0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 7 16:31:23 2017 -0800

    nodal projection: clean up

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 3e3fbeceb41aeeb1cb818d878f09b0f83bf81cc8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 7 15:55:12 2017 -0800

    nodal projection: zero out dirichlet boundary

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit b421f22f389fb0bee052243f8310c13f9c43a4c3
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 7 15:50:03 2017 -0800

    fix warning.

Src/Base/AMReX_FACopyDescriptor.H

commit 1183af431d1c6d25095b7a491b6110330545db6f
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 7 15:14:22 2017 -0800

    prepost updates for plotfiles.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 841884a8186fcc0022518138d2695d36dd08d665
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 7 15:11:57 2017 -0800

    prepost updates for plotfiles.

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp

commit 8377b337e28561a9da7df5ad64915cf3d44ba62e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 7 14:23:23 2017 -0800

    nodal projection: fix a bug

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90

commit a189955131e44701e729b5f379ae4396188e63b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 7 13:41:13 2017 -0800

    nodal projection: interpolation

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 5871d31efd561b20799e545201e4a00fdc889be7
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Dec 7 12:49:51 2017 -0800

    more examples of geometries

Tutorials/EB/GeometryGeneration/exec/GNUmakefile
Tutorials/EB/GeometryGeneration/exec/parabolaWithSphere.cpp
Tutorials/EB/GeometryGeneration/exec/parabolaWithSphere.inputs
Tutorials/EB/GeometryGeneration/exec/surfaceOfRevolution.cpp
Tutorials/EB/GeometryGeneration/exec/surfaceOfRevolution.inputs

commit 6e193e1c55ca5e11c0a995fccc5b3cd68ce91af4
Author: kngott <kngott@lbl.gov>
Date:   Thu Dec 7 12:22:29 2017 -0800

    Addition of regions data checks to -check batch function.

Src/Extern/ProfParser/AMReX_RegionsProfStats.H
Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp
Src/Extern/amrdata/AMReX_DataServices.cpp

commit 65fbebb92d5c454aee7f7f837fe41283046c6c82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 7 12:17:10 2017 -0800

    add virtual MLLinOp::interpolation

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 02c504212cdf00337e03baf5a41b44f51d0459e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 7 11:20:17 2017 -0800

    nodal projection: add nodal owner mask

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit f6f38ea7027dfe0e4e7f8eef22f1d8e82d8d8468
Merge: 9fa65935e 746e975ff
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Dec 7 11:17:25 2017 -0800

    Merge remote-tracking branch 'origin/development' into marc/geom_surface

commit 9fa65935e2578af43ab994dd91f886a7f72adc0c
Merge: aeb83d730 a0db3f296
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Dec 7 11:15:54 2017 -0800

    Merge remote-tracking branch 'origin/development' into marc/geom_surface

commit c694cc2946df0fe080a04d4b23f97eee4e8ffada
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 7 11:15:41 2017 -0800

    add MultiFab::Dot for nodal with mask

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.f90
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit 128a4dbb7992547d657b671ea0495845365751b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 7 10:17:54 2017 -0800

    nodal projection: restriction

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 21d4d950441a1cd5b42510b2ac94f5735d4843e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 7 10:16:34 2017 -0800

    add free function coarsen for BoxArray

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit 746e975ff3954eeefde79e0e735a8fd610651b2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 7 08:45:54 2017 -0800

    update CHANGES

CHANGES

commit ede5cec780c2d072a4d52ce04a4ec9cd7ac57eeb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 7 06:33:17 2017 -0800

    update LoadBalance tutorial

Tutorials/Particles/LoadBalance/main.cpp

commit d1e2b573aab9f2e942d1ab464eae6f360a886190
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 7 06:32:45 2017 -0800

    add lo-dim versions of these functions too

Src/Particle/AMReX_KDTree_1d.F90
Src/Particle/AMReX_KDTree_2d.F90

commit e378d696a107823355974dcd32ca4c04c85e4dcc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Dec 7 06:24:23 2017 -0800

    also add 1D and 2D versions of this function.

Src/Particle/AMReX_KDTree_1d.F90
Src/Particle/AMReX_KDTree_2d.F90

commit c7209aa8e0c4a642a7295421425124fa68649312
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Dec 6 20:01:08 2017 -0800

    don't let the KD-tree create 0 cost boxes.

Src/Particle/AMReX_KDTree_3d.F90
Src/Particle/AMReX_KDTree_F.H
Src/Particle/AMReX_LoadBalanceKD.cpp

commit 9f7d73014b9bff79622a6af38488ab58708c0606
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 6 16:58:29 2017 -0800

    nodal projection: add virtual restriction method

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 28a1e34bfdf018de69f3749caec8c080865c4108
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 6 16:21:09 2017 -0800

    nodal projection: applybc

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 13aa60c6ce9ab685022b4c80157436690254ec69
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Dec 6 16:00:25 2017 -0800

    more examples of geometry generation

Tutorials/EB/GeometryGeneration/exec/GNUmakefile
Tutorials/EB/GeometryGeneration/exec/sphere.cpp
Tutorials/EB/GeometryGeneration/exec/sphere.inputs
Tutorials/EB/GeometryGeneration/src/CommonCode.cpp
Tutorials/EB/GeometryGeneration/src/Make.package
Tutorials/EB/GeometryGeneration/src/WriteEBPlotFile.H
Tutorials/EB/GeometryGeneration/src/WriteEBPlotFile.cpp

commit 52c99014d0cb3293d0e382dde9a137d7c828769d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 6 15:32:47 2017 -0800

    nodal projection: fillbc for sigma

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit aeb83d730bf31b1ff3096369e21fe51e98942ec1
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Dec 6 13:04:05 2017 -0800

    Separate out the IO of the eb surface file in order to better manage writes in parallel

Src/GeometryShop/AMReX_EBISLevel.cpp

commit 76719409abe8ff83230077a31f244033f405d0ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 6 10:43:48 2017 -0800

    nodal projection: 2d Jacobi smoothing

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 0a6d58ef417c4d587682d310a4b8d102bcedd00b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 6 10:18:23 2017 -0800

    fix a minor bug

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H

commit 04681b615d48bec594d88461625e21507eaf91af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 6 10:18:23 2017 -0800

    fix a minor bug

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H

commit 012d0577db9fffb530ca2807a91bc2dcc289f379
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 6 09:45:28 2017 -0800

    nodal projection: 2d A dot x

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 5506aba529d74fde55dd363a5695aee2d2307ed0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Dec 5 16:38:10 2017 -0800

    starting on tutorial where I show how to make a bunch of different geometries.

Tools/C_util/Convergence/GNUmakefile
Tutorials/EB/GeometryGeneration/exec/GNUmakefile
Tutorials/EB/GeometryGeneration/exec/sphere.cpp
Tutorials/EB/GeometryGeneration/exec/sphere.inputs
Tutorials/EB/GeometryGeneration/src/CommonCode.H
Tutorials/EB/GeometryGeneration/src/CommonCode.cpp
Tutorials/EB/GeometryGeneration/src/Make.package
Tutorials/EB/GeometryGeneration/src/WriteEBPlotFile.H
Tutorials/EB/GeometryGeneration/src/WriteEBPlotFile.cpp

commit df6d1c3a5ea7ff7b9adefb5029a44101e0a5babf
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Tue Dec 5 15:31:37 2017 -0800

    build the body of an AMR task hierarchy

Src/AmrTask/AMFIter/AMReX_AmrTask.H
Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/main.cpp
Src/Base/AMReX_FabArrayBase.H

commit b859895909b70d4d83f598cbb23705d337c93d0c
Merge: 1dfc44c80 59a354728
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Dec 5 14:03:00 2017 -0800

    merging with dev branch

commit 59a35472825a77155ae0b9bfd6a21dc67f75cdaf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 5 09:51:51 2017 -0800

    stdint.h -> cstdint because this is C++

Src/Base/AMReX_IntConv.H

commit 130775c9412cc19c8cedaab44c71e3bf00497aad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 5 09:43:59 2017 -0800

    fix template specialization

Src/Base/AMReX_IntConv.cpp

commit 56c05b67a18adeb2fc0bc67688da6bafd909d446
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 5 09:38:37 2017 -0800

    Revert "use the new VectorIO routines in the particle checkpoint and restart routines."
    
    This reverts commit 3c44f13d61ff821c8a21e6058feeaf2a3322fdf5.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit b66f3b17af3739c4dee4ef36cfe0519fe804a292
Merge: 53df579af 548e4c314
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Dec 5 09:08:27 2017 -0800

    Merge pull request #176 from AMReX-Codes/portable_particle_io
    
    Functions for writing Vectors of ints, longs, and Reals to disk in a portable manner.

commit 548e4c31484b9c666484e8d187c8b2e855415013
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Dec 4 22:43:53 2017 -0800

    clean up endianness macros

Src/Base/AMReX_FPC.cpp

commit 9ac178350bb20f5fda6486e920a086de437d1cce
Author: kngott <kngott@lbl.gov>
Date:   Mon Dec 4 18:06:33 2017 -0800

    ClickHistory and Send/Recv List Button.

Src/Extern/ProfParser/AMReX_BLProfStats.H
Src/Extern/ProfParser/AMReX_BLProfStats.cpp
Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp
Src/Extern/ProfParser/AMReX_CommProfStats.H
Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp
Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp
Src/Extern/amrdata/AMReX_DataServices.H
Src/Extern/amrdata/AMReX_DataServices.cpp

commit 1dfc44c80ff23328a191685670f42328df574643
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Dec 4 17:20:38 2017 -0800

    redid the math for rk3 case---still not stable.  Maybe I need to do something leastsquares-ish or add higher order terms.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit 3c44f13d61ff821c8a21e6058feeaf2a3322fdf5
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Dec 4 16:49:35 2017 -0800

    use the new VectorIO routines in the particle checkpoint and restart routines.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 53df579af7b8b3f2506f2f9fd404ee67082f90eb
Merge: ffd2e6e44 1d6531c89
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Dec 4 16:45:47 2017 -0800

    Merge pull request #175 from JBlaschke/development
    
    fix macros leading to incorrec endianness in fab io

commit 1d6531c8948c18b3d4e12c5f5f9225f40ee5cf2c
Author: Johannes Blaschke <jpblaschke@lbl.gov>
Date:   Mon Dec 4 16:28:08 2017 -0800

    fix macros leading to incorrec endian-ness in fab io

Src/F_BaseLib/fabio_c.c

commit f797650fe4c6b18838209dd65f4f949ba1b3691a
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Dec 4 13:25:07 2017 -0800

    consolidate the vector IO functions into a file.

Src/Base/AMReX_IntConv.H
Src/Base/AMReX_IntConv.cpp
Src/Base/AMReX_VectorIO.H
Src/Base/AMReX_VectorIO.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tests/Particles/TypeDescriptor/main.cpp

commit 9deadc73846007838f6ddab9f51cfd8f39b3836d
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Dec 4 13:12:22 2017 -0800

    also testing real data.

Tests/Particles/TypeDescriptor/main.cpp

commit 6f31e4149950117e644cf14305d56ee187d0d7bf
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Dec 4 12:37:29 2017 -0800

    typo fix in comment.

Src/Base/AMReX_FabConv.H

commit ec87ebdba7ddc3df173e3d2c8887a1a2e7b2cf71
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Dec 4 12:32:14 2017 -0800

    include negatives in test.

Tests/Particles/TypeDescriptor/main.cpp

commit 3e2fb6e004cd6633004846f89c5a74f24b9c9ca7
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Dec 4 12:23:33 2017 -0800

    also support long data; some reorganization.

Src/Base/AMReX_IntConv.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tests/Particles/TypeDescriptor/main.cpp

commit ffd2e6e44ad58fe87b4a189d06ff5b06ba7e257c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 4 10:30:23 2017 -0800

    Fortran octree: add support for amr.max_grid_size_x, _y and _z

Src/F_Interfaces/Octree/AMReX_octree_fi.cpp

commit ff52c7c5eb7d87dbbe3eac9bd11dd851e92f2486
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Dec 4 10:28:22 2017 -0800

    also read/write the IntDescriptor to a header file.

Tests/Particles/TypeDescriptor/main.cpp

commit 438c463e9c529f5b2575ea2bc596605b9af8473b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 2 13:42:40 2017 -0800

    WIP: nodal projection

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit 704b2092f407b74ce7c9eb90967f476c6cc5abfa
Author: atmyers <atmyers2@gmail.com>
Date:   Sat Dec 2 12:55:45 2017 -0800

    move the int conversion stuff to Base and install the header

Src/Base/AMReX_IntConv.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tests/Particles/TypeDescriptor/Make.package
Tests/Particles/TypeDescriptor/main.cpp

commit 78690bd1678eac2b0f9a2da9fbca661838b24363
Author: atmyers <atmyers2@gmail.com>
Date:   Sat Dec 2 12:48:20 2017 -0800

    swap bytes for unsigned as well.

Tests/Particles/TypeDescriptor/Convert.H

commit 3633a3c8cdb63b3703c96cd49c8c1b89f992a0bd
Author: atmyers <atmyers2@gmail.com>
Date:   Sat Dec 2 12:42:08 2017 -0800

    handle short

Tests/Particles/TypeDescriptor/main.cpp

commit 8b264bc66a7210928a3cd1f1cd6f7d13ae0eb173
Author: atmyers <atmyers2@gmail.com>
Date:   Sat Dec 2 12:39:02 2017 -0800

    handle endianness

Tests/Particles/TypeDescriptor/Convert.H
Tests/Particles/TypeDescriptor/main.cpp

commit 6f0c80aec159dee02a291d255f80a02b98bbe0cc
Author: atmyers <atmyers2@gmail.com>
Date:   Sat Dec 2 12:28:36 2017 -0800

    add a test for the more portable io stuff

Tests/Particles/TypeDescriptor/Convert.H
Tests/Particles/TypeDescriptor/GNUmakefile
Tests/Particles/TypeDescriptor/Make.package
Tests/Particles/TypeDescriptor/main.cpp

commit 8ef30bfc0744ee5cd7c5768f8c83aa1dfd077ac4
Author: atmyers <atmyers2@gmail.com>
Date:   Sat Dec 2 12:27:44 2017 -0800

    some BoxLib -> AMReX

Src/Base/AMReX_FabConv.H

commit 27b004984bdfb39230032954eddd6ff4aa54b0b6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Dec 2 10:07:55 2017 -0800

    fix bug with rcv count caching in the neighbor particle code.

Src/Particle/AMReX_NeighborParticlesI.H

commit 01f7ad64a46f9fff0d998e907c83c082019cb537
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Dec 1 18:23:46 2017 -0800

    Protect against negative grid ID in BuildLevelMask

Src/Particle/AMReX_NeighborParticlesI.H

commit c44c338c8acc6de06e143e6f89f3be04dd2ab761
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Dec 1 13:50:35 2017 -0800

    implement io operators for the IntDescriptor

Src/Base/AMReX_FabConv.H
Src/Base/AMReX_FabConv.cpp

commit b13a356ad17120ab39d38424bbcfcf6e09a24dbe
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Dec 1 13:05:05 2017 -0800

    adding a NativeIntDescriptor.

Src/Base/AMReX_FPC.H
Src/Base/AMReX_FPC.cpp
Src/Base/AMReX_FabConv.H

commit 57c73b8a146415433e37f0e1a7b34eb4c5198b0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 1 10:48:58 2017 -0800

    average down edge coefficients

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H

commit 90a16a8cbc4573576d02145fa929d66c16df635a
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 1 09:09:36 2017 -0800

    WIP: collect intersections from geo server into distributed data structure, connect up contour lines or triangulated surface patches, and write...if ebis.build_eb_surface=true

Src/GeometryShop/AMReX_AllRegularService.H
Src/GeometryShop/AMReX_AllRegularService.cpp
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_FlatPlateGeom.H
Src/GeometryShop/AMReX_FlatPlateGeom.cpp
Src/GeometryShop/AMReX_GeomIntersectUtils.H
Src/GeometryShop/AMReX_GeomIntersectUtils.cpp
Src/GeometryShop/AMReX_GeometryService.H
Src/GeometryShop/AMReX_GeometryService.cpp
Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/Make.package

commit 031881908216b2226d9e8831896e6002bbb9b4d6
Merge: 2e48372f3 1b9f11d96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 1 08:40:29 2017 -0800

    Merge branch 'development'

commit 1b9f11d969b59f686b5f2f7288e372e7405b5d7a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 30 17:30:58 2017 -0800

    Add more missing files to CMakeLists.txt

Src/GeometryShop/CMakeLists.txt

commit 108cf2ae7068da33c410c4fa3a1d65514c0039e0
Author: kngott <kngott@lbl.gov>
Date:   Thu Nov 30 17:18:45 2017 -0800

    Comment distinguishing backtrace options.

Src/Base/AMReX_BLBackTrace.H

commit b3ed443c5c4cc06cb9c2382d670674844689eeeb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 30 16:58:15 2017 -0800

    add index type

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp

commit fabd348388b632ab049a7acc25bcbfd5ecf03599
Merge: 40c595ee5 e2557be8c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 30 16:52:42 2017 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 40c595ee5bb416f5be40f6d207063288ed1b2d0b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 30 16:52:34 2017 -0800

    Add missing .H file

Src/GeometryShop/CMakeLists.txt

commit 8ab4852c02f1890aeccb2d81f585af34924342bd
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Nov 30 16:30:04 2017 -0800

    redid the calculations for rk4.   still not showing the right convergence.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit 9f52734e24e5c725fec217f0d5ea4834c76ab8d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 30 16:23:51 2017 -0800

    move MLCellLinOp specific stuff from base class MLLinOp

Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H

commit d93a7d3b7f933bc90eef4bfe2ab2eb8013a01a4a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 30 14:38:35 2017 -0800

    nodal projection: compute divu

Src/Boundary/AMReX_LO_BCTYPES.H
Src/Boundary/AMReX_lo_bctypes_mod.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit e2557be8c3ff77b12b6f84297e6fbff572833999
Merge: 756870317 db024ced3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 30 13:44:43 2017 -0800

    Merge pull request #174 from emotheau/master
    
    update

commit db024ced3e685ea7cc64035e5c03d1605d603d90
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Thu Nov 30 13:41:59 2017 -0800

    move file

Tools/C_util/Convergence/AVGDOWN_1D.F

commit cdf57746f077a9bcde4ae31a6836cab4af910665
Merge: 716456a53 cd31e1451
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Thu Nov 30 13:29:24 2017 -0800

    Merge pull request #1 from emotheau/emotheau-patch-1
    
    Add missing file for 1D convergence test

commit cd31e145164a8deb3990d36f42f99c4a79db5316
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Thu Nov 30 13:28:31 2017 -0800

    Add missing file for 1D convergence test

AVGDOWN_1D.F

commit 7568703173fc607e0403b5f4b96769d94b0b7769
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 30 12:57:18 2017 -0800

    Add AMReX_AnisotropicIF.H to the CMakeLists.txt

Src/GeometryShop/CMakeLists.txt

commit 0651232b15c53443e1794945b91f987af10888bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 30 10:01:43 2017 -0800

    split MLLinOp into MLCellLinOp and MLNodeLinOp

Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/Make.package

commit d2be80bac77cde2da2d403163772eb1888f3c5ac
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 30 06:15:26 2017 -0800

    fix assertion.

Src/Particle/AMReX_NeighborParticlesI.H

commit d5fc770aae596a2b4643164a205931f73862e9ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 29 17:15:27 2017 -0800

    average nodal coefficients from cell centers to edges

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp

commit 56b56bb68b4b33c0aae27fc4a2e1f4802ed4b704
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 29 15:07:33 2017 -0800

    start nodal projection

Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp
Src/LinearSolvers/MLMG/Make.package

commit ecd3e1dc81119c774158cc154b0f7f732a513ca1
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Nov 29 09:56:59 2017 -0800

    put back in abort message in CNS that disallows ansiotropic dx

Tutorials/EB/CNS/Source/CNS.cpp

commit 28c2e679e28025c82758070223f43314429d0918
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Nov 29 09:55:54 2017 -0800

    added general anisotropic dx implicit function (along with an example in CNS that calls it)

Src/GeometryShop/AMReX_AnisotropicIF.H
Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_init_eb.cpp

commit 654d0d8b8d029c064e9d817890a5e6fe47d3eeeb
Merge: 024bc0414 669721809
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Nov 29 09:36:28 2017 -0800

    Merge branch 'development' into dtg_branch

commit 669721809c2b5a6dde5ab3d36efe338e61565a07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 29 09:25:37 2017 -0800

    add amrex::second() that calls C++ clock.  use it in TinyProfiler

Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_TinyProfiler.cpp
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit a22364564bb47eacca8548bd43924510cd922acc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 28 16:15:10 2017 -0800

    Don't need prob_domain in that routine

Src/Particle/AMReX_NeighborParticlesI.H

commit 024bc0414f37e7e71e81d98b19c43355fea94492
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Nov 28 12:30:52 2017 -0800

    found a bug in jbb version of time interpolation.  rk3 looks very good.  have to check math for rk4 again.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit df61cbb63bc1ad68c974f41a9e9ba016d60182da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 28 09:04:32 2017 -0800

    TinyProfiler: disable BL_PROFILE_REGION_START and STOP so that the output is smaller

Src/Base/AMReX_BLProfiler.H

commit 76b8cb95a0ec3ed15e18a706571c56bfaf472b39
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Nov 27 18:59:01 2017 -0800

    Add 3D code to dump triangulated surface.

Src/GeometryShop/AMReX_GeometryShop.cpp

commit 76887cd60ce6e5990ccc84926e0b2cc37e947667
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Nov 27 18:03:11 2017 -0800

    reuse some original Amr code

Src/AmrTask/Amr/AMReX_AmrLevelTask.H
Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp
Src/AmrTask/Amr/AMReX_AmrTask.cpp
Src/AmrTask/Amr/Make.package
Src/AmrTask/Amr/Makefile
Src/AmrTask/AmrCore/AMReX_FillPatchUtil.H
Src/AmrTask/AmrCore/AMReX_FillPatchUtil.cpp

commit 3bf78515fc16708a455a256836db20359c5ec062
Merge: 57e70699a 4799d37c9
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Nov 27 17:56:16 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 57e70699a57d842b70ec75b9d49ab5d907f23a42
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Nov 27 17:56:05 2017 -0800

    writing a fully asynchronous version of the Advection code

Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/CMakeLists.txt
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/Make.Adv
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Make.package
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Prob.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/probin
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Make.package
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probin
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/README
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Adv_F.H
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.H
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/LevelBldAdv.cpp
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Make.package
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/Make.package
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/slope_2d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/Make.package
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/slope_3d.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_nd/Make.package
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_nd/tagging_params.f90
Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/main.cpp

commit 4799d37c95385e20fb8719a34830e9840c898e80
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 27 17:53:08 2017 -0800

    add some regional profilers to MLMG

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp

commit 3a77463784a08a646b9f344309a8f87b5c70b69c
Merge: ac1bd0420 4f89f4f92
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Nov 27 17:51:29 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ac1bd042083545d2166e1952973bfc365508abe6
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Nov 27 17:51:17 2017 -0800

    add AmrTask support

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_AmrLevel.H
Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H
Src/AmrTask/AMFIter/Makefile
Src/AmrTask/Makefile
Src/AmrTask/arch/arch.mpi.generic
Src/AmrTask/graph/AMReX_AbstractTask.H

commit 4f89f4f92ee09a11443b7a3cd8fae8c651e0653f
Merge: 020a0623a bcff6c682
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 27 17:39:43 2017 -0800

    Merge branch 'tprof-region' into development

commit 8264aadcf52a5fddf490ba95cbd88cf0c2488383
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Nov 27 16:35:55 2017 -0800

    Fix scaling of intercept points.

Src/GeometryShop/AMReX_GeometryShop.cpp

commit 020a0623a65f12ff908120c7f9a5c7d508146d0b
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Nov 27 15:49:23 2017 -0800

    CMake: include MLMG in build

Src/LinearSolvers/CMakeLists.txt

commit a82870e14dbdd33181603f9b6d9ff1510d0a589d
Merge: 4abf1dc03 a0db3f296
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Nov 27 15:40:48 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d5c7d14693b8db3b5be442084439f6ec21abf9bd
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Nov 27 15:40:30 2017 -0800

    coded yet another version of time interpolation.   the simple polynomial version seems to work best.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit 6ab3ed65b8e71667293d85d3d911a16043784476
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Nov 27 15:39:52 2017 -0800

    WIP: Extracting intersections

Src/GeometryShop/AMReX_GeometryShop.cpp
Tests/GeometryShop/stencilTestbed/exec/GNUmakefile
Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp
Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90
Tests/GeometryShop/stencilTestbed/exec/sphere.inputs
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp

commit bcff6c6826a73587684f8798c702498ddcf457bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 27 10:53:29 2017 -0800

    add TinyProfileRegion class

Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp

commit a0db3f296dd98b1b7bd2729772ee878d7cd9e505
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 26 20:07:38 2017 -0800

    put a global variable into anonymous namespace

Src/Base/AMReX_Utility.cpp

commit 6dcedf4316930939cea468e211f8e3079614ca23
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 26 15:12:15 2017 -0800

    Regional profiling support in TinyProfiler

Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit 571d6268141964c48a96ad506cef400e08997fc1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 26 12:08:15 2017 -0800

    TinyProfiler ctor optimization

Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp

commit eeb628c1149a2fc48c37b495e8bbfa45a5534bc5
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Nov 26 13:45:16 2017 -0500

    Add method to swap old/new data with another StateData

Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp

commit eb6d6567928f4209252acff0f5304f866bbfefe2
Merge: 709c3375f f48d503d7
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Nov 24 17:04:11 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 709c3375f0e1c74df384166a857f1c9ab4040339
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Nov 24 17:03:47 2017 -0800

    remove an anonymous namespace

Src/Amr/AMReX_Amr.cpp

commit f48d503d79fb593a4648e3ab51fdd991ae222263
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 24 16:50:44 2017 -0800

    make: if AMREX_HOME string contains ~, replace it because make won't like it and the error message cannot be easily understood.

Tools/GNUMake/Make.defs

commit 6018be5399320ddb82468a1e46b6f5d971cbf634
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Nov 24 13:20:05 2017 -0500

    Ensure uniform gcc version number reporting with -dumpfullversion

Tools/F_mk/comps/gfortran.mak
Tools/GNUMake/comps/gnu.mak

commit 306d63ab5d491925cb8cac927875f475f83a09c1
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Nov 24 13:14:23 2017 -0500

    Throw error if gcc < 4.8 (F_mk)

Tools/F_mk/comps/gfortran.mak

commit 2d9a952ca9d13f7941c03822aae026bba9b6291d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 24 08:40:25 2017 -0800

    throw error if gcc < 4.8

Tools/GNUMake/comps/gnu.mak

commit 4abf1dc03f130f2bd67cee7b7b00d282c11efbec
Merge: d5c9e4828 1a00814ec
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Nov 22 14:36:34 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 22b62209a9bd0125a7e324e24efe3a6f30fa3d44
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Nov 22 13:48:32 2017 -0800

    we now have three versions of time interpolation.   for super smooth problems, the simply polynomial seems to work best.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit 1a00814ec3856d41880d4dfe55543004ae7cb953
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Nov 22 13:04:33 2017 -0800

    add a function that returns the number of data states

Src/Amr/AMReX_AmrLevel.H

commit 95755b87e46a1fbda5ef45eabae95247e37e3caa
Merge: 2b4070db9 2d891c709
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 22 11:51:38 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2b4070db918915fe66be2bdd76eabdfe0746db73
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Nov 22 11:51:28 2017 -0800

    functions for growing all the boxes in a BoxArray in a given direction on only the lo / hi side.

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit 2d891c70997a0407b883fe7f2b25d650f49fe4db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 22 11:30:07 2017 -0800

    fix thread id

Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.cpp

commit ac781886570ac32b95fcefd9437d4e40a644e732
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 22 11:20:14 2017 -0800

    hopefully I fixed it this time. Shouldn't have done this before going out shopping

Src/Base/AMReX_BoxArray.cpp

commit 583ed71182b7ad8cb801064081e22de05b5d277c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 22 11:12:10 2017 -0800

    fix a bug

Src/Base/AMReX_BoxArray.cpp

commit 5ea41e9c788c80da049c2b9987652062f1ffb502
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 22 11:06:16 2017 -0800

    fix a typo

Src/Base/AMReX_BoxArray.cpp

commit 1b616d4829fe00f624e4e6afd3546c07c79f4e8a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 22 11:02:27 2017 -0800

    optimizatin of BoxList::complementIn

Src/Base/AMReX_BoxList.cpp

commit 27010e10ba9f80568df50782378f619562b6a929
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 22 11:02:00 2017 -0800

    OMP BoxArray::minimalBox()

Src/Base/AMReX_BoxArray.cpp

commit 3f2118a29236e187d7c439f4b5eccc2fe5eccac0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 22 07:46:29 2017 -0800

    added BoxList::swap and some minor changes

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp

commit fd2590dadea5ceb42e4acced3249ae1c13ef83f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 22 07:33:47 2017 -0800

    OMP BoxList::complementIn

Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp

commit ac8964896c1fb1ebaf83ce8158c077d4443392ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 22 07:21:19 2017 -0800

    A faster way of removing dupliates (which may break some regression tests).  Added BoxList::reserve

Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BoxList.H

commit 2062722db8d7f7310ca4c7ea2b6ec41f25c1425e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 22 07:06:00 2017 -0800

    fix typos

Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp

commit 0152dbf6c3067e859a1b6716614b280dda4bb39a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Nov 21 15:53:40 2017 -0800

    redid the math and recoded time interpolation for rk3/4.   I am still losing an order in solution error but it looks pretty good.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit d891f85135cf1745a87ebe1b2011cdbb675a3da1
Merge: f528f097e 66407a7a8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 21 14:56:18 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f528f097ec8019e8a991714bb62a79b6861f2ecb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 21 14:56:06 2017 -0800

    enable users to turn off the MPI communication of certain particle components when filling ghost particles.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 66407a7a8fc4c81d51024ccc12b6da3fd5c4232c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 21 14:54:10 2017 -0800

    Tutorials/LinearSolvers/ABecLaplacian_C

Tools/RegressionTesting/AMReX-tests.ini
Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile
Tutorials/LinearSolvers/ABecLaplacian_C/Make.package
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/MyTestPlotfile.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/MyTest_F.H
Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp
Tutorials/LinearSolvers/ABecLaplacian_C/init_prob.F90
Tutorials/LinearSolvers/ABecLaplacian_C/inputs
Tutorials/LinearSolvers/ABecLaplacian_C/inputs-rt-abeclap-com
Tutorials/LinearSolvers/ABecLaplacian_C/inputs-rt-poisson-lev
Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp

commit 9169e44a90c19ab1ff8aa6d49530c3186d1f910a
Merge: 73a469c04 312c9a460
Author: kngott <kngott@lbl.gov>
Date:   Tue Nov 21 13:17:08 2017 -0800

    Merge branch 'profvis' of https://github.com/AMReX-codes/amrex into profvis

commit ec1329f5f55161f6695b374f6337a89880e10b83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 21 08:49:35 2017 -0800

    add amrex::

Src/Base/AMReX_ParallelDescriptor.H

commit 38d453427b3a1c0a5d677e7edd9c4d8fbdd9ef5c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Nov 20 16:46:27 2017 -0800

    more debugging hooks.  new time interpolation not there yet.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit d27a90ff44b9640e180b12841ed761f4e8510186
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 20 13:14:08 2017 -0800

    use 5 digits in DATA_ string.  we need to sync thses sizes.

Src/Particle/AMReX_ParticleContainerI.H

commit 98bf4e1532ea6d30fc2a01bef70985bb1c7616b0
Merge: 6db2b7ba4 896a2aa4a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Nov 17 20:44:59 2017 -0800

    Merge pull request #165 from bcfriesen/EB_updates
    
    EB updates

commit 6db2b7ba4d52006616667ca700edc699a70036ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 17 20:42:35 2017 -0800

    add README to the Fortran linear solver tutorial

Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H
Tutorials/LinearSolvers/ABecLaplacian_F/README

commit 5227757747c5b159c1efd561f6849fe014a6a41c
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 17 18:16:46 2017 -0800

    remove diagnostic.

Src/Base/AMReX_NFiles.cpp

commit fd64246b2b1e091dc113cfe79620eb300d9fb33a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 17 17:00:54 2017 -0800

    update regression tests

Tools/RegressionTesting/AMReX-tests.ini
Tutorials/LinearSolvers/ABecLaplacian_F/inputs-rt-abeclap-lev
Tutorials/LinearSolvers/ABecLaplacian_F/inputs-rt-poisson-com

commit 43aa6c6929536ade9c252ed4eb357c92b7f99f4f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Nov 17 15:57:13 2017 -0800

    have rk3 and rk4 time interpolation coded in john's new way.   Now I Have to figure out whether my algebra or my coding (or both) are incorrect

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs

commit 01477544ef432da90c2d37977fe23a8a98978b1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 17 15:48:01 2017 -0800

    Fixed a bug that causes segfault when making alias FabArray of alias.  The bug was introduced 3 days in a255e56940fbf57 by me.

Src/Base/AMReX_FabArray.H

commit 43dace8bd4baf1649e3fcd1fe668f31c03ee55f0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 17 15:20:15 2017 -0800

    don't need to do this intersection any more.

Src/Particle/AMReX_NeighborParticlesI.H

commit 7e39e6f2eddffa31f7c769666a730a243daa15a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 17 15:19:08 2017 -0800

    finished Fortran linear solver tutorial

Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90

commit ccdb0141f2247c3d967e138ec68273fe8cd02af8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 17 13:04:41 2017 -0800

    implement amrex_abeclaplacian_module

Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_mod.F90
Src/F_Interfaces/LinearSolvers/AMReX_linear_solver_mod.F90

commit f8d735915992f10ffddc6a2506ba049faef4a677
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 17 14:04:33 2017 -0800

    this loop only needs to go over the real particles, not the real + neighbors.

Src/Particle/AMReX_NeighborParticlesI.H

commit af0c7e9350f65274dd4c5fb2cb98166ae49e2be3
Merge: f319ddeb4 18cee043e
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 17 13:33:48 2017 -0800

    merge fixes.

commit f319ddeb43f76a3c488276da95a15f67839eec4c
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 17 13:21:47 2017 -0800

    use dss from nfilesiter.

Src/Base/AMReX_NFiles.H
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp

commit 92ef11309d72453cd9316638dd61f6c3ce80f1aa
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Nov 17 12:55:08 2017 -0800

    added in new style fourth-order limiting

Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit 285b10a86168a316e2b51b01b8102a14d8e2fb09
Merge: 81abe9f17 0cda1c36d
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 17 12:35:42 2017 -0800

    Merge branch 'partio' of https://github.com/AMReX-Codes/amrex into partio

commit 0cda1c36da278f9c33382b2c1c913ef4342310cd
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 17 12:35:20 2017 -0800

    use long.

Src/Extern/ProfParser/AMReX_CommProfStats.cpp

commit 81abe9f17987d4323eb830807375d2a5b3aad75a
Merge: 83c6c4c74 c181bb6d8
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 17 12:25:06 2017 -0800

    merge fix.

commit 83c6c4c7428ba2a22f06ab930200630a71bf9f51
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 17 12:23:45 2017 -0800

    init value.

Src/Particle/AMReX_ParticleContainerI.H

commit e91469f63543cbe9576f91a9f1e9be8695c4d242
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 17 12:23:14 2017 -0800

    parser fixes.

Src/Extern/ProfParser/AMReX_CommProfStats.H
Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp

commit bf086cb8ec3e9047b782aca90182ef425ea5b76e
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 17 12:20:30 2017 -0800

    fix comment.

Src/Base/AMReX_NFiles.H
Src/Base/AMReX_VisMF.cpp

commit c181bb6d88bacdf3159dbc4744160b5c2ff64c93
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 17 12:15:47 2017 -0800

    use rank for sparse file number.

Src/Base/AMReX_NFiles.cpp
Src/Base/AMReX_VisMF.cpp

commit 18cee043e05fa5338db7cd88eb9994ef0f4870f0
Merge: e1a858220 7ce6a4548
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 17 11:06:46 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit e1a858220bab450533684019e4752f766aa45d85
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 17 10:57:04 2017 -0800

    removing a couple of now un-needed functions.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 7ce6a45484395a3803aa9dabe64b62f869404ed9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 17 10:56:04 2017 -0800

    add amrex_average_cellcenter_to_face to amrex_multifabutil_module

Src/F_Interfaces/Base/AMReX_multifabutil_fi.cpp
Src/F_Interfaces/Base/AMReX_multifabutil_mod.F90
Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90

commit dc30bacc6132435781f30090e4d15ade2831fd6f
Merge: d3f65bab6 9b74a8305
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 17 10:39:52 2017 -0800

    merging.

commit d3f65bab68e3d6cb9f7d42df3cfdda74ee0c0f58
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 17 10:33:43 2017 -0800

    reduce temporary copies in the neighbor particle code.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 48413f69cada425f28c435005a55731e43425cb4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 17 10:33:06 2017 -0800

    more efficient to insert these at the end, rather than the beginning.

Src/Particle/AMReX_ParticleContainerI.H

commit 9b74a83053f5e74b8d26cb3a39f5fb8071ef1db9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 17 10:14:40 2017 -0800

    port more features of MFIter from C++ to Fortran

CHANGES
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 24f8e11af67dad62e49efee627ee636e9d2e73ea
Merge: 5fd547e94 e5af0134f
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 16 17:54:09 2017 -0800

    Merge branch 'partio' of https://github.com/AMReX-Codes/amrex into partio

commit e5af0134f78a2dc10e4b0cd12246046de7f11a49
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 16 17:52:55 2017 -0800

    header diagnostics for sparse fabarray writes.

Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_NFiles.H
Src/Base/AMReX_NFiles.cpp
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp

commit 9176ca9099da3801cf7b240bc9415692f40a0765
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 16 17:50:21 2017 -0800

    temp flush fix.

Src/Amr/AMReX_Amr.cpp

commit 263a73e28b7230f6e29b60d82dfa3b3dd83df089
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 16 17:11:43 2017 -0800

    Fortran linear solver tutorial: init abeclapacian coefficients

Tests/LinearSolvers/MLMG/fort_3d.F90
Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90

commit 5b0fa5675d5efe2dc8dd976d3d454afc491f085a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 16 16:45:11 2017 -0800

    Fortran linear solver tutorial: level by level poisson solve works

Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90

commit 609a17077141c675c67c52e05c8ceb7de37f2b60
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 16 15:03:57 2017 -0800

    rename setBCWithCoarseData to setCoarseFineBC

Src/F_Interfaces/LinearSolvers/AMReX_linop_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_linop_mod.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90

commit 7b63c32b65698544f114102a82260af55f582c16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 16 14:31:51 2017 -0800

    Fortran linear sovler tutorial works for compsite Poisson

Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90

commit 77126202317d23dcc4774dbf89e5f3fe27c8de75
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 16 14:25:23 2017 -0800

    add more functions to Fortran amrex_multifab_module

CHANGES
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit d5c9e482836b59717245d0fcac0ca0624af32094
Merge: a7024ad0c 15db38af6
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Nov 16 14:20:49 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 15db38af63a46440a4e356a6648a826fea254b48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 16 13:10:03 2017 -0800

    fix typo in amrex_multigrid_module

Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90

commit ff7b3f55f8ae7be16ae89785a8362f8a5c5805c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 16 12:05:37 2017 -0800

    fix omp bug in amrex_geometry_module; more on the linear solver tutorial

Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90

commit 35866fe0668082eb70823ce01a74687cf4f25876
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 16 12:03:29 2017 -0800

    fix omp bug in amrex_geometry_module; more on the linear solver tutorial

Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90

commit 0efcc01d92b1c955cf5780494274402e9cfcd33f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 16 12:02:21 2017 -0800

    fix omp bug in amrex_geometry_module

Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Tutorials/Basic/HeatEquation_EX1_F/init_phi.f90
Tutorials/LinearSolvers/ABecLaplacian_F/Make.package
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90

commit 84e1d694df425f34daad112697df0ce1703b13dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 16 10:30:11 2017 -0800

    amrex_box_module: add coarsen and refine

Src/F_Interfaces/Base/AMReX_box_mod.F90

commit 78051c2ed5c13b2b22030895f30e6daab7725563
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 16 09:34:31 2017 -0800

    add some functions to amrex_geometry_module for setting coordinates, problem domain and periodicity through funcitons instead of inputs

Src/F_Interfaces/Base/AMReX_geometry_mod.F90

commit a2a86b437d8a201b746f22538466d43db04e2f7a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 16 08:55:06 2017 -0800

    MLMG: test singularity on the bottom instead because it's cheaper

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp

commit c517c5959ca53429bd881146c16ba9073740d423
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Nov 16 08:50:09 2017 -0800

    bug fixes in 4th order limiting.

Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90

commit 2fd71f2228bd25ea66c6da69afee5b1476d162c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 15 18:09:11 2017 -0800

    F_Interfaces/LinearSolvers: finished amrex_multigrid_module

Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90
Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90

commit 7ced2c8ce73e481fa64638115efaac622f3ce3e0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Nov 15 16:30:00 2017 -0800

    slogged my way through writing the limiting code a la mccorquodale.  The limiting versions still untested.

Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90

commit 72a6278864ec4bbf0580ba83aaad6981cf79cd61
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Nov 15 14:56:40 2017 -0800

    IOBenchmark: make only master thread flush and close file in thread-shared IO

Tests/IOBenchmark/IOTestDriver.cpp

commit 902435948747cf50fddb54a0c572386cd943a41b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 15 14:28:31 2017 -0800

    F_Interfaces/LinearSolvers: wip

Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_mod.F90
Src/F_Interfaces/LinearSolvers/AMReX_linear_solver_mod.F90
Src/F_Interfaces/LinearSolvers/AMReX_linop_mod.F90
Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90
Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90
Src/F_Interfaces/LinearSolvers/Make.package
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90

commit b6e09aa1ab794b50fb64f6b560ce320d013c2610
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 15 13:14:25 2017 -0800

    F_Interfaces/LinearSolvers: WIP

Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_linop_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_linop_mod.F90
Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90
Src/F_Interfaces/LinearSolvers/AMReX_poisson_fi.cpp
Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90
Src/F_Interfaces/LinearSolvers/Make.package
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90

commit 3efacbb06ef95101622f8e524de5428a0c3cae1e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 15 09:40:56 2017 -0800

    start F_Interfaces/LinearSolvers

Src/Base/AMReX_string_mod.F90
Src/Boundary/AMReX_LO_BCTYPES.H
Src/Boundary/AMReX_lo_bctypes_mod.F90
Src/Boundary/CMakeLists.txt
Src/Boundary/Make.package
Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_mod.F90
Src/F_Interfaces/LinearSolvers/AMReX_linear_solver_mod.F90
Src/F_Interfaces/LinearSolvers/AMReX_linop_mod.F90
Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90
Src/F_Interfaces/LinearSolvers/Make.package
Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile
Tutorials/LinearSolvers/ABecLaplacian_F/Make.package
Tutorials/LinearSolvers/ABecLaplacian_F/inputs
Tutorials/LinearSolvers/ABecLaplacian_F/main.F90
Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90

commit 3eeeb89db8f401093820df4b0eee5edd75622b84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Nov 15 13:57:03 2017 -0500

    add the total time to the summary page

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/test_report.py

commit ad6616dacc116cbb1e70db271dccc7867a635f48
Merge: 4d4d4fa19 b2d4214db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Nov 15 13:38:51 2017 -0500

    Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development

commit 4d4d4fa19e318a7d33f30f0b5d0118e8ab1b161e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Nov 15 13:38:41 2017 -0500

    quote slack posts

Tools/RegressionTesting/regtest.py

commit b2d4214db788e2a1293c2a83d38c8273b65b84a2
Merge: 3ffe320c9 b443b6f50
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Nov 15 08:09:03 2017 -0800

    Merge pull request #167 from AMReX-Codes/fillpatchadd
    
    Add a FillPatch that adds, not copies

commit b443b6f5027273844d5a5d275dc0ed3982e36506
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed Nov 15 01:59:44 2017 -0500

    Add a FillPatch that adds, not copies

Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp

commit eaf87c41596d4fc59d6f079b5a92b184d8941b84
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Nov 14 16:07:00 2017 -0800

    put in hooks and started code for fourth order limiting.  This stuff is complex.

Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90

commit 3ffe320c9a67c374e0d97716975bdc601c903da3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 14 15:49:10 2017 -0800

    MLMG: make some changes so that Cy can put in his mapping

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 5fd547e942a2552624feb818dcc85abf82795dae
Merge: 581231929 6e277ef9c
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 14 13:46:09 2017 -0800

    Merge branch 'partio' of https://github.com/AMReX-Codes/amrex into partio

commit 6824aa2be64a1a14ea61601e10306004fac7c316
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 14 13:42:20 2017 -0800

    update CHANGES

CHANGES

commit f0d03f16b365994e90255fba3c354005d4160484
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 14 13:21:51 2017 -0800

    Tutorials/Amr/Advection_AmrCore: add memory log

Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 839cbf6a99c85c8e9d5ba0e551a3a6b0745af45f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 14 13:20:26 2017 -0800

    manually write MultiFab move ctor so that build can be logged

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit a255e56940fbf57b75683c4f236d03b1b2bff645
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 14 12:48:05 2017 -0800

    FabArray: clear before define; Tutorials/Amr/Advection_AmrCore: use Vector<MultiFab>

Src/Base/AMReX_FabArray.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 2b858dda315c969cb447c60fe63e463fff0b4f14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 14 11:45:10 2017 -0800

    add clear() to FluxRegister

Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BndryRegister.cpp

commit 6b7df9a9b50c7a425ccf00eb282c1cd106375375
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 14 11:22:44 2017 -0800

    implement move assignment operator for FabArray

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_iMultiFab.H

commit 736829d5382596454ef846c6b3c3e18156f38adc
Merge: 1844db91f bea583464
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 14 09:14:04 2017 -0800

    Merge branch 'development' into moveassign

commit bea583464af6d06e2ac09e09d992ad5a213f18d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 14 09:13:22 2017 -0800

    add GetVecOfPtrs again for FabArray types only

Src/Base/AMReX_Vector.H

commit 93b2b2eadd9b5fd89dcb14ebb06e91cd66d4fa9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 13 20:49:05 2017 -0800

    revert

Src/Base/AMReX_Vector.H

commit 1844db91fc7526b3e58895bdf5f6d5cb4c185156
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 13 17:35:31 2017 -0800

    start writing move assignment for MultiFab and FabArray

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.H

commit 6c7b3162e8347142749c179b569fa1caa0759b78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 13 17:34:12 2017 -0800

    add GetVecOfPtrs

Src/Base/AMReX_Vector.H

commit 6e277ef9c1a80baf89a88784834099cf24552087
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 13 17:31:46 2017 -0800

    remove flush.

Src/Amr/AMReX_Amr.cpp

commit 5812319295280292890b6ee5d707c35abda62ff2
Merge: f6732ebc5 ddadcab92
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 13 16:28:29 2017 -0800

    Merge branch 'partio' of https://github.com/AMReX-Codes/amrex into partio

commit ddadcab9232f9c1c2559e77894989b32cd408df6
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 13 16:19:13 2017 -0800

    additions for pre and post checkpoint functions for i/o optimization.

Src/Base/AMReX_NFiles.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 0039b3b0a6ba896cdb37ee68e3f547e3b78c6c1c
Merge: 8a7a43eaf ec0eb76a8
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Nov 13 15:54:37 2017 -0800

    merging with dev

commit 8a7a43eaf07e9b698eeb584ec9d77ab2dbe45acd
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Nov 13 15:52:34 2017 -0800

    added the hooks in the fortran to make limiting optional

Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/slope_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/slope_3d.f90

commit ec0eb76a8174e352e08d593e4071de753e89ec02
Merge: 7fcd29430 4f87f1010
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 13 14:32:17 2017 -0800

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 7fcd29430ce25aff458bff267e4317f8e91ea162
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 13 14:32:02 2017 -0800

    add a CountCells function

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit ebfac58b1bb6cb9bab1a2250d3fb1150a6a0b387
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Nov 13 14:11:45 2017 -0800

    cleaned up code--can now switch algorithm choice via the input file

Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp

commit 4f87f10102033b3709ef3e4b43e738f662423cb8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 13 13:21:14 2017 -0800

    add MLMG to libamrex

GNUmakefile.in
Tools/libamrex/configure.py

commit 12f13ece08e31e9e78ad79908776e6bfae1a698c
Merge: 45e0c71de a7923daf3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 13 13:23:28 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2b625353c2cc6e4df1d48d1cb43bdb46a92a8456
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 13 13:00:09 2017 -0800

    additions for pre and post checkpoint functions for i/o optimization.

Src/Particle/AMReX_Particles.H

commit 9e4ef2f3f77ecc732fe775b743f7a2d25a3136c0
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 13 12:59:13 2017 -0800

    added particle nfiles.

Docs/Readme.io

commit b03d1b24f632169b2b7d6ef4835f35dfa7d3f328
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 13 12:52:00 2017 -0800

    additions for pre and post checkpoint functions for i/o optimization.

Src/Particle/AMReX_ParticleContainerI.H

commit fca80946282c6c83563fb9aaf4fd5f3001882e73
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 13 12:51:10 2017 -0800

    increase default nfiles.

Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_VisMF.cpp

commit 7323cd6e3345fcbb0a25f8c23b9e32e37ee15203
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 13 12:49:27 2017 -0800

    additions for pre and post checkpoint functions for i/o optimization.

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp

commit c53f60503806118693a73ef0fb4a967856c796c7
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Nov 13 12:01:09 2017 -0800

    made progress on algorithm document

Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex
Tutorials/Amr/ScalarAdvectionDiffusion/Doc/references.bib

commit a7923daf30310a6be28917083b15975e9a1bac3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 13 11:00:18 2017 -0800

    MLMG: some experimental approaches in consolidation

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 45e0c71de17f9acbff8ba31d2b03e8f3dfab15b8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 13 10:38:23 2017 -0800

    exit early from Redistribute if particle is invalidated.

Src/Particle/AMReX_ParticleContainerI.H

commit a54a1c1292f0e8341f0e1bc4e506d415861f0fb0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 11 20:39:39 2017 -0800

    add some profilers

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit a049f7deff2314ba007e2ea9eede013cd989146b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 11 12:09:51 2017 -0800

    fix a new bug in MLMGBndry

Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp

commit da8312a8a9ba375a0c8fe729c676813301fcb093
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 11 10:48:04 2017 -0800

    omp parallel

Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp

commit 2d0d0e2d248ea16bdc35a4d2d9e0a85c0b8c23e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 11 10:30:52 2017 -0800

    add MLMGBndry

Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_LO_BCTYPES.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H
Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp
Src/LinearSolvers/MLMG/Make.package

commit 2089f4f6b92115163d9e3c8371d1fcfc5099385b
Merge: f39f47096 d789da394
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Nov 11 01:42:45 2017 -0500

    Merge branch 'development' into gpu

commit d789da39407902d684bb6b6e3ad195839cde847b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 10 17:52:14 2017 -0800

    MLMG: add ReflectOdd and divide flux by beta

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H

commit 312c9a4604af3f6c7faa965f6be3956f3741f059
Author: kngott <kngott@lbl.gov>
Date:   Fri Nov 10 14:53:38 2017 -0800

    Optimization tweaks.

Src/Extern/amrdata/AMReX_DataServices.cpp

commit 2b71112585323ba25ab05384221be6dcd15b928a
Merge: 973281396 650b8c04c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 10 14:20:10 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 973281396cda107ff214b54da265fc1e1b92845b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Nov 10 14:19:49 2017 -0800

    some optimizations for neighbor particle finding and updating.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 650b8c04c9dd4a001b7f8720e0a01a54e49a411e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 10 12:00:15 2017 -0800

    MLMG: fix 2d

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 780458f37412f83dd84def7305150b2e4b95108a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 10 11:51:42 2017 -0800

    MLMG: remove static memebers

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit b8fc8db9028d57f13abc2877bb1ad89046861095
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 10 10:26:26 2017 -0800

    MLMG: option to disable metric terms

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 73a469c041f0bcde2f0dc5b1b152ec93b6fb63c3
Merge: febfc2b63 085004c86
Author: kngott <kngott@lbl.gov>
Date:   Thu Nov 9 18:09:04 2017 -0800

    Merge branch 'partio' into profvis
    
    Conflicts:
            Src/Particle/AMReX_ParticleContainerI.H
            Src/Particle/AMReX_Particles.H

commit febfc2b63a1ffe2404b2ed19b575561e10ffd73c
Author: kngott <kngott@lbl.gov>
Date:   Thu Nov 9 17:31:45 2017 -0800

    One more adjustment.

Src/Extern/ProfParser/AMReX_CommProfStats.cpp

commit 377a54534cf7ab2d1128753120621caeb1d5924d
Author: kngott <kngott@lbl.gov>
Date:   Thu Nov 9 17:27:29 2017 -0800

    OpenStreams adjustment.

Src/Extern/ProfParser/AMReX_CommProfStats.cpp
Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp

commit 7c437eae5d103343b8d0dd75956edfaea7f12a72
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 9 16:44:15 2017 -0800

    MLMG: option to fill final bc

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 979ea8c53ba5920b258af925c12d0132575d135f
Author: kngott <kngott@lbl.gov>
Date:   Thu Nov 9 16:26:20 2017 -0800

    bl_profprof

Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp

commit c317be1565c7078fcb829e847f7a3b2759d9f860
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Nov 9 16:06:37 2017 -0800

    working on more detailed document for this tutorial

Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex
Tutorials/Amr/ScalarAdvectionDiffusion/Doc/references.bib
Tutorials/Amr/ScalarAdvectionDiffusion/Doc/working_notes.tex

commit db78cafabd41d218098679bbd217ea91110a8601
Author: kngott <kngott@lbl.gov>
Date:   Thu Nov 9 15:41:36 2017 -0800

    Additional/Corrected profiling flags in profiler.

Src/Extern/ProfParser/AMReX_BLProfStats.cpp
Src/Extern/ProfParser/AMReX_CommProfStats.cpp
Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp
Src/Extern/amrdata/AMReX_DataServices.cpp

commit 7b6b5093b49b848c49c29dcd4d8c4223c9242bc0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 9 14:50:40 2017 -0800

    MLMG: fix periodic boundary

Src/Base/AMReX_Geometry.H
Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_FabSet.H
Src/Boundary/AMReX_FabSet.cpp
Src/Boundary/AMReX_InterpBndryData.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 62059c1cb79cd2d60de31848e98878b930a63006
Merge: 17ea691dc 4e9d84d14
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Nov 9 13:50:36 2017 -0800

    merging with dev branch

commit 4e9d84d1405b880b8cdac5528c55f6107357cc1b
Author: kngott <kngott@lbl.gov>
Date:   Thu Nov 9 12:41:28 2017 -0800

    Fixed incorrect bool. proxMap -> statsCollected

Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp
Src/Extern/amrdata/AMReX_DataServices.cpp

commit 17ea691dc7e59843bc680acc2cd5b0e697f45b7e
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Nov 9 12:39:54 2017 -0800

    fixed time interpolation for TVD RK3

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp

commit fc290d8d358581a9c88905e54b50bc47abe3e8a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 9 11:15:42 2017 -0800

    MLMG: fix the special case of alpha is zero

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp

commit 00799f9ccaf30bba79e3a47408ea7253cbde4a97
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 9 10:54:32 2017 -0800

    MLMG: fix spherical

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit cb53b2160cb878b3159d666a5c2c9d7db5991562
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 9 10:49:22 2017 -0800

    MLMG: skip applying metric terms in Cartesian

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 085004c861884a5d8158e05b765b144684b6b0f9
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 8 17:57:57 2017 -0800

    add sparse vismf write for fabarrays with data on fewer mpi procs than nfiles.

Src/Base/AMReX_NFiles.H
Src/Base/AMReX_NFiles.cpp
Src/Base/AMReX_VisMF.cpp

commit f97ef7d806351c3ed5640ed3a69843a3c28a0e8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 8 17:39:18 2017 -0800

    MLMG test: option to do fine level solve only

Tests/LinearSolvers/MLMG/inputs.boxes
Tests/LinearSolvers/MLMG/main.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit 7b253814ef83f7b7ee209c70c2a2970d2a63603f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 8 17:29:27 2017 -0800

    MLMG test: option to read grids

Tests/LinearSolvers/MLMG/grids/gr.3_128cubed
Tests/LinearSolvers/MLMG/grids/gr.3_256cubed
Tests/LinearSolvers/MLMG/grids/gr.3_2boxes_a
Tests/LinearSolvers/MLMG/grids/gr.3_2x3x4
Tests/LinearSolvers/MLMG/grids/gr.3_512cubed
Tests/LinearSolvers/MLMG/grids/gr.3_big
Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_a
Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_b
Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_c
Tests/LinearSolvers/MLMG/grids/gr.3_mac_tst
Tests/LinearSolvers/MLMG/grids/gr.3_shiftedUp
Tests/LinearSolvers/MLMG/grids/gr.3_small_a
Tests/LinearSolvers/MLMG/grids/gr.3_stack_a
Tests/LinearSolvers/MLMG/grids/grids.15456.REMOVED.git-id
Tests/LinearSolvers/MLMG/grids/grids.213
Tests/LinearSolvers/MLMG/grids/grids.25600.REMOVED.git-id
Tests/LinearSolvers/MLMG/grids/grids.5034
Tests/LinearSolvers/MLMG/inputs.boxes
Tests/LinearSolvers/MLMG/main.cpp

commit fa99de392d90827ea580526d2024fc419b55b30c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Nov 8 16:58:32 2017 -0800

    fixed loop bound bug in 3d fortran

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90

commit 496b09ca925fcee7b9cf21f3f65cc5bff8586f1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 8 16:24:15 2017 -0800

    MLMG: if scalar a is zero, we can simply set coefficient to zero

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp

commit 550b0f395d53d018d01608b38875fc345bf226b0
Author: kngott <kngott@lbl.gov>
Date:   Wed Nov 8 14:09:38 2017 -0800

    Testing and turning off of persistent streams for profparser when number of files is extremely large.

Src/Extern/ProfParser/AMReX_CommProfStats.H
Src/Extern/ProfParser/AMReX_CommProfStats.cpp
Src/Extern/ProfParser/AMReX_RegionsProfStats.H
Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp

commit e027b66a1b4ba761a05fcb98751390d4f7027362
Author: kngott <kngott@lbl.gov>
Date:   Wed Nov 8 13:56:49 2017 -0800

    Output cleanup for MoveAllFabs and MoveFabs.

Src/Base/AMReX_FabArray.H

commit 4e707546b2af7a6e7fc1283387e19de4ab95b159
Author: kngott <kngott@lbl.gov>
Date:   Wed Nov 8 13:45:26 2017 -0800

    MoveAllFabs adjustment to allow testing at any number of procs.

OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp

commit cd5ebbd1571457a5a318a216da49d413e20ff528
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Nov 8 13:37:17 2017 -0800

    convergence results look pretty good

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs

commit d10e8470208a1d76b444edb9583c5e0404d3b308
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Nov 8 13:20:41 2017 -0800

    finished coding time interpolation for TVD rk3 scheme.

Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit 41566c1f9f47082f3da7aebc930286de914ba96b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 8 09:36:53 2017 -0800

    MLMG test: add option to do level by level solve

Tests/LinearSolvers/MLMG/inputs
Tests/LinearSolvers/MLMG/main.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit a2538e19815c237825fc4926bbef1d48a5722400
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 8 09:36:21 2017 -0800

    MLMG: agglomeration and consolidation flags need to be static because they are used by the constructor

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit c81eba6fa74fb73e5fe3291a42178befb414422d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 7 16:55:12 2017 -0800

    MLMG: 1d implemented but not tested

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 0ad3ad6dc2e888e7ece7d58a814190c23d45fd1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 7 16:39:59 2017 -0800

    MLMG: 1d

Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90

commit 78979b7305bc92d97a4d4eed7b78f0bcc6ed4b33
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 7 15:59:29 2017 -0800

    MLMG: add getGradSolution function

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/Make.package

commit cbe027384af687c83dd68cbed0c729bdc9978cc5
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 7 15:52:05 2017 -0800

    more information for errors.

Src/Extern/amrdata/AMReX_DataServices.cpp

commit ff8c0751f321975fbbaea9dd0495c107b2878d04
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 7 15:22:42 2017 -0800

    MLMG: metric terms for ABecLaplacian

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp

commit 850adf15363ee50e0267abac1bc99f5b6bd017c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 7 13:56:44 2017 -0800

    MLMG: 2d and cylindrical coordinates

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H

commit 896a2aa4ac6b4329da493b9f461b64cea6d5aff8
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Nov 7 14:16:08 2017 -0800

    EB: change type of get_neighbor_cells_int_single() function from PURE to ELEMENTAL
    
    ELEMENTAL is a stronger statement about the function's behavior, and implies
    PURE anyway.

Src/EB/AMReX_ebcellflag_mod.F90

commit c310946090f2b27113312d1777630f53807f5e02
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Nov 7 14:08:47 2017 -0800

    now seeing third order solution error with AMR

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp

commit 4474ad6259312e9bcece9040f8b4f698a6f1a367
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Nov 7 12:58:54 2017 -0800

    EB, Combustor: add function get_neighbor_cells_int_single()
    
    This function behaves similarly to get_neighbor_cells_int(), except it returns
    a single value for the requested neighbor cell, rather than returning a 3x3x3
    array containing values for all neighbors. This single-value approach is
    friendlier to function inlining and vectorization, and also yields better
    memory access patterns because a compiler attempting to vectorize a loop which
    calls this function need not generate private 3x3x3 arrays for each lane of a
    vector processing unit.

Src/EB/AMReX_ebcellflag_mod.F90
Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90

commit 68e96074df6e8716f6ac61a92214929cb16299c3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 7 12:40:41 2017 -0800

    also cache the grown_gridbox in EnforcePeriodicWhere.

Src/Particle/AMReX_ParticleContainerI.H

commit a4ed403519a45d0d6cd7bc75e360dfefe265427a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Nov 7 12:31:29 2017 -0800

    now getting fourth order truncation error with AMR

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/fourthOrderCFInterpTest.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/test.inputs

commit 6192580e7b8c1529b5bad9679c40baf579f4c933
Merge: ff6173777 ae8d7ea1c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 7 11:26:08 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ff61737775b2c3b9f02074fd22f86ad00065f880
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Nov 7 11:25:57 2017 -0800

    reset the pld cache after trying the grown particle locate (the next one might not have the same nGrow)

Src/Particle/AMReX_ParticleContainerI.H

commit ae8d7ea1c76494e7b30f3fdee1fcd53cb39cbc94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 7 10:16:29 2017 -0800

    PlotFileUtil: option to pre-build extra directories in plotfile

Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_PlotFileUtil.cpp

commit 1b478778da7e95ce970a5c251d3635625cf2e243
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 7 09:37:30 2017 -0800

    PlotFileUtil: use default in VisMF

Src/Base/AMReX_PlotFileUtil.cpp

commit f39f4709642a8331f9b83f9bb2f6fa53d245d69d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Nov 6 21:34:22 2017 -0500

    Add C binding to get_loop_bounds

Src/Base/AMReX_Device.H
Src/Base/AMReX_fort_mod.F90

commit a7024ad0cfeabb9566cdf0b0fc0a2215c8577ad0
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Nov 6 18:22:35 2017 -0800

    Lower limit error mag for computing order

Tools/C_util/Convergence/RichardsonConvergenceTest.cpp

commit 7d6fab52063b6b9a4443085f737301c3c79c9d04
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 6 17:43:26 2017 -0800

    try four.

build_and_deploy.sh

commit 5d4b2e4899741d27d664ef20e869f7dffbcfb9f2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 6 17:37:56 2017 -0800

    try two make jobs

build_and_deploy.sh

commit cf29cf52eda2dccd328453587cf482dc00fa0dc0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 6 17:31:18 2017 -0800

    do serial build.

build_and_deploy.sh

commit 5472034128a5d7e6e33159e95a40a468734f5fac
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 6 17:25:23 2017 -0800

    have travis build libamrex on each push.

.travis.yml
build_and_deploy.sh

commit 72110d805a00b6cd7ae13281f3d2c2beee7bd08f
Merge: 2b373b845 cb6b1ab7e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Nov 6 20:23:55 2017 -0500

    Merge branch 'development' into gpu

commit cb6b1ab7e578dc529bf33b74e7941749bf7965e1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 6 16:45:37 2017 -0800

    another Redistribute optimization.

Src/Particle/AMReX_ParticleContainerI.H

commit 8896ca2c14963003854bd2de255adac0ceced00e
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Nov 6 16:17:38 2017 -0800

    added test for coarse-fine interpolation.  FillPatchUtil with quartic_interp is indeed fourth order

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/fourthOrderCFInterpTest.cpp

commit ec981019492f6c73fd07cd324b60069806e74ea1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 6 16:14:47 2017 -0800

    an optmization for ParticleContainer::Redistribute

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 08215dad8381537a48fcca632760ccf3bb5dfdd0
Merge: b3befde03 a2963d91e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Nov 6 12:10:43 2017 -0800

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a2963d91ed59bae3e40c23cfd2046ffa44466ef5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 5 12:46:41 2017 -0800

    MLMG make applybc work for any d

Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90
Src/LinearSolvers/MLMG/Make.package

commit 3ba47937101ce88c1170ac43d06e1843a8237fa1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 5 12:23:50 2017 -0800

    MLMG: implement 2D version of some funcitons

Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90

commit 40cacbba99d1bafb1c321a4c18531124f116642e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 3 09:08:05 2017 -0700

    fix for the most vexing parse in C++

Src/F_Interfaces/Base/AMReX_geometry_fi.cpp

commit 4bf59972097749a540528d7bee0e2727ce380b98
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 3 09:05:28 2017 -0700

    fix particle module for 1d

Src/Particle/AMReX_Particle_mod_1d.F90

commit 5dc6ec5b0fc641ec56d1b4a4822ac1bb1dd05d87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Nov 3 11:43:11 2017 -0400

    warn if analysis failed and store analysis output

Tools/RegressionTesting/regtest.py

commit b410e11279c3063a81287e8085ae80fb8469eb88
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Nov 2 20:03:16 2017 -0400

    quote slack posts

Tools/RegressionTesting/regtest.py

commit 2e48372f3271dbefb95e12bd79b1ab90ca714147
Author: Neil Carlson <neil.n.carlson@gmail.com>
Date:   Thu Nov 2 12:55:13 2017 -0600

    Use amrex_constants_module in amrex_filcc_2d

Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90

commit 19807295d3d4dd637a7d986f732191d0680470ef
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Nov 2 14:09:41 2017 -0400

    Add protections against accessing invalid dimensions

Src/Base/AMReX_filcc_mod.F90

commit 929b4d6362a1d7dcfa35dffff6b932223ab6db65
Author: Neil Carlson <neil.n.carlson@gmail.com>
Date:   Thu Nov 2 10:41:13 2017 -0600

    Use amrex_constants_module in amrex_filcc_3d; trivial nag fix

Src/Base/AMReX_FILCC_3D.F90
Src/Base/AMReX_filcc_mod.F90

commit 6f01652b4c44f523e984f2cca34f2853d3d434d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 1 17:23:50 2017 -0700

    use amrex_constants_module in amrex_filcc_module

Src/Base/AMReX_filcc_mod.F90

commit 4af830ad50d04d634a46a4bbeaa2d60d095ed82b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 1 17:20:25 2017 -0700

    add amrex_constants_module and make bl_constants_module use it

Src/Base/AMReX_constants_mod.f90
Src/Base/CMakeLists.txt
Src/Base/GPackage.mak
Src/Base/Make.package
Src/F_BaseLib/bl_constants.f90

commit 77691daf7dcc00e0db09cec4e2b5ccfc32f3f049
Merge: c1cc71bf7 520fc965d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 2 12:52:03 2017 -0700

    Merge branch 'weiqun/mlmg' into development

commit 520fc965d9a84099893d62d508ae125d39aa35c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 2 12:51:22 2017 -0700

    MLMG: must use the fine dx for bc location on coarse MG levels

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit c1cc71bf72064d4f6a12f46f1673d296b6813363
Merge: cddd586d7 be53255a3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Nov 2 11:59:51 2017 -0700

    Merge pull request #163 from nncarlson/constants-fix
    
    Use amrex_constants_module in amrex_filcc_2d

commit be53255a3ed57f024ad259198a8b81a64bb99101
Author: Neil Carlson <neil.n.carlson@gmail.com>
Date:   Thu Nov 2 12:55:13 2017 -0600

    Use amrex_constants_module in amrex_filcc_2d

Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90

commit cddd586d7f1c9fc9064f79d119eaf59c7ae6b532
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Nov 2 14:09:41 2017 -0400

    Add protections against accessing invalid dimensions

Src/Base/AMReX_filcc_mod.F90

commit b3befde0304276200a0db6b1a11787573e11dea2
Merge: b395f0b6c 5dc0a3e70
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Nov 2 10:05:04 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 63759e3ef979b1f5214013e44ddafbe1a1897998
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 2 10:02:44 2017 -0700

    MLMG: simplify norm_inf calls

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit 5dc0a3e704ccd79bddafc8648bf7b37f3595032a
Merge: 114ccf19f cbc8b284b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Nov 2 09:47:49 2017 -0700

    Merge pull request #161 from nncarlson/nag-fixes
    
    Use amrex_constants_module in amrex_filcc_3d; trivial nag fix

commit cbc8b284b267a7e08f1f7ab20f3cfad3d47eddc4
Author: Neil Carlson <neil.n.carlson@gmail.com>
Date:   Thu Nov 2 10:41:13 2017 -0600

    Use amrex_constants_module in amrex_filcc_3d; trivial nag fix

Src/Base/AMReX_FILCC_3D.F90
Src/Base/AMReX_filcc_mod.F90

commit 81c763f1b3a75a30c82032fee6df725b35a853fd
Merge: 8d239421c 114ccf19f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 2 08:48:00 2017 -0700

    Merge branch 'development' into weiqun/mlmg

commit 8d239421cce7dfcd63baf69c94718d5cb9883540
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 2 08:47:56 2017 -0700

    minor

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit bb10dc27368452c1b564f11f63d007e4bdece9ef
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Nov 2 08:40:48 2017 -0700

    EB: change INTENT of neighbor lists in get_neighbor_cells() to OUT

Src/EB/AMReX_ebcellflag_mod.F90

commit 114ccf19f9ff2790345212bff201b1d36083d906
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Nov 1 18:12:34 2017 -0700

    revert testing stuff for now.

.travis.yml
build_and_deploy.sh

commit 2b762c52fdd139c16f5eca68119d1f0291cfc22d
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Nov 1 18:02:39 2017 -0700

    try openmpi and gfortran

.travis.yml

commit 57e997bf4dfab94e46bd823d5fd496dafee87dca
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Nov 1 17:55:12 2017 -0700

    add mpich to the packages to install

.travis.yml

commit cf76d815920c1f42c03507fbf73597ead13ece79
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Nov 1 17:36:24 2017 -0700

    also test whether we can build libamrex in travis.

build_and_deploy.sh

commit 1ada4807558c72eb6a47324646244e3f99c19e5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 1 17:23:50 2017 -0700

    use amrex_constants_module in amrex_filcc_module

Src/Base/AMReX_filcc_mod.F90

commit 49a1cb8943feef3f85cfdfb47eaa7cf75477d2f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 1 17:20:25 2017 -0700

    add amrex_constants_module and make bl_constants_module use it

Src/Base/AMReX_constants_mod.f90
Src/Base/CMakeLists.txt
Src/Base/GPackage.mak
Src/Base/Make.package
Src/F_BaseLib/bl_constants.f90

commit c41595104c57a2d4a4e44b4ce5d82f9c3e6cf2d1
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Nov 1 17:03:27 2017 -0700

    always return true from both git commit and git push.

build_and_deploy.sh

commit ce609c69963f43997c9e0897615b9bc9b48c6ee7
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Nov 1 16:28:16 2017 -0700

    bug fix in time interpolation

Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp

commit 117d5f84788482c765fd13f7a94dfb04a31700c8
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Nov 1 16:26:06 2017 -0700

    exit successfully if there are no changes.

build_and_deploy.sh

commit c17a6e7d170fdd38b6cf809b280788e20023557c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 1 16:08:01 2017 -0700

    MLMG: fix bugs

Src/Base/AMReX_ParallelDescriptor.cpp
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp

commit 6e6ca6ab64f5675b833bd106d9a920d9b4be2178
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Nov 1 15:58:06 2017 -0700

    always return true from git push

build_and_deploy.sh

commit 1e07ff7f52eb221845f1399ad29c4028c56f75c7
Merge: 5b921ffee c9043b6db
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Nov 1 15:47:11 2017 -0700

    Merge pull request #160 from nncarlson/F2003-pure-fix
    
    Add argument intent for pure subroutine required by F2003

commit c9043b6dbd08ab3bb03c750ec8c18a5545837a8c
Author: Neil Carlson <neil.n.carlson@gmail.com>
Date:   Wed Nov 1 16:17:31 2017 -0600

    Add argument intent for pure subroutine required by F2003

Src/F_Interfaces/Base/AMReX_boxarray_mod.F90

commit 7a0b52263d280004104b28d81eabdcd4bbe51fe6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 1 15:01:38 2017 -0700

    MLMG: distribution map consolidation

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 2156567cb3d6deee8a1bcc19523040ec594a5fdf
Merge: fd9053f10 5b921ffee
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Nov 1 14:15:30 2017 -0700

    keeping up with dev branch

commit fd9053f10c9784c8631b04a8a2e97912759308a6
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Nov 1 14:15:17 2017 -0700

    added some small debugging hooks

Tools/C_util/Convergence/DebugDump.H
Tools/C_util/Convergence/DebugOut.H
Tools/C_util/Convergence/DebugOut.cpp
Tools/C_util/Convergence/Make.package
Tools/C_util/Convergence/RichardsonConvergenceTest.cpp

commit 387d95c85655924ae6af71142fb0ce8a5232a565
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Nov 1 14:09:24 2017 -0700

    now have fourth order interpolation running without NaN's---on to testing

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Tagging_nd.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit 062f29e1cc18f2f3be54872c4b6c3eedf10ac466
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Nov 1 14:03:39 2017 -0700

    added a hook to avoid dividing by zero in BaseFab::linInterp

Src/Base/AMReX_BaseFab.H

commit 64fdbb8898d629481cca5dd22f627d3c05de2004
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 1 13:42:05 2017 -0700

    MLMG: jump the sequence number before bottom solve and and then reset afterwards

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 5432c777e6e8956cabfc9b0f71b860a4226edf0b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 1 13:29:35 2017 -0700

    MLMG: fix bug

Src/Base/AMReX_ParallelReduce.H

commit 501b3fa8fcdfbc1baf237e91dc227782eebe2f58
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 1 11:34:58 2017 -0700

    minor

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H

commit 7f1b52c79acf7adaf5a1a35e1618c8baf68603f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 1 11:23:57 2017 -0700

    MLMG::bottomSolve: use subcommunicator for allreaduce of sum

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 00ac2b2a5477e297fc6fe8da84b052b6d6eac6b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 1 11:16:39 2017 -0700

    MLMG: build subcommunicator for bottom

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 1a9ba2fecaa0aecdb6a7fb2576cce219e3b943e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 1 09:27:14 2017 -0700

    MLMG: only bottom needs a subcommunicator

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 5b921ffee623c74f0a5d2c981012320d02c90a73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 1 08:48:03 2017 -0700

    add 17.11 to CHANGES

CHANGES

commit 08a0fc9a68babd9b0fd9d4c69f513268275884fa
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 31 17:42:00 2017 -0700

    fix for alternate bl_prof directory names.

Src/Base/AMReX_BLProfiler.cpp

commit a23edc28a04822c7a68f96bec672334659ce16f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 31 16:51:48 2017 -0700

    MLMG: use sub communicator

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_ParallelReduce.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H

commit f993ac382ade5af515118139cd761372d176f2f2
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 31 16:53:41 2017 -0700

    added rk4 time interpolation

Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90

commit b395f0b6ce69314e0f063989a3fc83aa9b4e7bea
Merge: a86145b67 db8b99896
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 31 16:09:30 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit db8b998966db1a061724a740c3e78426359168b7
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Oct 31 15:41:37 2017 -0700

    helps if you use the right format so Doxygen can parse it.

Src/Particle/AMReX_Particles.H

commit 736bf63ec115dd347abffa6fd8ded729c76ec0cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 31 15:11:54 2017 -0700

    MLMG: store communicators

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit ffd29fa4a859157e16a3476756b41f1bf855ed81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 31 14:40:02 2017 -0700

    MLMG: build special distributionmapping

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H

commit 68104f056c12bc252c621290d6c786f6743f7333
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Oct 31 14:37:01 2017 -0700

    don't need to remove this here.

build_and_deploy.sh

commit f1f0c7dde9cfe938bc892f6ebb9368b8d08b2c20
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Oct 31 14:36:01 2017 -0700

    only make new directories if they don't already exist.

build_and_deploy.sh

commit 85b0495c23d3d39f803ba3a4a021024349700902
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Oct 31 14:27:08 2017 -0700

    add a doxygen-formated brief for ParticleContainer to test the Travis CI stuff.

Src/Particle/AMReX_Particles.H

commit 710a4ce1bf82efb47f0443ab0c6d858389e9748c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 31 14:13:05 2017 -0700

    diffusion convergence rates are now correct, as well.  On to time interpolation for AMR

Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90

commit 30aaccfe83ce51f5c66ac9cb9a4bac3853160e31
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Oct 31 14:09:59 2017 -0700

    adding deploy script and configuration for Travis CI

.travis.yml
build_and_deploy.sh
id_rsa_travis.enc

commit f4f7358def9951658520c2a6b4eadde616cf16d1
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Oct 31 14:01:25 2017 -0700

    remove ystatic from html_static_path entry.

Docs/sphinx/source/conf.py

commit e47d58e050f360250ff1b9e20ce955af618d6053
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Oct 31 13:58:13 2017 -0700

    update link location for the doxygen documentation.

Docs/sphinx/source/intro.rst

commit c27666d4da14bad759210d0b0883f5199f1eab45
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Oct 31 12:06:45 2017 -0700

    turn off latex in the doxygen build.

Docs/Doxygen/doxygen.conf

commit cf7bb88fbd14c19b3db7531a0a553f337897526b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 31 11:43:37 2017 -0700

    bug fix

Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90

commit f8d1b8a43572d2a8415c4ba24f2b41941349eec4
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 31 11:31:31 2017 -0700

    bug fix in diffusion flux stencil

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90

commit 2b373b8454ca1554db028f3de65da8a701175c8f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Oct 31 13:28:48 2017 -0400

    Restore device copy of nvar

Src/Base/AMReX_BaseFab.H

commit 545fc98640ce8efa02142bb512580ed0216b32db
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Oct 31 13:00:15 2017 -0400

    Update to use cellsize again

Tutorials/GPU/HeatEquation_EX1_C/advance.cpp

commit ce7505c03209a0f28ecfdb49abda2ee1e4c3c1f8
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Oct 31 12:59:51 2017 -0400

    Add device notation to dimensional filcc

Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90

commit 0d2a8f3cbfb4797c6a532cb301325ddaed422522
Merge: d838d490a 1ce310701
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Oct 31 12:49:38 2017 -0400

    Merge branch 'development' into gpu

commit 1ce31070154e8da0edbd6c791d8d552c509f6ffd
Merge: 1de358b03 dedf46cde
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Oct 31 09:38:40 2017 -0700

    Merge pull request #154 from AMReX-Codes/filcc
    
    Have old filcc's call new filccn

commit 1de358b039ed26e7e8cbe4c44ad6788408e16745
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 31 09:08:27 2017 -0700

    F_Interfaces: add nodal_type function to multifab, imultifab and boxarray

Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit d124e1c7b156782b0eb6e0c563c6c7c80b372f9c
Merge: 0bc29ba36 20938ba48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 30 17:54:35 2017 -0700

    Merge branch 'development' into weiqun/mlmg

commit 0bc29ba36aeaf60e187a6e8b25ed53d6825bbe45
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 30 17:54:07 2017 -0700

    MLMG: fix bugs in agglomeration

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 4d7838dc5768b8d995217a1160fa5c90e68e938f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 30 17:37:02 2017 -0700

    MLMG: build bc conditions and locations for each MG level

Src/Base/AMReX_LayoutData.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit a9f02a4d2c5f7c2effbcca590675016d8d6eda42
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Oct 30 17:03:47 2017 -0700

    Apparently, using pi=4.0d0*atan(1.0d0) is not an accurate enough representation of pi to avoid RK integrators producing bogus results at periodic boundaries (using this, I was getting sin(2.0d0*pi*1.0d0) = O(10^-7) instead of something near roundoff).   Who knew?   Now all looks correct in the convergence universe.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90

commit bb1f3ccfeac4b3e8d57de8bad7303f53a2ce5c17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 30 15:24:12 2017 -0700

    MLMG: use the new applybc

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 9b03c17984cd0e72de0c05494b22e6fe679c8c4b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Oct 30 13:41:50 2017 -0700

    bug fixes for rk4

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90

commit a86145b67e7d07abf5396eae2915122f92a22407
Merge: 3dd5c8a5b 20938ba48
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Oct 30 10:43:29 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 20938ba48c43d98a828cf4e339dd1de8fe0b49dd
Merge: aa26fd407 a4da1d763
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Oct 30 09:23:33 2017 -0700

    Merge pull request #156 from zingale/development
    
    if we are doing `print-`, then don't do dependency checking

commit a4da1d763f0d87edc513fd197aa54c9c25a8f6a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Oct 30 12:08:19 2017 -0400

    if we are doing `print-`, then don't do dependency checking

Tools/GNUMake/Make.rules

commit a1e346574c88f9737965d5b2f115e9f443ee0c8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 29 16:00:32 2017 -0700

    WIP MLMG: more on applybc

Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H

commit f905946b976b46e273c5ac16b0b38b7e23274749
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 29 11:32:32 2017 -0700

    MLMG: wip

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 14ca211234a769dce627a492d825876057137e2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 29 08:16:20 2017 -0700

    MLMG: add some fortran files in preparation for rewriting applybc

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/Make.package

commit 2ffa3ed3e34b50caeac7b1f5dec3e79d4d19cfb7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 28 21:28:16 2017 -0700

    MLMG: finish first pass of agglomeration without consolidation

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit b6097f97fd49081510cd7448ced67a729acf2766
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 28 15:42:17 2017 -0700

    make averag_down_faces more general

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit cde0c9ec7dbd36d80ce8938263a439f62ae602f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 28 14:09:53 2017 -0700

    MLMG: agglomeration WIP

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 12986d5567d12964117e4c4ffc2428de27c7705c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 28 13:21:22 2017 -0700

    min width argument for coarsenable function

Src/Base/AMReX_Box.H
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit d838d490a4be0aac48a2bd85f2d6637375e3f6e5
Merge: d86564079 aa26fd407
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Oct 28 14:45:17 2017 -0400

    Merge branch 'development' into gpu

commit aa26fd407eff9fe9df2fb37085b1b7566cd42013
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 27 19:37:42 2017 -0400

    fix omp atomic form

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit 319941aa7558fd5809db163a5b7b7b0991efe92a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Oct 27 16:06:18 2017 -0700

    more hooks and options

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugDump.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90

commit 6712330a0284df0c379bab9257575da920221bb0
Author: kngott <kngott@lbl.gov>
Date:   Fri Oct 27 15:53:45 2017 -0700

    Making it run again.

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.H

commit af56c14de92f5be252fa7fb9111d4f458ace5b07
Author: kngott <kngott@lbl.gov>
Date:   Fri Oct 27 15:25:24 2017 -0700

    Removal of proximity mapping options.

Src/Amr/AMReX_Amr.cpp
Src/Base/AMReX_DistributionMapping.H

commit 07461bb4a6c068c6428a4c404f5a6c444647eaa5
Author: kngott <kngott@lbl.gov>
Date:   Fri Oct 27 14:58:15 2017 -0700

    Constant reference adjustment.

Src/Base/AMReX_BLBackTrace.H
Src/Base/AMReX_BLBackTrace.cpp

commit f593d88598a44784c6d69019df24bc6dd32534aa
Author: kngott <kngott@lbl.gov>
Date:   Fri Oct 27 14:46:19 2017 -0700

    Addition of BoxArray and DistributionMapping hashing functions for comparison across MPI. Also, adjustment of BroadcastDistributionMapping to include color.

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit 951a7c425f668b5868519e2f50c7122f07d0e7c2
Author: kngott <kngott@lbl.gov>
Date:   Fri Oct 27 14:43:52 2017 -0700

    Function that outputs a backtrace but does not abort.

Src/Base/AMReX_BLBackTrace.H
Src/Base/AMReX_BLBackTrace.cpp

commit 800930247b77f0994ec67c307669b00467da36c0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 27 12:48:37 2017 -0700

    Need to reflect FILCC change in the CMakeLists.txt

Src/Base/CMakeLists.txt

commit e04186e9bb19fb7af4d6afc8af95d7c80773e938
Merge: 78af29598 8b8a91189
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 27 12:47:19 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 78af29598be35d55ff7d44eb4946284e05451e14
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 27 12:47:14 2017 -0700

    Fix typo

Docs/AMReXUsersGuide/EB/EB.tex

commit f6732ebc5a4e3f081943bb07ba1690fbcffddf33
Merge: fa12fcb8f 8b8a91189
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 27 11:57:53 2017 -0700

    Merge branch 'development' into partio

commit dedf46cde76b2bb6f77288d073b5bd4dff197edd
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 27 11:16:32 2017 -0400

    Have old filcc's call new filccn

Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90

commit 8b8a91189d721125c2236e211307a3676cdf1a01
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 27 02:57:46 2017 -0400

    Move the FILCC functions to F90 files

Src/Base/AMReX_FILCC_1D.F
Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F
Src/Base/AMReX_FILCC_3D.F90
Src/Base/Make.package

commit d86564079b72809952d0bcd79a6fffb760f1c5bd
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 27 02:05:19 2017 -0400

    Wrap a CUDA-only parameter in an ifdef

Src/Base/AMReX_FabArrayBase.cpp

commit 07674bbd15ddac2a0e4938a44f2e12e236ae2055
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 27 01:55:04 2017 -0400

    Move .F90 FILCC files back to .F

Src/Base/AMReX_FILCC_1D.F
Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F
Src/Base/AMReX_FILCC_3D.F90
Src/Base/Make.package

commit b063eda1d5a35e7baf6d795d5b25c24aa606b1a9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 27 01:33:13 2017 -0400

    Use a larger string size for bl_error/warning

Src/Base/AMReX_BLBoxLib_F.f

commit 93daa461b18f0959b17271ab0a626882d4712c2f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 27 01:28:00 2017 -0400

    Sync up heat equation with development

Tutorials/Basic/HeatEquation_EX1_C/main.cpp

commit 4400397b595cd587a90819033099ce8ea835c541
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 27 01:16:33 2017 -0400

    Update sites for CORAL early access systems

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/Linux_pgi.mak
Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.llnl
Tools/GNUMake/sites/Make.olcf
Tools/GNUMake/sites/Make.unknown

commit a2e1f642f1af2f03a0e835eebed11fc8ac440bac
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 27 01:24:37 2017 -0400

    summit -> summitdev

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/Linux_pgi.mak

commit c9534a554c5fb62fb31fd960fc4b887121957d3b
Merge: fb02ada5a 216a6b1f9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 27 00:57:22 2017 -0400

    Merge branch 'development' into gpu

commit 216a6b1f9a3891b2c925010e0d701576dec355a8
Merge: 0e80fb68b dd94eebcb
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Oct 26 16:18:35 2017 -0700

    Merge pull request #152 from AMReX-Codes/filcc
    
    Create a dimension agnostic, multi-component filcc

commit dd94eebcb660c3342daa5f8d77e73248f17f185e
Merge: e9dd8330a 79b5b0100
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 26 16:04:39 2017 -0700

    Merge pull request #153 from AMReX-Codes/fillcc2
    
    move some if tests out of nested i-j-k loops

commit 0e80fb68b47816d78cc264c99f06e4c0557977ac
Merge: 4edd05624 0402d624e
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 26 15:58:10 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 4edd05624d7577d4a4607d1b7533e8950c183bf7
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 26 15:57:46 2017 -0700

    added 1-e/i percent time to html output.

Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp

commit 0402d624eb4e943c00a150e613e3fdd173929c80
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 26 13:34:31 2017 -0700

    MLMG: fix ref ratio of 4

Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90

commit 79b5b0100bfa49936a8250ef19277f465642dab6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 26 13:19:04 2017 -0700

    move some if tests out of nested i-j-k loops

Src/Base/AMReX_filcc_mod.F90

commit fb02ada5a1ecfcec87a1a34fdc56a44c16246b96
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 26 12:11:01 2017 -0400

    Revert to CUDA 8 default

Tools/F_mk/GMakedefs.mak
Tools/GNUMake/Make.defs

commit 44568675f717308699bd1b6881eeb4706102e503
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 26 12:10:22 2017 -0400

    Specify CUDA_VERSION at compile time for the PGI compiler

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/Linux_pgi.mak
Tools/GNUMake/Make.defs
Tools/GNUMake/comps/pgi.mak

commit 9b27d62538ec9cc893e6440c9289d1af59c83693
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 25 17:56:33 2017 -0700

    make sure relative tolerance is not less than 1.e-13

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 6ea2bab5aa01869cd44d7ed51b02398ff74b8e31
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 25 17:35:08 2017 -0700

    MLMG: in case crse bc data is not provides, use zero

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit fef809999bcca3bc1f136a887148d27382843ea6
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 25 16:51:35 2017 -0700

    work on the profiler flush interval.

Src/Amr/AMReX_Amr.cpp
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BLProfiler.cpp

commit 614262db02dceb4ed7fb18a7a0a0af19681b5417
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 25 16:48:39 2017 -0700

    fix assertion

Src/Boundary/AMReX_YAFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister.cpp

commit 9b9b6325943791827f8dfd3f74ad66c0da8fb93b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 25 16:47:05 2017 -0700

    fix bug in YAFluxRegister

Src/Boundary/AMReX_YAFluxRegister.cpp
Src/Boundary/AMReX_YAFluxRegister_1d.F90
Src/Boundary/AMReX_YAFluxRegister_2d.F90
Src/Boundary/AMReX_YAFluxRegister_3d.F90
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_2d.F90
Src/EB/AMReX_EBFluxRegister_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 47f01cb94fbb572099527fe8b550ef7460f74688
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Oct 25 16:07:37 2017 -0700

    fillboundary needs to know about periodicity

Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90

commit 4c43c187c41fa6f79242ea4dbfd8d4a1ac1c5e18
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Oct 25 15:51:52 2017 -0700

    ScalarAdvectionDiffusion now fourth order for non-AMR calcs.  Now on  the hard part.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90

commit e9dd8330a1caa2e6706ddba5fa0875d89cc59a28
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 25 17:17:57 2017 -0400

    Create a dimension agnostic, multi-component filcc
    
    This version of filcc is both dimension agnostic, and works over an arbitrary
    number of components. It gives the same results as the dimensionful versions of
    filcc. It will be necessary for performance reasons to use a version like this
    on the GPU.
    
    This also applies the new filcc to amrex_fab_filcc.

Src/Base/AMReX_filcc_mod.F90

commit 3dd5c8a5b1e164824ac8062b37503f76f54d7677
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 25 14:17:28 2017 -0700

    remove unused variable.

Src/Particle/AMReX_NeighborParticlesI.H

commit 5d832b5b9cf00b43fed24a57a47e731dce3f6c9d
Merge: 0c83d0ce7 295b479de
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 25 17:16:57 2017 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 0c83d0ce7abcffee5c15f8e39971b8a3f8a7bdef
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 25 16:54:10 2017 -0400

    Bring over a few stub functions from gpu branch

Src/Base/AMReX_BLFort.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_fort_mod.F90
Tools/GNUMake/Make.defs

commit aa76a4b59b6447c8fc362acbcb969a17778083c5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 25 14:16:07 2017 -0700

    add profiling to amrex::get_slice_data

Src/Base/AMReX_MultiFabUtil.cpp

commit 295b479de94e29cbb79836bfaf12ea16ec8794bf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 25 13:53:25 2017 -0700

    MLMG: add getFluxes and compResidual

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 6a0c2a5ff9e7d7ade521481a2c6a6e7e239e13c3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 25 16:44:57 2017 -0400

    Compile fix for ppc64le

Src/Base/AMReX_FPC.cpp

commit c399423ba612f63dbfe95c8a39ab4fe5396a1943
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 25 15:42:49 2017 -0400

    Simplify logic for copying Box data

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_RealBox.H

commit 2cea01808d8893eb18e31e10fd172ea00827e892
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 25 14:42:50 2017 -0400

    CUDA-awareness in MPI is now a runtime option

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Tools/GNUMake/Make.defs

commit dede1487697b003c279860d2881dd2171a3fb35c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 25 14:29:41 2017 -0400

    Remove unnecessary device synchronizations

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_Geometry.cpp

commit d9903f823ab152e3056aaaf8d6afaa09a09a74b9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 25 14:14:07 2017 -0400

    Reduce more diffs with development

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H

commit 5b7e23595589db907b6c7353c98667a4f95c3495
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 25 11:02:46 2017 -0700

    update Users Guide for Array -> Vector

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/EB/EB.tex
Docs/AMReXUsersGuide/amrexsymbols.tex

commit 4655eba643ad0945a6917280690490a4b62badf8
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 25 13:56:48 2017 -0400

    Remove functionality to have device data in Fab's/MF's/StateData
    
    This may be introduced in a future GPU release, but is currently unnecessary.

Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StateDescriptor.H
Src/Amr/AMReX_StateDescriptor.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabFactory.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit f33851033635b3e399c5a67862587f7a3ec29459
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 25 10:46:39 2017 -0700

    add macros AMREX_ASSERT_WITH_MESSAGE and AMREX_ALWAYS_ASSERT_WITH_MESSAGE

CHANGES
Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_BLassert.H

commit 810367b513e6f91b119c2975ce22f216454deb2a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Oct 25 10:44:50 2017 -0700

    put check for isotropic dx back into CNS

Tutorials/EB/CNS/Source/CNS.cpp

commit e5c7d3d8d8d4f3c3309513850ba1327367cbd1b0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 25 13:29:56 2017 -0400

    Reduce some diffs with development

Src/Amr/AMReX_StateData.cpp

commit e091e5030f62c1fb54271036b41bc48e933c1806
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 25 09:57:59 2017 -0700

    MLPoisson: fix bug

Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90

commit 35144dd3714e4f5ea8a9c340946368b7244ff977
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 24 17:20:10 2017 -0700

    minor typo

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 03818260ce790373c10fe5166eb9524e23e55ea2
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 25 12:43:20 2017 -0400

    No longer need a special gcc configuration for PGI on summitdev

Tools/GNUMake/comps/pgi.mak

commit b0ba9646420d56b163cfc14b2e43898c384ea0f1
Merge: 04f8c26f4 aba804ad0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 25 09:17:52 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 04f8c26f44dd52078b2247e28f51273d62708798
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 25 09:17:07 2017 -0700

    Update BuildingAMReX chapter of the sphinx docs

Docs/sphinx/source/BuildingAMReX.rst

commit aba804ad00e8096274e130619bfe2690bc94dd71
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Oct 25 09:09:18 2017 -0700

    added new header to CMakeLists.txt

Src/GeometryShop/CMakeLists.txt

commit d0ba79a5ddd8d300d6d8ac49b2322d255e1a4f1d
Merge: 915e6a47e fa36fbbfe
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Oct 25 09:06:37 2017 -0700

    Merge branch 'dtg_branch' into development

commit fa36fbbfe11f139edd218a6638c7668bab5b43a3
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Oct 25 09:05:52 2017 -0700

    bug fix (needed to also add new factory function)

Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H
Src/GeometryShop/AMReX_PlaneIF.H

commit 915e6a47ebc91bd0b4614f7924a887ba90bce077
Merge: 17a79637b b06bc2025
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Oct 25 08:50:20 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 17a79637b43bd9846acc649512d3add9a55cb1f9
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Oct 25 08:49:24 2017 -0700

    adding missing file

Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H

commit b06bc2025d752c6c440b07848add15aa742e369a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 24 16:58:06 2017 -0700

    MLPoisson: rm member m_Anorm

Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit a60f5e31155297b76b699903a1ca270ee025c8d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 24 16:31:44 2017 -0700

    add MLPoisson::Anorm

Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp

commit 35aee01c061060750b378e5e32cc61a0771444e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 24 16:21:59 2017 -0700

    add amrex_mlpoisson_gsrb

Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H

commit 517c283dc9274b658cb295d3436cc9d8c0756c30
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Oct 24 19:14:09 2017 -0400

    Remove remaining calls to get_host_pointer

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_Box.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MFIter.H

commit 8f79e5e20320b2e52195f9b20ec50c910a47f190
Merge: 04b4fec26 8c1f6819f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 24 16:11:39 2017 -0700

    Merge pull request #151 from AMReX-Codes/dtg_branch
    
    merging with dev so Jordan can get implicit function for plane with anistropic dx.

commit 8c1f6819fd59be79cf75aaa38f366439d796e279
Merge: 78e6f0357 04b4fec26
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 24 16:09:32 2017 -0700

    Merge branch 'development' into dtg_branch

commit 78e6f0357506fda57f249d89b440ef9f8a64f6a7
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 24 16:08:45 2017 -0700

    added Plane geometry for anistropic dx.  I tested it on CNS and it seems to give the right geometry

Tools/C_util/TV_TempWrite.H
Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_init_eb.cpp

commit 611bbb99de8e8e9293d57bbe3dabac91d8e8bc5c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Oct 24 18:54:33 2017 -0400

    Remove RealBox::loF/hiF

Src/Amr/AMReX_AmrLevel.cpp
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp

commit 7ea77a1a5117db2ff85d8e62cf99c0773ef2d050
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 24 15:45:30 2017 -0700

    more debugging hooks

Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90

commit 2b31264b98a928cb8dca959c2c45031b4b146caa
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Oct 24 18:40:33 2017 -0400

    Remove Geometry::CellSizeF()

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_CoordSys.H

commit b8aa8f007f166b6b42384905e1896c8798586821
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Oct 24 18:39:23 2017 -0400

    Avoid using write-combined pinned memory
    
    This can in theory provide a performance benefit, but in practice it probably
    never will matter, and we want to switch to using a uniform pointer for pinned
    memory between the host and device, which means we need to avoid WC memory
    if we want to skip the use of cudaHostGetDevicePointer().

Src/Base/AMReX_CUDA.F90

commit 04b4fec2643e73bf33c8baf2654d80d08bc22484
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 24 15:31:22 2017 -0700

    start MLPoisson

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp
Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H
Src/LinearSolvers/MLMG/Make.package

commit 0ba63bf6fa1454ad241f9ac5912a7d05bd427f0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 24 13:41:27 2017 -0700

    minor tweak of amrex_array_to_vector.sh

Tools/Migration/amrex_array_to_vector.sh

commit f3e10c4939b1f1bc012b330a51fcc19ba3119af6
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 24 13:10:59 2017 -0700

    added a pile of debugging hooks.   fluxes are fourth order.

Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_serial_driver.py

commit b0d71a3887ade6fd473bf6f2b0145939cb6ee62e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 24 13:03:05 2017 -0700

    MLMG: use more restrictive convergence criteria for CG

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 4b4c0e25e4fb3701f60551897dcb9dd09e64b476
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 24 11:12:31 2017 -0700

    MLMG: need to apply bc before reflux

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit b8cc03559a9dc0eee80847161a2ba090dac8ca9b
Merge: 0901389ea a0b6c9db3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Oct 24 09:24:21 2017 -0700

    Merge pull request #150 from bcfriesen/update_F_mk_for_intel
    
    F_mk: add support for compiling with Intel v17 and v18

commit a0b6c9db31f90255f39f380223e82ff82569ad66
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Oct 24 09:01:42 2017 -0700

    F_mk: add support for compiling with Intel v17 and v18

Tools/F_mk/comps/Linux_intel.mak

commit 0901389eaff285e284fd7103d0c176c8a0f4c165
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 24 08:58:53 2017 -0700

    MLMG: isSingular virtual function

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 8056ce9b452f205764070d7fe2983b8dfeb76606
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 23 17:04:11 2017 -0700

    MLMG: solvability WIP

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 85b06d9de1c196f2a630cce59620b4a9e4e33f32
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 23 15:16:44 2017 -0700

    MLMG: enforce solvability

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/init_prob.cpp
Tests/LinearSolvers/MLMG/main.cpp

commit 71e0b3fe43ebaa31ef5d698b879bb1370e76d12a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 23 11:16:13 2017 -0700

    MLMG: add m_singular vector

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 2e38c1b1177ae767e54304bf0c7d0c4e5adfe42b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 23 10:41:59 2017 -0700

    MLMG test: set up periodic and Neumann

Tests/LinearSolvers/MLMG/fort.H
Tests/LinearSolvers/MLMG/fort_3d.F90
Tests/LinearSolvers/MLMG/init_prob.cpp
Tests/LinearSolvers/MLMG/inputs
Tests/LinearSolvers/MLMG/prob_par.H
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit 88149ddd29158d374afe72dcfb773a3aa8d21c6e
Merge: 11daa8a9b 2157ae2df
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Oct 23 17:02:46 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 11daa8a9b8a3241b19d2feb35caeb90ed9a03cad
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Oct 23 17:02:29 2017 -0700

    add a version of MakeMFIter that overrides the default tiling setting.

Src/Particle/AMReX_Particles.H

commit 2157ae2df397bc6c95bceeaa072b3adf39e9e914
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 23 16:45:39 2017 -0700

    Default for ENABLE_EB should be off.

Tools/CMake/AMReX_Options.cmake

commit 835290342df36420cd345c3c22ea8af51d565d89
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 23 16:44:44 2017 -0700

    Fix bug where there were 0 neighbors and we were trying to fill an array with zero values.

Src/Particle/AMReX_NeighborParticlesI.H

commit c1eace42e12b15bda80282db2f98d0ba27374184
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Oct 23 16:36:20 2017 -0700

    added interior box option as an example

Tutorials/EB/CNS/Source/CNS_init_eb.cpp

commit 3087bd06491c2a7fa1487d7791447d5583ce138c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Oct 23 18:09:55 2017 -0400

    Add CUDA suffix for F90 builds

Tools/F_mk/GMakedefs.mak

commit b547111dbe55a2b681db9db87df2e1c4d309be83
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Oct 23 14:42:26 2017 -0700

    some bug fixes.  dphi/dt for MOL code still only second order.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_serial_driver.py

commit 724375bb085e9883efe9b462c38d3e188555caf5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Oct 23 17:13:19 2017 -0400

    Update to CUDA 9 in F90 build system

Tools/F_mk/comps/Linux_pgi.mak

commit 8b2e0c1402adc0829ed6054a1c14f39d6b2113b7
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Oct 23 16:28:30 2017 -0400

    Support CUDA module in F90 build

Src/Base/AMReX_CUDA.F90
Tools/F_mk/GMakedefs.mak

commit 8f09a3022ee683c96a18cdbc235994907c5918a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 23 10:06:06 2017 -0700

    MLMG: no longer requires AmrCore

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/GNUmakefile

commit a3ee38c5622faace0b3eb49ed9b107ce56d71d13
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 23 10:03:54 2017 -0700

    MLMG: cleanup

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 08fbe3ca18c9dee7735333b3c78320e1ec9677fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 22 12:26:03 2017 -0700

    MLMG: set bc interface

Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_InterpBndryData.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit 6897a5d99083d56446aed440b23a7988e57e29b3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 22 17:08:27 2017 -0700

    Update the EBParticles Tutorial with 1) 3d bounce routine , 2) replace 0.0005 by dt in bounce.

Tutorials/Particles/EBParticles/EBParticleContainer.H
Tutorials/Particles/EBParticles/EBParticleContainer.cpp
Tutorials/Particles/EBParticles/GNUmakefile
Tutorials/Particles/EBParticles/ebparticles_2d.f90
Tutorials/Particles/EBParticles/ebparticles_3d.f90
Tutorials/Particles/EBParticles/ebparticles_F.H
Tutorials/Particles/EBParticles/main.cpp

commit b2cd6bcf5bae1ad70095c20e102224114127e7ec
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Oct 21 18:12:01 2017 -0700

    Fix some typos

Docs/AMReXUsersGuide/EB/EB.tex

commit ac427e54c207c0e178a1223abfa2da837e0594df
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Oct 21 14:47:25 2017 -0700

    added fixed_dt option so I can do proper convergence tests

Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90

commit 5cf3b28e559b758d3ab1b2b6a9f1ad310fe6e325
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Oct 21 13:31:17 2017 -0700

    added a python utility for convergence tests

Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_serial_driver.py

commit d2b1b9d6afcc396c78afec0adf280bf890d105d1
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Oct 20 17:42:43 2017 -0700

    CMake: fix few bugs

Src/Boundary/CMakeLists.txt
Src/GeometryShop/CMakeLists.txt

commit cc2b5fd0ce6a54e6f41095679d319e6c9707f224
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 20 17:14:01 2017 -0700

    Fix another typo

Src/GeometryShop/CMakeLists.txt

commit acb1c6024103bfaac55a2142524d9f89dd0800ac
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 20 17:13:07 2017 -0700

    Fix typo

Src/GeometryShop/CMakeLists.txt

commit 1d11389f8049f2190303055afbfa3bbc6d20c28c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 20 17:11:50 2017 -0700

    Fix typos

Src/EB/CMakeLists.txt

commit 07998f9d11acf840706ee312e875b999c7e0628b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 20 16:58:48 2017 -0700

    Adding more cmake support for using EB

Src/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake

commit 3497a01f6f465efd3ef4789f25f2674fcd9f34ae
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 20 16:50:49 2017 -0700

    Adding CMakeLists.txt for EB and GeometryShop

Src/EB/CMakeLists.txt
Src/GeometryShop/CMakeLists.txt

commit 709bbc49208aa9eaa125c8c8690d900cecb8daa6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 20 16:34:18 2017 -0700

    improve amrex_array_to_vector.sh

Tools/Migration/amrex_array_to_vector.sh

commit fa12fcb8f3943d1f21cf94a9cd44a33af76ab43d
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 20 15:55:18 2017 -0700

    more support for precreate directories and particle io.

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp
Src/Base/AMReX.cpp
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BLProfiler.cpp
Src/Particle/AMReX_ParticleContainerI.H

commit 8375fab5df2ee3935ac920b3b3e27ac2f5cb175e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 20 15:07:51 2017 -0700

    MLMG: use linear interp for amr level prolongation

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 41400efb2e9839d40771da6f3ebbc1d8df54c63f
Merge: ef990f1ba b43ab36b5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 20 15:11:38 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ef990f1ba10eb71578468b9007b86337fcfc99f4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 20 15:09:13 2017 -0700

    add utility functions for filling slices of data from a Multifab.

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_MultiFabUtil_nd.F90

commit b43ab36b50a80fab45166c03597cc500c9660ec7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 20 15:00:41 2017 -0700

    MLMG: fix linear interp

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLMG_F.H
Src/LinearSolvers/MLMG/Make.package

commit f454ea63fffaec61da2977188331a5c3d0927c62
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 20 13:59:05 2017 -0700

    move heap allocation out of mfiiter

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit a3a3b0d72f9895f273454d017eff16793cee2ff2
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 20 13:35:42 2017 -0700

    more support for precreate directories.

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Particle/AMReX_Particles.H

commit 7ac36b0726de377d218f7549b9bcc89d4c4a02b8
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Oct 20 13:13:41 2017 -0700

    some bug fixes

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.2d.convtest.sh
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.3d.convtest.sh
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs

commit 1cb4e5a485947d4162b0f87330ccd60fae18640c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Oct 20 11:49:27 2017 -0700

    added (exact) smooth initial condition, confirmed via convergence test

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/debug.inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.2d.convtest.sh
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.3d.convtest.sh
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/probdata.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/probin
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs

commit add92f07a71d74770536f0fdefdbfa9960bf5b79
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 20 11:36:26 2017 -0700

    shorten profiling names.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H

commit 35383e945ff938206e8a74d41d292cac6628aa5c
Merge: 36004bb31 3356b77ff
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 20 10:32:51 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 3356b77ffb2e32fc7527db080d18c93495dd8950
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 20 10:31:22 2017 -0700

    MLMG: remove nu0 and fix mini-cycle

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit a244adb70185c9ff01e6af8643406499a23184c2
Merge: 243601df9 165250c37
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Oct 20 09:51:39 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 243601df9c6f815b1287aa269df6afe622cbbd1a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Oct 20 09:51:24 2017 -0700

    CMake: add header to cmake list

Src/Base/CMakeLists.txt

commit 165250c37b8ec2a20e269bcadb2971ae97a2446d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 20 09:41:55 2017 -0700

    MLMG: fix a minor bug

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 06331c176f762a31f05710daf3f7ada6836e6a3f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 20 09:32:48 2017 -0700

    MLMG:: add profilers

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/main.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit b37f7493768e6fa4137f498b1f3338c51b9e7cb0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 20 09:07:05 2017 -0700

    MLMG test: add inputs

Tests/LinearSolvers/MLMG/init_prob.cpp
Tests/LinearSolvers/MLMG/inputs
Tests/LinearSolvers/MLMG/prob_par.H

commit 001693af5f833ce111d704652f685698eb51a1f0
Merge: 3531a2da4 1783235eb
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Fri Oct 20 10:36:58 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 1783235eb6fce8af3c326149fd6eecbab7c5824d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 19 18:26:11 2017 -0700

    Add rst files for the rest of the user guide chapters.

Docs/sphinx/source/Amr.rst
Docs/sphinx/source/AmrCore.rst
Docs/sphinx/source/Basics.rst
Docs/sphinx/source/Boundary.rst
Docs/sphinx/source/BuildingAMReX.rst
Docs/sphinx/source/CVODE.rst
Docs/sphinx/source/Chapter2.rst
Docs/sphinx/source/Chapter3.rst
Docs/sphinx/source/Chapter4.rst
Docs/sphinx/source/EB.rst
Docs/sphinx/source/Fortran.rst
Docs/sphinx/source/GettingStarted.rst
Docs/sphinx/source/Particles.rst
Docs/sphinx/source/Profiling.rst
Docs/sphinx/source/Visualization.rst
Docs/sphinx/source/index.rst
Docs/sphinx/source/intro.rst

commit c5e94f640482263a06c10efade1c5ff01d382698
Merge: 5866e8876 e94ac4743
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 19 20:52:42 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 5866e8876c95b85d728ae279b55b382b27c8b115
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 19 19:55:14 2017 -0400

    Correct the reporting of how many total GPUs are available

Src/Base/AMReX_Device.cpp

commit ffb8ac25363202e10449530c628d483b4d437c57
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 19 19:22:19 2017 -0400

    Use the same CPU-GPU matching algorithm without MPI

Src/Base/AMReX_Device.cpp

commit 489a05b2c6f6542fb4db908d99d250f9a84004ad
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 19 16:11:02 2017 -0700

    Fix subsections

Docs/sphinx/source/Basics.rst

commit 81d24557b52d24fff2e4b1a23c30f915a73d0e97
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 19 16:03:57 2017 -0700

    Fix the index

Docs/sphinx/source/index.rst

commit ef470f7b3c4fbb6710a31cd22473923381f0717f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 19 15:59:29 2017 -0700

    Add Basics/Basics.tex

Docs/sphinx/source/Basics.rst
Docs/sphinx/source/index.rst

commit e5fcc1605905faa45cdca7697170694fa313fd97
Merge: b84c96233 afe5db5e0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 19 15:55:03 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit b84c962338f70017fad238c021268d7f237443ab
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 19 15:54:48 2017 -0700

    Missing curly brackets in emph lines

Docs/AMReXUsersGuide/Basics/Basics.tex

commit c35f2c3b10b73e364ea3c25c1a522185abab651e
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Oct 19 15:46:47 2017 -0700

    added an algorithm description to the notes

Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90

commit afe5db5e048e4d7558d2478d1f68cde85c425d9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 19 15:37:13 2017 -0700

    MLMG: remove unnecessary fillboundary

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 6657db1d047c1bd642dd902bbadcf159b9997ca7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 19 15:17:28 2017 -0700

    sphinx for github.io pages

Docs/sphinx/Makefile
Docs/sphinx/source/conf.py
Docs/sphinx/source/index.rst
Docs/sphinx/source/intro.rst

commit 55be57f368ac947af7e8da423281609fb0cec85a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 19 14:36:58 2017 -0700

    MLMG: fix bug

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 8041ec23e0edad724943c54f3586e161a0038108
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 19 14:23:05 2017 -0700

    MLMG: refactor and comments

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit b20e34c373d2b7ea03939c9c912615f39c062490
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Oct 19 14:19:36 2017 -0700

    added fourth order fortran routines.   On to testing.

Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90

commit e94ac4743a1901d6899858b450f5a4e7f2275def
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Thu Oct 19 17:09:38 2017 -0400

    Add BL_USE_F_BASELIB as a preprocessor variable for F90 build system.
    
    This fixes CUDA compilation for the Microphysics test_react unit test.

Tools/F_mk/GMakedefs.mak

commit 7b7f6c6644d318aefc03fcbd27149025e7cb39bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 19 10:52:21 2017 -0700

    MLMG: avoid recursive function

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 94c695a1c42cd97bff666674e9121d86c54543e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 19 10:40:31 2017 -0700

    MLMG test: add max_fmg_iter parameter

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit 5e1e8870dadf9ef7eb4471b6c129c70568229804
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 19 10:20:27 2017 -0700

    MLMG: add linear interpolation

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 28f3f6c6956e0a98fcf17015912cf6a40f86f585
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 19 06:17:10 2017 -0400

    Make NVML mandatory

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Tools/GNUMake/Make.defs

commit b42918cc086a6cb691484f6f92f49da8ccfd945e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 19 06:05:09 2017 -0400

    Clean up the code for assigning ranks to GPUs

Src/Base/AMReX_Device.cpp

commit 01f6eb80941e09f30b436172ac0f3ee56dc55bb8
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 19 06:04:33 2017 -0400

    Add an NVML error check macro

Src/Base/AMReX_Device.H

commit 7653d72bc54430ed67d03e6637d08e4264fd5dd3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 19 05:14:33 2017 -0400

    Do not divide up GPUs that are not visible to CUDA

Src/Base/AMReX_Device.cpp

commit d6277acb8907b112edd5cc2b91e1f30d4177429e
Merge: cdf41e262 9db5c57a8
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 19 05:13:45 2017 -0400

    Merge branch 'development' into gpu

commit cdf41e262e3cc5cb52ac371c933677a26ef54704
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 19 02:07:35 2017 -0400

    Allow disabling of CUDA-aware MPI at compile time

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Tools/GNUMake/Make.defs

commit 094afe6dbd17c116cb4373a29286e97bdf65b144
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 18 21:57:42 2017 -0700

    MLMG: use swap

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit af9c9822ca94e392fe344c6d0ef5b61558a463f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 18 21:51:02 2017 -0700

    MLMG: remove a temp mf

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 8f05cf9f7af8678570b7fa0823d2d8b17d718653
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 18 23:19:46 2017 -0400

    Only link in NVTX if profiling

Tools/GNUMake/Make.defs

commit c0ead92e8989237dd9b228af83987bd1c3ea2784
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 18 23:06:58 2017 -0400

    Update to CUDA 9 (requires PGI 17.9+)

Tools/GNUMake/comps/pgi.mak
Tools/GNUMake/sites/Make.olcf

commit 9db5c57a8bc2a1793864ce10b0e1a476b6e8f126
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 18 17:39:14 2017 -0700

    MLMG: better name

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 2ba2f09bdd47f119ca2ca93f4700a19c0aca8140
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 18 17:35:23 2017 -0700

    MLMG: implement FMG cycle

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 8ab5878a4e7dc09aa8c5ca7b897c978e45de3d15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 18 12:13:07 2017 -0700

    MLMG: some timers

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 4bf4df2f4f2470d5d52ceb708fad60f893bec58f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 18 11:02:28 2017 -0700

    MLMG: some cleanup

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/ComparisonTest/compute_norm.cpp
Tests/LinearSolvers/MLMG/GNUmakefile

commit 7b406ce1c7342f160853b2c3c616030d80fb0058
Merge: bbd321df6 884ecf5f7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 18 16:37:50 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit bbd321df631458bceab8ef3e71d6eb0ba3c42abc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 18 16:28:43 2017 -0700

    change the value of insideRegular to be consistent with the above example, which has the solution domain on the inside of the sphere.

Docs/AMReXUsersGuide/EB/EB.tex

commit 0814e362b7c8e16d46ad1ad1f94cd458b3d20f52
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Oct 18 15:19:24 2017 -0700

    added in fortran framework

Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90

commit 884ecf5f79c1330991f31dac6f8148b92b8c084e
Merge: 09a3e78ad 1d4a618d9
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Oct 18 14:41:29 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 09a3e78ad7ff40409f47f68a66a6acc91650b65f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Oct 18 14:40:40 2017 -0700

    CMake: add support for Cray compiler

Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Config.cmake

commit c12b6682fbeac7ccc17572ea59d487081eef9b3f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Oct 18 14:05:55 2017 -0700

    added some more notes and put in 4th order framework for advance

Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp

commit 33b23537d92fbff26683e3c6a2c14e9829e48d8b
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Oct 18 14:00:11 2017 -0700

    CMake: remove cmake file copied by mistake in Tutorials/ScalarAdvectionDiffusion

Tutorials/Amr/ScalarAdvectionDiffusion/CMakeLists.txt

commit 1d4a618d9fc8a2ffe5eba91e84e4d91798beacb9
Merge: 603280d1f 96d26fa5d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 18 12:17:28 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 603280d1f42b1ba3b78118a028531576b266358d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 18 12:17:15 2017 -0700

    clean up main.

Tutorials/Particles/EBParticles/main.cpp

commit 6d366d29cca7537695e514de25fe0e051422ae99
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 18 12:16:20 2017 -0700

    clean up inputs file.

Tutorials/Particles/EBParticles/inputs

commit 73c8043a65108c0e61e9272e273ba7d08adbe132
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 18 12:09:41 2017 -0700

    Tutorial for particles that interact with embedded boundaries.

Tutorials/Particles/EBParticles/EBParticleContainer.H
Tutorials/Particles/EBParticles/EBParticleContainer.cpp
Tutorials/Particles/EBParticles/GNUmakefile
Tutorials/Particles/EBParticles/Make.package
Tutorials/Particles/EBParticles/ebparticles_2d.f90
Tutorials/Particles/EBParticles/ebparticles_3d.f90
Tutorials/Particles/EBParticles/ebparticles_F.H
Tutorials/Particles/EBParticles/inputs
Tutorials/Particles/EBParticles/main.cpp

commit 96d26fa5d0b9b8103306cea53e0ac1a8d170102b
Merge: 9ebec95a8 d81e4b85c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Oct 18 11:37:44 2017 -0700

    Merge pull request #148 from AMReX-Codes/dtg_branch
    
    moving a couple of things to dev so Marc can get the convergence test utility

commit d81e4b85c79bbb01463382ab709d07f2a234e909
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Oct 18 11:36:20 2017 -0700

    added full Richardson convergence test utility to save some of the manual labor of convergence tests

Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Convergence/RichardsonConvergenceTest.cpp

commit 9ebec95a8b3827742e07d1613583a57bf59ddfb0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 18 08:54:41 2017 -0700

    add inputs for regression only

Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt

commit f2d4f20fcec0236ffadc982a5fbe6279349fb684
Author: Max Katz <katz12@llnl.gov>
Date:   Wed Oct 18 04:31:28 2017 -0700

    Correctly handle the case with fully interior boxes

Src/Amr/AMReX_StateData.cpp

commit b12244f8897309d732bbfa2a996b5c08690f01fe
Author: Max Katz <katz12@llnl.gov>
Date:   Wed Oct 18 04:31:10 2017 -0700

    Insert sanity check: positive number of CUDA threads/blocks

Src/Base/AMReX_CUDA.F90

commit dbf11c9bb3d8200defae2c17a29e599bda2be913
Author: Max Katz <katz12@llnl.gov>
Date:   Wed Oct 18 03:46:56 2017 -0700

    Add CORAL EA systems at LLNL

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.llnl

commit fcd99f8270bdff91763fbbda12121af0f41e7168
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 17 18:08:39 2017 -0700

    MLMG: fix mask for compute residual

Src/Base/AMReX_BaseFab_nd.f90
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 9a567a316dbf49aea6452df7a9f0f7b569d6e6cb
Author: Max Katz <katz12@llnl.gov>
Date:   Tue Oct 17 17:49:17 2017 -0700

    Add a second sanity check on number of threads

Src/Base/AMReX_CUDA.F90

commit 9f5438a48ba2a5a8c01ebecd1b84ea157eb563f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 17 17:42:20 2017 -0700

    add a new function to compute masked inf norm

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.f90
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_Print.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 31db08adc4cc44015e3db8dea02236e41e471c93
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 17 16:33:58 2017 -0700

    added some working notes

Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp

commit a90c09d424e6b1059d772c5e2094d655e14e6906
Author: Max Katz <katz12@llnl.gov>
Date:   Tue Oct 17 15:48:18 2017 -0700

    Use the C++ CUDA error checker

Src/Base/AMReX_Device.cpp

commit e7035c31b874d30395cc738aaf9b29269bf2156b
Merge: 6cd14f429 a8fa411f2
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 17 15:47:35 2017 -0700

    Merge pull request #146 from AMReX-Codes/dtg_branch
    
    bringing convergence tool fixes over to dev branch

commit a8fa411f22d48e01e115f4539863b8c2c24e73a9
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 17 15:45:13 2017 -0700

    all the tools except for ComputeAmrNorms compile.   ComputeAmrNorms has no main.

Tools/C_util/Convergence/DiffSameDomainRefined.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Convergence/PltFileNormB.cpp

commit 19995b3461327d379a413c8cf009d0f6ef7ec360
Author: Max Katz <katz12@llnl.gov>
Date:   Tue Oct 17 15:44:42 2017 -0700

    Error check routines do not need to be on a single line

Src/Base/AMReX_Device.H

commit fd408c9bfd17f5aacc90f00e6022e57e347557d5
Author: Max Katz <katz12@llnl.gov>
Date:   Tue Oct 17 15:44:24 2017 -0700

    Add Spectrum MPI to list of known implementations

Tools/GNUMake/sites/Make.unknown

commit 6cd14f429ffc8b43f9c4241adb484865b060c29a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 17 14:11:03 2017 -0700

    MLMG: need to update coarse level solution bc

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 62c609f5c8ed1e2610d51611abb26424bb4c09e0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 17 13:44:51 2017 -0700

    more progress toward getting these tools working again.   On a bunch of them, the MultiFab declarations need to be reworked

Tools/C_util/Convergence/Add.cpp
Tools/C_util/Convergence/ComputeAmrDataNorms.H
Tools/C_util/Convergence/DiffFab.cpp
Tools/C_util/Convergence/DiffSameDomainRefined.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp
Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileNormB.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp

commit 689e694e9a8be90816c208b5059cd209b6409b7f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 17 12:58:17 2017 -0700

    take out wrong assertion

Src/Boundary/AMReX_YAFluxRegister.cpp

commit 187bef0f999bc85115f520374d71a87630a86220
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 17 12:41:27 2017 -0700

    Revert "tiling: make sure tile boxes are generally coarsenable"
    
    This reverts commit 616c5b59e8a4338147ba398a386833100c1da61d.

Src/Base/AMReX_FabArrayBase.cpp

commit 14f7e82b0f74f4030ac286cbe8efa38243e27249
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Oct 17 12:41:52 2017 -0700

    Add dest_comp argument to YAFluxRegister::Reflux

Src/Boundary/AMReX_YAFluxRegister.H
Src/Boundary/AMReX_YAFluxRegister.cpp

commit ebd5c2198b14fa5b17bfcfd2c634a6ba3a9a221b
Merge: a5215de5c a9e81e7b7
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 17 11:13:43 2017 -0700

    merging with dev to get convergence tools

commit a9e81e7b7b299070b86f59db720af6d1adef0710
Merge: 616c5b59e 738a1a696
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Oct 17 10:58:33 2017 -0700

    Merge pull request #143 from AMReX-Codes/migrate_Convergence_util
    
    Migrate convergence util

commit 616c5b59e8a4338147ba398a386833100c1da61d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 17 09:28:10 2017 -0700

    tiling: make sure tile boxes are generally coarsenable

Src/Base/AMReX_FabArrayBase.cpp

commit a5215de5c616bbec708585633d1cd95461d843f9
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Oct 16 14:19:05 2017 -0700

    MOL2nd order now seems to work even with AMR.  YAFluxRegister makes more sense in this context than FluxRegister.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp

commit 4551e3404a306fa4c8014d8c91a8830ba290b6d4
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Oct 16 12:00:45 2017 -0700

    added some debugging tools and I got MOL to work without AMR.   Still something off with AMR, however.

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugDump.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/main.cpp

commit 6eb1c642f02f44522a087dba62da2541ebc70bbf
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sun Oct 15 12:51:27 2017 -0700

    godunov version works fine.  MOL version needs work.

Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Make.Adv
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp

commit 2263a1b4685c3b5bb42fe0c679f77f9983e8b9ba
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Oct 14 21:39:37 2017 -0700

    couple of dimension-specific bug fixes

Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90

commit 0e6602b9fc4ea2097c250f49afaf8dadffef88ec
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Oct 14 21:36:49 2017 -0700

    bunch of bug fixes

Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Make.Adv.Diff
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90

commit 417a3c272be94b1c1a7beacb0a104b8f47d323c2
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Oct 13 20:54:47 2017 -0700

    changed adv diff  integrator to 2nd Order MOL.

Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90

commit 8997f302d77da01febbb11f867c3fba63abdd7e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 13 18:05:29 2017 -0700

    MLMG test: add more parameters

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit 4a9dc2e528583c28e567a61a5fff3f88895c7bed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 13 17:41:55 2017 -0700

    MLMG: fix data type

Src/LinearSolvers/MLMG/AMReX_MLMG.H

commit b0bd068ded9a880473b36f228570a29517a60b90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 13 17:36:04 2017 -0700

    MLMG: set cg parameters

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit b9edf16acb9fba677bd989665e182cd59cb5dc10
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 13 17:32:58 2017 -0700

    MLMG: fix cg tolerance

Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 5d0af86864f5a3723fe223aecc28a62a1e6d1b63
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 13 17:19:02 2017 -0700

    CG for MLMG

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H
Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/Make.package

commit bca731ab245f644a2ca3a9162037f3ae75ef838d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 13 14:14:34 2017 -0700

    add anonymous namespace aroung some functions in CGSolver

Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit aa3d3df67fd417072447752188f892d17d7e5c40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 13 12:16:40 2017 -0700

    MLLinOp::setMaxOrder

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 3348b9f66ac494c3185e1589f5e4d708bf3c0447
Merge: 04dbce1b0 50639530a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 13 14:54:16 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 04dbce1b025d91b575ea7c3bb90c6845d291d662
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 13 14:54:04 2017 -0700

    clarify comment.

Docs/AMReXUsersGuide/EB/EB.tex

commit b4e5e4a1cf729c4bd90a1ace83b512619e8cd756
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Oct 13 14:29:00 2017 -0700

    advection/diffusion (in Godunov mode) reproduces advection tutorial.

Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs
Tutorials/Amr/ScalarAdvectionDiffusion/README
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90

commit 50639530a7cedf3acc28990dfe3dd8641f07067b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 13 11:16:32 2017 -0700

    MLMG: bottomSolve

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit c281ee7826c8bf1ddbd81e707022a779ce756fd9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 13 11:19:33 2017 -0700

    handle low dimensionality in the neighbor particle finding.

Src/Particle/AMReX_NeighborParticlesI.H

commit 81f5dbe0fc2fdd31ca7a4245077a8ac282599ec1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 13 10:59:21 2017 -0700

    fix a couple more typos.

Docs/AMReXUsersGuide/EB/EB.tex

commit 1329352b58835d75ca3d8344a084669aa1ae3176
Merge: 357b28e65 a5fcb9fad
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 13 13:36:12 2017 -0400

    Merge branch 'development' into gpu

commit a5fcb9fad10d0a9351851d526fedb6f2fa2d7d69
Merge: 43b6f3a8f 310fb01ef
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 13 10:28:13 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 43b6f3a8f6cb2943c9bb4dc7eecc180935a4cff8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 13 10:27:57 2017 -0700

    fix minor formatting issue.

Docs/AMReXUsersGuide/EB/EB.tex

commit 310fb01efa72f75d48a850e285d19d5421f620f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 13 10:24:23 2017 -0700

    MLMG: add more set methods

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/main.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit 357b28e65463535b15a6be7892265eea070b8412
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 13 13:14:59 2017 -0400

    Add sanity check on total number of CUDA threads

Src/Base/AMReX_CUDA.F90

commit 55e641dbbd8551976a5a99499f0633a91e381846
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Oct 13 10:14:11 2017 -0700

    fix typo in EB docs.

Docs/AMReXUsersGuide/EB/EB.tex

commit cf32ab2d0c5f28da240b7e0b4261763b7b2c4827
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 13 13:06:40 2017 -0400

    Deal appropriately with varying box sizes in FillBoundary

Src/Amr/AMReX_StateData.cpp

commit 244ed5b5f06ac8f298fdf238d8fcdc272ce92b05
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 12 18:39:44 2017 -0700

    Changes to be compatible with Sam's latest changes to HPGMG for Nyx.

Src/Extern/hpgmg/BL_HPGMG.H
Tools/GNUMake/packages/Make.hpgmg

commit d9035a577093b617376fbe175d195966c3486af3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 12 17:10:53 2017 -0700

    MLMG test: add some runtime parameters

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/main.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit 2f3a3e1fa4eb90eedb0f099a64aae4ad119c8233
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 12 16:37:13 2017 -0700

    MLMG: mgCycle

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 117ba8be282ab1246fb00772e5ca4601d592c7ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 12 15:09:16 2017 -0700

    MLMG: up the amr v-cycle

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 9636228613e36d39ae00d385b4dbc467a36df523
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 12 13:35:32 2017 -0700

    MLMG: save BndryRegister used in updating bc

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit cc68406f85a08f08f911e3908fbc0ededa669ec0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 12 19:41:58 2017 -0400

    Set a minimum threadblock size for StateData::FillBoundary

Src/Amr/AMReX_StateData.cpp

commit c49ab6bb2822aedfe431b14bd166dcfd2cade63b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 12 19:12:19 2017 -0400

    Sync threads in between BC fill dimensions

Src/Base/AMReX_filcc_mod.F90

commit 56cf18cf099bc47479beb3692cd7ed61bf34eaff
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 12 19:11:55 2017 -0400

    Add capability to set minimum number of CUDA threads

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit fbda66160467ecd75051ed8d5f6a2c1d222b69a9
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Oct 12 15:34:36 2017 -0700

    added advection-(explicit)diffusion example.   Just starting to get this organized.

Tutorials/Amr/ScalarAdvectionDiffusion/CMakeLists.txt
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Make.Adv
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs.tracers
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/probin
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/Prob.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/face_velocity_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/probdata.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/probin
Tutorials/Amr/ScalarAdvectionDiffusion/README
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H
Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/LevelBldAdv.cpp
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/slope_2d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/slope_3d.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Adv_nd.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Make.package
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Tagging_nd.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/tagging_params.f90
Tutorials/Amr/ScalarAdvectionDiffusion/Source/main.cpp

commit ccc4acfa770ed9b687244a4120e87f9718f1694f
Merge: 832162f68 6bd9f1a2a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 12 15:26:45 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 832162f686d0fdf8f344a7fb2a706d1fedf1c429
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 12 15:26:33 2017 -0700

    avoid allocating memory for temporaries in threaded regions.

Src/Particle/AMReX_NeighborParticlesI.H

commit 6bd9f1a2a4bac46c452d818f4b04dfcacdd90f5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 12 13:13:39 2017 -0700

    MLMG: updateSolBC

Src/Base/AMReX_IntVect.H
Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_MacBndry.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit c6b08523bc8901cda26860d1374d4b31532692a7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 12 12:42:43 2017 -0700

    constructing a ParIter with an MFItInfo should not imply tiling=true.

Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParIterI.H

commit 0dfa00600f5d0f1fe8c7fcab5e801e1efe4f81f1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 12 11:07:48 2017 -0700

    use async MPI communication in the particle neighbor fill

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 957aacfc3c6e41cdcf7381c71f0b24a843aaa606
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 12 11:07:14 2017 -0700

    move the duplicate helper function to AMReX_Vector.H so it can be used elsewhere as well.

Src/Base/AMReX_Vector.H

commit 2d6a3290751c3a34667c3f0aca38bf55218d29b3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 12 09:59:03 2017 -0700

    std::vector -> amrex::Vector

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit d56131a803f1a00a9dba1de9b6b845fc580818eb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 12 09:56:41 2017 -0700

    encapsulate remove duplicates from a vector into a function.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit a040ce97258312011566652dbed951f92bb6d40b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 12 08:58:51 2017 -0700

    MLMG: clean up the interface and fix dx in reflux

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit a5b7eb48635a6c54079b44fa0d9b9def91a80325
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 12 06:20:19 2017 -0400

    Wrap CUDA launch in its own block

Src/Base/AMReX_BLFort.H

commit 6f171b160b11e51ac813b24c4edac1a0e6287ffd
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 12 04:31:30 2017 -0400

    Unify on a single filccn

Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90
Src/Base/AMReX_filcc_mod.F90

commit 317f43b4f05b8493fd02270c3816da11d0516577
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 12 03:58:44 2017 -0400

    Decrease default number of max CUDA threads

Src/Base/AMReX_CUDA.F90
Tools/GNUMake/Make.defs

commit 568dfbb218402f8a6f7a94cb0db35f7e2a62e7d9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 12 03:46:43 2017 -0400

    Update heat equation GPU test

Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90

commit 9990f28a0d4a13fc885d44b7b49d0569b057932f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 12 03:38:56 2017 -0400

    Remove SUBROUTINE from macro names

Src/Base/AMReX_BaseFab_nd.F90
Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90
Src/Base/AMReX_filcc_mod.F90
Src/Base/AMReX_fort_mod.F90
Tools/GNUMake/Make.defs

commit 2d779c24a32f76c2498b81a8c147088d80f24bf0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 12 03:31:02 2017 -0400

    Use device subroutine macro

Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90
Src/Base/AMReX_fort_mod.F90
Tools/GNUMake/Make.defs

commit 95b012686d5f6f9d2822014c28104b8d2ce0026c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 12 03:22:39 2017 -0400

    Call filcc directly from C++

Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_filcc_f.H
Src/Base/AMReX_filcc_mod.F90

commit 007af5f0dcb16c4c723f66922992039a22865324
Merge: a6438f466 c2cae79dd
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Oct 12 00:19:20 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a6438f466d4b0fa6977eaffa76044f045df6febf
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Oct 12 00:19:08 2017 -0700

    add SMC code

Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/GNUmakefile
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/LiDryer.c
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/Make.package
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC.H
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC.cpp
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC_F.H
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC_advance.cpp
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC_init.cpp
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC_io.cpp
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/chemistry_module.f90
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/derivative_stencil.f90
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/init_data.f90
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/inputs_SMC
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/kernels.f90
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/main.cpp
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/make_plot.f90
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/transport_properties.f90
Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/variables.f90

commit c2cae79ddb6869525f4777e779cc89b056224a5e
Merge: 92caaad3b 8bbdbb188
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Oct 11 16:45:38 2017 -0700

    Merge pull request #145 from bcfriesen/pmi_fixes
    
    PMI: change computation of unique groups/chassis/slots from unordered_set to vector

commit 8bbdbb188f49195b4c7baed0d279b8d786f9469e
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Oct 11 16:39:55 2017 -0700

    PMI: change computation of unique groups/chassis/slots from unordered_set to vector
    
    This has better performance for large arrays.

Src/Base/AMReX_ParallelDescriptor.cpp

commit 92caaad3bbffb9e9be187ab5ced736c5c1083cbd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 11 16:22:47 2017 -0700

    MLMG: prolongation of correction from coarse to fine amr level

Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/GNUmakefile

commit bf6f597a523d57a7fbcba424bcf4118f0f672817
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 11 15:35:38 2017 -0700

    MLMG: Reflux

Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 2d36421cc8a3a899ce8dcf0b55036d1fcb6e8e00
Merge: 76cac72c0 3057a29ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 11 15:10:35 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 76cac72c03a072b3596c14650cabea25b13062d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 11 15:09:10 2017 -0700

    MLMG: coarse part of reflux

Src/Boundary/AMReX_YAFluxRegister.H
Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 3057a29baba50b5fd2825b19fea5213d29505a89
Merge: 4b3f2fe17 a972c2553
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Oct 11 13:59:55 2017 -0700

    Merge pull request #144 from bcfriesen/add_pmi_support
    
    Base: add support for querying Process Management Interface (PMI)

commit a972c2553b921d3a082d70b5b12f482479a9694c
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Oct 11 13:36:07 2017 -0700

    Base: print simple header to STDOUT before PMI statistics

Src/Base/AMReX_ParallelDescriptor.cpp

commit 01a0eff33beefedd8b2ed18eaef91fe1db596c4a
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Oct 11 13:35:53 2017 -0700

    Base: "PMI" -> "AMREX_PMI"

Src/Base/AMReX.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Tools/GNUMake/Make.defs

commit 4b3f2fe17bb1c98d07862906772adfc3f2ac1e9a
Author: kngott <kngott@lbl.gov>
Date:   Wed Oct 11 13:19:38 2017 -0700

    Adjustments to test output and general cleanup of MoveAllFabs.

Src/Base/AMReX_FabArray.H

commit 9ab7fe886949599e65f9df8969bedd94ca53acbf
Author: kngott <kngott@lbl.gov>
Date:   Wed Oct 11 13:10:18 2017 -0700

    Change AddCompsToProc in FabSet to properly allocate FluxRegister FabArrays

Src/Boundary/AMReX_FabSet.H

commit 4bf5d960e8b54515b40fa5a7f86e19bc67b04d88
Author: kngott <kngott@lbl.gov>
Date:   Wed Oct 11 13:07:46 2017 -0700

    Rewrite a comment from Array to Vector

Src/Amr/AMReX_Amr.H

commit b6073af307442cac501c0370e1baac83e7d41c68
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Oct 6 13:17:33 2017 -0700

    Base: add support for querying Process Management Interface (PMI)
    
    PMI is available on Cray systems and provides information about the topology of
    the job on the network. One can use this information to apply optimizations at
    run time which exploit higher bandwidth, lower-latency connections between
    particular groups of processes on the network.
    
    PMI support is disabled by default, and can be activated by setting
    USE_PMI=TRUE in the makefile.

Src/Base/AMReX.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Tools/GNUMake/Make.defs

commit c761748c12167e88ac21c1206b0df3c113b734f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 11 12:25:29 2017 -0700

    move YAFluxRegister to Boundary/

Src/AmrCore/Make.package
Src/Boundary/AMReX_YAFluxRegister.H
Src/Boundary/AMReX_YAFluxRegister.cpp
Src/Boundary/AMReX_YAFluxRegister_1d.F90
Src/Boundary/AMReX_YAFluxRegister_2d.F90
Src/Boundary/AMReX_YAFluxRegister_3d.F90
Src/Boundary/AMReX_YAFluxRegister_F.H
Src/Boundary/AMReX_YAFluxRegister_nd.F90
Src/Boundary/CMakeLists.txt
Src/Boundary/Make.package
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/write_plotfile.cpp

commit 7889d091d00817d3223de9d56198f887a5808f3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 11 10:37:39 2017 -0700

    MLMG: smooth

Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 36004bb31b4a7b5aaeeba4168eccdc406b8de66f
Merge: 1e51f8610 1596e8c24
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 11 10:23:07 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 1596e8c248726c18c19537690e011adf7d9ec64f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 11 09:36:38 2017 -0700

    MLMG: finish applyBC

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp

commit 86599d1e04b90ca04848dc203c8cc3b1257504ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 11 07:46:24 2017 -0700

    Array is used by Fortran BoxLib and in that case cannot include AMReX_SPACE.H

Src/Base/AMReX_Array.H

commit ac6a8b5685031bc456311d121ce30eab2164a282
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 10 16:55:52 2017 -0700

    MLMG: applyBC WIP

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_LayoutData.H
Src/Boundary/AMReX_BndryData.H
Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_MacBndry.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/GNUmakefile
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit 1e51f8610899ba8eb721a29d915cabbdcf752994
Merge: 038539afd fcdefa3f2
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 10 15:03:46 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit b0112558b9e52a0fe81e9be7c7c7ee5acd3ee616
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 10 13:31:17 2017 -0700

    MLMG: wip

Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit 1a352f817fa16e7d881785e35433da9ddadf8842
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Oct 10 15:59:35 2017 -0400

    Fix rank <-> GPU identification for MPS case

Src/Base/AMReX_Device.cpp

commit fcdefa3f29d83d0f2a92c649b3d92b4a0df5f180
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 10 12:41:26 2017 -0700

    MLMG: add A dot x

Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90
Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/Make.package

commit 9e5efc7b8e3086988c387d834e0193b6ea7df30d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 10 11:06:45 2017 -0700

    add a few virtual function stubs to MLLinOp

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit acfe5325ec8009b6cbec25ff1bd0e2af41ca5de4
Merge: 57b41fc69 58e4fd369
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 10 10:31:15 2017 -0700

    Merge branch 'weiqun/mlmg' into development

commit 58e4fd369ef05d76f1354ddce14236dcf1b6ca1b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 10 10:30:35 2017 -0700

    MLMG: WIP

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp

commit bad73ccc91f23a36da4bb49598136c8c8a7d09cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 9 17:23:58 2017 -0700

    WIP

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/main.cpp

commit 57b41fc69d53db2ab4ca371e187415b8ccdeae12
Merge: ae90dbfd4 ec3110776
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Oct 9 16:36:50 2017 -0700

    fixing merge conflict

commit 5e53b9f733bd31af429f355731d9bbeb99dcbe0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 8 12:06:21 2017 -0700

    MLMG: notes

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit 14bbb92b548bab77c9ec9f9545177b68b7ad843e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Oct 8 06:39:10 2017 -0400

    Fix a compile fail without MPI

Src/Base/AMReX_Device.cpp

commit a55517b78527f0414d940fd4e14ed291d600b04a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Oct 8 01:51:32 2017 -0400

    Use 512 threads per block
    
    Note that for Pascal, this means you need to limit the number of
    registers per function to 128.

Src/Base/AMReX_CUDA.F90

commit 04e77cc5d5db4d90cc960d512944728923e1d154
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Oct 8 01:19:50 2017 -0400

    Do not tile threadblock size; this hurts performance

Src/Base/AMReX_CUDA.F90

commit 1897612dd67748378d6fc1d980dd683edc23678c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Oct 7 22:00:51 2017 -0400

    Move the loop over components to the top level

Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90

commit d914d5f7afced9efb110596863ec1d5da3a81747
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Oct 7 21:02:32 2017 -0400

    filccn loops over all n variables

Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90
Src/Base/AMReX_filcc_mod.F90

commit d67523c9358a704f04526144ad8e83aa613dc251
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 7 15:48:43 2017 -0700

    WIP: MLMG

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/main.cpp

commit 36520d83b07f435a81b9b24b15ac84b5deea881b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 7 13:30:40 2017 -0700

    MLMG: prepare for solve

Src/Base/AMReX_Array.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit d3fcbb948196f1d3eed0708c159898e0ba3c20b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 6 17:12:30 2017 -0700

    MLMG::solve WIP

Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/main.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit d98329a3bedf1513a95db42471d851c4143673f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 6 16:49:18 2017 -0700

    MLMG constructor

Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit e24efe2f04270851132dfefe908d0e11719f6469
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 6 16:36:51 2017 -0700

    set ABecLaplacian coefficients

Src/Base/AMReX_MultiFabUtil.cpp
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit 96c3a8cd7eb50a8aac07e426966c9c2811a86c39
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 6 15:08:44 2017 -0700

    MLLinOp and MLABecLaplacian constructors

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Tests/LinearSolvers/MLMG/main.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit 038539afd3b72d98099235c45dff2c6fda61905b
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 6 14:41:02 2017 -0700

    remove debug diagnostic.

Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp

commit ea61045fe1534a75304786b6b60f87d6e1bd477b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 6 12:35:15 2017 -0700

    Array --> Vector in mlmg test

Tests/LinearSolvers/MLMG/init_prob.cpp
Tests/LinearSolvers/MLMG/main.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp
Tests/LinearSolvers/MLMG/write_plotfile.cpp

commit 3d8be64878ab61817a88ddea2381be417aca6a09
Merge: e7c5b1dcf ec3110776
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 6 12:32:19 2017 -0700

    Merge branch 'development' into weiqun/mlmg
    
    Conflicts:
            Src/Base/AMReX_Array.H

commit 738a1a696824d80e16f9110368fbe917b229e961
Merge: 7feb1c361 ec3110776
Author: rgrout <rgrout@users.noreply.github.com>
Date:   Fri Oct 6 13:20:28 2017 -0600

    Merge branch 'development' into migrate_Convergence_util

commit 7feb1c361398ac55b1cbef73289e5f920c3bcb5c
Author: Ray Grout <ray.grout@nrel.gov>
Date:   Fri Oct 6 09:30:05 2017 -0700

    Updates to track AMReX development

Tools/C_util/Convergence/ComputeAmrDataNorms.H
Tools/C_util/Convergence/ComputeAmrDataNorms.cpp
Tools/C_util/Convergence/DiffSameGrid2.cpp
Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Convergence/Make.package
Tools/C_util/WritePlotFile.H
Tools/C_util/WritePlotFile.cpp

commit ec31107762d7ed12e82d49d6a0d7d1c4cb8064a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 6 08:53:01 2017 -0700

    Array --> Vector in Tools

Tools/AMRProfParser/TestCodes/BLProfCallTimes.cpp
Tools/AMRProfParser/TestCodes/Pieces.cpp
Tools/AMRProfParser/TestCodes/SendTest0.cpp
Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp
Tools/C_util/Convergence/ComputeAmrDataNorms.H
Tools/C_util/Convergence/ComputeAmrDataNorms.cpp
Tools/C_util/Convergence/DiffSameDomainRefined.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGrid2.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileNormB.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp
Tools/C_util/Statistics/ComputeAmrDataStat.H
Tools/C_util/Statistics/ComputeAmrDataStat.cpp
Tools/C_util/Statistics/PltFileFluxAve.H
Tools/C_util/Statistics/PltFileFluxAve.cpp
Tools/C_util/Statistics/PltFileList.cpp
Tools/C_util/Statistics/PltFileStat.cpp
Tools/C_util/Statistics/PltFileXAve.H
Tools/C_util/Statistics/PltFileXAve.cpp
Tools/C_util/ViewMF/mfMinMax.cpp
Tools/C_util/WritePlotFile.H
Tools/C_util/WritePlotFile.cpp
Tools/C_util/dbgTools/crsGrids.cpp
Tools/C_util/dbgTools/intersectGrids.cpp

commit 68544a54fa5cbe5fcf7c62e271d421f0ee15c226
Merge: a274becd1 945759d46
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Oct 6 01:15:39 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a274becd1542d5f383c8212a7c67609b477fb015
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Oct 6 01:15:30 2017 -0700

    fix a memory leak bug

Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H

commit e2d9950f1860ad21bebedfef5087d13773aaf1e0
Merge: 669a6a9ba 945759d46
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 6 03:11:53 2017 -0400

    Merge branch 'development' into gpu

commit 669a6a9badc2a3ba62fc3a5a9ee669a1557395e9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Oct 6 02:07:33 2017 -0400

    Give simplified initial output if device is not verbose

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 537f635792e5e264fbff6fd72f60905b343c8395
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 5 22:01:58 2017 -0400

    Add device.verbose output parameter

Src/Base/AMReX.cpp
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 945759d46ba1bd3a0e00b1b125fc703966afad5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 17:48:51 2017 -0700

    update CHANGES

CHANGES

commit faa0d57083c3abee8c1b659b8fc90b793cc063dc
Merge: d6785a628 bb60bc275
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Oct 5 17:39:25 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d6785a6281e56a28811ba62cb305b39a769f3b2d
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Oct 5 17:39:04 2017 -0700

    grant friend access to MFGraph and Action classes

Src/Base/AMReX_FabArray.H

commit e65447ec7130090d5045e4d2cd5da1363d4888f7
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Oct 5 17:36:45 2017 -0700

    runtime support for AMFIter

Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H
Src/AmrTask/AMFIter/AMReX_AsyncMFIter.cpp
Src/AmrTask/AMFIter/AMReX_Connections.H
Src/AmrTask/AMFIter/Makefile
Src/AmrTask/graph/AMReX_AbstractTask.H
Src/AmrTask/graph/AMReX_TaskGraph.H
Src/AmrTask/rts_impls/MPI_Generic/Makefile
Src/AmrTask/rts_impls/MPI_Generic/rts.C
Src/AmrTask/tutorials/MiniApps/HeatEquation/advance.cpp
Src/AmrTask/tutorials/MiniApps/HeatEquation/inputs_3d

commit bb60bc275816f0ad98a63f0426c8aff2f82251d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 17:35:05 2017 -0700

    Array --> Vector in Docs

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/Boundary/Boundary.tex
Docs/AMReXUsersGuide/EB/EB.tex
Docs/AMReXUsersGuide/Particle/Particle.tex
Docs/Readme.sidecars
Tools/Migration/amrex_array_to_vector.sh

commit f19ceb6d5d36ad99b55c5ae8aadfb4e8a62bb59f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 17:29:43 2017 -0700

    a script for Array --> Vector

Tools/Migration/amrex_array_to_vector.sh

commit 67db2c14fcf8daa675bc44d26efbe608007e38ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 17:27:21 2017 -0700

    Array --> Vector in Tutorials

Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Tutorials/Basic/HeatEquation_EX1_C/main.cpp
Tutorials/Basic/HeatEquation_EX2_C/advance.cpp
Tutorials/Basic/HeatEquation_EX2_C/main.cpp
Tutorials/Basic/HeatEquation_EX2_C/myfunc.H
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_init_eb.cpp
Tutorials/EB/CNS/Source/CNS_setup.cpp
Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H
Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp
Tutorials/Particles/ElectrostaticPIC/main.cpp
Tutorials/Particles/LoadBalance/main.cpp

commit 8dac4ff5ca7c480c38d9f602bef37150276ccb4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 17:26:31 2017 -0700

    Array --> Vector in Tests

Tests/BBIOBenchmark/BBIOTest.cpp
Tests/C_BaseLib/BcastClasses/BcastClasses.cpp
Tests/C_BaseLib/tFB.cpp
Tests/C_BaseLib/tMF.cpp
Tests/C_BaseLib/tParmParse.cpp
Tests/C_BaseLib/tProfiler.cpp
Tests/C_BaseLib/tRABcast.cpp
Tests/EBAMRTools/regression/aggpwlfpTest.cpp
Tests/EBAMRTools/regression/divergenceOpTest.cpp
Tests/EBAMRTools/regression/ebCoarseAveTest.cpp
Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp
Tests/EBAMRTools/regression/ebFineInterpTest.cpp
Tests/EBAMRTools/regression/fluxRegTest.cpp
Tests/EBAMRTools/regression/gradientOpTest.cpp
Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp
Tests/EBAMRTools/regression/simpleMeshRefine.cpp
Tests/FillBoundaryComparison/main.cpp
Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp
Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp
Tests/GeometryShop/flatPlate/flatPlateTest.cpp
Tests/GeometryShop/ramp/main.cpp
Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp
Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp
Tests/GeometryShop/vofStructures/umapTest.cpp
Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp
Tests/LinearSolvers/C_TensorMG/testVI.cpp
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp
Tests/LinearSolvers/ComparisonTest/compute_norm.cpp
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp
Tests/LinearSolvers/ComparisonTest/writePlotFile.H
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp
Tests/Particles/AssignMultiLevelDensity/main.cpp
Tests/Particles/ParticleIterator/main.cpp
Tests/Particles/main.cpp

commit 205418320396c9d6172b9acfe08c2c5bc2f4cf2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 17:25:01 2017 -0700

    Array --> Vector in OldTutorials

OldTutorials/DataServicesTest0/DataServicesTest0.cpp
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp
OldTutorials/GettingStarted_C/main.cpp
OldTutorials/HeatEquation_EX2_C/main.cpp
OldTutorials/MeshRefinement/MyAmr.H
OldTutorials/MeshRefinement/MyAmr.cpp
OldTutorials/MeshRefinement/main.cpp
OldTutorials/MultiColor_C/main.cpp
OldTutorials/MultiFabTests_C/GridMoveTest.cpp
OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp
OldTutorials/MultiFabTests_C/MultiFabFillBoundary.cpp
OldTutorials/MultiFabTests_C/MultiFabReadWrite.cpp
OldTutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp
OldTutorials/MultiGrid_C/main.cpp
OldTutorials/PGAS_HEAT/main.cpp
OldTutorials/PIC_C/single_level.cpp
OldTutorials/PIC_C/solve_for_accel.cpp
OldTutorials/PIC_C/solve_with_f90.cpp
OldTutorials/PIC_C/two_level.cpp
OldTutorials/Sidecar_EX1/DestMFTest.cpp
OldTutorials/Sidecar_EX1/NSidecarsTest.cpp
OldTutorials/Sidecar_EX1/SidecarResizeTest.cpp
OldTutorials/Sidecar_EX1/TestRankSets.cpp
OldTutorials/Tiling_Heat_C/main.cpp
OldTutorials/TwoGrid_PIC_C/main.cpp
OldTutorials/TwoGrid_PIC_C/solve_for_accel.cpp
OldTutorials/TwoGrid_PIC_C/solve_with_f90.cpp
OldTutorials/TwoGrid_PIC_C/split_boxes.cpp
OldTutorials/libamrex_C/MyAmr.H
OldTutorials/libamrex_C/MyAmr.cpp
OldTutorials/libamrex_C/main.cpp

commit c02d0ca36b8e247696f7c635acd9b33a28bc88bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 17:21:44 2017 -0700

    Array --> Vector in MiniApps

MiniApps/PGAS_SMC/SMC.H
MiniApps/PGAS_SMC/SMC.cpp
MiniApps/PGAS_SMC/SMC_init.cpp

commit 5fecfa6e986de5dbfbf0c26ec39c504b4acd4a04
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 16:20:21 2017 -0700

    Array --> Vector in Src/

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_Derive.H
Src/Amr/AMReX_Derive.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StateDescriptor.H
Src/Amr/AMReX_StateDescriptor.cpp
Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_AmrParGDB.H
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_ErrorList.H
Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/AmrCore/AMReX_YAFluxRegister.H
Src/AmrCore/AMReX_YAFluxRegister.cpp
Src/AmrTask/tutorials/MiniApps/HeatEquation/main.cpp
Src/AmrTask/tutorials/MiniApps/HeatEquation/physbc.cpp
Src/Base/AMReX_Array.H
Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCRec.cpp
Src/Base/AMReX_BCUtil.H
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxDomain.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabConv.H
Src/Base/AMReX_FabConv.cpp
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp
Src/Base/AMReX_LayoutData.H
Src/Base/AMReX_MFCopyDescriptor.H
Src/Base/AMReX_MFCopyDescriptor.cpp
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_NFiles.H
Src/Base/AMReX_NFiles.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ParmParse.H
Src/Base/AMReX_ParmParse.cpp
Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_TinyProfiler.cpp
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp
Src/Base/AMReX_iMultiFab.cpp
Src/Base/AMReX_parmparse_fi.cpp
Src/Boundary/AMReX_BndryData.H
Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_MacBndry.cpp
Src/Boundary/AMReX_MultiMask.cpp
Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBInterpolater.H
Src/EB/AMReX_EBInterpolater.cpp
Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H
Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp
Src/EBAMRTools/AMReX_DivergenceOp.cpp
Src/EBAMRTools/AMReX_EBCFInterp.H
Src/EBAMRTools/AMReX_EBCFInterp.cpp
Src/EBAMRTools/AMReX_EBCoarseAverage.cpp
Src/EBAMRTools/AMReX_EBFineInterp.H
Src/EBAMRTools/AMReX_EBFineInterp.cpp
Src/EBAMRTools/AMReX_EBLevelDataOps.H
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Src/EBAMRTools/AMReX_GradientOp.H
Src/EBAMRTools/AMReX_GradientOp.cpp
Src/EBAMRTools/AMReX_MeshRefine.H
Src/EBAMRTools/AMReX_MeshRefine.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/ProfParser/AMReX_BLProfStats.H
Src/Extern/ProfParser/AMReX_BLProfStats.cpp
Src/Extern/ProfParser/AMReX_BLProfUtilities.H
Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp
Src/Extern/ProfParser/AMReX_BLWritePlotFile.H
Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp
Src/Extern/ProfParser/AMReX_CommProfStats.H
Src/Extern/ProfParser/AMReX_CommProfStats.cpp
Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp
Src/Extern/ProfParser/AMReX_RegionsProfStats.H
Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp
Src/Extern/amrdata/AMReX_AmrData.H
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/Extern/amrdata/AMReX_DataServices.H
Src/Extern/amrdata/AMReX_DataServices.cpp
Src/Extern/amrdata/AMReX_XYPlotDataList.H
Src/Extern/amrdata/AMReX_XYPlotDataList.cpp
Src/F_BaseLib/MultiFab_C_F.cpp
Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp
Src/F_Interfaces/Base/AMReX_distromap_fi.cpp
Src/F_Interfaces/Base/AMReX_init_fi.cpp
Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp
Src/F_Interfaces/Octree/AMReX_octree_fi.cpp
Src/GeometryShop/AMReX_AggStencil.H
Src/GeometryShop/AMReX_AggStencilI.H
Src/GeometryShop/AMReX_AllRegularService.H
Src/GeometryShop/AMReX_AllRegularService.cpp
Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_BaseEBCellFABI.H
Src/GeometryShop/AMReX_BaseEBFaceFAB.H
Src/GeometryShop/AMReX_BaseEBFaceFABI.H
Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBArith.cpp
Src/GeometryShop/AMReX_EBCellFAB.cpp
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBDebugOut.H
Src/GeometryShop/AMReX_EBDebugOut.cpp
Src/GeometryShop/AMReX_EBFaceFAB.cpp
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISBox.H
Src/GeometryShop/AMReX_EBISBox.cpp
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp
Src/GeometryShop/AMReX_FabArrayIO.H
Src/GeometryShop/AMReX_FaceIterator.H
Src/GeometryShop/AMReX_FaceIterator.cpp
Src/GeometryShop/AMReX_FlatPlateGeom.H
Src/GeometryShop/AMReX_FlatPlateGeom.cpp
Src/GeometryShop/AMReX_GeometryService.H
Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_GraphNode.H
Src/GeometryShop/AMReX_GraphNode.cpp
Src/GeometryShop/AMReX_IntVectSet.H
Src/GeometryShop/AMReX_IntVectSet.cpp
Src/GeometryShop/AMReX_IntersectionIF.H
Src/GeometryShop/AMReX_IntersectionIF.cpp
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_IrregNode.cpp
Src/GeometryShop/AMReX_LSquares.H
Src/GeometryShop/AMReX_LSquares.cpp
Src/GeometryShop/AMReX_Moments.H
Src/GeometryShop/AMReX_Moments.cpp
Src/GeometryShop/AMReX_PolyGeom.H
Src/GeometryShop/AMReX_PolyGeom.cpp
Src/GeometryShop/AMReX_PolynomialIF.H
Src/GeometryShop/AMReX_PolynomialIF.cpp
Src/GeometryShop/AMReX_RedistStencil.cpp
Src/GeometryShop/AMReX_SlabService.H
Src/GeometryShop/AMReX_SlabService.cpp
Src/GeometryShop/AMReX_Stencils.H
Src/GeometryShop/AMReX_UnionIF.H
Src/GeometryShop/AMReX_UnionIF.cpp
Src/GeometryShop/AMReX_VoFIterator.H
Src/GeometryShop/AMReX_VoFIterator.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp
Src/Particle/AMReX_LoadBalanceKD.H
Src/Particle/AMReX_LoadBalanceKD.cpp
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_ParGDB.H
Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit dd050be633bce59c18e65e24e39c6e6a0023c8aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 16:12:14 2017 -0700

    include AMReX_Vector.H in addition to AMReX_Array.H

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateDescriptor.H
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_Cluster.H
Src/AmrCore/AMReX_ErrorList.H
Src/AmrCore/AMReX_TagBox.H
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_Box.H
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabConv.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_Utility.H
Src/Base/AMReX_parmparse_fi.cpp
Src/EB/AMReX_EBMultiFabUtil.H
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Src/Extern/ProfParser/AMReX_BLProfUtilities.H
Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp
Src/Extern/ProfParser/AMReX_CommProfStats.H
Src/Extern/ProfParser/AMReX_RegionsProfStats.H
Src/Extern/amrdata/AMReX_AmrData.H
Src/Extern/amrdata/AMReX_DataServices.H
Src/Extern/amrdata/AMReX_XYPlotDataList.H
Src/F_Interfaces/Base/AMReX_init_fi.cpp
Src/F_Interfaces/Octree/AMReX_octree_fi.cpp
Src/GeometryShop/AMReX_IntersectionIF.H
Src/GeometryShop/AMReX_LSquares.H
Src/GeometryShop/AMReX_Moments.H
Src/GeometryShop/AMReX_PolyGeom.H
Src/GeometryShop/AMReX_SlabService.H
Src/GeometryShop/AMReX_UnionIF.H
Src/GeometryShop/AMReX_UnionIF.cpp
Src/GeometryShop/AMReX_VoFIterator.H
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H
Src/Particle/AMReX_ParGDB.H
Src/Particle/AMReX_Particles.H

commit e7c5b1dcf8998f9b819363153bc7cbf6b5703ccf
Merge: 94a465e2f 5a6178be9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 15:57:43 2017 -0700

    Merge branch 'development' into weiqun/mlmg

commit 5a6178be9654b662d3bd30244e28ee406e89d501
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 15:57:14 2017 -0700

    add amrex::Vector

Src/Base/AMReX_Vector.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 94a465e2f83782694c950dfa9eafb79b3e3d27bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 15:47:48 2017 -0700

    MLMG test: wip

Tests/LinearSolvers/MLMG/Make.package
Tests/LinearSolvers/MLMG/init_prob.cpp
Tests/LinearSolvers/MLMG/main.cpp
Tests/LinearSolvers/MLMG/prob_par.H
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp

commit b306d7d96d1447adc1e726b1323269d4002deaf7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 14:42:03 2017 -0700

    set up a test problem for MLMG

Src/Base/AMReX_Array.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Tests/LinearSolvers/MLMG/GNUmakefile
Tests/LinearSolvers/MLMG/Make.package
Tests/LinearSolvers/MLMG/fort.H
Tests/LinearSolvers/MLMG/fort_3d.F90
Tests/LinearSolvers/MLMG/init_prob.cpp
Tests/LinearSolvers/MLMG/main.cpp
Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp
Tests/LinearSolvers/MLMG/write_plotfile.cpp

commit dc1e602b560ecfeb825da5b2607445a9b203c442
Merge: 85d76e883 cbb336a40
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Oct 5 11:21:41 2017 -0700

    Merge branch 'development' into mr-cmake

commit cbb336a4012b027b75bd8b76aa5a6b3576e56453
Merge: 36ac652b6 3441bfde2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Oct 5 10:44:24 2017 -0700

    Merge pull request #142 from zingale/development
    
    sync up with fcompare

commit 36ac652b627d61050f7a694c8981996e194c624a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Oct 5 10:22:50 2017 -0700

    update changelog

CHANGES

commit bd0179deb38c4943ee6d2080e822de0aa75e4966
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 5 10:20:33 2017 -0700

    start MLMG

Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H
Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp
Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp
Src/LinearSolvers/MLMG/AMReX_MLMG.H
Src/LinearSolvers/MLMG/AMReX_MLMG.cpp
Src/LinearSolvers/MLMG/Make.package
Tests/LinearSolvers/MLMG/GNUmakefile
Tests/LinearSolvers/MLMG/Make.package
Tests/LinearSolvers/MLMG/main.cpp

commit d6df9c293b057db4e473e3785372d40574f77c2f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 5 05:01:55 2017 -0400

    Fix an error testing against a possibly empty vector

Src/Base/AMReX_MFIter.cpp

commit d1722ed0697e437609bc910eb06faa3351c5c166
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 5 05:01:33 2017 -0400

    Allow for multi-node CPU<->GPU mappings

Src/Base/AMReX_Device.cpp

commit 3531a2da499f929cc620fc766e10c564e8711ee0
Merge: d7ca2bc19 74aa06398
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Thu Oct 5 01:38:33 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 85e3ea22d2ff90973862621d84e4af9cee739585
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Oct 5 02:10:54 2017 -0400

    Use a distinct (non-coalesced) memory arena for FabArray

Src/Base/AMReX_Arena.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 74aa06398304e0f2cf71cfeb9d1e1c6c3b61cab4
Merge: 7a060dfbd 95ed12916
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Oct 4 18:32:57 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 7a060dfbd23fdd3ed7c2a44916e50ecd4c97104c
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Oct 4 18:31:48 2017 -0700

    add sort=.false. to the boxarray constructor for the diff multifab
    
    it fixes problems with this utility when the input plotfile boxarray are not in the "sorted" order

Tools/Postprocessing/F_Src/fcompare.f90

commit 3441bfde27d002247cd8fc96231d377430d50cff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 4 20:43:08 2017 -0400

    sync up with fcompare
    
    you now don't need to use --infile1 and --infile2, just list the
    plot files after the command
    
    the 2 features it doesn't do that fcompare does is compare ghost
    cells (not sure if it makes sense with different boxes) and
    output a plotfile with the difference between plotfiles

Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90

commit 95ed12916155eb12a072544c660a9d0fc545f854
Merge: 9593e9577 9e9865508
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Oct 4 17:34:27 2017 -0700

    Merge pull request #141 from AMReX-Codes/parallel_print_to_file
    
    Parallel print to file

commit 9e9865508d2041b5319a05b9448f11be68cc2ac0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 4 16:58:48 2017 -0700

    trading some code duplication for some clarity.

Src/Base/AMReX_Print.H
Tests/Particles/ParticleIterator/main.cpp

commit efedbbe60f3a3dc9874e3577a61656004eeb1eb5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Oct 4 19:50:40 2017 -0400

    Add C++ CUDA error checking

Src/Base/AMReX_BLFort.H
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 25b862b52fb84cc0e076b4f615392433140ad9b8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 4 15:31:58 2017 -0700

    update this test to demonstrate the new amrex::Print() capability

Tests/Particles/ParticleIterator/GNUmakefile
Tests/Particles/ParticleIterator/main.cpp

commit f19c64a8e8e194a9619686eeb22b61879862dc9d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Oct 4 15:31:21 2017 -0700

    new versions of amrex::Print() that send the output to a different file for each proc (and for each thread if called inside a parallel region).

Src/Base/AMReX_Print.H

commit 85d76e88359e9fd8e3a88db80025b17b70ccda72
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Oct 4 15:29:53 2017 -0700

    Remove garbage

Tutorials/Amr/Advection_octree_F/CMakeLists.txt

commit 9593e9577645d26ae2b767556bc953532ff0af94
Merge: 1a9dcfe79 6e5eda778
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 4 15:12:02 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 5c222f5eaeb3ed998c607edc91e67f8ae8086b58
Merge: 45c70be70 6e5eda778
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Oct 4 13:55:04 2017 -0700

    Merge branch 'development' into mr-cmake
    
    Conflicts:
            Src/AmrCore/CMakeLists.txt
            Tutorials/Amr/Advection_AmrCore/CMakeLists.txt

commit 6e5eda7789de63c1e3d3bbe9bab0b31afff33173
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 4 08:50:41 2017 -0700

    clean up old files

Src/EB/AMReX_EBFaceFlag.H
Src/EB/AMReX_EBFaceFlag.cpp
Src/EB/AMReX_EBLevel.H
Src/EB/AMReX_EBLevel.cpp
Src/EB/Make.package

commit eaaeca7a11d30a1545c557ad5fec201584302927
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 3 17:50:46 2017 -0700

    EB/CNS: tagging on density gradient

Tutorials/EB/CNS/Exec/ShockRef/inputs.amr
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/fortran/CNS_tagging.F90
Tutorials/EB/CNS/Source/fortran/Make.package

commit 1a9dcfe7912dcfeba5ebbabfd6ae55ebffc8a18c
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 3 16:09:03 2017 -0700

    fix comments.

Src/Base/AMReX.H

commit 3e7487ca9ddc2f96e091389c2d2d28593d4de060
Merge: 0cd099cf4 3e44cf771
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Oct 3 15:53:47 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 0cd099cf436a4c5f989c60b8a2c16be38c459878
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Oct 3 15:53:27 2017 -0700

    CMake: update CMakeLists.txt in Tutorials

Tutorials/Amr/Advection_AmrCore/CMakeLists.txt

commit 3e44cf771a2472917a3bc82e511d54a33b06e1bb
Merge: 35691dd7e 32a121d8e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 3 15:41:34 2017 -0700

    Merge branch 'weiqun/eb' into development

commit 35691dd7edfd00900277494e9694ee554bf13121
Merge: 7f47b5442 39aa4f48f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 3 15:27:43 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 7f47b5442c0e603eb21dca5d105a609ddf0df659
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Oct 3 15:26:50 2017 -0700

    added some timers

Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90

commit f634d9b94cf47683622034aafdfee235ca7e5663
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 3 14:42:50 2017 -0700

    move file into Extern/ProfParser.

Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp
Src/Extern/ProfParser/Make.package
Tools/AMRProfParser/GNUmakefile

commit d0b7cfabb9b662771ac441297b403ce3920560eb
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 3 14:22:56 2017 -0700

    move the amrprofparser into amrex tools.
    the parser functionality will be replaced by amrvis.

Tools/AMRProfParser/AMReX_ProfParserBatch.cpp
Tools/AMRProfParser/BLProfParser.cpp
Tools/AMRProfParser/GNUmakefile
Tools/AMRProfParser/TestCodes/AMRProfTest0.cpp
Tools/AMRProfParser/TestCodes/BLProfCallTimes.cpp
Tools/AMRProfParser/TestCodes/GNUmakefile
Tools/AMRProfParser/TestCodes/Pieces.cpp
Tools/AMRProfParser/TestCodes/SendTest0.cpp
Tools/AMRProfParser/TestCodes/TokenizeTest.cpp

commit 8d9338393645477c8c169819a5d98c09fdb2b7ac
Merge: 2a2cb9403 39aa4f48f
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 3 14:07:30 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 2a2cb9403840f64008cdc2517ece55afde05284a
Merge: e3441f0cd 0f51486ef
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 3 14:07:28 2017 -0700

    merge fix.

commit 39aa4f48f9d8e8ccb55ef615438bd64c4b245655
Merge: 6b68a5271 0f51486ef
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 3 13:28:41 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6b68a52713d904b810576652e85171e8cb746d14
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Oct 3 13:28:25 2017 -0700

    add ability to load balance based on the square of the particle count.

Src/Particle/AMReX_KDTree_3d.F90
Src/Particle/AMReX_KDTree_F.H
Src/Particle/AMReX_LoadBalanceKD.H
Src/Particle/AMReX_LoadBalanceKD.cpp

commit 32a121d8ed48268b03bb1f70907f9141bef9a5ff
Merge: f44c383ee 0f51486ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 3 12:50:06 2017 -0700

    Merge branch 'development' into weiqun/eb

commit f44c383ee8b9d6cbbb544729b24f0b45a7b71a92
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 3 12:48:43 2017 -0700

    fine tune # of ghost cells

Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_FabArrayBase.cpp
Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_EBTower.cpp
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/main.cpp

commit e3441f0cdf84fb801f3107dcc165fc9346317a67
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 3 12:19:22 2017 -0700

    update for amrex.

OldTutorials/Sidecar_EX1/SidecarResizeTest.cpp

commit e550df3759446a23e2fdb2d927fc1e07cbae942f
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 3 12:17:22 2017 -0700

    fix comment.

Src/Base/AMReX_ParallelDescriptor.H

commit 0f51486ef8dd1ea3bfe96f70de10fb5abecb7e1e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 3 10:05:29 2017 -0700

    Revert "simplify overloaded calls to InterpFromCoarseLevel and FillPatchTwoLevels"
    
    This reverts commit b984bd551bb96802bb0896d63e4ca7ca8132955f.

Src/AmrCore/AMReX_FillPatchUtil.cpp

commit b747bf33304a8cecaf267110a6309d3a3844cb94
Merge: 3aa540ff8 fa6163cb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 3 09:43:38 2017 -0700

    Merge branch 'development' into weiqun/eb

commit 3aa540ff8faa25c7461510156a083767961065b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 3 09:43:26 2017 -0700

    more clean up of EBMultiFabUtil

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_F.H
Src/EB/AMReX_EBMultiFabUtil_nd.F90
Tutorials/EB/CNS/Source/CNS.cpp

commit 1122ee807e939c04b7264d249f511a27c732c879
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 3 09:30:54 2017 -0700

    EBTower: bug fix

Src/EB/AMReX_EBTower.cpp

commit f81e3c6165170b47d514f7994decbcbf2e70a38c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 3 09:18:32 2017 -0700

    clean up

Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp

commit fa6163cb4e3b27e7e1ea3c3b8ca0ce712a385b2b
Merge: 914a64625 b984bd551
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Oct 2 23:31:39 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 914a646257466ee306ba038af78bbe2693816c48
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Oct 2 23:31:15 2017 -0700

    handle case where a level is lost on restart in Particle::Redistribute()

Src/Particle/AMReX_ParticleContainerI.H

commit b984bd551bb96802bb0896d63e4ca7ca8132955f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Oct 2 17:42:51 2017 -0700

    simplify overloaded calls to InterpFromCoarseLevel and FillPatchTwoLevels

Src/AmrCore/AMReX_FillPatchUtil.cpp

commit 61b5aefd418faf1e4d7fa9df5603a8081423eae6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 2 17:32:16 2017 -0700

    fix no-mpi

Src/Base/AMReX_Box.cpp

commit 65198ccbfbe35c0f39e2770c1a021bfe9e2ffd51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 2 17:10:06 2017 -0700

    update EB average down and fix local copy of CutFab

Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_3d.F90
Src/EB/AMReX_EBMultiFabUtil_F.H
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp

commit 6349b636f83e393c505324e7441c1f82477d1d41
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Oct 2 17:00:40 2017 -0700

    boundary condition documentation, example cleanup

Docs/AMReXUsersGuide/Boundary/Boundary.tex
Src/Base/AMReX_PhysBCFunct.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 5a36ae5a4aab19dbf3a63d1ab5fd5107c69ec6a2
Merge: cca88eb0d 5760d5a78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 2 16:29:08 2017 -0700

    Merge branch 'development' into weiqun/eb

commit cca88eb0d0316e1faad6c72831661f548b8a289f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 2 16:28:54 2017 -0700

    ParallelCopy for MultiCutFab

Src/Amr/AMReX_AmrLevel.cpp
Src/Base/AMReX_FabArray.H
Src/EB/AMReX_EBFArrayBox.cpp
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp

commit 7da89b98d0403c2272e5043f538ff5c37d438794
Merge: 73cac8afe c79b8f8f7
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Oct 2 13:52:42 2017 -0700

    removing this file
    
    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development
    
    Conflicts:
            Tutorials/Amr/Advection_AmrCore_Boundary/CMakeLists.txt

commit 73cac8afe29c62459a44a785b32ce5537684bb68
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Oct 2 13:50:47 2017 -0700

    greatly cleaned up the Advection_AmrCore example so now it includes physical boundary conditions
    
    removed the derived AmrAdvPhysBC.H class, it wasn't needed and now uses PhysBCFunct class in amrex/Src/Base so there are less local files/classes

Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdvPhysBC.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/Amr/Advection_AmrCore/Source/Make.package
Tutorials/Amr/Advection_AmrCore/Source/bc_fill_nd.F90
Tutorials/Amr/Advection_AmrCore_Boundary/CMakeLists.txt
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/Make.Adv
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/Make.package
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/Prob.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_AmrCore_Boundary/README
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv_F.H
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Make.package
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/Make.package
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/slope_2d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/Make.package
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/compute_flux_3d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/slope_3d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_nd/Make.package
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_nd/Tagging_nd.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/main.cpp

commit 4fe6565fb6cdce54af4d306722d8a1351ea99f00
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Oct 2 13:39:52 2017 -0700

    further simplification of this tutorial to rely on amrex-native classes

Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.H
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.cpp
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv_F.H
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Make.package
Tutorials/Amr/Advection_AmrCore_Boundary/Source/bc_fill_nd.F90

commit 8ee6aa8f330f468a92ac75e1096ddc3f402755c1
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Oct 2 13:38:49 2017 -0700

    overloaded FillPatchTwoLevels and InterpFromCoarseLevel to allow
    
    const BCRec& bcs
    
    as an option for input instead of
    
    const Array<BCRec>& bcs

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp

commit e022a2bf28f38e35af701cf2bc8650949197e034
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Oct 2 13:16:15 2017 -0700

    boundary condition work in progress

Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.H
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.cpp

commit c79b8f8f739f58d6a1d204214b28888c0975e06a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Oct 2 12:43:56 2017 -0700

    give this executable a different name so the cmake install will work.

Tutorials/Amr/Advection_AmrCore_Boundary/CMakeLists.txt

commit 1124a21ca4358b33c8404aeef73701b815814521
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Oct 2 12:35:54 2017 -0700

    start of expanded documenation on domain boundary conditions

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/Boundary/Boundary.tex
Docs/AMReXUsersGuide/GNUmakefile
Tutorials/Basic/HeatEquation_EX2_C/advance.cpp

commit 5760d5a780fbe44d6c8d61ce6a76ed04dfe6fc79
Merge: 2bc3b4ddf f47d9cbaa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 2 08:29:44 2017 -0700

    Merge branch 'development'

commit f47d9cbaada52932155596a0a4e194a9b9146f45
Author: kngott <kngott@lbl.gov>
Date:   Sun Oct 1 16:52:44 2017 -0700

    Fix some OldTutorials/MultiFabTests_C and OldTutorials/Sidecar_EX1 to function again.

OldTutorials/MultiFabTests_C/MultiFabReadWrite.cpp
OldTutorials/Sidecar_EX1/DestMFTest.cpp
OldTutorials/Sidecar_EX1/GNUmakefile
OldTutorials/Sidecar_EX1/GridMoveTest.cpp
OldTutorials/Sidecar_EX1/InTransitAnalysis.H
OldTutorials/Sidecar_EX1/SidecarResizeTest.cpp

commit f9d5c866ca5352e9b4a008a87920f17b91930d35
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 1 16:09:31 2017 -0700

    update EB/CNS to use cached geometry data

Src/EB/AMReX_EBFabFactory.H
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp

commit db5571b31376c99d0a961f04cd9902eb9ce01c45
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 1 15:55:15 2017 -0700

    fill bndrycent, areafrac and facecent

Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp

commit cc57b80dff8c73f4aba2c1e40157cc77e0301345
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 1 15:08:43 2017 -0700

    MultiCutFab: remove regular and covered fabs

Src/Base/AMReX_FabArray.H
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp

commit 9126e3f35589307e4af20ebffb3fecff598afb84
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 1 14:56:49 2017 -0700

    EBDataCollection: define bndrycent, areafrac and facecent

Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp

commit 8f70156b2cfb06ad2bf85c3ef859e979d4ba1fc6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 1 12:55:24 2017 -0700

    EBTower: added bndrycent, areafrac and facecent

Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Src/EB/AMReX_MultiCutFab.H
Src/EB/AMReX_MultiCutFab.cpp
Src/EB/Make.package

commit 4f265ca8ee53ebb2bb889bfdfcc133046f256c6a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Sep 30 19:24:56 2017 -0400

    Broadcast plot_and_continue to all processors

Src/Amr/AMReX_Amr.cpp

commit da101cb65518d9ba4fc40cfb93f87bd2b5519e03
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Sep 30 18:38:44 2017 -0400

    Add small_plot_and_continue file checker

Src/Amr/AMReX_Amr.cpp

commit ae185e2f97db3dab24e0552586416a08cb59ba18
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Sep 30 18:38:21 2017 -0400

    Add a level option to fdump

Tools/Postprocessing/F_Src/fdump.f90

commit dd7145c62c144cf36080b89fbabf7f720c5a4afb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 30 13:23:45 2017 -0700

    function to delete the EBIndexSpace singleton

Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Tutorials/EB/CNS/Source/main.cpp

commit 4e33c7289bcce57378eb2e869bd30641bc6cec06
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 29 18:05:56 2017 -0700

    WIP: get volume fraction

Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp

commit 9b503de64e4a1839059d4fba065892803d76b33f
Merge: 9674d2e24 c9abf710c
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Sep 29 19:21:37 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 9674d2e24f35215099e62ece45da3e0bc95a7d43
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Sep 29 19:21:26 2017 -0700

    comments

Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.cpp

commit c9abf710c458a8d470ab8f30dffa64ead45ad987
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 29 18:05:19 2017 -0700

    EB/CNS: fix RK2

Tutorials/EB/CNS/Source/CNS_advance.cpp

commit 4fb0028b716100e7c4f138ed96796059c58a394e
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Sep 29 17:20:59 2017 -0700

    new Tutorial showing how to do walls (homogeneous Neumann) scalar bc's in the AmrCore framework

Tutorials/Amr/Advection_AmrCore_Boundary/CMakeLists.txt
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/Make.Adv
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/Make.package
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/Prob.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_AmrCore_Boundary/README
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.H
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.cpp
Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv_F.H
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Make.package
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/Make.package
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/slope_2d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/Make.package
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/compute_flux_3d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/slope_3d.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_nd/Make.package
Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_nd/Tagging_nd.f90
Tutorials/Amr/Advection_AmrCore_Boundary/Source/main.cpp

commit ec0a3f441c6aa012b3603a65b233cc18d88e5680
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 29 16:50:01 2017 -0700

    WIP: EBTower: volume fraction

Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBSupport.H
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/main.cpp

commit a9f214e2067033311519366a93193c45e9c87556
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 29 14:26:12 2017 -0700

    WIP: EBTower: fill cell flags for EBDataCollection

Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabFactory.H
Src/Base/AMReX_MultiFab.H
Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFArrayBox.H
Src/EB/AMReX_EBFArrayBox.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBSupport.H
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Src/EB/Make.package
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp

commit 59aaa3aa9033d727118e0c9e658c4a76d71af86f
Merge: 90b62388d d791f53cf
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 29 11:14:42 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit d791f53cf230c43d0e044fb317d3ed88ded6865c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 29 10:40:57 2017 -0700

    add ostream& operator<< for BoxArray::RefID, DistributionMapping::RefID and FabArrayBase::BDKey

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit bb73713264704d76da109d27e8a04ca166d4eb85
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 28 19:09:41 2017 -0700

    Fix Oops  in AMReX_DistributionMapping.cpp

Src/Base/AMReX_DistributionMapping.cpp

commit 6943a9aa980bc22e3c896226793d1062886000ff
Merge: fada55b92 ebeafa803
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 28 19:04:27 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development
    
    Conflicts:
            Src/Base/AMReX_DistributionMapping.H
            Src/Base/AMReX_DistributionMapping.cpp

commit fada55b92c6692a2eb0412006d4f9410d714240e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 28 19:02:00 2017 -0700

    Add the ability to call makeKnapsack with a list of weights rather than the boxes themselves --
    this is what we want to do within the KD Load Balancing algorithm

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Particle/AMReX_LoadBalanceKD.H

commit 90b62388d6f139816e1afbada3323a825ab3b79a
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 28 18:11:05 2017 -0700

    make html headers consistent with output.

Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp

commit b42d19524c324687c6b846be554212ab45c95e4a
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 28 17:27:03 2017 -0700

    some cleanup.

Src/Extern/amrdata/AMReX_DataServices.H
Src/Extern/amrdata/AMReX_DataServices.cpp

commit cfb5bd8e4519bb651833e5c448bb4c7d7bc755a1
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 28 17:14:02 2017 -0700

    fix compiler warnings.

Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp
Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp
Src/Extern/ProfParser/AMReX_CommProfStats.cpp
Src/Extern/amrdata/AMReX_DataServices.cpp

commit ebeafa80315b361a7629117baaf5a9202925149f
Merge: d5da75fad 4bc1cd000
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 28 14:50:36 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit d5da75fadcfd7dff874c4178430f3d7cdec14c4a
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 28 14:37:17 2017 -0700

    fix compiler warnings.

Src/Extern/amrdata/AMReX_AmrData.cpp

commit edc20dd682da2eec9f4773e1d9db6bbbd6d77ee1
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 28 14:24:04 2017 -0700

    fix compiler warning.

Src/Extern/ProfParser/AMReX_CommProfStats.H

commit 4bc1cd0004a20ab66a6e210d9f120b32f2848988
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 28 13:45:27 2017 -0700

    parameter to limit the number of boxes can be assigned to a single process in load balance

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit 0bb7117f0d5eeb9a32fb56bdc1203e976e918ccc
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 28 14:14:30 2017 -0700

    fix compiler warning.

Src/Base/AMReX_BLProfiler.H

commit 000350842fb103cb49260571a8f55a9ae8bcf374
Merge: 7a3277b19 6a0551057
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 28 14:05:37 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 7a3277b194766aede5782cd50c784f0dab50ffa5
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 28 14:03:05 2017 -0700

    added show body flag for eb.

Src/Extern/amrdata/AMReX_AmrData.H
Src/Extern/amrdata/AMReX_AmrData.cpp

commit 6a0551057e7b658da5384bd11e6ce7a33e64c643
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 28 13:09:28 2017 -0700

    fix cmake install

Src/AmrCore/CMakeLists.txt

commit c2e41219618cdabf5d087a2091924e7016f44ce9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 27 17:30:44 2017 -0700

    added EBDataCollection

Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_FabArrayBase.cpp
Src/EB/AMReX_EBDataCollection.H
Src/EB/AMReX_EBDataCollection.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBTower.H
Src/EB/Make.package

commit 104438a509d17c4bb0894a68ab571808b1c60cb2
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 27 16:55:18 2017 -0700

    add Dirichlet boundary conditions

Tutorials/Basic/HeatEquation_EX2_C/AMReX_FILCC_2D.F
Tutorials/Basic/HeatEquation_EX2_C/AMReX_FILCC_3D.F

commit 44be6cfbf1855a07cb09211de27eab89abf32ec8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 27 16:21:50 2017 -0700

    cache EBCellFlags

Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp

commit 45c70be70d318fdf072f890fa37e9c9539d3feff
Merge: 17029dee6 ac86317c5
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Sep 27 15:31:49 2017 -0700

    Merge branch 'development' into mr-cmake
    
    Conflicts:
            Src/AmrCore/CMakeLists.txt
            Src/Base/CMakeLists.txt
            Src/Particle/CMakeLists.txt

commit 32af9438456346ea5309679594ce7f8ae5371086
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 27 15:25:24 2017 -0700

    started EBTower

Src/EB/AMReX_EBTower.H
Src/EB/AMReX_EBTower.cpp
Src/EB/Make.package
Tutorials/EB/CNS/Source/main.cpp

commit 95bb13388d31417e97583a8b5cfaab0d5b70ca59
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 27 15:23:57 2017 -0700

    access to some EB internal data

Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBIndexSpace.H

commit d462b5bf16706a2db4adfd80f6a1d6edd098110c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 27 15:23:02 2017 -0700

    added a new BoxList constructor that takes rvalue Array<Box>

Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp

commit effe379bbd459f9c3c6631987add8782a83ba017
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 27 15:22:16 2017 -0700

    added amrex::AllGatherBoxes

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp

commit ac86317c5ff9057ce47f31b4cd68f5a87ee0fb1b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 27 10:31:45 2017 -0700

    EB/CNS: update plotfile

Tutorials/EB/CNS/Source/CNS_io.cpp

commit 26c49a90c6e7cc37c7f9b762621ff810b3bd1012
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 27 10:12:58 2017 -0700

    add CartGrid-V2.0 to plotfile types

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/plotfile.f90

commit b203331883deedb53fd93b83ff3c57cc7de44701
Merge: adf127359 d2d923298
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 27 09:00:45 2017 -0700

    Merge pull request #140 from bcfriesen/cvode_docs_fix
    
    Docs: add note to CVODE compilation about the examples linking dynamically

commit d2d92329806df5bf4837eefa528785efac22c876
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Sep 26 21:12:34 2017 -0700

    Docs: add note to CVODE compilation about the examples linking dynamically

Docs/AMReXUsersGuide/CVODE/CVODE.tex

commit adf127359acc07aeafcd6d53371d46565df2fbf2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 26 17:20:47 2017 -0700

    don't profile this function - called too many times.

Src/Particle/AMReX_ParticleContainerI.H

commit 281435ab09c3f47232c1b68d4669be8ed9370ccf
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 26 17:20:15 2017 -0700

    fix some parameters shadowings.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H

commit c066df38544070ae3349f7e881e32149841b3e35
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 26 16:39:08 2017 -0700

    EB/CNS: use Amr's load balance approach

Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs
Tutorials/EB/CNS/Exec/Combustor/inputs
Tutorials/EB/CNS/Exec/Combustor/inputs.regt
Tutorials/EB/CNS/Exec/Combustor/inputs.testing
Tutorials/EB/CNS/Exec/Combustor/inputs_combustor
Tutorials/EB/CNS/Exec/Pulse/inputs
Tutorials/EB/CNS/Exec/Pulse/inputs.regt
Tutorials/EB/CNS/Exec/ShockRef/inputs
Tutorials/EB/CNS/Exec/ShockRef/inputs.regt
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_setup.cpp
Tutorials/EB/CNS/Source/main.cpp

commit a3582a42b3ebb72d8317ddafa9d4f348b6d2eabf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 26 16:21:10 2017 -0700

    update CHANGES

CHANGES

commit 3bdb7d118cbb22ed2bebd25fb42cccd4583b0032
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 26 16:14:41 2017 -0700

    add amr.loadbalance_with_workestimates and amr.loadbalance_level0_int

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H

commit 321e416282eb5bcccbee99a162f1056661750a84
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 26 15:33:23 2017 -0700

    Tweaks to some of the text in the User Guide

Docs/AMReXUsersGuide/EB/EB.tex

commit ae90dbfd4d517d8300a6f81377c4c15eb516a85f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 26 13:12:45 2017 -0700

    also turn it on for building the neighbor list.

Src/Particle/AMReX_NeighborParticlesI.H

commit a7cbcc8b194b1695bb660ac05efaa27e5874f5a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 26 12:20:50 2017 -0700

    EB/CNS: update plotfile to CartGrid-V2.0

Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS_io.cpp

commit 7e4caedb99a85b24fb365427bdf622c1142188f2
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 25 17:24:44 2017 -0700

    implemented periodic, zero-flux, and Dirichlet options

Tutorials/Basic/HeatEquation_EX2_C/advance_2d.f90
Tutorials/Basic/HeatEquation_EX2_C/advance_3d.f90
Tutorials/Basic/HeatEquation_EX2_C/inputs_2d
Tutorials/Basic/HeatEquation_EX2_C/inputs_3d
Tutorials/Basic/HeatEquation_EX2_C/main.cpp

commit c483132e6c4d4fde05003d1c9d3080b260b5b619
Merge: c46db98b8 8128fa703
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Sep 25 15:27:29 2017 -0700

    merging with dtg_branch to get documentation changes over

commit 8128fa7034c8ba7aca0ec780c48d047f7e701d0a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Sep 25 15:25:46 2017 -0700

    added more geometry examples

Docs/AMReXUsersGuide/EB/EB.tex
Docs/AMReXUsersGuide/EB/EB_example.fig.bak
Docs/AMReXUsersGuide/EB/eb_fluxes.fig.bak
Docs/AMReXUsersGuide/EB/parabsphere.pdf
Docs/AMReXUsersGuide/EB/parabsphere.ps.REMOVED.git-id
Docs/AMReXUsersGuide/EB/revolution.pdf
Docs/AMReXUsersGuide/EB/revolution.ps.REMOVED.git-id

commit 9daf62c8ba9e3468906ce3974988c38ad69d16da
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Sep 25 15:09:07 2017 -0700

    added polynomial geometry

Src/GeometryShop/AMReX_PolynomialIF.H
Src/GeometryShop/AMReX_PolynomialIF.cpp
Src/GeometryShop/Make.package

commit 40f405c2c1224524d3371900e11143fc9f3235bb
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Sep 25 15:08:48 2017 -0700

    added a couple more geometry options

Tutorials/EB/CNS/Source/CNS_init_eb.cpp

commit c46db98b874513a64399996a093c7615649c1a6f
Merge: ef626dd22 6d919a782
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 25 15:01:12 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit ef626dd22195a672a7bb58a75bf3f4146d327b64
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 25 15:00:02 2017 -0700

    split the Basic/HeatEquation_EX1_C into EX1 and EX2.  EX1 is periodic, EX2 will support Neumann and Dirichlet conditions eventually (WIP)

Tutorials/Basic/HeatEquation_EX1_C/Make.package
Tutorials/Basic/HeatEquation_EX1_C/advance.cpp
Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90
Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90
Tutorials/Basic/HeatEquation_EX1_C/inputs_2d
Tutorials/Basic/HeatEquation_EX1_C/inputs_3d
Tutorials/Basic/HeatEquation_EX1_C/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/myfunc.H
Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H
Tutorials/Basic/HeatEquation_EX1_C/physbc.cpp
Tutorials/Basic/HeatEquation_EX2_C/GNUmakefile
Tutorials/Basic/HeatEquation_EX2_C/Make.package
Tutorials/Basic/HeatEquation_EX2_C/advance.cpp
Tutorials/Basic/HeatEquation_EX2_C/advance_2d.f90
Tutorials/Basic/HeatEquation_EX2_C/advance_3d.f90
Tutorials/Basic/HeatEquation_EX2_C/init_phi_2d.f90
Tutorials/Basic/HeatEquation_EX2_C/init_phi_3d.f90
Tutorials/Basic/HeatEquation_EX2_C/inputs_2d
Tutorials/Basic/HeatEquation_EX2_C/inputs_3d
Tutorials/Basic/HeatEquation_EX2_C/main.cpp
Tutorials/Basic/HeatEquation_EX2_C/myfunc.H
Tutorials/Basic/HeatEquation_EX2_C/myfunc_F.H

commit 6d919a7821c8117459d51dfb39f701a4adb0ed01
Merge: ab0f44f07 c0dd93eae
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Sep 25 13:16:05 2017 -0700

    Merge pull request #139 from zingale/development
    
    add stub versions of the new broadcasts

commit c0dd93eae18f98677f6f444398a69cf69aba4c27
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 25 16:11:58 2017 -0400

    add stub versions of the new broadcasts

Src/F_BaseLib/parallel_stubs.f90

commit eb6e1823af64a065914de277dab6ec1e38d5151d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Sep 25 13:05:42 2017 -0700

    fix some dynamic scheduling bugs.

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H

commit ab0f44f0745bc37adc7bdacc2184f15e37f27243
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 25 12:55:54 2017 -0700

    VisMF::Exist(const std::string&) returns ture iff a MultiFab with such name exists

Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp

commit d530a2cabaaea7d70c4af6e86753e2955715638c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 25 09:16:48 2017 -0700

    update EB regression test to include amr

Tutorials/EB/CNS/Exec/Pulse/inputs.regt

commit eeb265b083a80758bb0dd8608f822d7b8ba457da
Merge: 3d469e562 4598e9253
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Sep 25 08:48:03 2017 -0700

    Merge pull request #138 from AMReX-Codes/multid_bcast
    
    Add 2D, 3D, 4D parallel_bcast

commit 3d469e56245aa61ad225dba009a7b0c73d678a2d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Sep 25 01:37:52 2017 -0400

    Add index options to fdump

Tools/Postprocessing/F_Src/fdump.f90

commit 208e72e458a29e510eb9147154337f38830033b1
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Sep 25 01:14:32 2017 -0400

    Add minimum and maximum value options to fdump

Tools/Postprocessing/F_Src/fdump.f90

commit 4598e9253b4d1f5e5558445a7ac0ffc0cfb79939
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Sep 24 23:26:20 2017 -0400

    Add 2D, 3D, 4D parallel_bcast

Src/F_BaseLib/parallel.f90

commit f3843a48e3ab88eb2684c8d07d50ef263b37cd5e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Sep 24 20:00:28 2017 -0400

    Default last_smallplotfile to -1
    
    This allows for a quick test to see if the user has requested any
    small plot files at all; the number will end up >= 0 if so, and stay
    negative if not.

Src/Amr/AMReX_Amr.cpp

commit cb9d9e95bacafa3f542f8413b3410d067268d444
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Sep 24 07:48:41 2017 -0400

    Add function to set level_count

Src/Amr/AMReX_Amr.H

commit fe85124be95b26dede0906fcf9e4209163343501
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 23 13:13:47 2017 -0700

    EB/CNS: turn off various profiling

Src/Base/AMReX_BoxArray.cpp
Tutorials/EB/CNS/Exec/Combustor/GNUmakefile

commit 57dfc3335aa0bb1b67371111d4cb870dbf976085
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 23 12:17:28 2017 -0700

    fix 2d

Src/EB/AMReX_EBFluxRegister_2d.F90

commit 1271f3b23049ffb7d74a9be23e2680a617289a50
Merge: 3b9a6cc0e 02a84a62a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 23 12:14:42 2017 -0700

    Merge branch 'weiqun/eb' into development

commit 02a84a62a3a62bff6d39a5e73dc3c499bbd4b121
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 23 12:14:22 2017 -0700

    Merge branch 'development' into weiqun/eb

Docs/AMReXUsersGuide/EB/EB.tex

commit 14b635b5942fc69cb8e92658b7e80385e44a285c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 23 12:13:40 2017 -0700

    refactor EBFluxRegister

Src/EB/AMReX_EBFluxRegister.H
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_2d.F90
Src/EB/AMReX_EBFluxRegister_3d.F90
Src/EB/AMReX_EBFluxRegister_F.H
Tutorials/EB/CNS/Exec/Pulse/inputs.debug

commit 3b9a6cc0e2e8efaab28e601122893ae098412bfa
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Sep 22 20:15:14 2017 -0700

    Work the EB section of the doc a bit

Docs/AMReXUsersGuide/EB/EB.tex

commit fb6273f4cc016210f1dd1b213c2f203b03ca812b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 22 17:30:47 2017 -0700

    re-re-redistribution

Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_3d.F90

commit 584a8361fcbef100ef6a84a2a6da22de0392c913
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 22 17:06:55 2017 -0700

    WIP: Re-reflux

Src/AmrCore/AMReX_YAFluxRegister.H
Src/AmrCore/AMReX_YAFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister.H
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_3d.F90
Src/EB/AMReX_EBFluxRegister_F.H
Tutorials/EB/CNS/Source/CNS.cpp

commit 331da41f6cd57c11818eeaf5f28c20de7a406410
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 22 15:38:39 2017 -0700

    fixed error messages.

Src/Extern/amrdata/AMReX_DataServices.cpp

commit 711a729c7f7eada8938a5704ebb07a4529508602
Merge: 7f8e6b8c2 0eb10b979
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 22 09:46:37 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 7f8e6b8c2a8803c5d97ebfed52f298a27e2669dc
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 22 09:45:49 2017 -0700

    bug fixes  in EB.tex

Docs/AMReXUsersGuide/EB/EB.tex

commit 0eb10b979666ae8934c44eb4a1d18fd44c603a8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 22 09:41:29 2017 -0700

    YAFluxRegister: update comment

Src/AmrCore/AMReX_YAFluxRegister.cpp

commit 4ba8e0d03aa6f3fc0c5fcf6b74e79820abffe083
Merge: 31bb27991 bda96126b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 22 09:27:43 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 31bb2799128c04370f0178311551e7c9a6d05563
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 22 09:26:07 2017 -0700

    added surface of revolution section

Docs/AMReXUsersGuide/EB/EB.tex

commit bda96126bf2006527a63507fd46ef8b146edf12a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 22 09:21:19 2017 -0700

    EB/CNS: add cns.do_reflux

Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_io.cpp

commit 51c928fcb35c77dc4ff1c1c08a518341b89cb58b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 22 09:11:43 2017 -0700

    option to disable reredistribution for testing

Src/EB/AMReX_EBFluxRegister_nd.F90
Tutorials/EB/CNS/Source/fortran/CNS_f.F90

commit 3bec2a3ed99624d4215dcf0b75f54d9a041db129
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 21 17:56:11 2017 -0700

    inputs for John to hack

Tutorials/EB/CNS/Exec/Pulse/inputs.debug

commit 3e99b9ea51ebc6346e0b61e8cb46f8342a056085
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 21 17:47:46 2017 -0700

    yet another flux register

Src/AmrCore/AMReX_FillPatchUtil_1d.F90
Src/AmrCore/AMReX_YAFluxRegister.H
Src/AmrCore/AMReX_YAFluxRegister.cpp
Src/AmrCore/AMReX_YAFluxRegister_1d.F90
Src/AmrCore/AMReX_YAFluxRegister_2d.F90
Src/AmrCore/AMReX_YAFluxRegister_3d.F90
Src/AmrCore/AMReX_YAFluxRegister_F.H
Src/AmrCore/AMReX_YAFluxRegister_nd.F90
Src/AmrCore/CMakeLists.txt
Src/AmrCore/Make.package
Src/EB/AMReX_EBFluxRegister.H
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_2d.F90
Src/EB/AMReX_EBFluxRegister_3d.F90
Src/EB/AMReX_EBFluxRegister_F.H
Src/EB/AMReX_EBFluxRegister_nd.F90

commit 4f673b6f4021a4dd14e1e9a0ae66d9b4fc0443d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 21 13:12:33 2017 -0700

    add re-redistribution threshold

Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_2d.F90
Src/EB/AMReX_EBFluxRegister_3d.F90
Src/EB/AMReX_EBFluxRegister_nd.F90
Src/EB/Make.package
Tutorials/EB/CNS/Source/fortran/CNS_divop.F90

commit 08c2aafabf0fd003525b471d7bc549cb20fca78e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 21 10:05:11 2017 -0700

    EBFluxRegister: fix periodic boundary

Src/EB/AMReX_EBFluxRegister.H
Src/EB/AMReX_EBFluxRegister.cpp

commit 75cd1b21ec40370d94f7d3ecf75c7620be8585e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 21 10:03:16 2017 -0700

    add a free function converting iMultiFab to MultiFab

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_MultiFabUtil_nd.F90
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit ac6f7631a75d912a54200fa569a175d975c0f533
Merge: 65f093b90 6b37c2125
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Sep 21 16:29:29 2017 -0700

    merging documentation changes over to dev so others can see them

commit 6b37c21251ed03dd249e71d8a7ae0ee64c3a01dc
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Sep 21 16:27:34 2017 -0700

    some missing files

Docs/AMReXUsersGuide/EB/redist.eps
Docs/AMReXUsersGuide/EB/redist.fig
Docs/AMReXUsersGuide/EB/redist.pdf

commit 096535a23d09c417d328c133093646887bee9b66
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Sep 21 16:27:12 2017 -0700

    started on documentation revisions of EB stuff per John and Marc's recommendations

Docs/AMReXUsersGuide/EB/EB.tex
Docs/AMReXUsersGuide/EB/EB_example.eps
Docs/AMReXUsersGuide/EB/EB_example.fig
Docs/AMReXUsersGuide/EB/EB_example.pdf
Docs/AMReXUsersGuide/EB/areas_and_volumes.eps
Docs/AMReXUsersGuide/EB/areas_and_volumes.fig
Docs/AMReXUsersGuide/EB/areas_and_volumes.pdf
Docs/AMReXUsersGuide/EB/eb_fluxes.eps
Docs/AMReXUsersGuide/EB/eb_fluxes.fig
Docs/AMReXUsersGuide/EB/eb_fluxes.pdf

commit 65f093b9061c50ccef0dd06da6ae5067d2bfd3e0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 21 14:26:12 2017 -0700

    Fix the flags getting passed to HPGMG

Tools/GNUMake/packages/Make.hpgmg

commit 1c0abd4a9d6ecf3ae4e5ee8c88b831c126ed9e2e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 21 14:19:44 2017 -0700

    First stab at making the particle iterator able to use dynamic scheduling with OpenMP.

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborList/inputs
Tutorials/Particles/NeighborList/main.cpp

commit 2f3c976249f6291d57199f67a71133d0881ed220
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 21 11:57:34 2017 -0700

    John's which --> that corrections.

Docs/AMReXUsersGuide/CVODE/CVODE.tex

commit b51a66addedc244f996ed8f8d8453e6b115e4848
Merge: 3e49497ed 65e58ca25
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Sep 21 09:03:32 2017 -0700

    Merge pull request #137 from bcfriesen/update_cvode_docs
    
    Docs: update CVODE docs

commit e08851e43c184ba50012010bebe60cab85827212
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Sep 21 03:57:02 2017 -0400

    Move BaseFab kernels to FORT_LAUNCH

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit c7273b65ba3dc759a58a5bd0ebe4fd35b2c4f8b2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Sep 21 03:56:46 2017 -0400

    Do not pass MFIter to FORT_LAUNCH

Src/Base/AMReX_BLFort.H
Tutorials/GPU/HeatEquation_EX1_C/advance.cpp

commit 6d3762f6b9d8d5dafdef5b04c90bd1da480fc042
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Sep 21 03:56:19 2017 -0400

    Add static current CUDA stream

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit e9b44e2a98140e72bd98bf7461fdb16398456c2d
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Sep 21 03:08:10 2017 -0400

    Fix non-GPU compilation of heat equation

Tutorials/GPU/HeatEquation_EX1_C/main.cpp

commit bb860b5ab5dbcf0d67349791855d8dcc34a41af6
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Sep 21 03:04:18 2017 -0400

    Use subroutine defines in heat equation example

Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90

commit 8607140cf87bf220f1bdf632cd6dcee4d8fe2d4a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Sep 21 03:04:01 2017 -0400

    Rename CUDA defines to all caps

Tools/GNUMake/Make.defs

commit d58ec09f4bd49de2b9a43cf8fa67f9910d107c25
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Sep 21 02:58:01 2017 -0400

    Launch heat equation kernels from C++

Tutorials/GPU/HeatEquation_EX1_C/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H

commit 7f8997df8c2d5bae79bd4ac090411ede77d498e9
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Sep 21 02:52:07 2017 -0400

    Add FORT_LAUNCH and FORT_LAUNCHABLE macros for CUDA kernels

Src/Base/AMReX_BLFort.H

commit c1b4ee9e99ec7c50c8db7b987446e5ec1e936c9e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Sep 21 02:51:37 2017 -0400

    Add helper routines for launching kernels from C++

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 65e58ca25af4f4f5aaff1585ee7db5bbc7b22f69
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Sep 20 22:30:18 2017 -0700

    Docs: add a new section describing the CVODE Tutorials

Docs/AMReXUsersGuide/CVODE/CVODE.tex

commit 2e8cbf25c1e73b776c1b1e79cda10c45b06690af
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Sep 20 22:29:47 2017 -0700

    Docs: revise the wording of the CVODE Fortran 2003 interface description

Docs/AMReXUsersGuide/CVODE/CVODE.tex

commit 569acbbde053531f304d2fb096f1ffc240ec7ef3
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Sep 20 22:28:54 2017 -0700

    Docs: add note discouraging FCVODE in favor of the Fortran 2003 interface

Docs/AMReXUsersGuide/CVODE/CVODE.tex

commit 454bf7a1be9fee46f5ba564251e348d9985db7d2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Sep 21 01:01:37 2017 -0400

    Handle the bl_error difference between the C++ and F90 build systems

Src/Base/AMReX_CUDA.F90

commit ef077c76ac761c73e4d97074dcefbdc773827e56
Merge: 0c5f20049 3e49497ed
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Sep 21 00:51:52 2017 -0400

    Merge branch 'development' into gpu

commit 3e49497ed702495ef141ea0de11928de24c94952
Merge: 9e78f21e0 762fd0f5d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 20 14:59:33 2017 -0700

    Merge branch 'development' into threaded_neighbor_particles

commit 762fd0f5d3fcfb490798f3efa18893d02de20b91
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 20 14:26:44 2017 -0700

    fix errors in comments

Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 2bc3b4ddf1aea4c54fb9fdc36d812165a73ad118
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 20 14:18:51 2017 -0700

    Revert "fix comments regarding regridding functions"
    
    This reverts commit 3dfec1d7158bc40188427d88c8bc2a900291907f.

Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 3dfec1d7158bc40188427d88c8bc2a900291907f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 20 14:11:38 2017 -0700

    fix comments regarding regridding functions

Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit b9e92afa0c4fafa4694a9448037657809dc80209
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 20 13:13:19 2017 -0700

    check signal_handling for F_BaseLib too

CHANGES
Src/F_BaseLib/backtrace_c.cpp

commit 9e78f21e0f5e27ddd1736a4e85e6e5b4c1b125df
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 20 13:12:50 2017 -0700

    avoid rellocating this vector repeatedly in parallel region.

Src/Particle/AMReX_NeighborParticlesI.H

commit d4ea49ddd688d107292bcbc58ed831f6b95922e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 20 13:05:15 2017 -0700

    runtime parameter amrex.signal_handling for disabling signal handling

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_ParallelDescriptor.cpp

commit 864fe23295896a08ea8b8c2adbb28ba8b7987b3b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 20 12:25:01 2017 -0700

    just use regular parallel for regions here.

Src/Particle/AMReX_NeighborParticlesI.H

commit 974ccdb4f263e81c2a7e0646b49893ca72e30c66
Merge: 1020dc1cf 99ea7a69b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 20 12:03:12 2017 -0700

    Merge pull request #136 from AMReX-Codes/dtg_branch
    
    with these fixes, I was able to run Pele with threads

commit 99ea7a69b380339475ec21bca06583e013bf0a33
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 20 11:59:40 2017 -0700

    took out some debugging statements

Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp

commit ca44e491657f840b8811905c3e1ecede1f9911ba
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 20 11:57:19 2017 -0700

    I added some return values to AMReX_RegionsProfStats.cpp for cases where it is being called incorrectly just to shut up the compiler.   I also fixed EBGraph::fillIntMask to make it thread safe

Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp

commit 9e340d0e526b72e1f5dd95ce3a3bcff38efac31e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 20 11:08:01 2017 -0700

    the local temporaries need entries for the neighboring tiles, too.

Src/Particle/AMReX_NeighborParticlesI.H

commit 84810a96158ab75738e019a9ef25d35018147eae
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 20 10:45:49 2017 -0700

    correctly build map for remote particles in serial to allow for multithreaded processing.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 1020dc1cf209f3dd0ffadab13358d638abe43b71
Merge: 8bb972a61 d9c5cfe39
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 20 09:14:48 2017 -0700

    Merge pull request #134 from AMReX-Codes/dtg_branch
    
    missed one

commit d9c5cfe39248d13b745befbe004d095a46ff34d4
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 20 09:13:31 2017 -0700

    translation amount in ebinit was wrong if maxlev > 0

Tutorials/EB/CNS/Source/CNS_init_eb.cpp

commit 8bb972a612d72fbb9be5060d5d31a77b0ab3c8d0
Merge: 8644824c8 10c0e13f1
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 20 09:07:15 2017 -0700

    Merge pull request #133 from AMReX-Codes/dtg_branch
    
    minor bug fix

commit 10c0e13f191f9e90781b7c5ca9796b9cf1d0ae4c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 20 09:05:44 2017 -0700

    volume fraction variable has to be named vfrac in order for visit to work

Tutorials/EB/CNS/Source/CNS_io.cpp

commit 8644824c847d497a10ca1557597974fc3cccd116
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 19 16:38:51 2017 -0700

    We now pass in "cell_weight" as the initialization for the weight of each cell.
    To this we will add the number of particles in that cell.

Src/Particle/AMReX_LoadBalanceKD.H

commit c69e7fea037aaacf6e1a09df66400861dd57b815
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 19 16:38:28 2017 -0700

    Remove write statement "actually rebuilding"

Src/Particle/AMReX_NeighborParticlesI.H

commit a551b8584b0027cfa53419fae4cfad1beb1525b1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 19 16:22:31 2017 -0700

    remove some more debugging crap

Src/Particle/AMReX_NeighborParticlesI.H

commit c3d64fff7ac5e0a1687b82df990cbbc2ea42b923
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 19 16:21:57 2017 -0700

    handle update neighbors too.

Src/Particle/AMReX_NeighborParticlesI.H

commit 7796d91cf3d73d7d5b005205e2500245cf1b697c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 19 16:13:41 2017 -0700

    handle threading for the local neighbor particles in fillNeighbors.

Src/Particle/AMReX_NeighborParticlesI.H

commit a148a7405d92df57e726ad8d24dc89ddffbb8283
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 19 15:48:17 2017 -0700

    EB/CNS: inputs parameters for fine level grids placement

Src/Base/AMReX_RealBox.H
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp

commit b0e9d196f892a3be38c8e6f46447788702bb20d7
Merge: ee69438fb 55606925d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 19 15:41:50 2017 -0700

    Merge pull request #132 from cmsquared/osx_fix
    
    add missing library to link line for gfortran in osx

commit 55606925de8a4f2b93723ed1a63c09563d481fd3
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Tue Sep 19 16:27:11 2017 -0600

    add missing library to link line for gfortran in osx

Tools/F_mk/comps/gfortran.mak

commit 3fb94bd4c78dac745d7ad3f62fdc622cc66632df
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 19 15:21:38 2017 -0700

    handle threading for the remote neighbor particles.

Src/Particle/AMReX_NeighborParticlesI.H

commit ee69438fbdd16f654a18dc86de00adb597eaad94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 19 14:54:41 2017 -0700

    #if 0 some debug code

Tutorials/EB/CNS/Source/CNS.cpp

commit e4ee971c763c8cd711966a4234884383e7efee51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 19 14:52:09 2017 -0700

    EB/CNS: minor tweak

Tutorials/EB/CNS/Source/fortran/CNS_divop.F90
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90

commit 1c405bb2f1cc55b9e5a09efe506e4166672d0dea
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Sep 19 13:24:58 2017 -0700

    added some timers

Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBGraph.cpp

commit 5a5d94573a876ddfef700ac27df51ad3a0acab6d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 19 12:41:36 2017 -0700

    remove some debugging junk.

Src/Particle/AMReX_NeighborParticlesI.H

commit d3416799245751667d0dec419ff1d94f4329c8af
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Sep 19 12:40:32 2017 -0700

    refactor the neighbor particle code to make it easier to thread.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 63e513836cc4c9435b01c2802b9002db465e9b58
Merge: e04d0d974 b5f6e9b4f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Sep 19 10:32:26 2017 -0700

    Merge pull request #131 from AMReX-Codes/dtg_branch
    
    merging with development to get EBCellFlagFab caching in place

commit b5f6e9b4ffca7ccf5df4a716c221704c81d8a5ea
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Sep 19 10:31:07 2017 -0700

    took out some debugging statements

Src/EB/AMReX_EBLevel.cpp

commit 882e3fb4d8e0d84d218532a87de53b85b3ad52f8
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Sep 19 10:26:20 2017 -0700

    added cache of EBCellFlagFab inside EBGraph.   For the CNS benchmark problem, this appears to speed things up quite a lot.

Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBLevel.cpp
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISBox.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.cpp

commit e04d0d974c9af64535933c657b6689e563d7e842
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 19 10:16:51 2017 -0700

    add CHANGES

CHANGES

commit f3e29086fc21483a5aad7f9f18448b50362c11b4
Merge: 3910d99c3 84e8516eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 19 10:08:59 2017 -0700

    Merge branch 'development' into weiqun/eb
    
    Conflicts:
            Tutorials/EB/CNS/Source/fortran/CNS_divop.F90

commit 3910d99c39e7dabdca5e627bc5ad4bbc7884276b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 19 10:07:33 2017 -0700

    EBFluxRegister: finish 2D

Src/EB/AMReX_EBFluxRegister_2d.F90

commit 77980206952d232b2d10dde97ff6d07807ef0d49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 19 09:44:56 2017 -0700

    add some comments to EBFluxRegister

Src/EB/AMReX_EBFluxRegister.H

commit 84e8516ebe32fe2826824c8984e29a3fb8d4f409
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Sep 19 04:29:17 2017 -0400

    Allow small plotfile to have derived variables

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp

commit dab85aaf63d26e3c8de7b524c7d6c2a0eeb0baba
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Sep 18 17:41:44 2017 -0700

    remove an app

Src/AmrTask/tutorials/AMReXApps/3DJacobi/3DJacobi.C
Src/AmrTask/tutorials/AMReXApps/3DJacobi/Makefile

commit b54d07134a97045a3abbabb59b5e36965651f3c4
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Sep 18 17:37:57 2017 -0700

    add heat solver

Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H
Src/AmrTask/graph/AMReX_WorkerThread.H
Src/AmrTask/graph/AMReX_WorkerThread.cpp
Src/AmrTask/rts_impls/MPI_Generic/rts.C
Src/AmrTask/tutorials/MiniApps/HeatEquation/.DS_Store
Src/AmrTask/tutorials/MiniApps/HeatEquation/GNUmakefile
Src/AmrTask/tutorials/MiniApps/HeatEquation/Make.package
Src/AmrTask/tutorials/MiniApps/HeatEquation/advance.cpp
Src/AmrTask/tutorials/MiniApps/HeatEquation/advance_2d.f90
Src/AmrTask/tutorials/MiniApps/HeatEquation/advance_3d.f90
Src/AmrTask/tutorials/MiniApps/HeatEquation/init_phi_2d.f90
Src/AmrTask/tutorials/MiniApps/HeatEquation/init_phi_3d.f90
Src/AmrTask/tutorials/MiniApps/HeatEquation/inputs_2d
Src/AmrTask/tutorials/MiniApps/HeatEquation/inputs_3d
Src/AmrTask/tutorials/MiniApps/HeatEquation/main.cpp
Src/AmrTask/tutorials/MiniApps/HeatEquation/myfunc.H
Src/AmrTask/tutorials/MiniApps/HeatEquation/myfunc_F.H
Src/AmrTask/tutorials/MiniApps/HeatEquation/physbc.cpp

commit 9c6347ad1dcb7d704b2c34f9b03bb632d33b0c21
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Sep 18 16:50:46 2017 -0700

    relocate files

Src/AmrTask/graph/AMReX_AsyncMFIter.H
Src/AmrTask/graph/AMReX_AsyncMFIter.cpp

commit 30a4434bd9fdfbee6410d1a333020ac4f28d6930
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Sep 18 16:47:26 2017 -0700

    async MFIter interface

Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H
Src/AmrTask/AMFIter/AMReX_AsyncMFIter.cpp
Src/AmrTask/AMFIter/Makefile
Src/AmrTask/Makefile
Src/AmrTask/arch/arch.mpi.generic
Src/AmrTask/graph/RTS.H
Src/AmrTask/rts_impls/MPI_Generic/rts.C
Src/AmrTask/rts_impls/Serial/rts.C
Src/AmrTask/tutorials/UnitTests/001_TokenRing.C
Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C
Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C

commit bb8670270a0fd99dab7342061f78e51de213e008
Merge: 32466a1de 00a90a9aa
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 18 16:36:16 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 32466a1ded09f391583e8293a97d4f07b0b81c95
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 18 16:36:01 2017 -0700

    fix comment

Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 0bbeb22c6272930defb5718df6527363c148138f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 18 16:01:42 2017 -0700

    fix octree tutorial

Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90

commit 00a90a9aa0933008ba320b1d9a856b3756770b49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 18 16:01:42 2017 -0700

    fix octree tutorial

Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90

commit 9ef77637302f285b91e26b1a5767e76e9b8a1603
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Sep 18 15:57:46 2017 -0700

    CVODE: "CVODE" -> "\cvode"

Docs/AMReXUsersGuide/CVODE/CVODE.tex

commit f2d70e7001ffea40c0aeec61f3428764c1da8678
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Sep 18 15:27:32 2017 -0700

    CVODE: Move FCVODE doc cite from inline to a footnote

Docs/AMReXUsersGuide/CVODE/CVODE.tex

commit a3ab937e6c2bcc2869a889b00c492ac0ec51c99a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 18 13:26:09 2017 -0700

    fix more gcc shadow warnings

Src/Amr/AMReX_Amr.cpp
Src/EB/AMReX_EBFArrayBox.cpp
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_EBCellFAB.cpp
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_FaceIndex.cpp
Src/GeometryShop/AMReX_Stencils.cpp
Src/GeometryShop/AMReX_TransformIF.cpp
Tutorials/EB/CNS/Source/CNS_io.cpp

commit 623b7194670d7219a243eaf30148dffe9c9a9e40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 18 13:03:15 2017 -0700

    fixed some gcc -Wshadow warnings

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_Derive.cpp
Src/Amr/AMReX_StateDescriptor.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BCRec.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_CArena.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_ParmParse.cpp
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_VisMF.cpp
Src/Base/AMReX_iMultiFab.cpp
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_MacBndry.cpp
Src/Boundary/AMReX_Mask.cpp
Src/GeometryShop/AMReX_EBArith.cpp
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_FlatPlateGeom.cpp
Src/GeometryShop/AMReX_PolyGeom.H
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp

commit c219b596a0cc6763a9b9f31d65f206021574be38
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 18 12:40:22 2017 -0700

    for gcc >= 6, add -Wnull-dereference in DEBUG mode

Tools/GNUMake/comps/gnu.mak

commit ed8c1bec1ab2a06b515a564dff92a76e90efe139
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Sep 18 11:46:50 2017 -0700

    added volume mask to GeometryShop--on to testing it.

Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBGraph.H

commit 60a644c79f5b90bc07852e90ed6b77421653cde5
Merge: d05a04fb1 a0f804794
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Sep 18 11:02:05 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d05a04fb168d71846add91cf5effa863e6cd8f17
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Sep 18 11:01:46 2017 -0700

    Give the NeighborParticleContainer a regrid method and update the necessary internal data structures.

Src/Particle/AMReX_LoadBalanceKD.H
Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit a0f80479472bfe2441bc003e2035f160c67f21bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 18 09:16:20 2017 -0700

    add -Wshadow to gcc flags in DEBUG

Tools/GNUMake/comps/gnu.mak

commit c206280f9c3b7f207b2ffe43f4a6a1be10ef9378
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 18 09:01:40 2017 -0700

    tidy

Src/EB/AMReX_EBFluxRegister.cpp

commit d6824375683f7b000ca62135e46f7a2d1c9bab6d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 16 21:36:59 2017 -0700

    EBFluxRegister: omp atomic

Src/EB/AMReX_EBFluxRegister_3d.F90

commit 9b43b9507993d6f95a677f4ee0778fe5aace2195
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 16 21:18:46 2017 -0700

    EB/CNS: fix re-redistribution scaling and cleanup

Src/EB/AMReX_EBFluxRegister.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/fortran/CNS_divop.F90

commit c878f7f7b1b3d04ea31454d9b6ab01472fa2fca2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 16 14:51:41 2017 -0700

    EB/CNS: minor change for clarity

Tutorials/EB/CNS/Source/fortran/CNS_divop.F90

commit b1ddb21395616573a325a6d1f4d22c8f2693d683
Merge: d9a675afb 06734196f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Sep 16 13:53:43 2017 -0700

    moving minor optimiizations over to development

commit 06734196fec15c96c41252ab7dc81c206ea77827
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Sep 16 13:41:24 2017 -0700

    Some clean up and optimization of  EBLevel::defineDoIt.   It did not speed stuff up as much as I had hoped (amounted to 20 seconds off a 500 second run).

Src/EB/AMReX_EBLevel.H
Src/EB/AMReX_EBLevel.cpp

commit caa8ecbceda956440e6516d7dff3ce6c7f1e116f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 16 12:51:31 2017 -0700

    EB/CNS: rename some variables

Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/fortran/CNS_divop.F90
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90

commit d9a675afbd29d07dc77c170a73ca50e6e4557c1c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri Jul 7 01:28:08 2017 -0700

    Fix Intel Fortran compiler preprocessing of AMReX_REAL.H

Src/Base/AMReX_REAL.H

commit 274f409965b514ab94eddfbe02e5b2f43b044986
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 15 17:19:02 2017 -0700

    EB Re-redistribution: fix scaling

Src/EB/AMReX_EBFluxRegister_3d.F90
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/fortran/CNS_divop.F90
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90

commit 67f2f797fc9c58ceb6772358c4dff1ed0c4d1e06
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 15 18:02:10 2017 -0700

    Fix oops in last commit

Tools/Postprocessing/F_Src/GNUmakefile

commit 3563e1a9a3a5be8a9b586561f66005914a62f1df
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 15 17:41:14 2017 -0700

    Update plt_compare_diff_grids so that it measures the relative error the same as fcompare does --
    instead of dividing error by value pointwise it sums the error and sums the values and divides the sums.

Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90

commit 1437e3b1952bb55ed01f4bec5e14cc338db12cb8
Merge: cf0633d1c b55839956
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 15 17:20:00 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit cf0633d1cedbaa5c5e36ad842a217feb21a04a68
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 15 17:19:47 2017 -0700

    File should be fcompare not fcompareFinest

Tools/Postprocessing/F_Src/GNUmakefile

commit e0e68e7c329e3e34f05bf575603e818bf3ba59b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 15 16:05:11 2017 -0700

    EB/CNS: pass level to fortran just in case

Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90

commit b558399561e067acece29b938ab90dd86e98f822
Author: John Bell <jbbell@lbl.gov>
Date:   Fri Sep 15 15:23:37 2017 -0700

    added new options for eb redsitribution weighting

Tutorials/EB/CNS/Source/fortran/CNS_divop.F90
Tutorials/EB/CNS/Source/fortran/CNS_f.F90

commit 22101c638f74a8fede638c050212786110c57491
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 15 14:44:59 2017 -0700

    EB/CNS: add level mask

Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_3d.F90
Src/EB/AMReX_EBFluxRegister_F.H
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/fortran/CNS_divop.F90
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90
Tutorials/EB/CNS/Source/fortran/CNS_f.F90

commit f5875b18d1112a1d4a9ca52f7cdd0cc78bcae9ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 15 13:10:44 2017 -0700

    EB/CNS: fix bug

Tutorials/EB/CNS/Source/fortran/CNS_divop.F90

commit 2499be719cbb358a9a9552a830bfc856ff24d137
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 15 13:10:44 2017 -0700

    EB/CNS: fix bug

Tutorials/EB/CNS/Source/fortran/CNS_divop.F90

commit 073d8862d949d325ef812c10f917470ddc5047f2
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 15 13:02:31 2017 -0700

    turned on all the profiling flags I could find and I added some refinements on the benchmark inputs

Tutorials/EB/CNS/Exec/Combustor/GNUmakefile
Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs

commit 810e7bc00c2d50a0bbc9fe8958f4ff70d9e6d663
Merge: 766b12430 06499fa81
Author: jbb <jbbell@lbl.gov>
Date:   Fri Sep 15 12:47:48 2017 -0700

    Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development

commit 766b12430700e7112dc618679719b155fe301156
Author: jbb <jbbell@lbl.gov>
Date:   Fri Sep 15 12:45:33 2017 -0700

    added combustor inputs

Tutorials/EB/CNS/Exec/Combustor/inputs_combustor

commit ee46d14734f227b5813c3e3c97a09b9912371a7b
Author: jbb <jbbell@lbl.gov>
Date:   Fri Sep 15 12:44:52 2017 -0700

    added other swirling combustor

Tutorials/EB/CNS/Exec/Combustor/bc_fill_nd.F90_jbb
Tutorials/EB/CNS/Exec/Combustor/cns_prob.F90_jbb

commit 06499fa816b19df882eec249fc5597cdd5897f19
Merge: 52175793e 457d51713
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 15 11:57:34 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 52175793ea5ee17009185fbed11e032722658558
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 15 11:57:19 2017 -0700

    return from ReadData if filetype is PROFDATA.

Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp
Src/Extern/amrdata/AMReX_AmrData.cpp

commit 457d517137f3115ca4d924a72f1f30441830221c
Merge: 80c802c7f 30cbcb646
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 15 11:31:08 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 80c802c7ffddcaf148581e138cd99c817cf334a1
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 15 11:30:43 2017 -0700

    found some more macro usages that needed to be removed for intel

Src/EBAMRTools/AMReX_EBFortND.F90

commit 14677fe7361c55218acc585322c62a44f8b1f003
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 15 11:18:16 2017 -0700

    WIP: Re-Redistribution

Src/EB/AMReX_EBFluxRegister.H
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_3d.F90
Src/EB/AMReX_EBFluxRegister_F.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/fortran/CNS_divop.F90
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90

commit 30cbcb646221279d6676c848a99c94da9764bff8
Merge: bcdad3a71 094da2513
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 15 11:16:36 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit bcdad3a71467f15f68c61d8481ac1b852355dd8a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 15 11:10:58 2017 -0700

    miscellaneous bug fixes for the new neighbor filling stuff.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 094da2513c51e2f837245f417424202be8e602bb
Merge: c81ddf8e0 b36435f9d
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 15 11:05:37 2017 -0700

    getting fortran fix for intel compilers over

commit b36435f9d138df1f713991452e48662620027fac
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 15 11:02:38 2017 -0700

    took out CONSTANTS.H macro usage because it was breaking on intel compilers

Src/EBAMRTools/AMReX_EBFortND.F90

commit c81ddf8e0b70b9b63bd560dc3a28cce62275b59f
Merge: dc6fe6be1 9bf676407
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Sep 15 09:11:44 2017 -0700

    Merge pull request #129 from bcfriesen/fcompare_openmp
    
    Postprocessing: add OpenMP to fcompare tool

commit 9bf676407ae31b7aba51043724fb9e6b1953c34a
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Sep 14 20:53:41 2017 -0700

    Postprocessing: add COLLAPSE(2) to OpenMP PARALLEL DO in fcompare
    
    This will likely result in better load balance across threads where there are
    lots of threads.  E.g., on Xeon Phi on Cori, 2 threads per core means 136
    threads total, which is comparable to the trip count of the outermost loop.

Tools/Postprocessing/F_Src/fcompare.f90

commit 03c603ec13c970c94a5a4038786f732a3e83923d
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Sep 14 17:54:32 2017 -0700

    Postprocessing: add OpenMP to fcompare tool

Tools/Postprocessing/F_Src/fcompare.f90

commit dc6fe6be1c4f1cb50650026c97177b7df75852c3
Merge: a14f96da2 be8dfc87a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 14 18:20:02 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a14f96da2aa63a450a6fef5a7288df7e81af4f4b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 14 17:13:46 2017 -0700

    Fix bug in fillNeighbors when KDTree is used.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 6e7ae15062fb9a0ca9d97b4246cec56a153e67f0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Sep 14 16:55:10 2017 -0700

    turned profiling on and added a benchmark inputs file

Tutorials/EB/CNS/Exec/Combustor/GNUmakefile
Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs

commit 917c000cd94b6da565f8ee42a8766446dc2ee264
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 14 14:45:05 2017 -0700

    EBFluxRegister 2D

Src/EB/AMReX_EBFluxRegister_2d.F90
Src/EB/AMReX_EBFluxRegister_3d.F90

commit be8dfc87a1e49b99d179ace7e54dc42234a3cd04
Merge: c84ec9f48 b41647d4d
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Sep 14 14:41:27 2017 -0700

    merging so people can see EB section of the User's guide

commit b41647d4dbd75ef13fd8d70b675fe86b815c96a0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Sep 14 14:40:04 2017 -0700

    added EBFArrayBox fortran example section to user's guide

Docs/AMReXUsersGuide/EB/EB.tex

commit 7ccb52dcd29d284e144eabecaa60198cbf5985cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 14 14:20:05 2017 -0700

    EB Reflux works in 3D

Src/EB/AMReX_EBFluxRegister.H
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_3d.F90
Src/EB/AMReX_EBFluxRegister_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/fortran/CNS_divop.F90
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90

commit 0e9f79093852a4093fdf0a44d23e98faa5bdc8a3
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Sep 14 14:16:06 2017 -0700

    added EBFArrayBox section to user's guide

Docs/AMReXUsersGuide/EB/EB.tex

commit c84ec9f48f171c4f7502820c9cfeea80172e53ba
Merge: 05807f4d3 85a5ea98b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 17:22:56 2017 -0700

    Merge branch 'development' into weiqun/eb
    
    Conflicts:
            Src/GeometryShop/AMReX_EBISLevel.cpp
            Src/GeometryShop/AMReX_GeometryShop.cpp

commit 85a5ea98bc7febb09927253425d99f0385d06969
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 17:03:12 2017 -0700

    EB regression tests inputs

Tools/RegressionTesting/AMReX-tests.ini
Tutorials/EB/CNS/Exec/Combustor/inputs.regt
Tutorials/EB/CNS/Exec/Pulse/inputs.regt
Tutorials/EB/CNS/Exec/ShockRef/inputs.regt

commit 81381380355dd1553eeb3ae63f9d085c995456ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 16:34:06 2017 -0700

    EB/CNS: for regression test, zero out Cost_Type

Tutorials/EB/CNS/Source/CNS_io.cpp

commit ef39b7fbe33c67e9138e67bee6a125f96a3821b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 16:12:12 2017 -0700

    BaseIFFABI: whenever copying from memory, avoid copying nan

Src/GeometryShop/AMReX_BaseIFFABI.H

commit 7a0303245be8e4659efbdf2f67fd57dd37be1e0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 15:42:08 2017 -0700

    EBData: use qnan instead of snan because gcc 4.8.4 crahes on calling std::isnan with snan

Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp

commit 86504d0682651a5ffa70942f7654d82ece5a65a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 15:19:55 2017 -0700

    always initialize EBData to snan.  we can then use std::isnan to detect whether a face has good data

Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_EBData.cpp
Tests/GeometryShop/ramp/main.cpp

commit 65d5babaa21d870912d5de7bdf63609bd6d15324
Merge: 0f36e3dbb 8f4af5eb1
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 13 14:56:06 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 0f36e3dbb1e525624bcbc28dffc074417289cc1a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 13 14:56:02 2017 -0700

    added dirname to inputs, updated readme.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/IOBenchmark/README
Tests/IOBenchmark/inputs.dirname
Tests/IOBenchmark/inputs.small

commit 8f4af5eb11302f850f786f66101d5d826b140b26
Merge: 5e86daf00 06802b31d
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 13 14:52:37 2017 -0700

    Merge branch 'development' into dtg_branch
    
    Conflicts:
            Src/GeometryShop/AMReX_BaseIFFAB.H
            Src/GeometryShop/AMReX_BaseIFFABI.H
            Src/GeometryShop/AMReX_EBData.cpp
            Src/GeometryShop/AMReX_GeometryShop.cpp

commit 06802b31d63e5d1e69aace154f17b4d73317e824
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 14:44:20 2017 -0700

    mod ramp test for debugging

Tests/GeometryShop/ramp/GNUmakefile
Tests/GeometryShop/ramp/main.cpp

commit 5e86daf004fd83fe0d8b21984ff15bea1ed0cdde
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 13 14:40:04 2017 -0700

    took out debugging statements and fixed Weiqun's test so that it has some chance of passing

Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp
Tests/EBAMRTools/regression/runalltests.serial.sh
Tests/GeometryShop/regression/ebio.cpp

commit fa46476619667a919742e6f33f8ce3b382c83a1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 14:26:23 2017 -0700

    BaseIFFAB copy in FabArray copy is not thread safe

Src/GeometryShop/AMReX_BaseIFFAB.H

commit 60fde578759f0f6ce7e6b671dd5260b2bbd87195
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 14:24:25 2017 -0700

    comment out some debug codes

Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp

commit c294ad02da3ebd50fe107e5ed2658c44422c18a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 13:58:38 2017 -0700

    add an assertion

Src/GeometryShop/AMReX_BaseIFFAB.H

commit a6faad7fa81c9c18ad08e15c13e8c27314c56368
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 13:55:24 2017 -0700

    The FabArray constructor that takes array of pointers must define factory data member too

Src/Base/AMReX_FabArray.H

commit a001a2f78ac2ae9dd9429c402403ee644dc530d5
Merge: a11c2f83c 1dfa291b5
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 13 13:09:42 2017 -0700

    Merge pull request #127 from AMReX-Codes/dtg_branch
    
    Ann wanted this merged over mostly because of EB user's guide

commit 1dfa291b560cb0d241b2af547f9741d865dd3108
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 13 13:07:12 2017 -0700

    fixed more regression tests that were broken by recent interface changes

Tests/EBAMRTools/regression/GNUmakefile
Tests/EBAMRTools/regression/aggpwlfpTest.cpp
Tests/EBAMRTools/regression/divergenceOpTest.cpp
Tests/EBAMRTools/regression/ebCoarseAveTest.cpp
Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp
Tests/EBAMRTools/regression/ebFineInterpTest.cpp
Tests/EBAMRTools/regression/fluxRegTest.cpp
Tests/EBAMRTools/regression/gradientOpTest.cpp
Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp
Tests/EBAMRTools/regression/runalltests.mpi.sh
Tests/EBAMRTools/regression/simpleMeshRefine.cpp

commit f9990e8c1e8d11a9aa97ec848ea1c986aad8ebb5
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 13 12:44:24 2017 -0700

    fixed regression tests that were broken by recent interface changes

Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp
Tests/GeometryShop/ebgraphDistributed/GNUmakefile
Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp
Tests/GeometryShop/ebgraphSingleGrid/GNUmakefile
Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp
Tests/GeometryShop/flatPlate/GNUmakefile
Tests/GeometryShop/flatPlate/flatPlateTest.cpp
Tests/GeometryShop/ramp/main.cpp
Tests/GeometryShop/regression/GNUmakefile
Tests/GeometryShop/regression/runalltests.mpi.sh
Tests/GeometryShop/runalltests.serial.sh
Tests/GeometryShop/sparseDataSingleGrid/GNUmakefile
Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp

commit 3a27131e93c070bbf9eb2e2d4731b222c5aad81f
Merge: 67042afc3 61564822f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 13 09:33:44 2017 -0700

    Merge branch 'development' into dtg_branch

commit 61564822f7e89c378eb6f4aaaf5485d3f6355c7b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 13 09:33:35 2017 -0700

    make default debug=true

Tests/GeometryShop/ramp/GNUmakefile

commit a11c2f83c74ec02bd223eddee94dacafa6cba6a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 09:01:17 2017 -0700

    fix compilation

Src/EB/AMReX_EBAmrUtil.cpp
Src/EB/AMReX_EBMultiFabUtil.cpp
Tests/GeometryShop/ramp/GNUmakefile

commit a92048dbb86dc6b0e789967453cd2c3f13345e39
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 08:53:29 2017 -0700

    fix make

Tests/GeometryShop/ramp/GNUmakefile

commit 67042afc3ec5b2c583645bc5474f7e94bb8da5cd
Merge: 384ff38d4 32fe4adbb
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Sep 13 08:48:46 2017 -0700

    Merge branch 'development' into dtg_branch

commit 32fe4adbb2ed25295ab5c10ca8264188a2a013af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 13 08:44:35 2017 -0700

    modify test for debugging

Tests/GeometryShop/ramp/inputs
Tests/GeometryShop/ramp/main.cpp

commit 05807f4d3749ffb46635ad0ef3bd54eda07feb54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 12 20:32:02 2017 -0700

    typo

Src/GeometryShop/AMReX_EBData.cpp

commit 384ff38d4df699e9fc35bb6fe8ab803c7ab1062d
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Sep 12 16:23:28 2017 -0700

    more user's guide stuff.

Docs/AMReXUsersGuide/EB/EB.tex

commit 288e591acc1f67984d3d64557dc64ae0ce754428
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 12 15:27:37 2017 -0700

    more const&

Src/GeometryShop/AMReX_EBData.cpp

commit f8b76565080a0f23aff2b3ff6258c17f8cf15537
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Sep 12 15:13:45 2017 -0700

    starting to flesh out EB user's guide

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/EB/EB.tex
Docs/AMReXUsersGuide/EB/graph.pdf
Docs/AMReXUsersGuide/EB/multidivide.pdf
Docs/AMReXUsersGuide/EB/volume.pdf
Docs/AMReXUsersGuide/GNUmakefile
Docs/AMReXUsersGuide/Particle/Particle.tex

commit 23e9adb138e2d67e3aee0e79f899ff3809454969
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 12 14:48:23 2017 -0700

    constexpr instead of macros

Src/GeometryShop/AMReX_EBDataVarMacros.H

commit a06e99f07a079c4fa09f7b87c4b58dd349dea68f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 12 13:49:03 2017 -0700

    prefer make_shared; tidy

Src/GeometryShop/AMReX_EBData.H

commit 9185120b51d2dd040a9a268f9d86d6e5e89824b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 12 13:15:59 2017 -0700

    built-in array to std::array; pass shared_ptr by reference

Src/GeometryShop/AMReX_EBDataFactory.H
Src/GeometryShop/AMReX_GraphNode.H
Src/GeometryShop/AMReX_GraphNode.cpp

commit d7ca2bc19e2e95cb396e41703209a77bebfd1e21
Merge: 3256cd29b cc292eb70
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Tue Sep 12 14:49:36 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 32d0fb8b5b08f62894310d983d8708a88da054fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 12 11:56:42 2017 -0700

    small changes

Src/GeometryShop/AMReX_EBGraph.cpp

commit 87d0f813e1fa4e9054617ca7dc72f5ecf34d0251
Merge: 3fa322b97 cc292eb70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 16:24:50 2017 -0700

    Merge branch 'development' into weiqun/eb
    
    Conflicts:
            Src/GeometryShop/AMReX_EBGraph.cpp

commit cc292eb708aa2f36da1e97b39fdfbf595e481e47
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 16:23:38 2017 -0700

    remove unused and wrong functions with Dan's approval

Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp

commit 3fa322b9724985a9b0ef2a97688f3b00e167b3eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 16:10:34 2017 -0700

    tidy

Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp

commit 7a46a0fb24918b98e0f91dad7713b7e51e16dc87
Merge: e7ae77cf0 3bfd7f931
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 13:15:19 2017 -0700

    Merge branch 'development' into weiqun/eb

commit 3bfd7f93186329a7b9a5e329846093d21c2e40f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 13:15:02 2017 -0700

    move LayoutData class from GeometryShop to Base

Src/Base/AMReX_LayoutData.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/GeometryShop/Make.package

commit f7bffd26fa7670a8464d2919c973afd9ed00f6ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 12:24:47 2017 -0700

    add assertion to LayoutData

Src/GeometryShop/AMReX_LayoutData.H

commit e7ae77cf04255e7ccc19933f1197f4452e30cd82
Merge: bfe33e931 4273e5007
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 12:40:43 2017 -0700

    Merge branch 'development' into weiqun/eb

commit 4273e50079d9593e4608f92eaca4ab5869de032d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 12:40:11 2017 -0700

    LayoutData: operator[] now takes global index

Src/GeometryShop/AMReX_BaseIVFactory.H
Src/GeometryShop/AMReX_IrregFABFactory.cpp
Src/GeometryShop/AMReX_LayoutData.H

commit bfe33e93142161bbfb5df55b1d4a4be9ffc1fafc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 12:24:47 2017 -0700

    add assertion to LayoutData

Src/GeometryShop/AMReX_LayoutData.H

commit 6f06c1fef9ec50fbb9885865467a069a1924779f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 12:06:50 2017 -0700

    EB/CNS: test domain boundary in CNS_eb_fixup_geom

Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/fortran/CNS_nd.F90

commit 4dc5ff41c79124bc5d54f2c662b48316a2ec211f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 11:18:17 2017 -0700

    tidy

Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp

commit 402abe3aa3bd7a499351dcb00031af36e17f5a34
Merge: b91ff99ad 78b741cfa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 09:49:50 2017 -0700

    Merge branch 'development' into weiqun/eb

commit b91ff99ad2a7bf272836efdd00f75ad95c734677
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 09:28:37 2017 -0700

    use <algorithm> instead of our own code

Src/GeometryShop/AMReX_EBIndexSpace.cpp

commit 78b741cfa4b5d1f7e9aca56a36428cbdb998571b
Merge: 9ff691f8a fe8de1796
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Sep 11 09:25:39 2017 -0700

    Merge pull request #125 from AMReX-Codes/dtg_branch
    
    merging some bug fixes back over to development

commit fe8de17961ebe04242c44486c9f5af910ceef615
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Sep 11 09:24:18 2017 -0700

    in GeometryShop::fixRegularNextToCovered, corner cells outside the domain were recognized as such, causing some faces to be incorrectly labelled as non-boundary

Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_IrregNode.cpp

commit 0bc910e519c8969652abc05b9261d5c2d52efd43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 11 09:11:35 2017 -0700

    raw pointer -> unique_ptr

Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp

commit 2aeef0ef626f06102ac698a21b96d3ed60147159
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Sep 11 09:11:59 2017 -0700

    bug fix identified by Weiqun

Src/GeometryShop/AMReX_GeometryShop.cpp

commit 3f4b3f961929c31afad07fce1d073f0648fbe1e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 10 12:58:59 2017 -0700

    minor

Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_Moments.H

commit 8bdc08ee631fc3b2080cb2403bcd22cfde1c5bf4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 22:27:19 2017 -0700

    tidy

Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_IrregNode.cpp

commit 7bb8bb92488ea860dc45ec1815753b7ca1188583
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 21:39:53 2017 -0700

    tidy

Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_GraphNode.cpp

commit 4f2a93595a01be646431984de5e94de57eb0a3da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 21:31:10 2017 -0700

    built-in array -> std::array

Src/GeometryShop/AMReX_IrregNode.H

commit 9ff691f8ac695acf0b693951f44717d64a782ff5
Merge: fdacbd6c5 380c31595
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Sep 9 17:50:54 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit fdacbd6c56dfdb89113611b4caa141580c79c216
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Sep 9 17:50:38 2017 -0700

    Fix logic that enforces a minimum split size in the KD Tree load balancer.

Src/Particle/AMReX_LoadBalanceKD.cpp

commit 4d7bf209a7fb177fce50a9fbeef80e8962fffe89
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 15:48:20 2017 -0700

    tidy

Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp

commit 49f80f65be68e8dcd6a4b1918bb003769d43b395
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 15:24:48 2017 -0700

    builtin array to std::array

Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp

commit e8d8068df7db44ca2e0b574f48517cc898ab1732
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 14:59:43 2017 -0700

    tidy

Src/GeometryShop/AMReX_GeometryService.H
Src/GeometryShop/AMReX_GeometryService.cpp

commit 380c31595502172d9d2066396ebee0f732034f0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 14:44:32 2017 -0700

    add back ivsFine

Src/EBAMRTools/AMReX_EBCoarseAverage.cpp

commit 820f3d26e7fff790a725f83d3200ee549f79502b
Merge: f9ca99bcf 0a2601b6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 14:21:26 2017 -0700

    Merge branch 'development' into weiqun/eb

commit 0a2601b6af1a36a3d255b1c1cd5b4a1cd1ab27e5
Merge: bda85a342 3597566b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 13:09:50 2017 -0700

    Merge branch 'weiqun/cu' into development

commit bda85a342934ccd39b15d2d0bc47c4827d7fdba1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 13:06:37 2017 -0700

    remove virtual from IrregFAB and IVFAB

Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_EBDataFactory.H
Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_IrregFAB.H
Src/GeometryShop/AMReX_LoHiSide.cpp

commit f9ca99bcf41158913572f3e6d7216bc98349d327
Merge: 5cf42c37e 8ae698a4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 13:01:23 2017 -0700

    merge

commit 8ae698a4c1a411969e31e5a76cd73ce7a9ada6f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 12:56:45 2017 -0700

    vector -> Array

Src/GeometryShop/AMReX_EBISLevel.cpp

commit bbf38391af0d3443ef39f77e3eeb7d50d9bab68d
Merge: 71037d4de 4a9d39d3b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Sep 9 12:06:34 2017 -0700

    Merge pull request #124 from AMReX-Codes/dtg_branch
    
    Getting some important bug fixes into development

commit 4a9d39d3b4d122defeaa17ecd906d704ce481955
Merge: fa0cbfbf1 71037d4de
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Sep 9 12:06:13 2017 -0700

    Merge branch 'development' into dtg_branch

commit fa0cbfbf19d333ce9521e3c8a38cd1487c9cff2b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Sep 9 12:00:24 2017 -0700

    took out debugging statements

Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp

commit 93250eabfcd28bed2b7e5a86a14101a4258f8cc3
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Sep 9 11:47:03 2017 -0700

    after much wailing and gnashing of teeth (and quite a bit of software refactoring), I have fixed the nan bug that Weiqun identified.   There are still a bunch of debugging statements in the code.  I will remove them before merging with development

Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp

commit 71037d4de9ee784136ab8cf87f7c0d269b81a542
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 08:16:33 2017 -0700

    vector -> Array

Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H
Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp
Src/EBAMRTools/AMReX_DivergenceOp.cpp
Src/EBAMRTools/AMReX_EBCFInterp.H
Src/EBAMRTools/AMReX_EBCFInterp.cpp
Src/EBAMRTools/AMReX_EBCoarseAverage.cpp
Src/EBAMRTools/AMReX_EBFineInterp.H
Src/EBAMRTools/AMReX_EBFineInterp.cpp
Src/EBAMRTools/AMReX_EBLevelDataOps.H
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Src/EBAMRTools/AMReX_GradientOp.H
Src/EBAMRTools/AMReX_GradientOp.cpp
Src/EBAMRTools/AMReX_MeshRefine.H
Src/EBAMRTools/AMReX_MeshRefine.cpp

commit 0ee0828ccfc8985b0975e4aa171900967417f07e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 9 08:03:18 2017 -0700

    vector -> Array to get bound checking in debug mode

Src/GeometryShop/AMReX_AggStencil.H
Src/GeometryShop/AMReX_AggStencilI.H
Src/GeometryShop/AMReX_AllRegularService.H
Src/GeometryShop/AMReX_AllRegularService.cpp
Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_BaseEBCellFABI.H
Src/GeometryShop/AMReX_BaseEBCellFactory.H
Src/GeometryShop/AMReX_BaseEBFaceFAB.H
Src/GeometryShop/AMReX_BaseEBFaceFABI.H
Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/AMReX_ComplementIF.H
Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBArith.cpp
Src/GeometryShop/AMReX_EBCellFAB.cpp
Src/GeometryShop/AMReX_EBCellFactory.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBDebugOut.H
Src/GeometryShop/AMReX_EBDebugOut.cpp
Src/GeometryShop/AMReX_EBFaceFAB.cpp
Src/GeometryShop/AMReX_EBFluxFAB.H
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISBox.H
Src/GeometryShop/AMReX_EBISBox.cpp
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp
Src/GeometryShop/AMReX_FabArrayIO.H
Src/GeometryShop/AMReX_FaceIterator.H
Src/GeometryShop/AMReX_FaceIterator.cpp
Src/GeometryShop/AMReX_FlatPlateGeom.H
Src/GeometryShop/AMReX_FlatPlateGeom.cpp
Src/GeometryShop/AMReX_GeometryService.H
Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_GraphNode.H
Src/GeometryShop/AMReX_GraphNode.cpp
Src/GeometryShop/AMReX_IntVectSet.H
Src/GeometryShop/AMReX_IntVectSet.cpp
Src/GeometryShop/AMReX_IntersectionIF.H
Src/GeometryShop/AMReX_IntersectionIF.cpp
Src/GeometryShop/AMReX_IrregFAB.H
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_LSquares.H
Src/GeometryShop/AMReX_LSquares.cpp
Src/GeometryShop/AMReX_LatheIF.H
Src/GeometryShop/AMReX_LayoutData.H
Src/GeometryShop/AMReX_Moments.H
Src/GeometryShop/AMReX_Moments.cpp
Src/GeometryShop/AMReX_PolyGeom.H
Src/GeometryShop/AMReX_PolyGeom.cpp
Src/GeometryShop/AMReX_RedistStencil.cpp
Src/GeometryShop/AMReX_SlabService.H
Src/GeometryShop/AMReX_SlabService.cpp
Src/GeometryShop/AMReX_Stencils.H
Src/GeometryShop/AMReX_TransformIF.H
Src/GeometryShop/AMReX_TransformIF.cpp
Src/GeometryShop/AMReX_UnionIF.H
Src/GeometryShop/AMReX_UnionIF.cpp
Src/GeometryShop/AMReX_VoFIterator.H
Src/GeometryShop/AMReX_VoFIterator.cpp
Tutorials/EB/CNS/Source/CNS_init_eb.cpp

commit 3597566b56f5b4cdf6f7fdaa00ea8bde4ae80132
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 8 21:47:05 2017 -0700

    add virtual override

Src/GeometryShop/AMReX_GeometryShop.H

commit a3b305611d1e5d2b46010e2178696623a7f2289f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 8 21:38:49 2017 -0700

    removed virtual from BaseIVFAB and IrregFAB

Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_EBDataFactory.H
Src/GeometryShop/AMReX_IrregFAB.H
Src/GeometryShop/AMReX_LoHiSide.cpp

commit 96dad9a1f5422c983e831fa6649f43a0b2f329c9
Merge: 4e978226a e828afba9
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Sep 8 17:28:19 2017 -0700

    Merge pull request #123 from AMReX-Codes/threaded_redistribute
    
    Threaded redistribute

commit 4e978226a91ff0b47de3125b3fe5957175fca7a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 8 17:24:41 2017 -0700

    override and minor cleanup

Src/GeometryShop/AMReX_GeometryService.H
Src/GeometryShop/AMReX_GeometryService.cpp
Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_IntVectSet.cpp

commit 9444122207e707041c4ee4ea0936529cd6f4f974
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 8 17:17:19 2017 -0700

    minor clean up

Src/GeometryShop/AMReX_PlaneIF.H
Src/GeometryShop/AMReX_PlaneIF.cpp

commit 5cf42c37e056493c718a28b9ef4c22f157a618ab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 8 16:20:36 2017 -0700

    EB/CNS: new parameter cns.refine_cutcells=1

Src/Amr/AMReX_Amr.cpp
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp

commit 1733839ceba5ea05119132cc4a345e7442f528cc
Merge: 1b256042a ab6f6eec6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 8 16:13:20 2017 -0700

    Merge branch 'development' into threaded_neighbor_list

commit 3a876f474464e21f885abd6ced802d1ae610a09d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 8 14:27:02 2017 -0700

    move some scattered EB files into a new directory Src/EB

Src/AmrCore/Make.package
Src/Base/Make.package
Src/EB/AMReX_EBAmrUtil.H
Src/EB/AMReX_EBAmrUtil.cpp
Src/EB/AMReX_EBAmrUtil_F.H
Src/EB/AMReX_EBAmrUtil_nd.F90
Src/EB/AMReX_EBCellFlag.H
Src/EB/AMReX_EBCellFlag.cpp
Src/EB/AMReX_EBCellFlag_F.H
Src/EB/AMReX_EBFArrayBox.H
Src/EB/AMReX_EBFArrayBox.cpp
Src/EB/AMReX_EBFabFactory.H
Src/EB/AMReX_EBFabFactory.cpp
Src/EB/AMReX_EBFaceFlag.H
Src/EB/AMReX_EBFaceFlag.cpp
Src/EB/AMReX_EBFluxRegister.H
Src/EB/AMReX_EBFluxRegister.cpp
Src/EB/AMReX_EBFluxRegister_1d.F90
Src/EB/AMReX_EBFluxRegister_2d.F90
Src/EB/AMReX_EBFluxRegister_3d.F90
Src/EB/AMReX_EBFluxRegister_F.H
Src/EB/AMReX_EBInterp_F.H
Src/EB/AMReX_EBInterpolater.H
Src/EB/AMReX_EBInterpolater.cpp
Src/EB/AMReX_EBLevel.H
Src/EB/AMReX_EBLevel.cpp
Src/EB/AMReX_EBMultiFabUtil.H
Src/EB/AMReX_EBMultiFabUtil.cpp
Src/EB/AMReX_EBMultiFabUtil_2d.F90
Src/EB/AMReX_EBMultiFabUtil_3d.F90
Src/EB/AMReX_EBMultiFabUtil_F.H
Src/EB/AMReX_EBMultiFabUtil_nd.F90
Src/EB/AMReX_ebcellflag_mod.F90
Src/EB/AMReX_ebinterp_1d.F90
Src/EB/AMReX_ebinterp_2d.F90
Src/EB/AMReX_ebinterp_3d.F90
Src/EB/Make.package
Tutorials/EB/CNS/Exec/Make.CNS

commit e828afba93b6d517348edcf832e761771dc760c3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 8 14:13:09 2017 -0700

    Pass in the explicit tile size to the dummy mfiter

Src/Particle/AMReX_ParticleContainerI.H

commit ab6f6eec605771b7ef747943a195b9a254b69872
Merge: 5481f113c f9b1a78c3
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Sep 8 13:48:15 2017 -0700

    Merge pull request #122 from bcfriesen/fix_vtune_linking
    
    GNUMake: update the env var pointing to the VTune directory at NERSC

commit 5481f113ced48df34650384630ef3cb0944e85c7
Merge: 66a19c3ec 96d92f72c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Sep 8 13:45:02 2017 -0700

    Merge pull request #121 from bcfriesen/fix_cvode_linking
    
    GNUMake: remove links to FCVODE, the old Fortran wrapper to CVODE

commit c70905079eef087d2c58657256a1a4277314d076
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 8 13:31:58 2017 -0700

    set default tiling back to false.

Src/Particle/AMReX_ParticleContainerI.H

commit 9674db7c5092546c1c555b6054e76e84eab824b5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 8 12:58:27 2017 -0700

    fix dumb mistake

Src/Particle/AMReX_ParticleContainerI.H

commit 66a19c3ecc3ee66ef289082d89fc95db125dac14
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 8 12:45:58 2017 -0700

    Slight typo corrections

Docs/Migration/Migration.md

commit d146a132f0aee6594573d506a63b9d1655cc5fe8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 8 12:45:45 2017 -0700

    also handle the soa data in the threaded redistrbute.

Src/Particle/AMReX_ParticleContainerI.H

commit f9b1a78c3b96f32a7973193273ee96b0aaea17b6
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Sep 8 12:16:47 2017 -0700

    GNUMake: update the env var pointing to the VTune directory at NERSC
    
    The default version at NERSC is now VTune 2017, so we need to update this
    environment variable or else compiling will fail.

Tools/GNUMake/tools/Make.vtune

commit 96d92f72c533637fac3a8362fcd6ab34cfd2fad9
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Sep 8 12:10:53 2017 -0700

    GNUMake: remove links to FCVODE, the old Fortran wrapper to CVODE
    
    FCVODE comes with CVODE and provides a Fortran interface to the CVODE library,
    but is not thread-safe. Recently the SUNDIALS developers provided us with a
    Fortran 2003 interface to CVODE which uses iso_c_binding to most of the
    functions in the library. So remove the links to the old FCVODE library since
    we don't need it anymore.

Tools/GNUMake/packages/Make.cvode

commit 1efcea0c0f7d9eccd5f3547d2a3b4a783833a49a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 8 11:29:19 2017 -0700

    removed this by mistake.

Src/Particle/AMReX_ParticleContainerI.H

commit 83db808e2ef5ff1456ffce0c432949eaefff8776
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 8 11:20:35 2017 -0700

    fix bug affecting hydrid MPI / OpenMP redistribute.

Src/Particle/AMReX_ParticleContainerI.H

commit 2aeb42bae67a2a6636454d7be6b461fd6539f95d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 8 10:43:29 2017 -0700

    also reset has_hashmap here.

Src/Base/AMReX_BoxArray.cpp

commit 3562ad544c2d3622fb4c2620eb61560207abc47e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 8 10:38:27 2017 -0700

    reset has_hashmap when the map is cleared.

Src/Base/AMReX_BoxArray.cpp

commit b39013fadf61f06f880d77a1fd74cbb008b4c218
Merge: 6a2bbc6a9 cfb1c765f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 8 10:24:25 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6a2bbc6a910585ff643ce3509d323dd56544aea5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Sep 8 10:24:14 2017 -0700

    enforce a min box size in the KDTree load balancer.

Src/Particle/AMReX_LoadBalanceKD.H
Src/Particle/AMReX_LoadBalanceKD.cpp

commit bd8781d7cbd9b5ee7ff6b93cfb6b02a349b7d729
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 8 09:33:19 2017 -0700

    2D EBFluxRegister

Src/AmrCore/AMReX_EBFluxRegister_2d.F90

commit 00a51112a23a7682a8e897fb0547858b9a53811d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 8 09:21:59 2017 -0700

    minor

Src/AmrCore/AMReX_EBFluxRegister_3d.F90
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp

commit 8f09e58bc35b0c10927d2ef1f2b64df5faded98e
Merge: f5cd89f4c cfb1c765f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 8 08:22:39 2017 -0700

    merging with development to get weiqun's test

commit 3256cd29b1fa6b77179b16ce7dac4e0f285e8403
Merge: d04f9491d cfb1c765f
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Fri Sep 8 00:13:18 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d1b136bbc2a9b3a76b329f76889563c9cde2117b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 7 17:31:36 2017 -0700

    EB: fix init_snan

Src/GeometryShop/AMReX_EBData.cpp

commit cfb1c765fdb5b4da0b8e422f7472f7e4f799da1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 7 17:31:36 2017 -0700

    EB: fix init_snan

Src/GeometryShop/AMReX_EBData.cpp

commit 8a532558cfdf61942b5277076b86f2b19be0c800
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 7 17:09:38 2017 -0700

    initialize EB data to snan to help debug

Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp

commit 26eac8250c42f46e9123ac5f25cd0844c6d77fc4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 7 17:10:58 2017 -0700

    EB/CNS: pass mpi rank to fortran to help debugging

Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_setup.cpp
Tutorials/EB/CNS/Source/fortran/CNS_f.F90

commit 00b2fe91270e5458a0ce43b849c54b4bf2b093f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 7 17:09:38 2017 -0700

    initialize EB data to snan to help debug

Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp

commit 16fb58c4c738eb79a36585e3c97db8dbc76947ba
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 7 16:54:43 2017 -0700

    need to create any missing map entries in serial here before the parallel reduction.

Src/Particle/AMReX_ParticleContainerI.H

commit b4fbcdc83637bc304a2908469743d2afe35250f8
Merge: 697ed7c85 cba746153
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 7 16:13:16 2017 -0700

    Merge branch 'development' into weiqun/eb

commit 03913d3939c0f7be117c18d0417445a5a93481ca
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 7 15:33:14 2017 -0700

    Don't want to perform this check inside a critical region, since in particle code we call this a lot from threaded regions.

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit f5cd89f4c66a1588604e077fecf0ea6788703cb9
Merge: fdfe0bfa2 cba746153
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Sep 7 15:17:24 2017 -0700

    Merge branch 'development' into dtg_branch

commit fdfe0bfa2ce5e50051e2d5369e1d870658826813
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Sep 7 15:02:52 2017 -0700

    more bugs found.  need to pivot toward writing documents now.

Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Tests/EBAMRElliptic/exec/conductivitySolve.cpp

commit 697ed7c85a12d603472448dd33ef581b71d16823
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 7 14:57:50 2017 -0700

    WIP: don't tag covered cells

Src/AmrCore/AMReX_EBAmrUtil_nd.F90

commit 25f9f6a6fe24a69578302dbabafe6bf45651ba54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 7 14:27:37 2017 -0700

    WIP: EBFluxRegister: bug fix

Src/AmrCore/AMReX_EBFluxRegister.cpp
Src/AmrCore/AMReX_EBFluxRegister_3d.F90

commit 9543fbb09f9db9e4972860069afee860180bbe26
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 7 13:22:24 2017 -0700

    WIP: EBFluxRegister::Reflux

Src/AmrCore/AMReX_EBFluxRegister.H
Src/AmrCore/AMReX_EBFluxRegister.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp

commit 10960f4d68c7c265c67ea94f78b5c676b71f9765
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 7 12:41:06 2017 -0700

    WIP: EBFluxRegister::FineAdd

Src/AmrCore/AMReX_EBFluxRegister.H
Src/AmrCore/AMReX_EBFluxRegister.cpp
Src/AmrCore/AMReX_EBFluxRegister_3d.F90
Src/AmrCore/AMReX_EBFluxRegister_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90

commit 32e1d7f4fdf8e9f7f596efe28a8982f02039ccc4
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Sep 7 12:05:47 2017 -0700

    conductivity op seems to work now.  God I hate fortran.

Src/EBAMRElliptic/AMReX_EBEllipticFort.F90
Src/EBAMRElliptic/AMReX_VCAggStencil.cpp
Tests/EBAMRElliptic/exec/cond.inputs

commit ed1313d174c6a4878c182daed79a68e8d1b8cde6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 7 10:46:51 2017 -0700

    accidently screwed up caching by moving this - fixing.

Src/Particle/AMReX_ParticleContainerI.H

commit 3c247fdb0c80aefdd25668bc8fa496bfca0cb752
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Sep 7 10:07:20 2017 -0700

    give the AoS insert and delete methods and use them.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit cba746153c6709602da02cfb4179cfa36f223a9f
Merge: da7eb4e48 69eaea40d
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Sep 7 08:47:17 2017 -0700

    Merge pull request #120 from kweide/development
    
    Expose MFIter's index() method to Fortran code as grid_index()

commit 69eaea40d056f8193e2e9a1ad3d0e4e954e69416
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Wed Sep 6 22:08:10 2017 -0500

    Expose MFIter's index() method to Fortran code as grid_index()
    
    The Fortran multifab already has a dataPtr() method that takes an
    index, so there should also be a way to get such an index from
    an iterator over a multifab.
    
    analogous to the AMReX_octree iterator's grid_index(), whence the name

Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 6cdb82016121e80a9e59c75294c2151573927dc3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 6 17:38:03 2017 -0700

    WIP: EBFluxRegister

Src/AmrCore/AMReX_EBFluxRegister.H
Src/AmrCore/AMReX_EBFluxRegister.cpp
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp

commit fbd891715c3f28992e4028167e86adce66007637
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 6 16:58:34 2017 -0700

    in the first pass, thread over tiles instead of threading over the particles on a tile.

Src/Particle/AMReX_ParticleContainerI.H

commit 25f695f651c9d34b0046e1170f94b495f312ebd9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 6 16:18:19 2017 -0700

    WIP: EBFluxRegister

Src/AmrCore/AMReX_EBFluxRegister.H
Src/AmrCore/AMReX_EBFluxRegister.cpp
Src/AmrCore/AMReX_EBFluxRegister_1d.F90
Src/AmrCore/AMReX_EBFluxRegister_2d.F90
Src/AmrCore/AMReX_EBFluxRegister_3d.F90
Src/AmrCore/AMReX_EBFluxRegister_F.H
Src/AmrCore/Make.package
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_io.cpp
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90

commit 6a51f1a19bf96953f7866d18df69a7b90fd3d771
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 6 15:53:03 2017 -0700

    OpenMP support in Redistribute compiles and gives the right answers.

Src/Particle/AMReX_ParticleContainerI.H

commit da7eb4e480f804438b93dff773087442368bdad5
Merge: 09006ab32 c80c209dc
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 6 14:30:42 2017 -0700

    Merge pull request #119 from bcfriesen/add_arch_suffix
    
    GNUMake: add arch suffix to exe name when building on a Cray

commit c80c209dccd4ec7027d909df28fdd1158cb81f70
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Sep 6 14:21:07 2017 -0700

    GNUMake: add arch suffix to exe name when building on a Cray
    
    Cross-compiling on Cray systems is common, so adding the target architecture to
    the exe suffix clarifies which instruction set the binary was compiled with.

Tools/GNUMake/Make.defs

commit 09006ab325fff2e66d9219a3eedf89fb21e884a9
Merge: 49caf2c07 121d363fb
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Sep 6 13:16:17 2017 -0700

    Merge pull request #118 from bcfriesen/print_build_target_on_cray
    
    Print build target on Cray

commit 121d363fb9c98067680c8fdca908681f1dc37714
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Sep 6 12:56:38 2017 -0700

    GNUMake: print the build target at link time if running on a Cray
    
    AMReX does not have separate compiler flags for different architectures on Cray
    systems, e.g., separate compile flags for AVX2 vs. AVX-512 instructions. The
    user is responsible for choosing the correct build target, via the
    "craype-<arch>" modules. To make clear which target the user is compiling for,
    print the target at link time.

Tools/GNUMake/Make.rules

commit 4e8bead59e45a6f498167c72cca6bbbc2e48e77b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 6 12:32:47 2017 -0700

    do reduction over threads for the non-local buffer.

Src/Particle/AMReX_ParticleContainerI.H

commit 6b59b0ce70cc1053b0cdfd642ff47c6a29f988a2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 6 11:23:52 2017 -0700

    only add entries to the remote tmp map on demand

Src/Particle/AMReX_ParticleContainerI.H

commit f1834d6bebdef8419f2a7d7506af3ac7d6a6c143
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 6 11:16:34 2017 -0700

    EB/CNS: add tagging on cutcells

Src/AmrCore/AMReX_EBAmrUtil.H
Src/AmrCore/AMReX_EBAmrUtil.cpp
Src/AmrCore/AMReX_EBAmrUtil_F.H
Src/AmrCore/AMReX_EBAmrUtil_nd.F90
Src/AmrCore/AMReX_EBFluxRegister.H
Src/AmrCore/AMReX_EBFluxRegister.cpp
Src/AmrCore/Make.package
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_error.cpp
Tutorials/EB/CNS/Source/CNS_io.cpp
Tutorials/EB/CNS/Source/CNS_setup.cpp
Tutorials/EB/CNS/Source/Make.package

commit 9476d7228af7aa391be20a00274f2ed560da001f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 6 10:49:39 2017 -0700

    threading the non-local tmp container.

Src/Particle/AMReX_ParticleContainerI.H

commit 4c3ca285b51cd08ae9bacd5ace306efaa046bf61
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Sep 6 09:52:52 2017 -0700

    about the start threading the redistribute method.

Src/Particle/AMReX_ParticleContainerI.H

commit 96281ce5240b7d339daa02f3644a457bfa223958
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Sep 5 15:54:16 2017 -0700

    found some bugs and added some debugging tools

Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H
Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/GeometryShop/AMReX_EBDebugDump.H
Src/GeometryShop/AMReX_EBDebugOut.H
Src/GeometryShop/AMReX_EBDebugOut.cpp
Src/GeometryShop/AMReX_Stencils.H
Src/GeometryShop/AMReX_Stencils.cpp
Tests/EBAMRElliptic/exec/cond.inputs
Tests/EBAMRElliptic/exec/conductivitySolve.cpp

commit 49caf2c07bd5dcc8f87500a10cae6bba4eb7b720
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 5 15:09:57 2017 -0700

    make GraphNode thread safe

Src/Base/AMReX_EBLevel.cpp
Src/Base/AMReX_EBMultiFabUtil.cpp
Src/GeometryShop/AMReX_GraphNode.cpp

commit d427a655a317dece25b463c3114fa8da88357e0a
Merge: 8fc2572b6 6feff0818
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 5 12:03:10 2017 -0700

    Merge pull request #117 from nncarlson/dfloat-fix
    
    Eliminate use of non-standard Fortran dfloat intrinsic

commit 8fc2572b600509c31c03e257daa09793782d36c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 5 10:26:30 2017 -0700

    remove BL_USE_FORT_STAR_PRECISION

Src/Base/AMReX_REAL.H
Src/Boundary/AMReX_LO_UTIL.F

commit d0bfe568d169ccbd5f042730fb824ec5e04b17c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 5 10:12:44 2017 -0700

    add linear solvers to libamrex

GNUmakefile.in
Src/Base/Make.package
Tools/libamrex/configure.py

commit 4af0473f23c97f4e6e089d060563415df4467549
Merge: 0caf60f6f e2527a8a6
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Sep 5 09:18:25 2017 -0700

    Merge pull request #116 from AMReX-Codes/weiqun/sort
    
    BaseIVFAB and BaseIFFAB

commit 6feff0818cc39ed53caf831e0ddc1a28ea18abcd
Author: Neil Carlson <neil.n.carlson@gmail.com>
Date:   Tue Sep 5 10:11:38 2017 -0600

    Eliminate use of non-standard Fortran dfloat intrinsic (fixes #115)

Src/AmrCore/AMReX_INTERP_3D.F

commit 0caf60f6f87a9e5b132dbf3369725ecc9f7056ed
Merge: 05741bbfc 89f965dec
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Sep 5 08:54:14 2017 -0700

    Merge pull request #114 from nncarlson/imultifab-additions
    
    Additions to the Fortran imultifab interface

commit 05741bbfc6e71ff940c110751acb2909e802b747
Merge: 152687b14 a82d58178
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Sep 5 08:50:39 2017 -0700

    Merge pull request #111 from AMReX-Codes/weiqun/cfivs
    
    replace simple loop over grids with BoxArray's fast complement function

commit 89f965dec521b6d8da85582eeeb42e3d9a3857cf
Author: Neil Carlson <neil.n.carlson@gmail.com>
Date:   Mon Sep 4 21:53:12 2017 -0600

    Additions to the Fortran imultifab interface
    
    This extends the Fortran imultifab interface to include the setval
    method, and adds the optional nodal argument to amrex_imultifab_build,
    as defined for amrex_multifab_build.

Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit e2527a8a6c4914749063c3e9503b6b453568c747
Merge: 696b95b62 b2e9e9293
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 3 12:11:55 2017 -0700

    merge

commit 696b95b62f578b53cf17cd464c383a1ee28a0165
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 3 12:08:01 2017 -0700

    optimize IFFAB

Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFABI.H

commit f2718bd0461b2368118284337bca7d03763c9b22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 3 11:04:50 2017 -0700

    refactor IVFAB to make getIndex faster

Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_BaseIVFABI.H

commit b2e9e9293a5aa2c485505b76b1cd53162149aab4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 3 11:04:50 2017 -0700

    refactor IVFAB to make getIndex faster

Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_BaseIVFABI.H

commit 152687b14154ce0775fbf56d28a44cdff2eba9c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 2 12:48:17 2017 -0700

    inline operator== for VolIndex and FaceIndex and switch the order of comparison by comparing int first

Src/GeometryShop/AMReX_FaceIndex.H
Src/GeometryShop/AMReX_FaceIndex.cpp
Src/GeometryShop/AMReX_VolIndex.H
Src/GeometryShop/AMReX_VolIndex.cpp

commit e502a626bff4ed29d391a8c2618b8e0f93250955
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 2 12:48:17 2017 -0700

    inline operator== for VolIndex and FaceIndex and switch the order of comparison by comparing int first

Src/GeometryShop/AMReX_FaceIndex.H
Src/GeometryShop/AMReX_FaceIndex.cpp
Src/GeometryShop/AMReX_VolIndex.H
Src/GeometryShop/AMReX_VolIndex.cpp

commit 58e0bad3c96c66b82ac72fcf0c3d54e4490ec134
Merge: ae1276aaf a82d58178
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 1 22:01:27 2017 -0700

    Merge branch 'weiqun/cfivs' into weiqun/eb

commit ae1276aaf68e26a8cb3ba7ac2b652d37a8cf7604
Merge: a580f6fa1 96e32bda6
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 1 19:40:57 2017 -0700

    Merge pull request #110 from AMReX-Codes/weiqun/iffabcopy
    
    optimization of IFFAB copy

commit a82d581786424c929a353d6ddb7a3e971614a075
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 1 17:58:19 2017 -0700

    replace simple loop over grids with BoxArray's fast complement function

Src/GeometryShop/AMReX_EBLevelGrid.cpp

commit 96e32bda6d42f8f3e87c6c7aac7827d54444667d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 1 16:40:13 2017 -0700

    optimization of IFFAB copy

Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_IntVectSet.H
Src/GeometryShop/AMReX_IntVectSet.cpp

commit bb82781bc39adfaf8be425cc4bcdc24cf8d78cb5
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 1 16:23:52 2017 -0700

    some simplification and debugging of EB solvers

Src/EBAMRElliptic/AMReX_EBConductivityOp.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp
Src/EBAMRTools/AMReX_EBCoarseAverage.cpp

commit a580f6fa148ca44cbf26077fabb75fc89bb7fc7c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 1 15:14:57 2017 -0700

    add some profilers

Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBLevelGrid.cpp

commit 694800f558c84f131027050a898ff7e335816f98
Merge: 447adfb57 3fc3b5713
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 1 13:31:11 2017 -0700

    Merge pull request #109 from AMReX-Codes/dtg_branch
    
    putting some tweaks to IntVectSet into development

commit 3fc3b5713a46aaeeca75fe1462df6bea525290aa
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 1 13:29:14 2017 -0700

    with Weiqun's advice, I was able to restore the move constructors to IntVectSet.

Src/GeometryShop/AMReX_IntVectSet.H

commit 447adfb57217e3e0e1b88530bfb28c34160dcc44
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 1 13:25:04 2017 -0700

    have to remove noexcept because gcc 4 does support

Src/GeometryShop/AMReX_IntVectSet.H

commit 38409c0999ea3c91976a62da93e4ee3ed1eae2ce
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 1 12:59:56 2017 -0700

    my compiler was not eating some of weiqun's more sophistocated c++11-isms so I made IntVectSet old school again.

Src/GeometryShop/AMReX_IntVectSet.H

commit e440e0aeea3fd17948504aa717abe7af98409076
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 1 12:52:18 2017 -0700

    fixed compilation bug in IntVectSet

Src/GeometryShop/AMReX_IntVectSet.H

commit ca11d79c749b609024665aeaf39b9b6e9b62b785
Merge: b7977940e 4701db386
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 1 12:49:17 2017 -0700

    Merge branch 'development' into dtg_branch

commit 4701db3860a5769ed3c5dda1fb8689cc30dc0686
Merge: 8b7c6e452 fdd41ce8a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 1 12:47:33 2017 -0700

    Merge pull request #108 from AMReX-Codes/weiqun/intvectset
    
    Internal container of IntVectSet

commit b7977940edb000c57550b45c8f270d666d18031a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Sep 1 11:30:48 2017 -0700

    eb plotfile routines now work.

Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Tests/EBAMRElliptic/exec/cond.inputs
Tests/EBAMRElliptic/exec/conductivitySolve.cpp

commit fdd41ce8af89ad9e324b924e389a074c22cdc58d
Merge: 5d24abaac 8b7c6e452
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 1 11:25:11 2017 -0700

    Merge branch 'development' into weiqun/intvectset

commit 8b7c6e452aa95cef7af840a3553e60a2804eff3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 1 11:24:20 2017 -0700

    more BL_PROFILE

Src/GeometryShop/AMReX_EBLevelGrid.cpp

commit 5d24abaace034783d766fda41d7e8315cf546148
Merge: c672e69c9 fa26cdcf4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 1 11:02:29 2017 -0700

    Merge branch 'development' into weiqun/intvectset

commit fa26cdcf4913ff9fa500af0ac12e4ac7a578a113
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 1 10:59:43 2017 -0700

    add/rmove some BL_PROFILEs

Src/Amr/AMReX_Amr.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp
Tutorials/EB/CNS/Source/CNS.cpp

commit c672e69c931adf2e9a2352805477d5c7253bac96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 1 10:56:59 2017 -0700

    IntVectSet: reimplement it with unordered_set rather than set

Src/GeometryShop/AMReX_IntVectSet.H
Src/GeometryShop/AMReX_IntVectSet.cpp

commit 1e4f61b72815b1d003b683228711fa2f57aff19c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 31 21:30:02 2017 -0700

    EB/CNS: flooring

Tutorials/EB/CNS/Source/fortran/CNS_f.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90

commit cffba664b9c6763bb68f35cfea4959fd71b4ae1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 31 16:08:51 2017 -0700

    Disable MPI checking if NO_MPI_CHECKING=TRUE.

Tools/GNUMake/Make.local.template
Tools/GNUMake/sites/Make.unknown

commit 8af7220616a2a49a90d7661ef7671750e321cabb
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Aug 31 15:43:50 2017 -0700

    added utilities to output visit and amrvis-compliant plot files from EB data. I also added a debugging utility that allows data to be visualized from inside a debugger..

Src/EBAMRTools/AMReX_EBLevelDataOps.H
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBDebugOut.cpp
Tests/GeometryShop/ramp/GNUmakefile
Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp

commit 61cc4f0cc0333775fb3b9b32879340572b9a552f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 31 14:59:18 2017 -0700

    less verbose

Src/Amr/AMReX_Amr.cpp

commit 34676fbbd26d38f6d733d34b72d3d00c9696245f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 31 14:56:55 2017 -0700

    EB/CNS: override post_restart to fix up geometry

Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp

commit 9e965c6f90531e3f7a05a46ce8a9fdebb48e34c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 31 13:58:08 2017 -0700

    EB/CNS: add testing inputs

Tutorials/EB/CNS/Exec/Combustor/inputs.testing

commit 92e7f0c4cda2da188a6dd342f036d15b4f769ff3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 31 13:49:52 2017 -0700

    fix restart for EB

Src/Base/AMReX_EBLevel.H
Src/Base/AMReX_EBLevel.cpp

commit 30e5c131435b9303e87d6dfd7d4e51d47a2f09b1
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Aug 31 11:05:00 2017 -0700

    bug fix to conductivityopfactory

Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp

commit 59b86dd7edaffcf9a231631ecd1b930b27954ef1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 31 09:22:40 2017 -0700

    commented out FaceFlag stuff

Src/Base/AMReX_EBLevel.H
Src/Base/AMReX_EBLevel.cpp

commit a4e89e1d72a14e677342f22d90d8a088bfc5e86c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 31 09:17:55 2017 -0700

    EB/CNS: pass amr.max_level into EBIndexSpace::define so that we don't have to build extra coarse levels

Tutorials/EB/CNS/Source/CNS_init_eb.cpp

commit 1d3ddd1a0ceaafbf4ea5b30404c16e55f6bb0379
Merge: 2670989ab 501ee3674
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 31 09:13:33 2017 -0700

    Merge branch 'development' into weiqun/eb

commit 2670989abceffd31e491cf06b488186f204aff7b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 31 09:12:55 2017 -0700

    EB/CNS: if interior plus one ghost are all regular, no need to call eb functions

Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90

commit 9418e7ac132081cdc518fd0ff1f392ce985a0209
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 30 16:02:31 2017 -0700

    EB/CNS: vectorization of riemann solver

Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90
Tutorials/EB/CNS/Source/hydro/analriem3d.F90
Tutorials/EB/CNS/Source/hydro/cns_eb_hyp_wall.F90

commit 501ee3674c572168ee2f36fac5a954b7c0b56f2e
Merge: d23315ae7 e5154a3e4
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Aug 30 18:12:00 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d23315ae704cb2e5723a4a9c8a154c51c34bfe02
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Aug 30 18:11:50 2017 -0700

    add task association feature to support dynamic task parallelism

Src/AmrTask/graph/AMReX_AbstractTask.H
Src/AmrTask/graph/AMReX_AbstractTask.cpp
Src/AmrTask/graph/AMReX_DataTypes.H
Src/AmrTask/graph/AMReX_TaskGraph.H
Src/AmrTask/rts_impls/MPI_Generic/mylock.h
Src/AmrTask/rts_impls/MPI_Generic/rts.C
Src/AmrTask/rts_impls/MPI_Generic/rts_graphimpl.H
Src/AmrTask/rts_impls/MPI_Generic/rts_taskimpl.H
Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C
Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C

commit e5154a3e4f7c15b0a9766bea17b5ff25050924bd
Merge: 50a63610b 0fac5be3c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Aug 30 15:56:00 2017 -0700

    Merge pull request #106 from AMReX-Codes/dtg_branch
    
    merging over improved serialization of EBGraph and a bug fix to BaseIFFAB.

commit 0fac5be3c45db7ed9a4617ed7cc850a9f08b1d26
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Aug 30 15:54:23 2017 -0700

    I reworked EBGraph serialization so that it will preserve the sparse nature of the object if it can.   I also fixed a subtle bug in BaseIFFAB that may have been causing our valgrind troubles.

Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Src/GeometryShop/AMReX_EBLevelGrid.cpp
Tests/GeometryShop/regression/ebio.cpp

commit d04f9491debd8db6f7cff554353b1594441fa973
Merge: 29989ea3b 50a63610b
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Wed Aug 30 14:51:36 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit fb1a21727aeeda3f2b30af8f84dcb21d4e3f498c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 30 10:41:15 2017 -0700

    dynamic OpenMP scheduling in MFIter

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp

commit 17d6d71fe3caa9b1a27937facac0a66d383c7cee
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Aug 30 08:57:53 2017 -0700

    bug found by weiqun

Src/GeometryShop/AMReX_EBIndexSpace.cpp

commit 50a63610b60fb089be9285282b06e561440b4b9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 30 08:49:22 2017 -0700

    not thread safe

Src/Base/AMReX_EBLevel.cpp

commit 6f973598eb9fce331d404aed4149e576b5facd3f
Author: kngott <kngott@lbl.gov>
Date:   Wed Aug 30 03:09:46 2017 -0700

    Add functions to allow access and updating of cached DistributionMappings in StateData, AmrLevel and AmrMesh objects. Used to fix functionality with MoveAllFabs.

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.H

commit 4fa3c012f97d602049148bbc68fec656431890ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 29 21:04:34 2017 -0700

    turn off openmp for some eb codes because they are not thread safe yet

Src/Base/AMReX_EBMultiFabUtil.cpp

commit 12b4e5eaf84156fabea5ca5a6892fd6d3cdb21e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 29 15:15:57 2017 -0700

    add headers to makefile

Src/GeometryShop/Make.package

commit 8f46475790f3685d56ba0e35c45536e5d3e1cc3f
Merge: 70989affa 89f17aa43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 29 14:22:29 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 70989affad94c74c21022f7622df49c75565efb7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 29 14:22:20 2017 -0700

    EB/CNS: tile size

Tutorials/EB/CNS/Source/CNS_advance.cpp

commit 89f17aa43cb7b7a1d1bf44009de36708e56690a0
Merge: 8164710a0 3e33ec4cd
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 29 13:25:17 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8164710a0f9b072b3a2254211e987453e2179777
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 29 13:25:08 2017 -0700

    option to graph top pct in write summary, extra information in call trac, replace spaces in function names.

Src/Extern/ProfParser/AMReX_BLProfStats.H
Src/Extern/ProfParser/AMReX_BLProfStats.cpp
Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp
Src/Extern/ProfParser/AMReX_RegionsProfStats.H
Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp
Src/Extern/amrdata/AMReX_DataServices.H
Src/Extern/amrdata/AMReX_DataServices.cpp

commit 3e33ec4cd713ffb4df084488c48f4428c89e709c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 29 13:01:58 2017 -0700

    EB/CNS: don't have to go through all the eb stuff if interior plus one ghost cell are all regular

Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90

commit 29989ea3b6865ca7031def4e364ce081620b2ad2
Merge: 3a35a3d6c 69e7b416e
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Tue Aug 29 14:54:42 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 69e7b416e377d6a63815d15df7b46dd2d885857e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 29 12:20:04 2017 -0700

    use fortran for cell type counting

Src/Base/AMReX_EBCellFlag.cpp
Src/Base/AMReX_EBCellFlag_F.H
Src/Base/AMReX_ebcellflag_mod.F90
Src/Base/Make.package

commit cb6c06805d2a4ca8b4bc5b75e38a6497fe2795d9
Merge: 574196ddd fe0a0c67f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 29 11:14:15 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 574196dddd5fa593920666d015de1c165d0a6d19
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 29 11:13:53 2017 -0700

    EB/CNS: disable initial load balance

Tutorials/EB/CNS/Source/CNS.cpp

commit fe0a0c67f24d863cd5075a2bb304330a3eda142b
Merge: 373997795 917c3b458
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 29 10:10:23 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 37399779517e3862beb4ce6432599f18d30c0818
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 29 10:10:06 2017 -0700

    make sure the Geometry offset is consistent with the RealBox.

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp

commit 612add1f966ae81347e40e254b328869c9d8d963
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 29 10:04:29 2017 -0700

    EB/CNS: dynamic load balance

Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_setup.cpp
Tutorials/EB/CNS/Source/fortran/CNS_nd.F90
Tutorials/EB/CNS/Source/main.cpp

commit 3a35a3d6c1cd04084ba18bb4658177b6f8bb2d57
Merge: fec330191 917c3b458
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Tue Aug 29 12:01:28 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 7dded4bf9ed3f5eb666a2a90e851d9c8867cc569
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 29 08:41:15 2017 -0700

    EB utility function for setting single valued cells

Src/Base/AMReX_EBMultiFabUtil.H
Src/Base/AMReX_EBMultiFabUtil.cpp
Src/Base/AMReX_EBMultiFabUtil_F.H
Src/Base/AMReX_EBMultiFabUtil_nd.F90

commit 917c3b458811da2c8a38a412aded94bbd9b2f88f
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Aug 28 17:53:40 2017 -0700

    support local load balancing

Src/AmrTask/graph/RTS.H
Src/AmrTask/rts_impls/MPI_Generic/README
Src/AmrTask/rts_impls/MPI_Generic/rts.C
Src/AmrTask/rts_impls/Serial/rts.C
Src/AmrTask/tutorials/UnitTests/001_TokenRing.C
Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C
Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C

commit 7d3f2ef3ffa5a4bac336f4e8b47f83f2c23f5e96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 28 16:45:51 2017 -0700

    EB/CNS: load balance

Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/main.cpp

commit d02c9ad6e48c64882efd1494c52fff9a76cfb5f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 28 16:45:14 2017 -0700

    new EB_set_covered function

Src/Base/AMReX_EBMultiFabUtil.H
Src/Base/AMReX_EBMultiFabUtil.cpp

commit e12a3cbcbc7c15c07bceb679cd9745d160784c69
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 28 16:44:46 2017 -0700

    add a new function to Amr for load balance

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp

commit 3ea409f0d62733cd140a3d9af120da3dcf67903e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 28 15:47:51 2017 -0700

    EB/CNS: fix a bug

Tutorials/EB/CNS/Source/CNS_advance.cpp

commit 5cb7214b367679cc17ffad92d2cb4b8a4a5148e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 28 15:04:36 2017 -0700

    EB/CNS: set inflow velocity correctly

Tutorials/EB/CNS/Exec/Combustor/bc_fill_nd.F90
Tutorials/EB/CNS/Exec/Combustor/cns_prob.F90
Tutorials/EB/CNS/Exec/Combustor/inputs

commit a961c0b7d2f3b53b6672a4f29dc186aea5f29519
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 28 13:34:07 2017 -0700

    EB/CNS: Combustor test

Tutorials/EB/CNS/Exec/Combustor/GNUmakefile
Tutorials/EB/CNS/Exec/Combustor/Make.package
Tutorials/EB/CNS/Exec/Combustor/bc_fill_nd.F90
Tutorials/EB/CNS/Exec/Combustor/cns_prob.F90
Tutorials/EB/CNS/Exec/Combustor/inputs

commit 368ed03c06bedbab61c8ac74bd981bf29315fda7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 28 12:20:16 2017 -0700

    fix up cells that have volume fraction and apertures be exactly one but with a covered neighbor cell touching the corner

Src/Base/AMReX_ebcellflag_mod.F90
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/fortran/CNS_nd.F90

commit 5ddc4bbfb6b0cecc503e40924d18d4ac382eacd9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 28 10:25:54 2017 -0700

    EB/CNS: more debug info

Tutorials/EB/CNS/Source/fortran/CNS_divop.F90
Tutorials/EB/CNS/Source/hydro/cns_eb_hyp_wall.F90

commit 3c324806776edb894e92d0cb54dca5dd589a36ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 28 09:57:33 2017 -0700

    EB/CNS: save volume fraction in plotfile

Tutorials/EB/CNS/Source/CNS_io.cpp

commit 8c50b33a88319a0a2eb47970b82bd85beb3bf3f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 21:13:44 2017 -0700

    EBFluxFAB is alos thread safe

Src/GeometryShop/AMReX_EBFluxFAB.H

commit b206c56c4ec99cf174b582d2d76cf4274b5ba5e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 21:12:14 2017 -0700

    update FillBoundary for thread safety too

Src/Base/AMReX_FabArray.H

commit b166a1cbe961773d8116e9e774f297cb90a4302c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 21:04:58 2017 -0700

    some GeometryShop classes are thread safe

Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_BaseEBFaceFAB.H
Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIVFAB.H

commit 7f5afb59032c1f5fd973a5a4291f6bb3c9077a40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 20:50:18 2017 -0700

    fix AmrLevel and StateData Restart

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp

commit bd90c4a4e2fba14804a013b130f8a83491d2fc99
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 16:43:18 2017 -0700

    add BaseFab::isCopyOMPSafe() function so that ParallelCopy can turn off omp for unsafe FABs; add this to all EB Fabs.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_BaseEBFaceFAB.H
Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBFluxFAB.H
Src/GeometryShop/AMReX_EBGraph.H

commit 341272dadea88178b6168a0a88c8911ecaa207a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 15:02:31 2017 -0700

    EB/CNS: fix a bug

Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90

commit c3219de40804d8fb5b6e2d6fcb5cc38060d2f5ba
Merge: f5ffec25b d0c919e89
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sun Aug 27 14:00:49 2017 -0700

    Merge pull request #103 from AMReX-Codes/dtg_branch
    
    merging some small bug fixes into devlopment for weiqun

commit d0c919e89d1572d4fef448d38e1bd27a07f5ac3c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sun Aug 27 13:58:46 2017 -0700

    using the MFIter(FabArray) constructor was breaking in EBISLevel because it seems to magically invoke OMP stuff.   I switched it to MFIter(BoxArray, DM) and now it seems to work

Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Tests/GeometryShop/ramp/GNUmakefile

commit 5df6451bc81045516dd8e158e2dd56caf7efead5
Merge: 864329306 f5ffec25b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sun Aug 27 13:39:38 2017 -0700

    Merge branch 'development' into dtg_branch

commit f5ffec25b5cd787edf4d84c44f18e8179b627a9a
Merge: 2fb3140e4 71b81bb8a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 13:34:53 2017 -0700

    Merge branch 'development' into weiqun/eb

commit 8643293065b4d4c885acecbf5bf745ecc02e28ef
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sun Aug 27 13:34:22 2017 -0700

    fixed some logic in GeometryShop

Src/GeometryShop/AMReX_GeometryShop.cpp

commit 2fb3140e4c9da35adb91c52c5cfea1b6712aea6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 13:08:52 2017 -0700

    add -lubsan for llvm when FSANITIZER is TRUE

Tools/GNUMake/comps/llvm.mak

commit 2823e3691e41951651fdc91fc8b60de3a9ad736c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 13:04:17 2017 -0700

    remove an unnecessary move

Src/Base/AMReX_BoxList.cpp

commit 114c88a7468ad45e8a0b690b53ab465529ac133d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 12:36:06 2017 -0700

    clear some warnings

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_StateData.cpp
Src/AmrCore/AMReX_ebinterp_3d.F90
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_EBLevel.H
Src/Base/AMReX_iMultiFab.H
Src/GeometryShop/AMReX_BaseEBCellFactory.H
Src/GeometryShop/AMReX_BaseIVFactory.H
Src/GeometryShop/AMReX_EBCellFactory.H
Src/GeometryShop/AMReX_EBDataFactory.H
Src/GeometryShop/AMReX_EBFluxFactory.H
Src/GeometryShop/AMReX_IrregFABFactory.H
Tutorials/EB/CNS/Source/hydro/analriem3d.F90

commit 82762138a7f1c8230489b974bf49ed115f35d205
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 12:18:02 2017 -0700

    EB/CNS: add some override

Tutorials/EB/CNS/Source/CNS.H

commit 929b13741b874a82393d7b3f076edebe91e58511
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 11:49:17 2017 -0700

    remove unused variable

Src/Base/AMReX_EBMultiFabUtil.cpp

commit 71b81bb8a3b9b4461132149959878c876b2597a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Aug 27 14:43:35 2017 -0400

    remove unused argument that Cray complains about

Src/LinearSolvers/F_MG/mg.f90

commit d78ec64d669f70586db3f5e171fea64944ace9db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 11:27:45 2017 -0700

    EB/CNS: LAZY := TRUE

Tutorials/EB/CNS/Exec/Make.CNS
Tutorials/EB/CNS/Source/CNS.cpp

commit ddc6ac16a16c1fec3dd47d29a56569da5b80393a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 11:17:09 2017 -0700

    EB/CNS: omp

Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp

commit 7638584b3c031af8a2dff291b578cad0ea3cc75b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 27 11:01:58 2017 -0700

    EB/CNS: add profiler

Src/Base/AMReX_EBLevel.cpp
Src/Base/AMReX_EBMultiFabUtil.cpp
Tutorials/EB/CNS/Exec/Pulse/GNUmakefile
Tutorials/EB/CNS/Exec/ShockRef/GNUmakefile
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_init_eb.cpp
Tutorials/EB/CNS/Source/CNS_io.cpp
Tutorials/EB/CNS/Source/main.cpp

commit 302fa7007c8f0bca7c20c348c1e0c4d7cbfea2eb
Merge: 0b7562d0b 1a0d27705
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Aug 26 20:07:43 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 0b7562d0b2feee6100b459326afd03eaa76ca687
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Aug 26 20:07:23 2017 -0700

    don't let the kdtree load balancer make empty boxes

Src/Particle/AMReX_KDTree_3d.F90
Src/Particle/AMReX_LoadBalanceKD.cpp

commit d3c8d6c8322c5785bc443a7c8870bc071925bb40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 26 15:20:10 2017 -0700

    EB/CNS: minor

Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90

commit 5bbb4c5562c131b521fc39a4db5a640454f3319c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 26 14:45:07 2017 -0700

    EB/CNS: fix bug

Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90

commit 985babb32991032f9bea9ded53d1a2438a269172
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 26 11:19:03 2017 -0700

    EB/CNS: cleanup

Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90
Tutorials/EB/CNS/Source/fortran/CNS_derive.F90
Tutorials/EB/CNS/Source/fortran/CNS_divop.F90
Tutorials/EB/CNS/Source/fortran/CNS_f.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90

commit 003eb98fbb297e7d439177959319997aed9ff5d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 26 07:25:56 2017 -0700

    EB/CNS: clean up

Tutorials/EB/CNS/Exec/ShockRef/inputs
Tutorials/EB/CNS/Source/diffusion/diff_coef_mod.F90
Tutorials/EB/CNS/Source/fortran/CNS_nd.F90
Tutorials/EB/CNS/Source/fortran/CNS_physics.F90

commit ff80e01a1591af10e97244ada1f6eec8c7f0750d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 26 07:08:37 2017 -0700

    CNS/EB: file reorganization

Tutorials/EB/CNS/Exec/Make.CNS
Tutorials/EB/CNS/Source/Make.package
Tutorials/EB/CNS/Source/fortran/CNS_derive.F90
Tutorials/EB/CNS/Source/fortran/CNS_divop.F90
Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90
Tutorials/EB/CNS/Source/fortran/CNS_f.F90
Tutorials/EB/CNS/Source/fortran/CNS_nd.F90
Tutorials/EB/CNS/Source/fortran/CNS_physics.F90
Tutorials/EB/CNS/Source/fortran/Make.package
Tutorials/EB/CNS/Source/fortran/bc_fill_nd.F90

commit 109a07154bc704e9b4aa3d752561d3cfef89de8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 26 07:02:27 2017 -0700

    EB/CNS: fix a bug in parameter initialization for constant viscosity

Tutorials/EB/CNS/Source/CNS_physics.F90

commit f3c9760d3f6973bb866fae80ed1bc978e532fcc4
Merge: b3ed17f7e 1a0d27705
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 26 07:01:11 2017 -0700

    Merge branch 'development' into weiqun/eb

commit 7bb8ed6b012fd16ca77f9cefcec38dfec5f7f543
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Aug 26 06:31:13 2017 -0700

    commented out debugging statement

Src/GeometryShop/AMReX_EBISLevel.cpp

commit 1a0d2770517e02ac7817155aa7dae0e3fb7b18fb
Merge: 3c43ff6ae 4f2786224
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Aug 26 06:14:36 2017 -0700

    Merge pull request #102 from AMReX-Codes/dtg_branch
    
    fixed another bug Weiqun identified.  EBGraph linearization needs a l…

commit 4f27862240847c95f1bcf66f90245449e7c15d16
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Aug 26 06:08:05 2017 -0700

    fixed another bug Weiqun identified.  EBGraph linearization needs a little work but I will commit this first because this version of linearization works.

Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp

commit b3ed17f7e586a42fb775e51788c9aeb3874ebcf9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 25 18:43:54 2017 -0700

    EB/CNS: fix index bugs

Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90
Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90

commit 7ccda851e493cf9219209c3d935de290a68d3557
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 25 17:09:41 2017 -0700

    EB/CNS: add a parameter for using total energy for weighting

Tutorials/EB/CNS/Exec/ShockRef/inputs
Tutorials/EB/CNS/Source/CNS_divop.F90
Tutorials/EB/CNS/Source/CNS_f.F90

commit 7732f125894911449f9c26bb0bd8ac4692400e5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 25 17:03:51 2017 -0700

    EB/CNS: use noslipwall for shock reflection test

Tutorials/EB/CNS/Exec/ShockRef/inputs

commit 3c43ff6ae2893f8bbde9d51446479d534f5bbaf8
Merge: 2eeaef73e fbec03000
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 25 16:31:28 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 2eeaef73ea2aebf89b89a8436b955e3dbf6a5c96
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 25 16:31:04 2017 -0700

    we want to compile these functions even without _OPENMP.

Src/Particle/AMReX_OMPDepositionHelper_nd.F90
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit fbec0300081ac628c0009f2fd426c0f3b42430c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 25 16:02:55 2017 -0700

    modify GeomtryShop test

Tests/GeometryShop/ramp/main.cpp

commit 172c25bff6baabae20eb85c70a0f924aaf22d78d
Merge: d090d7b7d 571231849
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 25 15:48:25 2017 -0700

    Merge branch 'eb_development' into weiqun/eb

commit 9db5e45e092d9d3b618c6a68efefbf95b4b7a959
Merge: cfe29f843 d6cc2763f
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Aug 25 15:40:37 2017 -0700

    Merge pull request #100 from emotheau/convtools
    
    New Convergence tool to compute the composite error. Was made with Bo…

commit d6cc2763f51e4599bddd643e8c685a49b880fdf0
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Fri Aug 25 15:29:11 2017 -0700

    New Convergence tool to compute the composite error. Was made with BoxLib, we have to convert it to amrex

Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp
Tools/C_util/Convergence/GNUmakefile

commit 5712318497fa841e83e4889be751f4da9669f035
Merge: f42e5cd9c cfe29f843
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 25 15:23:52 2017 -0700

    Merge branch 'development' into eb_development
    
    Conflicts:
            Src/Base/AMReX_FabArrayBase.H
            Src/Base/AMReX_FabArrayBase.cpp

commit d090d7b7d64afbe94d9a7d72b9ee3c6c96d4ef10
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 25 15:03:31 2017 -0700

    EB/CNS: minor

Tutorials/EB/CNS/Source/CNS_init_eb.cpp

commit cfe29f843c23f6c12643cd54f76dea9d4c9bd8e2
Merge: fbdd83e68 1ce16162e
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Aug 25 14:54:05 2017 -0700

    Merge pull request #99 from AMReX-Codes/dtg_branch
    
    moving bug fixes to development

commit 1ce16162e38515e2b7e5b0c061374b0858258d0a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Aug 25 14:52:33 2017 -0700

    fixed parallel bug identified by Weiqun

Src/EBAMRTools/AMReX_EBFineInterp.cpp
Src/GeometryShop/AMReX_EBArith.cpp
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp
Tests/GeometryShop/ramp/main.cpp

commit 7d364ac678f581b26bd7258d98dde305ac72356c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 25 14:30:31 2017 -0700

    EB/CNS: add contiguous

Tutorials/EB/CNS/Source/CNS_dudt.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90

commit b29260f49ac08168e185ba756c6354a310b44e68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 25 13:56:32 2017 -0700

    EB/CNS: print mementa and energy too

Tutorials/EB/CNS/Source/CNS.cpp

commit 7238c7533e1d24227005ff7ae40963c6f707f97f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 25 13:36:28 2017 -0700

    EB/CNS: parameter to turn off diffusion

Tutorials/EB/CNS/Source/CNS_physics.F90

commit fbdd83e683285d8a6669b1313513905862a4cfb4
Merge: 1eb820739 b3c35096f
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Aug 25 13:26:46 2017 -0700

    Merge pull request #97 from kweide/development
    
    give the octree iterator a clear() method

commit 4a5cf90288237015979d996f2d301ae6ae5002ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 25 13:11:15 2017 -0700

    EB/CNS: add const viscosity

Tutorials/EB/CNS/Exec/ShockRef/inputs
Tutorials/EB/CNS/Source/CNS_divop.F90
Tutorials/EB/CNS/Source/CNS_physics.F90
Tutorials/EB/CNS/Source/diffusion/diff_coef_mod.F90

commit a47243cb88cd5178941edee9016d44de9ea3673c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 25 12:14:48 2017 -0700

    EB/CNS: need one more ghost cell

Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS_dudt.F90
Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90

commit 1eb82073950ca122642fd96f12935577c284020b
Merge: 014103e8e ff899c593
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Aug 25 11:46:17 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 014103e8eb84e26103b8f6729ccc713c9db2f43f
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Aug 25 11:45:43 2017 -0700

    MPI runtime implementation

Src/AmrTask/rts_impls/Utils/dl_malloc.c
Src/AmrTask/rts_impls/Utils/dl_malloc.h
Src/AmrTask/rts_impls/Utils/sysInfo.C
Src/AmrTask/rts_impls/Utils/sysInfo.H

commit 4eb75f0224a362cc4e733d431241b60883a4803a
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Aug 25 11:45:06 2017 -0700

    MPI runtime implementation

Src/AmrTask/rts_impls/MPI_Generic/Makefile
Src/AmrTask/rts_impls/MPI_Generic/README
Src/AmrTask/rts_impls/MPI_Generic/mylock.h
Src/AmrTask/rts_impls/MPI_Generic/rts.C
Src/AmrTask/rts_impls/MPI_Generic/rts_graphimpl.H
Src/AmrTask/rts_impls/MPI_Generic/rts_taskimpl.H

commit ff899c5938fc3b685c3937c727cbbe63c2694bbd
Merge: 478d0c8b3 c089232c4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 25 11:33:01 2017 -0700

    Merge pull request #98 from MaxThevenet/compile_on_theta
    
    Add possibility to compile on Theta ALCF

commit c089232c400908260db5a243f53da8e39c576887
Author: Maxence Thevenet <mthevenet@lbl.gov>
Date:   Fri Aug 25 11:19:25 2017 -0700

    Add possibility to compile on Theta ALCF

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.alcf

commit b3c35096ffbf35fda8bda4dcc23f4f0b77227acb
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Fri Aug 25 13:18:42 2017 -0500

    give the mfiter (Fortran) iterator a fabbox() method (tested only compilation and linking so far)

Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit a9d92656f533591c5ab65259a77c17f639bb0609
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 25 11:11:49 2017 -0700

    EB/CNS: first pass of diffusion wall flux

Tutorials/EB/CNS/Source/CNS_divop.F90
Tutorials/EB/CNS/Source/CNS_dudt.F90
Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90

commit c9f236cb44037840abbbfbdb6f5f3a75d7af9939
Merge: 3ad2a9bc9 478d0c8b3
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Fri Aug 25 13:02:25 2017 -0500

    Merge branch 'development' into kw-development

commit 3ad2a9bc953c92c54ddd5429f7506afc2abe94cd
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Fri Aug 25 09:05:10 2017 -0500

    give the octree iterator a clear() method

Src/F_Interfaces/Octree/AMReX_octree_mod.F90

commit 478d0c8b3547f24ba7c0d1b160c7eed1ee6ea284
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Aug 25 04:24:05 2017 -0700

    add a multithreaded runtime implementation

Src/AmrTask/Makefile
Src/AmrTask/arch.common
Src/AmrTask/arch/arch.mpi.generic
Src/AmrTask/arch/arch.serial
Src/AmrTask/graph/AMReX_AbstractTask.H
Src/AmrTask/graph/AMReX_AbstractTask.cpp
Src/AmrTask/graph/RTS.H
Src/AmrTask/rts_impls/Serial/Makefile
Src/AmrTask/rts_impls/Serial/rts.C
Src/AmrTask/todolist
Src/AmrTask/tutorials/UnitTests/001_TokenRing.C
Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C
Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C
Src/AmrTask/tutorials/UnitTests/Makefile

commit e93949680c042525cd59816f64342883f99487f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 24 14:29:58 2017 -0700

    EB/CNS: fake 2D

Tutorials/EB/CNS/Exec/ShockRef/inputs
Tutorials/EB/CNS/Source/CNS_dudt.F90
Tutorials/EB/CNS/Source/CNS_f.F90

commit 1ef1a7170b95b4aec4edb3b4e2717a03fc08c848
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 24 14:21:47 2017 -0700

    EB/CNS: use current density for redistribution

Tutorials/EB/CNS/Source/CNS_divop.F90

commit 9acb920316c89b6c6b27b9489018f54a5232ab00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 24 13:47:55 2017 -0700

    EB/CNS: add a parameter to PLM

Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90
Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90

commit 869961a7a620e784297881c833508cd5af56090e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 24 13:26:26 2017 -0700

    EB/CNS: pass bndry centrold into Fortran

Src/Base/AMReX_EBMultiFabUtil.H
Src/Base/AMReX_EBMultiFabUtil.cpp
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_divop.F90
Tutorials/EB/CNS/Source/CNS_dudt.F90
Tutorials/EB/CNS/Source/CNS_physics.F90
Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90

commit b99c61c80d15c3496946d4d7998803987b34f133
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Aug 24 13:16:40 2017 -0700

    fixed the bug that was breaking MPI in this branch

Src/Base/AMReX_FabArrayBase.cpp

commit f42e5cd9cd7b88b991b455bef51a260e1f40ebbd
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Aug 24 12:54:21 2017 -0700

    removed constant declaration from argument

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 2c206d1a1899769f72bc4a382ad402cebe2144d8
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Aug 24 12:49:40 2017 -0700

    simplified geometry generation stuff somewhat

Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp

commit 46dfbbc71845001f2b895d535cb3b0fc34edd8a9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Aug 24 10:57:45 2017 -0700

    remove unused variable.

Src/Base/AMReX_FabArray.H

commit bb026eebbc20e91ca54e9dc54d6ae137bb490409
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Aug 24 10:12:59 2017 -0700

    take care of unused variable warning in parallel copy

Src/Base/AMReX_FabArray.H

commit 23e756d99d29deb6a1ca57d928d00a6ddf038063
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Aug 24 09:41:11 2017 -0700

    took out  const declaration in FabArrayBase to fix USE_MPI=TRUE compile

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 82561bac434c611195f8be303e6016d35f38ab84
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Aug 24 08:45:58 2017 -0700

    merging with branch eb_development

Tests/EBAMRTools/regression/GNUmakefile

commit b8e14d9effe9652aa8b1cd7b94950c05e054adb7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 23 18:00:37 2017 -0700

    EB/CNS: minor memory leak

Tutorials/EB/CNS/Source/CNS_init_eb.cpp

commit baecd41317593ffdc6e75605fb66859301a846cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 23 17:33:41 2017 -0700

    EB/CNS: prepare for diffusion wall flux

Tutorials/EB/CNS/Source/CNS_divop.F90
Tutorials/EB/CNS/Source/CNS_dudt.F90
Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90
Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90
Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90

commit 315f305f738fddc85e00048f4391946d993756ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 23 17:01:38 2017 -0700

    EB/CNS: start diffusion wall flux module

Tutorials/EB/CNS/Source/CNS_divop.F90
Tutorials/EB/CNS/Source/CNS_dudt.F90
Tutorials/EB/CNS/Source/Make.package
Tutorials/EB/CNS/Source/diffusion/Make.package
Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90
Tutorials/EB/CNS/Source/hydro/Make.package

commit c604114190b2f7100555e988d3291efc7427fb63
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 23 16:40:49 2017 -0700

    EB/CNS: fix EB diffusion flux

Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90

commit 09a2cdf685ac6214fa83ed33bb4f77b107954bda
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 23 16:12:38 2017 -0700

    need to check for the __powerpc__ macro as well

Src/Base/AMReX_FPC.cpp

commit aa60aaf80f29d024987ce084f9c87a5fdef61f7d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 23 13:00:58 2017 -0700

    a few more signed/unsigned

Src/Base/AMReX_TinyProfiler.cpp

commit 8c3d4fb9368db403fa08e3992700808c39ec23e7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 23 12:58:26 2017 -0700

    fix unused variable warning.

Src/Particle/AMReX_ParticleContainerI.H

commit ffce1ba11af2a89df7a258156c35bba789fe137b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 23 12:53:38 2017 -0700

    switch from C-style arrays to std::arrays to avoid zero-length array warning.

Src/Particle/AMReX_Particles.H

commit 6bbb7edc6ecfcc39136883d3e85a70ccd9726595
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 23 10:21:42 2017 -0700

    fix signed/unsigned comparison.

Src/Base/AMReX_Array.H

commit fbddf3e352f36e3ad985bc1e30dd67f4fc6fd497
Merge: bd561295f 616b5de7d
Author: kngott <kngott@lbl.gov>
Date:   Tue Aug 22 22:40:38 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-codes/amrex into development

commit bd561295f1f2d50fe1c09d1a5b90e9f9dd5f0715
Author: kngott <kngott@lbl.gov>
Date:   Tue Aug 22 22:40:34 2017 -0700

    MoveAllFabs fix and updated test

OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp
Src/Base/AMReX_FabArray.H

commit 616b5de7d2376e1b98a24e347b6e3ffc4560e419
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 22 22:02:46 2017 -0700

    refactor the new amrex_boxarray_build for FLASH

Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90

commit 46a38a05dc37a04989a915ab8e954d027ce60d8e
Merge: c063a1355 92c19a1e7
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 22 21:37:50 2017 -0700

    Merge pull request #93 from kweide/development
    
    Add specific build routines for constructing boxarrays and distromaps from user-provided lists in Fortran

commit cf038b5098abe20a92c4f2de66e757715d8bb036
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 22 18:08:28 2017 -0700

    EB/CNS: EB diffusion flux

Src/Base/AMReX_ebcellflag_mod.F90
Tutorials/EB/CNS/Source/CNS_dudt.F90
Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90
Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90

commit a59ce2eaf23a3af46db550569069d337405706ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 22 16:49:13 2017 -0700

    EB/CNS: split hydro and diffsion fluxes

Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_dudt.F90
Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90
Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90

commit c063a1355a9473a961b469957b12c2ca04c58ca5
Merge: 69bc0a7ed 5ecff6d27
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Aug 22 16:18:55 2017 -0700

    Merge pull request #95 from AMReX-Codes/perf-docs
    
    update Documentation: added IPM section to Profiling.tex

commit 5ecff6d27d0d9ac35a0a05ba7b3e3098dbf3edb8
Merge: b9e7e42d2 00e9dd08d
Author: Cy Chan <cychan@lbl.gov>
Date:   Tue Aug 22 16:15:22 2017 -0700

    Merge branch 'development' into perf-docs

commit b9e7e42d28d5b8ad67a66129e761c4df9a35d718
Author: Cy Chan <cychan@lbl.gov>
Date:   Tue Aug 22 16:07:27 2017 -0700

    update Documentation
      added IPM section to Profiling.tex

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Profiling/Profiling.tex
Docs/AMReXUsersGuide/Profiling/figs/commtopo.png
Docs/AMReXUsersGuide/Profiling/figs/mpi.png
Docs/AMReXUsersGuide/Profiling/figs/msgsizes.png
Docs/AMReXUsersGuide/Profiling/figs/papi.png
Docs/AMReXUsersGuide/Profiling/figs/summary.png
Docs/AMReXUsersGuide/Profiling/figs/timings.png

commit 3e40ca33e6319cf79c4369f2ee1bd0ea2184c9a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 22 15:18:08 2017 -0700

    EB/CNS: regular diffusion terms

Tutorials/EB/CNS/Source/CNS_dudt.F90
Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90
Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90

commit fec330191747a3c4c86a301b19ab0bd6c20f21a4
Merge: ed330ba6a 69bc0a7ed
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Tue Aug 22 15:09:32 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 69bc0a7ed576f247b7bdf4be9ffaee508b089bea
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 22 11:37:48 2017 -0700

    add move all fabs test.

OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp

commit 2688726e0f3e6bdd2bee638445b16438449366b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 22 11:26:44 2017 -0700

    EB/CNS: use future mass for weighting

Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_dudt.F90
Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90

commit dc18f279ffb7222c2575524cd59a585ad0ad3ce0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 22 10:58:16 2017 -0700

    EB/CNS: reorganization

Tutorials/EB/CNS/Exec/Make.CNS
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_dudt.F90
Tutorials/EB/CNS/Source/CNS_nd.F90
Tutorials/EB/CNS/Source/Make.package
Tutorials/EB/CNS/Source/diffusion/Make.package
Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90
Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90
Tutorials/EB/CNS/Source/diffusion/diff_coef_mod.F90
Tutorials/EB/CNS/Source/hydro/Make.package

commit 180f7cf217df91cf4bb938a7e82c0522d169ec77
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 21 14:45:30 2017 -0700

    EB/CNS: use air as initial condition

Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90
Tutorials/EB/CNS/Exec/Pulse/inputs

commit 82cadae4bdc01de79b2219fd6d44eee7cc563cfd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 21 14:23:18 2017 -0700

    EB/CNS: add a module computing viscosity and thermal conductivity

Tutorials/EB/CNS/Source/CNS_physics.F90
Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90
Tutorials/EB/CNS/Source/hydro/Make.package
Tutorials/EB/CNS/Source/hydro/cns_diff_mod.F90
Tutorials/EB/CNS/Source/hydro/cns_eb_diff_mod.F90
Tutorials/EB/CNS/Source/hydro/diff_coef_mod.F90

commit 7074ca4192429d0ae465c22b53862dfcd152b71f
Merge: a0491c979 bbe4d0d0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 21 13:53:36 2017 -0700

    Merge branch 'weiqun/eb' into eb_development

commit 00e9dd08de14d59a6444c30eb128b243d651beb4
Merge: f56a800da cbb7c8b8e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Aug 21 13:47:44 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f56a800da65b8d14b181b9b6ceddfc8457bf7fb7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Aug 21 13:47:26 2017 -0700

    remove some debugging junk I checked in by mistake.

Src/Particle/AMReX_ParticleInit.H

commit bbe4d0d0d55d514398b661aee9693295a625a68d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 21 13:43:11 2017 -0700

    EB/CNS: fix a bug

Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90

commit 89ecb4e0c358c944af0207c02d801c7b5d7287cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 21 10:34:09 2017 -0700

    EB/CNS: make sure flux outside the domain is not used

Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90

commit ed330ba6ad24b7cd49059667df8510b5fec4c1d9
Merge: 8910997e9 cbb7c8b8e
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Mon Aug 21 08:07:02 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cbb7c8b8ea23d0757d8ffe3dbd89988108d7769f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 19 13:05:59 2017 -0700

    add assertion making sure BoxArray::set is not called on non-trivial objects

Src/Base/AMReX_BoxArray.cpp

commit a139b16a12d52272e5ad2ae8611f79d0f264c06e
Merge: 81038c6ba 16b829705
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Aug 18 16:04:19 2017 -0700

    Merge pull request #91 from AMReX-Codes/compiler_warnings
    
    Compiler warnings

commit 16b82970563ccd793de0a6ec96f5c6655b56627e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 16:00:42 2017 -0700

    give this a more descriptive name

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_Utility.H

commit a0491c979bf3785842b8c543d0834e189c6dc880
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 18 15:05:20 2017 -0700

    a GeometryShop test

Tests/GeometryShop/ramp/GNUmakefile
Tests/GeometryShop/ramp/Make.package
Tests/GeometryShop/ramp/inputs
Tests/GeometryShop/ramp/main.cpp

commit 19c826e9470276d0eb57c74f0c0173225f84027e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 15:43:40 2017 -0700

    remove some vlas

Src/Amr/AMReX_Amr.cpp

commit 007cca18dfdf51b86f21e0b4b70a234a56471fe7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 15:28:15 2017 -0700

    some more cleanup

Src/Base/AMReX.cpp
Src/Base/AMReX_BCUtil.H
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_BC_TYPES.H
Src/Particle/AMReX_LoadBalanceKD.H
Src/Particle/AMReX_Particles_F.H

commit 309b21221b338eb4109d6303da5b420ab81059f5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 15:13:00 2017 -0700

    initialize this variable

Src/Base/AMReX_BaseFab.cpp

commit 79f64a84709cd01e54f39b877d9bb822c11738a9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 15:08:25 2017 -0700

    switch this back to no by default.

Tools/GNUMake/comps/gnu.mak

commit 6bc9dd95583c42491ec8968ab1c7915af834a981
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 15:06:40 2017 -0700

    fix bug in llvm.mak

Tools/GNUMake/comps/llvm.mak

commit 824d9432795c81ba7d3c141e84508d6b53ad0218
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 14:52:56 2017 -0700

    turn on -Wsign-compare in Debug mode.

Tools/GNUMake/comps/gnu.mak

commit 9dcc8eb0afe0813af6278de5b5e906311e96aa4c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 14:46:54 2017 -0700

    yet another signed/unsigned

Src/Amr/AMReX_StateDescriptor.cpp

commit baa4aa552c3df7101f8bd0e656f1fd72bbe5f917
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 14:38:26 2017 -0700

    a few more signed / unsigned

Src/Amr/AMReX_AmrLevel.cpp

commit 92c19a1e76a8518045c2aa221f9db27a2ae71349
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Fri Aug 18 16:00:41 2017 -0500

    Add specific build routines for constructing boxarrays and distromaps from explicit Fortran data

Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_distromap_fi.cpp
Src/F_Interfaces/Base/AMReX_distromap_mod.F90

commit dab6cc101a49c0275a6850213086a22a9b57f5f4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 13:53:00 2017 -0700

    another signed/unsigned

Src/Base/AMReX_DistributionMapping.cpp

commit 2672a734580dc1dd99aebd69eb4f64217af24e7b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 13:51:21 2017 -0700

    ignore this unused variable.

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_Utility.H

commit e750e60ac076b7c1c58d534fc2c3a995f2ad59f6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 13:37:22 2017 -0700

    fix some signed / unsigned comparisons.

Src/AmrCore/AMReX_FluxRegister.cpp
Src/Base/AMReX_Array.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_NFiles.cpp
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ParmParse.cpp
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_VisMF.cpp
Src/Base/AMReX_parmparse_fi.cpp

commit bfbf52d2a1f914a407bce1b48fb646ce5898afd8
Merge: b8a701a3d 1ab5dd248
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 18 13:18:33 2017 -0700

    Merge branch 'dtg_branch' into weiqun/eb

commit b8a701a3d524fdedd495eb82232bda6b88c9af8c
Merge: 3c5c42e57 81038c6ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 18 13:18:19 2017 -0700

    Merge branch 'development' into weiqun/eb

commit 3c5c42e5716704da8c161826872a60aa47e5cef5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 18 12:49:14 2017 -0700

    we may not even have a probin file

Src/Amr/AMReX_Amr.cpp

commit 9a2aaf961397d5bcd9fc72dd4bb12e28b053ecb8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 18 12:36:59 2017 -0700

    EB/CNS: mod inputs

Tutorials/EB/CNS/Exec/ShockRef/cns_prob.F90
Tutorials/EB/CNS/Exec/ShockRef/inputs

commit 17029dee6e74c1840417b015188fecf23e31e892
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Aug 18 11:58:29 2017 -0700

    CMake: update config file

Tools/CMake/AMReXConfig.cmake.in

commit a2689c3b90ba7236decb612793f27b39c67bcf5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 18 10:51:20 2017 -0700

    EB/CNS: using mass weighting instead of volume weighting

Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90

commit f6b2f90dea5c6a47bcdde7a489a58072a61aced7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 18 10:49:17 2017 -0700

    EB/CNS: some parmparse parameters for the shock reflection test

Tutorials/EB/CNS/Exec/ShockRef/cns_prob.F90

commit 81038c6ba1b554662c11d4e4c6b18ff56867b23a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 10:07:18 2017 -0700

    Fix offset bug when initializing particle integer data.

Src/Particle/AMReX_ParticleInit.H

commit 7b426c29bec02ebbae8f193cfc7303b3bc34890d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 10:04:29 2017 -0700

    Fix copy/paste issue in comment.

Src/Particle/AMReX_ParticleInit.H

commit bd2045e20bf9c6e6924c65488ba5b6b41603cf72
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Aug 18 10:02:25 2017 -0700

    Real -> amrex::Real

Src/Particle/AMReX_LoadBalanceKD.H

commit bb497048504639db8bc9b93b6215e78be5fbc045
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 18 09:23:45 2017 -0700

    EB/CNS: fix a bug in 2-shock riemann solver; add HLL; floor density and pressure

Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_nd.F90
Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90
Tutorials/EB/CNS/Source/hydro/analriem3d.F90

commit 8910997e93b0615893409f8535f36af862d79fa7
Merge: bf061aef5 8457d4770
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Fri Aug 18 07:36:41 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 0c5f20049fa650711fe78403a1a017f6be2fef4f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Aug 18 01:35:09 2017 -0700

    Add a missing device ifdef

Src/Base/AMReX_BaseFab.H

commit 16dd1d1f5d646cf8db32f1743530163e15cce02b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Aug 18 01:54:12 2017 -0400

    Fix the summitdev library typo

Tools/GNUMake/comps/pgi.mak

commit 822c257b896a4e74c939e1854251d0903822518d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Aug 17 17:29:05 2017 -0700

    Doc: fix typo

Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex

commit 5b445a60018eebdc087512a61005b0c08518c0fa
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Aug 17 17:27:36 2017 -0700

    CMake: update exports

Tools/CMake/AMReXConfig.cmake.in

commit 1455939bd55d710ca16e8b13a665fc3a8d32f018
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Aug 17 17:17:28 2017 -0700

    CMake: update doc

Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex
Tools/CMake/AMReX_Defines.cmake

commit 93280c1536824becc995230a101c159306623a0f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Aug 17 16:57:20 2017 -0700

    CMake: update
      * Add support for ProfParser
      * Re-factor souce files lists
      * Change some config args.

Src/Amr/CMakeLists.txt
Src/AmrCore/CMakeLists.txt
Src/Base/CMakeLists.txt
Src/Boundary/CMakeLists.txt
Src/CMakeLists.txt
Src/Extern/CMakeLists.txt
Src/F_BaseLib/CMakeLists.txt
Src/F_Interfaces/CMakeLists.txt
Src/LinearSolvers/CMakeLists.txt
Src/Particle/CMakeLists.txt
Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake
Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt
Tutorials/Amr/Advection_F/CMakeLists.txt
Tutorials/Amr/Advection_octree_F/CMakeLists.txt

commit 1ab5dd24815edfb49ecb5216025ad3a04d9975e0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Aug 17 16:29:05 2017 -0700

    yet another attempt to silence valgrind

Src/GeometryShop/AMReX_EBISBox.cpp

commit 8457d4770517bee7461e4a8d1fce01693aae60b7
Merge: 756c8e7ea 81ff56778
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Aug 17 16:26:57 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ceea83872e9f2d4e9a76a9d0f14dceb71350c51d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 17 15:56:12 2017 -0700

    EB/CNS: minor

Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90

commit 90c0c0afcbee04c53b2c297a68a67ea776eb92ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 17 15:21:30 2017 -0700

    EB/CNS: make sure dx == dy == dz

Tutorials/EB/CNS/Exec/ShockRef/inputs
Tutorials/EB/CNS/Source/CNS.cpp

commit 81ff56778011e69c19d811b7f392eea51cedfaf1
Merge: a10911ad6 25c1a3f22
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 17 15:19:07 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit a10911ad6499613a1a3afd23291ed34da49eeb37
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 17 15:18:29 2017 -0700

    uniqify coarsened boxarray.

Src/Extern/amrdata/AMReX_DataServices.cpp

commit 927e862b85d2262879bcb150a99889024f42d343
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 17 15:13:31 2017 -0700

    make uniqify public.

Src/Base/AMReX_BoxArray.H

commit 272f46a29abe6579761ce74c4e1027fec77a7dab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 17 14:25:01 2017 -0700

    EB/CNS: add Shock Reflection problem

Src/Amr/AMReX_Amr.cpp
Tutorials/EB/CNS/Exec/Pulse/GNUmakefile
Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90
Tutorials/EB/CNS/Exec/ShockRef/GNUmakefile
Tutorials/EB/CNS/Exec/ShockRef/Make.package
Tutorials/EB/CNS/Exec/ShockRef/cns_prob.F90
Tutorials/EB/CNS/Exec/ShockRef/inputs
Tutorials/EB/CNS/Source/CNS_f.F90
Tutorials/EB/CNS/Source/CNS_physics.F90

commit 756c8e7ea0c8b290f00b8a33ceebf8d7b15980e4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Aug 17 12:41:06 2017 -0700

    1D and 2D versions of the KDTree fortran helper routines.

Src/Particle/AMReX_KDTree_1d.F90
Src/Particle/AMReX_KDTree_2d.F90
Src/Particle/AMReX_KDTree_3d.F90

commit 415d779733a94d9e0053b4a0853013547cf08c71
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Aug 17 12:34:03 2017 -0700

    move the load balancing stuff to Src/Particle

Src/Particle/AMReX_KDTree_3d.F90
Src/Particle/AMReX_KDTree_F.H
Src/Particle/AMReX_LoadBalanceKD.H
Src/Particle/AMReX_LoadBalanceKD.cpp
Src/Particle/CMakeLists.txt
Src/Particle/Make.package
Tutorials/Particles/LoadBalance/Make.package
Tutorials/Particles/LoadBalance/kdtree_F.H
Tutorials/Particles/LoadBalance/main.cpp
Tutorials/Particles/LoadBalance/visualize_output.ipynb
Tutorials/Particles/LoadBalance/visualize_output.ipynb.REMOVED.git-id

commit 25c1a3f222cb9f0a6fbdbf696c6a5b49de0c85bc
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Aug 17 11:19:10 2017 -0700

    This needs to be a 'C' header so it will be installed when building amrex as a library.

Src/Particle/Make.package

commit 30c9d83f2fc160dc7bc1059e1df5f9c33b02b114
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Aug 17 10:46:22 2017 -0700

    some more reorganization.

Tutorials/Particles/LoadBalance/main.cpp

commit 78cfae09c131f51f33a3da79eb536a661a4d0d4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 17 10:42:38 2017 -0700

     EB/CNS: forgot to call mpi reduce

Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90

commit a8a1cba2eff6985b701c316fb4027c8521fa2cb3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Aug 17 10:23:16 2017 -0700

    some reorganization.

Tutorials/Particles/LoadBalance/main.cpp

commit a8c4aeefcece2a728549d7c9c89f095b8af6a69e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 16 18:04:27 2017 -0700

    EB/CNS: minor

Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90

commit c1dd21ca4009755b3a32c72d7fb201341cf3bbef
Merge: 0d4ce81e9 bf061aef5
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Wed Aug 16 19:52:40 2017 -0500

    Merge branch 'development' into kw-development

commit bf061aef54d5e726895b0e78649f87d6179277b7
Merge: 8b55b4bed 52cf20bc7
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Wed Aug 16 19:45:18 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cc571d7014f71dc4cf136c5120eec43513739f52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 16 17:23:07 2017 -0700

    EB/CNS: print out the total mass

Tutorials/EB/CNS/Exec/Pulse/inputs
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp

commit 32d72bc3871e049108d84a2ff854a890385dd746
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 16 16:57:26 2017 -0700

    EB/CNS: bug fix

Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90
Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90
Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90

commit 52cf20bc7262bde110c492c18253f2503243f851
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 16 16:51:24 2017 -0700

    minor tweaks.

Tutorials/Particles/LoadBalance/create_binary_particle_file.py
Tutorials/Particles/LoadBalance/inputs
Tutorials/Particles/LoadBalance/main.cpp
Tutorials/Particles/LoadBalance/visualize_output.ipynb.REMOVED.git-id

commit 2a8be21157da02d4f171156c56340ff7e88e4be9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 16 16:51:04 2017 -0700

    checked this file in by mistake.

Tutorials/Particles/LoadBalance/binary_particle_file.dat.REMOVED.git-id

commit 075bd73e771ebbdb586b916a3d9bc4f319d0a03c
Merge: 65b4b71de 3051886b8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 16 16:29:28 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 65b4b71de9fbb034b7f4c05cee625f6204c46c91
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Aug 16 16:29:13 2017 -0700

    some works towards using a kdtree for load balancing particles

Tutorials/Particles/LoadBalance/GNUmakefile
Tutorials/Particles/LoadBalance/Make.package
Tutorials/Particles/LoadBalance/binary_particle_file.dat.REMOVED.git-id
Tutorials/Particles/LoadBalance/create_binary_particle_file.py
Tutorials/Particles/LoadBalance/inputs
Tutorials/Particles/LoadBalance/kdtree_3d.f90
Tutorials/Particles/LoadBalance/kdtree_F.H
Tutorials/Particles/LoadBalance/main.cpp
Tutorials/Particles/LoadBalance/visualize_output.ipynb.REMOVED.git-id

commit f0a7342c21522c1ceab75ff30088f2ca0f0d7335
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 16 15:22:22 2017 -0700

    EB/CNS: clean up

Tutorials/EB/CNS/Source/hydro/comp.F90
Tutorials/EB/CNS/Source/hydro/comp_2d.F90
Tutorials/EB/CNS/Source/hydro/comp_3d.F90
Tutorials/EB/CNS/Source/hydro/wall.F

commit 19b4f798272bf7b03bd9e39a7fe887efe69ae663
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 16 15:20:20 2017 -0700

    EB/CNS: add wall flux and the first simple test seems to work now

Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90
Tutorials/EB/CNS/Source/hydro/Make.package
Tutorials/EB/CNS/Source/hydro/analriem3d.F90
Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90
Tutorials/EB/CNS/Source/hydro/cns_eb_hyp_wall.F90

commit 0d4ce81e9c699b0ebc242ad0202aa2a0f8b43d64
Merge: 85ebfd03b 3051886b8
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Wed Aug 16 17:19:10 2017 -0500

    Merge branch 'development' into kw-development

commit 469546bf05a400a69fbe24a11e8da3bc39a56bf9
Merge: 2b291b988 3051886b8
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Aug 16 14:46:04 2017 -0700

    Merge branch 'development' into mr-cmake

commit 2b291b98848486db8f8a306670cb135da0d48b53
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Aug 16 14:45:08 2017 -0700

    CMake: modify implementation of user options

Tools/CMake/AMReX_Options.cmake

commit a608f2676b92a4a73f2011a79443969cbe24d690
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 16 11:17:33 2017 -0700

    EB/CNS: add parmparse to probin

Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90
Tutorials/EB/CNS/Exec/Pulse/inputs

commit 76b208b9635728c54ff2b338da6f8a0ba25f6f86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 16 10:54:53 2017 -0700

    fix a number of index problems

Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90
Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90

commit b572dc4528ea447ef265b86c313f1b496e64e98c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 15 18:07:33 2017 -0700

    EB/CNS: fix bug

Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90

commit 114b302cfa913d89454d1464de373cac522d4e1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 15 17:52:06 2017 -0700

    EB/CNS: compute eb diffop

Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_nd.F90
Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90
Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90

commit 3051886b8b2e9e635cbb2a955c3d9ffbd1cf3eca
Merge: f760b0a09 f55c3669d
Author: kngott <kngott@lbl.gov>
Date:   Tue Aug 15 17:51:50 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-codes/amrex into development

commit f760b0a09b63bf74e58f19c5449ea324ce233271
Author: kngott <kngott@lbl.gov>
Date:   Tue Aug 15 17:51:07 2017 -0700

    Update to make system for profiling and new profparser setup. Uses separate PROFILE and USE_PROFPARSER variables in GNUmakefiles and eliminates depreciated NOLINEVALUES directive.

OldTutorials/DataServicesTest0/GNUmakefile
Src/Extern/ProfParser/Make.package
Src/Extern/amrdata/AMReX_DataServices.H
Src/Extern/amrdata/AMReX_DataServices.cpp
Src/Extern/amrdata/AMReX_XYPlotDataList.H
Src/Extern/amrdata/AMReX_XYPlotDataList.cpp
Src/Extern/amrdata/Make.package
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 06b391b23ef9ffdcde9358d0041bcf90491c6ea4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Aug 15 17:43:14 2017 -0700

    CMake: modify way of adding include dirs

Src/Amr/CMakeLists.txt
Src/AmrCore/CMakeLists.txt
Src/Base/CMakeLists.txt
Src/Boundary/CMakeLists.txt
Src/CMakeLists.txt
Src/Extern/CMakeLists.txt
Src/F_BaseLib/CMakeLists.txt
Src/F_Interfaces/CMakeLists.txt
Src/LinearSolvers/CMakeLists.txt
Src/Particle/CMakeLists.txt
Tools/CMake/AMReX_Utils.cmake

commit f55c3669da938aa3ed8b12ad2d401cd63663903e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 15 17:31:45 2017 -0700

    This approach to testing whether the grids cover the domain is much more memory efficient and should be equivalent if the grids are non-overlapping.

Src/Particle/AMReX_ParticleContainerI.H

commit 0e6f2031335c049a293890b37a2c371c857258df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 15 16:41:22 2017 -0700

    build area fraction and face centroid

Src/Base/AMReX_EBMultiFabUtil.H
Src/Base/AMReX_EBMultiFabUtil.cpp
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp

commit 11775c1e07595e97f1464484d3790a0bc152134e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Aug 15 16:28:42 2017 -0700

    CMake: remove unused functions.

Tools/CMake/AMReX_Utils.cmake

commit 402e62b153ec2fbe328a28f5fc02cbec47c200b5
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Aug 15 16:20:46 2017 -0700

    CMake: move config of macro definitions to separate file

Src/Extern/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Defines.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_Utils.cmake

commit 026aca295230b4a9042e2d3c4355daa960756205
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 15 15:19:21 2017 -0700

    EB/CNS: first pass of eb flux module

Tutorials/EB/CNS/Source/hydro/Make.package
Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90

commit d6a7d2073f34c14577ff7066b00dbccb0d91b6a0
Merge: 645d4fc05 ac1109be5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 15 15:07:33 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 645d4fc0563a1e01a141268ca6c87bbbbd30d5d2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 15 15:07:16 2017 -0700

    Restore some variable names that were changed by some over-aggresive find/replacing.

Src/Particle/AMReX_ParticleInit.H

commit f46229d9d088fb19b8406ad830a9358aa686e9c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 15 12:30:31 2017 -0700

    EB/CNS: get comp_3d compile

Tutorials/EB/CNS/Source/hydro/Make.package
Tutorials/EB/CNS/Source/hydro/comp_3d.F90

commit 04021d3b0cdfe2b5886d2be5431d57180d2ed56e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 15 10:44:07 2017 -0700

    EB/CNS: add john's code

Tutorials/EB/CNS/Source/hydro/comp_3d.F90

commit e43325580a0e05f35e047727f47de865613fc0e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 15 10:42:21 2017 -0700

    EB/CNS: fix physical boundary without EB

Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90

commit c515ddaab69d0095b0dd1484a1f6eeacedd9ce48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 14 17:49:05 2017 -0700

    EB/CNS: fix some bugs

Tutorials/EB/CNS/Exec/Pulse/inputs
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90
Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90
Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90

commit c4078a1926b64be81cf1bd680c3c8e559b71b8dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 14 16:51:41 2017 -0700

    EB/CNS: merge John's eb hyperbolic code

Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90
Tutorials/EB/CNS/Source/hydro/Make.package
Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90
Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90

commit 275fef46b8f6e9433b9a4b3eb3453e81d612cf61
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 14 15:43:35 2017 -0700

    EB/CNS: second order hydro with regular geometry works

Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90

commit ac1109be58434e24b154d22dad90198a26cc96d1
Author: kngott <kngott@lbl.gov>
Date:   Mon Aug 14 15:26:24 2017 -0700

    Added BLProfParser parser files to the realclean command. Used specific names to ensure there are not accidental deletions.

Tools/GNUMake/Make.rules

commit 28aac30a4c2220178b6869924625242172d6c230
Author: kngott <kngott@lbl.gov>
Date:   Mon Aug 14 15:21:43 2017 -0700

    A simple 3D TRACE profiling fix.

Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp

commit 9383f7ce56acf4ca8e370ab8076087eaab0312ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 14 15:09:50 2017 -0700

    EB/CNS: first order hydro with regular geometry works

Tutorials/EB/CNS/Exec/Make.CNS
Tutorials/EB/CNS/Exec/Pulse/inputs
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_f.F90
Tutorials/EB/CNS/Source/CNS_nd.F90
Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90
Tutorials/EB/CNS/Source/hydro/Make.package
Tutorials/EB/CNS/Source/hydro/analriem3d.F90
Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90

commit 3df1ab1dfc3aa0a3469edad4dbedb2ad57f64f2e
Author: kngott <kngott@lbl.gov>
Date:   Mon Aug 14 14:30:31 2017 -0700

    Addition of profile specific requirements to standard amrex make. Should only require PROFILE=TRUE.

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 8d813b2d44ead910551b1aea46eb61d35a76099c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 14 11:04:58 2017 -0700

    EB/CNS: rename to F90

Tutorials/EB/CNS/Source/hydro/analriem3d.F90
Tutorials/EB/CNS/Source/hydro/comp.F90
Tutorials/EB/CNS/Source/hydro/comp_2d.F90
Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90
Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90
Tutorials/EB/CNS/Source/hydro/wall.F

commit 2b92f4c3041c358758c09b7f30e45dcab670f7fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 14 11:01:29 2017 -0700

    EB/CNS: more code from John

Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90
Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90
Tutorials/EB/CNS/Source/hydro/analriem3d.f
Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.f90
Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.f90

commit 9d996d3ce69ad544d806990f5464dfc00d803889
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 14 10:43:13 2017 -0700

    EB/CNS: john's hydro code

Tutorials/EB/CNS/Source/hydro/comp.f
Tutorials/EB/CNS/Source/hydro/comp_2d.f
Tutorials/EB/CNS/Source/hydro/wall.f

commit 56a92eee92cd2f55edc47569db4a73cf385de7f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 14 10:39:37 2017 -0700

    EB/CNS: set up RK2 and plotfile

Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90
Tutorials/EB/CNS/Exec/Pulse/inputs
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_io.cpp

commit 070f9423e7e88efc2356c0f9c36f2e74bde04008
Merge: 6ffe1527b e9ef96335
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Aug 14 10:36:33 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 6f57b41dd899a0ef9b3be716e57493dea1a22368
Merge: 14dbe9043 e9ef96335
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Aug 14 01:44:02 2017 -0700

    Merge branch 'development' into gpu
    
    Conflicts:
            Src/Base/AMReX.cpp
            Src/Base/AMReX_BaseFab_f.H
            Src/Base/AMReX_BaseFab_nd.f90
            Src/Base/AMReX_parmparse_mod.F90
            Tools/GNUMake/Make.rules
            Tools/GNUMake/comps/pgi.mak

commit 0a8ff6e0e71800584f89be5f9755c9d982f7f21a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 13 08:00:29 2017 -0700

    EB/CNS: initialzie EB

Tutorials/EB/CNS/Exec/Pulse/inputs
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_init_eb.cpp
Tutorials/EB/CNS/Source/Make.package
Tutorials/EB/CNS/Source/main.cpp

commit e9ef96335aefdf9b655621ed5c3119618e732e5f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 12 16:25:13 2017 -0700

    Remove unused variables

Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Extern/amrdata/AMReX_AmrData.cpp

commit c5de995c20a0ca228560a0720dc6eb62e9643a44
Merge: 207e7af3b c763f9b41
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Aug 12 15:49:23 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 207e7af3b1c6508fa398cff1103135a4d19ef465
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Aug 12 15:49:19 2017 -0700

    add Dynamic Task Parallelism support

Src/AmrTask/graph/AMReX_AbstractTask.H
Src/AmrTask/graph/AMReX_DataTypes.H
Src/AmrTask/graph/AMReX_TaskGraph.H
Src/AmrTask/graph/RTS.H
Src/AmrTask/rts_impls/Serial/rts.C
Src/AmrTask/rts_impls/Serial/rts_taskimpl.H
Src/AmrTask/tutorials/UnitTests/001_TokenRing.C
Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C
Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C
Src/AmrTask/tutorials/UnitTests/Makefile

commit c763f9b41bab389c51ebc4f229d6985168309536
Author: kngott <kngott@lbl.gov>
Date:   Sat Aug 12 14:57:14 2017 -0700

    Preprocessing to protect profiler services from 3D simulations.

Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp
Src/Extern/amrdata/AMReX_DataServices.cpp

commit a2e739d73fc0412554bfdb33f5c5326caada3dd4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 12 12:23:33 2017 -0700

    EB/CNS: estimate dt

Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_nd.F90

commit be4fb4f4dcab40666a3288eaa54d12be7b5b564e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 12 12:03:51 2017 -0700

    EB/CNS: compute temperature

Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_nd.F90
Tutorials/EB/CNS/Source/Make.package

commit ee81d4aacac81205f04f3175618c4ccab5e6fe0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 12 11:37:02 2017 -0700

    EB/CNS: set up a simple test problem

Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90
Tutorials/EB/CNS/Exec/Pulse/inputs
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_f.F90
Tutorials/EB/CNS/Source/CNS_physics.F90

commit 1462329252451079cdabd7cdfbc4d2b14b466f72
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 11 21:48:24 2017 -0700

    CNS/EB: derive

Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_derive.F90
Tutorials/EB/CNS/Source/CNS_physics.F90
Tutorials/EB/CNS/Source/CNS_setup.cpp
Tutorials/EB/CNS/Source/Make.package

commit e1078134d0f8bcdc1349edbe1452ad75bf85e6d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 11 21:16:31 2017 -0700

    EB/CNS: add physics module

Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_f.F90
Tutorials/EB/CNS/Source/CNS_physics.F90
Tutorials/EB/CNS/Source/CNS_setup.cpp
Tutorials/EB/CNS/Source/Make.package

commit 3e3a8d07f2a887552649cc3a9e42d096e3ed8916
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 11 17:59:36 2017 -0700

    set up statedata

Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_setup.cpp
Tutorials/EB/CNS/Source/Make.package
Tutorials/EB/CNS/Source/bc_fill_nd.F90

commit 559a74cdc089b2addfde0010d1866d79f4c48038
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 11 17:43:31 2017 -0700

    EB/CNS: pass parameters to fortran

Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_ParallelDescriptor.H
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNS_F.H
Tutorials/EB/CNS/Source/CNS_f.F90
Tutorials/EB/CNS/Source/CNS_setup.cpp
Tutorials/EB/CNS/Source/Make.package

commit 3458e19420beb21ac731da1ebfd75bbfd1262003
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 11 15:16:27 2017 -0700

    skeleton for EB/CNS

Tutorials/EB/CNS/Exec/Make.CNS
Tutorials/EB/CNS/Exec/Pulse/GNUmakefile
Tutorials/EB/CNS/Exec/Pulse/Make.package
Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90
Tutorials/EB/CNS/Source/CNS.H
Tutorials/EB/CNS/Source/CNS.cpp
Tutorials/EB/CNS/Source/CNSBld.cpp
Tutorials/EB/CNS/Source/CNS_advance.cpp
Tutorials/EB/CNS/Source/CNS_error.cpp
Tutorials/EB/CNS/Source/CNS_io.cpp
Tutorials/EB/CNS/Source/CNS_setup.cpp
Tutorials/EB/CNS/Source/Make.package
Tutorials/EB/CNS/Source/main.cpp

commit d3567ffa10aab9c99dafcb3d09dd1555276d28de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 11 12:17:36 2017 -0700

    remove old ones

Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3d.f90

commit 4e2b49552eaf6f4b32039a9341649b08a7623adf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 11 12:11:55 2017 -0700

    move some eb fortran subrtoutines into new files

Src/Base/AMReX_EBMultiFabUtil_2d.F90
Src/Base/AMReX_EBMultiFabUtil_3d.F90
Src/Base/Make.package

commit 40328e250ad5e73c6541fd59f79e690ac6aeba62
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 11 09:55:46 2017 -0700

    Face neighbors: this is known to be flawed, but check in before we have a better alternative

Src/Base/AMReX_EBLevel.cpp

commit c6a33f3030f4247b8debfba51a54039749f8b34b
Merge: 69704c2aa 6e1aba2dd
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Aug 10 22:30:13 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 69704c2aa529a2db97dc8b22ab7b13bf83235a70
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Aug 10 22:30:06 2017 -0700

    add more routines to the runtime interface

Src/AmrTask/arch.common
Src/AmrTask/arch/arch.serial
Src/AmrTask/graph/AMReX_AbstractTask.H
Src/AmrTask/graph/AMReX_AbstractTask.cpp
Src/AmrTask/graph/AMReX_DataTypes.H
Src/AmrTask/graph/AMReX_TaskGraph.H
Src/AmrTask/graph/Makefile
Src/AmrTask/graph/RTS.H
Src/AmrTask/rts_impls/Serial/Makefile
Src/AmrTask/rts_impls/Serial/rts.C
Src/AmrTask/rts_impls/Serial/rts_graphimpl.H
Src/AmrTask/rts_impls/Serial/rts_taskimpl.H
Src/AmrTask/tutorials/UnitTests/001_TokenRing.C
Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C
Src/AmrTask/tutorials/UnitTests/Makefile

commit d2dc94047f610952b8b73537cfff2beb1d9a6cea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 10 17:06:25 2017 -0700

    wip: face neighbors

Src/Base/AMReX_EBLevel.H
Src/Base/AMReX_EBLevel.cpp

commit dc696a1b947fd7082fdb7750a87b0800d509798a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 9 15:54:21 2017 -0700

    wip: add EBFaceFlagFab

Src/Base/AMReX_EBCellFlag.H
Src/Base/AMReX_EBFabFactory.cpp
Src/Base/AMReX_EBFaceFlag.H
Src/Base/AMReX_EBFaceFlag.cpp
Src/Base/AMReX_EBLevel.H
Src/Base/AMReX_EBLevel.cpp
Src/Base/Make.package

commit 6e1aba2dd29e8bc7da1665a0235917f89fc024b7
Author: kngott <kngott@lbl.gov>
Date:   Wed Aug 9 15:24:38 2017 -0700

    Adding a count of MPI function calls to the timeline profiling option.

Src/Extern/ProfParser/AMReX_CommProfStats.cpp
Src/Extern/amrdata/AMReX_DataServices.cpp

commit 34bd65c03cf68ca08fb19879cf6975ba9f4bf390
Merge: 1402b2400 10dcd0152
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Aug 9 09:49:43 2017 -0700

    Merge pull request #89 from nncarlson/fix-char-kind
    
    Fix character kind declarations

commit 10dcd0152e9dcb51d4d291c5e86e786a34cfd7ac
Author: Neil Carlson <neil.n.carlson@gmail.com>
Date:   Wed Aug 9 09:12:32 2017 -0600

    Fix character kind declarations

Src/Base/AMReX_error_mod.F90
Src/F_BaseLib/bl_random_f.f90
Src/F_BaseLib/multifab_c.f90
Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90
Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90
Src/F_Interfaces/Base/AMReX_init_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Src/F_Interfaces/Base/AMReX_plotfile_mod.F90
Tutorials/Amr/Advection_F/Source/my_amr_mod.F90
Tutorials/Amr/Advection_F/Source/tagging_mod.F90
Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90
Tutorials/Amr/Advection_octree_F/Source/tagging_mod.F90

commit 1402b24002742190c5ab9e3c8731ec276a24fe21
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Aug 9 00:01:46 2017 -0700

    update jacobi test code

Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C
Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C

commit e1fbb8112ba1e8df60ae656c576e847b721943bf
Merge: f9f14534a 486e2149c
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 8 18:02:54 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit f9f14534a8ed452be51d1cc94a95365877215f1c
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 8 18:02:48 2017 -0700

    some fixes for profiling data.

Src/Extern/amrdata/AMReX_DataServices.H
Src/Extern/amrdata/AMReX_DataServices.cpp

commit 85153e63e60a4718f04d07964932c487cdf3228b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 8 13:20:53 2017 -0700

    renaming some functions

Src/AmrCore/AMReX_ebinterp_1d.F90
Src/AmrCore/AMReX_ebinterp_2d.F90
Src/AmrCore/AMReX_ebinterp_3d.F90
Src/Base/AMReX_EBMultiFabUtil_nd.F90
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_ebcellflag_mod.F90

commit a915391aaad606e9c61a9916b20aa7be89e73432
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 8 13:05:02 2017 -0700

    EBFlagFab --> EBCellFlagFab

Src/AmrCore/AMReX_EBInterpolater.cpp
Src/Base/AMReX_EBCellFlag.H
Src/Base/AMReX_EBCellFlag.cpp
Src/Base/AMReX_EBFArrayBox.H
Src/Base/AMReX_EBFArrayBox.cpp
Src/Base/AMReX_EBFabFactory.cpp
Src/Base/AMReX_EBLevel.H
Src/Base/AMReX_EBLevel.cpp
Src/Base/AMReX_EBMultiFabUtil.cpp

commit 83597ca590a0870e212af79f4011f6d8e9ceffe3
Merge: 1588dcb13 96e30a474
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 8 12:37:29 2017 -0700

    Merge branch 'eb_development' into weiqun/eb

commit 96e30a474d3f302d5fe02c29e29d3d79ad76dce7
Merge: 01d63265e 26b81847e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 8 12:37:10 2017 -0700

    Merge branch 'dtg_branch' into eb_development

commit 26b81847ed5540c514e20a02d62a35126e4e5d4c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Aug 8 12:25:43 2017 -0700

    bug fix in FlatPlate

Src/GeometryShop/AMReX_FlatPlateGeom.cpp

commit 1588dcb13184278f2d7eeb65ee64463ac615b526
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 8 10:03:10 2017 -0700

    some pure --> elemental

Src/Base/AMReX_ebcellflag_mod.F90

commit fbcf4c1ad81191bc0b4de6f2d886b5c3f8be2b2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 8 10:00:59 2017 -0700

    fillpatch now works for single-valued cells when eb is close to coarse/fine boundary

Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_EBInterp_f.H
Src/AmrCore/AMReX_EBInterpolater.cpp
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrCore/AMReX_ebinterp_1d.F90
Src/AmrCore/AMReX_ebinterp_2d.F90
Src/AmrCore/AMReX_ebinterp_3d.F90
Src/AmrCore/Make.package
Src/Base/AMReX_EBMultiFabUtil.H
Src/Base/AMReX_EBMultiFabUtil.cpp
Src/Base/AMReX_ebcellflag_mod.F90

commit 486e2149cfc07525f94f4b3c54efb3b7c36b3e37
Merge: 369513b85 073c1582c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Aug 7 19:00:05 2017 -0700

    Merge pull request #88 from AMReX-Codes/dtg_branch
    
    merging to development to get bug fix over

commit 073c1582c66bbc1c21ca2a6242dea81d7c0700d7
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Aug 7 18:57:15 2017 -0700

    tweak to Polygeom to try to satisfy valgrind

Src/GeometryShop/AMReX_PolyGeom.cpp

commit f4baf1afca3e21f0385aa5e6bbff442ad2340c25
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Aug 7 18:55:35 2017 -0700

    bug fix to divergence op

Src/EBAMRTools/AMReX_DivergenceOp.cpp

commit 369513b856ab27b0058b84bbbfe1f14058384beb
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Mon Aug 7 15:22:21 2017 -0700

    task graph prototype

Src/AmrTask/Makefile
Src/AmrTask/arch.common
Src/AmrTask/arch/arch.serial
Src/AmrTask/graph/AMReX_AbstractTask.H
Src/AmrTask/graph/AMReX_AbstractTask.cpp
Src/AmrTask/graph/AMReX_Affinity.H
Src/AmrTask/graph/AMReX_Affinity.cpp
Src/AmrTask/graph/AMReX_AsyncMFIter.H
Src/AmrTask/graph/AMReX_AsyncMFIter.cpp
Src/AmrTask/graph/AMReX_DataTypes.H
Src/AmrTask/graph/AMReX_TaskGraph.H
Src/AmrTask/graph/AMReX_TaskGraph.cpp
Src/AmrTask/graph/AMReX_WorkerThread.H
Src/AmrTask/graph/AMReX_WorkerThread.cpp
Src/AmrTask/graph/Makefile
Src/AmrTask/graph/RTS.H
Src/AmrTask/make_defaults/Cori
Src/AmrTask/make_defaults/Edison
Src/AmrTask/make_defaults/Summit-dev
Src/AmrTask/rts_impls/README
Src/AmrTask/rts_impls/Serial/Makefile
Src/AmrTask/rts_impls/Serial/rts.C
Src/AmrTask/tutorials/AMReXApps/3DJacobi/3DJacobi.C
Src/AmrTask/tutorials/AMReXApps/3DJacobi/Makefile
Src/AmrTask/tutorials/UnitTests/001_TokenRing.C
Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C
Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C
Src/AmrTask/tutorials/UnitTests/Makefile

commit 2b6c406fa41f4c63199188a67523b61fdfcbf82d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 7 14:27:59 2017 -0700

    add EBInterpolater stub

Src/Amr/AMReX_AmrLevel.H
Src/AmrCore/AMReX_EBInterpolater.H
Src/AmrCore/AMReX_EBInterpolater.cpp
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/Make.package

commit 4866203db7fb7945a692a5883c1aafdcdb0855a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 7 13:41:09 2017 -0700

    fix graph walking

Src/Base/AMReX_EBLevel.cpp

commit d722e7a42bf8c0a9d0f9a309c3b530e7d41b30b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 7 13:14:29 2017 -0700

    fix dangling pointer/reference due to return-by-value in some EB data structure

Src/Base/AMReX_EBFArrayBox.H
Src/Base/AMReX_EBFArrayBox.cpp
Src/Base/AMReX_EBFabFactory.H
Src/Base/AMReX_EBFabFactory.cpp
Src/Base/AMReX_EBLevel.H
Src/Base/AMReX_EBLevel.cpp
Src/Base/AMReX_EBMultiFabUtil.cpp

commit 66058db9273f8bd32ea9ef3e2c502864e06782d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 7 12:35:23 2017 -0700

    add more access functions

Src/Base/AMReX_EBFArrayBox.H
Src/Base/AMReX_EBFArrayBox.cpp
Src/Base/AMReX_EBLevel.H
Src/Base/AMReX_EBLevel.cpp
Src/Base/AMReX_EBMultiFabUtil.cpp
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_MultiFab.H

commit 812eeb1c45ae08756418f95f96eaaea39e048270
Merge: 03b34a8ff 01d63265e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 7 11:05:48 2017 -0700

    Merge branch 'eb_development' into weiqun/eb

commit 01d63265e35d9522917af211c9d18e012565995a
Merge: d9bdacd3a 723231eee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 7 11:04:49 2017 -0700

    Merge branch 'development' into eb_development

commit 723231eee37cc6ce2f02038aa585ccf918a610cf
Merge: 7138cc9bd 005062c42
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Aug 7 11:03:09 2017 -0700

    Merge pull request #87 from nncarlson/add-nag
    
    [WIP] Add GNUmakefile support for the NAG Fortran compiler

commit 7138cc9bdfae58409df6da2323a69aebc71ae73a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 7 10:47:36 2017 -0700

    move Tests/LinearSovlver/F_MG to boxlib test list

Tools/CompileTesting/compiletesting.py

commit 8630683cf98bba37dbb8afc8081589d88ae537dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 7 10:38:33 2017 -0700

    update compiletesting.py

Tools/CompileTesting/compiletesting.py

commit 1404633e0a1d8ed21ec19421545ed4d0aeaec75c
Merge: f1faeae18 39be65269
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Aug 7 10:13:21 2017 -0700

    Merge pull request #76 from akreienbuehl/clrdDiffuSolve
    
    clrdDiffuSolve

commit f1faeae18dc73066a4454f68c7e7841cd26bf821
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 7 10:12:47 2017 -0700

    fix compilation of a test

OldTutorials/MultiFabTests_C/GNUmakefile

commit 9c56eccad3f0ee39f3fcf78c085176c6ff1c3f41
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 7 09:58:10 2017 -0700

    update compiletesting.py

Tools/CompileTesting/compiletesting.py

commit 03b34a8ffa6e9389a9c68401dfcef195dee658b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 7 09:43:35 2017 -0700

    save pointers to ebflag fab in EbFArrayBox

Src/Base/AMReX_EBFArrayBox.H
Src/Base/AMReX_EBFArrayBox.cpp

commit 005062c424c76c83b9b0dfb23c5b64c4f063cc6f
Author: Neil Carlson <neil.n.carlson@gmail.com>
Date:   Sun Aug 6 08:45:04 2017 -0600

    Add GNUmakefile support for the NAG Fortran compiler

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/nag.mak
Tools/libamrex/configure.py
Tools/libamrex/mkconfig.py

commit 39be65269f41b8624b81696dbe0a2180ba4a3d8d
Merge: 369b3b700 5f825d5a2
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Sun Aug 6 12:36:36 2017 -0700

    Merge branch 'clrdDiffuSolve' of https://github.com/akreienbuehl/amrex into clrdDiffuSolve

commit 369b3b7009bc20044d76a9bfd0460633d07fde2f
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Sun Aug 6 12:35:54 2017 -0700

    Introduced variable `m_clr_map` along the lines of `m_nCommColors`

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit 7559314b97c211fbce55fb6182168bd36266b1f0
Merge: e1fdeabdb e02cf3da5
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Sun Aug 6 09:36:40 2017 -0700

    Merge branch 'development' into clrdDiffuSolve

commit 14dbe9043c64d8560a43e6e31e2dc1c59ed86ac7
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 5 19:23:59 2017 -0400

    Add a new wrapper around Device functions

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StateDescriptor.H
Src/Amr/AMReX_StateDescriptor.cpp
Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_BArena.H
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabFactory.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_MFIter.cpp
Src/Base/Make.package
Tools/GNUMake/Make.defs

commit 29517f3735940adaf24dfe301700e195a1a1a65c
Merge: 6b474fbeb 3a726a1f3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 5 18:00:19 2017 -0400

    Merge branch 'development' into gpu
    
    Conflicts:
            Src/Base/AMReX_RealBox.H
            Src/Base/AMReX_RealBox.cpp
            Tools/GNUMake/Make.defs

commit 6b474fbebd80ab99ad2a98f9a9ba390baed6c032
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Aug 5 17:48:49 2017 -0400

    Replace CUDA macro with AMREX_USE_CUDA

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_nd.F90
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp
Src/Base/AMReX_filcc_mod.F90
Src/Base/AMReX_fort_mod.F90
Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp
Tools/GNUMake/Make.defs
Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90

commit 417f0208030fb766ba2fef8f7ab70321a5f58e5a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Aug 4 19:11:38 2017 -0700

    my tweak to the make system that should never be pushed

Tools/GNUMake/comps/gnu.mak

commit e02cf3da53ae3e431039fa3f8fe47142588b4f8b
Merge: c34d2728c 5c4ecd7b8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 4 18:55:14 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 9e4904eff515ca502be79657939e739e70878e99
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Aug 4 18:31:28 2017 -0700

    Add back changes to EB fortran in divflux...lost in merge conflict resolution

Src/EBAMRTools/AMReX_EBFortND.F90

commit 2f5614277663173f2f5bb13f618745fd45664ee8
Merge: fd5da5154 d9bdacd3a
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Aug 4 18:22:18 2017 -0700

    Merge branch 'eb_development' into weiqun/eb

commit d9bdacd3ad30b64ffbe11def098832e11ddf3db6
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Aug 4 18:21:24 2017 -0700

    Undo adding of declaration...sorting out multiple merges

Src/EBAMRTools/AMReX_EBFortND.F90

commit 988d1ad5082562eb2eb864cd2d9ce5126a1e83bb
Merge: 77d5ebff4 c66804f1e
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Aug 4 18:14:43 2017 -0700

    Conflict resolution with dtg_branch

commit fd5da515488e20c39418aac529c446390ff3038b
Merge: fbe93e238 77d5ebff4
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Aug 4 18:03:50 2017 -0700

    Merge branch 'eb_development' into weiqun/eb

commit 77d5ebff4d7c7513d71237cdd01da5de62d13876
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Aug 4 18:02:30 2017 -0700

    Add declaration for flag

Src/EBAMRTools/AMReX_EBFortND.F90

commit fbe93e238551d86febf042bee2f26592acd3aaa6
Merge: 52905cb16 5b1f8ff3c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 4 17:45:03 2017 -0700

    Merge branch 'eb_development' into weiqun/eb
    
    Conflicts:
            Src/EBAMRTools/AMReX_EBFortND.F90

commit 5b1f8ff3cdf02bb01bf07c69f369eaef26c6b0d5
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Aug 4 17:08:21 2017 -0700

    resolve conflicts

Src/EBAMRTools/AMReX_EBFortND.F90

commit 52905cb16550033248052b511f880139f5c6c1bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 4 17:12:43 2017 -0700

    fix 3d avgdown

Src/Base/AMReX_EBMultiFabUtil.cpp

commit 0f9ffcbcccafe51259d8d6c5a08fa79ff845a787
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 4 17:01:15 2017 -0700

    missed an enddo

Src/Base/AMReX_MultiFabUtil_3d.f90

commit d07dbc1316182e681cfc6fe5e8385307f7487db0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 4 16:59:59 2017 -0700

    finish eb average down

Src/Base/AMReX_EBMultiFabUtil.H
Src/Base/AMReX_EBMultiFabUtil.cpp
Src/Base/AMReX_EBMultiFabUtil_F.H
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3d.f90

commit f323967efd42deaf0b4f7013c13458b203b92dff
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 4 16:16:16 2017 -0700

    fix comment.

Src/Base/AMReX_Utility.H

commit 2ba3bae0a43f0ff1fe0ca91a19b9241df6441df2
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 4 16:00:10 2017 -0700

    removed old files.

Src/Extern/ProfParser/backup/AMReX_AVGDOWN_2D.F
Src/Extern/ProfParser/backup/AMReX_AVGDOWN_3D.F
Src/Extern/ProfParser/backup/AMReX_AVGDOWN_F.H
Src/Extern/ProfParser/backup/AMReX_BLProfStats.H
Src/Extern/ProfParser/backup/AMReX_BLProfStats.cpp
Src/Extern/ProfParser/backup/AMReX_BLProfUtilities.cpp
Src/Extern/ProfParser/backup/AMReX_BLWritePlotFile.H
Src/Extern/ProfParser/backup/AMReX_BLWritePlotFile.cpp
Src/Extern/ProfParser/backup/AMReX_CommProfStats.H
Src/Extern/ProfParser/backup/AMReX_CommProfStats.cpp
Src/Extern/ProfParser/backup/AMReX_RegionsProfStats.H
Src/Extern/ProfParser/backup/AMReX_RegionsProfStats.cpp
Src/Extern/ProfParser/backup/AMReX_XYPlotDataList.H
Src/Extern/ProfParser/backup/AMReX_XYPlotDataList.cpp
Src/Extern/ProfParser/backup/BLProfParser.l
Src/Extern/ProfParser/backup/BLProfParser.y
Src/Extern/ProfParser/backup/Make.package

commit d52df0586905bcba57561afa40e988b98b8450bd
Merge: 83bdb1a82 5c4ecd7b8
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 4 15:52:45 2017 -0700

    Merge branch 'development' into profvisDS

commit 83bdb1a824148c1f7238a1f60ef906e2a00e5e8e
Merge: b47795248 21a614905
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 4 15:44:19 2017 -0700

    sync with original code.

commit c66804f1ea08a8dda58ecddba7500c22dd5b0451
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Aug 4 15:08:57 2017 -0700

    added sphere option to redistribution test

Tests/GeometryShop/regression/levelRedistTest.cpp
Tests/GeometryShop/regression/levelredist.inputs

commit 6ffe1527b7ea55cc635f45207de2cabb009cc11d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Aug 4 14:51:07 2017 -0700

    CMake: update docs.

Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex
Tools/CMake/AMReX_Options.cmake

commit ef42e7ebd54d1f387799f462f61ba3bee25fecc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 4 14:13:03 2017 -0700

    finish EB_set_volume_fraction

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_EBCellFlag.cpp
Src/Base/AMReX_EBLevel.cpp
Src/Base/AMReX_EBMultiFabUtil.cpp
Src/Base/AMReX_FabFactory.H

commit c40fc3892cd592fe4e692aba99b25a1d700afcc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 4 13:44:05 2017 -0700

    fix regular average_down

Src/Base/AMReX_EBFabFactory.cpp
Src/Base/AMReX_MultiFabUtil.cpp

commit 88345e1c39f2b1740c1f969a971311225acf3e55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 4 13:26:23 2017 -0700

    EBFArrayBox can now get type info from EBLevel

Src/Base/AMReX_EBFArrayBox.H
Src/Base/AMReX_EBFArrayBox.cpp
Src/Base/AMReX_EBFabFactory.cpp

commit f811aa41b33e29522b56ca46425c19ca1b8cd584
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 4 13:09:59 2017 -0700

    EBLevel: add FabType

Src/Base/AMReX_EBCellFlag.H
Src/Base/AMReX_EBCellFlag.cpp
Src/Base/AMReX_EBLevel.H
Src/Base/AMReX_EBLevel.cpp
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FabFactory.H

commit 279dcc440e9b3414ee7cd9c2d018c4c6520f1d33
Merge: a893470d3 bc4aa94a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 4 12:32:24 2017 -0700

    Merge branch 'eb_development' into weiqun/eb
    
    Conflicts:
            Src/EBAMRTools/AMReX_DivergenceOp.cpp

commit bc4aa94a58000139ce05b883d3c2cce62a8b14f6
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Aug 4 12:17:28 2017 -0700

    Fix a couple bugs resulting from me not correctly specifying Dans jobs...my bad.
    
    Conflicts:
            Src/EBAMRTools/AMReX_DivergenceOp.cpp

Src/EBAMRTools/AMReX_DivergenceOp.cpp

commit ccc79dcad23af8534bc3d773a8ab98de3490f6ae
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Aug 4 12:16:49 2017 -0700

    CMake: fix defines for comm-profiling

Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Utils.cmake

commit a893470d3d2a7cb8751410bcf854b69f6f4b83c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 4 11:27:19 2017 -0700

    add armrex::EB_set_volume_fraction stub

Src/Base/AMReX_EBMultiFabUtil.H
Src/Base/AMReX_EBMultiFabUtil.cpp

commit 93931db6ad0d8a2f77cd421bbe193094b10b8dd4
Merge: faee24afa 5c4ecd7b8
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Aug 4 11:13:08 2017 -0700

    Merge branch 'development' into mr-cmake

commit c3d739fede0a1cca2bdb5bf705f82e17c0dbafb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 4 10:56:18 2017 -0700

    fix BoxIterator for empty box

Src/Base/AMReX_BoxIterator.cpp

commit 5c4ecd7b8912c7761fd9333b32dc5df20076a0c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 4 10:17:58 2017 -0700

    Fortran: boxarray%maxsize now has three versions: single integer size, three integers and an integer array of size 3

Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90

commit 3a2cb2fa8fba3db6a236370effbc676a0aeebab8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 3 22:17:54 2017 -0700

    fix include hell

Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabFactory.H

commit c34d2728cf901c0fe9df82c4e4df2cc501c3f4e6
Merge: e24e66af4 12adbcf1e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 3 18:31:48 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 12adbcf1ecd4b2a31ce1044f814b0da90bba84bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Aug 3 20:47:06 2017 -0400

    more git error control
    sometimes if the repo is dirty or a branch doesn't exist the checkout
    of the branch can silently fail

Tools/RegressionTesting/repo.py

commit faee24afa700f812733f125571c95a2b80d779f3
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Aug 3 17:34:11 2017 -0700

    CMake: add support for trace and comm profiling

Src/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake

commit 0ac96265a2eff183475f169482982201782279b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 3 17:06:37 2017 -0700

    use fortran to set covered cells to min vals

Src/Base/AMReX_EBLevel.H
Src/Base/AMReX_EBLevel.cpp
Src/Base/AMReX_EBMultiFabUtil.cpp
Src/Base/AMReX_EBMultiFabUtil_F.H
Src/Base/AMReX_EBMultiFabUtil_nd.F90
Src/Base/Make.package

commit da58c40dcfbb1536152963e595ffdeff2c3509db
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Aug 3 16:46:22 2017 -0700

    CMake: fix typo

Src/CMakeLists.txt

commit bd9c4ecd0c7700c91774ec587f5b002555bf8f0a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Aug 3 16:08:17 2017 -0700

    CMake: enable user to turn on/off AMReX components

Src/CMakeLists.txt
Src/LinearSolvers/CMakeLists.txt
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake

commit b83cecb577656160df7b1190ef4d24f4682ce523
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 3 15:55:16 2017 -0700

    need this for pgi compiler

Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90

commit 228c8ff1fbd0b6ddcd95168813a2db6544cb538e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 3 15:47:33 2017 -0700

    save a copy of EBLevel in EBFabFactory, which is in turn stored in MultiFab

Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_EBFabFactory.H
Src/Base/AMReX_EBFabFactory.cpp
Src/Base/AMReX_EBLevel.H
Src/Base/AMReX_EBLevel.cpp
Src/Base/AMReX_EBMultiFabUtil.cpp
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_FabFactory.H
Src/Base/AMReX_MultiFab.H
Src/Base/Make.package
Src/GeometryShop/AMReX_IrregFABFactory.H
Src/GeometryShop/AMReX_IrregFABFactory.cpp
Src/GeometryShop/AMReX_LayoutData.H

commit 5045e89137fcd3291912abf648391b977dd51db3
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Aug 3 15:08:34 2017 -0700

    got the conductivity solver to run to completion.  still wrong.  back to writing documents.

Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp
Src/GeometryShop/AMReX_EBArith.cpp
Tests/EBAMRElliptic/exec/cond.inputs
Tests/EBAMRElliptic/exec/conductivitySolve.cpp

commit 653ad5666d348ebf5e945a4221445291f824f3a1
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Aug 3 14:47:39 2017 -0700

    CMake: fix minor bugs

Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Utils.cmake

commit 98a6d1151e0dcca201b18405243e91d02d4e31f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 3 14:21:26 2017 -0700

    fix c_real in mempool module

Src/Base/AMReX_fort_mod.F90
Src/Base/AMReX_mempool_f.f90
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/amrex_fort_mod.f90

commit c036bd1f3f984cc0966359644aab6dbacf42fac0
Author: Ondřej Čertík <ondrej.certik@gmail.com>
Date:   Thu Aug 3 13:43:40 2017 -0600

    Compare real kinds directly
    
    In order to determine if the real kinds are equal, one can just compare them
    directly, they are just integers. This is simpler, and also allows these lines
    to be compiled with NAG. For some reason NAG does not seem to have `c_sizeof()`
    as part of the `iso_c_binding` module and so it fails on these lines. This
    commit fixes it.

Src/F_Interfaces/Base/AMReX_parallel_mod.F90

commit 716456a53d4be2954fefe613c64b969d57c68259
Merge: 952dd930c 4466b9a4a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Aug 3 13:22:34 2017 -0700

    Merge pull request #80 from certik/size_of_fix
    
    Compare real kinds directly

commit 4466b9a4a7e04b7b5c3b3cd8bd37e1cbcea26544
Author: Ondřej Čertík <ondrej.certik@gmail.com>
Date:   Thu Aug 3 13:43:40 2017 -0600

    Compare real kinds directly
    
    In order to determine if the real kinds are equal, one can just compare them
    directly, they are just integers. This is simpler, and also allows these lines
    to be compiled with NAG. For some reason NAG does not seem to have `c_sizeof()`
    as part of the `iso_c_binding` module and so it fails on these lines. This
    commit fixes it.

Src/F_Interfaces/Base/AMReX_parallel_mod.F90

commit ea9351af4533b3fcc4870d754bd0c7293f7b2a3d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 3 11:42:23 2017 -0700

    have to intersect with the domain because there is no eb information outside the domain

Src/Base/AMReX_EBLevel.cpp

commit 0ef222e4ed3cb720448cc019bf1029c05d52a6fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 3 11:28:37 2017 -0700

    add Fortran module for ebcellflag

Src/Base/AMReX_ebcellflag_mod.F90
Src/Base/Make.package

commit dd6d7f97e194dda7e0901b7d8a3f30cd309e541a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 3 10:43:56 2017 -0700

    set and get number of VoFs

Src/Base/AMReX_EBCellFlag.H
Src/Base/AMReX_EBLevel.cpp

commit 1d78eff7f38ce501229d34affa859d8847a65266
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 3 09:46:04 2017 -0700

    reserve 3 bits for number of multi-valued cells and clean up CellFlag

Src/Base/AMReX_EBCellFlag.H
Src/Base/AMReX_EBCellFlag.cpp

commit 5f825d5a2f7cc58db946777b8356fa16151f76e8
Merge: e1fdeabdb ad1ca154c
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Thu Aug 3 08:35:23 2017 -0700

    Merge branch 'development' into clrdDiffuSolve

commit acf5e862ad929976d8c8d72bf5206974a82830c7
Merge: 33e9bc102 ad1ca154c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Aug 2 20:35:46 2017 -0700

    Merge pull request #78 from AMReX-Codes/development
    
    trying to get bug fixes for DivergenceOp into weiqun/eb branch

commit ad1ca154cbbbcd56152576824cd52c696155183d
Merge: 5c3517e85 eef52795c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Aug 2 20:31:42 2017 -0700

    Merge pull request #77 from AMReX-Codes/dtg_branch
    
    getting some bug fixes over to development branch

commit 33e9bc1022ac4016cfa6f33a3d10b4ef928c08bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 2 17:36:23 2017 -0700

    finish setting up EBCellFlag in C++

Src/Base/AMReX_EBCellFlag.H
Src/Base/AMReX_EBCellFlag.cpp
Src/Base/AMReX_EBLevel.cpp
Src/Base/Make.package

commit f1c290e71036a613701388b9799b8926aee10c55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 2 14:25:47 2017 -0700

    wip because pge is cutting power

Src/Base/AMReX_EBCellFlag.H
Src/Base/AMReX_EBLevel.cpp

commit 5c3517e85d50f9d720fd1f9057b46b92295a5a32
Merge: 4795dfe9a 21a614905
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Aug 2 17:06:36 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development

commit 4795dfe9aed30f39a859d9cae2e9463c5540b98d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Aug 2 17:06:18 2017 -0400

    fix compilation + add a DO_ALL macro

Tools/Postprocessing/F_Src/GNUmakefile
Tools/Postprocessing/F_Src/fdump.f90

commit 86acfafa7b37c4568705d10a77d8533c0683649b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 2 10:20:18 2017 -0700

    start EBLevel and EBCellFlag

Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Base/AMReX_EBCellFlag.H
Src/Base/AMReX_EBLevel.H
Src/Base/AMReX_EBLevel.cpp
Src/Base/Make.package

commit e24e66af425813e8a05cad5c5c777c8d5f252ed0
Merge: 63d07dec9 21a614905
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 2 09:47:51 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit e1fdeabdb399ec502b650212910408bf4ded398d
Merge: 71036bd13 21a614905
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Wed Aug 2 09:36:07 2017 -0700

    Merge branch 'development' into clrdDiffuSolve

commit 7e1263217243f6e4e3d9eb08a47cc6ad02f05166
Merge: 0263ace78 21a614905
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 2 09:24:53 2017 -0700

    Merge branch 'development' into eb_development

commit 21a614905db98fbbd8a99728074ea82cb4429f3e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 1 17:48:30 2017 -0700

    Need an option for mvapich (cooley.alcf.anl.go) as well in Make.unknown

Tools/GNUMake/sites/Make.unknown

commit 952dd930c4491283c9182fdcd8b4953d15939c9c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 1 17:48:30 2017 -0700

    Need an option for mvapich (cooley.alcf.anl.go) as well in Make.unknown

Tools/GNUMake/sites/Make.unknown

commit 63d07dec9687cd1a57ee6f1a65da1715b8246d36
Merge: 27c708160 648e13f76
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 1 17:48:55 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 27c708160869b0808e9588bd41bd760aa6a6815f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 1 17:48:30 2017 -0700

    Need an option for mvapich (cooley.alcf.anl.go) as well in Make.unknown

Tools/GNUMake/sites/Make.unknown

commit 648e13f76615a5fd67ce3b75b9070758b3034c72
Merge: 7d2f62471 76eb8fd5e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Aug 1 17:12:35 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 7d2f62471e50f62e7244c2b9a6c79bff873ebac3
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Aug 1 17:12:24 2017 -0700

    CMake: update exported info

Tools/CMake/AMReXConfig.cmake.in

commit 76eb8fd5e67473fe22b244dc5c1dcaf8ff5933fc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 1 16:54:56 2017 -0700

    Fix AMReX_HOME -- one more directory down

Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile

commit 1de881a22807de459c938c95427a3d37b6bdfac1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 1 16:54:25 2017 -0700

    Fix AMREX_HOME -- one more directory down

Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile

commit 0263ace78357009ad756a8eb2950d3fd1c4f7fc1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 1 16:53:24 2017 -0700

    update fillpatch for eb

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 7d75c9432fa32ef88b3a6f7cf3b2f92b892b7268
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Aug 1 16:38:47 2017 -0700

    CMake: make assertions opt-in

Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake

commit eef52795c68d40315518895ae72dc8b36be1ff4d
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Aug 1 16:20:56 2017 -0700

    EBAMRElliptic's big redesign of Chombo's elliptic stuff now compiles

Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H
Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp
Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp
Src/EBAMRElliptic/AMReX_EBSimpleSolver.H
Src/EBAMRElliptic/AMReX_EBSimpleSolver.cpp
Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.H
Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp
Src/EBAMRElliptic/AMReX_VCAggStencil.cpp
Src/EBAMRElliptic/Make.package
Tests/EBAMRElliptic/exec/cond.inputs
Tests/EBAMRElliptic/exec/conductivitySolve.cpp

commit 58849bf57ce13feba3e6dcb28bd721d5a2b8211a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Aug 1 18:51:09 2017 -0400

    make this work with python3

Tools/Py_util/plotsinglevar.py

commit 1b256042ae582edd05f98b72f1b9da9b63859cf0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Aug 1 14:41:53 2017 -0700

    threading the buildNeighborList method.

Src/Particle/AMReX_NeighborParticlesI.H

commit 71036bd1382515a79dcd107618b7c17e9b660f6d
Merge: 89a439891 60b2d443e
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Tue Aug 1 13:27:54 2017 -0700

    Merge branch 'clrdDiffuSolve' of https://github.com/akreienbuehl/amrex into clrdDiffuSolve

commit 89a439891e985ad579182cc505cc26d3f0071302
Merge: 49e39e991 1ed2afc00
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Tue Aug 1 13:27:15 2017 -0700

    Merge branch 'development' into clrdDiffuSolve

commit 8caa162eb46d9e395fd4c09c5e5c0afc1cf7fd54
Merge: df2c09264 f49e2e502
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 1 13:12:00 2017 -0700

    Merge branch 'weiqun/eb' into eb_development

commit f49e2e502f71e1becf18f64f680c00e79c460936
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 1 13:00:06 2017 -0700

    use factory member variable

Src/Base/AMReX_FabArray.H

commit 9272161d43f8c592a95619377783893a5ff7c7f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 1 12:17:32 2017 -0700

    fix FabType for nodal EBFArrayBox

Src/Base/AMReX_EBFArrayBox.cpp

commit efc473880db1a307918748fb28e7def92e65f1e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 1 12:14:09 2017 -0700

    add a strict mode in which one must pass factory to FabArray constructor

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AuxBoundaryData.cpp
Src/Amr/AMReX_Extrapolater.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_VisMF.cpp
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp
Src/Boundary/AMReX_FabSet.cpp
Src/Boundary/AMReX_MultiMask.cpp
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_FabArrayIO.H
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp
Tools/GNUMake/Make.defs

commit df2c0926454f9a5fa17949ec78cf2798c2627308
Merge: f9b1f0486 d9500ba4f
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Aug 1 11:27:21 2017 -0700

    Merge branch 'vof-work' into eb_development

commit d9500ba4f52eb6753db36b341a58b407d0385fd0
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Aug 1 11:25:43 2017 -0700

    Pass the stencil box to further clean fort code

Tests/GeometryShop/vofStructures/nbrsTest.cpp
Tests/GeometryShop/vofStructures/nbrsTest_nd.f90

commit b5d9f84326d3108d8e6073bdff5fbb2addaf841e
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Aug 1 11:16:03 2017 -0700

    Use better macros, clean resulting code

Tests/GeometryShop/vofStructures/nbrsTest.cpp
Tests/GeometryShop/vofStructures/nbrsTest_nd.f90

commit f9b1f0486d113864dac882189a43e3b6490a7df4
Merge: 9fc162ad5 1ed2afc00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 1 10:00:28 2017 -0700

    Merge branch 'development' into weiqun/eb

commit 1ed2afc00c3c4acc6f0d1febfc4f594ccf5c1b9a
Merge: 103bcf0cd ea47076aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 1 09:52:12 2017 -0700

    Merge branch 'development'
    
    Conflicts:
            Tools/CMake/AMReX_Config.cmake

commit 91806eb7fbb61ed57b4c17747d61fec539fd1702
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jul 31 19:42:40 2017 -0700

    Add a test code to make a simple redistribution stencil and apply it. Needs more generalization, but it shows one method of passing such data to fortran.

Tests/GeometryShop/vofStructures/AMReX_EBRedist.H
Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/nbrsTest.cpp
Tests/GeometryShop/vofStructures/nbrsTest_mod.F90
Tests/GeometryShop/vofStructures/nbrsTest_nd.f90

commit 9fc162ad54b947c315e6f542378c39c38e176288
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 31 17:57:22 2017 -0700

    AmrLevel: new MultiFabs should be built with factory member

Src/Amr/AMReX_AmrLevel.cpp

commit f0bd8daf3e21fe6a0ce40b65a18d3502d45b601e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 31 17:46:28 2017 -0700

    store a copy of eb factory in AmrLevel

Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp

commit e466d7533a7da76e2266dd2d23772ad8b356c93c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 31 17:00:55 2017 -0700

    because we don't have geometry information outside domain

Src/Base/AMReX_EBFArrayBox.cpp

commit 6a5bd5d2811cf3071c15d5c079c9dba5ec74efb9
Merge: 8318082b0 d28bc5f3e
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jul 31 16:46:38 2017 -0700

    Merge branch 'dtg_branch' into vof-work

commit 319621700fc85a356347f2e0a28b0624544f0aef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 31 16:37:18 2017 -0700

    get EBISLayout from eb factory

Src/Base/AMReX_FabFactory.H

commit bba2ad1b0f1d518dbbe129b8cd506c209ffb98af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 31 16:36:45 2017 -0700

    add a eb utility function to set all covered to the min val for the temporary purpose of visualization

Src/Base/AMReX_EBMultiFabUtil.H
Src/Base/AMReX_EBMultiFabUtil.cpp
Src/Base/Make.package

commit 676463eec089909eb46eded7697114fb932a993e
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Jul 31 16:29:18 2017 -0700

    made EBGraph::fillIntMask more closely resemble what Marc wants.

Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp

commit 777979fe8bfbbb2f65261799e6866852b1ed7ef2
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Jul 31 12:10:40 2017 -0700

    made DivergenceOp able to support fluxes that have area multiplied in to support PeleC

Src/EBAMRTools/AMReX_DivergenceOp.H
Src/EBAMRTools/AMReX_DivergenceOp.cpp
Src/EBAMRTools/AMReX_EBFortND.F90
Src/EBAMRTools/AMReX_EBFortND_F.H

commit ea47076aa986c37fb148c78762f208018b88d99e
Merge: d4d1481f1 3465e0e9f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jul 31 12:08:00 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit d4d1481f1acec809a451dac1fd3585d4043ddb3c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jul 31 12:07:14 2017 -0700

    CMake:manually force C++11 compliance for Intel compiler

Tools/CMake/AMReX_CMakeVariables.cmake

commit 3465e0e9f42c4be515506e4bda0076e5dec26991
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 31 10:36:00 2017 -0700

    make this test work in 2D and 3D.

Tests/Particles/AssignMultiLevelDensity/main.cpp

commit 520abd3b50640ccabf3db6c2501f26312032692f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 31 10:35:41 2017 -0700

    consolidate OMP Deposition helpers.

Src/Particle/AMReX_OMPDepositionHelper_1d.F90
Src/Particle/AMReX_OMPDepositionHelper_2d.F90
Src/Particle/AMReX_OMPDepositionHelper_nd.F90
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit c08cb8371590ae070acbd14ab954dd898db25f5f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 31 10:11:37 2017 -0700

    use PCInterp in the multilevel density deposition.

Src/Particle/AMReX_ParticleContainerI.H

commit c98c4024856f1a75c2784366fd1d3e7f676335eb
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Jul 31 09:54:46 2017 -0700

    bug fix in DivergenceOp

Src/EBAMRTools/AMReX_DivergenceOp.cpp
Src/EBAMRTools/AMReX_EBLevelDataOps.H
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp

commit 8318082b06d78e57a9b95d795cfe08704616e7f6
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jul 31 09:23:42 2017 -0700

    Add back code to set fluid cells to unity so that amrvis2d smooth works correctly.  Just for demo purposes, keep code more explicitly handling the different types of cells.

Tests/GeometryShop/vofStructures/umapTest.cpp

commit 8c3bea70653e8823a2c63fb13df0433fa9d4dc7a
Merge: 227a7e486 b94043a26
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 29 11:49:05 2017 -0700

    merge branch 'development' into weiqun/eb

commit 227a7e4861c938169b483b52a1238fa8c7801d52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 29 11:48:17 2017 -0700

    update comments

Src/Base/AMReX_FArrayBox.H

commit b94043a2657d3b9bb8c830675ef57de57910ede3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 29 11:45:31 2017 -0700

    make FabArray friend of DistributionMapping for sidecar's moveallfabs

Src/Base/AMReX_DistributionMapping.H

commit 76e19d60ee9c8a82ae3370193971645a63d3c567
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 28 23:51:15 2017 -0700

    fix typo

Src/Amr/AMReX_AmrLevel.cpp

commit 06ff71da6e0e9459e80a7e2374b3b23f941a260b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 28 23:49:31 2017 -0700

    add factory and eb to AmrLevel and StateData

Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp

commit bc6b548f11e1bddb579a30f80df305a122d91bb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 28 22:59:59 2017 -0700

    change default factory of MultiFab

Src/Base/AMReX_EBFabFactory.cpp
Src/Base/AMReX_FabFactory.H

commit 4e070a04ef2aaf04db35887cd97d0cdc5f394520
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 28 22:36:53 2017 -0700

    add clone function to FabFactory

Src/Base/AMReX_EBFabFactory.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabFactory.H
Src/GeometryShop/AMReX_BaseEBCellFactory.H
Src/GeometryShop/AMReX_BaseIFFactory.H
Src/GeometryShop/AMReX_BaseIVFactory.H
Src/GeometryShop/AMReX_EBCellFactory.H
Src/GeometryShop/AMReX_EBDataFactory.H
Src/GeometryShop/AMReX_EBFluxFactory.H
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_IrregFABFactory.H

commit 636506e5b35e5c730c2c10e5d9347828f6b87445
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 28 17:41:53 2017 -0700

    add FabType

Src/Base/AMReX_EBFArrayBox.H
Src/Base/AMReX_EBFArrayBox.cpp
Src/Base/AMReX_EBFabFactory.cpp
Src/Base/AMReX_FArrayBox.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBISBox.H

commit d096056423fbbda248ecbcd80069431e720301f1
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 28 17:27:07 2017 -0700

    CMake: update source file list

Src/F_Interfaces/CMakeLists.txt

commit 7a17b4c6d3436c828b694881e2ef45353793c6f7
Merge: 64110cd18 d42d02031
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 28 17:21:41 2017 -0700

    Merge branch 'mr-cmake' into development

commit d42d0203127dff40b17a0c2906f7b75548ca3cae
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 28 17:21:08 2017 -0700

    CMake: update documentation

Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex

commit 3029ece748429fc2c2cfa9e84ed62c7e388558c6
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 28 17:07:53 2017 -0700

    CMake: add AMReX version info

Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Utils.cmake

commit 02f89ec0404e28e5b8efcd7847771b5bc658b2ca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 28 16:52:28 2017 -0700

    add optional factory to MultiFab constructor

Src/Base/AMReX_EBFabFactory.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit 082e929545b1f2c5dc9e4fc89c885885b8e2da2e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 28 16:37:17 2017 -0700

    CMake: build Amr tutorials

CMakeLists.txt
Tools/CMake/AMReX_Utils.cmake
Tutorials/Amr/Advection_AmrCore/CMakeLists.txt
Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt
Tutorials/Amr/Advection_F/CMakeLists.txt
Tutorials/Amr/Advection_octree_F/CMakeLists.txt
Tutorials/CMakeLists.txt

commit d72644067493a2e4f87df16053f24e5b9ff519e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 28 16:35:28 2017 -0700

    FArrayBoxFactory

Src/Base/AMReX_EBFabFactory.cpp
Src/Base/AMReX_FabFactory.H
Src/Base/AMReX_MultiFab.H
Src/GeometryShop/AMReX_EBFluxFactory.H
Src/GeometryShop/AMReX_EBISLayout.H

commit 80bb2b858477a4deaa48d64f29110021298f508c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 28 16:34:06 2017 -0700

    CMake: remove FindCCSE

Tools/CMake/FindCCSE.cmake

commit 5ae49e9ae7b745f41175945e4e59c64094e7826b
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 28 16:32:34 2017 -0700

    CMake: build fortran interfaces by default

Tools/CMake/AMReX_Config.cmake

commit 2596d629ff3982e5df45854b2a755b351bfdf74e
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jul 28 15:55:57 2017 -0700

    bit more progress toward eb elliptic solvers

Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp

commit 5536b2bb23ac248a73a731bc55e61dd1e8b71763
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 28 15:27:33 2017 -0700

    add EBFArrayBox

Src/Base/AMReX_EBFArrayBox.H
Src/Base/AMReX_EBFArrayBox.cpp
Src/Base/AMReX_EBFabFactory.cpp
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FabFactory.H
Src/Base/Make.package

commit a70f9b611b03db5d0e727b693ecc9b8d2fe2f6ad
Merge: 282c0ab5e 64110cd18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 28 14:42:10 2017 -0700

    Merge branch 'development' into weiqun/eb

commit 64110cd18dfb67aea1087c15c4f7ec7e095c23b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 28 14:38:56 2017 -0700

    use std::function instead of function pointer for flexibility

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/F_Interfaces/Base/AMReX_init_fi.cpp

commit c15224322e54f974fa9c3f99b054183b2bd879ab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 28 14:23:09 2017 -0700

    have to link with pgfortran if pgi is used and the main is in Fortran

Src/F_Interfaces/Base/Make.package
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/pgi.mak

commit e08eb8197b2d28a86cdc406e0d57f22e7ccec4a8
Merge: 1b1eb7d2d e031e40ca
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jul 28 11:28:02 2017 -0700

    Merge pull request #73 from AMReX-Codes/dtg_branch
    
    syncing with dtg_branch so Ray can get the combustor geometry tools.

commit e031e40cade125644da5430d338992cd2d4beeac
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jul 28 11:26:08 2017 -0700

    to give Ray the combustion geometry, I added Terry's transformation functions for implicit functions (Lathe (surfaces of revolution), Complement, Union, Intersection, Transforms (scale, translate, rotate)

Src/GeometryShop/AMReX_ComplementIF.H
Src/GeometryShop/AMReX_ComplementIF.cpp
Src/GeometryShop/AMReX_IntersectionIF.H
Src/GeometryShop/AMReX_IntersectionIF.cpp
Src/GeometryShop/AMReX_IrregFABFactory.cpp
Src/GeometryShop/AMReX_LatheIF.H
Src/GeometryShop/AMReX_LatheIF.cpp
Src/GeometryShop/AMReX_TransformIF.H
Src/GeometryShop/AMReX_TransformIF.cpp
Src/GeometryShop/AMReX_UnionIF.H
Src/GeometryShop/AMReX_UnionIF.cpp
Src/GeometryShop/Make.package

commit 1b1eb7d2da8d78a6a8893c01eaf440045dd7d7ab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 28 11:06:13 2017 -0700

    have to do this for pgi

Src/Base/AMReX_parmparse_mod.F90
Src/F_Interfaces/Base/AMReX_box_mod.F90
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_distromap_mod.F90
Src/F_Interfaces/Base/AMReX_fab_mod.F90
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 1d1b0824465d6e002cbb846a03bfc5b3eac0fb5a
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jul 28 10:43:41 2017 -0700

    CMake: add missing files

Src/Base/CMakeLists.txt

commit 60b2d443ec8caaabc626f181f9a5275ce7ee769e
Merge: 7cbf4c1f0 49e39e991
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Fri Jul 28 07:07:53 2017 -0700

    Merge branch 'clrdDiffuSolve' of https://github.com/akreienbuehl/amrex into clrdDiffuSolve

commit 7cbf4c1f06879927b9b879b4b2b70567704c5082
Merge: 1697df7cb 682f56e58
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Fri Jul 28 07:07:34 2017 -0700

    Merge remote-tracking branch 'upstream/development' into clrdDiffuSolve

commit 49e39e99144bb58e75db058a76d6deac2beecd42
Merge: 1697df7cb 682f56e58
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Fri Jul 28 07:02:49 2017 -0700

    Merge remote-tracking branch 'upstream/development' into clrdDiffuSolve

commit 282c0ab5ed48049d23136a4d9cfc761e33004f52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 27 17:10:35 2017 -0700

    add USE_EB to make system

Tools/GNUMake/Make.defs

commit 07d53579414d42df37fc7516474bc103bfd77090
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jul 27 16:46:14 2017 -0700

    CMake: default to Release if no build type is specified

Tools/CMake/AMReX_Options.cmake

commit 682f56e581b310e36f6f07d2211dfc6fe0b7daf3
Merge: d8fa2267f 5079de8f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 27 19:37:28 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit d8fa2267f31c452c5fccc0cbe12c878bfe05c133
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 27 19:36:39 2017 -0400

    add keyword support to tests
    each test can now give a comma-separated lists of keywords
    with the `--keyword key` option, we can run only those tests with
    a specific keyword (e.g. gravity).

Tools/RegressionTesting/params.py
Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_util.py

commit d28bc5f3eee4401191c8830db1bd3282eaf9f884
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jul 27 16:10:29 2017 -0700

    fixed parallel bug identified by Marc.

Src/EBAMRTools/AMReX_DivergenceOp.cpp
Src/GeometryShop/AMReX_BaseIVFactory.H
Src/GeometryShop/AMReX_EBLevelRedist.H
Src/GeometryShop/AMReX_EBLevelRedist.cpp
Src/GeometryShop/AMReX_IrregFABFactory.cpp

commit df342fb53fc5926b2ec4634a50d9cb12d06c38ee
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jul 27 16:04:11 2017 -0700

    CMake: remove old cmake files

Src/CMakeLists.txt
Src/Particle/CMakeLists.txt
Tools/CMake/CCSEConfig-install.cmake.in
Tools/CMake/CCSEConfigReport.cmake
Tools/CMake/CCSEConfigVersion-install.cmake.in
Tools/CMake/CCSELinkLine.cmake
Tools/CMake/CCSEOptions.cmake
Tools/CMake/CMakeParseArguments.cmake
Tools/CMake/ExampleBoxLibConfig.cmake
Tools/CMake/ExampleCMakeLists.txt_CCSEApp
Tools/CMake/InstallManager.cmake
Tools/CMake/ParseLibraryList.cmake

commit 5079de8f329ea3198aee72eba0220d9762742fed
Merge: ca8b11467 d699c2a2f
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 27 15:50:07 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit ca8b11467b46143a0a5eb6c5809e6cce4ae78550
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 27 15:49:52 2017 -0700

    remove diagnostic.

Src/Base/AMReX_DistributionMapping.cpp

commit bcd7cb8fcdf62554b24b60ee31504e66fc8c0ac4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jul 27 15:31:53 2017 -0700

    CMake: modify install process

CMakeLists.txt
Src/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Config.cmake

commit d699c2a2f05c54312b44ce884fec824ca75b9da1
Merge: 17813fc99 116e1d89a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jul 27 12:57:50 2017 -0700

    Merge pull request #72 from AMReX-Codes/dtg_branch
    
    merging some bug fixes over

commit aff1032c6032ce1f84e00434018c5b3562001a9c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jul 27 11:37:51 2017 -0700

    CMake:clean-up obsolete CMakeLists.txt

Src/CMakeLists.txt
Src/Extern/amrdata/CMakeLists.txt
Src/LinearSolvers/C_CellMG/CMakeLists.txt
Src/LinearSolvers/C_CellMG4/CMakeLists.txt
Src/LinearSolvers/C_TensorMG/CMakeLists.txt
Src/LinearSolvers/C_to_F_MG/CMakeLists.txt
Src/LinearSolvers/F_MG/CMakeLists.txt
Tools/CMake/AMReX_Utils.cmake

commit 230de365b7cca99a28f5361364b5e12947ff18e5
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jul 27 11:31:44 2017 -0700

    CMake: modify structure of the build

CMakeLists.txt
Src/Amr/CMakeLists.txt
Src/AmrCore/CMakeLists.txt
Src/Base/CMakeLists.txt
Src/Boundary/CMakeLists.txt
Src/CMakeLists.txt
Src/Extern/CMakeLists.txt
Src/F_BaseLib/CMakeLists.txt
Src/F_Interfaces/CMakeLists.txt
Src/LinearSolvers/CMakeLists.txt
Src/LinearSolvers/F_MG/sparse_solve.f90
Src/Particle/CMakeLists.txt
Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Utils.cmake

commit 17813fc99aa1670561f23504c6b13cdca5e94982
Merge: 0beb09ac0 e63696fa6
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 27 10:28:49 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 116e1d89a9dcf4b1e5684d076d9f6666d7c0e0bc
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jul 27 10:23:57 2017 -0700

    Changed MultiGrid.H to EBMultiGrid.H and AMRMultiGrid.H to AMREBMultiGrid.H per Marc's request.

Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp
Src/EBAMRElliptic/AMReX_EBMultiGrid.H
Tests/EBAMRElliptic/exec/conductivitySolve.cpp

commit e63696fa6824d8b5e240eeaa92e0dd56d4d43c59
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 27 10:19:00 2017 -0700

    fix call to mpi_finalize

Tutorials/Basic/main_F/main.F90

commit d8502c443611fdc5a5d334aa3978d3d70595e3b2
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jul 27 10:11:49 2017 -0700

    bug fixes and another argument to DivergenceOp to allow fortran bit to be bypassed

Src/EBAMRTools/AMReX_DivergenceOp.H
Src/EBAMRTools/AMReX_DivergenceOp.cpp
Src/EBAMRTools/AMReX_EBFortND.F90

commit 1697df7cb05cd7fcfa9b72f8878ee89ec90abefa
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Thu Jul 27 07:13:45 2017 -0700

    Simplified color-map selection

Src/Base/AMReX_ParallelDescriptor.cpp

commit 7b004fd92939471b16a9ccd5058167f17bcd0b6c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 27 06:29:53 2017 -0700

    fix datatype

Src/F_Interfaces/Base/AMReX_parallel_mod.F90
Tutorials/Basic/main_F/main.F90

commit 0ede85f8427660ebb77e1dfdb47876a30477abae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 26 18:08:47 2017 -0700

    new Tutorials/Basic/main_C

Tutorials/Basic/main_C/GNUmakefile
Tutorials/Basic/main_C/Make.package
Tutorials/Basic/main_C/main.cpp

commit b477952485e256749364b6b24f68491c19cef976
Author: kngott <kngott@lbl.gov>
Date:   Wed Jul 26 17:50:55 2017 -0700

    First attempt to transfer ProfDataServices to amrex::DataServices.

OldTutorials/DataServicesTest0/GNUmakefile
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Src/Extern/ProfParser/AMReX_AVGDOWN_2D.F
Src/Extern/ProfParser/AMReX_AVGDOWN_3D.F
Src/Extern/ProfParser/AMReX_AVGDOWN_F.H
Src/Extern/ProfParser/AMReX_BLProfStats.H
Src/Extern/ProfParser/AMReX_BLProfStats.cpp
Src/Extern/ProfParser/AMReX_BLProfUtilities.H
Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp
Src/Extern/ProfParser/AMReX_BLWritePlotFile.H
Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp
Src/Extern/ProfParser/AMReX_CommProfStats.H
Src/Extern/ProfParser/AMReX_CommProfStats.cpp
Src/Extern/ProfParser/AMReX_RegionsProfStats.H
Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp
Src/Extern/ProfParser/AMReX_XYPlotDataList.H
Src/Extern/ProfParser/AMReX_XYPlotDataList.cpp
Src/Extern/ProfParser/BLProfParser.l
Src/Extern/ProfParser/BLProfParser.y
Src/Extern/ProfParser/Make.package
Src/Extern/ProfParser/backup/AMReX_AVGDOWN_2D.F
Src/Extern/ProfParser/backup/AMReX_AVGDOWN_3D.F
Src/Extern/ProfParser/backup/AMReX_AVGDOWN_F.H
Src/Extern/ProfParser/backup/AMReX_BLProfStats.H
Src/Extern/ProfParser/backup/AMReX_BLProfStats.cpp
Src/Extern/ProfParser/backup/AMReX_BLProfUtilities.cpp
Src/Extern/ProfParser/backup/AMReX_BLWritePlotFile.H
Src/Extern/ProfParser/backup/AMReX_BLWritePlotFile.cpp
Src/Extern/ProfParser/backup/AMReX_CommProfStats.H
Src/Extern/ProfParser/backup/AMReX_CommProfStats.cpp
Src/Extern/ProfParser/backup/AMReX_RegionsProfStats.H
Src/Extern/ProfParser/backup/AMReX_RegionsProfStats.cpp
Src/Extern/ProfParser/backup/AMReX_XYPlotDataList.H
Src/Extern/ProfParser/backup/AMReX_XYPlotDataList.cpp
Src/Extern/ProfParser/backup/BLProfParser.l
Src/Extern/ProfParser/backup/BLProfParser.y
Src/Extern/ProfParser/backup/Make.package
Src/Extern/amrdata/AMReX_DataServices.H
Src/Extern/amrdata/AMReX_DataServices.cpp

commit 71233602c7383ee0205603eb4f76e4e82325666f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 26 17:17:10 2017 -0700

    We have to pass a function adding parameters to amrex::Initialize, otherwise it might be too late.

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/F_Interfaces/Base/AMReX_init_fi.cpp
Src/F_Interfaces/Base/AMReX_init_mod.F90
Tutorials/Basic/main_F/main.F90

commit 0beb09ac036d4fc7a35db5d3dc7b357554c1ec6a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 26 17:08:42 2017 -0700

    merge fix.

Docs/Notes.io_implementation
Src/Amr/AMReX_Amr.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Boundary/AMReX_FabSet.H
Src/Particle/AMReX_Particles.H
Tests/IOBenchmark/IOTestDriver.cpp

commit abc9f69daca4fe4f4acf22952b58c06beb3d555c
Merge: 6deffc253 8849f70ba
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 26 16:31:44 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6deffc2532a0026847f46b932c47a6087a83466e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 26 16:31:34 2017 -0700

    Adding a thread-safe random normal distribution to amrex.

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit 8849f70baf8c47cf734d20ccc076ce9183e2a526
Merge: 66a38bbb4 062ed4553
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 26 15:49:19 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 66a38bbb43bc8e491ead43a7011047262cb93991
Merge: 4ee7b2554 f295dcdd6
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 26 15:49:03 2017 -0700

    merge fix.

commit 062ed4553989fea6eddefc3739eb9eab3a86ef98
Merge: 727c64337 f295dcdd6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 26 15:34:50 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4ee7b2554f55b2ed83b08d527629e012e8eafc5a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 26 15:22:54 2017 -0700

    some profiler optimizations.

Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit ee7eb3477b5caab85552a18dae72142fbdf79a4a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 26 15:13:54 2017 -0700

    minor tutorial changes.

Tests/IOBenchmark/GNUmakefile

commit 4f51e6a051d896eb81fc3855bc058e1fe67aadd1
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 26 15:11:42 2017 -0700

    minor tutorial changes.

OldTutorials/DataServicesTest0/GNUmakefile
OldTutorials/MultiFabTests_C/GNUmakefile
OldTutorials/MultiFabTests_C/Make.package
OldTutorials/Sidecar_EX1/NSidecarsTest.cpp

commit f295dcdd670d68743731cb3e870c488fd6ba0fc7
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 26 15:01:18 2017 -0700

    dont send or clean up unused messages.

Src/Base/AMReX_NFiles.H
Src/Base/AMReX_NFiles.cpp
Tests/IOBenchmark/GNUmakefile
Tests/IOBenchmark/IOTest.cpp

commit 727c643377ee6467de4d4f6059923235c643257f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 26 14:58:50 2017 -0700

    Fortran: fix non MPI

Src/F_Interfaces/Base/AMReX_parallel_mod.F90

commit 7a99e7e20d7d44279738b47a1ad55cf7ad464938
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 26 14:52:30 2017 -0700

    Fortran: allow users pass their own communicator and skip building parmparse database from command line arguments

Src/Base/AMReX.cpp
Src/Base/AMReX_ParmParse.cpp
Src/F_Interfaces/Base/AMReX_init_fi.cpp
Src/F_Interfaces/Base/AMReX_init_mod.F90
Src/F_Interfaces/Base/AMReX_parallel_mod.F90
Tutorials/Basic/main_F/main.F90

commit d6fda8aa96d670065b3ea33d8ad6909118973e02
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Wed Jul 26 13:12:05 2017 -0700

    Introduced input parameter for choice of color-map

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit f301c71445bf0f986b527ecedfbca6b97da630d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 26 10:49:54 2017 -0700

    Fortran parmparse: add optional return flag to query functions

Src/Base/AMReX_parmparse_fi.cpp
Src/Base/AMReX_parmparse_mod.F90

commit a706f382ee50d57b73d8e9582e540ab18d83044c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 26 10:29:51 2017 -0700

    update User's Guide

Docs/AMReXUsersGuide/Fortran/Fortran.tex

commit 7e38d370eb0c1d8cf67341f91f11ec1a28aa388a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 26 10:17:54 2017 -0700

    remove old Fotran miniapp

MiniApps/AMR_Adv_Diff_F90/GNUmakefile
MiniApps/AMR_Adv_Diff_F90/GPackage.mak
MiniApps/AMR_Adv_Diff_F90/advance.f90
MiniApps/AMR_Adv_Diff_F90/compute_flux.f90
MiniApps/AMR_Adv_Diff_F90/init_phi.f90
MiniApps/AMR_Adv_Diff_F90/inputs_2d
MiniApps/AMR_Adv_Diff_F90/inputs_3d
MiniApps/AMR_Adv_Diff_F90/main.f90
MiniApps/AMR_Adv_Diff_F90/prob.f90
MiniApps/AMR_Adv_Diff_F90/update_phi.f90
MiniApps/AMR_Adv_Diff_F90/write_plotfile.f90

commit 2a9d06f096a5a34ec77f39cfa6f960031b897d50
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 26 10:16:14 2017 -0700

    Fortran: removed C++ main

GNUmakefile.in
Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90
Src/F_Interfaces/Base/AMReX_fi_main.cpp
Src/F_Interfaces/Base/AMReX_init_mod.F90
Src/F_Interfaces/Base/Make.package
Tutorials/Amr/Advection_F/Source/fmain.F90
Tutorials/Amr/Advection_F/Source/my_amr_mod.F90
Tutorials/Amr/Advection_octree_F/Source/fmain.F90
Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90
Tutorials/Basic/HeatEquation_EX1_F/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_F/fmain.f90
Tutorials/Basic/HelloWorld_F/fmain.f90
Tutorials/Basic/main_F/GNUmakefile

commit be3e897f205cfb5b5f149303e8c79e7254f65074
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 26 07:07:53 2017 -0700

    Fortran ParamParse: disable some functions for gfortran 4 because of (I believe) compiler bug

Src/Base/AMReX_parmparse_mod.F90
Tutorials/Basic/main_F/main.F90

commit ad57f50837a7518d296bc64cf46e3d68131f8f95
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 25 21:38:41 2017 -0700

    Fortran parmparse: trim before adding string

Src/Base/AMReX_parmparse_mod.F90

commit de5584e1b5ac4300ff2c8184fd46725d1c0a7731
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 25 21:30:30 2017 -0700

    Fortran ParmParse: implement add and refactor string

Src/Base/AMReX_parmparse_fi.cpp
Src/Base/AMReX_parmparse_mod.F90
Src/Base/AMReX_string_mod.F90
Src/F_Interfaces/Base/AMReX_init_fi.cpp
Tutorials/Basic/main_F/main.F90

commit 197c1eee98e06b9e2f1cc08b20d1fc10ba7fdea3
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jul 25 13:13:24 2017 -0700

    Modify way of add include paths

CMakeLists.txt
Src/Amr/CMakeLists.txt
Src/AmrCore/CMakeLists.txt
Src/Base/CMakeLists.txt
Src/Boundary/CMakeLists.txt
Src/CMakeLists.txt
Src/Extern/amrdata/CMakeLists.txt
Src/F_BaseLib/CMakeLists.txt
Src/F_Interfaces/CMakeLists.txt
Src/LinearSolvers/C_CellMG/CMakeLists.txt
Src/LinearSolvers/C_CellMG4/CMakeLists.txt
Src/LinearSolvers/C_TensorMG/CMakeLists.txt
Src/LinearSolvers/C_to_F_MG/CMakeLists.txt
Src/LinearSolvers/F_MG/CMakeLists.txt
Src/Particle/CMakeLists.txt

commit 96d672397ae877601975f4a180989f2af1eab649
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jul 25 11:44:11 2017 -0700

    Add utility to find subdirectories

Tools/CMake/AMReX_Utils.cmake

commit abff22ecb303c68c9fef81e679775381e4a1c65a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 25 06:46:28 2017 -0700

    forgot to check in new files

Src/F_Interfaces/Base/AMReX_init_fi.cpp
Src/F_Interfaces/Base/AMReX_init_mod.F90

commit 5255bbad8cc31beb4f2b5efd6391ed734e986035
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 25 06:45:43 2017 -0700

    fix relative path

Tutorials/Amr/Advection_F/Exec/Make.Adv
Tutorials/Amr/Advection_octree_F/Exec/Make.Adv

commit 0b1bc2f5fc5c5765acf5d101657f6af4c1f6af70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 24 17:31:27 2017 -0700

    Fortran: allow main in Fortran

GNUmakefile.in
Src/Base/AMReX_ParallelDescriptor.cpp
Src/F_Interfaces/Base/AMReX_base_mod.F90
Src/F_Interfaces/Base/AMReX_fi_main.cpp
Src/F_Interfaces/Base/Make.package
Tutorials/Basic/main_F/GNUmakefile
Tutorials/Basic/main_F/Make.package
Tutorials/Basic/main_F/main.F90

commit 9f0b9d5f6280fc03d780d6358eac1fdf194d2368
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jul 24 14:43:10 2017 -0700

    wip

Tests/GeometryShop/vofStructures/umapTest.H
Tests/GeometryShop/vofStructures/umapTest.cpp
Tests/GeometryShop/vofStructures/umapTest_mod.f90
Tests/GeometryShop/vofStructures/umapTest_nd.f90

commit 894e15d5a8f1d4a67fe17cc389127b9fb59e76b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 24 14:17:11 2017 -0700

    Fortran: add sum_boundary and average_sync

Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit f191bb8ac6bfaaddd05a45a32ad54dc4f07554cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 24 12:57:06 2017 -0700

    OwnerMask is now iMultiFab

Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.f90
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 9f78b74a256d57020b300e9c1ca6e11440495788
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jul 24 15:06:47 2017 -0400

    util_module -> box_util_module

Tools/Postprocessing/F_Src/fnan.f90

commit cdddbf656f6056a0adcc0b36fedc4421251a6510
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 24 11:59:19 2017 -0700

    add some specialized ifab functions

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.f90

commit 724c202b0ee52205fb31346091fa7116e2dfadd5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 21 17:28:36 2017 -0700

    reverting

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 8c5d9228859cb030e0f76232412ab32248af2c56
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 21 16:00:19 2017 -0700

    revert the periodic shift optimization for now

Src/Particle/AMReX_NeighborParticlesI.H

commit 979eee688c3ade49525b3347d0e1c63a8deea066
Merge: db71b1c74 3a726a1f3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 21 15:22:49 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit db71b1c74e52111d5957f50a3de3e270568706d8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 21 15:22:41 2017 -0700

    some minor optimization /refactoring of the neighbor particle code.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit bf663f5ffebadfa895a89b1822e163688060386b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jul 21 11:23:02 2017 -0400

    Link against the IBM OpenMP library

Tools/GNUMake/comps/ibm.mak

commit 3a726a1f3b49b971fb5e41888739a1996f33baf3
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jul 20 17:39:01 2017 -0700

    added a makeSFC distribution mapping interface (similar to the knapsack and roundrobin cases)

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit c52d2b3788feaa067c22f512c090a4ef73fb54ca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 20 15:34:54 2017 -0700

    F_Interfaces: owner mask and override_sync

Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 18834c9f86f28a5989df733f9c712ba15c3f03ec
Merge: 030f1c504 aa6f31235
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 20 14:54:46 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 030f1c5049a4e933154551f319ce73037f31411d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 20 14:54:37 2017 -0700

    Update these Tutorials to account for the recent changes to NeighborParticleContainer.

Tutorials/Particles/NeighborList/GNUmakefile
Tutorials/Particles/NeighborList/NeighborListParticleContainer.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborList/neighbor_list_2d.f90
Tutorials/Particles/NeighborList/neighbor_list_3d.f90

commit aa6f31235278767b927713389b219c30416627ab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 20 14:46:00 2017 -0700

    fix comment

Src/Base/AMReX_MultiFab.H

commit bb5e29def605c9f4b2654c6a77feaad855940ad8
Merge: d2b4e447d c7eb385b4
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jul 20 14:16:30 2017 -0700

    Merge pull request #61 from AMReX-Codes/dtg_branch
    
    fixed some bugs and wrote gradient operator that Marc wanted.

commit c7eb385b4779e1cc0d9f3a66433a08f4fbb770d2
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jul 20 14:15:02 2017 -0700

     a few random bug fixes along with a brand new EB gradient operator that passes its test.

Src/EBAMRTools/AMReX_DivergenceOp.H
Src/EBAMRTools/AMReX_DivergenceOp.cpp
Src/EBAMRTools/AMReX_EBFortND.F90
Src/EBAMRTools/AMReX_EBFortND_F.H
Src/EBAMRTools/AMReX_GradientOp.H
Src/EBAMRTools/AMReX_GradientOp.cpp
Src/EBAMRTools/Make.package
Src/GeometryShop/AMReX_AggStencilI.H
Tests/EBAMRTools/regression/GNUmakefile
Tests/EBAMRTools/regression/aggpwlfp.inputs
Tests/EBAMRTools/regression/aggpwlfpTest.cpp
Tests/EBAMRTools/regression/divop.inputs
Tests/EBAMRTools/regression/ebcoarave.inputs
Tests/EBAMRTools/regression/gradientOpTest.cpp
Tests/EBAMRTools/regression/gradop.inputs
Tests/EBAMRTools/regression/nwoebquadcfi.inputs

commit d2b4e447dd4ef4c6aadcf3f0fd09a1ca15f48577
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 20 14:08:20 2017 -0700

    add OwnerMask and OverrideSync functions that let owners override nonowners

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit 8a60deec2dafbd83e1a0cd2055c781abc82560d0
Merge: 747210d86 9aae7fdb2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 20 14:05:50 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 747210d86b3d3d597cdb2227772e9b605bbb200e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 20 14:05:40 2017 -0700

    remove openmp pragmas from neighbor list code for now.

Src/Particle/AMReX_NeighborParticlesI.H

commit 9aae7fdb23ec9e4c5aedb7dec496d87bf7942597
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 20 10:01:47 2017 -0700

    add a function performing nodal data sync via averaging

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit 61e3fb1bd76022885f34c9ac302cbd544cd7c805
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 20 10:37:49 2017 -0700

    left out a #ifdef for MPI.

Src/Particle/AMReX_NeighborParticlesI.H

commit 5c670eea608e1c69bec43431eda3e181735f49f0
Merge: 6365f16e6 8f367b16e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 20 10:25:54 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6365f16e61d634444ae7375dde6e2827a3835a28
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 20 10:25:42 2017 -0700

    do not recompute the number of snds / rcvs unless it changes.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 8f367b16e472f871a45ce840bc19df5d6205165c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 20 09:34:47 2017 -0700

    fix typo

Docs/AMReXUsersGuide/Basics/Basics.tex

commit e2b8a7c9f3b8200de4b991a2210e09f1de37d189
Merge: df1242597 7da68d2f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 20 09:35:08 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 5a9d0179355781420c735635cffc705a3707ce71
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jul 19 17:53:42 2017 -0700

    WIP for umap tests

Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90
Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/umapTest.H
Tests/GeometryShop/vofStructures/umapTest.cpp
Tests/GeometryShop/vofStructures/umapTest_mod.f90
Tests/GeometryShop/vofStructures/umapTest_nd.f90

commit 7da68d2f53b90b754dc3c5e29504c2b5e84edc3f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 19 13:57:05 2017 -0700

    don't hard-code this cutoff.

Src/Particle/AMReX_Particle_mod_3d.F90

commit e0d53c5c79393eeec3d527ada99b0c7b79d930e1
Merge: 6a289a2b9 9e88860b9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 19 13:21:39 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6a289a2b9af95cb71b45f9a1538976d9959a1fb5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jul 19 13:21:22 2017 -0700

    add method to update the neighbor buffers without refilling them.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 9e88860b9ca33790ea7b4399477427b8011fc6c3
Merge: 9b702218a 826506003
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jul 19 12:30:09 2017 -0700

    Merge pull request #59 from zingale/development
    
    rewrite some of the area and volume terms

commit 82650600310c60fc97a044ae95bf1f39d07fa616
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 19 14:45:25 2017 -0400

    rewrite some of the area and volume terms
    this reduces roundoff for large values of r
    also use Pi and other constants from the constants header
    
    this closes #29

Src/Base/AMReX_COORDSYS_1D.F
Src/Base/AMReX_COORDSYS_2D.F

commit df1242597e2bf521c749d6444b32bd9953cb409d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 19 10:22:38 2017 -0700

    quiet compiler

Src/Amr/AMReX_StateData.H

commit 69dc79e990078b69d6876bfeb20b6fbeea3b6d0d
Merge: 7309fe78a 9b702218a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 19 10:01:17 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9b702218aa5cc660c5ba3c4d6c1f4c5d737e7841
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 19 10:00:50 2017 -0700

    replace UINT32_MAX with std::mt19937::max()

Src/F_BaseLib/bl_random_c.cpp

commit 7309fe78a27113abbd36a385c1d589e23a614a76
Merge: b94723333 1a785555e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 19 09:41:14 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 1a785555ee96f74b2a36b6f084c537aa38f90cb9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 18 17:41:19 2017 -0700

    Fortran version of buildNeighborList

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H
Src/Particle/AMReX_Particle_mod_3d.F90
Src/Particle/AMReX_Particles_F.H

commit 90a144e617d268e31b2ebfd5aaa2d42fb71fa465
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Jul 18 15:10:44 2017 -0700

    bug fix in divergenceop

Src/EBAMRTools/AMReX_DivergenceOp.cpp

commit 1ca92b8f4f226f2b910cd1d8f021a6dd22654683
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jul 18 13:42:51 2017 -0700

    Update documentation

Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex

commit 5b16bdd57508b0ff778846b2fb92c8b3b84ae474
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jul 18 13:33:49 2017 -0700

    Provide default install dir other than /usr/local

Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Config.cmake

commit ffffd78dde1ce8ac86df88ce8fb5a5fd7410eab4
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jul 18 12:44:39 2017 -0700

    Add CMake options to turn on/off FPE compiler flags

Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake

commit 65997e8a0acfcfcbc2fe98374adadc56cc9e1fbf
Merge: 757a5606b ed2d324be
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Jul 18 11:15:52 2017 -0700

    Merge pull request #58 from AMReX-Codes/dtg_branch
    
    some bug fixes and a new divergence operator

commit ed2d324be0a61571c83f6c23e35461ace7806643
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Jul 18 11:14:39 2017 -0700

    DivergenceOp now passes its test.

Src/EBAMRTools/AMReX_DivergenceOp.cpp
Src/EBAMRTools/AMReX_EBFortND.F90
Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp
Tests/EBAMRTools/regression/divergenceOpTest.cpp

commit 05aeba879056087ddb90dd6cf9cb27c1d34e3867
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Jul 17 16:54:47 2017 -0700

    Per Marc's request, I added a standalone hybrid divergence operator.   It compiles but testing is not complete

Src/EBAMRTools/AMReX_DivergenceOp.H
Src/EBAMRTools/AMReX_DivergenceOp.cpp
Src/EBAMRTools/AMReX_EBFortND.F90
Src/EBAMRTools/AMReX_EBFortND_F.H
Src/EBAMRTools/Make.package
Src/GeometryShop/AMReX_EBLevelRedist.H
Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H
Tests/EBAMRTools/regression/GNUmakefile
Tests/EBAMRTools/regression/divergenceOpTest.cpp
Tests/EBAMRTools/regression/divop.inputs

commit 757a5606b3838eb46a125b1019702e994f781d5c
Merge: fb7491037 9a48811f2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 17 14:48:19 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit fb7491037db632cf492f7dd311087d01917eece3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 17 14:48:09 2017 -0700

    optimizing / simplifying the neighbor list code.

Src/Particle/AMReX_NeighborParticlesI.H

commit 9a48811f2e0cd81f0ea3a7e3ee57343a35bcd7c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 17 12:47:26 2017 -0700

    assert that we are not using tag that's too large

Src/Base/AMReX_NFiles.cpp

commit f922ac3337cde11212673e726fddf921cb7b8920
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 17 12:42:06 2017 -0700

    Abort if MPI_Comm_get_attr failes to get MPI_TAG_UB.  Add ParallelDescriptor::MaxTag()

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit acb7b7ad36244b708741624fd5569c7564886a2c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 17 10:33:16 2017 -0700

    check getcwd error code.

Src/F_BaseLib/backtrace_c.cpp

commit 4d8fb6de09bb630cf5a714680dbb70f9573f00f8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 17 10:20:08 2017 -0700

    check return code of std::system in amrex::UtilCreateDirectoryDestructive

Src/Base/AMReX_Utility.cpp

commit 99cec8974d387ef7a5e07a8cd817e7343cf2e165
Merge: 6c6497e23 6eb1678eb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 17 09:59:06 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6c6497e2355d5c0028e117cd20a78956c3e7c670
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 17 09:58:55 2017 -0700

    add option to sort nl after constructing it (useful for exactly comparing against the N^2 calculation.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit 6eb1678eb93c82b883b6b2cbbd3b25b4c5ecb577
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 15 16:42:43 2017 -0700

    more reduce funcitons

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit 525d961ac4a74e7fb697a05cf8e9776a69c9bd9b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 15 16:17:15 2017 -0700

    add more reduce functions that do multiple reductions without user packing and unpack into arrays

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit e55d878024c5e7a0dd7d62eb7399b9657a2a5c34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 15 15:50:54 2017 -0700

    reorganize reduce functions

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit cf34b31589dca8772b973c87484fe7afd175ff2d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 15 04:13:58 2017 -0400

    Fix the offset in copytomem/copyfrommem again

Src/Base/AMReX_BaseFab_nd.F90

commit 9a522156ac25d0141c2016db3e43816c7301e0d4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 15 03:51:01 2017 -0400

    Add device syncs after copyToMem/copyFromMem

Src/Base/AMReX_FabArray.H

commit 083347f1b96fc97b4940cf8552cfc8ada8fcb16f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 15 02:02:31 2017 -0400

    Only do reductions when CUDA is enabled

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit e9ccf955d511f97018807b502ac9720fc4f3dcb8
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 15 01:45:50 2017 -0400

    Fix the offset in copytomem/copyfrommem

Src/Base/AMReX_BaseFab_nd.F90

commit 4ab1a8865ccb8f84558c7a4bdc92f1f930cb8acc
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 15 00:11:16 2017 -0400

    Do not perform Device operations for non-CUDA code

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_Device.H
Src/Base/AMReX_MFIter.H

commit 481ce13b15b56ad858a7f363f756a3b5a0d849cd
Merge: 278078c16 bf70914ee
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 14 17:21:18 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 278078c16c9c0b514f4c158dd2141cbce15ff7c8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 14 17:19:55 2017 -0700

    also creating neighbor lists for ghost particles.

Src/Particle/AMReX_NeighborParticlesI.H

commit 435377ef4e1fda98c4f2b7aaff2e1ae83d848b83
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jul 14 16:45:27 2017 -0700

    more progress on EBAMRElliptic.  Parking this for now so I can write Pele operators.

Src/EBAMRElliptic/AMReX_AMRMultiGrid.H
Src/EBAMRElliptic/AMReX_BaseBCFuncEval.H
Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H
Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp
Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOp.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp
Src/EBAMRElliptic/AMReX_EBEllipticFort.F90
Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H
Src/EBAMRElliptic/AMReX_MultiGrid.H
Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp
Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H
Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp
Src/EBAMRElliptic/AMReX_NoOpSolver.H
Src/EBAMRElliptic/AMReX_VCAggStencil.H
Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBArith.cpp

commit bf70914ee57cd835ca6213a85e26ae98e619b353
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 14 16:09:28 2017 -0700

    hypre: provide initial guess and add BoomerAMG to inputs

Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Tutorials/HYPRE/ABecLaplacian/inputs

commit 955b3806ff8a3ca5790de08693776b17c213266d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 14 15:56:14 2017 -0700

    Hypre tutorial: print out error

Tutorials/HYPRE/ABecLaplacian/ABL.H
Tutorials/HYPRE/ABecLaplacian/ABL.cpp
Tutorials/HYPRE/ABecLaplacian/ABL_F.F90
Tutorials/HYPRE/ABecLaplacian/ABL_F.H

commit d7ddf9ba42b5d082b53b294f04dc239d77d6198c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 14 14:28:53 2017 -0700

    first pass of Hypre Boomer AMG

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.H
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H
Tutorials/HYPRE/ABecLaplacian/ABL.cpp

commit 3348b9c21b4822a93ccbc9cfbdf2e2ac775e10e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 14 10:31:37 2017 -0700

    remove the inclusion of Hypre's Make.package from Make.hypre

Tools/GNUMake/packages/Make.hypre
Tutorials/HYPRE/ABecLaplacian/GNUmakefile

commit 141307673586a9616d8297b1415ccd2cfa890541
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 14 15:12:29 2017 -0700

    Offset the neighbor particle number by Np

Src/Particle/AMReX_NeighborParticlesI.H

commit b94723333e7d5436453cbf7860b41c70024d8c9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 14 10:23:47 2017 -0700

    Abort if message sizes in parallel copy and fillboundary do not match

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 1b0b3262d13fb544ebcc516cd0ff7ee7b9a1f234
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 13 21:05:02 2017 -0700

    flush AMReX::Print by default

Src/Base/AMReX_Print.H

commit b0e893766c9ae802602a15e1eef9a767667563d7
Merge: ad88aa397 77c323b3f
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 14 12:21:49 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 61bb9c0a634679e45ca42bd1db4b7099d191dc3c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jul 14 12:19:39 2017 -0700

    you know you have been staring at stuff too long when it pisses you off that Dirichlet and Neumann have different numbers of letters

Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp
Tests/EBAMRElliptic/exec/conductivitySolve.cpp

commit ad88aa3974d369e4f4d02eae652b383e05ac2a72
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 14 12:19:07 2017 -0700

    call CleanUpMessages for nfilesiter.

Src/Base/AMReX_NFiles.cpp

commit 77c323b3f152cf863e34ccb95d72d357191cf2f5
Merge: 203267a6f ed780271e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 14 10:54:41 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 203267a6fd3685bea912d76917a14c8ccd6ed2c1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jul 14 10:54:30 2017 -0700

    update the short range force tutorials to reflect recent changes in NeighborParticleContainer.

Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborList/main.cpp
Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp
Tutorials/Particles/ShortRangeParticles/main.cpp

commit ed780271e9f530a11c71125f06dfe816e0c06dde
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 13 21:42:56 2017 -0700

    Add the ability to pass weights into the knapsack and round robin
    strategies -- the algorithms then use the weights instead of numpts.

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit 6e88e97fdd66f8387ad67c1041959289cb770da6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 13 19:04:12 2017 -0700

    fixing fill neighbors for the case of ng>1

Src/Particle/AMReX_NeighborParticlesI.H

commit 7d64ddbafb2daabb46c8a50e9371e5d2bdc7a5e8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 13 18:59:27 2017 -0700

    fixing another bug...

Src/Particle/AMReX_NeighborParticlesI.H

commit 425d87b75fa79484b3a2c3d2b17e91dd2933ed3f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 13 18:56:59 2017 -0700

    got a sign wrong here.

Src/Particle/AMReX_NeighborParticlesI.H

commit e34b429e1d0165268c4fa81ff3dadba6519ddba4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 13 18:53:08 2017 -0700

    make these protected instead of private.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit aa3e8c835c817e227a9a31143796dc954df3a0cc
Merge: 14efed3d1 d1299272c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 13 18:21:32 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 14efed3d1ccff85cb2c886f8ba1dea67ab2653d2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 13 18:21:19 2017 -0700

    use the input dmap and geom rather than getting it from the pc.

Src/Particle/AMReX_NeighborParticlesI.H

commit d1299272c15acf4dbd18b562fb78a5baa7daa690
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 13 18:12:31 2017 -0700

    BoxArray intersection for a corner case in which the box array has a single nodal box with a single node in one of the directions

Src/Base/AMReX_Box.H
Src/Base/AMReX_BoxArray.cpp

commit a3bd15fdec1e4ea147f553d1abd455e8602c067f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 13 17:45:43 2017 -0700

    make the applyPeriodic and packGhost functions take the lev

Src/Particle/AMReX_NeighborParticlesI.H

commit a2e5fa893d1712b67f816161d85a3c7b5cef2f28
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 13 17:42:37 2017 -0700

    fix another typo.

Src/Particle/AMReX_NeighborParticlesI.H

commit c8ec9b8fd8e0e798c8776b88c80c0316f6dd2b2e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 13 17:40:59 2017 -0700

    fix typo

Src/Particle/AMReX_NeighborParticles.H

commit 5d394139359e36e5c5bd73083db76c507078dd16
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 13 17:38:09 2017 -0700

    Add some asserts for safety.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit afb6b010a8041492f7e3308da87c7e99227a1da5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jul 13 17:02:32 2017 -0700

    add a ParGDB constructor to the neighbor particle container.

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp

commit abb2495db5188530c830db4386d68fdcc684dbd0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jul 13 16:17:10 2017 -0700

    EBAMRElliptic continues to slouch toward Bethlehem

Src/EBAMRElliptic/AMReX_AMRMultiGrid.H
Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H
Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp
Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H
Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp
Src/EBAMRElliptic/Make.package
Tests/EBAMRElliptic/exec/GNUmakefile
Tests/EBAMRElliptic/exec/conductivitySolve.cpp

commit 2989b715fc67fdee00730f02a774537900c4f4c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 13 11:08:21 2017 -0700

    remove plt_compare_diff_grids

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py

commit f3739b0f4d2f0b85c6a6b17be0fe8ed4c5b6c324
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 11 18:28:24 2017 -0700

    WIP: hypre BoomerAMG

Src/Extern/HYPRE/AMReX_HABEC_3D.F90
Src/Extern/HYPRE/AMReX_Hypre.H
Src/Extern/HYPRE/AMReX_Hypre.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap.H
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABecLap2.H
Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp
Src/Extern/HYPRE/AMReX_HypreABec_F.H
Src/Extern/HYPRE/Make.package
Tutorials/HYPRE/ABecLaplacian/ABL.H
Tutorials/HYPRE/ABecLaplacian/ABL.cpp

commit 88c0f585ca11c6c892030689cbfc7d2e0290eb25
Merge: c65d02c68 6d3bc9b4e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jul 13 12:05:47 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 6d3bc9b4e71c22cd1495f922fc9f8bda2e22a523
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 12 19:24:30 2017 -0400

    fix the case where no B params are specified

Tools/F_scripts/write_probin.py

commit 8dadd2905f96ed28f6fe03f77984bc8daac0a4d9
Author: Donald Willcox <eugene.willcox@gmail.com>
Date:   Wed Jul 12 16:54:29 2017 -0400

    In write_probin, use --managed flag to turn on CUDA managed probin vars (off by default).

Tools/F_scripts/write_probin.py

commit a7c486085e81fd5cf456c9590b29ed7f3552a57f
Author: Donald Willcox <eugene.willcox@gmail.com>
Date:   Wed Jul 12 16:33:42 2017 -0400

    Modified write_probin to use argparse instead of getopt.

Tools/F_scripts/write_probin.py

commit 5f13821bd47581a8961f84315db4d9a7be51e86d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 12 12:46:56 2017 -0700

    fix for AddProcsToComp.

Src/Amr/AMReX_Amr.cpp

commit 0037cfce44defd4c009efd0f957dfe545fb0d5bb
Author: Donald Willcox <eugene.willcox@gmail.com>
Date:   Wed Jul 12 03:14:02 2017 -0400

    Modified write_probin to use managed memory.

Tools/F_scripts/write_probin.py

commit 15e586b02fe8b6c4bce92914286f47e97ae2a8c8
Merge: d44b8df6e d8fb51dd2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jul 11 17:18:39 2017 -0700

    Merge pull request #56 from zingale/development
    
    add a print_state (and print_state_n) method

commit d8fb51dd2c5e5c2b324963dfc2c45d19bf40c8d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 11 20:17:05 2017 -0400

    wrong one -- single component gets more precision

Src/Base/AMReX_MultiFabUtil.cpp

commit 2000c345b39c35a8c3cf48fda899c3ca76905986
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 11 20:15:00 2017 -0400

    max precision

Src/Base/AMReX_MultiFabUtil.cpp

commit f879e99c784895b067fb1d573e687f46bc5037cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 11 20:02:59 2017 -0400

    much nicer C++ implementation of print_state (thanks to Weiqun for
    pointers)

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_F.H

commit 09a8dc7a486e64b1e32ca052f4f8b7a66e97d591
Merge: e06c008c7 d44b8df6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 11 19:28:20 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit d44b8df6e8027afb084fc9a9b2b02df6f82286fb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 11 16:18:35 2017 -0700

    adding a new test for tracer particles

Tools/RegressionTesting/AMReX-tests.ini

commit 1b7eeb231998e04d3545d0056877b0f053ab2414
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 11 16:17:23 2017 -0700

    adding myself to the list of people who get emailed if the AMReX tests fail.

Tools/RegressionTesting/AMReX-tests.ini

commit c840d0d44781ee0ff72d1b75e2e89e7f634cac22
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 11 16:16:03 2017 -0700

    set up one of the advection tutorials to use tracer particles.

Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers

commit e06c008c7c02dd73986a9cdb75d03f365a0ff53c
Merge: e2c59d4f2 8f6badf40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 11 19:00:18 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit 8f6badf4064f2a0e52896d25f2db808462b947a8
Merge: 27cba3e54 6a8a0e561
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 11 15:02:37 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 27cba3e54062b5c024e126f5f3ab61c088803b8b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 11 15:01:47 2017 -0700

    some extra documentation for the Base code

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/Basics/figs/flowchart.odg
Docs/AMReXUsersGuide/Basics/figs/flowchart.pdf
Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex

commit e2c59d4f28726364d614101512067be9c75d0c7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 11 17:33:34 2017 -0400

    add a print_state (and print_state_n) method
    Useful for dumping out the state for a single zone, for debugging

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_F.H

commit 6a8a0e561d6fc976486a13beb377b0e9e3a6ae84
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 11 14:06:13 2017 -0700

    1D and 2D versions of the deposit_particle_dx routines, while I'm at it.

Src/Particle/AMReX_Particle_mod_1d.F90
Src/Particle/AMReX_Particle_mod_2d.F90

commit 1f90147991d77bb289ff72b51f6a04c0f7f0e1d0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 11 13:17:15 2017 -0700

    Fix a couple of bugs in the routine I just added.

Src/Particle/AMReX_Particle_mod_3d.F90

commit 1f7d650e0a2f41bb016f864b31127e922fa4724d
Merge: 9bb4e5bc9 049b71662
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 11 12:47:10 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 049b7166273fe64bce52a23df609ab5b115d69d5
Merge: 49750ac87 f4cf063d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 11 12:37:26 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 49750ac879216cb7abe4fe885030df9c753d48bf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 11 12:37:15 2017 -0700

    fix memory profiling for BoxArray

Src/Base/AMReX_BoxArray.cpp

commit 9bb4e5bc9593d7754cb750f6210e9fc93e229c2d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 11 11:04:10 2017 -0700

    Fix copy/paste error.

Src/Particle/AMReX_Particle_mod_3d.F90

commit e23c5c3b658ebf596f7282af2615023bbbc75d3e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 11 10:53:02 2017 -0700

    Fortran routine for deposition when dx != particle_dx

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_Particle_mod_3d.F90
Src/Particle/AMReX_Particles_F.H

commit f4cf063d242d5dfa067771f6bd37ac4da38ed372
Merge: ee888fd91 3984c7aa0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 11 09:28:52 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ee888fd91413634296b89905f688552d8be86347
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jul 11 09:28:39 2017 -0700

    can't assume one ghost cell here because of sub-cycling

Src/Particle/AMReX_ParticleContainerI.H

commit 3984c7aa0e1024654464c5fd20aea5118a8a7f47
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Jul 11 00:17:16 2017 -0700

    DistributionMapping() -> DistributionMap() - the Mapping() version actually constructs an empty dm instead of returning the one used by this mf.

Src/Base/AMReX_MultiFab.cpp

commit 480376b3cfddaea98367540e1070740cb33742be
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 10 18:30:59 2017 -0700

    Remove unused pmap

Src/Particle/AMReX_ParticleContainerI.H

commit ca48266eb160a5fe6be9f021c236af744443c151
Merge: bad9d47de f6aa3ca0f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 10 17:53:05 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit bad9d47dec8e188cb760e232d94f18a493eed418
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jul 10 17:52:29 2017 -0700

    add some stuff to the docs about neighbor lists.

Docs/AMReXUsersGuide/Particle/Particle.tex
Docs/AMReXUsersGuide/Particle/neighbor_list.pdf
Docs/AMReXUsersGuide/Particle/neighbor_list.tex

commit f6aa3ca0f1884307f4d640f92d41bf706beaf0b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 10 17:05:02 2017 -0700

    hypre: no need to make a new distributionmapping

Src/Extern/HYPRE/AMReX_HypreABecLap.cpp

commit 3bde0ea24193aa78f250fd40d1cdf392c2e92027
Merge: ed5bc4729 ffac06fd3
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jul 10 16:48:01 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ed5bc4729314da931e1d089dcbf1bde63e421ad5
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jul 10 16:47:19 2017 -0700

    Turn on OpenMP by default in the NeighborList Tutorial.

Tutorials/Particles/NeighborList/GNUmakefile

commit b37e65b498c67080d83668191077028496a7225e
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jul 10 16:46:56 2017 -0700

    turn on tiling and domain decomposition by default in the NeighborList Tutorial inputs file.

Tutorials/Particles/NeighborList/inputs

commit 4d0575b33a1145ef9d3b3b61529d6a8cb57c05d8
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jul 10 16:37:38 2017 -0700

    Much of the functionality of these tutorials is now implemented in AMReX.

Tutorials/Particles/NeighborList/NeighborListParticleContainer.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborList/inputs
Tutorials/Particles/ShortRangeParticles/GNUmakefile
Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H
Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp
Tutorials/Particles/ShortRangeParticles/inputs
Tutorials/Particles/ShortRangeParticles/main.cpp

commit 1ff0614519e38166979941821931ae86eeb59129
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jul 10 16:36:47 2017 -0700

    move the neighbor list stuff to Src/Particle

Src/Particle/AMReX_NeighborParticles.H
Src/Particle/AMReX_NeighborParticlesI.H

commit ffac06fd3dba3295388a5bf86285c069a14d26a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 10 16:34:58 2017 -0700

    add inputs

Src/Extern/HYPRE/AMReX_HypreABecLap.H
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Tutorials/HYPRE/ABecLaplacian/ABL.cpp
Tutorials/HYPRE/ABecLaplacian/inputs

commit a3d5f26018ab4ccbb7c07d59548cb778791aaa57
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jul 10 16:22:24 2017 -0700

    slight change to the check_pair method.

Tutorials/Particles/NeighborList/NeighborListParticleContainer.H

commit b3679c6f6c8e9bdcb133b212450a67a227e0cf9e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 10 16:14:56 2017 -0700

    hypreabeclap: add communicator

Src/Extern/HYPRE/AMReX_HypreABecLap.H
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp

commit 0556a141d21fd018b4ef20b762480fa641ce2bf2
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Jul 10 16:10:51 2017 -0700

    progress made in EBAMRElliptic.   I am close to where I can start actually trying to run stuff.

Src/EBAMRElliptic/AMReX_EBConductivityOp.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp
Src/EBAMRElliptic/AMReX_EBSimpleSolver.H
Src/EBAMRElliptic/AMReX_EBSimpleSolver.cpp
Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBArith.cpp

commit 4ac962cabc6e096c5d70ff0688a8a48eb66ce372
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 10 16:02:08 2017 -0700

    add hypre tutorial

Tutorials/HYPRE/ABecLaplacian/ABL.H
Tutorials/HYPRE/ABecLaplacian/ABL.cpp
Tutorials/HYPRE/ABecLaplacian/ABL_F.F90
Tutorials/HYPRE/ABecLaplacian/ABL_F.H
Tutorials/HYPRE/ABecLaplacian/GNUmakefile
Tutorials/HYPRE/ABecLaplacian/Make.package
Tutorials/HYPRE/ABecLaplacian/main.cpp

commit ea19c1d7c72360f9dcd539a1607ec0b8a034e9ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 10 16:01:00 2017 -0700

    more hypre

Src/Boundary/AMReX_LO_BCTYPES.H
Src/Extern/HYPRE/AMReX_HypreABecLap.H
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp

commit a263823cb346e09745a7d8382957203c927e55f0
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jul 10 15:49:32 2017 -0700

    make the distance function a 'check_pair' function.

Tutorials/Particles/NeighborList/NeighborListParticleContainer.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp

commit 289a15595c723df2073e174605fd2642efb35133
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jul 10 15:38:56 2017 -0700

    Moving the neighbor particle stuff into Src/Particle so it can be re-used elsewhere.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 4357692d5fc31d69f1bfa0be2f37050596326916
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jul 10 15:37:05 2017 -0700

    making these static constexpr seems to improve performance slightly.

Tutorials/Particles/NeighborList/NeighborListParticleContainer.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp

commit 286323caabf7ab2ccf448065f0cfbf790f2c6f66
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 10 11:16:13 2017 -0700

    add some support for Hypre

Src/Extern/HYPRE/AMReX_HypreABecLap.H
Src/Extern/HYPRE/AMReX_HypreABecLap.cpp
Src/Extern/HYPRE/AMReX_HypreABec_3D.F
Src/Extern/HYPRE/AMReX_HypreABec_F.H
Src/Extern/HYPRE/Make.package
Tools/GNUMake/Make.defs
Tools/GNUMake/packages/Make.hypre

commit e84a38298527fd06238de244dc0eae06f1211fe7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 10 10:19:20 2017 -0700

    converting size to int instead of int to unsigned. this is what the compiler implicitly does for us.

Src/Base/AMReX_FabArray.H

commit 1452440a99222f4e22d0679a7684d008dbf985b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 10 10:13:35 2017 -0700

    move Make.local to the last

Tools/GNUMake/Make.defs

commit 43bf4f11919910769f750ec7734a0e82e2f20eed
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jul 10 10:08:28 2017 -0700

    fix unsigned to signed integer comparison.

Src/Base/AMReX_FabArray.H

commit 5136b5385de7693e18244ba9b6a93a2c30d7ea10
Merge: bcae199f7 3d4394b1f
Author: asalmgren <asalmgren@lbl.gov>
Date:   Sun Jul 9 16:32:48 2017 -0700

    Merge pull request #55 from bcfriesen/add_craypat_docs_part1
    
    Docs: add section describing simple profiling with CrayPat

commit 3d4394b1fa6f7aa1181fdd75f39e7f671efd64af
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jul 9 16:24:36 2017 -0700

    Docs: add section describing simple profiling with CrayPat
    
    Info about advanced profiling techniques with CrayPat will come
    separately.

Docs/AMReXUsersGuide/Profiling/Profiling.tex

commit bcae199f717e93a82c17a82bc7c79703eabe7239
Merge: 6b1bec72c 0441a7a7b
Author: asalmgren <asalmgren@lbl.gov>
Date:   Sun Jul 9 14:53:55 2017 -0700

    Merge pull request #51 from atmyers/development
    
    Have the test suite also send an email if it has to abort for…

commit 6b1bec72ce2eec5775129aa3619375e60b30d918
Merge: 260590e08 8518e5a3d
Author: asalmgren <asalmgren@lbl.gov>
Date:   Sun Jul 9 14:53:31 2017 -0700

    Merge pull request #54 from bcfriesen/add_craypat
    
    Add CrayPAT support

commit 8518e5a3d5bbabbb7fed80fd27b97616fc1acea2
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jul 7 09:24:48 2017 -0700

    Tools: add support for tracing user-defined regions with CrayPAT

Tools/GNUMake/Make.defs
Tools/GNUMake/tools/Make.craypat

commit 4dc8e8782ffe3d501d4afe972af3f0ac632c384a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Jul 8 18:26:46 2017 -0700

    needed some functions to get FabArray<EBFluxFAB> to compile

Src/GeometryShop/AMReX_EBFluxFAB.H

commit c65d02c6838926ccef1c8aa9dff90ce2ba4f21c1
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 8 21:24:03 2017 -0400

    Prefer L1 cache to shared memory when available

Src/Base/AMReX_CUDA.F90

commit 22d28d234dadea2aeda70bbff2bebc05e15b9fe9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 8 20:20:25 2017 -0400

    Fix the kernel bounds in AmrLevel::Derive

Src/Amr/AMReX_AmrLevel.cpp

commit 4fea0da1fa71eb547921cff325e6f82e3a74b426
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 8 20:11:30 2017 -0400

    Turn off CUDA 8 support on Titan

Src/Base/AMReX_CUDA.F90
Tools/GNUMake/Make.defs
Tools/GNUMake/sites/Make.olcf

commit 67988f08ffd0b388566899f67edbb2f6f0abe82a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 8 20:10:48 2017 -0400

    Return value to suppress compiler warning

Src/Base/AMReX_MFIter.H

commit 00417f9ada4061be9abcd07ed5654f972e9c2017
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Jul 8 17:10:11 2017 -0400

    Use correct deleter on operator new[] data

Src/Base/AMReX_Device.H

commit 19bf27838695cd7ca32f8c1c67b5fc4641250512
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 8 16:14:43 2017 -0400

    Use smaller hunk sizes for small data

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_RealBox.cpp

commit 2868ddcc03d1eadcf038e5fde96e87f173ce12a5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 8 15:59:46 2017 -0400

    Use the correct RealBox lo expression in derive

Src/Amr/AMReX_AmrLevel.cpp

commit f5e9c542c870a677f7eb5a0a7dbbb021e912c139
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 8 15:59:29 2017 -0400

    Fix the nullification of RealBox data

Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp

commit fe3b0b548670c512ffd63fda494d2aa1c2fdd927
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 8 01:37:46 2017 -0400

    Clean up various parts of BaseFab

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit c7f5a1755cbe4838f52da1e5f2401dff07e2f1e9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 8 01:31:05 2017 -0400

    Port copyToMem and copyFromMem to GPU

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit 83a89e162698c89c8275a52696d45cb962717eba
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 8 01:15:55 2017 -0400

    Make copyToMem and copyFromMem void and thread-safe

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit c09c8fd61ceac96217afbac25028dd5041c33e34
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 8 01:15:15 2017 -0400

    Add missing return statement

Src/Base/AMReX_Device.H

commit 23f70eee5a967bdd249257b0dc6c9fc36b732777
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 8 00:38:52 2017 -0400

    Port BaseFab::norm, sum, dot product to GPU

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit eea091f190e705b20e11d04aa25fb075320eaf93
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 8 00:38:34 2017 -0400

    Add a function to create a device pointer

Src/Base/AMReX_Device.H

commit 260590e08bf78f42564b404c988f1d4709e50bf2
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Jul 7 19:07:03 2017 -0700

    move building the neighbor list into the compute forces routine.

Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp

commit 220d3b3facbb416cefadd31d3e7226ab8f05be61
Merge: d432a3f6c 5b239ce3a
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Jul 7 16:14:10 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d432a3f6c645e73845fb6d3401651e758b0e1b1b
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Jul 7 16:13:56 2017 -0700

    A tutorial that shows how to do neighbor lists for particles the see short-range forces.

Tutorials/Particles/NeighborList/GNUmakefile
Tutorials/Particles/NeighborList/Make.package
Tutorials/Particles/NeighborList/NeighborListParticleContainer.H
Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp
Tutorials/Particles/NeighborList/compare.py
Tutorials/Particles/NeighborList/inputs
Tutorials/Particles/NeighborList/main.cpp
Tutorials/Particles/NeighborList/neighbor_list_2d.f90
Tutorials/Particles/NeighborList/neighbor_list_3d.f90
Tutorials/Particles/NeighborList/neighbor_list_F.H

commit 5b239ce3a1f34fe5bd3f44aa0eb4c3739f4db18e
Merge: 5a8fbc29a ee4c5bbf2
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jul 7 15:16:58 2017 -0700

    Merge pull request #53 from AMReX-Codes/dtg_branch
    
    Bug fix pull request.

commit ee4c5bbf26a0b10862bbe7a2198630266fb7b335
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jul 7 13:45:53 2017 -0700

    got face averaging to work. found subtle bug in EBFaceFAB in the process

Src/EBAMRTools/AMReX_EBCoarseAverage.cpp
Src/EBAMRTools/AMReX_EBFortND.F90
Src/EBAMRTools/AMReX_EBFortND_F.H
Src/GeometryShop/AMReX_BaseEBFaceFABI.H
Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp
Tests/EBAMRTools/regression/ebcoarave.inputs

commit 9c12241f566123eb96b5df591d569716475dbe20
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jul 7 08:10:42 2017 -0400

    Make cudaSetDevice be the first thing we do

Src/Base/AMReX_CUDA.F90

commit dc1231993fdff49e5e373152140364311adbcae4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jul 7 07:09:39 2017 -0400

    Clean up the output about which GPU we're using

Src/Base/AMReX_CUDA.F90

commit e2f9fd0cd5d0fd7a94554d350bc2c2118a975ca7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri Jul 7 01:28:08 2017 -0700

    Fix Intel Fortran compiler preprocessing of AMReX_REAL.H

Src/Base/AMReX_REAL.H

commit f1bc3ca1596dd109aee1d3267f388f2d1110d8c4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jul 7 03:15:16 2017 -0400

    Add some math functions to amrex_fort_module

Src/Base/AMReX_fort_mod.F90

commit f60b74cc9879490cb173730d2a1825a9782188f9
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jul 6 16:21:51 2017 -0700

    added the ability to averaging face centered data with EB.  Does not pass its test yet.

Src/EBAMRElliptic/AMReX_EBEllipticFort.F90
Src/EBAMRTools/AMReX_EBCoarseAverage.H
Src/EBAMRTools/AMReX_EBCoarseAverage.cpp
Src/EBAMRTools/AMReX_EBFortND.F90
Src/EBAMRTools/AMReX_EBFortND_F.H
Tests/EBAMRTools/README
Tests/EBAMRTools/regression/GNUmakefile
Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp

commit 5a8fbc29a49e15b057e2ae37577e95e7c231a357
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 6 15:43:23 2017 -0700

    fix one-sided MPI

Src/Base/AMReX_FabArray.H

commit 103bcf0cde8c29e89cab42d506941fe978fdc0ef
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jul 6 10:12:52 2017 -0700

    Fix typo in Cmake files.

Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake

commit 9d32f94b125e75f67234e8351dcffca6ebabc060
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jul 6 10:12:52 2017 -0700

    Fix typo in Cmake files.

Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake

commit 1155ebf72b7edb32860fe901eb4862cc5dce6521
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jul 6 07:36:34 2017 -0400

    Use an Arena to store device reducer data

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit fe71a5173edd6a42c3b819f4d8277d45fd3a3fc3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jul 6 06:36:07 2017 -0400

    Add a MFIter reduction operation for Reals

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 630421c06292ed6e8fede222657c5c41d86fa9ae
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jul 6 04:06:28 2017 -0400

    Add a MFIter function to register a RealBox

Src/Amr/AMReX_AmrLevel.cpp
Src/Base/AMReX_MFIter.H

commit bc253977bf347ad274789fecaa982c22d3012d85
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jul 5 15:47:58 2017 -0700

    Just to keep these messages different, I am looking for synonyms for 'slog'.  Trudge?   Schlep?

Src/EBAMRElliptic/AMReX_AMRMultiGrid.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp
Src/EBAMRElliptic/AMReX_EBEllipticFort.F90
Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H
Src/EBAMRElliptic/Make.package
Tests/EBAMRElliptic/exec/GNUmakefile
Tests/EBAMRElliptic/exec/cond.inputs
Tests/EBAMRElliptic/exec/conductivitySolve.cpp

commit f71b74c71c6922baa87ebd40e4428948d6d58c78
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed Jul 5 01:13:17 2017 -0400

    Make the CUDA device ID public

Src/Base/AMReX_CUDA.F90

commit 5f231e7221f43a5c27c713704b3a0f20db80de16
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Jul 4 19:10:00 2017 -0400

    Get F90 build with CUDA working again

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/GPackage.mak

commit e655d4a9ff90e9190c7d4739679a1b0f970c5bf9
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Jul 4 18:36:15 2017 -0400

    Do not compile dim3 without using nvcc

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 5112d1eb055a105a4c6a4c339ef4ac19da62acb4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jul 4 03:18:32 2017 -0400

    Fix the synchronize strategy in ParallelCopy

Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_FabArray.H

commit 94d5605b5a6ff22a0533fdf49e68961251240c09
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jul 4 01:53:24 2017 -0400

    Make StateData::FillBoundary asynchronous

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp

commit c31ccc764e598b094925b4c6245665a357aa44d0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Jul 3 15:45:03 2017 -0700

    Continued the EBAMRElliptic slog.  There is a lot  here.

Src/EBAMRElliptic/AMReX_EBConductivityOp.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRElliptic/AMReX_EBEllipticFort.F90
Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H
Src/EBAMRTools/AMReX_EBLevelDataOps.H
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBArith.cpp

commit f8df87ff2af5d73e0689e355f3868bbc905ec031
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 3 18:34:01 2017 -0400

    Disable FabArrayBase tiling when using CUDA

Src/Base/AMReX_FabArrayBase.cpp

commit 5486da25d003f5c44fc3bcc261d44e33df7a03fe
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 3 17:43:54 2017 -0400

    Use MFIter pointer registration in AmrLevel::Derive

Src/Amr/AMReX_AmrLevel.cpp

commit ed99ef01a179cfe66be66bf4dddb963a68b0edbb
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 3 17:18:25 2017 -0400

    Add MFIter::get_fortran_pointer to assist with scalar values for device routines
    
    There are cases in the code where we pass scalar values like the current time
    to a Fortran kernel, and we pass it by reference. An example is AmrLevel::Derive.
    For backward compatibility we do not want to change the interface -- that would break
    a lot of codes. But we also want to pass a device pointer for the CUDA version, and
    to allow asynchrony across MFIter indices. The solution is to store a shared_ptr with
    a pinned host (or device, but I've gone with pinned host for now to avoid a cudaMemcpy call)
    copy of the data, so that the lifetime of the data is the lifetime of the MFIter.
    For the CPU version of the code, the function effectively does nothing.

Src/Base/AMReX_MFIter.H

commit 010b8ff1f0b3305e7e022d59ef8b3695f172efec
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 3 16:38:55 2017 -0400

    Clean up temporary pointer creation

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_Device.H

commit 282f5cec222d6fa889f02f81dd6ed19131a07ca5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Jul 2 17:07:19 2017 -0700

    Fix the construction of the cost function in makeKnapSack

Src/Base/AMReX_DistributionMapping.cpp

commit d66f8057dd2d3c4c986e73f1ef3a0159424068b4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 3 05:28:07 2017 -0400

    Add hook to start profiler

Tutorials/GPU/HeatEquation_EX1_C/main.cpp

commit 9e7792564cf370817b9e6c293082d2451b08ad8f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 3 05:09:01 2017 -0400

    Avoid use of parallel module in CUDA initialization

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 28cddce212be7ca9098019963e14fb787eb493df
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 3 04:46:06 2017 -0400

    Avoid calls to cudaFree/cudaFreeHost at end of program

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 5d6d86864a73efbe82d678e51df52dd86af5597f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 3 04:03:48 2017 -0400

    Do not throw error for CUDA runtime unloading

Src/Base/AMReX_CUDA.F90

commit 4dd5f01065936020a26c8bec33ecc2206a96a140
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 3 03:37:35 2017 -0400

    Delay initialization of the RealBox device memory
    
    Geometry contains a static RealBox object, and it was creating problems
    that a CUDA API call (to allocate memory) was being called before we
    got to the initialize_cuda step. By delaying allocation of the device
    memory until the first time we actually access the data, we still get
    the desired behavior from RealBox while not breaking the intended
    behavior that no CUDA API calls are done until we've mapped the MPI ranks
    to GPUs.

Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp

commit 4cfab94b8efd870c769554a4f8f3de142df586b7
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 3 01:59:38 2017 -0400

    Enable round-robin assignment of MPI ranks to GPUs

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 9d9191ba0d3043f83b1913d1b8b305663e084c1e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 3 01:59:14 2017 -0400

    Use nvcc as the MPI host compiler

Tools/GNUMake/sites/Make.olcf

commit bdcc57c67a3ff16e45e6a42396dfc0412f844f6d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jul 3 01:58:43 2017 -0400

    Define a host compiler variable

Tools/GNUMake/comps/ibm.mak
Tools/GNUMake/comps/pgi.mak

commit 41e091eb86ce558cceaf983a79fcb52b38e6ea64
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jul 2 21:14:14 2017 -0400

    Add NVML build support

Tools/GNUMake/Make.defs
Tools/GNUMake/sites/Make.olcf

commit 402845a474d71b0dc71d96fd8411bd27411b4475
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Jul 2 17:07:19 2017 -0700

    Fix the construction of the cost function in makeKnapSack

Src/Base/AMReX_DistributionMapping.cpp

commit e2ddb568d4a141464dd1845c13c1d982b82794d9
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jul 2 17:59:28 2017 -0400

    Port more BaseFab routines to the GPU

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit a5733db482c59bdd2eeeded48f529a30042f9a63
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jul 2 16:36:17 2017 -0400

    Add function to get threads and blocks in C++

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 23da7b926a347f9f31d7370ed45ecb6c3dbcafca
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jul 2 16:35:56 2017 -0400

    Remove the CUDA compiler

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/cuda.mak

commit 70e4805d195fadc7f756e3642e5ce71115de498d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jul 2 16:33:33 2017 -0400

    Use nvcc/g++ as C/C++ compiler when using CUDA with IBM

Tools/GNUMake/comps/ibm.mak

commit 7017151f3dcd824f455ce97390a34fd8a40fca4d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jul 2 13:56:15 2017 -0400

    Use nvcc/g++ as C/C++ compiler when using CUDA with PGI

Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/pgi.mak

commit 4ffdac87df294a2152dd72654a366f5abd75ff39
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jul 2 13:50:04 2017 -0400

    Use the new dx call in advance

Tutorials/GPU/HeatEquation_EX1_C/advance.cpp

commit d5942652745d3f154c9ab755ea6b702c026a5fbe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 2 08:47:47 2017 -0700

    avoid self-move

Src/Particle/AMReX_ParticleContainerI.H

commit 489b30dd72f44ab5ef140bbde6f0121e2cd69c88
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jul 2 05:12:32 2017 -0400

    Use pinned data for RealBox and CoordSys

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp

commit 3f37361285e09a0385d697abf6e6ff5d8e1e87fc
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jul 2 05:11:48 2017 -0400

    Make get_host_pointer a no-op for non-CUDA builds

Src/Base/AMReX_Device.cpp

commit 6935925bff74344e7b6d16b616b9515eca613047
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jul 2 03:50:49 2017 -0400

    Insert a device synchronize after MultiFab creation

Src/Base/AMReX_FabArray.H

commit b2264768035b9bd2029e390481ec6cd2fca49426
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 1 07:45:02 2017 -0400

    Get FillDomainBoundary working on the GPU

Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F90
Src/Base/AMReX_filcc_mod.F90

commit 2e4eec0d6221c02c88d6d6cc222a38020e1778c0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 1 07:29:07 2017 -0400

    Fix error in the BaseFab arenas

Src/Base/AMReX_BaseFab.cpp

commit 9192d5f7301d3e0a2abc66b0d7225b1291c0a314
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 1 07:20:23 2017 -0400

    Make some some arguments const

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 7eb20c26eb92c52fa07de7bae74a203a8799991a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 1 05:20:04 2017 -0400

    Port the 1D and 2D filcc to GPU-friendly versions

Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90

commit 5faa9223b2c34fc02f6f3992d01d400eab842cff
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 1 04:09:40 2017 -0400

    Complete GPU-friendly port of 3D filcc

Src/Base/AMReX_FILCC_3D.F90

commit bdae016df0e7ed1de63eedec5b2f04758caa6847
Merge: 5d5adbb6f ae5bba0f5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 1 00:52:08 2017 -0400

    Merge branch 'gpu' into gpu_lessmanaged

commit ae5bba0f5cd6d1596d3d6ee09cfedd69aaef9940
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jul 1 00:51:27 2017 -0400

    Use a new thread block layout

Src/Base/AMReX_CUDA.F90

commit 38073b46d734547aa52f9d5e33577d7cbd288583
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jun 30 15:44:13 2017 -0700

    the slog continues

Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H
Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRElliptic/AMReX_EBEllipticFort.F90
Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H
Src/EBAMRElliptic/AMReX_VCAggStencil.H
Src/EBAMRElliptic/AMReX_VCAggStencil.cpp
Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBArith.cpp
Tests/EBAMRTools/regression/GNUmakefile
Tests/EBAMRTools/regression/aggpwlfpTest.cpp
Tests/EBAMRTools/regression/simpleMeshRefine.cpp

commit 0441a7a7b4459c6fd758c225232e54ae0ba301a0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 30 15:35:49 2017 -0700

    Have the test suite also send an email if it has to abort for whatever reason (if emails are turned on...)

Tools/RegressionTesting/params.py
Tools/RegressionTesting/test_util.py

commit ecedcbc9ed0b4b5ef1776d144e9dde03a34ec59d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 30 15:03:01 2017 -0700

    option to turn off checkInput()

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit ea023eb640ede33b00c912f689f1d9ccb6f112a1
Merge: 79153d30b c86200557
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 30 12:23:07 2017 -0700

    Merge branch 'master' into development
    
    Conflicts:
            Tools/CMake/PreprocessAMReXFortran90.cmake

commit 79153d30bda597c06628c431839e819ea8801bd4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jun 30 09:44:23 2017 -0700

    Fix the sizing and offset of mf_to_be_filled in AssignDensityFort.

Src/Particle/AMReX_ParticleContainerI.H

commit 3d88f58fd35891655f08f7ab8f3570c4eec9d91d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 29 23:00:29 2017 -0700

    fix momentum deposition for Nyx.

Src/Particle/AMReX_Particle_mod_3d.F90

commit d754f3d7aa7de087861a65fd939cc2a7b0f63dee
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 29 22:58:49 2017 -0700

    don't need my own plot file routine for this test.

Tests/Particles/AssignDensity/main.cpp

commit 5d5adbb6fb0c01755f066a51cbfcea64f9a0f1ce
Merge: 09ee3bc4f db80a1a43
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jun 30 01:47:28 2017 -0400

    Merge branch 'gpu' into gpu_lessmanaged

commit 09ee3bc4fcacae9c89c1f4c82b8aa6de8c1bda57
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jun 30 01:43:56 2017 -0400

    Remove managed memory in Box class

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp

commit db80a1a43045c26882fd96f150f8f5d01488ed49
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri Jun 30 01:14:22 2017 -0400

    Fix the obsolete macros

Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90

commit 0aca9e5e419aaf707520dcb943d51c8c047e3b4a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jun 30 01:09:54 2017 -0400

    Add some forgotten files to the heat equation case

Tutorials/GPU/HeatEquation_EX1_C/advance.cpp
Tutorials/GPU/HeatEquation_EX1_C/myfunc.H
Tutorials/GPU/HeatEquation_EX1_C/physbc.cpp

commit 43856da0ad863b52f560b57e93bd61155a98e54d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jun 30 01:00:52 2017 -0400

    Set the null stream as the default stream

Src/Base/AMReX_CUDA.F90

commit 72397fcc1ff73e7a5626989d7d57f4d70acb1c30
Merge: 9b8bd5e90 afd51fb2c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jun 30 00:58:12 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit f496f22e98a8ca3d92913360abd3ec844042fb7f
Merge: d5c6d1b63 232da02dd
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 29 17:27:16 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit d5c6d1b630dfe9ee3f5cd107287bb26b9e0ef426
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 29 17:27:12 2017 -0700

    fixes for 1d slicing.

Src/Extern/amrdata/AMReX_DataServices.cpp

commit 232da02dd7ee903b5d809743a40344347b5046d2
Merge: 615cd94e2 5ab90a41f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 29 17:26:14 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 615cd94e2ebafcd0d84c909d8a2405ad069c322d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 29 17:25:57 2017 -0700

    Make eps an optional argument instead of a static member of RealBox.

Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp

commit 5ab90a41f8495085975d04d2a8ebb817d1b73799
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 29 16:39:02 2017 -0700

    Add some checking of input parameters -- the tests here are a subset
    of the tests that Amr.cpp does.

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit c6a065498ae7c9106acabfad2cab110db4273b5d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 29 16:38:49 2017 -0700

    Fix the error messages

Src/Amr/AMReX_Amr.cpp

commit a3c4bb7d7e22ec2302a3a0f3543e2623aada515e
Merge: 456c37688 ebc701840
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 29 12:52:42 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 456c3768867272bfa7b7c70597c86ffdc19db17f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 29 12:50:05 2017 -0700

    Update how grids are created (section 5.3.5)

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex

commit ebc701840d2a94537bf7df92dc2e9c4ce5405be9
Merge: 01d058330 8696d1b3e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 29 12:37:37 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 01d05833066cf1209fcb2ef5858bc6b9ff26f478
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 29 12:37:24 2017 -0700

    Some Cmake clean-up

CMakeLists.txt
Tools/CMake/TransformVersion.cmake

commit afd51fb2c243fcdce2fa29cd1c5f584f677fd970
Merge: dc35e9b28 8696d1b3e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 29 04:44:04 2017 -0400

    Merge branch 'development' into gpu

commit 8696d1b3e53af8bc935e71c8053036c3fdce5035
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 28 17:31:57 2017 -0700

    fix amrex_particle_real for typecheck

Tools/GNUMake/Make.rules

commit 247574b6590b96287306f75645a3d40968ad5b17
Merge: cfc4d5f7b 0ca8d80d9
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 28 17:11:57 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit cfc4d5f7b47fdcb4bea6ed1a6321e68484aae070
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 28 17:11:42 2017 -0700

    added to the profiling and visualization documentation.

Docs/AMReXUsersGuide/Profiling/Profiling.tex
Docs/AMReXUsersGuide/Visualization/Visualization.tex

commit 0ca8d80d9ac422c9e9036a964bcae1c1b83507c7
Merge: 4a7597617 1115ee894
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jun 28 16:55:17 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 4a75976175a060c7503f0d9f98240c2aae829381
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jun 28 16:54:44 2017 -0700

    Update the Grid Creation subsection.

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex

commit e578f94691799e6b8370acf5449eecfdfafe35db
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jun 28 16:54:33 2017 -0700

    fix typo in comment

Src/AmrCore/AMReX_AmrMesh.cpp

commit 1115ee8945fe22c05fd28d12a9fdbb5a50d8e433
Merge: 8b8b39e77 a7ab67e2c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 28 16:29:22 2017 -0700

    Merge branch 'mr-cmake' into development

commit a7ab67e2cd4115faf8cc56f21677572f8c1ab069
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 28 16:28:37 2017 -0700

    Update documentation on cmake

Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex

commit 550972afaac237dc26f1e0d5f5b5a3c3f45930b8
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 28 15:52:00 2017 -0700

    Add new pre-preprocessor flags to cmake implementation

Tools/CMake/AMReX_Config.cmake

commit e5dec5966738a17e52f231e052ba0250b31a04f3
Merge: 3c88bb047 9e591871e
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 28 15:34:44 2017 -0700

    Merge branch 'development' into mr-cmake

commit 8b8b39e7796232d7b2aac1e7f9776400ad0ec89a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 28 15:28:59 2017 -0700

    User's Guide: wip

Docs/AMReXUsersGuide/Debugging/Debugging.tex

commit 7c472ae911762f4341a9c681d56fe7beaaa83e26
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 28 15:22:46 2017 -0700

    update deprecated gfortran option

Tools/GNUMake/comps/gnu.mak

commit 3c88bb047c6633f041434e33ef4f769e2a2713eb
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 28 14:57:44 2017 -0700

    Some clean-up

Tools/CMake/InstallManager.cmake

commit 786958cf7d9d4ec5e1ffbdf9c46161b21606d418
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 28 13:29:04 2017 -0700

    Fix typo

CMakeLists.txt

commit e51728ed19fd87a820b565dfd1b13c517d9ca4f7
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 28 13:03:22 2017 -0700

    More changes to cmake system

CMakeLists.txt
Src/Amr/CMakeLists.txt
Src/AmrCore/CMakeLists.txt
Src/Base/CMakeLists.txt
Src/Boundary/CMakeLists.txt
Src/Extern/amrdata/CMakeLists.txt
Src/F_BaseLib/CMakeLists.txt
Src/LinearSolvers/C_CellMG/CMakeLists.txt
Src/LinearSolvers/C_CellMG4/CMakeLists.txt
Src/LinearSolvers/C_TensorMG/CMakeLists.txt
Src/LinearSolvers/C_to_F_MG/CMakeLists.txt
Src/LinearSolvers/F_MG/CMakeLists.txt
Src/Particle/CMakeLists.txt
Tools/CMake/AMReXConfig.cmake.in
Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_Utils.cmake
Tools/CMake/InstallManager.cmake

commit 9e591871ecc4555469433e4ec9955d1fb14abdd8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jun 28 10:02:29 2017 -0700

    switch order of these loops.

Src/Particle/AMReX_OMPDepositionHelper_1d.F90
Src/Particle/AMReX_OMPDepositionHelper_2d.F90
Src/Particle/AMReX_OMPDepositionHelper_3d.F90

commit 98a3e56f6025c90710f2289923afbb7f83ccac3f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jun 28 09:27:20 2017 -0700

    Resolve amrex namespace problems.

Src/Extern/hpgmg/BL_HPGMG.H
Src/Extern/hpgmg/BL_HPGMG.cpp

commit 3b310d13e3fe3e97e63e2886bc9ecd02eae6109a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 27 18:10:42 2017 -0700

    Make sure to resize the local fab to be tile_size*ncomp (to allow for ncomp > 1)

Src/Particle/AMReX_ParticleContainerI.H

commit b11da912796adf3e2311ca5316278ee7315b7fc3
Merge: 814538ec5 0bb538de1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 27 17:44:37 2017 -0700

    merging

commit 814538ec531d5395effa499e37dc0ce52ebbe77b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 27 17:43:35 2017 -0700

    Forgot to turn off ncomp check here.

Src/Particle/AMReX_ParticleContainerI.H

commit 0bb538de18e73c41b53bc4e1a8be1a06624232ca
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 27 17:43:11 2017 -0700

    1) Fix incorrect print statement
    2) Remove assertion on (ncomp == 1) in AssignDensityFort since we now correctly take ncomp > 1 cases.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H

commit a85084617cd5c73aec11009dcce39a08f4dd5785
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 27 16:57:27 2017 -0700

    Fix initialization of nthreads -- move it into InitRandom

Src/Base/AMReX_Utility.cpp

commit 4f09beb593fd62c373f72205f68520598add716e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 27 16:41:15 2017 -0700

    generalize fortran deposition routines to use ncomps.

Src/Particle/AMReX_OMPDepositionHelper_1d.F90
Src/Particle/AMReX_OMPDepositionHelper_2d.F90
Src/Particle/AMReX_OMPDepositionHelper_3d.F90
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particle_mod_1d.F90
Src/Particle/AMReX_Particle_mod_2d.F90
Src/Particle/AMReX_Particle_mod_3d.F90
Src/Particle/AMReX_Particles_F.H

commit 4c789f63fe7f63edb196f0aab1e12515b711e39a
Merge: fa21635cd 99603c558
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 27 16:00:16 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit fa21635cd38d307e252b3abc6467a4703ff0535c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 27 16:00:01 2017 -0700

    Added run-time parameters and an explanation of how grids are created

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex

commit 99603c558ff47362f9f7e5481ca037a3eff2fc81
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 27 15:25:13 2017 -0700

    updates to doc

Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex
Docs/AMReXUsersGuide/Introduction/Introduction.tex

commit df8a80c977f191902d0f8a311f9f2bb8cd4973e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 27 10:14:16 2017 -0700

    User's Guide: octree

Docs/AMReXUsersGuide/Fortran/Fortran.tex

commit 4ba990a7a5d91af69138365c61b9b2dcd08d804b
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Jun 27 08:58:35 2017 -0700

    Add source file for tiny profiling

Src/Base/CMakeLists.txt

commit 7c9415eae07538212b996b123e28188dcb444cec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 27 06:33:29 2017 -0700

    remove old license

Src/Base/OpenSource.txt

commit 55fd11d0ca138d92a1b94b03989de024db21d487
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 27 06:28:08 2017 -0700

    fix tutorials

Tutorials/Amr/Advection_F/Source/my_amr_mod.F90
Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90

commit 9b8bd5e90b0911db404cafe9f9c5627f16224917
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 26 23:51:58 2017 -0400

    Start the profiler at the end of Amr initialization

Src/Amr/AMReX_Amr.cpp

commit d0af2865040b0d15d8d3704958deeba913b9d279
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 26 23:46:11 2017 -0400

    Add C++ hooks to start and stop the profiler

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit cadf29a89d13eb2d39b0a5ae1b0834d0b4e6e894
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 26 18:05:24 2017 -0700

    User's Guide: AMR in Fortran interface

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Docs/AMReXUsersGuide/Fortran/Fortran.tex
Docs/AMReXUsersGuide/GNUmakefile

commit 8c867b1d67d65a02006e359a2115f4f4a34878cb
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jun 26 17:40:13 2017 -0700

    Add option for tiny profiling

Tools/CMake/AMReX_Config.cmake

commit 5763df03a787f543bd8e11d14ebcacc7397a4f29
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 26 16:46:53 2017 -0700

    F_Interfaces: fix component index bug

Docs/AMReXUsersGuide/Fortran/Fortran.tex
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit ebc2e4f15a974b3e824b04cba8eed85f9f2c4e3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 26 14:18:58 2017 -0700

    User's Guide: Fortran interface basics

Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/Fortran/Fortran.tex
Tutorials/Basic/HeatEquation_EX1_F/advance.f90

commit 8b55b4bedb74fc8d9d93974d5617b3c17d53a4ad
Merge: 61c9d955f f55be70bf
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Mon Jun 26 15:14:10 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f55be70bfdd5f33ef7fecf0c6d5e6c9fa0cc3af1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 26 12:40:26 2017 -0700

    F_interfaces: fix bug in setval and parallelcopy; note that the component index starts with 1 in Fortran

Src/Base/AMReX_fort_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 61c9d955fa08d5f0387c2fcee037868f8609db90
Merge: dd6e4360b e2abf3f8e
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Mon Jun 26 11:26:44 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit dc35e9b2837ff419e4d68e290e84d2f1e8563653
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 26 05:05:51 2017 -0400

    fix linking with IBM XL and CUDA

Tools/GNUMake/comps/ibm.mak
Tools/GNUMake/sites/Make.olcf

commit 68952a5265ce175479f181507044bdaed16ed38d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 26 03:06:51 2017 -0400

    Skip finalization routine if using XL

Src/Base/AMReX_parmparse_mod.F90

commit 2e5f43273d5165ae8206826753a06ed4a608e8f5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 26 02:52:34 2017 -0400

    Remove CUF kernels; these should be replaced with real CUDA later

Src/Base/AMReX_BaseFab_nd.F90

commit 463a3a4f72775ca00eaf64aa013267e9283411ec
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 26 02:48:24 2017 -0400

    Replace logical with integer to satisfy bind(c) property

Src/Base/AMReX_CUDA.F90

commit 3973c3bff8f7e3c4358e1bc27d045da1bc2141cb
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 26 02:41:19 2017 -0400

    Create interface to cudaProfilerStart/cudaProfilerStop

Src/Base/AMReX_CUDA.F90

commit 1fcb19e22cdfb6614c82f0807cbf224cab68edd2
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 26 02:30:09 2017 -0400

    Use thread-safe XL compiler when using CUDA

Tools/GNUMake/comps/ibm.mak

commit ce35354fa6c5f8ff529f067866bb9656c912cb3b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 26 01:40:24 2017 -0400

    Redefine the CUDA attributes(global/device) macros

Tools/GNUMake/Make.defs

commit 17ffe789826d0f3685755d7fa8dce2efe61a4e33
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 26 01:09:13 2017 -0400

    Create device copies of data in AmrLevel::derive

Src/Amr/AMReX_AmrLevel.cpp

commit 2cd7e86550eab1c1f532ace078b8995f80104ea3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 26 00:27:39 2017 -0400

    Create device copies of data in FillBoundary

Src/Amr/AMReX_StateData.cpp

commit dfdeb01f14489a453e5012d8ece676c8d422ec1c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 25 17:21:39 2017 -0400

    Add Device hook for stream synchronize

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit e2abf3f8e2cbb14a2aaaf44e15a77b1133b66a5a
Author: atmyers <atmyers2@gmail.com>
Date:   Sun Jun 25 11:33:03 2017 -0700

    don't need to define partMF in this test anymore.

Tests/Particles/AssignMultiLevelDensity/main.cpp

commit 2496146ee560c0e196c5919d8d1d55ed7b82a554
Author: atmyers <atmyers2@gmail.com>
Date:   Sun Jun 25 11:30:46 2017 -0700

    make behavior of AssignDensityFort consistent with AssignDensity in that the mfs don't need to be defined before being passed in.

Src/Particle/AMReX_ParticleContainerI.H

commit b109461da16346cb6f1a07cc51e2c9de5837220e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 25 06:01:40 2017 -0400

    Have registerBox return the box

Src/Base/AMReX_MFIter.H

commit 896b2c7de8ccdac6b8a83971089a4448ec159f1c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 25 05:11:02 2017 -0400

    Add Device hooks for malloc, free, memcpy

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit c4f048ffdcb29d1e16b1985c3999184ec76352a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 24 22:09:06 2017 -0700

    F_Interfaces: add amrex_multifab%parallel_copy

Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 1dd25ae16d681a6f136fa8406672a1aaedde58e5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 24 21:19:08 2017 -0400

    Use long x-blocks for coalesced memory access

Src/Base/AMReX_CUDA.F90

commit 732be31ad965d38d16251926676328e2187786be
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jun 24 16:57:16 2017 -0700

    Remove all references to STATIONDATA, SLABSTAT or MAKESLICE
    in AMReX_Amr* or Make.package or CMakelists.txt

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/CMakeLists.txt
Src/Amr/Make.package

commit aeb8df3acd9e76d7f3f7cf2b19293c6408cda379
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jun 24 16:53:27 2017 -0700

    None of the applications use MAKESLIDE_3D any more (and it can always be recovered
        from git history and/or the old BoxLib repo)

Src/Amr/AMReX_MAKESLICE_3D.F
Src/Amr/AMReX_MAKESLICE_F.H

commit 9fdd37e2a9b03e2cf1ed23c55a454baaff6067ec
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jun 24 16:52:17 2017 -0700

    None of the applications use SlabStat any more (and it can always be recovered
        from git history and/or the old BoxLib repo)

Src/Amr/AMReX_SLABSTAT_1D.F
Src/Amr/AMReX_SLABSTAT_2D.F
Src/Amr/AMReX_SLABSTAT_3D.F
Src/Amr/AMReX_SLABSTAT_F.H
Src/Amr/AMReX_SlabStat.H
Src/Amr/AMReX_SlabStat.cpp

commit 814b8242225c7dccc0d81d5ac9a49e1d362e59db
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jun 24 16:49:49 2017 -0700

    None of the applications use StationData any more (and it can always be recovered
    from git history and/or the old BoxLib repo)

Src/Amr/AMReX_StationData.H
Src/Amr/AMReX_StationData.cpp

commit fe4de436ba9ef6463043fbd5408c70c3e2e4e9c7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jun 24 16:47:52 2017 -0700

    Update the Profiling section and spell-check the entire document.

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex
Docs/AMReXUsersGuide/Fortran/Fortran.tex
Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex
Docs/AMReXUsersGuide/Particle/Particle.tex
Docs/AMReXUsersGuide/Profiling/Profiling.tex
Docs/AMReXUsersGuide/Visualization/Visualization.tex

commit 67a5ce31f1c2d46d2bb0933b08ff2480f7595ba7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jun 24 16:31:45 2017 -0700

    Add material from Readme.profiling -- but this still needs Vince to make a pass.

Docs/AMReXUsersGuide/Profiling/Profiling.tex

commit cc2a94927e841b873af7f8c4f90f6f558a11f40f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 24 18:07:12 2017 -0400

    Sync up HeatEquation with development
    
    The filcc call had to be modified temporarily until we get the
    BCs working on the GPU.

Src/Base/AMReX_BCUtil.cpp
Tutorials/GPU/HeatEquation_EX1_C/Make.package
Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/inputs_2d
Tutorials/GPU/HeatEquation_EX1_C/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H

commit 9043be6156adcdd9ab75f91103aa6d21f5fbba72
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 24 17:35:33 2017 -0400

    Create a device pointer for a FAB's nvar

Src/Base/AMReX_Arena.H
Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp

commit 85ebfd03b27b0c9f2810d28f3959aa42a9fd3860
Merge: dd6e4360b 798a23f1b
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Sat Jun 24 16:15:19 2017 -0500

    Merge branch 'development' into kw-development

commit 637f96c9ccb212c931dd1fa146fbab9894da2334
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 24 17:04:05 2017 -0400

    Set blocks and threads before entering Fortran

Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_StateData.cpp
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_nd.F90
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit da0a5391b4ac1f9ec330112e5147d5bbf334b2f3
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 24 16:24:51 2017 -0400

    Create a current CUDA stream variable

Src/Base/AMReX_BaseFab_nd.F90
Src/Base/AMReX_CUDA.F90

commit 798a23f1b9944fe07387e406ba90de046ce94c5d
Merge: 142b1d40a 0c4a25ff5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Jun 24 12:56:46 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 142b1d40ab51cc79cfad9c489768671da0809f8b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Jun 24 12:56:24 2017 -0700

    A version of the electrostatic pic tutorial that works in 2D.

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H
Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp
Tutorials/Particles/ElectrostaticPIC/GNUmakefile
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_2d.f90
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H
Tutorials/Particles/ElectrostaticPIC/inputs
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit 002721675fa5b3612dea66bec74b543cf007df52
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 24 12:57:51 2017 -0400

    Clarify intent of dm

Src/F_BaseLib/knapsack.f90

commit 6cfd3a24d614cae9e76c323be158a97ead0346e9
Merge: 074362db1 3b9a83664
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 24 09:55:55 2017 -0700

    Merge pull request #47 from dwillcox/gpu
    
    Workaround for AMReX Issue 46

commit 074362db10bb23b2c4cfcb1624d3b860d4109408
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 24 03:08:09 2017 -0400

    Lower the optimization level when using CUDA

Tools/GNUMake/comps/pgi.mak

commit e58e2d4f8917472d1d0a32b46a4bf5dc6d004084
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 24 01:43:39 2017 -0400

    Do not set default stream, to avoid compiler bug

Src/Base/AMReX_CUDA.F90

commit 3b9a83664ec612ddd61c8242d734af61aeb62e73
Merge: 6b967d0f4 f48070b78
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Sat Jun 24 00:54:07 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 6b967d0f42e3d6071a5fa6a65b9cf09e368006a2
Author: dwillcox <eugene.willcox@gmail.com>
Date:   Sat Jun 24 00:53:25 2017 -0400

    Pass dm to function make_box_key as workaround for suspected PGI 17.4 bug.

Src/F_BaseLib/knapsack.f90

commit f48070b78c9c09716a8ea65ef30ae51d7f05ba62
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jun 23 23:15:15 2017 -0400

    Initialize with NULL value for non-CUDA

Src/Base/AMReX_Device.cpp

commit 7bfff2613f28bf43beb239889d90d078e6c69dcc
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jun 23 23:14:09 2017 -0400

    Remove unnecessary CUDA ifdef

Src/Base/AMReX_Device.cpp

commit 297f2d35e96e033f892269cd167e2ff13362a972
Merge: 007719d19 0c4a25ff5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Fri Jun 23 23:10:48 2017 -0400

    Merge branch 'development' into gpu

commit 0c4a25ff5c794939c7ab1befd2b132daa561f59a
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jun 23 18:48:22 2017 -0700

    updates to Amr source doc

Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex

commit 17bc75c1aa2d06dd6085fac333bbacb8e5a40e2f
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jun 23 18:04:14 2017 -0700

    Downgrade cmake minimum required version to 3.3

CMakeLists.txt

commit 87de2655f18183bfd58a4e2479ec7375c88c2795
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jun 23 15:07:05 2017 -0700

    note on running particles in Advection_AmrLevel

Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex

commit 84bfb385d8f481b4746be819c8eb7e3297c7b260
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jun 23 15:02:04 2017 -0700

    particle stuff in Advection_AmrLevel

Src/Amr/AMReX_AmrLevel.H
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/inputs

commit ca8b2d30c19b3c37404aa03eebe1b4b77047728a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jun 23 13:52:35 2017 -0700

    fixed a broken test.  now all the EBAMRTools tests also run in parallel

Tests/EBAMRTools/regression/ebFineInterpTest.cpp
Tests/EBAMRTools/regression/runalltests.mpi.sh

commit 9efec27a4fd07891d866a044a9f7d7c86ecb8594
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jun 23 13:16:36 2017 -0700

    Fix bugs in new cmake implementation

Src/AmrCore/CMakeLists.txt
Src/Particle/CMakeLists.txt
Tools/CMake/FindCCSE.cmake

commit dd6e4360b037f9e6284af8d2ae8b985121ad6f39
Merge: c62cab7fb 4de9874ca
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Fri Jun 23 14:31:06 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4de9874ca28b16592cf394ac1cab19ff4f57d612
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jun 23 11:55:40 2017 -0700

    various small cleanups to tutorial code

Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/probin
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/tagging_params.f90

commit 59006ca0794d8340e1c775d13b22785d481c300d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jun 23 11:19:36 2017 -0700

    Comment out 'Find Perl' code

Tools/CMake/FindCCSE.cmake

commit 029be9937c2ab6e255f5703485ea8e8b5b41afdb
Merge: cdbb70905 f1ea38539
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jun 23 10:26:12 2017 -0700

    Merge pull request #45 from AMReX-Codes/dtg_branch
    
    Push parallel fixes to development.

commit c62cab7fbedb35679fce45294c362f38dd1aa889
Merge: 3c83c7d20 cdbb70905
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Fri Jun 23 11:56:14 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f1ea385394dad42075be12d0ae5d650bfbef6f0c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jun 23 09:32:22 2017 -0700

    All EB tests now work in parallel, including I/O.

Src/Base/AMReX_SPMD.H
Src/Base/AMReX_SPMDI.H
Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Tests/GeometryShop/regression/ebio.2.inputs
Tests/GeometryShop/regression/ebio.cpp
Tests/GeometryShop/regression/runalltests.mpi.sh

commit cdbb70905b5d34d34b6e343b5582f34e9b23d9a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 23 06:47:24 2017 -0700

    remove ifdef USE_PARTICLES around function declarations

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles_F.H

commit 5670d4e368b9e4e0836736a370aed9aa96b3d9db
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jun 22 18:19:56 2017 -0700

    Remove old BoxLib docs.  You can find the tex in the BoxLib repo if you need it (or in the git history here)

Docs/BoxLibUsersGuide/C_AdvancedTopics/C_AdvancedTopics.tex
Docs/BoxLibUsersGuide/F_AdvancedTopics/F_AdvancedTopics.tex
Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example1.eps
Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example1.fig
Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example2.eps
Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example2.fig
Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example3.eps
Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example3.fig
Docs/BoxLibUsersGuide/F_AdvancedTopics/subcycling_algorithm.eps
Docs/BoxLibUsersGuide/GNUmakefile
Docs/BoxLibUsersGuide/GettingStarted/GettingStarted.tex
Docs/BoxLibUsersGuide/GettingStarted/VisIt_2D.eps
Docs/BoxLibUsersGuide/GettingStarted/VisIt_3D.eps
Docs/BoxLibUsersGuide/GettingStarted/edison.run
Docs/BoxLibUsersGuide/GettingStarted/edison_omp.run
Docs/BoxLibUsersGuide/Introduction/AMR.eps
Docs/BoxLibUsersGuide/Introduction/Introduction.tex
Docs/BoxLibUsersGuide/Introduction/boxlib_directory_bw2.eps
Docs/BoxLibUsersGuide/Introduction/castro_scaling.eps
Docs/BoxLibUsersGuide/Introduction/data_loc.odg
Docs/BoxLibUsersGuide/Introduction/data_loc2.eps
Docs/BoxLibUsersGuide/Introduction/index_grid.odg
Docs/BoxLibUsersGuide/Introduction/index_grid2.eps
Docs/BoxLibUsersGuide/Introduction/lmc_scaling.eps
Docs/BoxLibUsersGuide/Introduction/maestro_scaling.eps
Docs/BoxLibUsersGuide/Introduction/varden1.eps.REMOVED.git-id
Docs/BoxLibUsersGuide/Introduction/varden2.eps.REMOVED.git-id
Docs/BoxLibUsersGuide/Introduction/varden3.eps.REMOVED.git-id
Docs/BoxLibUsersGuide/Introduction/varden4.eps.REMOVED.git-id
Docs/BoxLibUsersGuide/LinearSolvers/LinearSolvers.tex
Docs/BoxLibUsersGuide/Preface/Preface.tex
Docs/BoxLibUsersGuide/README
Docs/BoxLibUsersGuide/Regression/test_suite.tex
Docs/BoxLibUsersGuide/Regression/testsuite.eps
Docs/BoxLibUsersGuide/UsersGuide.tex

commit a106491ec30ca57e6ab3ff9ff9a5dcb125dcc395
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jun 22 18:04:39 2017 -0700

    more doc work

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex

commit 6ddf6afba1f88f620673f0be6dc792841c9e2d57
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jun 22 17:43:12 2017 -0700

    docs update

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex
Docs/AMReXUsersGuide/AmrLevel/figs/flowchart.odg
Docs/AMReXUsersGuide/AmrLevel/figs/flowchart.pdf
Tutorials/Amr/Advection_AmrCore/Exec/Make.Adv
Tutorials/Amr/Advection_AmrLevel/Exec/Make.Adv

commit 5399420b861636340fd0eaaccf221c3d3d970a6a
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 22 16:40:23 2017 -0700

    Start eb fortran work by copying the test code for inf norm.  Also, build face aperatures and eb geom info in a form suitable for passing to fortran.

Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/umapTest.cpp
Tests/GeometryShop/vofStructures/umapTest_nd.f90

commit 1896b077308726d3898a759002133040bfe95bb4
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jun 22 16:32:52 2017 -0700

    make AmrLevel::thePlotFileType() and AmrLevel::okToContinue virtual (and not pure virtual)
    
    removed overriding functions from tutorial

Src/Amr/AMReX_AmrLevel.H
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit 43eac5cc24fb0e9678487d8c555ecb6650a93377
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 22 16:26:14 2017 -0700

    Disable c++11 gnu extensions

CMakeLists.txt

commit 5b56f85f01b792df59ef3ed5f8ecaf8bccf44c1c
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 22 16:14:13 2017 -0700

    Fix some bugs with new cmake

CMakeLists.txt
Src/Base/CMakeLists.txt
Src/CMakeLists.txt
Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Utils.cmake

commit 110516c2dc0c02ba956763a2e355498752488811
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jun 22 16:13:04 2017 -0700

    AmrLevel::writePlotFile is no longer pure virtual (it is simply virtual with a default implementation)
    
    change the Advection_AmrLevel tutorial to call the default implementation.

Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit de4352bb221c9a969660538d46cc23912a69eb72
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 22 15:51:10 2017 -0700

    Create eb data structrues in order to facilitate building lapl op, for example.

Tests/GeometryShop/vofStructures/umapTest.cpp

commit 2e49665f47a079af81baf3efde63a77e520d30a6
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 22 15:50:21 2017 -0700

    Comment out unused variables in BaseUmap.H

Src/Base/AMReX_BaseUmap.H

commit 5ada997ad4a2b3fd1cf14ebbb63190e8e1fb0a76
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 22 14:59:15 2017 -0700

    Move some utility functions in AMReX_Utils.cmake

Src/CMakeLists.txt
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Utils.cmake
Tools/CMake/PreprocessAMReXFortran.cmake

commit 374f524a971252e8113bc5c73c79f4c332891a1f
Merge: 7c8dd3cb6 1e2d71c6e
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 22 13:29:54 2017 -0700

    Merge branch 'rgrout/sparse_fab' into vof-work

commit 7c8dd3cb6c8a7c5256742e214d59746f4ee26400
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 22 13:28:45 2017 -0700

    WIP: nothing interesting

Tests/GeometryShop/vofStructures/umapTest.cpp

commit 06c25fca883cdb203df5d5602600bf915be5e07c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 22 13:03:08 2017 -0700

    do domain decomposition by default.

Tutorials/Particles/ElectrostaticPIC/inputs
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit 0aeda4d83c1564f9c79f4f4456b4863573569aa3
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 22 12:44:32 2017 -0700

    Re-organize CMake structure

CMakeLists.txt
Src/CMakeLists.txt
Tools/CMake/AMReX_CMakeVariables.cmake
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake
Tools/CMake/AMReX_Utils.cmake

commit 1e2d71c6e071b00ec45632790eb328c6142d440f
Merge: ec39f28d4 98103684f
Author: Grout <ray.grout@nrel.gov>
Date:   Thu Jun 22 11:18:18 2017 -0600

    Merge branch 'rgrout/sparse_fab' of github.com:AMReX-Codes/amrex into rgrout/sparse_fab

commit ec39f28d44bfb15ce3df6a8ac7ea0e1c2d7e8eb1
Author: Grout <ray.grout@nrel.gov>
Date:   Thu Jun 22 11:17:55 2017 -0600

    Stripped allocation check that did not make sense with new object

Src/Base/AMReX_BaseUmap.H

commit 484da6a088ed93a8d63e78a5b1ecd19a2715b602
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 22 10:01:24 2017 -0700

    removing some more unused variables.

Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit 2a3f318178f7dadded12a65b56288f500f6041ee
Merge: 805bfeb92 b06249277
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 22 09:53:30 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 805bfeb92ffde7696321b4121c27732130e0efa1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 22 09:52:54 2017 -0700

    remove some more no-longer-needed temporaries.

Tutorials/Particles/ElectrostaticPIC/main.cpp

commit 55d3f8999a3fe72d7c5c8d2d7457aac53f9f31c8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 22 09:51:57 2017 -0700

    remove tmp_phi, which is not actually used anymore.

Tutorials/Particles/ElectrostaticPIC/main.cpp

commit c327b0fc3112c2fa5f95240d4eeec646e8cf2870
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 22 09:50:51 2017 -0700

    Change the setup of this test to match Vay et. al. 2012.

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp
Tutorials/Particles/ElectrostaticPIC/inputs
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit b0a90efdede70856c7c618b7698e7433f26da89f
Merge: bee2c1079 98103684f
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 22 09:49:03 2017 -0700

    Merge branch 'rgrout/sparse_fab' into vof-work

commit b062492771eac7e2365aff1b058cd36e6670ca4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 22 09:40:20 2017 -0700

    The plot file type needs to be "HypreCLaw-V1.1", not "AMReX".

Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit 5516e530fad13cd15d94db5e79d8ea6342e91227
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 22 09:35:50 2017 -0700

    fix path to amrex home

Tutorials/Amr/Advection_F/Exec/Make.Adv
Tutorials/Amr/Advection_octree_F/Exec/Make.Adv

commit 007719d19fd41682e1d43439c4443813fdf97ae5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 22 06:02:16 2017 -0400

    Fix a logic error in when to update the device copies

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_RealBox.H

commit 342f9da65a40e98b049798a2c14919d98eaddfdb
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 22 03:50:51 2017 -0400

    Insert device synchronizes in DEBUG mode

Src/Base/AMReX_MFIter.cpp

commit 0c88bc1b8727af7836fa8dd8087b18014f786461
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 22 02:37:03 2017 -0400

    Refactor a little to hide CUDA in Device class

Src/Base/AMReX.cpp
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_MultiFab.cpp

commit 8e078bb9a77bac32883cc60224d16774c3ffdbfd
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 22 02:00:35 2017 -0400

    Do error checking in MFIter

Src/Base/AMReX_MFIter.cpp

commit 23fca5156778f588a3b2ec065b844d53c3486fc1
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 22 02:00:21 2017 -0400

    Add a test for any runtime/kernel launch errors

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 56deb77ce559f261a707c4aa6a72c0e96b28cc41
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 22 01:40:01 2017 -0400

    Use loVectF/hiVectF in BL_TO_FORTRAN macros

Src/Base/AMReX_ArrayLim.H

commit bee2c1079fcb540279dfa8543c3ecca879416ef5
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jun 21 17:57:09 2017 -0700

    WIP: Remove debugging info

Tests/GeometryShop/vofStructures/umapTest.cpp

commit 98103684f8817a3ec9634601122928f91db8823f
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jun 21 17:54:06 2017 -0700

    Fix case on include file

Tests/C_BaseLib/tUMap.cpp

commit caa4c4f980e0dfb700e0f2488ea5aefafbf52930
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jun 21 17:34:43 2017 -0700

    WIP: rework umap test to build CutCells and CutFaces with cell index of parent coarse object to allow that multi-level eb operations can be done in Fortran.

Tests/GeometryShop/vofStructures/flatplate.inputs
Tests/GeometryShop/vofStructures/sphere.inputs
Tests/GeometryShop/vofStructures/umapTest.cpp

commit 8df2cea69466efe6ddbb6ee0132fb77649e6c167
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 21 16:50:11 2017 -0700

    User's Guide: start Fortran chapter

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Fortran/Fortran.tex
Docs/AMReXUsersGuide/GNUmakefile
Tutorials/Basic/HelloWorld_F/GNUmakefile
Tutorials/Basic/HelloWorld_F/fmain.f90

commit dd66e7cd9ddaf002a9be0523917cabe7203ca7d8
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 21 14:01:41 2017 -0700

    tutorial cleanup

Tutorials/Amr/Advection_AmrLevel/Source/main.cpp

commit de13f1e51b92f89ae79fa19faa87054294fe9678
Author: Grout <ray.grout@nrel.gov>
Date:   Wed Jun 21 14:32:15 2017 -0600

    Add skeleton of how to access Umap from fortran; temporarily turn off failure for non-existant data; test to compute norm using fortran interface

Src/Base/AMReX_BaseUmap.H
Src/Base/AMReX_BaseUmap_f.H
Src/Base/AMReX_BaseUmap_nd.f90
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/tUMap.cpp

commit e792ce1a20faa7cfcc2e487fe3e370ee839a623a
Merge: 48daaedb5 06bfb7e6c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 21 12:46:50 2017 -0700

    Merge pull request #43 from kweide/development
    
    some simple corrections to UsersGuide

commit 3c83c7d20c9efaeba8f59bf67ab0af78d5f54473
Merge: 06bfb7e6c 48daaedb5
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Wed Jun 21 14:36:02 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 48daaedb58ad014def2e96e09b359507498e6dfd
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 21 11:22:24 2017 -0700

    cout -> amrex::Print()

Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Tutorials/Amr/Advection_AmrLevel/Source/main.cpp

commit 9ce323f59f537d29848eb5473c119b9dd06e36c5
Merge: 8929a2223 b0c1a59d1
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 21 11:05:30 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 8929a2223e8b98dd82a84d0c5a10a5c16e5499c0
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 21 11:05:07 2017 -0700

    State_Type -> Phi_Type (to avoid confusion)
    
    more documentation

Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp

commit 9ed7257d8c9454c534f5bfa75c82a5c7b06899f4
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 21 11:03:38 2017 -0700

    State_Type -> Phi_Type (avoid confusion)

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex

commit b0c1a59d13b723a645fd77ea0dc87e951ca536be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 21 10:12:36 2017 -0700

    move some new Fortran tutorials from OldTutorials to Tutorials

Tutorials/Amr/Advection_F/Exec/Make.Adv
Tutorials/Amr/Advection_F/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_F/Exec/SingleVortex/Make.package
Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob.f90
Tutorials/Amr/Advection_F/Exec/SingleVortex/face_velocity_2d.F90
Tutorials/Amr/Advection_F/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_F/Exec/SingleVortex/inputs.physbc
Tutorials/Amr/Advection_F/Exec/SingleVortex/inputs.rt
Tutorials/Amr/Advection_F/README
Tutorials/Amr/Advection_F/Source/Make.package
Tutorials/Amr/Advection_F/Source/Src_2d/Make.package
Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/Amr/Advection_F/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/Advection_F/Source/Src_2d/slope_2d.f90
Tutorials/Amr/Advection_F/Source/amr_data_mod.F90
Tutorials/Amr/Advection_F/Source/averagedown_mod.F90
Tutorials/Amr/Advection_F/Source/bc_mod.F90
Tutorials/Amr/Advection_F/Source/compute_dt_mod.F90
Tutorials/Amr/Advection_F/Source/evolve_mod.F90
Tutorials/Amr/Advection_F/Source/fillpatch_mod.F90
Tutorials/Amr/Advection_F/Source/fmain.F90
Tutorials/Amr/Advection_F/Source/initdata.F90
Tutorials/Amr/Advection_F/Source/my_amr_mod.F90
Tutorials/Amr/Advection_F/Source/plotfile_mod.F90
Tutorials/Amr/Advection_F/Source/tagging_mod.F90
Tutorials/Amr/Advection_octree_F/Exec/Make.Adv
Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/Make.package
Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/Prob.f90
Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/face_velocity_2d.F90
Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/inputs.rt
Tutorials/Amr/Advection_octree_F/README
Tutorials/Amr/Advection_octree_F/Source/Make.package
Tutorials/Amr/Advection_octree_F/Source/Src_2d/Make.package
Tutorials/Amr/Advection_octree_F/Source/Src_2d/advect_2d_mod.F90
Tutorials/Amr/Advection_octree_F/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/Advection_octree_F/Source/Src_2d/slope_2d.f90
Tutorials/Amr/Advection_octree_F/Source/amr_data_mod.F90
Tutorials/Amr/Advection_octree_F/Source/averagedown_mod.F90
Tutorials/Amr/Advection_octree_F/Source/bc_mod.F90
Tutorials/Amr/Advection_octree_F/Source/compute_dt_mod.F90
Tutorials/Amr/Advection_octree_F/Source/evolve_mod.F90
Tutorials/Amr/Advection_octree_F/Source/fillpatch_mod.F90
Tutorials/Amr/Advection_octree_F/Source/fmain.F90
Tutorials/Amr/Advection_octree_F/Source/initdata.F90
Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90
Tutorials/Amr/Advection_octree_F/Source/plotfile_mod.F90
Tutorials/Amr/Advection_octree_F/Source/tagging_mod.F90

commit cf87a98cdf10be8003ef59e2d1cadbeedfa6bfeb
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 21 09:59:08 2017 -0700

    added back in check to make sure a fine level already hasn't been regridded from a coarser level regrid

Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp

commit 9037d3e6396e3a03dba5640c4d2f4056547ce542
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Jun 21 09:46:46 2017 -0700

    Start re-writing of AMReX Cmake

CMakeLists.txt
Tools/CMake/AMReX_Config.cmake
Tools/CMake/AMReX_Options.cmake

commit ed2e194ba59f8340c01e47926649910ff857f535
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 21 09:29:50 2017 -0700

    cleanup tutorial

Tutorials/Amr/Advection_AmrLevel/Source/Adv.cpp
Tutorials/Amr/Advection_AmrLevel/Source/Adv_advance.cpp
Tutorials/Amr/Advection_AmrLevel/Source/Adv_dt.cpp
Tutorials/Amr/Advection_AmrLevel/Source/Adv_io.cpp
Tutorials/Amr/Advection_AmrLevel/Source/Adv_setup.cpp
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H
Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp
Tutorials/Amr/Advection_AmrLevel/Source/LevelBldAdv.cpp
Tutorials/Amr/Advection_AmrLevel/Source/Make.package

commit 9d68e3c300ca2f9959e03e3aeadb615c09321aa9
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 21 08:56:36 2017 -0700

    move AMR_Adv_C example into Tutorials/Amr/Advection_AmrLevel and get it compiling/running again

OldTutorials/AMR_Adv_C/README
Tutorials/Amr/Advection_AmrLevel/Exec/Make.Adv
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/Make.package
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/Prob.f90
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/probin
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/Make.package
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/inputs
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90
Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/probin
Tutorials/Amr/Advection_AmrLevel/README
Tutorials/Amr/Advection_AmrLevel/Source/Adv.H
Tutorials/Amr/Advection_AmrLevel/Source/Adv.cpp
Tutorials/Amr/Advection_AmrLevel/Source/AdvBld.cpp
Tutorials/Amr/Advection_AmrLevel/Source/Adv_F.H
Tutorials/Amr/Advection_AmrLevel/Source/Adv_advance.cpp
Tutorials/Amr/Advection_AmrLevel/Source/Adv_dt.cpp
Tutorials/Amr/Advection_AmrLevel/Source/Adv_io.cpp
Tutorials/Amr/Advection_AmrLevel/Source/Adv_setup.cpp
Tutorials/Amr/Advection_AmrLevel/Source/Make.package
Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Make.package
Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/slope_2d.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/Make.package
Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/slope_3d.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Make.package
Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90
Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/tagging_params.f90
Tutorials/Amr/Advection_AmrLevel/Source/main.cpp

commit ee45cbd6b9e48fbb59c9c6223cb25fb57ab36244
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 21 08:26:09 2017 -0700

    cleanup of tutorial and associated documentation

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdvPhysBC.H
Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv_F.H
Tutorials/Amr/Advection_AmrCore/Source/Make.package
Tutorials/Amr/Advection_AmrCore/Source/main.cpp

commit 717c03163a4d4960758f606ec8bbf4fe868998c0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 21 05:01:56 2017 -0400

    Use default stream to simplify logic

Src/Base/AMReX_CUDA.F90

commit 8d7abb2b29d649b537178c70efe23c6ef656939f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 21 04:58:38 2017 -0400

    Create a gpu_error function

Src/Base/AMReX_CUDA.F90

commit ea621137507c077270534618ae81206ad0386203
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 21 04:43:10 2017 -0400

    Add a hook to set the GPU stack limit

Src/Base/AMReX_CUDA.F90

commit ad95089007d20c28c6c83be4f9c01f1e57eb690f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 21 04:15:47 2017 -0400

    Avoid undefined non-CUDA behavior

Src/Base/AMReX_Device.cpp

commit f33ff3cba9714d02990f794f76f183d1c6b64205
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 21 04:12:57 2017 -0400

    Add BaseFab hook to return pinned Box memory

Src/Base/AMReX_BaseFab.H

commit b4fdaf1d2197f2047529d47a85e3b5a6aea67044
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 21 03:31:37 2017 -0400

    Add a pinned memory version of Box data

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp

commit 1994e0cb31329e14604e1a2566cd061cfd0cb431
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 21 03:14:38 2017 -0400

    Use BL_TO_FORT macro in HeatEq again

Tutorials/GPU/HeatEquation_EX1_C/main.cpp

commit d9b1f4209f570d8d7a6180c29138b1361bc23afb
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 21 02:53:39 2017 -0400

    Add C++ hook to get host pointer for pinned memory

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit a4307741bcc36a25c0040711fe7586a0b110845e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 21 02:36:43 2017 -0400

    Reset to the default stream on MFIter destruction

Src/Base/AMReX_MFIter.cpp

commit 8a9ff32d271d5a229973c1d5bb174c53fcd374db
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 21 02:36:16 2017 -0400

    Add cuda_streams(0) as the default stream

Src/Base/AMReX_CUDA.F90

commit f8c0dc7d023304d221013e6bb34ca1739af9d1ff
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 21 02:17:10 2017 -0400

    Add function to return current stream index

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit e61b3a031ffe03c0444584b5f12c8d991c6d12ee
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 21 01:49:42 2017 -0400

    Register a box for asynchronous execution

Tutorials/GPU/HeatEquation_EX1_C/main.cpp

commit 06bfb7e6c53db039a05432955466f4e74c52364a
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Wed Jun 21 00:29:59 2017 -0500

    triv

Docs/AMReXUsersGuide/Basics/Basics.tex

commit fac5319c6725fe2a517afff87999329623c7168f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 21 01:04:35 2017 -0400

    Update the RealBox device pointer in more cases

Src/Base/AMReX_RealBox.H

commit 114aba6485afa5519f24b7ed9c9f2bb3dd87d040
Merge: 59481acf2 18965fd7d
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Tue Jun 20 23:52:48 2017 -0500

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 59481acf207906d34dbc12a39c6217c18978611a
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Tue Jun 20 23:52:30 2017 -0500

    trivial edits

Docs/AMReXUsersGuide/Basics/Basics.tex

commit 18965fd7d0c564d32f3dfd2be56b19d2f0d605fb
Merge: a17ab5210 1218dcc45
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 20 21:27:14 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a17ab52101a4a854116af9a8f50e0b4e6817fa81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 20 21:26:35 2017 -0700

    make bl_random_f seeding thread safe

Src/F_BaseLib/bl_random_c.cpp
Src/F_BaseLib/bl_random_f.f90

commit 1218dcc4542e4e06fdf72c9a6725ac658f96c399
Merge: 6d9d4114b c1323257d
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 20 21:00:01 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 6d9d4114bce6591b1e4a202b71ceac33a94f7f82
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 20 18:04:14 2017 -0700

    more documentation

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex

commit 0a2f40ef15592d4d0b20c432fa8002ca2a5bff68
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 20 17:37:20 2017 -0700

    comments

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp

commit a4cb9427d420aa67b8daf104e4e3bdab14590ac5
Merge: 99219b039 c1323257d
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jun 20 17:32:03 2017 -0700

    Merge branch 'development' into vof-work

commit c1323257d2448bb7180f6fc7e69d61de1de34e4d
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jun 20 17:31:37 2017 -0700

    Indexing bug in VolIndex output function

Src/GeometryShop/AMReX_VolIndex.cpp

commit d7af48a635c2ccdad6cfe2ee706865e66ff894d6
Merge: 4a558260d d6a60f0a1
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Jun 20 17:18:40 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 4a558260df130c2f4dd3fd46dc164b95d7bb4d84
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Jun 20 17:18:29 2017 -0700

    use enum instead of integer for specifying cartesian coordinates in the tutorials.

Tests/Particles/AssignDensity/main.cpp
Tests/Particles/AssignMultiLevelDensity/main.cpp
Tests/Particles/ParticleIterator/GNUmakefile
Tests/Particles/ParticleIterator/main.cpp
Tests/Particles/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/main.cpp
Tutorials/CVODE/EX1/main.cpp
Tutorials/CVODE/EX2/main.cpp
Tutorials/Particles/ElectrostaticPIC/main.cpp
Tutorials/Particles/ShortRangeParticles/main.cpp

commit d6a60f0a1ee86f63cbb689daa33bb400b11cc1fe
Merge: d8cf76812 71a5bce22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 20 16:21:02 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit d8cf7681225f409a235ac0e644b440c3e271ef31
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 20 16:20:56 2017 -0700

    make max_grid_size and blocking_factor IntVect

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp

commit 71a5bce22e246c5053339f3a2e37487a3295fcb3
Merge: a7d733ff7 de95d45d7
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jun 20 16:14:23 2017 -0700

    Merge pull request #42 from AMReX-Codes/dtg_branch
    
    bunch of small parallel fixes

commit de95d45d7fddb94c757ae7c7558a34992dfa3a63
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Jun 20 16:08:12 2017 -0700

    put in the repo the working input file

Tests/GeometryShop/regression/ebio.inputs

commit a7d733ff78b9e4e9d155175632b98000002564d2
Merge: 023a758e2 bb8a8c46f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 20 14:14:33 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 023a758e2eef70f3d8a379297c56ffc1b718e51e
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 20 14:14:19 2017 -0700

    minor updates to doc

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp

commit bb8a8c46fcf79f9c710ddda27b657fc67d1c1af7
Merge: fd7e44d71 7a16363b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 20 13:27:25 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit fd7e44d71c7ddedbacbdadadc62bdbc23cdd61aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 20 13:27:13 2017 -0700

    add assertion to FabArray::operator[] making sure DistributionMapping is the same

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MFIter.H

commit 7a16363b1b727bb71d607230a43a654003f05633
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 20 13:25:08 2017 -0700

    more AmrCore doc and some code cleanup

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp
Tutorials/Amr/Advection_AmrCore/Source/main.cpp

commit e576c0f996f5a6e42582d30da635d97506ce1fd0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Jun 20 12:00:43 2017 -0700

    parallel I/O of FabArray objects is now correct

Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_FabArrayIO.H
Tests/GeometryShop/regression/fabio.cpp

commit a9d90c7e5f172649f98280bda37b9afc60f2b2e5
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jun 12 17:20:04 2017 -0700

    Modify main CMakeLists.txt

CMakeLists.txt
Tools/CMake/AMReX_Utils.cmake

commit 7d293ce0f32f47382acfd9157498585ac36a0a4d
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Jun 12 14:13:04 2017 -0700

    Add missing file from source list

Src/Base/CMakeLists.txt

commit 2bfad9e4eb28bb1ee6f208c1e5700571f324a669
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jun 9 15:30:21 2017 -0700

    Modify previous fix to circular dependency problem

Tools/CMake/FindCCSE.cmake

commit d241ec9475ef9bd47b4b239350bb4a2acaeb7550
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jun 9 10:06:39 2017 -0700

    Force VERBOSE ON by default

CMakeLists.txt

commit 36ae8d1ff64e98472313a657cfbb747b06c403f7
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 8 15:59:33 2017 -0700

    Modify preprocessing for F77 files

Tools/CMake/PreprocessAMReXFortran.cmake

commit cada0fc97e3aa43b49bb9cc365102f6c9a8d61f6
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 8 10:46:20 2017 -0700

    Get rid of PreprocessAMReXFortran90

CMakeLists.txt
Src/Base/CMakeLists.txt
Src/CMakeLists.txt
Tools/CMake/PreprocessAMReXFortran90.cmake

commit fbfe92005748ed7c5b6ed6830676a8a3e60f8c77
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 20 00:05:03 2017 -0400

    Further restrict the device synchronizes

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_Geometry.cpp

commit d435c1af44f05b8dc5951c78ea0b042e94184db5
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 23:53:21 2017 -0400

    Suppress warning about driver shutting down

Src/Base/AMReX_CUDA.F90

commit a61330bb7317d697b8375d83ad6595561ef10004
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 23:28:53 2017 -0400

    Use a less restrictive device sync policy

Src/Base/AMReX_Device.H
Src/Base/AMReX_FabArray.H

commit efb282fb5557fb1aa08ba0362f34a8f16c95da1f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 23:14:32 2017 -0400

    Add a GPU synchronize on MFIter destruction

Src/Base/AMReX_MFIter.cpp

commit 54a23fd33c69cca3ffc60a2b9be49b4ea7e101a1
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 23:13:17 2017 -0400

    Add a stream synchronize hook

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H

commit 04c83f566c0cb3c96c1abe75ff17f718c0ff9b9a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 22:42:31 2017 -0400

    Handle device stream index automatically in MFIter

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MFIter.cpp
Src/Base/AMReX_MultiFab.cpp

commit 99219b03962f1da2695c24de1f459b2a985b41fe
Merge: 538f0f068 6387464b5
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 19 19:14:33 2017 -0700

    Merge branch 'development' into vof-work

commit 0c97825edae2c0749031f8014f63024032816670
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 22:14:22 2017 -0400

    Revert "Remove an unnecessary device synchronize"
    
    This reverts commit 0b597e8cd4f99fd400285ae1af4edf5a67a59b2d.

Src/Base/AMReX_Device.H

commit 6387464b59148e1d803a41b3f78e5e3ed4507d54
Merge: eff3a77d4 52adb7ac9
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 19 19:14:06 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit eff3a77d4db73a444db5e266a8a252ec1102db8e
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 19 19:13:53 2017 -0700

    Rename dummy arguments in EBLevelGrid.H for refine function

Src/GeometryShop/AMReX_EBLevelGrid.H

commit 63c962bf7df1da407948054150a97045fec9cbfd
Merge: 83f484574 c62802ca6
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 21:25:51 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit c62802ca68e92418acbfc688b0bd8fbc62e3d2ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 19 21:22:59 2017 -0400

    prevent ppc and little_endian from clashing on IBM power 8

Src/Base/AMReX_FPC.cpp

commit 64eab00e6a3559e1679a20ba44441133d8f54303
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 19 21:17:03 2017 -0400

    wrap the comments in #if 0 ... #endif so we can compile with xlf

Src/Base/AMReX_REAL.H

commit 538f0f068e76dbf536b602692f5660ae1261af9d
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 19 16:30:37 2017 -0700

    Fix a problem associated with reference-counted semantics

Tests/GeometryShop/vofStructures/umapTest.cpp

commit 39c627a4129b22adeef3fdfa756cd06b209bc8ce
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Jun 19 15:52:11 2017 -0700

    fixed nasty little parallel bug that was only happening when the EB ends near a box boundary.  I/O is still broken in parallel but the other stuff seems to work.

Src/GeometryShop/AMReX_BaseEBCellFABI.H
Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBLevelGrid.cpp
Src/GeometryShop/AMReX_GraphNode.cpp
Tests/GeometryShop/regression/fabio.cpp

commit 52adb7ac9138927f1ecf9f2a4e4a2113308163a1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 19 12:48:12 2017 -0700

    Use PCInterp instead of CellConservativeLinear in multi-level assign density.

Src/Particle/AMReX_ParticleContainerI.H

commit a239e83e1dc54c50c523e631f14b94b571ac599a
Merge: 61cbc7c5f 33040bdb1
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 19 12:39:35 2017 -0700

    Merge branch 'development' into vof-work

commit c30b4d0f69e4e450b53f20a15e6f5319db342107
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jun 19 12:26:21 2017 -0700

    Add more detail about single precision particles in the docs.

Docs/AMReXUsersGuide/Particle/Particle.tex

commit 61cbc7c5fbd0822767b2813fc5aab28a67ada5b5
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 19 12:15:08 2017 -0700

    Remove ebXXXID

Tests/GeometryShop/vofStructures/AMReX_EBStruct.H
Tests/GeometryShop/vofStructures/umapTest.cpp

commit dae257ae487b7874c9f18f0ffc8571cfe9e36421
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 19 12:11:19 2017 -0700

    WIP: Remove vofStructure sample code, choosing Umap structures over the original Node (IntVect-based) concept.

Tests/GeometryShop/vofStructures/AMReX_EBStruct.H
Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90
Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/vofStructures.cpp
Tests/GeometryShop/vofStructures/vofStructures_2d.F90
Tests/GeometryShop/vofStructures/vofStructures_3d.F90

commit 233ccdd4ed05a12bb9926ca6b271ff176fd7cdd6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 19 11:14:06 2017 -0700

    move amrex_particle_real to AMReX_fort_mod.F90

Src/Base/AMReX_fort_mod.F90
Src/Particle/AMReX_Particle_mod_1d.F90
Src/Particle/AMReX_Particle_mod_2d.F90
Src/Particle/AMReX_Particle_mod_3d.F90
Tutorials/Particles/ShortRangeParticles/short_range_2d.f90
Tutorials/Particles/ShortRangeParticles/short_range_3d.f90

commit 07f2a413762133147fa68370263fb7aeb438430b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 19 10:57:38 2017 -0700

    Allow for single precision particles to be handled by Fortran routines.

Src/Particle/AMReX_Particle_mod_1d.F90
Src/Particle/AMReX_Particle_mod_2d.F90
Src/Particle/AMReX_Particle_mod_3d.F90
Src/Particle/AMReX_Particles_F.H
Tools/GNUMake/Make.defs
Tutorials/Particles/ShortRangeParticles/main.cpp
Tutorials/Particles/ShortRangeParticles/short_range_2d.f90
Tutorials/Particles/ShortRangeParticles/short_range_3d.f90

commit 83f484574473e088d5c5647c7253be530342f679
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 05:09:13 2017 -0400

    Handle stream indices more cleanly and consistently

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.cpp

commit c1a30df5016d268ee1aaa007309942089c75b12c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 04:43:42 2017 -0400

    Prevent OpenMP when using CUDA

Tools/GNUMake/Make.defs

commit abe66b8813415eb76c28cec0d4cf19af6bb60e66
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 03:10:09 2017 -0400

    Make the device index thread safe

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 8252c4fb601c048b8648c11f4b21ab65d55e4cde
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 02:38:19 2017 -0400

    Return to old MFIter style since boxes are now saved

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.cpp

commit e114240c9e49bce2d2ed97102415e437ed7907ea
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 02:37:38 2017 -0400

    Register boxes created by MFIter

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit ccfe89826096262453585a534376d3edf06d9dda
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 01:58:50 2017 -0400

    Remove index from Fab interfaces

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit 380dc18253c3bc397528e115f9eaffe52c39b297
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 01:50:07 2017 -0400

    Make the MultiFab operations asynchrony-safe

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.cpp

commit 0b597e8cd4f99fd400285ae1af4edf5a67a59b2d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 01:33:22 2017 -0400

    Remove an unnecessary device synchronize

Src/Base/AMReX_Device.H

commit 16345f8e9736645b22209cc126a1e3c99370e79e
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 19 01:07:55 2017 -0400

    Add a stream index variable

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H

commit 2c5f181b475ea06b9dceb8793ce381248ad1947c
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 18 23:12:03 2017 -0400

    Add PGI compiler major and minor version definitions

Tools/GNUMake/comps/pgi.mak

commit 7b0ce1069ac441fef42d52335caee8d24e509e18
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jun 18 20:55:29 2017 -0400

    ifdef out some CUDA stuff

Src/Base/AMReX_Device.cpp

commit fdb26d77ea2d99900b82c024236a8b77e1495226
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 18 20:24:08 2017 -0400

    Automatically pick up CUDA path on Titan and Summitdev

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.machines
Tools/GNUMake/comps/pgi.mak
Tools/GNUMake/sites/Make.olcf

commit dfd783874eabcb55911cebb8977292580cc6b0f4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 18 16:43:06 2017 -0400

    Get the CUDA device ID from Fortran

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit 740b51d609046f5d7caff0bc47093ce3fdb1c37f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 18 16:30:49 2017 -0400

    Drive CUDA initialization from C++

Src/Base/AMReX.cpp
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp

commit f010bb54e54d4019774ee1b83cdf7c1094fce789
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 18 15:29:37 2017 -0400

    Query GPU properties, use in avoiding unsupported calls

Src/Base/AMReX_CUDA.F90

commit 93f82c0c82c73839edbd99ffbcd45d5708590855
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 18 15:29:14 2017 -0400

    Initialize CUDA before class initializations

Src/Base/AMReX.cpp

commit 18d30437c70e96c6cd73afd265aa810ad337adac
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 18 01:17:12 2017 -0400

    Create managed copy of RealBox data

Src/Amr/AMReX_AmrLevel.cpp
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp

commit 191110e8fdb96a826cc7a75d8c0835c14a24165b
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sun Jun 18 00:48:40 2017 -0400

    Add function to return number of MFIter indices

Src/Base/AMReX_MFIter.H

commit 39e40e7c63ff5cecd828198daec6b82243005df7
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 17 23:14:26 2017 -0400

    Fix the argument passing to cudaMemAdvise

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_Device.H

commit 7aa44d177838e7cf17048404c4e720868b8d6776
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 17 22:00:19 2017 -0400

    Insert CUDA finalization

Src/Base/AMReX.cpp
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H

commit efe94d3fcd600e2e58fcee8b14c42f5f22fe5c26
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 17 21:13:23 2017 -0400

    Disable broken error checking for cudamemadvise

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_CUDA.F90

commit 7665f2ea0da333c160e337c858c21ce5c2022edd
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 17 20:32:45 2017 -0400

    Add capability to use hostalloc'ed data

Src/Base/AMReX_Arena.H
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_CArena.cpp

commit 83aab7793d4fbdcf54e94aebc3307a81368bcb4a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 17 20:31:10 2017 -0400

    Clean up CUDA functions, add error checking

Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H

commit c6af601ee59ea74e13a9625b5ccda35442c21e7f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 17 20:30:11 2017 -0400

    Increase length of error string

Src/Base/AMReX_BLBoxLib_F.f

commit 69faf1ba2e9007c7c2fc812fbeccae64a1439bd8
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sat Jun 17 16:14:08 2017 -0700

    took out unnecessary fillboundary calls

Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_EBDebugOut.cpp
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBLevelGrid.cpp

commit 79ca2e3d891012a7f217f6359527c1c8198cb1f1
Merge: 124f2fc46 8467ae21d
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 17 06:31:37 2017 -0700

    Merge pull request #40 from atmyers/gpu
    
    An approach to managed memory for particle data

commit 124f2fc46030a389e055c0cb18b3b1da553b7cb7
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 17 09:04:34 2017 -0400

    Always use CArena in Box

Src/Base/AMReX_Box.cpp

commit ecaa7cc951c212e6c268b4ddeb45f2068453f379
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 17 05:13:53 2017 -0400

    Rely on data that is now managed

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90

commit 07c65a5804c96d5775a5bf9f910ff7158faff33a
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 17 04:17:07 2017 -0400

    Add an option to use cudaMalloc, not cudaMallocManaged

Src/Base/AMReX_Arena.H
Src/Base/AMReX_CArena.cpp

commit d4a8dadf0b98bdc23baf377c2d73eea87bccff58
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat Jun 17 04:13:21 2017 -0400

    Use the default stream if passed an invalid index

Src/Base/AMReX_CUDA.F90

commit 193ee594da3ed6d75851580972a99b5de7869c25
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jun 16 19:29:25 2017 -0700

    Add faces to graph in Umap form.

Src/Base/AMReX_BaseUmap.H
Tests/GeometryShop/vofStructures/AMReX_EBStruct.H
Tests/GeometryShop/vofStructures/flatplate.inputs
Tests/GeometryShop/vofStructures/umapTest.cpp

commit 8467ae21dec1bbf0b38f700b3c5cef8901516dd8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 16 17:28:36 2017 -0700

    removing file checked in by mistake.

Tests/Particles/ManagedCUDADeposition/make.out

commit 79fcb387ec77e88ba86d9feb3c358d18f29a5734
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 16 17:17:37 2017 -0700

    check in test problem for Managed Cuda particle deposition.

Tests/Particles/ManagedCUDADeposition/GNUmakefile
Tests/Particles/ManagedCUDADeposition/Make.package
Tests/Particles/ManagedCUDADeposition/MyParticleContainer.H
Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp
Tests/Particles/ManagedCUDADeposition/cuda_deposit_3d.f90
Tests/Particles/ManagedCUDADeposition/deposit_3d.f90
Tests/Particles/ManagedCUDADeposition/deposit_F.H
Tests/Particles/ManagedCUDADeposition/inputs
Tests/Particles/ManagedCUDADeposition/main.cpp
Tests/Particles/ManagedCUDADeposition/make.out
Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp
Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp

commit b0f351e28d988bd1aae88c77b8256c6bdaf1a398
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 16 17:16:59 2017 -0700

    remove old version of custom allocator from problem directory

Tests/Particles/CUDADeposition/CUDAManagedAllocator.H

commit 95492c92dd2563c4c7415a4968195f06f0dc7d00
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 16 17:16:18 2017 -0700

    Add a custom allocator that uses Cuda managed memory and use it in the ParticleContainer when Cuda is enabled.

Src/Particle/AMReX_CudaManagedAllocator.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Src/Particle/Make.package

commit b17d1aea59291cbe0f6f5e280b1a3a25530f5fe9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 16 17:14:01 2017 -0700

    modify AMReX_Array to optionally take a custom allocator (off by default)

Src/Base/AMReX_Array.H

commit 5304b747bb2cdfb3b95068215d002303d079da5f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jun 16 16:48:12 2017 -0700

    more AmrCore documentation

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Docs/AMReXUsersGuide/AmrCore/figs/flowchart.odg
Docs/AMReXUsersGuide/AmrCore/figs/flowchart.pdf

commit 87785dad84c1d8b7a3a51f56e4b42df46cf8e822
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jun 16 15:17:19 2017 -0700

    Enabling OpenMP in the ShortRangeParticleContainer and adding timers.

Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp

commit 0a4b577c2ac11dc934a0eea49f391075b8a41201
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 16 14:47:39 2017 -0700

    User's Guide: proofread

Docs/AMReXUsersGuide/Basics/Basics.tex

commit 2ac8c8ba4a691d708be014dcae5f4c4d80f75c23
Merge: 137c4c92b b57c5c272
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 16 12:46:37 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 137c4c92b76bd619761f91a1757d765eadefdec3
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 16 12:46:23 2017 -0700

    fix uniform_int_distribution call to be consistent with header comments.

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit b57c5c27295156d6cef222a88d04cb0afcfc67f8
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Jun 16 11:25:22 2017 -0700

    Clean up use of Fortran intent / const in the Particle tutorials.

Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H
Tutorials/Particles/ShortRangeParticles/short_range_F.H

commit 2d33d99daade673866b0621da164e616905c3d8f
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jun 16 11:10:25 2017 -0700

    For BaseUmap::const_iterator, add access to IntVect, L and n.

Src/Base/AMReX_BaseUmap.H
Tests/GeometryShop/vofStructures/umapTest.cpp

commit 70c5d484ee39bb24da1553791c295f8549803552
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Jun 16 11:03:54 2017 -0700

    Proofreading pass of particle documentation.

Docs/AMReXUsersGuide/Particle/Particle.tex
Docs/AMReXUsersGuide/Visualization/Visualization.tex

commit 99efc96b4ed419e4fb4552f0bce408c2e07151fb
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jun 16 10:59:01 2017 -0700

    Add an iterator to BaseUMap to allow iterating over all explicitly defined data....needs some work though

Src/Base/AMReX_BaseUmap.H
Tests/GeometryShop/vofStructures/umapTest.cpp

commit 5c018b61ace9578c09aa342e834777137d9d46ad
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jun 16 09:58:35 2017 -0700

    Merge vof-work and sparse-fab stuff...wip

Src/Base/AMReX_BaseUmap.H
Src/Base/Make.package
Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/umapTest.cpp
Tests/GeometryShop/vofStructures/vofStructures.cpp

commit 2a380324ae19138da3edab66f52b09cac504853f
Merge: 305e93470 806ded972
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jun 16 10:00:09 2017 -0600

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 305e934705f4d0f7cbb5d905e3da1bc55426a204
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Jun 16 10:00:02 2017 -0600

    CMake: disable tiny_profiler for the time being

Src/Base/CMakeLists.txt
Tools/CMake/CCSEOptions.cmake

commit 806ded9721db45b8145d662a1fb13d2db7aef801
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 15 19:43:20 2017 -0700

    use an explicit amrex:: namespace in the BL_PROFILE macro definitions.

Src/Base/AMReX_BLProfiler.H

commit 2f20baa62e801244198df3f2e2ec614bedb31f6a
Merge: 22f6db05c 74110f274
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 15 17:25:28 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 22f6db05c9c4c88426e5094895679e7edd26d4e3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 15 17:23:04 2017 -0700

    Same for the interpolation operation.

Src/Particle/AMReX_ParticleContainerI.H

commit 5b850929f9ea30e97175edc6854bfb4d3dd8c027
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 15 17:10:02 2017 -0700

    Make the deposition operation OpenMP-capable.

Src/Particle/AMReX_ParticleContainerI.H

commit 74110f274a38441c64ba62ef6bea383178fda490
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 15 17:01:39 2017 -0700

    minor changes

Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex
Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex

commit 2d81ce3930a6c1ece9cd45299c5393153c926c92
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 15 16:49:48 2017 -0700

    Functions to assist with particle deposition with OpenMP.

Src/Particle/AMReX_OMPDepositionHelper_1d.F90
Src/Particle/AMReX_OMPDepositionHelper_2d.F90
Src/Particle/AMReX_OMPDepositionHelper_3d.F90
Src/Particle/AMReX_Particles_F.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 0a6f897c38c561a5d920f1361cf13b589e2a496e
Merge: 5cbacf4da 51d12f21f
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 15 16:48:40 2017 -0700

    Merge branch 'rgrout/sparse_fab' into vof-merge

commit 33040bdb1c788c2fa5f2e7af048da45836720cec
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jun 15 16:44:49 2017 -0700

    cleaned up tutorial code, added lots of comments

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrMesh.H
Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvError.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvEvolve.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvIO.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvInit.cpp
Tutorials/Amr/Advection_AmrCore/Source/Make.package
Tutorials/Amr/Advection_AmrCore/Source/main.cpp

commit 7e2076993edeebec59ee73b35c83daedc01aa7fd
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jun 15 15:13:14 2017 -0700

    another parallel bug found.  More stuff works but not everything.

Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBLevelGrid.cpp
Src/GeometryShop/AMReX_IrregFABFactory.cpp
Tests/GeometryShop/regression/fabio.cpp
Tests/GeometryShop/regression/runalltests.mpi.sh
Tests/GeometryShop/regression/serialization.cpp
Tests/GeometryShop/regression/serialization.inputs

commit 410211f4a17a6de45b67279eeeddc55aa4aafb64
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 15 14:59:42 2017 -0700

    User's Guide: Boundary

Docs/AMReXUsersGuide/Basics/Basics.tex

commit 63be359c8b0b7f1638f50113146485e325de6364
Merge: 314708a25 bfb61626e
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jun 15 14:35:50 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 314708a2593bd6e72c57a2d7635df1a30b4f46bc
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jun 15 14:35:34 2017 -0700

    small documentation adds

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvEvolve.cpp

commit 19586607365c18bad8c4c98c5092e611b9d6b84f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jun 15 14:28:24 2017 -0700

    tex version of subcycling fig

Docs/AMReXUsersGuide/AmrCore/figs/subcycling.tex

commit bfb61626e33ca23553e9b81a71b59987a9b3329d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 15 14:27:06 2017 -0700

    adding in the *.tex files for the new figures.

Docs/AMReXUsersGuide/Particle/neighbor_particles.tex
Docs/AMReXUsersGuide/Particle/particle_arrays.tex

commit 12f128bfa8ed32c4d2bf186915f14fdb97af1a0e
Merge: f73536e3e 6d5e3acb2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jun 15 14:25:41 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6d5e3acb2b9021bad282d6bb30f30615166847c2
Merge: c5e9b0400 db5e371b3
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Jun 15 14:20:50 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit c5e9b0400222e47cc52f4e9e00295bb3d6359e6b
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Jun 15 14:20:35 2017 -0700

    adding a couple of figures to the particle section of the user's guide.

Docs/AMReXUsersGuide/Particle/Particle.tex
Docs/AMReXUsersGuide/Particle/neighbor_particles.pdf
Docs/AMReXUsersGuide/Particle/particle_arrays.pdf

commit db5e371b3f7b5b0f5a6292e565d9b5c28fafcf18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 15 13:44:31 2017 -0700

    update heat equation tutorial using the new amrex::FillDomainBoundary function

Tutorials/Basic/HeatEquation_EX1_C/advance.cpp
Tutorials/Basic/HeatEquation_EX1_C/myfunc.H
Tutorials/Basic/HeatEquation_EX1_C/physbc.cpp

commit 9bcf46202a949265b7388e3952173c784c46c4a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 15 13:39:56 2017 -0700

    add some helper functions for filling physical domain boundary conditions

Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCUtil.H
Src/Base/AMReX_BCUtil.cpp
Src/Base/AMReX_BC_TYPES.H
Src/Base/AMReX_BLassert.H
Src/Base/AMReX_bc_types_mod.F90
Src/Base/AMReX_filcc_f.H
Src/Base/AMReX_filcc_mod.F90
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/F_Interfaces/Base/Make.package
Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_C/Make.package
Tutorials/Basic/HeatEquation_EX1_C/inputs_2d
Tutorials/Basic/HeatEquation_EX1_C/inputs_3d
Tutorials/Basic/HeatEquation_EX1_C/main.cpp

commit cc7908541e2269aab60fe36ba5b50156f42e2718
Merge: 6168d6a11 2a2b423dd
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 15 14:00:40 2017 -0600

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 51d12f21fdbe629d7f258b099f771d4c7aca697f
Merge: c5b480ac5 2a2b423dd
Author: Grout <ray.grout@nrel.gov>
Date:   Thu Jun 15 13:59:20 2017 -0600

    Merge branch 'development' of github.com:AMReX-Codes/amrex into rgrout/sparse_fab

commit 6168d6a113789d3df4aa2beb5c72c36a1261e144
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 15 13:57:11 2017 -0600

    Make TinyProfiler the deault profiling tool

Src/Base/CMakeLists.txt
Tools/CMake/CCSEOptions.cmake

commit 5cbacf4dacadce08148826fd5be11127fb3c2ab9
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 15 12:52:11 2017 -0700

    WIP: Fixup test code for mv cells

Tests/GeometryShop/vofStructures/flatplate.inputs
Tests/GeometryShop/vofStructures/vofStructures.cpp
Tests/GeometryShop/vofStructures/vofStructures_2d.F90
Tests/GeometryShop/vofStructures/vofStructures_3d.F90

commit 937cb52dcaa310a2954f17ce31071b2f2c360836
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Jun 15 13:43:13 2017 -0600

    Update cmake with new source files

Src/Base/CMakeLists.txt

commit c5b480ac54c49ca521c3871e46a912f102be3a83
Author: Grout <ray.grout@nrel.gov>
Date:   Thu Jun 15 13:40:15 2017 -0600

    Start of sparse fab

Src/Base/AMReX_BaseUmap.H
Tests/C_BaseLib/tUMap.cpp

commit d6c962a1da2638d732033043aac188918bf785c6
Merge: cf8c05478 2a2b423dd
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Jun 15 12:21:05 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit fedfd6ce0aadda8c597bb9abd182de2fab98a34c
Merge: 7df5436cc 2a2b423dd
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 15 11:52:17 2017 -0700

    Merge branch 'development' into vof-work

commit 7df5436cc2de7316270d611da6398ec56c2fd211
Merge: 2e6000b81 afdf2c7ba
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 15 11:52:12 2017 -0700

    resolve merge conflicts

commit 2a2b423ddfbb1518ea43a8ee826c9d6cafa03183
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 15 11:49:31 2017 -0700

    Add arguments to pltfile functions that enable passing versionName to writer so we can make CartGrid_V2.0 files

Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_PlotFileUtil.cpp

commit 2e6000b8137ac1e7eaa019660637844745d7d396
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 15 11:47:35 2017 -0700

    WIP: Write plotfile with vfrac info

Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/vofStructures.cpp

commit d67ca9e5e8d2158ec6bc3ef47c934ec2e532393c
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jun 15 10:51:01 2017 -0700

    more bug fixes.  EB I/O still broken for nproc > 1

Src/GeometryShop/AMReX_FabArrayIO.H
Src/GeometryShop/AMReX_FabArrayIO.cpp
Src/GeometryShop/AMReX_IrregFABFactory.cpp
Tests/GeometryShop/regression/dataArith.cpp
Tests/GeometryShop/regression/runalltests.mpi.sh

commit 83e9ebf4dd03737490d9badb6c6923cefc8876ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 15 09:21:21 2017 -0700

    move OldTutorials/HelloWorld_CF Tutorials/HelloWorld_F

Tutorials/Basic/HelloWorld_F/GNUmakefile
Tutorials/Basic/HelloWorld_F/Make.package
Tutorials/Basic/HelloWorld_F/fmain.f90

commit 057034b1dc91462dc7818ce02b56f411b641e3e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 15 09:17:01 2017 -0700

    User's Guide: add some discussion on const& and return by value

Docs/AMReXUsersGuide/Basics/Basics.tex

commit 493aa1b85cbb9dc31584e56a0dc32850490a45dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 15 09:16:17 2017 -0700

    move OldTutorials/HeatEquation_EX1_CF to Tutorials/HeatEquation_EX1_F

Tutorials/Basic/HeatEquation_EX1_F/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_F/Make.package
Tutorials/Basic/HeatEquation_EX1_F/advance.f90
Tutorials/Basic/HeatEquation_EX1_F/fmain.f90
Tutorials/Basic/HeatEquation_EX1_F/init_phi.f90
Tutorials/Basic/HeatEquation_EX1_F/inputs

commit 9c2d95c7ae496648cecbe4322bab8763ff5538d6
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 15 10:23:45 2017 -0400

    Always reset device memory when applying a Box transformation
    
    The original idea was to only reset the shared pointer containing the memory
    for routines that returned a new box by value rather than modifying the
    existing box by reference. Thus we could keep the CUDA managed memory without
    reallocating it if one did Box bx = mfi.validbox(), but create a new allocation
    if one did Box bx = surroundingNodes(mfi.validbox()). However, this is defeated
    by the use case where one first creates the box copy, and then applies the
    transformation operation in a second step. So the only safe approach is to always
    reset the allocation if the box is transformed.

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp

commit 2322895e441ef854eacb776a2589a926f514e738
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 15 10:20:53 2017 -0400

    Do nothing with BL_TO_FORTRAN_3D when CUDA is enabled
    
    Since we are using managed memory to hold a copy of the box bounds,
    we want to directly access the pointer containing that memory, rather
    than save a temporary copy. The CUDA version automatically enables
    the same functionality as the macro because the lo and hi vectors
    contain zeroes in unused spatial dimensions.

Src/Base/AMReX_ArrayLim.H

commit b38b0b9d79b003086b5d8f5eb949d21d6c60c51b
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jun 14 19:14:28 2017 -0700

    WIP: prepare for multi-level work by making a couple of EBLevelGrid objects to start with.

Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/flatplate.inputs
Tests/GeometryShop/vofStructures/sphere.inputs
Tests/GeometryShop/vofStructures/vofStructures.cpp
Tests/GeometryShop/vofStructures/vofStructures_2d.F90
Tests/GeometryShop/vofStructures/vofStructures_3d.F90

commit e05e3124854227fc33b769ca81fd8ec645eeda57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 14 17:56:06 2017 -0700

    User's Guide: bl_allocate, Abort and ASSERT

Docs/AMReXUsersGuide/Basics/Basics.tex

commit f99d7b460b060b0411c1257513b549c5f8021ec5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 14 17:44:09 2017 -0700

    add AMREX_ASSERT and AMREX_ALWAYS_ASSERT

Src/Base/AMReX_BLassert.H

commit abd1c7563e44d9e69d25bd7e64cc2af9a95efedb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 14 16:31:43 2017 -0700

    remove debug line

Src/Base/AMReX_FabArray.H

commit d8d832aeea6a073832142507a42705d4dda15f5b
Merge: 56a7a3971 b51c18133
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 14 16:30:46 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 56a7a397137dfc9a4274a798aeb2dbf783aba883
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 14 16:30:41 2017 -0700

    User's Guide: IO

Docs/AMReXUsersGuide/Basics/Basics.tex

commit d2c02bd11319232f8d90ab0fdea414b71898a955
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jun 14 15:56:17 2017 -0700

    fixed IrregFABFactory parallel bug

Src/GeometryShop/AMReX_EBCellFactory.cpp
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_IrregFABFactory.H
Src/GeometryShop/AMReX_IrregFABFactory.cpp

commit f73536e3ee2de0e08f7ee7a90cc1368d3398dd42
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jun 14 15:33:23 2017 -0700

    remove some debugging junk from the ElectrostaticPIC example.

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90

commit b51c181338b0cbd8f384f4081c01e4ccb6e3beaf
Merge: cba1331ca 345fe63d8
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 14 14:52:40 2017 -0700

    Merge pull request #38 from AMReX-Codes/dtg_branch
    
    Peter M. wants some of the tools in dtg_branch and this should not break anything

commit 345fe63d8b3b33713ad3ae5a1893decbdfcd4aa6
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jun 14 14:47:29 2017 -0700

    took out debugging statements

Src/Base/AMReX_FabArray.H

commit 45349adf1a2939429eef10323f143ac53a24adc7
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jun 14 14:10:38 2017 -0700

    found subtle parallel bug.  More of the EB regression tests now pass in parallel.

Src/Base/AMReX_FabArray.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_GraphNode.H
Src/GeometryShop/AMReX_GraphNode.cpp
Tests/GeometryShop/regression/dataArith.cpp

commit cba1331caae2b4ca07cd111f14a99c6ab013abd0
Merge: 05e8e4bd8 ae613fb5b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 14 14:01:50 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 05e8e4bd8cb6bd5298611602f77ed2df595e8791
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 14 14:01:29 2017 -0700

    code comments, pseudocode of algorithm for AmrCore DesignDoc

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvError.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvEvolve.cpp

commit c2f322d6c3d6888a81afebfa383280ac259f892a
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 14 12:56:35 2017 -0700

    cleaning up the code, no functional changes

Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvIO.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvInit.cpp

commit cf8c05478b6279811856c826b29eec01679166b9
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Jun 14 12:35:16 2017 -0700

    Adding more information about neighbor particles.

Docs/AMReXUsersGuide/Particle/Particle.tex

commit e291805d77a9f81d372108543f5d0bb462bab628
Merge: 086253931 ae613fb5b
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Jun 14 12:12:26 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 08625393187ca09c3c9be32f1cd5dd853c002c0f
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Jun 14 12:12:17 2017 -0700

    Adding some stuff about the ShortRangeTutorial.

Docs/AMReXUsersGuide/Particle/Particle.tex

commit ae613fb5b27f21285d626bfaad1ed35c87915c94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 14 15:09:53 2017 -0400

    fix build

Docs/AMReXUsersGuide/Particle/Particle.tex

commit 8fa1d462bf6fa2d5412e8e3ef258f4042f0c22a1
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Jun 14 12:05:44 2017 -0700

    Particle IO section in docs.

Docs/AMReXUsersGuide/Particle/Particle.tex

commit 8168b8012f297bc37a85057bd21964d0a277d560
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 14 11:46:38 2017 -0700

    User's Guide: boundary

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/Debugging/Debugging.tex

commit bb4959ff683cc23bf9d98559fda7aceb9500e45e
Merge: df898fe92 3e7229ccd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 14 09:27:32 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit df898fe92463213d6715f1a7b1e199ab1b974c05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 14 09:26:20 2017 -0700

    merge

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Docs/AMReXUsersGuide/AmrCore/figs/Adv1.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv1.pdf
Docs/AMReXUsersGuide/AmrCore/figs/Adv2.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv2.pdf
Docs/AMReXUsersGuide/AmrCore/figs/Adv3.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv3.pdf
Docs/AMReXUsersGuide/AmrCore/figs/Adv4.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv4.pdf
Docs/AMReXUsersGuide/AmrCore/figs/Adv5.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv5.pdf
Docs/AMReXUsersGuide/AmrCore/figs/subcycling.eps
Docs/AMReXUsersGuide/AmrCore/figs/subcycling.pdf

commit 123f6d12b9ee0c0a0dcc9002a5cc79360a68d5fc
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 14 08:26:35 2017 -0700

    fix cropping issue in figure

Docs/AMReXUsersGuide/AmrCore/figs/subcycling.pdf

commit 856d80b314e865f5561d1573d1dc07f4cf64d78e
Merge: 716567b20 3e7229ccd
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed Jun 14 01:19:35 2017 -0400

    Merge branch 'development' into gpu

commit 716567b204b23bc30dc5b60fb9b06aafff9f9d5f
Merge: 9eeba24d3 060259bc2
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 13 21:34:40 2017 -0400

    Merge branch 'gpu' into gpu_var2

commit 9eeba24d3a9bb841d14c493c570d24b742087272
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 13 21:34:16 2017 -0400

    Define a CUDA attributes macro

Tools/GNUMake/Make.defs
Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90

commit e46062bc7a3edd670a38426b92f6224b13cd8acf
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 13 21:34:16 2017 -0400

    Clean up the update_phi interface

Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H

commit 63bcdff5eda1697e8c966eb282240614396b11a4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 13 21:34:16 2017 -0400

    Allocate the flux box bounds in C++ driver

Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/main.cpp

commit ddc68adf205ec820ff4570f9e9de94d0ff42241f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 13 21:34:16 2017 -0400

    Refactor to make directional splitting explicit

Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H

commit 07b1fc7eaf107364a5d0d79b890a08a032b4b0ea
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 13 21:34:16 2017 -0400

    Set readonly for CoordSys dx

Src/Base/AMReX_CoordSys.cpp

commit efbab18b9aac37f5c3c34c1544d951b99ca1baf0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 13 21:34:16 2017 -0400

    Set preferred on BaseFab arena

Src/Base/AMReX_BaseFab.cpp

commit 28f773007fc8ead0096fb6b28d0b8722050d9a12
Author: Max Katz <maxpkatz@gmail.com>
Date:   Tue Jun 13 21:34:16 2017 -0400

    Set read only to the Box arena

Src/Base/AMReX_Box.cpp

commit 0f74ed4a157519125c6490f243ee6afbe41bdeda
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 13 17:25:32 2017 -0700

    let's use BL_TO_FORTRAN_BOX

Src/AmrCore/AMReX_FillPatchUtil.cpp
Tutorials/Basic/HeatEquation_EX1_C/main.cpp

commit 3e7229ccd87669caf1e7b944206215079f3bcc88
Merge: e8e1bb408 c6cc2a0fb
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 13 17:18:04 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit e8e1bb408284b786eef25ae88976494a3a1a444a
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 13 17:17:48 2017 -0700

    convert eps to pdf.  some small updates to doc

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Docs/AMReXUsersGuide/AmrCore/figs/Adv1.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv1.pdf
Docs/AMReXUsersGuide/AmrCore/figs/Adv2.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv2.pdf
Docs/AMReXUsersGuide/AmrCore/figs/Adv3.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv3.pdf
Docs/AMReXUsersGuide/AmrCore/figs/Adv4.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv4.pdf
Docs/AMReXUsersGuide/AmrCore/figs/Adv5.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv5.pdf
Docs/AMReXUsersGuide/AmrCore/figs/subcycling.eps
Docs/AMReXUsersGuide/AmrCore/figs/subcycling.pdf

commit 060259bc2586a79164c064df1929f3b9cafcc21f
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Jun 13 17:13:44 2017 -0700

    An allocator that wraps cudaMallocManaged for use with std::vector

Tests/Particles/CUDADeposition/CUDAManagedAllocator.H
Tests/Particles/CUDADeposition/Make.package

commit c6cc2a0fb099cf2448b70b168d8ec9692082e9fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 13 17:12:57 2017 -0700

    User's Guide: calling Fortran

Docs/AMReXUsersGuide/Basics/Basics.tex

commit ccc82c1fb8b358e4b075821d3a2466df9c6f4887
Merge: 2ea416869 a04f0f661
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 13 16:25:41 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 2ea4168691ab01554a601be15628e3b60bd40bb2
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 13 16:25:10 2017 -0700

    added a short explanation of the AMR algorithm for explicit advection before going
    into code details

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Docs/AMReXUsersGuide/AmrCore/figs/Adv1.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv2.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv3.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv4.eps
Docs/AMReXUsersGuide/AmrCore/figs/Adv5.eps
Docs/AMReXUsersGuide/AmrCore/figs/subcycling.eps

commit a04f0f6617ff0af4bd86c4fe8887cce940195146
Merge: cfb354bb9 4e1fb3714
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 13 16:11:46 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cfb354bb990e095400156de7f409aaa547610a4e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 13 16:11:31 2017 -0700

    Use a mask to shift the interpolation to the coarse level for particles near boundary.

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H
Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H
Tutorials/Particles/ElectrostaticPIC/inputs
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit 215b0bbfadfe4bf0a49ff6d92eeace5edaffcef6
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 13 15:39:11 2017 -0700

    get rid of references to boxlib

Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90

commit d3c0c3cf81bab3ceda1cb9fe04337dd272b3b782
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 13 15:05:02 2017 -0700

    update problem description

Tutorials/Amr/Advection_AmrCore/README

commit 185a59447b51c6cb65fb85b2737a9f168c4dc8e7
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 13 14:46:20 2017 -0700

    boxlib ref -> amrex

Tutorials/Amr/Advection_AmrCore/README

commit 4e1fb371472843d7bba8800b2b4b56408b148e2e
Merge: 0e02cedcd eb8364aaa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 13 14:27:34 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 0e02cedcddf53a01f4a036e55d3ec18c78e07d23
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 13 14:27:26 2017 -0700

    move AmrCore advection tutorial out of OldTutorials

Tutorials/Amr/Advection_AmrCore/Exec/Make.Adv
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Make.package
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Prob.f90
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs
Tutorials/Amr/Advection_AmrCore/README
Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H
Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvBC.H
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvError.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvEvolve.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvIO.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrAdvInit.cpp
Tutorials/Amr/Advection_AmrCore/Source/AmrAdv_F.H
Tutorials/Amr/Advection_AmrCore/Source/Make.package
Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Make.package
Tutorials/Amr/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_2d/slope_2d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Make.package
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_3d/slope_3d.f90
Tutorials/Amr/Advection_AmrCore/Source/Src_nd/Make.package
Tutorials/Amr/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90
Tutorials/Amr/Advection_AmrCore/Source/main.cpp

commit eb8364aaa96f01402cd6ebfe8d353fc1fc76f100
Merge: abe54c2b0 77ded8cc1
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 13 14:26:24 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit abe54c2b07ea20560b4c6697dabc85ee1331c78a
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 13 14:26:09 2017 -0700

    start of doc for amrcore

Docs/AMReXUsersGuide/AmrCore/AmrCore.tex

commit 77ded8cc1735c65d0bacf4cc94f6851f7a433848
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 13 14:14:15 2017 -0700

    User's Guide: MFIter and tiling

Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/Basics/cc_growbox.pdf
Docs/AMReXUsersGuide/Basics/cc_tilebox.pdf
Docs/AMReXUsersGuide/Basics/cc_validbox.pdf
Docs/AMReXUsersGuide/Basics/ec_growbox.pdf
Docs/AMReXUsersGuide/Basics/ec_tilebox.pdf
Docs/AMReXUsersGuide/Basics/ec_validbox.pdf

commit eb777114255ef0262c3aa2dc3b073759a262764a
Merge: 6264479ab 8eb1b680c
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Jun 13 13:18:33 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6264479ab4d9ed629f0cc8081ed6400aaf3515ca
Author: atmyers <atmyers2@gmail.com>
Date:   Tue Jun 13 13:18:22 2017 -0700

    more work on the Particle docs.

Docs/AMReXUsersGuide/Particle/Particle.tex

commit afdf2c7ba882c5561b1c11a1e50738f41ae5fb86
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Jun 13 13:00:55 2017 -0700

    After much wailing and gnashing of teeth, I found the bug that was causing Marc's test to fail in initialization (it now fails in his code).

Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBDebugDump.H
Src/GeometryShop/AMReX_EBDebugOut.H
Src/GeometryShop/AMReX_EBDebugOut.cpp
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_FaceIndex.H
Src/GeometryShop/AMReX_FaceIndex.cpp
Src/GeometryShop/AMReX_FaceIterator.cpp
Src/GeometryShop/AMReX_VolIndex.H
Src/GeometryShop/AMReX_VolIndex.cpp
Tests/GeometryShop/vofStructures/vofStructures.cpp

commit c8c40c0638374010da400f594f1349be92b0ecb4
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jun 13 12:09:05 2017 -0700

    WIP: Rename Node.H

Tests/GeometryShop/vofStructures/AMReX_EBStruct.H
Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90
Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/vofStructures.cpp
Tests/GeometryShop/vofStructures/vofStructures_2d.F90
Tests/GeometryShop/vofStructures/vofStructures_3d.F90

commit 8eb1b680c4dc812e6715d2bc1f91f829e51c8723
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jun 13 11:32:06 2017 -0700

    fix sleep seconds.

Src/Base/AMReX_Utility.cpp

commit 5d32e0fbaeb4d2794e325b709fb9e96356728cdd
Merge: 19a5376ea 7ab8def26
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jun 13 11:30:55 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 193a1edbabf03370ff29f59cb85a2b28935b261f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Jun 13 13:47:54 2017 -0400

    Add Arena flags for cudaMemAdvise

Src/Base/AMReX_Arena.H
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H

commit 7ab8def26e9dd4ae3a58c1f863d4a446ec5d5f46
Merge: f18d1ffa4 454589a61
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jun 13 10:38:38 2017 -0700

    Merge pull request #36 from bcfriesen/misc_cvode
    
    Misc CVODE

commit f18d1ffa47d859f7dc37c74ef864b25134a8bd5b
Merge: 7162a5067 b8b1ea1fd
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jun 13 10:38:29 2017 -0700

    Merge pull request #37 from bcfriesen/update_cray_flags
    
    Update Cray flags

commit b8b1ea1fd5f5eb0d9d29794e731ba99602331461
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Jun 8 15:09:54 2017 -0700

    GNUMake: if DEBUG=TRUE, add Cray compiler flag that inits Fortran reals/complexes to NaN

Tools/GNUMake/comps/cray.mak

commit 0fb6c61723fbf606a96c14487871241aae466614
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Jun 7 16:02:56 2017 -0700

    Tools/GNUMake: add optimization report output to Cray compiler

Tools/GNUMake/comps/cray.mak

commit 454589a61f0ce8ef92a4b7faa22f2f8585c1ca3f
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Jun 13 10:12:14 2017 -0700

    VODE: add misc functions for querying integration statistics

Src/Extern/CVODE/Make.package
Src/Extern/CVODE/integrator_stats.f90

commit be3cca32619bc38ef3a4f3fb190d68208cc5e20e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Jun 13 12:57:28 2017 -0400

    Use an arena for Box data

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp

commit ca17549ea4cc3b6877e979d7700d1bf8b316272e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Jun 13 12:17:22 2017 -0400

    Avoid a Box conversion call if unnecessary

Src/Base/AMReX_BoxArray.cpp

commit c8481ebd4e42876ce29da4eaf8c5ad13b9690148
Merge: 673887ce0 82ea6cbb3
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Jun 13 08:38:48 2017 -0700

    merging with dtg_branch before fixing some bugs

commit 9916fc0e9099f143d81ddfbf513d26ad6efa282a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Jun 13 10:17:20 2017 -0400

    Move GPU heat equation example to new directory

Tutorials/Basic/HeatEquation_EX1_C/Make.package
Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90
Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90
Tutorials/Basic/HeatEquation_EX1_C/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H
Tutorials/GPU/HeatEquation_EX1_C/GNUmakefile
Tutorials/GPU/HeatEquation_EX1_C/Make.package
Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90
Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90
Tutorials/GPU/HeatEquation_EX1_C/init_phi_2d.f90
Tutorials/GPU/HeatEquation_EX1_C/init_phi_3d.f90
Tutorials/GPU/HeatEquation_EX1_C/inputs_2d
Tutorials/GPU/HeatEquation_EX1_C/inputs_3d
Tutorials/GPU/HeatEquation_EX1_C/main.cpp
Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H

commit fd020af2fa8010603a3cf75780423a13c1c26599
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Jun 13 10:01:13 2017 -0400

    Pass idir and dt by value

Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90
Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90

commit 673887ce0332504404230d3591e9ba570cdd8d7e
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 12 21:14:25 2017 -0700

    WIP: enforce that faces between regular and cut cells are regular, and seen that way from within the cut cell

Tests/GeometryShop/vofStructures/Node.H
Tests/GeometryShop/vofStructures/vofStructures.cpp
Tests/GeometryShop/vofStructures/vofStructures_2d.F90
Tests/GeometryShop/vofStructures/vofStructures_3d.F90

commit 5cfbce3238c6c2b220c412b6dc147dabc67e4c06
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Mon Jun 12 23:14:13 2017 -0400

    Rely on managed memory in heat equation

Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90
Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90
Tutorials/Basic/HeatEquation_EX1_C/main.cpp

commit 002c516328c7d827834ffc743ba98d0b5b583db3
Merge: 791c64814 1b9b259bb
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Mon Jun 12 23:05:30 2017 -0400

    Merge branch 'gpu' into gpu_var2

commit 791c64814c8abdbec69bdcfa0b1f1b2ccd17ebb8
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Mon Jun 12 22:48:52 2017 -0400

    Use a managed memory approach for the Box lo and hi bounds
    
    A shared pointer is created that stores the managed memory versions of
    lo and hi (which mirror what smallend and bigend store). The shared pointer
    is reset when a transforming function like surroundingNodes is called.

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp

commit 11099ff5ccc76e7ca33f9b546516c9b1179412ae
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 12 19:44:19 2017 -0700

    WIP: remove unused member data from local struct

Tests/GeometryShop/vofStructures/vofStructures.cpp

commit ce273baaa85fe14f36c4398a9ca86658827af909
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 12 19:39:31 2017 -0700

    WIP: move fort graph construction into function call

Tests/GeometryShop/vofStructures/vofStructures.cpp

commit 1b9b259bb40cf67882446c5694c24acac9d2d3dd
Merge: 5d1b92efb 86aeb3fca
Author: Max Katz <maxpkatz@gmail.com>
Date:   Mon Jun 12 19:30:20 2017 -0700

    Merge pull request #35 from xinshengqin/gpu2
    
    Add 3d cuda version of the heat equation tutorial

commit 7162a50671f7434dbba86ca2ae7f0174881742f8
Merge: 1e2e15468 f20bbf8d9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 12 17:51:10 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 1e2e154687e2d3e97bb64ed4a121e35981bb17e3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 12 17:33:12 2017 -0700

    generalize build mask to take a number of buffer cells instead of assuming 1.

Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit cc6c68c678b4be0d531a860ec5de9c1736cb04a9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 12 17:32:02 2017 -0700

    Need to special case num_levels = 1 here.

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp

commit f20bbf8d97e65448d2582054a670a8b3f86789c2
Merge: 73890f1d2 3aea35807
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 12 17:20:53 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 73890f1d2a2c4671e7fb1a475bc923c0d067119b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 12 17:20:24 2017 -0700

    added basic documentation for how to open 3d plotfiles and amrex particle data with paraview

Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex
Docs/AMReXUsersGuide/Introduction/Introduction.tex
Docs/AMReXUsersGuide/Visualization/ParaView.eps
Docs/AMReXUsersGuide/Visualization/ParaView_particles.eps.REMOVED.git-id
Docs/AMReXUsersGuide/Visualization/Visualization.tex
Docs/AMReXUsersGuide/amrexsymbols.tex

commit 3aea35807b425a11fc087578754672068be6be15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 12 16:56:22 2017 -0700

    User's Guide: MFiter without tiling

Docs/AMReXUsersGuide/Basics/Basics.tex

commit 593ffe74c96d613d3316c2e6c224368aaf8f118f
Merge: ba9ec36d8 acb7f17af
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jun 12 16:44:34 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ba9ec36d82a8c79d885532d8887b165f866e2c2a
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jun 12 16:44:27 2017 -0700

    fix comment.

Tutorials/Particles/ShortRangeParticles/short_range_2d.f90
Tutorials/Particles/ShortRangeParticles/short_range_3d.f90

commit 0846cb596d07ac5afb1111c21a22937373fbb36a
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jun 12 16:43:34 2017 -0700

    some more work on the Particle docs.

Docs/AMReXUsersGuide/Particle/Particle.tex

commit acb7f17afc0ef4316679e35e80775f9eac0cac50
Merge: af709e39c 001e00f82
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 12 16:22:59 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit af709e39ce27b7bae5984d59bf4dfa2cefb6dff7
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 12 16:22:20 2017 -0700

    for python script to convert amrex particle data to .vtp format, throw out extra four lines in header (after # of particles)

Tools/Py_util/amrex_particles_to_vtp/amrex_particles_to_vtp.py

commit 770aeebd51369c3dcea9c7ee3c47c59994608085
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Jun 12 16:22:08 2017 -0700

    bugs found in EBGraph, FaceIterator

Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_FaceIterator.cpp

commit 001e00f82749cc29f17c75059a54c54691ff96d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 12 15:32:41 2017 -0700

    User's Guide: parallel copy

Docs/AMReXUsersGuide/Basics/Basics.tex

commit 82ea6cbb3bd662bda2d099ea104479c173d07c39
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Jun 12 15:24:33 2017 -0700

    added some parallel debugging tools

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_SPMD.H
Src/Base/AMReX_SPMD.cpp
Src/Base/AMReX_SPMDI.H
Src/Base/AMReX_parstream.H
Src/Base/AMReX_parstream.cpp
Src/Base/Make.package
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_GraphNode.cpp
Src/GeometryShop/Make.package
Tests/GeometryShop/ebgraphDistributed/GNUmakefile
Tests/GeometryShop/ebgraphSingleGrid/GNUmakefile
Tests/GeometryShop/flatPlate/GNUmakefile
Tests/GeometryShop/regression/dataArith.cpp
Tests/GeometryShop/regression/dataarith.inputs
Tests/GeometryShop/regression/serialization.cpp
Tests/GeometryShop/regression/serialization.inputs
Tests/GeometryShop/runalltests.mpi.sh
Tests/GeometryShop/runalltests.serial.sh
Tests/GeometryShop/sparseDataSingleGrid/GNUmakefile
Tests/GeometryShop/sphere/GNUmakefile
Tests/GeometryShop/sphereEBISBox/GNUmakefile

commit 4dda54d4134b2768cb455e8c748e3b77399db046
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 12 15:20:12 2017 -0700

    WIP: Try to add flat plate geom, but there are issues...

Tests/GeometryShop/vofStructures/flatplate.inputs
Tests/GeometryShop/vofStructures/sphere.inputs
Tests/GeometryShop/vofStructures/vofStructures.cpp

commit e1b4d94939dda4eb13b66c727b3be281ad0ea6d9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 12 12:44:57 2017 -0700

    removing some commented-out code.

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H
Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90
Tutorials/Particles/ElectrostaticPIC/inputs
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit b20b85fdf3b29093b1a48fc6bf8214a1c84a4b2a
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 12 12:38:05 2017 -0700

    WIP: fix bug in eb f90 struct, add some checking of faces in fortran.

Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90
Tests/GeometryShop/vofStructures/vofStructures.cpp
Tests/GeometryShop/vofStructures/vofStructures_2d.F90
Tests/GeometryShop/vofStructures/vofStructures_3d.F90

commit 6c61218cec4d70d79cc558b269bb4a5bf5166a51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 12 11:19:46 2017 -0700

    User's Guide: FillBoundary

Docs/AMReXUsersGuide/Basics/Basics.tex

commit ac42272ee3c3b2de5eee46874f5bab61b85dcd76
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 12 11:18:01 2017 -0700

    WIP: Pass face-based structs to fortran, add note in README

Tests/GeometryShop/vofStructures/README.txt
Tests/GeometryShop/vofStructures/vofStructures.cpp
Tests/GeometryShop/vofStructures/vofStructures_2d.F90
Tests/GeometryShop/vofStructures/vofStructures_3d.F90

commit 7b7201919433b09aebb613a3f6e68a9c3e43a34c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 12 11:17:00 2017 -0700

    add ParallelCopy to FabArray to make the parallel part clearer

Src/Base/AMReX_FabArray.H

commit d0cb009134cd783f325a49850c21888bcd8fa920
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 12 10:52:33 2017 -0700

    WIP: Move eb struct def into mod file

Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90
Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/vofStructures_2d.F90
Tests/GeometryShop/vofStructures/vofStructures_3d.F90

commit e8370e9026fe349fbbd6c36189d3c33ccdf0710a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jun 12 10:36:14 2017 -0700

    check in working version of ES single particle test.

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H
Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H
Tutorials/Particles/ElectrostaticPIC/inputs
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit 86aeb3fca44b6ba76f897466e904547227a91285
Author: Xinsheng (Shawn) Qin <xinshengqin2014@gmail.com>
Date:   Sun Jun 11 14:33:19 2017 -0700

    change blo(2) and bhi(2) in advance_2d to blo(3) and bhi(3) to avoid warning

Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90

commit 5aa6b5cc6bcb1abb490b30811cc1e52f9e11f10e
Merge: 704cf79e8 5d1b92efb
Author: Xinsheng (Shawn) Qin <xinshengqin2014@gmail.com>
Date:   Sun Jun 11 14:01:23 2017 -0700

    Merge remote-tracking branch 'origin/gpu' into gpu2

commit 5d1b92efb22881519f1420f469f4c391f5d7d576
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jun 11 16:02:48 2017 -0400

    Fix loop bounds in update_phi_doit

Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90

commit 4ebaf67182602449724b3fd9682d3d0a486f6c39
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jun 11 14:56:57 2017 -0400

    Do not copy dx now that it is managed memory

Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90

commit 201cfc8f26dde726f065913b1c4c5435c3b3499f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jun 11 14:56:24 2017 -0400

    Create managed dx object in Geometry, returned by CellSize()

Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_Geometry.cpp

commit 704cf79e8fee0873cfe9eace07c513151eab8e2a
Author: Xinsheng (Shawn) Qin <xinshengqin2014@gmail.com>
Date:   Sat Jun 10 23:22:43 2017 -0700

    finish CUDA 3D version. Result tested.

Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90
Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90

commit 7325b12f3c19e0cbfd27e4d077eaffa857d02442
Merge: 923385c63 328915650
Author: Xinsheng (Shawn) Qin <xinshengqin2014@gmail.com>
Date:   Sat Jun 10 23:17:21 2017 -0700

    Merge remote-tracking branch 'origin/gpu' into gpu2

commit 9a7cd7db9d142ba725104ceb8be944dee2d22072
Merge: 38bcfcc22 a3dd3cd79
Author: Marc Day <MSDay@lbl.gov>
Date:   Sat Jun 10 19:34:38 2017 -0700

    Merge branch 'dtg_branch' into vof-work

commit 38bcfcc2299e6e14b9b1ef14450c3919b8ec5636
Author: Marc Day <MSDay@lbl.gov>
Date:   Sat Jun 10 19:33:54 2017 -0700

    WIP: Add 3d fort for vofstructures test

Tests/GeometryShop/vofStructures/vofStructures_3d.F90

commit 3289156503e1b93ab13af811ab1373befe0d51d1
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Jun 10 19:58:20 2017 -0400

    Move C interfaces into a module

Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90

commit bd180365a8e14f5a8bf6d47ab42d316dff1805a2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Jun 10 19:56:14 2017 -0400

    Launch kernels directly, avoiding CUDA wrappers

Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90

commit 923385c63f0e74909df81d5e30681a7a43e3906b
Author: Xinsheng (Shawn) Qin <xinshengqin2014@gmail.com>
Date:   Sat Jun 10 16:38:11 2017 -0700

    CUDA 3D version results checked

Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90

commit b21c68f10d81e81ac79576630934c164ef48c9c5
Author: Xinsheng (Shawn) Qin <xinshengqin2014@gmail.com>
Date:   Sat Jun 10 15:51:36 2017 -0700

    Fix some issues for CPU part. CPU results checked

Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90

commit ff7edb5bd49c68aaa9a8adad6deeb35845b4c6a9
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Jun 10 14:19:23 2017 -0400

    Fix some issues in the GPU heat equation

Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90
Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90
Tutorials/Basic/HeatEquation_EX1_C/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H

commit 6f2ecd77ae082ee758070c9af178404df9ab4e51
Merge: 53368ab5c 191c36a9f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Jun 10 12:17:46 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 0417d17cfc77e50dc75db752749d7ee446c23166
Author: Marc Day <MSDay@lbl.gov>
Date:   Sat Jun 10 00:44:12 2017 -0700

    Add a comment while I remember what I did.

Tests/GeometryShop/vofStructures/vofStructures.cpp

commit c7d297ee53c739351811dc6fe63f8c9ecf6848b4
Author: Marc Day <MSDay@lbl.gov>
Date:   Sat Jun 10 00:41:41 2017 -0700

    Add ebFaceID to CNode struct

Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/Node.H
Tests/GeometryShop/vofStructures/vofStructures.cpp
Tests/GeometryShop/vofStructures/vofStructures_2d.F90

commit a3dd3cd79472eae17c658c2decf8bd87e6d4ddeb
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri Jun 9 19:57:49 2017 -0700

    fixed IntVectSet to accomodate the fact that std::set is weird

Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_GraphNode.cpp
Src/GeometryShop/AMReX_IntVectSet.cpp

commit 191c36a9f781abcbac3450eb4674a914cb0b6ffb
Merge: 1619dddd7 9ee92ad86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jun 9 13:01:06 2017 -0400

    Merge branch 'development' into gpu

commit 9ee92ad8620fc6f865e5a5241f93cb01974002be
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Jun 9 12:51:05 2017 -0400

    CMakeLists.txt was missing this header file.

Src/AmrCore/CMakeLists.txt

commit 19a5376ea6563fa56ee0690a7f3b9a14950b487f
Merge: c345c6ef5 36408c018
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 9 09:37:36 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 36408c018fb29c38b50740db0f3e8fa50609c2df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 9 09:10:28 2017 -0700

    make: strip leading and trailing whitespace from many make variables

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.machines

commit 1619dddd7bb44e41d61434c5b81ec661f977d4d0
Merge: be4064f95 5864b47d7
Author: Andrew Myers <atmyers2gmail.com>
Date:   Fri Jun 9 11:40:21 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit be4064f95e4939eeac36bf0f8682106228b23b6d
Author: Andrew Myers <atmyers2gmail.com>
Date:   Fri Jun 9 11:40:15 2017 -0400

    some renaming.

Tests/Particles/CUDADeposition/MyParticleContainer.H
Tests/Particles/CUDADeposition/main.cpp

commit 53368ab5c3b676dee0b9fe72acb358aceb5e7efb
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri Jun 9 11:24:29 2017 -0400

    Strip out unnecessary CUDA wrappers

Src/Base/AMReX_BaseFab_nd.F90
Src/Base/AMReX_fort_mod.F90

commit 6c3eb230ef774877f17284b54ac4dbbe344bf24f
Author: Andrew Myers <atmyers2gmail.com>
Date:   Fri Jun 9 11:02:18 2017 -0400

    reorganizing the CUDA-enabled particle container.

Tests/Particles/CUDADeposition/MyParticleContainer.H
Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/inputs
Tests/Particles/CUDADeposition/main.cpp

commit 5864b47d7e39267c75388002114a085529848b23
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri Jun 9 08:45:29 2017 -0400

    Don't do threads_and_blocks without BL_SPACEDIM

Src/Base/AMReX_CUDA.F90

commit c1dd9f3cce7880cf0d57cd5e408f5f6405fe5d17
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Jun 8 22:23:37 2017 -0400

    Remove incorrect underscore

Src/Base/GPackage.mak

commit eccd5db4ad5e5b9d8e4c2e310d3c67a25217a683
Merge: a9db60c60 122e8534f
Author: Andrew Myers <atmyers2gmail.com>
Date:   Thu Jun 8 21:20:07 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit a9db60c60d3bc77965f69930f8434a569be0df1c
Author: Andrew Myers <atmyers2gmail.com>
Date:   Thu Jun 8 21:19:59 2017 -0400

    implementing multiple streams for the Cuda PIC example/

Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/cuda_deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_F.H
Tests/Particles/CUDADeposition/inputs
Tests/Particles/CUDADeposition/main.cpp

commit 1f85eaff2da7a4bfd48f8a32d5f7e442c29a224d
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 8 18:11:44 2017 -0700

    WIP: More testing of vof stuff in fortran

Tests/GeometryShop/vofStructures/Node.H
Tests/GeometryShop/vofStructures/vofStructures.cpp
Tests/GeometryShop/vofStructures/vofStructures_2d.F90

commit 00a9369ff37faddfc2c6dfe21e5fadce0fcb4fc6
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 8 17:06:48 2017 -0700

    WIP: Move defines for mask type into .H file

Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/Node.H
Tests/GeometryShop/vofStructures/vofStructures.cpp
Tests/GeometryShop/vofStructures/vofStructures_2d.F90

commit d237f080f14d9e9e4f384515c82811bfffa7830c
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 8 15:54:27 2017 -0700

    WIP: fix fortran and grow cell issue

Tests/GeometryShop/vofStructures/sphere.inputs
Tests/GeometryShop/vofStructures/vofStructures.cpp
Tests/GeometryShop/vofStructures/vofStructures_2d.F90

commit 122e8534f96e462e67d4d6eebb00674dcdbc0142
Merge: 27e9bfff2 638e331c0
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 8 18:40:34 2017 -0400

    Merge pull request #33 from xinshengqin/gpu2
    
    change Tools/GNUMake/Make.rules to be shell-independent

commit 638e331c0ef5fc0b4e36fd74a3f9fac37f72e778
Merge: 3757679ed 27e9bfff2
Author: Xinsheng (Shawn) Qin <xinshengqin2014@gmail.com>
Date:   Thu Jun 8 15:16:28 2017 -0700

    Merge remote-tracking branch 'origin/gpu' into gpu2

commit 3757679ed1e61b6eca2f9f0f4331f0b1f8804733
Author: Xinsheng (Shawn) Qin <xinshengqin2014@gmail.com>
Date:   Thu Jun 8 15:15:59 2017 -0700

    update Make.rules to use shell-independent if condition

Tools/GNUMake/Make.rules

commit 27e9bfff26f28643545a61f749edba445e0ea3c9
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Jun 8 17:50:42 2017 -0400

    Add in CUDA C++ to F90 build

Src/Base/GPackage.mak

commit eddf13ae61d4a7f57aed80d1261401c5a80212e7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Jun 8 17:03:37 2017 -0400

    Add an alternate FOEXTRAP version of filcc

Src/Base/AMReX_FILCC_3D.F90

commit 428a1520e4a33063fa6bb028ede17732894d937f
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 8 13:19:58 2017 -0700

    WIP: Try adding a grow cell...failure

Tests/GeometryShop/vofStructures/vofStructures.cpp

commit 9870052357ce78a80f03bc791093327c2a3c25db
Merge: 84b2b5abf bb03918ba
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu Jun 8 16:12:59 2017 -0400

    Merge pull request #32 from alancalder/gpu
    
    Gpu What should complete the cudaizing of the advance_3d.F90 routine for the Heat Equation Test.

commit f005aa2f94781767b255d51443bde291c6e0b7a1
Merge: cf56b7b80 13e0db1ad
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jun 8 13:03:38 2017 -0700

    Merge pull request #31 from bcfriesen/CVODE_tutorial_fixes
    
    Tutorials: fix pointer mistake in CVODE/EX1 and CVODE/EX2

commit 84b2b5abfd4e5a21b1ac7391e72c6c71901ddf36
Author: Andrew Myers <atmyers2gmail.com>
Date:   Thu Jun 8 16:01:41 2017 -0400

    use cuda streams when running with multiple boxes.

Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/cuda_deposit_3d.f90

commit bb03918ba345eb6d7d394feee381dae8b17dfe39
Author: Alan Calder <acalder@icsubmit01.sdcc.bnl.gov>
Date:   Thu Jun 8 15:57:10 2017 -0400

    Another pass at the advance_3d.F90 routine from the Heat Equation
    Test. Should be complete this time.

Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90

commit 13e0db1ad02d35034f82cf029e9e0969a4a28a39
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Jun 8 12:38:54 2017 -0700

    Tutorials: fix pointer mistake in CVODE/EX1 and CVODE/EX2
    
    I mistakenly thought that the CVODE function N_VMake_Serial() allocates
    a new C array and deep copies the data from the corresponding Fortran.
    But in fact it simply creates a C pointer that points to the Fortran
    data.

Tutorials/CVODE/EX1/integrate_ode.f90
Tutorials/CVODE/EX2/integrate_ode_no_jac.f90
Tutorials/CVODE/EX2/integrate_ode_with_jac.f90

commit 272e8df7624f6a9e287cc5b325aafe02ed0f25e3
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jun 8 12:38:12 2017 -0700

    WIP: Rework eb structures a bit, add fortran to test

Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/README.txt
Tests/GeometryShop/vofStructures/vofStructures.cpp
Tests/GeometryShop/vofStructures/vofStructuresA.cpp
Tests/GeometryShop/vofStructures/vofStructures_2d.F90

commit cf56b7b8055d97c4a9e3b95abc318978c3950d54
Merge: 307c5a7de a127bec01
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu Jun 8 12:36:31 2017 -0700

    Merge pull request #30 from AMReX-Codes/dtg_branch
    
    initial indications are that two-stage communication seems to be working

commit a127bec01d3a8e23137fb8ea022ad8249ad75c75
Merge: b698187b1 307c5a7de
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jun 8 12:22:49 2017 -0700

    merging with development branch

commit b698187b1f598a2423634b7b43ffc2676db62d91
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jun 8 12:21:35 2017 -0700

    took out some unused variables

Src/GeometryShop/AMReX_EBGraph.cpp

commit 987e5980cb0e291ca1ce4f19fd317add3261ff5a
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jun 8 11:08:17 2017 -0700

    made EBData holders (since they are templated) preallocatable = false without a ton of thought.   We can revisit this for template specializations where we know it to be true.

Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_BaseEBFaceFAB.H
Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBGraph.H

commit 04e10db39eeed060527e2eecd2fdafdb440eefd1
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jun 8 10:56:43 2017 -0700

    fixed merge bug

Src/EBAMRTools/AMReX_EBFortND_F.H

commit 1a50c06e827322e67d51bc3a958c3725e3a88303
Merge: d16c596bd 67ef79763
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jun 8 10:53:16 2017 -0700

    merging with weiqun/2passes

commit c6bb9dc74c98380c52b4bdd9cb51048e4e04035f
Author: Andrew Myers <atmyers2gmail.com>
Date:   Thu Jun 8 13:46:32 2017 -0400

    Adding another timer.

Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/main.cpp

commit ea1de653b6ef1d928457cf903f27a6c19f59c4b0
Author: Andrew Myers <atmyers2gmail.com>
Date:   Thu Jun 8 13:43:20 2017 -0400

    Also doing the Poisson solve.

Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/cuda_deposit_3d.f90
Tests/Particles/CUDADeposition/main.cpp
Tests/Particles/CUDADeposition/solve_for_accel.cpp

commit d16c596bd0634a364d7b9a0c6b8a9334eee1e8a8
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jun 8 10:40:24 2017 -0700

    EBIndexSpace read/write now works and is tested.

Src/Base/AMReX_Utility.cpp
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Tests/GeometryShop/README
Tests/GeometryShop/regression/ebio.cpp
Tests/GeometryShop/regression/ebio.inputs
Tests/GeometryShop/regression/fabio.cpp

commit d129fd85eb2687d2b6b147a7bfe61ac334350fd4
Merge: 78798d524 d1ec6c184
Author: Andrew Myers <atmyers2gmail.com>
Date:   Thu Jun 8 12:03:21 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit d1ec6c184d870a9c43f463d40ad5e5358ad16afe
Merge: bef191267 307c5a7de
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Jun 8 11:58:43 2017 -0400

    Merge branch 'development' into gpu

commit 307c5a7de6d86625fc7629c05732a379675ebf8e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Jun 8 11:55:34 2017 -0400

    Specify CUDA 8.0 for OpenACC

Tools/F_mk/comps/Linux_pgi.mak

commit 78798d524914dc962387fec237695d0dfa4dfa4d
Author: Andrew Myers <atmyers2gmail.com>
Date:   Thu Jun 8 11:49:21 2017 -0400

    fix capitalization issue.

Tests/Particles/CUDADeposition/Make.package

commit 185424ade5fb0c23a163adbf0f75cf18d6a04bbd
Author: Andrew Myers <atmyers2gmail.com>
Date:   Thu Jun 8 11:47:14 2017 -0400

    This compiles and runs correctly both with and without CUDA.

Tests/Particles/CUDADeposition/GNUmakefile
Tests/Particles/CUDADeposition/Make.package
Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/cuda_deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_F.H
Tests/Particles/CUDADeposition/main.cpp

commit 427c6db66b4fdc479f8a46ebb13ffe36069ffaf2
Author: Andrew Myers <atmyers2gmail.com>
Date:   Thu Jun 8 11:27:27 2017 -0400

    making this thing compile both with and without CUDA.

Tests/Particles/CUDADeposition/cuda_deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_3d.f90

commit e6177d9952e1382f2ea1bf1e3168f027b3f6dc8a
Author: Andrew Myers <atmyers2gmail.com>
Date:   Thu Jun 8 11:13:45 2017 -0400

    bringing over some stuff needed for the MG solves.

Tests/Particles/CUDADeposition/solve_for_accel.cpp
Tests/Particles/CUDADeposition/solve_with_f90.cpp

commit bef191267e50cee9a977a27a11a82f7145de3177
Merge: 3929652df c892d0c55
Author: Andrew Myers <atmyers2gmail.com>
Date:   Thu Jun 8 10:59:56 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 3929652dfe09285ffc4af8d60b7bceeb011c4c06
Author: Andrew Myers <atmyers2gmail.com>
Date:   Thu Jun 8 10:57:17 2017 -0400

    fixed double-counting issue.

Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_F.H
Tests/Particles/CUDADeposition/main.cpp

commit c892d0c556de86460647a3658d17aa72ed39978f
Merge: 1dcf8cd5f 441090acf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 8 10:51:30 2017 -0400

    Merge branch 'gpu' of ssh://github.com/AMReX-Codes/amrex into gpu

commit 1dcf8cd5f867670ca5efe77fb2e88a5175fdd0dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 8 10:51:14 2017 -0400

    remove the rest of the arraylim stuff for clarity

Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F90

commit 441090acfcbab43c2f319467896927d9981d88aa
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Jun 8 10:32:28 2017 -0400

    More cleanup of filcc interfaces

Src/Base/AMReX_FILCC_3D.F90

commit 8f1b7ee41c98faa32da199be2b8eb814bb676d82
Merge: cb7367be5 6ab429139
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 8 10:25:20 2017 -0400

    Merge branch 'gpu' of ssh://github.com/AMReX-Codes/amrex into gpu

commit cb7367be5eb8e8367aad95bcc2b30a50d94ebe42
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 8 10:25:07 2017 -0400

    remove dim macros for clarity

Src/Base/AMReX_FILCC_3D.F90

commit 6ab429139d61dcccc9353d651b91a2b3b34df17c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Jun 8 10:18:54 2017 -0400

    Add some FabArray/MultiFab profiling

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.cpp

commit 6e91722ed7c716490604d5da07fbcce4c1db6d63
Merge: 926e548db 5edf1a08d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 8 09:58:30 2017 -0400

    Merge branch 'gpu' of ssh://github.com/AMReX-Codes/amrex into gpu

commit 926e548dbee255798e2f522d8810aa42e4a1d95b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 8 09:58:11 2017 -0400

    make these free-form

Src/Base/AMReX_FILCC_1D.F
Src/Base/AMReX_FILCC_1D.F90
Src/Base/AMReX_FILCC_2D.F
Src/Base/AMReX_FILCC_2D.F90
Src/Base/AMReX_FILCC_3D.F
Src/Base/AMReX_FILCC_3D.F90
Src/Base/Make.package

commit 5edf1a08d2e1014d24157debd700232596f96a2d
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Jun 8 08:31:19 2017 -0400

    Fix CPU versions of saxpy and plus

Src/Base/AMReX_BaseFab_nd.F90

commit b6cc9419114ee7e83d73c414ce8459305b9f9c1d
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jun 7 20:17:30 2017 -0700

    WIP: Remove covered faces from data set

Tests/GeometryShop/vofStructures/vofStructuresA.cpp

commit 49bdddae98f157dfdd9c3a951909712db5bc8d3c
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jun 7 20:08:27 2017 -0700

    WIP: Rename FLUID to REGULAR

Tests/GeometryShop/vofStructures/vofStructuresA.cpp

commit 315d2476d2f2e9862eea97f190af9661dd2836d7
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jun 7 20:00:46 2017 -0700

    WIP: An alternative set of structures to chase the graph in Fortran.

Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/vofStructures.cpp
Tests/GeometryShop/vofStructures/vofStructuresA.cpp

commit 45e74d329fc82a303cb3ffca92edd5a5eaaac10b
Author: Andrew Myers <atmyers2gmail.com>
Date:   Wed Jun 7 21:55:59 2017 -0400

    fix to domain decomposed version.

Tests/Particles/CUDADeposition/deposit_3d.f90

commit fb84a237d95bf4cc6c3447c3355769f81b9c58f7
Merge: 9184fefc5 559bd89c7
Author: Andrew Myers <atmyers2gmail.com>
Date:   Wed Jun 7 20:25:51 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 9184fefc506e2a990bf68eeaa7628434a8daba22
Merge: 0d8e35929 df2f0a566
Author: Andrew Myers <atmyers2gmail.com>
Date:   Wed Jun 7 20:25:25 2017 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into gpu

commit 0d8e3592967a15d8e71e7095066143a7738e9f22
Author: Andrew Myers <atmyers2gmail.com>
Date:   Wed Jun 7 20:25:08 2017 -0400

    converting more pic kernels to cuda.

Tests/Particles/CUDADeposition/MyParticleContainer.H
Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_F.H
Tests/Particles/CUDADeposition/main.cpp

commit b19e739c665637831f6f8a52574cdf9bc61c84e8
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jun 7 16:24:10 2017 -0700

    fixed an I/O bug.  Added istream for RealVect.  On to trying out two-phase communication

Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Src/GeometryShop/AMReX_FabArrayIO.H
Tests/GeometryShop/regression/GNUmakefile
Tests/GeometryShop/regression/ebio.cpp
Tests/GeometryShop/regression/ebio.inputs
Tests/GeometryShop/regression/fabio.inputs

commit 559bd89c72e73e8b47633ea9a20318b941d60f63
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 7 19:14:27 2017 -0400

    enable CUDA for IBM

Tools/GNUMake/comps/ibm.mak

commit 5a6285ddd0ffc6940833f295152cc2554af6418a
Merge: 643512d6a df2f0a566
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 7 19:08:54 2017 -0400

    Merge branch 'development' into gpu

commit 67ef79763a05360d6540a5ae8039e7a9df526cf1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 7 15:23:46 2017 -0700

    fix deadlock in 2-pass communication

Src/Base/AMReX_FabArray.H

commit c8620055727f4c3e192c0bc9f7164eb532de801a
Merge: 24fe19abc 028d4088e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jun 7 15:06:45 2017 -0700

    Merge pull request #28 from AMReX-Codes/weiqun/tmp
    
    Add Intel to the list of compilers we test on to set the --traditiona…

commit 028d4088eb23246a865659530d80e4a19de9fdd5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jun 7 14:59:49 2017 -0700

    Add Intel to the list of compilers we test on to set the --traditional flag

Tools/CMake/PreprocessAMReXFortran90.cmake

commit df2f0a5669ab8c46da5b775a077078c32d5a3fdd
Merge: 65cc49582 65e038dd0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jun 7 15:00:07 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 65cc495822ba35048ccdb1710ad5a64e6fd9fe01
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jun 7 14:59:49 2017 -0700

    Add Intel to the list of compilers we test on to set the --traditional flag

Tools/CMake/PreprocessAMReXFortran90.cmake

commit 643512d6af6929f5c49f099595ed099896bdf9f3
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed Jun 7 17:45:39 2017 -0400

    Write proper kernels for copy, saxpy, setval, and plus

Src/Base/AMReX_BaseFab_nd.F90

commit 65fce5f9a15eedef4aae2cab4bfce7815e1cbdb0
Author: Andrew Myers <atmyers2gmail.com>
Date:   Wed Jun 7 17:18:10 2017 -0400

    some more work on the domain decomp stuff.

Tests/Particles/CUDADeposition/deposit_3d.f90
Tests/Particles/CUDADeposition/inputs

commit f190c26464098901b9be509c3bffc6b4384ab15a
Merge: f658e4830 85e4515c4
Author: Xinsheng (Shawn) Qin <xinshengqin2014@gmail.com>
Date:   Wed Jun 7 13:49:17 2017 -0700

    Merge remote-tracking branch 'origin/gpu' into gpu2

commit 6631f2851e8731b5020268f9c9271274825cd15d
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jun 7 13:37:19 2017 -0700

    I/O for FabArray<T> (for T = EBGraph, EBData and BaseEBCellFAB) seems to work fine.

Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_EBData.H
Tests/GeometryShop/regression/fabio.cpp
Tests/GeometryShop/regression/serialization.cpp
Tests/GeometryShop/regression/serialization.inputs

commit 85e4515c4a1afaeeac360f0e397bf54dae389d6e
Merge: 3ed3ca103 d0d8cfed9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 7 16:37:03 2017 -0400

    Merge pull request #27 from alancalder/gpu
    
    Alan's pass at cudaizing the 3-d advance routine for the heat

commit d0d8cfed904450a93ad11596b83428340175bcf5
Author: Alan Calder <acalder@icsubmit01.sdcc.bnl.gov>
Date:   Wed Jun 7 16:34:13 2017 -0400

    Fixed two bugs in advance_3d.F0 of the heat equation test identified
    by Mike and Max.

Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90

commit df6d1e500bf9ab9ed8a1aa15607eb415efefadb6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 7 13:30:12 2017 -0700

    have to sum up number of bytes for each communication tile because of metadata

Src/Base/AMReX_FabArray.H

commit 8074f4b1466c8401356d8612dff13778af65cce4
Author: Alan Calder <acalder@icsubmit01.sdcc.bnl.gov>
Date:   Wed Jun 7 15:59:24 2017 -0400

    Alan's pass at cudaizing the 3-d advance routine for the heat
    equation test.

Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90

commit 86c3ff799405cf95a3c183ea8d7490bbc0246406
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 7 12:42:21 2017 -0700

    Perform 2-pass communication if the receiver cannot preallocate the receive buffer.  FAB in FabArray<FAB> needs to have a preAllocatable() function indicate this.

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H

commit 33049a64e2bb97d1ed2bf6bee05de78d3887f16f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed Jun 7 11:45:14 2017 -0700

    serialization for everything in sight (EBGraph, EBData, BaseIFFAB, BaseIVFAB) seems to work in the test.

Src/GeometryShop/AMReX_BaseIFFABI.H
Tests/GeometryShop/regression/GNUmakefile
Tests/GeometryShop/regression/serialization.cpp

commit 3ed3ca103cbfa67b8130dd2f86ad42f94a4a9621
Merge: 6e20c0573 99328c051
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 7 14:25:38 2017 -0400

    Merge branch 'gpu' of ssh://github.com/AMReX-Codes/AMReX into gpu

commit 6e20c0573e7952d026ba6bb71464779f5b90c5ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 7 14:25:28 2017 -0400

    add an INCLUDE_LOCATIONS for CUDA

Tools/GNUMake/Make.defs

commit 99328c051f29763f945f5f231a3aa7f2e36ef903
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed Jun 7 14:20:52 2017 -0400

    Use CArena for CUDA

Src/Base/AMReX_CArena.cpp
Tools/GNUMake/Make.defs

commit 65c5f3702fca285a7169249dddae869b4aa5dfca
Merge: 8eb8e05ec dbd9220ca
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed Jun 7 14:19:32 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit f658e4830378337fc2da2b07c349b9b0a303702d
Merge: 44bbbe2e3 dbd9220ca
Author: Xinsheng (Shawn) Qin <xinshengqin2014@gmail.com>
Date:   Wed Jun 7 11:08:31 2017 -0700

    Merge remote-tracking branch 'origin/gpu' into gpu2

commit dbd9220caf910553060d56a9fa7d2252314a8a8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 7 13:09:54 2017 -0400

    fix compilation on summit with PGI

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/comps/Linux_pgi.mak

commit 4a1e50f6e36c32d37313d3deea42e247c33b979c
Author: Andrew Myers <atmyers2gmail.com>
Date:   Wed Jun 7 13:07:30 2017 -0400

    some work towards working with domain decomposition.

Tests/Particles/CUDADeposition/MyParticleContainer.H
Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_F.H
Tests/Particles/CUDADeposition/inputs

commit 94b10e3055a366b415a223ec1ceb4a6b54d3aa1e
Merge: e331e9370 65e038dd0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 7 13:00:57 2017 -0400

    Merge branch 'development' into gpu

commit e331e9370692e6b30581b050af0133ca56c1ab50
Merge: b09b1f141 2cdb022fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 7 12:21:08 2017 -0400

    Merge branch 'gpu' of ssh://github.com/AMReX-Codes/AMReX into gpu

commit 65e038dd08ea8f4d7bef609200652dac9d0e0483
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 7 11:54:09 2017 -0400

    some initial support for summit -- note, cpp doesn't work with -traditional
    there so we override

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak

commit 8eb8e05eccf6a9581bab6e54cca5cdf628f7b71e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed Jun 7 10:57:23 2017 -0400

    Use synchronize after phi update

Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90
Tutorials/Basic/HeatEquation_EX1_C/main.cpp

commit c17a4fe640b0d113a2816729058e48cd75d0ea11
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed Jun 7 10:23:47 2017 -0400

    Get the thread block count working in 2D

Src/Base/AMReX_CUDA.F90

commit 8fdff43e9ebf8aaa62f429271f67bdbe9904845f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed Jun 7 10:23:24 2017 -0400

    Get update_phi on the device

Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90
Tutorials/Basic/HeatEquation_EX1_C/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H

commit 2cdb022fca2aa157e78af13a007fdbc4ea218b4e
Merge: d65c0329e 9c6f2f0d6
Author: Andrew Myers <atmyers2gmail.com>
Date:   Wed Jun 7 09:37:56 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit d65c0329ecae14c9eb73d08cd47e3b930656f6c0
Author: Andrew Myers <atmyers2gmail.com>
Date:   Wed Jun 7 09:37:47 2017 -0400

    Fixing a couple more bugs.

Tests/Particles/CUDADeposition/GNUmakefile
Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/deposit_3d.f90

commit e5608ca5bd57681de9316af08dfcb4ca6b60583c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed Jun 7 09:35:19 2017 -0400

    Use separate streams in HeatEquation

Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90
Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90
Tutorials/Basic/HeatEquation_EX1_C/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H

commit b09b1f1418210e8786687a74267e6c1064cc672d
Merge: 9c6f2f0d6 48f0d4368
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 7 09:19:39 2017 -0400

    Merge branch 'development' into gpu

commit 9c6f2f0d69a74911905184ac25d701cde1c6f41a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed Jun 7 09:06:27 2017 -0400

    Fix errors in advance_2d

Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90

commit c9ca66fbf46d558e1b1fd26b432a8157332e1f08
Author: Andrew Myers <atmyers2gmail.com>
Date:   Tue Jun 6 23:43:35 2017 -0400

    a few bug fixes.

Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/deposit_3d.f90

commit 5376b7f7cfc39b91b93253462cf4b35f4f9f261d
Author: Andrew Myers <atmyers2gmail.com>
Date:   Tue Jun 6 22:10:10 2017 -0400

    Code that deposits a bunch of particles, with no domain decomposition for now.

Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/deposit_3d.f90
Tests/Particles/CUDADeposition/main.cpp

commit e7729ec065b93e10ef3b2a75acb32ddb967033b5
Merge: 2368092d7 77537d9f4
Author: Andrew Myers <atmyers2gmail.com>
Date:   Tue Jun 6 20:51:53 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 2368092d72de04412308777c2b4fd2edea1edd08
Author: Andrew Myers <atmyers2gmail.com>
Date:   Tue Jun 6 20:51:03 2017 -0400

    remove file added my mistake

Tests/Particles/CUDADeposition/.bashrc

commit ea29e96ca5c5585f403cbf6d422537fcfa70d902
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jun 6 17:48:56 2017 -0700

    Make vof struct pod

Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/Make.package
Tests/GeometryShop/vofStructures/vofStructures.cpp

commit d408872b1677c82e65235f12bd8da15db9b2bedf
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jun 6 20:42:05 2017 -0400

    successfully passing a chunk of particles to the GPU and processing them.

Tests/Particles/CUDADeposition/.bashrc
Tests/Particles/CUDADeposition/GNUmakefile
Tests/Particles/CUDADeposition/MyParticleContainer.H
Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_F.H
Tests/Particles/CUDADeposition/main.cpp

commit 8885c06cc0299d984e585141ffb438699f51e100
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue Jun 6 16:38:46 2017 -0700

    The Good News: EBGraph serializaton is correct to the degree that I can test it.  Bad news:  Parallel EB still broken until I can get two-pass communication.

Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Tests/GeometryShop/regression/serialization.cpp

commit 77537d9f4ee316a0b2d6a62e6a4b36fef89d3a98
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Jun 6 16:42:36 2017 -0400

    Disable tiling if CUDA is enabled

Src/Base/AMReX_FabArrayBase.cpp
Tools/GNUMake/Make.defs

commit 48f0d4368f5cdf451489ddb55284abae460f0046
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 6 11:26:26 2017 -0700

    add amrex:growLo and amrex::growHi for Box

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp

commit ba7d236b2cebc53add9332a668c792c4dd77b111
Merge: e42ca15ee 17f2ad918
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 6 12:04:35 2017 -0400

    Merge branch 'development' into gpu

commit e42ca15ee85d1c10717b29eb80868754c27a0883
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Jun 6 10:30:25 2017 -0400

    Put compute_flux on the GPU

Tutorials/Basic/HeatEquation_EX1_C/Make.package
Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90
Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90

commit 84c4da8553bfdb57752a6857b6233b881a7fcbc8
Author: Andrew Myers <atmyers@icsubmit01.sdcc.bnl.gov>
Date:   Tue Jun 6 10:01:09 2017 -0400

    Makings of a CUDA Deposition example program.

Tests/Particles/CUDADeposition/GNUmakefile
Tests/Particles/CUDADeposition/Make.package
Tests/Particles/CUDADeposition/MyParticleContainer.H
Tests/Particles/CUDADeposition/MyParticleContainer.cpp
Tests/Particles/CUDADeposition/deposit_3d.f90
Tests/Particles/CUDADeposition/deposit_F.H
Tests/Particles/CUDADeposition/inputs
Tests/Particles/CUDADeposition/main.cpp

commit 17f2ad91822408a4d0d69bfa7b80fef5b1062b6a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 6 09:20:16 2017 -0400

    fix spacing for global additions

Tools/RegressionTesting/params.py
Tools/RegressionTesting/regtest.py

commit cd654f099b35820600094d92bb9e4ae32668ff4b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 5 23:14:00 2017 -0400

    a .F90 version of the programs syntax

Tools/F_mk/GMakerules.mak

commit fe37819de9a5126c4e1f0a11da476ad43d979898
Merge: a568d043b 15e199d7d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 5 21:27:37 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit 15e199d7dfbe58a3991b04149baefc47fdc2aed1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 5 17:15:36 2017 -0700

    User's Guide: more on MultiFab

Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/Basics/indextypes.pdf
Docs/BoxLibUsersGuide/GettingStarted/GettingStarted.tex

commit bc6895445eeb8efbc43f35226e6ba3d3c0794f4b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon Jun 5 16:21:48 2017 -0700

    fixed some bugs in serialization.  There are more to find.

Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/AMReX_EBISBox.H
Src/GeometryShop/AMReX_FabArrayIO.H
Src/GeometryShop/AMReX_FabArrayIO.cpp
Src/GeometryShop/AMReX_SPMD.H
Tests/GeometryShop/README
Tests/GeometryShop/regression/GNUmakefile
Tests/GeometryShop/regression/serialization.cpp
Tests/GeometryShop/regression/serialization.inputs

commit 3ed86c9555edd3aede5ddc921c5b5ca5891a18f4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 5 15:28:20 2017 -0700

    fix memory profiler

Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_MultiFab.cpp

commit 44bbbe2e3b651e69514fd927fdc13006feefedd1
Merge: 9503eb510 0ce7d3362
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 5 13:42:37 2017 -0700

    Merge branch 'development' into gpu2

commit 0ce7d3362c53eacc97752abbc2ff6c73445da2e6
Merge: 6bdddd8ab 246815956
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 5 12:11:20 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6bdddd8ab3ac79edab990c7924137f68a3bf3666
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 5 12:11:16 2017 -0700

    User's Guide: FabArray

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/Basics/amrgrids.pdf

commit a568d043b64a25a9e308edeffe1f60d49a39f100
Merge: 8df048010 246815956
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 5 14:47:20 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit 2468159568b44df9dd783ce8651bcaae3d8ee3b3
Merge: ecf9eb9c1 8f21ae602
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jun 5 13:40:25 2017 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ecf9eb9c1101d7ed051aa4221782a1d9370908b7
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jun 5 13:40:10 2017 -0400

    fix silly mistake in convert script.

Tools/Py_util/amrex_particles_to_vtp/amrex_binary_particles_to_vtp.py

commit 9503eb51009f4c3bf8617c31e1cbf6fcf5c36153
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Mon Jun 5 12:24:28 2017 -0400

    Use CUDA 8.0

Tools/F_mk/comps/Linux_pgi.mak

commit a1e6d854482dd48cbf1b377e8c43bd792c64e790
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 5 08:50:05 2017 -0700

    typechecker: print debug information

Tools/typechecker/typechecker.py

commit 8f21ae602fc8319e664d6d372695d476e5400a20
Merge: a0b33efee f590f4998
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Jun 5 08:43:54 2017 -0700

    Merge pull request #25 from bcfriesen/update_cvode_docs
    
    Update CVODE docs

commit 7eac156f8c651302e2c5c508ea6d0c4379dadd8a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Mon Jun 5 10:31:28 2017 -0400

    Use streams for MultiFab operations

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.F90
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.cpp

commit ee219b502e03ffe8c945054054869b635cec1b57
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Mon Jun 5 10:24:23 2017 -0400

    Remove Castro-specific variable

Src/Base/AMReX_CUDA.F90

commit 8df048010af68745eb48460a5f2294b770a486b2
Merge: 7e10670b0 a0b33efee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 5 10:20:04 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit a0b33efee506851d150f0ffd5d7d600520712580
Merge: fb616cb79 3577dd316
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jun 4 22:37:46 2017 -0700

    Merge branch 'cvode_fixes' into development

commit 3577dd316640dc56c5ae22b7c2476a7259bce5ba
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jun 4 22:36:37 2017 -0700

    CVODE, Tools/GNUmake: add -DUSE_CVODE preprocessor flag when USE_CVODE=TRUE

Tools/GNUMake/packages/Make.cvode

commit fb616cb79caab95396ac193f66a68f7082f66bbf
Author: atmyers <atmyers2@gmail.com>
Date:   Mon Jun 5 01:20:47 2017 -0400

    Adding a script to write from the particle binary format to vtp.

Tools/Py_util/amrex_particles_to_vtp/README
Tools/Py_util/amrex_particles_to_vtp/amrex_binary_particles_to_vtp.py
Tools/Py_util/amrex_particles_to_vtp/amrex_particles_to_vtp.py

commit f590f4998a79492c204213b48d798fa1c95d4f1c
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jun 4 20:55:04 2017 -0700

    Docs: remove Readme.cvode
    
    The material in this Readme has been moved to the User Guide.

Docs/Readme.cvode

commit 070ae7e469bfb62a32b9d3fff8111190db5dee57
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jun 4 20:54:13 2017 -0700

    Docs: add chapter to user guide regarding CVODE with the new Fortran 2003 interface

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/CVODE/CVODE.tex
Docs/AMReXUsersGuide/amrexsymbols.tex

commit 17e6d94a95f285e5f5c3185149f74e46979ae8c4
Merge: e28aa1879 730487b3d
Author: atmyers <atmyers2@gmail.com>
Date:   Sun Jun 4 23:29:32 2017 -0400

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 730487b3dd1fb4d6d189cbe3f55c0e6e6864ab04
Merge: b230cc0ab c77b1b750
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jun 4 19:44:53 2017 -0700

    Merge branch 'use_f03_cvode' into development
    
    These commits add support for the new Fortran 2003 interface to CVODE.
    They also migrate the two CVODE tutorials ("EX1" and "EX2") to this new
    interface.

commit c77b1b75019185e9c3264e778986eedc52652ad4
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jun 4 19:41:41 2017 -0700

    Tutorials/CVODE/EX2: switch to new Fortran 2003 interface to CVODE

Tutorials/CVODE/EX2/Make.package
Tutorials/CVODE/EX2/fcvdjac.f90
Tutorials/CVODE/EX2/fcvfun.f90
Tutorials/CVODE/EX2/integrate_ode_no_jac.f90
Tutorials/CVODE/EX2/integrate_ode_with_jac.f90
Tutorials/CVODE/EX2/ode_mod.f90

commit f77e395a96ef6769dea4a1a3bf922ff4affd7a16
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jun 4 17:05:07 2017 -0700

    Tutorials/CVODE/EX1: switch to new Fortran 2003 interface to CVODE

Tutorials/CVODE/EX1/Make.package
Tutorials/CVODE/EX1/fcvfun.f90
Tutorials/CVODE/EX1/integrate_ode.f90
Tutorials/CVODE/EX1/ode_mod.f90

commit 65c3119c0c2755596f34785cd6420cf6708f4c20
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jun 4 17:02:39 2017 -0700

    CVODE: add Fortran 2003 interface to CVODE
    
    This interface uses iso_c_binding and enables one to call CVODE C
    functions directly from Fortran without using FCVODE. It also includes a
    few helper functions which ease programming by, e.g., converting C array
    pointers to Fortran array pointers. AMReX will compile these modules if
    the USE_CVODE variable is set to TRUE.
    
    This interface was contributed by the SUNDIALS team.

Src/Extern/CVODE/Make.package
Src/Extern/CVODE/cvode_interface.f90
Src/Extern/CVODE/fnvector_serial.f90
Src/Extern/CVODE/sundials_fdlsmat.f90
Tools/GNUMake/packages/Make.cvode

commit e28aa187924cf8c29673f0a7b3528fa8271a465c
Author: atmyers <atmyers2@gmail.com>
Date:   Sun Jun 4 17:16:06 2017 -0700

    Some work on the Particle section of the Users Guide.

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Particle/Particle.tex

commit ea79cf704375825d5197e668b95ede591a68aecc
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jun 4 13:27:30 2017 -0400

    Put the device synchronizes in a sane place

Src/Base/AMReX_BaseFab_nd.F90
Src/Base/AMReX_MultiFab.cpp

commit 62a39044ff61b8d23e1a30a4607599eb1c9d3028
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jun 4 11:37:47 2017 -0400

    Add CUDA to executable name

Tools/GNUMake/Make.defs

commit fe61a5a826d338834a02cfc2409c386e5665d61a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jun 4 11:25:28 2017 -0400

    Collapse the fab copy loop

Src/Base/AMReX_BaseFab_nd.F90

commit 671c5831ceb58544babbafbdeb437e194e9f47d0
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jun 4 04:28:34 2017 -0400

    Port more FAB functions

Src/Base/AMReX_BaseFab_nd.F90

commit ce402444bc6ed5c8cf6370c693fc93bfab1b70f8
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jun 4 03:31:43 2017 -0400

    Build in NVTX into TinyProfiler

Src/Base/AMReX_Device.H
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp

commit 39492303e8bc24e3766c545f7ca0901926275de8
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jun 4 03:05:23 2017 -0400

    Add support for NVTX

Src/Base/AMReX_Device.H
Tools/GNUMake/Make.defs

commit 43ab36a0d67744cd4b6227f35d3461dec98f3a58
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jun 4 02:13:50 2017 -0400

    Undo unintentionally committed comments

Src/Base/AMReX_BaseFab.H

commit c58e04fe220fad798e5b69b029b0aa6d646fd6db
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jun 4 02:11:58 2017 -0400

    Start putting FAB functionality on device

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab_nd.F90
Src/Base/Make.package

commit ac3c41bd910b57a1045208158b4354bdcac71014
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun Jun 4 02:11:35 2017 -0400

    Set preferred location to device

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H

commit b230cc0abef0e0eb8442026b36b2a23eec724617
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 3 16:30:54 2017 -0700

    it makes more sense to have SetPosition function in ParIter instead of ParIterBase

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H

commit 19ea6e2d3612422245b2cdd86e28c19ba477e37c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 3 14:30:02 2017 -0700

    fix ParConstIter

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H

commit dc30c17c7c26fb6e6622a7aa06558015b76c7b73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 3 13:18:50 2017 -0700

    fix ParContIter's enable_if

Src/Particle/AMReX_Particles.H

commit 3f9578118a55fd6c9a079c817ea9b7bd9fb80ee7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 3 13:05:19 2017 -0700

    add ParConstiter

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H

commit 95c921791277d4fab42ba6b64dbd8d47ca0d9781
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 2 19:04:16 2017 -0700

    option to turn off limiter

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FillPatchUtil_2d.F90
Src/AmrCore/AMReX_FillPatchUtil_3d.F90
Src/AmrCore/AMReX_FillPatchUtil_F.H

commit d416595f5d02fc358ced7ad1ed523923a2a5e46f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 2 18:40:10 2017 -0700

    fix a bug in the new interp function for warpx

Src/AmrCore/AMReX_FillPatchUtil_2d.F90

commit d073a9e070f7ebe15088c3c8b66938963affcda2
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jun 2 18:36:33 2017 -0700

    Start some new data structure dev/test code

Tests/GeometryShop/vofStructures/GNUmakefile
Tests/GeometryShop/vofStructures/Make.package
Tests/GeometryShop/vofStructures/sphere.inputs
Tests/GeometryShop/vofStructures/vofStructures.cpp

commit 63f48e85f0db4de5c998e22f512038b39b89d5ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 2 14:07:35 2017 -0700

    added some 2D functions for interpolation of EM fields

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FillPatchUtil_2d.F90
Src/AmrCore/AMReX_FillPatchUtil_3d.F90
Src/AmrCore/AMReX_FillPatchUtil_F.H
Src/Base/AMReX_fort_mod.F90

commit 6b75946e5c68aa180561cd28885f9514cc281bfe
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jun 1 16:25:49 2017 -0700

    Burrowing further into serialization routines.  The tea at this unbirthday party is terrible. Many more tests coming so I can work my way out of this stuff.

Src/GeometryShop/AMReX_BaseEBCellFABI.H
Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_IntVectSet.H
Src/GeometryShop/AMReX_IntVectSet.cpp
Src/GeometryShop/AMReX_IrregFAB.cpp

commit 230bfb540c3a37be223877d305e974ee25cd34f7
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu Jun 1 16:22:55 2017 -0700

    added a test for more fabarray objects

Tests/GeometryShop/regression/fabio.cpp

commit 7e10670b092b02463697d361d98b4784065b2b36
Merge: 1f2bc2ced 24fe19abc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 1 11:44:53 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit 08856a8ab6adaf9886e5efc06b11a350a2f63a3b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Jun 1 02:01:39 2017 -0400

    Also add -DCUDA to FPPFLAGS

Tools/F_mk/GMakedefs.mak

commit 1f165a03bb1ce40d2ad44c7dad5fbe71b087a288
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Jun 1 01:49:07 2017 -0400

    Add -DCUDA

Tools/F_mk/GMakedefs.mak

commit 24fe19abc762de0abd3ba75663427c77298f9373
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 31 17:21:17 2017 -0700

    User's Guide: BoxArray and DistributionMapping

Docs/AMReXUsersGuide/Basics/Basics.tex
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_FabArrayBase.cpp

commit 490d783ee7a78bd9d5325044ea00d27616460e39
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 31 16:02:40 2017 -0700

    This is an awfully deep rabbit hole.  And what kind of rabbit carries a pocket watch?

Src/GeometryShop/AMReX_BaseEBCellFABI.H
Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Src/GeometryShop/AMReX_FabArrayIO.H
Tests/GeometryShop/regression/fabio.cpp
Tests/GeometryShop/regression/fabio.inputs

commit ba901a1dccd3b6524162d8de4ef55b5ebb42992f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 31 16:01:47 2017 -0700

    added a utility to create a directory but moving the old one, it destroys it.  Will only work on Unix

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit d2f64e3b22fa849bb4c0029898099153bff5f148
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 31 14:24:57 2017 -0700

    User's Guide: BaseFab

Docs/AMReXUsersGuide/Basics/Basics.tex

commit 0145044c8d92a357a08a494521664ef95310146d
Author: hsitaram <hariswaran@gmail.com>
Date:   Wed May 31 14:49:41 2017 -0600

    python script added to convert ascii amrex particle files to vtp (#23)
    
    * python script added to convert ascii amrex particle files to vtp
    
    * deleted extra particle plotfiles

Tools/Py_util/amrex_particles_to_vtp/README
Tools/Py_util/amrex_particles_to_vtp/amrex_particles_to_vtp.py
Tools/Py_util/amrex_particles_to_vtp/samplefiles/particles00000
Tools/Py_util/amrex_particles_to_vtp/samplefiles/particles00001
Tools/Py_util/amrex_particles_to_vtp/samplefiles/particles00002
Tools/Py_util/amrex_particles_to_vtp/write_pview_file.py

commit 7f7923402cc342f14699c3239ff0a24ac5f2cba3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 31 12:24:23 2017 -0700

    Add the functionality to pass the variable names into WritePlotFile as well as into CheckPoint.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit efc81f58ce953968f65023b93d8fd604da2790e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 31 11:18:07 2017 -0700

    User's Guide: Geometry

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp
Tutorials/Basic/HeatEquation_EX1_C/main.cpp

commit b4475a6a8c2104a830b19b8d7f6b33153f538242
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed May 31 01:22:48 2017 -0400

    Add CUDA to PGI in F_mk

Tools/F_mk/comps/Linux_pgi.mak

commit 6152aa9d4bf37ce61acfe804e4570833d410e9f0
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue May 30 16:40:53 2017 -0700

    more progress on EB I/O.  Serialization ain't fun.

Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_BaseEBCellFABI.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_FabArrayIO.H
Src/GeometryShop/AMReX_IntVectSet.H
Src/GeometryShop/AMReX_IntVectSet.cpp

commit 11dda5523bf08f7aae758a1b4b142038ed0154d3
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue May 30 16:39:55 2017 -0700

    added a couple of funtions to Box and IntVect to make my life a bit easier

Src/Base/AMReX_Box.H
Src/Base/AMReX_IntVect.H

commit 1f2bc2ced639bb4dcca0f25b9a67d9537e7a8062
Merge: 202534854 ff0e93a93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 30 15:48:33 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit 063f196ec84955f6a40eb34b8860320637c48b32
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon May 29 16:39:33 2017 -0700

    More progress on I/O for EB.  Marc will be glad to hear that I added a couple of classes.

Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_BaseEBCellFABI.H
Src/GeometryShop/AMReX_BaseEBCellFactory.H
Src/GeometryShop/AMReX_FabArrayIO.H
Src/GeometryShop/AMReX_FabArrayIO.cpp
Tests/GeometryShop/regression/fabio.cpp

commit ff0e93a9368c8ae19f37f9d7465fd50c13712a2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 29 12:11:12 2017 -0700

    removeOverlap: option not to simplify

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit 202534854aea6bf31b09cea5c3fb339789e3e041
Merge: 16b28de67 e6fee826e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 29 12:07:16 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit e6fee826eaf7644928700bb5ab525025a8309bc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 29 07:19:28 2017 -0700

    move printGridSummary function from Amr to AmrCore

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp

commit 70497ac406edab15bd2deefe4516c8c4f95deabb
Author: dtgraves <dtgraves@lbl.gov>
Date:   Sun May 28 18:36:54 2017 -0700

    more progress toward (less general) I/O for more general objects

Src/GeometryShop/AMReX_FabArrayIO.H
Src/GeometryShop/AMReX_FabArrayIO.cpp
Src/GeometryShop/FabArrayIO.H
Src/GeometryShop/Make.package
Tests/GeometryShop/regression/fabio.cpp

commit 46e379a9cb7aff74a95610b37352947be6a1d0bb
Merge: a479739a2 9f40822e1
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 28 12:04:06 2017 -0400

    Merge branch 'development' into gpu

commit 16b28de67b87f9973e7fb21e8718a72dfd1b5ba0
Merge: bd22d1b55 9f40822e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun May 28 09:45:12 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit 9f40822e1c3322f8237bc07c74e2df9f9ff71ac0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 27 19:39:36 2017 -0700

    fix a bug in removeOverlap

Src/Base/AMReX_BoxArray.cpp

commit d180064514ada8f8cfa4a467f23f76784daa5fb0
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat May 27 18:02:36 2017 -0400

    Provide null implementation for post_restart

Src/Amr/AMReX_AmrLevel.H

commit a502e1d0b2592ea5a75ba27914ead7211bc47e24
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat May 27 17:45:36 2017 -0400

    Make post_restart not be pure virtual

Src/Amr/AMReX_AmrLevel.H

commit 759e172a0cfff0fc5fdee5eed8289caf264eaeed
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri May 26 16:32:09 2017 -0700

    started getting some EB elliptic stuff moved over

Src/EBAMRElliptic/AMReX_AMRMultiGrid.H
Src/EBAMRElliptic/AMReX_BaseBCFuncEval.H
Src/EBAMRElliptic/AMReX_BiCGStabSolver.H
Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H
Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp
Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H
Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOp.H
Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H
Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp
Src/EBAMRElliptic/AMReX_EBEllipticFort.F90
Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H
Src/EBAMRElliptic/AMReX_LinearSolver.H
Src/EBAMRElliptic/AMReX_MultiGrid.H
Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.H
Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp
Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H
Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp
Src/EBAMRElliptic/Make.package

commit b92b5126f9b923768c14283c8c763252928401e9
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri May 26 16:31:35 2017 -0700

    started the bare bones of more general I/O with lots of help from Vince

Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Src/GeometryShop/FabArrayIO.H
Tests/GeometryShop/regression/GNUmakefile
Tests/GeometryShop/regression/fabio.cpp
Tests/GeometryShop/regression/fabio.inputs

commit 7ad06248c190844a18eb41c5a9370151546067cc
Merge: ad1989bfe 03d0f1bb2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 26 15:40:02 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit ad1989bfe5c82c3b8c3c610247a5a9ecf1691daa
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 26 15:39:52 2017 -0700

    1D and 2D version of the particle deposition / interpolation operations.

Src/Particle/AMReX_Particle_mod_1d.F90
Src/Particle/AMReX_Particle_mod_2d.F90

commit 03d0f1bb26eae775190752c913114a816cc9bb14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 26 14:20:17 2017 -0700

    make FillBoundary work for overlapping BoxArray

Src/Base/AMReX_FabArrayBase.cpp

commit 5f17416b0e7532758fed0dc4988cac995529f43b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 26 13:53:52 2017 -0700

    Don't initialize integers with 0.d0

Tools/Postprocessing/F_Src/fextract.f90

commit 21b4f759dc1e1e2d223cb2212dfb0a059a6b63ab
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri May 26 13:37:17 2017 -0700

    Fix bug in fextract

Tools/Postprocessing/F_Src/fextract.f90

commit bd22d1b557d5dba04ce5bdb8cfd2fbcd0704a31a
Merge: c16c9de8d 9ef41cec8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 26 16:04:27 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit 9ef41cec81ed775533f49cff32aa93496cd75049
Merge: 6e5b8ca22 738b8363a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 26 10:57:32 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 6e5b8ca22980b1e110dca1caa6670fcdac6e3340
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 26 10:57:19 2017 -0700

    rename ghosts to neighbors to have a different name from Nyx-style ghost particles.

Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H
Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp
Tutorials/Particles/ShortRangeParticles/main.cpp
Tutorials/Particles/ShortRangeParticles/short_range_2d.f90
Tutorials/Particles/ShortRangeParticles/short_range_3d.f90
Tutorials/Particles/ShortRangeParticles/short_range_F.H

commit 738b8363a99208ded45a2aa38e8be506ca0a50db
Merge: 4bc3681a6 07cb175c0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 26 10:55:34 2017 -0700

    Merge pull request #21 from bcfriesen/cvode_tutorial_updates
    
    CVODE tutorial updates

commit 07cb175c03e4bdf20e2fd4a6244ce1a130fad9b8
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri May 26 10:50:38 2017 -0700

    Docs: added Readme.cvode with instructions for building CVODE/FCVODE

Docs/Readme.cvode

commit 3a35767592bc574b4302baeeaccca0696275c7fc
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri May 26 10:48:49 2017 -0700

    Tutorials/CVODE/EX1: replace custom writePlotFile() with amrex::WriteSingleLevelPlotfile()

Tutorials/CVODE/EX1/Make.package
Tutorials/CVODE/EX1/main.cpp
Tutorials/CVODE/EX1/writePlotFile.H
Tutorials/CVODE/EX1/writePlotFile.cpp

commit f09b877d53b9ce56210de04689b1b02c57aa9042
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri May 26 10:43:02 2017 -0700

    Tutorials/CVODE: added "EX2" tutorial
    
    This tutorial solves a set of 3 coupled ODEs in each cell. It is taken
    from the "fcvRoberts_dns.f" file in the CVODE examples.

Tutorials/CVODE/EX2/GNUmakefile
Tutorials/CVODE/EX2/Make.package
Tutorials/CVODE/EX2/fcvdjac.f90
Tutorials/CVODE/EX2/fcvfun.f90
Tutorials/CVODE/EX2/inputs
Tutorials/CVODE/EX2/integrate_ode_no_jac.f90
Tutorials/CVODE/EX2/integrate_ode_with_jac.f90
Tutorials/CVODE/EX2/main.cpp
Tutorials/CVODE/EX2/myfunc_F.H

commit 4bc3681a6a0f4118adfa0f9194c1d2888bd9d82f
Merge: 07be1d1f9 25ed2baa3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 26 10:23:13 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 07be1d1f93303b9f31e128340d102720048ee614
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 26 10:23:00 2017 -0700

    Handle periodic boundaries in the short range particle tutorial.

Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H
Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp

commit 25ed2baa3993ea336c4067e8d6a5f1d0c6680a6a
Merge: d228a420e 7ac299c22
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 26 09:29:40 2017 -0700

    Merge pull request #20 from akreienbuehl/clrdDiffuSolve
    
    Fixed `Make.unknown`

commit 7ac299c22a1803052cf9593e0b0056f7b7728a44
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Fri May 26 09:23:19 2017 -0700

    Made fix more readable

Tools/GNUMake/sites/Make.unknown

commit d301fbfd2e01e7dd742fb14abf345f80ce665a99
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Fri May 26 08:49:25 2017 -0700

    Fixed Makefile

Tools/GNUMake/sites/Make.unknown

commit d228a420eee8d15b891a6ae54c2181ef87ee72ba
Merge: 06de48459 7f29fa5c0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 26 08:45:17 2017 -0700

    Merge pull request #19 from AMReX-Codes/ibm_make
    
    add the ability to specify a prefix to preprocessor variables

commit 7f29fa5c09e61f539afdbda220e174b9b2d7f6cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 25 21:43:46 2017 -0400

    use the flush() intrinsic of Fortran 2003 instead of call flush() to get
    link issues resolved.
    
    Also add more to the library lines

Src/Base/AMReX_BLBoxLib_F.f
Src/F_BaseLib/layout.f90
Src/F_BaseLib/parallel.f90
Tools/GNUMake/comps/ibm.mak

commit 06de48459b3396b23205bf19a4d90907058aa7da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 25 16:54:58 2017 -0700

    fix ParallelDescriptor for non MPI

Src/Base/AMReX_ParallelDescriptor.cpp

commit b894bdf8d4cc6d710f8af9bc2f0eb7d20bade96f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 25 18:56:39 2017 -0400

    defer the initialization of prefixes to the CPP_FLAGS to allow
    for user-code defines to be caught

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit e508642075339ae42eb4539aaeb20e3537b20f99
Merge: 62437d0a3 2f66653ed
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu May 25 15:55:24 2017 -0700

    Merge pull request #18 from akreienbuehl/clrdDiffuSolve
    
    clrdDiffuSolve

commit 2f66653ede5b3cd13a15faa8daa5fd73fdd98453
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Thu May 25 15:38:10 2017 -0700

    Fixed issue with `std::vector::resize' and the MPICH installation prefix can now contain `mpich' in upper case as well

Src/Base/AMReX_ParallelDescriptor.cpp
Tools/GNUMake/sites/Make.unknown

commit c16c9de8d7449da9eb1073681af9ba197bc2aff8
Merge: 395f02dbd 62437d0a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 25 18:33:30 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit 62437d0a3c871e520f7ae6e9fd707c73b33d022b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 25 13:10:30 2017 -0700

    User's Guide: Box

Docs/AMReXUsersGuide/Basics/Basics.tex

commit 264831791a43d3a10aa779132cafe7f8fe16bd7c
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu May 25 12:30:38 2017 -0700

    Tutorials: move CVODE_EX1 to CVODE/EX1

Tutorials/CVODE/EX1/GNUmakefile
Tutorials/CVODE/EX1/Make.package
Tutorials/CVODE/EX1/fcvfun.f90
Tutorials/CVODE/EX1/inputs
Tutorials/CVODE/EX1/integrate_ode.f90
Tutorials/CVODE/EX1/main.cpp
Tutorials/CVODE/EX1/myfunc_F.H
Tutorials/CVODE/EX1/writePlotFile.H
Tutorials/CVODE/EX1/writePlotFile.cpp

commit b4d9e9f6668eed15e7b993aa2c8d8411a55a7480
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 25 15:06:02 2017 -0400

    this gets IBM to the link stage (if you hack the endianness stuff)

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/ibm.mak

commit 8034bb919842ee63e23c79ea96fb432ff998f96b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 25 14:00:06 2017 -0400

    use -gnu99 standard for C

Tools/GNUMake/comps/ibm.mak

commit 809b8db645361240f39aa1681a30ca009143ba9a
Merge: 6a0322d93 8d9718f7b
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Thu May 25 10:44:25 2017 -0700

    Merge pull request #17 from akreienbuehl/clrdDiffuSolve
    
    clrdDiffuSolve

commit 99fb87f256c14d603fbec5201e1da0210718b7fd
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu May 25 10:42:22 2017 -0700

    Tutorials/CVODE_EX1: add comment clarifying what the tutorial does

Tutorials/CVODE_EX1/main.cpp

commit 8d9718f7b53adfadf4e767923bdc9a1d6acea8f6
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Thu May 25 10:07:31 2017 -0700

    Improved initialization and color-free case

Src/Base/AMReX_ParallelDescriptor.cpp

commit e05eaef73fe5f9c073fa4a8a29e922645179c664
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Wed May 24 21:05:51 2017 -0700

    Added new var. `m_first_procs_clr' to header as well

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit 4547a69a747ae7b76d3d83d53b9302490d9e553f
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Wed May 24 16:37:47 2017 -0700

    Testing `nProcs%nClrs != 0'

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit 395f02dbd7169252eacacc8f400763a9fa0653ca
Merge: a5cd8de99 6a0322d93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 24 19:17:14 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit 6a0322d9344f29cd3a1216a4d584b2809b19a089
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 24 15:18:15 2017 -0700

    fix bug in amrex_interp_div_free_bfield

Src/AmrCore/AMReX_FillPatchUtil_3d.F90

commit 2e03841bae0c92a63d9ef0baf164776ecab25c00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 24 10:51:35 2017 -0700

    add optional arguments

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit de59b215f9ebf4bbc4c61100a06718e23357d83f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 24 10:01:35 2017 -0700

    added clarifying comment and made sure added EBGraph::fillIntMask does not reach outside domain

Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp

commit c62f46202c0d77eb146c1e7c58e09d435c63c54f
Merge: ce18382a4 fe5582c79
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 24 09:58:27 2017 -0700

    Merge pull request #16 from bcfriesen/yt_at_nersc
    
    Docs: add documentation for using yt

commit 0e7ff86d1f6054b444512626dec2c73b0efead9d
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 24 09:52:38 2017 -0700

    added EBGraph::fillIntMask

Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp

commit fe5582c7927f7649345c0cbff3c90e697b3a24a9
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed May 24 09:47:40 2017 -0700

    Docs: added section about visualization with yt
    
    This includes instructions for running yt on both a local workstation
    and at NERSC. The NERSC part is somewhat of a moving target because the
    dust is still settling on the implementation of Jupyter and IPython; the
    docs should be updated if those things change in the future.

Docs/AMReXUsersGuide/Visualization/Visualization.tex
Docs/AMReXUsersGuide/Visualization/yt_Nyx_density_slice.png
Docs/AMReXUsersGuide/Visualization/yt_Nyx_density_vol_rend.png

commit ce18382a45d84b7e37560bfdf7367b55923ae3d6
Merge: d910e9c85 ccc63c73c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 24 09:39:14 2017 -0700

    Merge pull request #14 from zingale/development
    
    define __LITTLE_ENDIAN__

commit d910e9c85e33315d7e8333455f005d7b9b7ed73e
Merge: de84aaf95 bf6d103cc
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 24 09:38:55 2017 -0700

    Merge pull request #12 from bcfriesen/add_cvode
    
    Add CVODE

commit de84aaf95cff34016da943c9c425093e234ff8f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 24 09:22:13 2017 -0700

    fix a bug in the new amrex_interp_efield

Src/AmrCore/AMReX_FillPatchUtil_3d.F90

commit 34aae37d664151bb83e38cc252e959ca4d080a5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 24 08:41:53 2017 -0700

    User's Guide: more place holders

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/AmrCore/AmrCore.tex
Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex
Docs/AMReXUsersGuide/Debugging/Debugging.tex
Docs/AMReXUsersGuide/GNUmakefile
Docs/AMReXUsersGuide/Particle/Particle.tex
Docs/AMReXUsersGuide/Profiling/Profiling.tex

commit b125f8eeae8e38cea5752f4fc598fa5fd1c1b324
Author: Andreas Kreienbuehl <akreienbuehl@lbl.gov>
Date:   Wed May 24 07:01:51 2017 -0700

    Toward `nProcs%nClrs != 0'

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp

commit 677e7d9878ac3640ea1299362b4baa33c64aa05c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 23 16:56:55 2017 -0700

    more options to CFinfo

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit cd7b1855ccefff5b6e460929129010a3ad8dcaa3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 23 12:17:49 2017 -0700

    Print: use the precision of the ostream argument

Src/Base/AMReX_Print.H

commit 80543a93a6fc8154f3edb27eb91b0064b2fd766c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 23 11:26:49 2017 -0700

    User's Guide: IntVect and IndexTyp

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex

commit 77992f833efbc266c33efa8f986c8dc0fcdd8122
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue May 23 11:23:55 2017 -0700

    revert the precision modifiers until we figure out how to set the global precision to be persistent

Src/Base/AMReX_Print.H

commit 1604428da3d96492a9f06befee1799eed48df3bd
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue May 23 10:49:09 2017 -0700

    create amrex::Print().Precision functionality that replicates std::cout.precision()

Src/Base/AMReX_Print.H

commit 2f250010c28654e343f15b5c1e65f31cf2fc1e02
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon May 22 17:47:57 2017 -0700

    Simply call std::map's clear here.

Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp

commit df8a995b14624bc52cf28cab1129522c0e6227cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 22 13:45:25 2017 -0700

    make IntVect::operator[] (int) const return a const& instead of value to avoid potentially passing addresss of temporary return value

Src/Base/AMReX_IntVect.H

commit 0499153d82bf10c1af01df8c1405b95c233d92a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 22 13:26:31 2017 -0700

    User's Guide: ParmParse

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
Src/Base/AMReX_REAL.H

commit 6eb59423c6f4661028b11be9a2ed8ced6cc0be12
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon May 22 12:49:45 2017 -0700

    Fix clearGhosts routine.

Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp

commit a5cd8de996f3722629301211021a8e23fdc08ad7
Merge: 7fa5cad68 f8b2b68e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 22 13:58:36 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit f8b2b68e0802704005a3a00a3a8bb603a22d9a51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 22 10:56:36 2017 -0700

    turn off ghost cells in amrex::WriteMultiLevelPlotfile

Src/Base/AMReX_PlotFileUtil.cpp

commit 98e29b5c109ccfd9e1bcfe69f5af882e40f01bc6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 22 09:56:07 2017 -0700

    add AMREX_SPACEDIM

Src/Base/AMReX_SPACE.H
Tools/GNUMake/Make.defs

commit 7cadc850414ef9339fe4e77533346510f8b1882c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 22 09:46:18 2017 -0700

    Remove some old scripts.  If you miss them, revert my commit.

Tools/C_scripts/boxlib-build.sh
Tools/C_scripts/compressor
Tools/C_scripts/gen_release_tarball

commit 5f3cd9f7dfe26fb749d5c53ff160993bafff060f
Merge: 59f0f0e15 eb4b2dd37
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat May 20 20:16:28 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 59f0f0e15ed9130aade587c05cf37dd838f5c3b2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat May 20 20:16:09 2017 -0700

    remove unused variable.

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp

commit 332b6d8906922710fc79599f6e4803768601483c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat May 20 20:15:48 2017 -0700

    properly fillpatch the ghost cells for phi.

Tutorials/Particles/ElectrostaticPIC/main.cpp

commit ccc63c73ced53f78f15502f4291f6f4e7d587f75
Merge: b8c02ea1d 7fa5cad68
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 20 20:13:08 2017 -0400

    Merge branch 'development' of ssh://github.com/zingale/amrex into development

commit b8c02ea1d2b3306e962dca9c83507c9a4e6e992d
Merge: a419688d3 eb4b2dd37
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 20 20:11:29 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit eb4b2dd378eb6a431f590bf6c205436cb42c2375
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 20 16:24:32 2017 -0700

    implement 3d amrex_interp_efield

Src/AmrCore/AMReX_FillPatchUtil_3d.F90

commit 16dc08cef9b46fdf40bef37c25b8cb4f30d625ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 20 18:40:58 2017 -0400

    a hack for summit to find libatomic.  This assumes that you've pointed PGI/17.4
    to the gcc/5.4.0 install using the makelocalrc in PGI

Tools/GNUMake/comps/pgi.mak

commit a419688d3d55cd304e15000a3de9bcb5b6031b1e
Merge: b21655933 7bf7d47d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 20 18:21:37 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit 7fa5cad686f9f0a0d7b239d19c882ea0e8b06110
Merge: 7bf7d47d6 db01f53c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 20 18:19:43 2017 -0400

    Merge branch 'development' of ssh://github.com/zingale/amrex into development

commit 7bf7d47d6d3eaeb6dbd9325e7905676a7c4ab5f6
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat May 20 17:44:51 2017 -0400

    Move internal subroutine out to avoid a PGI 17.4 bug

Src/F_BaseLib/multifab_c.f90

commit d87fa117441bd9a8082182442bbd904b6a240e38
Author: Max Katz <maxpkatz@gmail.com>
Date:   Sat May 20 17:44:29 2017 -0400

    Restrict a use statement to avoid a PGI 17.4 bug

Src/F_BaseLib/knapsack.f90

commit c2f3c228e48a64a7e3c34819efc5dcc09781cdff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 20 11:23:26 2017 -0700

    add amrex_intep_efield stub

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FillPatchUtil_1d.F90
Src/AmrCore/AMReX_FillPatchUtil_2d.F90
Src/AmrCore/AMReX_FillPatchUtil_3d.F90
Src/AmrCore/AMReX_FillPatchUtil_F.H

commit b216559334ddea6c3b44f7b6e4051d71ca1d0241
Merge: db01f53c9 6943903f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 20 13:34:11 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit 6943903f8c028781fce5e8e52ec99cb662112db8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 19 22:11:42 2017 -0400

    fix compilation error

Src/AmrCore/AMReX_FillPatchUtil_1d.F90

commit a09bd7425e72384d8a3fa00103605889f85bcf81
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 19 17:12:19 2017 -0700

    do the proper coarse/fine interpolation before computing the electric field.

Tutorials/Particles/ElectrostaticPIC/main.cpp

commit 5db5ea6c2af57e9c43733249ffa97aeebc624f8f
Merge: f3c141381 8936f9486
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 19 16:58:39 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit f3c141381e5a2978fc03c74bda3d98e48640a761
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 19 16:58:24 2017 -0700

    change the default inputs parameters

Tutorials/Particles/ElectrostaticPIC/inputs

commit c9aedf5cc3c4623137f4f3d62698ee9b07702256
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 19 16:58:00 2017 -0700

    Some tweaks to the nodal poisson solve.

Tutorials/Particles/ElectrostaticPIC/main.cpp

commit 27f1ce66f373457c13ffe9c5a583baa24fe9d3aa
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 19 16:57:46 2017 -0700

    Only initialize the particles on one process.

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp

commit 8936f948633b0762ad7c968a58868ea4f6304b28
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 19 10:58:14 2017 -0700

    fix a bug in SumBoundary

Src/AmrCore/AMReX_FillPatchUtil_3d.F90
Src/Base/AMReX_MultiFab.cpp

commit 9e1d9a8b9c382bf9addc72c8c2810039a90bd4ba
Merge: a2eb0eecd a02b449f0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 19 10:14:26 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit a2eb0eecdea426ee9a9b39a4f01d638b3a6bec84
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 19 10:14:13 2017 -0700

    Adding some commentary.

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H

commit a02b449f051eac7112e35db18d5985d96750207a
Merge: d1411bdee 51638c85f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 19 09:41:20 2017 -0700

    Merge branch 'weiqun/bfield' into development

commit a479739a2409db8641cd0cc6b0c96fb4d9e55a19
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri May 19 03:55:20 2017 -0400

    Place device updates in non-default streams

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 79abe67a8badcb758cf3ade371f201cfef8c5501
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri May 19 03:23:59 2017 -0400

    Enable CUDA in the PGI compiler

Tools/GNUMake/comps/pgi.mak

commit 05c721d93682b7ca4187b747fbb5f0850321a18f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri May 19 03:03:20 2017 -0400

    Move CUDA calls to Fortran

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CUDA.F90
Src/Base/AMReX_Device.H

commit d1411bdee788850d93847ed1ff0221f2fdc011dd
Merge: 781dc86a2 ba2b9481a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 18 17:10:59 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 781dc86a2c1d9a1791be443e9bf8f70258d0f4a1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 18 17:10:37 2017 -0700

    Some work on the ES PIC Tutorial

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H
Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H
Tutorials/Particles/ElectrostaticPIC/inputs
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit ba2b9481a65a5f58a61c34694fb98dc87a66c848
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 18 16:03:16 2017 -0700

    make it typechecker friendly

Src/EBAMRTools/AMReX_EBFortND_F.H
Src/EBAMRTools/Make.package

commit cbeed0e7ee2a3f775c2afe7b5d2826fd2a40f3fe
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu May 18 15:21:15 2017 -0700

    fixed some 3d bugs and I think finally have EBFineInterp working

Src/EBAMRTools/AMReX_EBFortND.F90
Src/GeometryShop/AMReX_EBArith.cpp
Src/GeometryShop/AMReX_PolyGeom.H
Src/GeometryShop/AMReX_PolyGeom.cpp
Tests/EBAMRTools/regression/ebFineInterpTest.cpp
Tests/EBAMRTools/regression/ebfineinterp.inputs

commit 49f5b9e68a7fe611186f28e3d0721bfabc6b5ac4
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu May 18 15:19:24 2017 -0700

    took out unwanted function

Src/Base/AMReX_BaseFab.H

commit a543984935bacb868e3211ff4b1dbe125854a5a9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 18 11:27:10 2017 -0700

    Adding a nodal average down function.

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_F.H

commit dec2d8bdb32d9ba5959aecbbb05a8329134c5f40
Merge: 01ad059fc 0569a5362
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu May 18 11:23:10 2017 -0700

    Merge branch 'mr-cmake' into development

commit 01ad059fc7591ad56d41e7b0466a97e212ef743f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu May 18 12:47:30 2017 -0400

    Revert "Create a unique MFIter index"
    
    This reverts commit f20630351987a9597814cf76d73ec3a541581361.

Src/Base/AMReX_MFIter.H

commit bf6d103ccdce06fe0aa96755ed25b5af6c7a0495
Merge: 4bdb389bb 64fd0eba3
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu May 18 09:42:20 2017 -0700

    Merge branch 'CVODE_EX1_cleanup' into add_cvode
    
    This cleans up a few misc problems with the CVODE_EX1 tutorial, and adds
    OpenMP tiling support (although currently FCVODE, the Fortran interface
    to CVODE, is not thread-safe).

commit 64fd0eba3f43580047fdda914bd758f4461ca91c
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu May 18 09:40:13 2017 -0700

    Tutorials/CVODE_EX1: remove incorrect comment

Tutorials/CVODE_EX1/main.cpp

commit 783d8c44028d6e0423edf5d2291d946abc53867c
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu May 18 09:39:52 2017 -0700

    Tutorials/CVODE_EX1: remove unused variable "dx[]"

Tutorials/CVODE_EX1/main.cpp

commit bde51e22842063ecae84c8e35b8c15706db1c0a9
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu May 18 09:39:21 2017 -0700

    Tutorials/CVODE_EX1: remove doubly declared variable "is_periodic[]"

Tutorials/CVODE_EX1/main.cpp

commit fa7dba0d099737e760d9d7c1961f770da02dac81
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu May 18 09:38:33 2017 -0700

    Tutorials/CVODE_EX1: add OpenMP tiling option

Tutorials/CVODE_EX1/inputs
Tutorials/CVODE_EX1/main.cpp

commit 8061d9abab6d35d6196234ae079b02c47be23c89
Merge: c9a1d862e f20630351
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu May 18 09:30:53 2017 -0700

    Merge branch 'development' into dtg_branch

commit c9a1d862e4b24152b3610889bafa860cc0cad543
Merge: 552f0c972 e3fae2b26
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu May 18 09:30:40 2017 -0700

    Merge branch 'dtg_branch' of https://github.com/AMReX-Codes/amrex into dtg_branch

commit 552f0c9727c1aee04f4c9919974c6ace0dc9d4f9
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu May 18 09:28:44 2017 -0700

    some progress toward higher order EBFineInterp

Src/EBAMRTools/AMReX_EBFineInterp.cpp
Src/EBAMRTools/AMReX_EBFortND.F90
Src/EBAMRTools/AMReX_EBFortND_F.H
Tests/EBAMRTools/regression/ebFineInterpTest.cpp

commit f20630351987a9597814cf76d73ec3a541581361
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 14 20:38:34 2017 -0400

    Create a unique MFIter index

Src/Base/AMReX_MFIter.H

commit db01f53c9bd518a4bffc18c5279457e873349d52
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 18 09:20:18 2017 -0400

    fix little endian locations

Src/Base/AMReX_FPC.cpp

commit dc7d2a360173b5b79ccbc7f68e10dca1ea487250
Merge: c7eb6a938 e3fae2b26
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 17 20:29:04 2017 -0700

    Merge pull request #13 from AMReX-Codes/dtg_branch
    
    EB bug fixes for Marc

commit e3fae2b267c6bdb08211d277b38bbd57191b1c8c
Merge: 1c99f720e c7eb6a938
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 17 19:04:19 2017 -0700

    Merge branch 'development' into dtg_branch

commit 4bdb389bb52409a823a761f28797d85f861d42e9
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed May 17 18:57:55 2017 -0700

    CVODE: move Make.cvode into Tools/GNUMake/packages

Tools/GNUMake/Make.defs
Tools/GNUMake/packages/Make.cvode

commit 4b1062fbd194ddc2341974951336f47b3e81d499
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 17 21:53:02 2017 -0400

    define __LITTLE_ENDIAN__

Src/Base/AMReX_FPC.cpp

commit c7eb6a938493b4d64eea218e4ee453752586c45c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 17 21:47:18 2017 -0400

    revert the CPP_PREFIX stuff required for IBM, since it breaks GNU.  THis means that
    IBM will not work until we find a better way to define preprocessor variables

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 74ff011c618aaa4ee3a1c907c4cf00077991733f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 17 21:17:56 2017 -0400

    some library fixes for GNU/summit

Tools/GNUMake/sites/Make.olcf

commit c4e424616067f72da47b90ac1c196976eda89b2d
Merge: 1d4ea3059 de38250fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 17 20:39:46 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit 1d4ea3059b2c9d9c480bf8265b9c8816d7c311d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 17 20:39:35 2017 -0400

    fix the dependency checking

Tools/GNUMake/Make.rules

commit de38250fcddeb7e58c8a15d8c63e9eef36cb3cba
Merge: cd475d2dd 7797ee7a1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 17 17:30:41 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit cd475d2dd484f1fd9f34b04e3e4933fd34942786
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 17 17:26:08 2017 -0700

    Adding a tutorial for electrostatic pic calculations.

Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H
Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp
Tutorials/Particles/ElectrostaticPIC/GNUmakefile
Tutorials/Particles/ElectrostaticPIC/Make.package
Tutorials/Particles/ElectrostaticPIC/PhysConst.H
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90
Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H
Tutorials/Particles/ElectrostaticPIC/inputs
Tutorials/Particles/ElectrostaticPIC/main.cpp

commit 0825460d6ec61b5ca18edf146d97eb7f75e96bbd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 17 17:25:41 2017 -0700

    Move the short range particles tutorial to the new tutorials directory.

Tutorials/Particles/ShortRangeParticles/GNUmakefile
Tutorials/Particles/ShortRangeParticles/Make.package
Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H
Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp
Tutorials/Particles/ShortRangeParticles/inputs
Tutorials/Particles/ShortRangeParticles/main.cpp
Tutorials/Particles/ShortRangeParticles/short_range_2d.f90
Tutorials/Particles/ShortRangeParticles/short_range_3d.f90
Tutorials/Particles/ShortRangeParticles/short_range_F.H

commit 7797ee7a1553f9eddb36566bd784dc345f072a7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 17 20:22:28 2017 -0400

    more progress with IBM -- only the F90 needs the -WF,-D... stuff.  Also,
    the .F has uses cpp directly, so no need for the prefix there

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/ibm.mak

commit 9844b9b2daddfee5ed6f6fcfdf6a57346b08384d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 17 17:15:13 2017 -0700

    use scientific notation in particle compare.

Tools/Postprocessing/C_Src/particle_compare.cpp

commit 51317c3384c40310a6ddedb25ab9cbb0ee439efe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 17 20:01:46 2017 -0400

    add a CPP_PREFIX option that should do nothing for all compilers except IBM XL,
    which wants the preprocessor directives in the form -WF,-DFOO=BAR

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/GNUMake/comps/ibm.mak

commit aaffb1ae6c83d67700a66d52a43a175400c84e8f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 17 19:33:51 2017 -0400

    initial support for the IBM xl-series compilers

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.machines
Tools/GNUMake/comps/ibm.mak

commit ce104b25ba111f22de8f37e3b5eff531c1b88c7d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 17 19:16:48 2017 -0400

    add summit -- hopefully this doesn't break titan  :)

Tools/GNUMake/sites/Make.olcf

commit 51638c85fd1be5d3fabbd95407a44e2b3254d041
Merge: 6c1d9d2dc 9aacd4cf2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 17 16:08:58 2017 -0700

    Merge branch 'development' into weiqun/bfield

commit 1c99f720e44214fa35528cc43e3ec3791d1d05ee
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 17 15:32:46 2017 -0700

    fixed a bug in graph coarsening that Marc found.

Src/EBAMRTools/AMReX_EBFortND.F90
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Tests/GeometryShop/sphereEBISBox/GNUmakefile

commit 6c1d9d2dca9d946be331514c1b65cf00fb20931c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 17 15:03:35 2017 -0700

    remove debug line

Src/AmrCore/AMReX_FillPatchUtil.cpp

commit 2fa20dd26cc3127a9c21f887439da907bb6f6692
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 17 14:58:35 2017 -0700

    first pass of 3d amrex_interp_div_free_bfield

Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FillPatchUtil_1d.F90
Src/AmrCore/AMReX_FillPatchUtil_2d.F90
Src/AmrCore/AMReX_FillPatchUtil_3d.F90
Src/AmrCore/AMReX_FillPatchUtil_F.H

commit 759d8bddfc795b0398f86361b7fdec46d5fd4689
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed May 17 12:47:24 2017 -0700

    CVODE: add link hooks, Readme, and tutorial for using CVODE

Tools/GNUMake/Make.cvode
Tools/GNUMake/Make.defs
Tutorials/CVODE_EX1/GNUmakefile
Tutorials/CVODE_EX1/Make.package
Tutorials/CVODE_EX1/fcvfun.f90
Tutorials/CVODE_EX1/inputs
Tutorials/CVODE_EX1/integrate_ode.f90
Tutorials/CVODE_EX1/main.cpp
Tutorials/CVODE_EX1/myfunc_F.H
Tutorials/CVODE_EX1/writePlotFile.H
Tutorials/CVODE_EX1/writePlotFile.cpp

commit b8b4b36f71c806e0406f18f0ecfeeb25887a1972
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 17 11:54:15 2017 -0700

    found a subtle bug in EBFineInterp.  Convergence rates are now correct.

Src/EBAMRTools/AMReX_EBCFInterp.H
Src/EBAMRTools/AMReX_EBFineInterp.H
Src/EBAMRTools/AMReX_EBFineInterp.cpp
Src/EBAMRTools/AMReX_EBFortND.F90
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Src/GeometryShop/AMReX_BaseEBCellFABI.H
Src/GeometryShop/AMReX_EBArith.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp
Tests/EBAMRTools/regression/ebFineInterpTest.cpp
Tests/EBAMRTools/regression/ebfineinterp.inputs

commit 9aacd4cf2950929314d17dc627d9bcc68228b4ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 17 11:01:20 2017 -0700

    remove BL_ALWAYS_FIX_DENORMALS

Src/Extern/amrdata/AMReX_AmrData.cpp
Tools/CMake/CCSEOptions.cmake

commit 5a14fb8201e04cf57947497b4fbdcfcf1946b701
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed May 17 13:39:23 2017 -0400

    Add AMReX_CUDA.F90

Src/Base/AMReX_CUDA.F90

commit 2c6db3bfb798919bba04093ea6cbc572e24fad03
Merge: 1cdeeb2cc c56164653
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed May 17 13:39:07 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 4e010f9a3003dd8731ebd96a6849ece3de3e29a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 17 10:30:47 2017 -0700

    removed a number of old if names: BL_AIX, BL_CRAY, BL_CRAYX1,
    BL_HOPPER, BL_SIM_HOPPER, BL_SIM_HOPPER_MAKE_TCFAB, and BL_T3E.

Src/AmrCore/AMReX_FLUXREG_3D.F
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_Utility.cpp
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F
Src/Extern/amrdata/AMReX_AmrData.cpp

commit c561646534c3e11f3c15b34d6a64333ad6bb9512
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 17 13:13:38 2017 -0400

    wrap a CUDA call

Src/Base/AMReX_Device.H

commit c307314b0ece87f54bc40d7f6574491f3e608a2a
Merge: e88a2d3b1 018ae35dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 17 13:02:13 2017 -0400

    Merge branch 'development' into gpu

commit 018ae35dc7d9f1642dd016ad755aa00484688b67
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 17 09:51:24 2017 -0700

    some BL_ --> AMREX_

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
OldTutorials/AMR_Adv_C/Source/Adv.cpp
OldTutorials/AMR_Adv_C/Source/Adv_F.H
OldTutorials/AMR_Adv_C/Source/Adv_advance.cpp
OldTutorials/AMR_Adv_C/Source/Adv_dt.cpp
OldTutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp
OldTutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H
OldTutorials/HeatEquation_EX2_C/main.cpp
OldTutorials/MeshRefinement/main.cpp
OldTutorials/MultiColor_C/main.cpp
OldTutorials/MultiGrid_C/main.cpp
OldTutorials/ShortRangeParticles/main.cpp
OldTutorials/Tiling_C/main.cpp
OldTutorials/TwoGrid_PIC_C/split_boxes.cpp
OldTutorials/libamrex_C/main.cpp
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_StationData.cpp
Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_ErrorList.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_INTERP_F.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCRec.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IndexType.cpp
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_Periodicity.H
Src/Base/AMReX_Periodicity.cpp
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp
Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp
Src/Base/AMReX_SPACE.H
Src/Base/AMReX_iMultiFab.cpp
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_InterpBndryData.cpp
Src/EBAMRTools/AMReX_EBCoarseAverage.cpp
Src/EBAMRTools/AMReX_EBFastFR.cpp
Src/EBAMRTools/AMReX_MeshRefine.cpp
Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp
Src/F_Interfaces/Base/AMReX_geometry_fi.cpp
Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp
Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/AMReX_EBArith.cpp
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBISBox.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_Moments.cpp
Src/GeometryShop/AMReX_PolyGeom.cpp
Src/GeometryShop/AMReX_VolIndex.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp
Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_Particles_F.H
Src/Particle/AMReX_TracerParticles.cpp
Tests/C_BaseLib/tVisMF.cpp
Tests/EBAMRTools/regression/regFluxRegTest.cpp
Tests/GeometryShop/sphere/sphereTest.cpp
Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/C_CellMG/main.cpp
Tests/LinearSolvers/C_TensorMG/testVI.cpp
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp
Tests/Particles/main.cpp
Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp
Tools/C_util/ViewMF/main.cpp
Tools/C_util/ViewMF/viewMFdiffHardWire.cpp
Tools/C_util/WritePlotFile.cpp
Tools/C_util/dbgTools/intersectGrids.cpp
Tutorials/Basic/HeatEquation_EX1_C/main.cpp

commit bfa937d85e50e29dac0aea63f03f28639244d998
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 17 09:36:02 2017 -0700

    D_EXPR --> BL_D_EXPR

Src/Base/AMReX_BCRec.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_IndexType.cpp
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp
Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp
Src/Base/AMReX_SPACE.H

commit 9bf3b325f6693d57fd10e0d0393b55408d1f5fa8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 17 09:32:06 2017 -0700

    D_TERM --> BL_D_TERM

OldTutorials/TwoGrid_PIC_C/split_boxes.cpp
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_StationData.cpp
Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BCRec.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IndexType.cpp
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp
Src/Base/AMReX_Periodicity.H
Src/Base/AMReX_RealBox.cpp
Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp
Src/Base/AMReX_SPACE.H
Src/Boundary/AMReX_InterpBndryData.cpp
Src/EBAMRTools/AMReX_EBCoarseAverage.cpp
Src/EBAMRTools/AMReX_EBFastFR.cpp
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBISBox.cpp
Src/GeometryShop/AMReX_Moments.cpp
Src/GeometryShop/AMReX_PolyGeom.cpp
Src/GeometryShop/AMReX_VolIndex.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_TracerParticles.cpp
Tests/EBAMRTools/regression/regFluxRegTest.cpp
Tests/GeometryShop/sphere/sphereTest.cpp
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/Particles/main.cpp
Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp

commit 081a7164f1152b8db71b149f1610250ed5e9ac20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 17 09:28:18 2017 -0700

    D_PICK --> BL_D_PICK

Src/Base/AMReX_SPACE.H
Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp

commit 4ee9528ecf04a518236d0224a057715d04d899c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 17 09:24:05 2017 -0700

    D_DECL --> BL_D_DECL

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
OldTutorials/AMR_Adv_C/Source/Adv.cpp
OldTutorials/AMR_Adv_C/Source/Adv_F.H
OldTutorials/AMR_Adv_C/Source/Adv_advance.cpp
OldTutorials/AMR_Adv_C/Source/Adv_dt.cpp
OldTutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp
OldTutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H
OldTutorials/HeatEquation_EX2_C/main.cpp
OldTutorials/MeshRefinement/main.cpp
OldTutorials/MultiColor_C/main.cpp
OldTutorials/MultiGrid_C/main.cpp
OldTutorials/ShortRangeParticles/main.cpp
OldTutorials/Tiling_C/main.cpp
OldTutorials/libamrex_C/main.cpp
Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/AMReX_ErrorList.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_INTERP_F.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCRec.cpp
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IndexType.cpp
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_Periodicity.H
Src/Base/AMReX_Periodicity.cpp
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp
Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp
Src/Base/AMReX_SPACE.H
Src/Base/AMReX_iMultiFab.cpp
Src/Boundary/AMReX_BndryRegister.cpp
Src/EBAMRTools/AMReX_MeshRefine.cpp
Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp
Src/F_Interfaces/Base/AMReX_geometry_fi.cpp
Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp
Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/AMReX_EBArith.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_Moments.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp
Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_Particles_F.H
Src/Particle/AMReX_TracerParticles.cpp
Tests/C_BaseLib/tVisMF.cpp
Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/C_CellMG/main.cpp
Tests/LinearSolvers/C_TensorMG/testVI.cpp
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp
Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp
Tools/C_util/ViewMF/main.cpp
Tools/C_util/ViewMF/viewMFdiffHardWire.cpp
Tools/C_util/WritePlotFile.cpp
Tools/C_util/dbgTools/intersectGrids.cpp
Tutorials/Basic/HeatEquation_EX1_C/main.cpp

commit 1a3c9272a3013933e0e5a45a61475443fc32ae02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 17 09:36:49 2017 -0700

    User's Guide add more place holders

Docs/AMReXUsersGuide/Basics/Basics.tex

commit e88a2d3b1f857a6038d6497628b2bea4d08d4c8a
Merge: a7ea94d02 ac3289be7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 17 08:35:26 2017 -0400

    Merge branch 'development' into gpu

commit ac3289be787409ebd72143b6f79daf29298c30b0
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed May 17 01:31:21 2017 -0400

    Initialize post_step_regrid to 0 in constructor

Src/Amr/AMReX_AmrLevel.cpp

commit 0569a536266a407789a3e2f27e8f457ddc8c65aa
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue May 16 17:16:56 2017 -0700

    Add section on CMake in AMReX documentation

Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex

commit 9177b6edab394dafba91e74664735c0d9f00dc52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 16 16:53:09 2017 -0700

    wip

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FillPatchUtil_1d.F90
Src/AmrCore/AMReX_FillPatchUtil_2d.F90
Src/AmrCore/AMReX_FillPatchUtil_3d.F90
Src/AmrCore/AMReX_FillPatchUtil_F.H
Src/AmrCore/CMakeLists.txt
Src/AmrCore/Make.package

commit c345c6ef51714259a01d3af83e4a92d1c237fec5
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 16 16:43:37 2017 -0700

    fix warnings for serial.  delete perstreams after read.

Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp

commit 2b17ae7aef99995315243e7f0464e6466ba83b97
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 16 16:23:21 2017 -0700

    profdata filetype.

Src/Extern/amrdata/AMReX_AmrvisConstants.H

commit efae9dfe83a71e3b74b295edf928e00cd320e05c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 16 13:25:14 2017 -0700

    add coarse fine boundary cache

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit a2f875b657037e0af509d41fe3b2396d280a1f50
Merge: 9401c0682 a90293dac
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 16 12:55:29 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9401c06825fb1be2936ebf8f7864241392390308
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 16 12:55:10 2017 -0700

    update the test suite to use the compiled particle compare utility.

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py

commit a90293dacfd54865837bb280272d4729388ec480
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 16 12:54:47 2017 -0700

    a few more tweaks to the particle compare utility.

Tools/Postprocessing/C_Src/particle_compare.cpp

commit 3e72a5c3a6c68c524373bdfcf82dc2ad92b45a08
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 16 11:29:13 2017 -0700

    User's Guide Basics

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_ccse-mpi.H

commit b08c817ed6c0b6ff7859e8b9e854d06b6c0cbb89
Merge: dcfdd989a 79ad54a08
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 16 11:13:08 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit dcfdd989a2d6384406b8294a343c52be511bf868
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 16 11:12:42 2017 -0700

    We need to update the dummy_mf after the grids have changed even if we haven't added levels.

Src/Particle/AMReX_ParticleContainerI.H

commit 7ef957e98fb39b6c51688b7d61d05c827ba50369
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue May 16 09:13:15 2017 -0700

    Fixed bug in graph coarsening.  EBFineInterp still needs some work.

Src/Base/AMReX_BaseFab.H
Src/EBAMRTools/AMReX_EBFineInterp.cpp
Src/GeometryShop/AMReX_EBDebugDump.H
Src/GeometryShop/AMReX_EBDebugOut.H
Src/GeometryShop/AMReX_EBDebugOut.cpp
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Tests/EBAMRTools/regression/ebFineInterpTest.cpp
Tests/EBAMRTools/regression/ebfineinterp.inputs

commit 79ad54a08bda5229ee6dbad134380fe71491b186
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 15 16:52:58 2017 -0700

    User's Guide: a little on basics

Docs/AMReXUsersGuide/Basics/Basics.tex

commit 1a1e956f8968ab57a9458346feff8309a671238f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 15 14:48:57 2017 -0700

    User's Guide: make

Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex
Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile
Tutorials/Basic/HelloWorld_C/GNUmakefile

commit 5335b1c86430de49f66e6f28c4818941df726e76
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 15 10:56:19 2017 -0700

    Force DIM to be set.  Minor edits in User's Guide

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/Basics/Basics.tex
Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex
Docs/AMReXUsersGuide/GNUmakefile
Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex
Tools/GNUMake/Make.defs
Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile
Tutorials/Basic/HelloWorld_C/GNUmakefile

commit c17683ee7b33454e70f012074456c1ff7e8d52d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 15 10:24:47 2017 -0700

    fix path to OldTutorials

OldTutorials/AMR_Adv_C/Exec/Make.Adv
OldTutorials/AMR_Adv_CF/Exec/Make.Adv
OldTutorials/AMR_Adv_CF_octree/Exec/Make.Adv
OldTutorials/AMR_Adv_C_v2/Exec/Make.Adv
OldTutorials/Sidecar_EX1/GNUmakefile

commit 1cdeeb2cc48336e4e240c395f35dc681a87464ac
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 14 20:38:34 2017 -0400

    Create a unique MFIter index

Src/Base/AMReX_MFIter.H

commit a7ea94d020024d786083246db60b4540dff9405b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 14 20:14:22 2017 -0400

    Create a CUDA fortran module

Src/Base/AMReX.cpp
Src/Base/AMReX_Device.H
Src/Base/Make.package

commit 37d7f5c60b1611f45b99574e79031cbd83238342
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 14 19:06:28 2017 -0400

    Move CUDA device ID into device class

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_FabArray.H

commit 8c2f793cc825c7ae0defb0690b250f2a955b9f80
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 14 18:51:32 2017 -0400

    Make a variable private

Src/Base/AMReX_Device.H

commit 26bac069d3dad525fd94d1e9ae5fdaf505454d4a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 14 18:23:31 2017 -0400

    Synchronize device at end of kernel region

Src/Base/AMReX_Device.H

commit bd35cfc0c974497e0647cf5f55840fb345467653
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 14 17:14:16 2017 -0400

    Add return type to null registerFab

Src/Base/AMReX_MFIter.H

commit da61eacbfcf2582d4272aabd747a3355bf273551
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 14 16:34:30 2017 -0400

    Use the result of registerFab

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MFIter.H

commit 8c92d7f9ccd8936c1c5a14a0737d5067adaf1dab
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 14 16:16:39 2017 -0400

    If in device launch region, return device pointer

Src/Base/AMReX_BaseFab.H

commit 1d8bb8523721403287aac011a64506ae2bf1b2cc
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 14 15:57:09 2017 -0400

    Only do device transfer if a FAB is not registered

Src/Base/AMReX_MFIter.H

commit 03030752b5bbe47bcd76e07158778279824f9f47
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 14 14:18:42 2017 -0400

    Move device code to a separate header

Src/Base/AMReX_Device.H
Src/Base/AMReX_Device.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp
Src/Base/Make.package

commit 627403e152c78d75907eae1b2bd86667d2f0c80b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 14 04:43:39 2017 -0400

    Fix registerFab

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 738571ee220651fede97910a3d46c2d8ed1e02fa
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 14 03:02:33 2017 -0400

    Add a device copy of data to BaseFab, with hooks up to StateData
    
    Using the MFInfo struct, a MultiFab can optionally allocate a device copy
    of its data. A hook has been added to StateData so that this can be done there
    as well. Right now the device implementation is for NVIDIA GPUs with CUDA,
    but in principle other devices that require offloading could be used.

Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StateDescriptor.H
Src/Amr/AMReX_StateDescriptor.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_BArena.H
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabFactory.H

commit 4c184ecab2d124cb41da2a87ff72cff4a744a6a5
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat May 13 23:22:43 2017 -0400

    Merge CUDArena into BArena

Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_CUDArena.H
Src/Base/AMReX_CUDArena.cpp
Src/Base/Make.package

commit fea98bbe3ede2a531685104553f176f4626d7f8e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat May 13 23:07:50 2017 -0400

    USE_CUDA_UM switches between managed and normal allocations

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_CUDArena.cpp
Tools/GNUMake/Make.defs

commit 8a16a0c7d771002c588fa9c0acd75b292570ce8f
Merge: 19488406c 364d92d8c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat May 13 20:49:59 2017 -0400

    Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu

commit 19488406c71eb946adb5e0862d93741eea4f8e4c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat May 13 20:49:42 2017 -0400

    Create toDevice and toHost in BaseFab

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MFIter.cpp

commit 89df80b669dc5ff2bb051abf4e5d8a0be49c5d2b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat May 13 20:14:48 2017 -0400

    Store FAB pointers instead of FAB member pointers

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 364d92d8c464a6209ab949f8f8317886e7706f06
Merge: 42150f4fa 53662d558
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 13 16:34:23 2017 -0400

    Merge branch 'gpu' of ssh://github.com/AMReX-Codes/amrex into gpu

commit 42150f4fa3f14e83849a2a30cfbf2f645cf89988
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 13 16:34:06 2017 -0400

    add cudafor to the ignores

Tools/F_scripts/dep.py

commit 9f0f2728982f0e9153621297a5dfa1dac050ec4b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 12 21:06:46 2017 -0700

    Revert "add optional argument to FillPatchUtil indicating ghost cells data are valid"
    
    This reverts commit e0d444086f00b5662edfec0816eb7cf7d9713586.

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp

commit a5b58b8ce4db1dd23b80576aa68de4b56e12cca8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 12 21:05:59 2017 -0700

    clean up comments

Src/AmrCore/AMReX_Interpolater.H

commit 3f5fdefb42678f7a6fc8950395f27dfbf67080ba
Merge: 9ae09d8dc fd67910c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 12 21:05:22 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9ae09d8dcff381892348a81c3541083bb4f7b1b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 12 21:04:55 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex
Docs/AMReXUsersGuide/Visualization/Amrvis_2d.eps
Docs/AMReXUsersGuide/Visualization/Amrvis_3d.eps
Docs/AMReXUsersGuide/Visualization/VisIt_2D.eps
Docs/AMReXUsersGuide/Visualization/VisIt_3D.eps
Docs/AMReXUsersGuide/Visualization/Visualization.tex
Tools/Postprocessing/C_Src/GNUmakefile
Tools/Postprocessing/C_Src/particle_compare.cpp

commit fd67910c6be38c6d38ce27ed975c0dfff8d7d617
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 12 17:50:04 2017 -0700

    Better error handling in the particle compare program.

Tools/Postprocessing/C_Src/GNUmakefile
Tools/Postprocessing/C_Src/particle_compare.cpp

commit 1ad6626258ebe4356bafdeaa1c848db2200db80b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri May 12 17:02:13 2017 -0700

    made some progress on more general interpolation but I have exposed a bug in EBIS coarsening.   Not fixed yet.

Src/EBAMRTools/AMReX_EBFineInterp.H
Src/EBAMRTools/AMReX_EBFineInterp.cpp
Src/EBAMRTools/AMReX_EBFortND.F90
Src/EBAMRTools/AMReX_EBFortND_F.H
Src/GeometryShop/AMReX_EBLoHiCenter.H
Src/GeometryShop/AMReX_EBLoHiCenter.cpp
Tests/EBAMRTools/regression/ebFineInterpTest.cpp

commit 3dd9da7df5c17ab71bb8351678064fc05a5998a3
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri May 12 15:53:35 2017 -0700

    more visualization stuff

Docs/AMReXUsersGuide/Visualization/Visualization.tex

commit 8d6f0e0c68b1b9460b143e3769342d58abf67119
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri May 12 15:20:38 2017 -0700

    added instructions for amrvis and visit

Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex
Docs/AMReXUsersGuide/Visualization/Amrvis_2d.eps
Docs/AMReXUsersGuide/Visualization/Amrvis_3d.eps
Docs/AMReXUsersGuide/Visualization/VisIt_2D.eps
Docs/AMReXUsersGuide/Visualization/VisIt_3D.eps
Docs/AMReXUsersGuide/Visualization/Visualization.tex

commit e0d444086f00b5662edfec0816eb7cf7d9713586
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 12 14:50:10 2017 -0700

    add optional argument to FillPatchUtil indicating ghost cells data are valid

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp

commit a4e1ff36489023ee305d65db326a5f38729a506d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 12 14:00:58 2017 -0700

    make default BCRec contain bogus bc instead of uninitialized values

Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCRec.cpp

commit 48953300ca9d93d6beb1516be7f42151ac8d97fd
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri May 12 13:53:29 2017 -0700

    start of a Vis section

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/GNUmakefile
Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex
Docs/AMReXUsersGuide/Visualization/Visualization.tex

commit 07b584d79bd8e70108f13bbdffa1eea67faa0497
Merge: e9f6a15f3 011e16a98
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri May 12 12:12:42 2017 -0700

    Merge pull request #9 from kweide/development
    
    support for Flash as a site, machine "asterix"

commit e9f6a15f3ceaac775535026490b50cc7e84c5a90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 12 11:12:21 2017 -0700

    a bit more on make

Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex
Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex

commit 653a0ec1797a7563706ed065d924ba33146d1dd4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 12 11:06:05 2017 -0700

    add BL_TO_FORTRAN_ANYD, update tutorial

Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BLFort.H
Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90
Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90
Tutorials/Basic/HeatEquation_EX1_C/init_phi_2d.f90
Tutorials/Basic/HeatEquation_EX1_C/init_phi_3d.f90
Tutorials/Basic/HeatEquation_EX1_C/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H

commit 16b59fc8d5c84a588d2489807550c4ea1efc6676
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 12 09:59:17 2017 -0700

    update AMREX_HOME

Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile
Tutorials/Basic/HelloWorld_C/GNUmakefile

commit 2be711e828629314f9e26be3986e6857db373900
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 12 09:53:17 2017 -0700

    move HelloWorld_C and HeatEquation_EX1_C

Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile
Tutorials/Basic/HeatEquation_EX1_C/Make.package
Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90
Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90
Tutorials/Basic/HeatEquation_EX1_C/init_phi_2d.f90
Tutorials/Basic/HeatEquation_EX1_C/init_phi_3d.f90
Tutorials/Basic/HeatEquation_EX1_C/inputs_2d
Tutorials/Basic/HeatEquation_EX1_C/inputs_3d
Tutorials/Basic/HeatEquation_EX1_C/main.cpp
Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H
Tutorials/Basic/HelloWorld_C/GNUmakefile
Tutorials/Basic/HelloWorld_C/Make.package
Tutorials/Basic/HelloWorld_C/main.cpp

commit d284bd5e8422c0aa5b8fe263b9fe167daff9e0c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 12 09:50:58 2017 -0700

    rename Tutorials to OldTutorials

OldTutorials/.gitignore
OldTutorials/AMR_Adv_C/Exec/Make.Adv
OldTutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile
OldTutorials/AMR_Adv_C/Exec/SingleVortex/Make.package
OldTutorials/AMR_Adv_C/Exec/SingleVortex/Prob.f90
OldTutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_2d.f90
OldTutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_3d.f90
OldTutorials/AMR_Adv_C/Exec/SingleVortex/inputs
OldTutorials/AMR_Adv_C/Exec/SingleVortex/probin
OldTutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile
OldTutorials/AMR_Adv_C/Exec/UniformVelocity/Make.package
OldTutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90
OldTutorials/AMR_Adv_C/Exec/UniformVelocity/face_velocity_2d.f90
OldTutorials/AMR_Adv_C/Exec/UniformVelocity/inputs
OldTutorials/AMR_Adv_C/Exec/UniformVelocity/probdata.f90
OldTutorials/AMR_Adv_C/Exec/UniformVelocity/probin
OldTutorials/AMR_Adv_C/README
OldTutorials/AMR_Adv_C/Source/Adv.H
OldTutorials/AMR_Adv_C/Source/Adv.cpp
OldTutorials/AMR_Adv_C/Source/AdvBld.cpp
OldTutorials/AMR_Adv_C/Source/Adv_F.H
OldTutorials/AMR_Adv_C/Source/Adv_advance.cpp
OldTutorials/AMR_Adv_C/Source/Adv_dt.cpp
OldTutorials/AMR_Adv_C/Source/Adv_io.cpp
OldTutorials/AMR_Adv_C/Source/Adv_setup.cpp
OldTutorials/AMR_Adv_C/Source/Make.package
OldTutorials/AMR_Adv_C/Source/Src_2d/Adv_2d.f90
OldTutorials/AMR_Adv_C/Source/Src_2d/Make.package
OldTutorials/AMR_Adv_C/Source/Src_2d/compute_flux_2d.f90
OldTutorials/AMR_Adv_C/Source/Src_2d/slope_2d.f90
OldTutorials/AMR_Adv_C/Source/Src_3d/Adv_3d.f90
OldTutorials/AMR_Adv_C/Source/Src_3d/Make.package
OldTutorials/AMR_Adv_C/Source/Src_3d/compute_flux_3d.f90
OldTutorials/AMR_Adv_C/Source/Src_3d/slope_3d.f90
OldTutorials/AMR_Adv_C/Source/Src_nd/Adv_nd.f90
OldTutorials/AMR_Adv_C/Source/Src_nd/Make.package
OldTutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90
OldTutorials/AMR_Adv_C/Source/Src_nd/tagging_params.f90
OldTutorials/AMR_Adv_C/Source/main.cpp
OldTutorials/AMR_Adv_CF/Exec/Make.Adv
OldTutorials/AMR_Adv_CF/Exec/SingleVortex/GNUmakefile
OldTutorials/AMR_Adv_CF/Exec/SingleVortex/Make.package
OldTutorials/AMR_Adv_CF/Exec/SingleVortex/Prob.f90
OldTutorials/AMR_Adv_CF/Exec/SingleVortex/face_velocity_2d.F90
OldTutorials/AMR_Adv_CF/Exec/SingleVortex/inputs
OldTutorials/AMR_Adv_CF/Exec/SingleVortex/inputs.physbc
OldTutorials/AMR_Adv_CF/Exec/SingleVortex/inputs.rt
OldTutorials/AMR_Adv_CF/README
OldTutorials/AMR_Adv_CF/Source/Make.package
OldTutorials/AMR_Adv_CF/Source/Src_2d/Make.package
OldTutorials/AMR_Adv_CF/Source/Src_2d/advect_2d_mod.F90
OldTutorials/AMR_Adv_CF/Source/Src_2d/compute_flux_2d.f90
OldTutorials/AMR_Adv_CF/Source/Src_2d/slope_2d.f90
OldTutorials/AMR_Adv_CF/Source/amr_data_mod.F90
OldTutorials/AMR_Adv_CF/Source/averagedown_mod.F90
OldTutorials/AMR_Adv_CF/Source/bc_mod.F90
OldTutorials/AMR_Adv_CF/Source/compute_dt_mod.F90
OldTutorials/AMR_Adv_CF/Source/evolve_mod.F90
OldTutorials/AMR_Adv_CF/Source/fillpatch_mod.F90
OldTutorials/AMR_Adv_CF/Source/fmain.F90
OldTutorials/AMR_Adv_CF/Source/initdata.F90
OldTutorials/AMR_Adv_CF/Source/my_amr_mod.F90
OldTutorials/AMR_Adv_CF/Source/plotfile_mod.F90
OldTutorials/AMR_Adv_CF/Source/tagging_mod.F90
OldTutorials/AMR_Adv_CF_octree/Exec/Make.Adv
OldTutorials/AMR_Adv_CF_octree/Exec/SingleVortex/GNUmakefile
OldTutorials/AMR_Adv_CF_octree/Exec/SingleVortex/Make.package
OldTutorials/AMR_Adv_CF_octree/Exec/SingleVortex/Prob.f90
OldTutorials/AMR_Adv_CF_octree/Exec/SingleVortex/face_velocity_2d.F90
OldTutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs
OldTutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs.rt
OldTutorials/AMR_Adv_CF_octree/README
OldTutorials/AMR_Adv_CF_octree/Source/Make.package
OldTutorials/AMR_Adv_CF_octree/Source/Src_2d/Make.package
OldTutorials/AMR_Adv_CF_octree/Source/Src_2d/advect_2d_mod.F90
OldTutorials/AMR_Adv_CF_octree/Source/Src_2d/compute_flux_2d.f90
OldTutorials/AMR_Adv_CF_octree/Source/Src_2d/slope_2d.f90
OldTutorials/AMR_Adv_CF_octree/Source/amr_data_mod.F90
OldTutorials/AMR_Adv_CF_octree/Source/averagedown_mod.F90
OldTutorials/AMR_Adv_CF_octree/Source/bc_mod.F90
OldTutorials/AMR_Adv_CF_octree/Source/compute_dt_mod.F90
OldTutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90
OldTutorials/AMR_Adv_CF_octree/Source/fillpatch_mod.F90
OldTutorials/AMR_Adv_CF_octree/Source/fmain.F90
OldTutorials/AMR_Adv_CF_octree/Source/initdata.F90
OldTutorials/AMR_Adv_CF_octree/Source/my_amr_mod.F90
OldTutorials/AMR_Adv_CF_octree/Source/plotfile_mod.F90
OldTutorials/AMR_Adv_CF_octree/Source/tagging_mod.F90
OldTutorials/AMR_Adv_C_v2/Exec/Make.Adv
OldTutorials/AMR_Adv_C_v2/Exec/SingleVortex/GNUmakefile
OldTutorials/AMR_Adv_C_v2/Exec/SingleVortex/Make.package
OldTutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90
OldTutorials/AMR_Adv_C_v2/Exec/SingleVortex/face_velocity_2d.f90
OldTutorials/AMR_Adv_C_v2/Exec/SingleVortex/face_velocity_3d.f90
OldTutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs
OldTutorials/AMR_Adv_C_v2/README
OldTutorials/AMR_Adv_C_v2/Source/AmrAdv.H
OldTutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
OldTutorials/AMR_Adv_C_v2/Source/AmrAdvBC.H
OldTutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp
OldTutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp
OldTutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp
OldTutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp
OldTutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H
OldTutorials/AMR_Adv_C_v2/Source/Make.package
OldTutorials/AMR_Adv_C_v2/Source/Src_2d/Adv_2d.f90
OldTutorials/AMR_Adv_C_v2/Source/Src_2d/Make.package
OldTutorials/AMR_Adv_C_v2/Source/Src_2d/compute_flux_2d.f90
OldTutorials/AMR_Adv_C_v2/Source/Src_2d/slope_2d.f90
OldTutorials/AMR_Adv_C_v2/Source/Src_3d/Adv_3d.f90
OldTutorials/AMR_Adv_C_v2/Source/Src_3d/Make.package
OldTutorials/AMR_Adv_C_v2/Source/Src_3d/compute_flux_3d.f90
OldTutorials/AMR_Adv_C_v2/Source/Src_3d/slope_3d.f90
OldTutorials/AMR_Adv_C_v2/Source/Src_nd/Make.package
OldTutorials/AMR_Adv_C_v2/Source/Src_nd/Tagging_nd.f90
OldTutorials/AMR_Adv_C_v2/Source/main.cpp
OldTutorials/AMR_Adv_F/Exec/SingleVortex/GNUmakefile
OldTutorials/AMR_Adv_F/Exec/SingleVortex/GPackage.mak
OldTutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90
OldTutorials/AMR_Adv_F/Exec/SingleVortex/inputs_2d
OldTutorials/AMR_Adv_F/Exec/SingleVortex/inputs_3d
OldTutorials/AMR_Adv_F/Exec/SingleVortex/set_velocity.f90
OldTutorials/AMR_Adv_F/Exec/UniformVelocity/GNUmakefile
OldTutorials/AMR_Adv_F/Exec/UniformVelocity/GPackage.mak
OldTutorials/AMR_Adv_F/Exec/UniformVelocity/init_phi.f90
OldTutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_2d
OldTutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_3d
OldTutorials/AMR_Adv_F/Exec/UniformVelocity/set_velocity.f90
OldTutorials/AMR_Adv_F/Source/GPackage.mak
OldTutorials/AMR_Adv_F/Source/advance.f90
OldTutorials/AMR_Adv_F/Source/compute_flux.f90
OldTutorials/AMR_Adv_F/Source/main.f90
OldTutorials/AMR_Adv_F/Source/slope.f90
OldTutorials/AMR_Adv_F/Source/tag_boxes.f90
OldTutorials/AMR_Adv_F/Source/update_phi.f90
OldTutorials/AMR_Adv_F/Source/write_plotfile.f90
OldTutorials/DataServicesTest0/DataServicesTest0.cpp
OldTutorials/DataServicesTest0/GNUmakefile
OldTutorials/Exp_CNS_NoSpec_F/CNSEquations.tex
OldTutorials/Exp_CNS_NoSpec_F/GNUmakefile
OldTutorials/Exp_CNS_NoSpec_F/GPackage.mak
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.c
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.h
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/GNUmakefile
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/bench.c
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.h
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.x86.c
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/Make.package
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/timer_c.c
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/Make.package
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/README
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/advance.f90
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/main.f90
OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/README
OldTutorials/Exp_CNS_NoSpec_F/README
OldTutorials/Exp_CNS_NoSpec_F/advance.f90
OldTutorials/Exp_CNS_NoSpec_F/init_data.f90
OldTutorials/Exp_CNS_NoSpec_F/inputs.jbb
OldTutorials/Exp_CNS_NoSpec_F/inputs_3d
OldTutorials/Exp_CNS_NoSpec_F/main.f90
OldTutorials/Exp_CNS_NoSpec_F/write_plotfile.f90
OldTutorials/GettingStarted_C/GNUmakefile
OldTutorials/GettingStarted_C/Make.package
OldTutorials/GettingStarted_C/main.cpp
OldTutorials/GettingStarted_C/work_on_data_2d.f90
OldTutorials/GettingStarted_C/work_on_data_3d.f90
OldTutorials/GettingStarted_F/GNUmakefile
OldTutorials/GettingStarted_F/GPackage.mak
OldTutorials/GettingStarted_F/main.f90
OldTutorials/GettingStarted_F/work_on_data.f90
OldTutorials/HeatEquation_EX1_C/GNUmakefile
OldTutorials/HeatEquation_EX1_C/Make.package
OldTutorials/HeatEquation_EX1_C/advance_2d.f90
OldTutorials/HeatEquation_EX1_C/advance_3d.f90
OldTutorials/HeatEquation_EX1_C/init_phi_2d.f90
OldTutorials/HeatEquation_EX1_C/init_phi_3d.f90
OldTutorials/HeatEquation_EX1_C/inputs_2d
OldTutorials/HeatEquation_EX1_C/inputs_3d
OldTutorials/HeatEquation_EX1_C/main.cpp
OldTutorials/HeatEquation_EX1_C/myfunc_F.H
OldTutorials/HeatEquation_EX1_CF/GNUmakefile
OldTutorials/HeatEquation_EX1_CF/Make.package
OldTutorials/HeatEquation_EX1_CF/advance.f90
OldTutorials/HeatEquation_EX1_CF/fmain.f90
OldTutorials/HeatEquation_EX1_CF/init_phi.f90
OldTutorials/HeatEquation_EX1_CF/inputs
OldTutorials/HeatEquation_EX1_F/GNUmakefile
OldTutorials/HeatEquation_EX1_F/GPackage.mak
OldTutorials/HeatEquation_EX1_F/advance.f90
OldTutorials/HeatEquation_EX1_F/init_phi.f90
OldTutorials/HeatEquation_EX1_F/inputs_2d
OldTutorials/HeatEquation_EX1_F/inputs_3d
OldTutorials/HeatEquation_EX1_F/main.f90
OldTutorials/HeatEquation_EX1_F/write_plotfile.f90
OldTutorials/HeatEquation_EX2_C/FILCC_2D.F
OldTutorials/HeatEquation_EX2_C/FILCC_3D.F
OldTutorials/HeatEquation_EX2_C/GNUmakefile
OldTutorials/HeatEquation_EX2_C/Make.package
OldTutorials/HeatEquation_EX2_C/advance_2d.f90
OldTutorials/HeatEquation_EX2_C/advance_3d.f90
OldTutorials/HeatEquation_EX2_C/bc_fill_nd.F90
OldTutorials/HeatEquation_EX2_C/init_phi_2d.f90
OldTutorials/HeatEquation_EX2_C/init_phi_3d.f90
OldTutorials/HeatEquation_EX2_C/inputs_2d
OldTutorials/HeatEquation_EX2_C/inputs_3d
OldTutorials/HeatEquation_EX2_C/main.cpp
OldTutorials/HeatEquation_EX2_C/myfunc_F.H
OldTutorials/HeatEquation_EX2_C/writePlotFile.H
OldTutorials/HeatEquation_EX2_C/writePlotFile.cpp
OldTutorials/HeatEquation_EX2_F/GNUmakefile
OldTutorials/HeatEquation_EX2_F/GPackage.mak
OldTutorials/HeatEquation_EX2_F/advance.f90
OldTutorials/HeatEquation_EX2_F/define_bc_tower.f90
OldTutorials/HeatEquation_EX2_F/init_phi.f90
OldTutorials/HeatEquation_EX2_F/inputs_2d
OldTutorials/HeatEquation_EX2_F/inputs_3d
OldTutorials/HeatEquation_EX2_F/main.f90
OldTutorials/HeatEquation_EX2_F/multifab_physbc.f90
OldTutorials/HeatEquation_EX2_F/write_plotfile.f90
OldTutorials/HeatEquation_EX3_F/GNUmakefile
OldTutorials/HeatEquation_EX3_F/GPackage.mak
OldTutorials/HeatEquation_EX3_F/advance.f90
OldTutorials/HeatEquation_EX3_F/define_bc_tower.f90
OldTutorials/HeatEquation_EX3_F/init_phi.f90
OldTutorials/HeatEquation_EX3_F/inputs_2d
OldTutorials/HeatEquation_EX3_F/inputs_3d
OldTutorials/HeatEquation_EX3_F/main.f90
OldTutorials/HeatEquation_EX3_F/multifab_physbc.f90
OldTutorials/HeatEquation_EX3_F/write_plotfile.f90
OldTutorials/HeatEquation_EX4_F/GNUmakefile
OldTutorials/HeatEquation_EX4_F/GPackage.mak
OldTutorials/HeatEquation_EX4_F/advance.f90
OldTutorials/HeatEquation_EX4_F/define_bc_tower.f90
OldTutorials/HeatEquation_EX4_F/init_phi.f90
OldTutorials/HeatEquation_EX4_F/inputs_2d
OldTutorials/HeatEquation_EX4_F/inputs_3d
OldTutorials/HeatEquation_EX4_F/main.f90
OldTutorials/HeatEquation_EX4_F/multifab_physbc.f90
OldTutorials/HeatEquation_EX4_F/write_plotfile.f90
OldTutorials/HeatEquation_EX5_F/GNUmakefile
OldTutorials/HeatEquation_EX5_F/GPackage.mak
OldTutorials/HeatEquation_EX5_F/advance.f90
OldTutorials/HeatEquation_EX5_F/define_bc_tower.f90
OldTutorials/HeatEquation_EX5_F/init_phi.f90
OldTutorials/HeatEquation_EX5_F/inputs-rt
OldTutorials/HeatEquation_EX5_F/inputs-rt-expl
OldTutorials/HeatEquation_EX5_F/inputs-rt-impl
OldTutorials/HeatEquation_EX5_F/inputs_2d
OldTutorials/HeatEquation_EX5_F/inputs_3d
OldTutorials/HeatEquation_EX5_F/main.f90
OldTutorials/HeatEquation_EX5_F/multifab_physbc.f90
OldTutorials/HeatEquation_EX5_F/write_plotfile.f90
OldTutorials/HelloWorld_C/GNUmakefile
OldTutorials/HelloWorld_C/Make.package
OldTutorials/HelloWorld_C/main.cpp
OldTutorials/HelloWorld_CF/GNUmakefile
OldTutorials/HelloWorld_CF/Make.package
OldTutorials/HelloWorld_CF/fmain.f90
OldTutorials/MeshRefinement/GNUmakefile
OldTutorials/MeshRefinement/Make.package
OldTutorials/MeshRefinement/MyAmr.H
OldTutorials/MeshRefinement/MyAmr.cpp
OldTutorials/MeshRefinement/main.cpp
OldTutorials/MultiColor_C/GNUmakefile
OldTutorials/MultiColor_C/Make.package
OldTutorials/MultiColor_C/ff.f90
OldTutorials/MultiColor_C/inputs
OldTutorials/MultiColor_C/main.cpp
OldTutorials/MultiFabTests_C/GNUmakefile
OldTutorials/MultiFabTests_C/GridMoveTest.cpp
OldTutorials/MultiFabTests_C/Make.package
OldTutorials/MultiFabTests_C/MultiFabFillBoundary.cpp
OldTutorials/MultiFabTests_C/MultiFabReadWrite.cpp
OldTutorials/MultiGrid_C/CMakeLists.txt
OldTutorials/MultiGrid_C/COEF_2D.F90
OldTutorials/MultiGrid_C/COEF_3D.F90
OldTutorials/MultiGrid_C/COEF_F.H
OldTutorials/MultiGrid_C/GNUmakefile
OldTutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H
OldTutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp
OldTutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F
OldTutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H
OldTutorials/MultiGrid_C/HypreABecLap/Make.package
OldTutorials/MultiGrid_C/Make.package
OldTutorials/MultiGrid_C/README
OldTutorials/MultiGrid_C/RHS_2D.F90
OldTutorials/MultiGrid_C/RHS_3D.F90
OldTutorials/MultiGrid_C/RHS_F.H
OldTutorials/MultiGrid_C/inputs
OldTutorials/MultiGrid_C/inputs-rt-c-neu
OldTutorials/MultiGrid_C/inputs-rt-c-ord2
OldTutorials/MultiGrid_C/inputs-rt-c-ord3
OldTutorials/MultiGrid_C/inputs-rt-f-neu
OldTutorials/MultiGrid_C/inputs-rt-f-ord2
OldTutorials/MultiGrid_C/inputs-rt-f-ord3
OldTutorials/MultiGrid_C/main.cpp
OldTutorials/MultiGrid_C/writePlotFile.H
OldTutorials/MultiGrid_C/writePlotFile.cpp
OldTutorials/MultiGrid_F/GNUmakefile
OldTutorials/MultiGrid_F/README
OldTutorials/MultiGrid_F/constants.f90
OldTutorials/MultiGrid_F/cycle_tower.f90
OldTutorials/MultiGrid_F/fmg_cycle.f90
OldTutorials/MultiGrid_F/init_coeffs.f90
OldTutorials/MultiGrid_F/init_rhs.f90
OldTutorials/MultiGrid_F/inputs_fmg_lin_2d
OldTutorials/MultiGrid_F/inputs_fmg_lin_3d
OldTutorials/MultiGrid_F/inputs_fmg_pc_2d
OldTutorials/MultiGrid_F/inputs_fmg_pc_3d
OldTutorials/MultiGrid_F/inputs_v_lin_2d
OldTutorials/MultiGrid_F/inputs_v_lin_3d
OldTutorials/MultiGrid_F/inputs_v_pc_2d
OldTutorials/MultiGrid_F/inputs_v_pc_3d
OldTutorials/MultiGrid_F/main.f90
OldTutorials/MultiGrid_F/solve.f90
OldTutorials/MultiGrid_F/traverse.f90
OldTutorials/MultiGrid_F/v_cycle.f90
OldTutorials/PGAS_HEAT/GNUmakefile
OldTutorials/PGAS_HEAT/Make.package
OldTutorials/PGAS_HEAT/advance_3d.f90
OldTutorials/PGAS_HEAT/init_phi_3d.f90
OldTutorials/PGAS_HEAT/inputs_3d
OldTutorials/PGAS_HEAT/main.cpp
OldTutorials/PGAS_HEAT/test-mpi3/main.cpp
OldTutorials/PGAS_HEAT/writePlotFile.H
OldTutorials/PGAS_HEAT/writePlotFile.cpp
OldTutorials/PIC_C/GNUmakefile
OldTutorials/PIC_C/Make.package
OldTutorials/PIC_C/README
OldTutorials/PIC_C/inputs
OldTutorials/PIC_C/main.cpp
OldTutorials/PIC_C/single_level.cpp
OldTutorials/PIC_C/solve_for_accel.cpp
OldTutorials/PIC_C/solve_with_f90.cpp
OldTutorials/PIC_C/two_level.cpp
OldTutorials/README_C
OldTutorials/README_F
OldTutorials/Random_F/GNUmakefile
OldTutorials/Random_F/GPackage.mak
OldTutorials/Random_F/main.f90
OldTutorials/ShortRangeParticles/GNUmakefile
OldTutorials/ShortRangeParticles/Make.package
OldTutorials/ShortRangeParticles/ShortRangeParticleContainer.H
OldTutorials/ShortRangeParticles/ShortRangeParticleContainer.cpp
OldTutorials/ShortRangeParticles/main.cpp
OldTutorials/ShortRangeParticles/short_range_2d.f90
OldTutorials/ShortRangeParticles/short_range_3d.f90
OldTutorials/ShortRangeParticles/short_range_F.H
OldTutorials/Sidecar_EX1/DestMFTest.cpp
OldTutorials/Sidecar_EX1/GNUmakefile
OldTutorials/Sidecar_EX1/GridMoveTest.cpp
OldTutorials/Sidecar_EX1/InTransitAnalysis.H
OldTutorials/Sidecar_EX1/InTransitAnalysis.cpp
OldTutorials/Sidecar_EX1/Make.package
OldTutorials/Sidecar_EX1/NSidecarsTest.cpp
OldTutorials/Sidecar_EX1/SidecarResizeTest.cpp
OldTutorials/Sidecar_EX1/TestRankSets.cpp
OldTutorials/Sidecar_EX1/inputs_3d
OldTutorials/Sidecar_EX1/inputs_sc
OldTutorials/Sidecar_EX1/run.sh
OldTutorials/Tiling_C/GNUmakefile
OldTutorials/Tiling_C/Make.package
OldTutorials/Tiling_C/main.cpp
OldTutorials/Tiling_C/work.f90
OldTutorials/Tiling_Heat_C/GNUmakefile
OldTutorials/Tiling_Heat_C/Make.package
OldTutorials/Tiling_Heat_C/advance_3d.f90
OldTutorials/Tiling_Heat_C/init_phi_3d.f90
OldTutorials/Tiling_Heat_C/inputs_3d
OldTutorials/Tiling_Heat_C/main.cpp
OldTutorials/Tiling_Heat_C/results/results.org
OldTutorials/Tiling_Heat_C/results/run-babbage.sh
OldTutorials/Tiling_Heat_C/results/run-edison.sh
OldTutorials/Tiling_Heat_C/writePlotFile.H
OldTutorials/Tiling_Heat_C/writePlotFile.cpp
OldTutorials/Tiling_Heat_F/GNUmakefile
OldTutorials/Tiling_Heat_F/GPackage.mak
OldTutorials/Tiling_Heat_F/advance.f90
OldTutorials/Tiling_Heat_F/init_phi.f90
OldTutorials/Tiling_Heat_F/inputs_3d
OldTutorials/Tiling_Heat_F/main.f90
OldTutorials/Tiling_Heat_F/results.txt
OldTutorials/Tiling_Heat_F/results/babbage_omp.run
OldTutorials/Tiling_Heat_F/results/results.txt
OldTutorials/Tiling_Heat_F/results/t1a.txt
OldTutorials/Tiling_Heat_F/results/t1b.txt
OldTutorials/Tiling_Heat_F/results/t2a.txt
OldTutorials/Tiling_Heat_F/results/t2b.txt
OldTutorials/Tiling_Heat_F/results/t3a.txt
OldTutorials/Tiling_Heat_F/results/t3b.txt
OldTutorials/Tiling_Heat_F/results/t4a.txt
OldTutorials/Tiling_Heat_F/results/t4b.txt
OldTutorials/Tiling_Heat_F/results/t5a.txt
OldTutorials/Tiling_Heat_F/results/t5b.txt
OldTutorials/Tiling_Heat_F/results/t6a.txt
OldTutorials/Tiling_Heat_F/results/t6b.txt
OldTutorials/Tiling_Heat_F/results/t7a.txt
OldTutorials/Tiling_Heat_F/results/t7b.txt
OldTutorials/Tiling_Heat_F/write_plotfile.f90
OldTutorials/TwoGrid_PIC_C/GNUmakefile
OldTutorials/TwoGrid_PIC_C/Make.package
OldTutorials/TwoGrid_PIC_C/main.cpp
OldTutorials/TwoGrid_PIC_C/solve_for_accel.cpp
OldTutorials/TwoGrid_PIC_C/solve_with_f90.cpp
OldTutorials/TwoGrid_PIC_C/split_boxes.cpp
OldTutorials/WaveEquation_C/GNUmakefile
OldTutorials/WaveEquation_C/Make.package
OldTutorials/WaveEquation_C/advance_2d.f90
OldTutorials/WaveEquation_C/advance_3d.f90
OldTutorials/WaveEquation_C/init_data_2d.f90
OldTutorials/WaveEquation_C/init_data_3d.f90
OldTutorials/WaveEquation_C/inputs_2d
OldTutorials/WaveEquation_C/inputs_3d
OldTutorials/WaveEquation_C/main.cpp
OldTutorials/WaveEquation_C/writePlotFile.H
OldTutorials/WaveEquation_C/writePlotFile.cpp
OldTutorials/WaveEquation_F/GNUmakefile
OldTutorials/WaveEquation_F/GPackage.mak
OldTutorials/WaveEquation_F/advance.f90
OldTutorials/WaveEquation_F/init_data.f90
OldTutorials/WaveEquation_F/inputs_2d
OldTutorials/WaveEquation_F/inputs_3d
OldTutorials/WaveEquation_F/main.f90
OldTutorials/WaveEquation_F/write_plotfile.f90
OldTutorials/libamrex_C/GNUmakefile
OldTutorials/libamrex_C/MyAmr.H
OldTutorials/libamrex_C/MyAmr.cpp
OldTutorials/libamrex_C/main.cpp
OldTutorials/libamrex_C/myf.f90

commit 011e16a98ecbac24afda1ebb20d167602e324db9
Author: Klaus Weide <klaus@flash.uchicago.edu>
Date:   Fri May 12 09:55:52 2017 -0500

    support for Flash as a site, machine "asterix"

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.flash

commit cab1dad14299b21f7af675db5d95ccce9c1c4585
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri May 12 02:22:09 2017 -0400

    Remove unnecessary device synchronize

Src/Base/AMReX_CUDArena.cpp

commit 53662d55847df16a76ae018d549abe1788911f05
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri May 12 01:50:48 2017 -0400

    Add capability to do UM prefetches to/from device
    
    By setting the new parameter do_device_transfers in MFIter, one can
    enable the ability to prefetch any FArrayBox accessed by that MFIter
    to the device. Then, when the MFIter index is incremented or the
    object is destroyed, all of the prefetches are reversed, bringing
    the data back to the host. For now, we default to moving everything
    to GPU 0. In the future, we should generalize this so that we can
    operate on multiple devices.

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 944f5332ea758a75e48cb13c52fce5986f311b56
Merge: 34a166e30 a28725065
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 11 20:52:27 2017 -0400

    Merge branch 'development' into gpu

commit 8b002e112fe14a289a5c6d705729764e5413bd7f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 11 17:29:20 2017 -0700

    Remove print statement that shouldn't have been committed.

Src/Particle/AMReX_ParticleContainerI.H

commit c861ab1a564e07de6dc593dc6d207916d926e751
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 11 16:13:08 2017 -0700

    add average_down_edges to MultiFabUtil

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/Make.package

commit ce901f4e7cc2678db41973338d5e449ed126ad06
Merge: 27cf2911e 5aff33b2c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 11 16:00:13 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 27cf2911e6f766690a008c4fbdba3c7b4e2a9eaf
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 11 15:59:47 2017 -0700

    A tool for comparing particle data in plt files for Regression testing.

Tools/Postprocessing/C_Src/GNUmakefile
Tools/Postprocessing/C_Src/Make.package
Tools/Postprocessing/C_Src/particle_compare.cpp

commit c6e0d7bb20ef17b6659dee10c2c6ac9cc33777d7
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu May 11 15:50:05 2017 -0700

    prolongation operator passes its first test

Src/EBAMRTools/AMReX_EBFineInterp.cpp
Tests/EBAMRTools/README
Tests/EBAMRTools/regression/GNUmakefile
Tests/EBAMRTools/regression/ebFineInterpTest.cpp
Tests/EBAMRTools/regression/ebfineinterp.inputs

commit ab41987195562bac7c35ba06825b00e26c68d140
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu May 11 15:09:54 2017 -0700

    EBCoarseAverage now does the right thing with the new fortran

Src/EBAMRTools/AMReX_EBCoarseAverage.cpp
Src/EBAMRTools/AMReX_EBFortND.F90

commit 1ad604fa6ffb61b6dba4d8649b66b6628aa917ac
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu May 11 15:08:48 2017 -0700

    fixed the new macros to actually work

Src/Base/AMReX_ArrayLim.H

commit f28805d15afe9b550522fe2c1b8bc5df22570b12
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu May 11 14:36:19 2017 -0700

    I added a macro to ArrayLim and a function to BaseFab to make calling Fortran slightly less painful.  Also I added some fortran source to EBAMRTools since the relevant MultiFab utilities did communication.

Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BaseFab.H
Src/EBAMRTools/AMReX_EBCFInterp.H
Src/EBAMRTools/AMReX_EBCoarseAverage.cpp
Src/EBAMRTools/AMReX_EBFineInterp.H
Src/EBAMRTools/AMReX_EBFineInterp.cpp
Src/EBAMRTools/AMReX_EBFortND.F90
Src/EBAMRTools/AMReX_EBFortND_F.H
Src/EBAMRTools/Make.package

commit 5aff33b2c69f87d6b946f3c5af3f019c9cd2a44b
Merge: b722ba3f2 d585ff2ff
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 11 14:17:16 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit b722ba3f230ee55dd933d9b3c3a17f3bef02a07c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 11 14:16:46 2017 -0700

    Must resize the dummy_mf when we resize m_particles in AddParticlesAtLevel

Src/Particle/AMReX_ParticleContainerI.H

commit d585ff2ffbe2227fc358c273f4a0b804e14999c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 11 13:36:53 2017 -0700

    add back BoxList BoxList intersection because Amrvis uses it

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp

commit 8676d5e489adc0c980ec148bdc5c0b00c430a9b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 11 13:21:18 2017 -0700

    clean up Tutorials/HeatEquation_EX1_C

Tutorials/HeatEquation_EX1_C/Make.package
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX1_C/myfunc_F.H
Tutorials/HeatEquation_EX1_C/writePlotFile.H
Tutorials/HeatEquation_EX1_C/writePlotFile.cpp

commit 234569709c5e4053350e3a7e9fac4f02c54a7890
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 11 10:41:44 2017 -0700

    User's Guide: add new file for Building AMReX

Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex
Docs/AMReXUsersGuide/GNUmakefile
Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex

commit 71a0b748c0552bd9edb754c1bce1f75a9e408372
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 11 10:32:45 2017 -0700

    User's Guide: Getting Started

Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex
Tutorials/HeatEquation_EX1_C/main.cpp

commit 1d01c139156e63191fa8dab92a810b4b53bc4b35
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 11 09:33:57 2017 -0700

    update typechecker for gcc 7

Tools/typechecker/typechecker.py

commit 57fb40e0fff376ba4e80090745b7623dd0ad443d
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 10 16:26:34 2017 -0700

    took out stray file

Src/EBAMRTools/AMReX_EBPWLFineInterp.H

commit f9637aa16df6c86c61342ce868721782bb6bb950
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 10 16:25:28 2017 -0700

    I am most of the way there to having (regridding, multigrid) interpolation/prolongation operator for EB.

Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H
Src/EBAMRTools/AMReX_EBCFInterp.H
Src/EBAMRTools/AMReX_EBCFInterp.cpp
Src/EBAMRTools/AMReX_EBFineInterp.H
Src/EBAMRTools/AMReX_EBFineInterp.cpp
Src/EBAMRTools/AMReX_EBPWLFineInterp.H
Src/EBAMRTools/AMReX_EBPWLFineInterp.cpp
Src/EBAMRTools/Make.package
Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBArith.cpp
Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp

commit a2872506558f631395fb25c876cb1f8cb0ed4748
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 10 10:13:16 2017 -0700

    If ref_ratio, n_error_buf, max_grid_size, or blocking_factor from inputs has fewer counts than the number of levels, fill the rest with the last value.  The old behavior was to abort except in the single value case.

Src/AmrCore/AMReX_AmrMesh.cpp

commit 5ad7574c62f4bbd99b751876324a95c0e973cf07
Merge: 9718535d0 aff70ea7e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed May 10 12:14:33 2017 -0700

    Merge pull request #8 from AMReX-Codes/dtg_branch
    
    stuff from dtg_branch requested by jrood

commit aff70ea7e30f00776c7f604fde50dae992c86e9e
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 10 11:52:10 2017 -0700

    ported over  some functions as requested by jrood

Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBArith.cpp
Src/GeometryShop/AMReX_EBLoHiCenter.H
Src/GeometryShop/AMReX_EBLoHiCenter.cpp
Src/GeometryShop/Make.package
Tests/EBAMRTools/regression/aggpwlfpTest.cpp

commit 34a166e3004d8d86f5b84b1a29b20bfb4fd17aa2
Merge: ed2ec40ab 9718535d0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 10 14:45:10 2017 -0400

    Merge branch 'development' into gpu

commit 4c3a8eef0fd9268bfdebeb7d5af09f7eb3509ae8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed May 10 11:20:22 2017 -0700

    Write out particle box array information to the plt / chk files.

Src/Particle/AMReX_ParticleContainerI.H

commit 9718535d0d14f016622d25255e2e1c8b4edd1f3c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 10 09:29:32 2017 -0700

    clean up BoxArray::GetBndryCells

Src/Base/AMReX_BoxArray.cpp

commit b7f1563975a9ce48a0778c111df814627f3b112f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 10 08:38:00 2017 -0700

    consistent names

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_FabArrayBase.cpp

commit 97bcd979e7d16ed99611eef6babb1d9087fd84ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 10 08:28:26 2017 -0700

    Revert "Remove unused variable."
    
    This reverts commit c16a1afb7b68c7aa67c4ab1703dd4f759ca539c2.

Src/Base/AMReX_IntVect.H

commit b51fb45f1c31130a3b52d1977e59aae1dd2b5133
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 10 08:25:24 2017 -0700

    High order CFInterp now works with as many ghost cells as you like (as long as the nesting radius supports it)

Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.H
Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp
Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp

commit ed2ec40ab55c8d2c06afdbad775b294b780c9df6
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed May 10 03:45:45 2017 -0400

    Use pgfortran as the linker

Tools/GNUMake/Make.rules
Tools/GNUMake/comps/cuda.mak

commit ee75a8480462dedd633ac1812bb2f6cecb515c00
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed May 10 03:15:41 2017 -0400

    Add in the cuda.mak file

Tools/GNUMake/comps/cuda.mak

commit 1d85d31a9258a59f6d13453c1778bbb0207d74a8
Merge: c16a1afb7 1f8544ed4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 9 20:36:22 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit c16a1afb7b68c7aa67c4ab1703dd4f759ca539c2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 9 20:35:32 2017 -0700

    Remove unused variable.

Src/Base/AMReX_IntVect.H

commit 97190a4b880843197d85f85f8a361df6ca6a9f88
Merge: de0fd9a14 1f8544ed4
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue May 9 21:13:18 2017 -0400

    Merge branch 'development' into gpu

commit 1f8544ed4b374d478448cfddb301341e1c72f1c7
Merge: bac340853 4dd384daf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 9 16:58:48 2017 -0700

    Merge branch 'development' into boxlist

commit 4dd384daf973a17d2ec73aac63a940f8c232f85c
Merge: 543cd0c99 f66117daf
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 9 16:50:35 2017 -0700

    Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development

commit 543cd0c99bb6ff66491592b5e9332ee86641d354
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 9 16:50:03 2017 -0700

    Remove unused variables.

Src/Particle/AMReX_ParticleInit.H

commit f66117dafc38a4a13a50ba6edfb53ff82109b497
Merge: 1f192b085 f845e4b49
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 9 16:32:36 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 1f192b0857ec437bad778bb55cb5613fcf2812ff
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 9 16:32:28 2017 -0700

    make num ghosts a property of the container.

Tutorials/ShortRangeParticles/ShortRangeParticleContainer.H
Tutorials/ShortRangeParticles/ShortRangeParticleContainer.cpp
Tutorials/ShortRangeParticles/main.cpp

commit 932509be51292e8bb562672ecdce301c2267c379
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue May 9 16:29:54 2017 -0700

    nwoEBQuadCFInterp has had many bug fixes

Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.H
Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp
Src/GeometryShop/AMReX_EBArith.cpp
Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp

commit bac34085347d8a44ed93bb6f211a022d68d3dea1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 9 16:17:48 2017 -0700

    fix recursive call

Src/Base/AMReX_BoxArray.cpp

commit b747c59ae5ca4743a24353a72862ca19e66d5d24
Merge: e61dc0cba f845e4b49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 9 16:04:24 2017 -0700

    Merge branch 'development' into boxlist

commit f845e4b49db2c053e296a3d70dfe3b1a46bdb569
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 9 15:54:41 2017 -0700

    Get rid of warning with DIM=1 about unused variable.

Src/Base/AMReX_BaseFab.H

commit e61dc0cba5bfa650ede68b9b8b4537cb0e450006
Merge: deaa1d13e b57929279
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 9 14:38:37 2017 -0700

    Merge branch 'development' into boxlist
    
    Conflicts:
            Tools/F_scripts/f90cat.py

commit deaa1d13e109a0ec1b2418cb89586bd71552aeec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 9 14:08:31 2017 -0700

    minor optimizations

Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.cpp

commit b57929279d56b4baa5cefd7bd5318c8e453aff31
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 9 14:32:40 2017 -0700

    Update advection tutorial to reflect changes in particle initialization routines.

Tutorials/AMR_Adv_C/Source/Adv.cpp

commit 842984e46754b3d9168fb42323ac7332c18aad76
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue May 9 14:00:52 2017 -0700

    bug fix for NWOEBQuadCFInterp

Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp

commit d1b713c1902ea4c9377d16cd392da961edb43f36
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 9 13:33:38 2017 -0700

    minor optimization
    BoxDomain: need to remove empty boxes

Src/Base/AMReX_BoxDomain.cpp

commit b891c6245ffffede1e3109bd89fd0643fda1fe68
Merge: fb6bab72e 207d23213
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 9 13:38:24 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit fb6bab72e650ae6735b5f882439e5a34cce57817
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 9 13:38:10 2017 -0700

    fix copy / paste error in previous commit.

Src/Particle/AMReX_ParticleInit.H

commit 207d23213d040d9376f528b283b5d4aafee730fa
Merge: 56eca3f73 389d7c754
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue May 9 13:22:58 2017 -0700

    Merge pull request #7 from AMReX-Codes/dtg_branch
    
    bug fixes from Dtg branch

commit 389d7c754727f9c43f635bf308527034f8ed930b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue May 9 13:11:33 2017 -0700

    more aggstencil pointer tricks for better performance.

Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp
Src/EBAMRTools/AMReX_EBCoarseAverage.cpp
Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.H
Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp

commit 56eca3f735984e8dba722a63c63a671d8270e297
Merge: 9604f3bb0 eddd07e43
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 9 12:43:59 2017 -0700

    Merge branch 'development' of github.com:AMReX-Codes/amrex into development

commit 9604f3bb0eb5ed16992c6020a10631ff209c2cfd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue May 9 12:43:45 2017 -0700

    Make the particle initialization routines agnostic as to the names of the components or how they are laid out in memory.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Tests/Particles/AssignDensity/main.cpp
Tests/Particles/AssignMultiLevelDensity/inputs
Tests/Particles/AssignMultiLevelDensity/main.cpp

commit d9cc550c4a8dcddc02b3041829031717c364b9b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 9 12:40:15 2017 -0700

    change plot_int

Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs

commit f2d564081e387bf67586f38377cce07e62d653c4
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue May 9 12:39:47 2017 -0700

    fixed another regression failure that Marc found

Src/GeometryShop/AMReX_IrregFABFactory.H

commit eddd07e4379f5298d2cf6be6922e3cf4968905dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 9 15:28:36 2017 -0400

    take a list of F90 files, determine their interdependencies and
    perform a topological sort.  Then output a single .F90 file
    with all input files concatenated together

Tools/F_scripts/f90cat.py

commit 5cf2ee163995182ce9d8af27d9f32af32454aba7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 9 12:02:34 2017 -0700

    remove unused function

Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp

commit 4d94543ec16dc653cd54d477ebae816e7d32c81e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 9 11:55:53 2017 -0700

    minor

Src/Base/AMReX_BoxList.cpp

commit 991062b2614e5d06c99e6938c052908b35ced897
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue May 9 11:42:24 2017 -0700

    bit of trickery to get more performance when making AggStencils

Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp

commit 6932733cd87719ce45b29796f2563ef4e9082b21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 9 11:01:02 2017 -0700

    change BoxList complement algorithm

Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.cpp

commit 813ff9da210500a3c163ce2679c4b8e5452ae0d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 9 10:26:24 2017 -0700

    wip: finished first pass

Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxDomain.H
Src/Base/AMReX_BoxDomain.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp

commit eff6ee383285037f20a0702786d5bd6cde2be273
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue May 9 09:11:00 2017 -0700

    Marc noticed one of the regression tests was failing.  This fixes that failure.

Src/GeometryShop/AMReX_BaseIVFactory.H
Src/GeometryShop/AMReX_RedistStencil.cpp

commit b1c9ef6256ce0959aa9067114785a0823a150b8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 8 22:58:37 2017 -0400

    concatenate a bunch of fortran files, first sorting them by dependency

Tools/F_scripts/f90cat.py

commit 202e3b83407c3cad6d4105ec6342fc98f868b299
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 8 18:10:28 2017 -0700

    wip: remove some unused functions

Src/Amr/AMReX_AuxBoundaryData.cpp
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp

commit 3066ddfce7229c307059b5048cb054e78dd977b3
Author: dtgraves <dtgraves@lbl.gov>
Date:   Mon May 8 16:44:55 2017 -0700

    Another day, another class.  I added high order coarse-fine interpolation (with EB).  The test does not show the proper convergence rate yet.

Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.H
Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp
Src/EBAMRTools/Make.package
Tests/EBAMRTools/README
Tests/EBAMRTools/regression/GNUmakefile
Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp
Tests/EBAMRTools/regression/nwoebquadcfi.inputs

commit b514fc87d14d6ca2182f30702a0cb3a451a64ef2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 8 12:07:03 2017 -0700

    wip: use Array instead of std::list as the internal data structure for BoxList

Src/Amr/AMReX_Amr.H
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxDomain.H
Src/Base/AMReX_BoxDomain.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp

commit ab6f8b893debf71201f4d04e2a573b68ee6bd0e3
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon May 8 15:19:39 2017 -0700

    Add amrex_fabio_c.f90 and amrex_timer_c.f90 to cmake build.

Src/F_BaseLib/CMakeLists.txt

commit 0ecd7a8a81e85207a3d3c8a02b06aa0a496e1447
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 7 16:55:27 2017 -0700

    unit test for typechecker

Tests/TypeCheck/GNUmakefile
Tests/TypeCheck/Make.package
Tests/TypeCheck/f.f90
Tests/TypeCheck/f_F.H

commit df66be77180c054938608e4ab87832261a2a0f70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 7 13:24:25 2017 -0700

    typecheck: add readme

Docs/Readme.typecheck

commit 085d8cf6d302b6d62affcfa97f27b713dae32018
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 7 13:03:49 2017 -0700

    type check: takes only the first part of the name

Tools/typechecker/typechecker.py

commit cb441f62c31fdb1560f545e6c93f2d145a1cdc57
Merge: 00525735c cd9ef8b41
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Sun May 7 12:10:32 2017 -0700

    Merge pull request #1 from AMReX-Codes/maxpkatz/post_timestep_regrid
    
    Add a hook so that an AmrLevel can force a post-timestep regrid

commit 00525735cc286f233bfbeac3072b6d67837262aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 7 07:44:11 2017 -0700

    fix print

Tools/typechecker/typechecker.py

commit 12061bd793e69a9fc3714fc5324921675af170ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 7 07:12:22 2017 -0700

    typechecker: get rid of global variables and print more info

Tools/typechecker/typechecker.py

commit fe4c415730941d339ab586978a630328d9492815
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 21:30:57 2017 -0700

    typo

Tests/C_BaseLib/TPROFILER_F.H

commit 5589ab1923bf562b5db34851d5de8a192f75ebe0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 19:09:14 2017 -0700

    fix conflict due to merge

Tutorials/ShortRangeParticles/short_range_F.H

commit 3d945cffd24fd798bddec557427afb5e63f70170
Merge: b5d3aff3d b470c44ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 19:06:52 2017 -0700

    merge

commit b470c44ef823525bd0aa33847e005723a50f93d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 16:51:02 2017 -0700

    type

Tools/typechecker/typechecker.py

commit 14a615d52de94aeaba0257b5c9942fe104aa31ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 15:37:59 2017 -0700

    typecheck: optimization

Tools/typechecker/typechecker.py

commit edae53ab6616a7743badb71e9249b25e30bb6c13
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 11:58:58 2017 -0700

    typecheck: remove whitespace lines because they mess up the block detection

Tools/typechecker/typechecker.py

commit 0f24dd850544b1ae958984c3fe3a81bed0a68bc9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 11:21:17 2017 -0700

    found missing argument thanks to typcheck

Src/AmrCore/AMReX_INTERP_1D.F

commit ed1deb22341a91ff19378f29fca922df2b2de135
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 11:20:48 2017 -0700

    better error message

Tools/typechecker/typechecker.py

commit c62a5ec9b9c758575e28032d2072352398ba7474
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 10:53:04 2017 -0700

    match void* with any fortran reference

Tools/typechecker/typechecker.py

commit 52bb8f9ad5a1a03deb2b6fc81320f2b9970f2479
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 08:49:45 2017 -0700

    fix sed

Tools/GNUMake/Make.rules

commit 5f4fff603b39d50f4f6858233c27a9713873cb63
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 08:42:59 2017 -0700

    minor tweak

Src/Base/AMReX_BLFort.H
Tools/GNUMake/Make.rules

commit 4ac86fbce5d45a24a76cabdd1764c639809d28f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 08:31:35 2017 -0700

    started #ifdef __cplusplus in EB tests, but quickly gave up

Tests/GeometryShop/stencilTestbed/src/lapl_nd_F.H

commit 658c6331875b94eb3d2a16f776893310e2251c0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 08:22:47 2017 -0700

    don't need to build executable to use typecheck, but we do still need to compile fortran codes

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit bc05f0cd7e8e6c08be91dcd56d5b415dfa91cc08
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 07:50:17 2017 -0700

    #ifdef __cplusplus

Tests/LinearSolvers/C_TensorMG/main_F.H

commit d04f3425e794020eaddb738c1dbd1ed6b6b01cb6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 07:43:27 2017 -0700

    remove non-existing header

Tests/LinearSolvers/C_CellMG/MACPROJ_2D.F
Tests/LinearSolvers/C_CellMG/MACPROJ_3D.F

commit 104f697a6e16af9d495a0f3ddd111d62a0712263
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 07:30:09 2017 -0700

    fix type(c_ptr), value and character(c_char)

Tools/typechecker/typechecker.py

commit 8a5e951c3ec8d81b74894c041a1056272c2447e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 07:19:38 2017 -0700

    fix node.args is NoneType

Tools/typechecker/typechecker.py

commit d5e62c9b39db68e9672830028740e80022d0a339
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 07:09:37 2017 -0700

    type errors in C_CellMG4

Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F

commit 51859250c795fca48fba78eeb0649277de436ac1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 07:07:44 2017 -0700

    fix type errors in C_CellMG4

Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F

commit dff5a7f0bde69dcefa7bda3ef30700e014657608
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 07:00:35 2017 -0700

    add variable name

Tools/typechecker/typechecker.py

commit 21ac7441bb9fd6eef2609ccf91ff09ebb732abfb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 06:54:43 2017 -0700

    add support for array such as int lo[]

Tools/typechecker/typechecker.py

commit f94403a8be883d414cee313d4df64a32fbcbd67f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 6 06:36:27 2017 -0700

    remove 2d FORT_SETVOLPT that didn't have correct function signature (thanks to typechecker)

Src/Base/AMReX_COORDSYS_2D.F
Tools/typechecker/typechecker.py

commit 4de68796548af45ef55c4c1c6ebb5eab1f89fa9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 5 23:48:45 2017 -0700

    typecheck .f and .F files too

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/typechecker/typechecker.py

commit bdb525e5c0f37f50d2466105f1cc5cfae9a1f0f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 5 23:00:27 2017 -0700

    tweak output of typecheck

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/typechecker/typechecker.py

commit b08561cffc189e5109e8cfab31b4d1d2103ff382
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 5 21:56:34 2017 -0700

    fix amrex::Real, amrex_real and &

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 1e3b1f1b66a12adf6aef860965599767d9f9d25c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 5 18:00:21 2017 -0700

    refactor typechecker to handle both module and non-moudle procedures. add missing headers

Src/AmrCore/AMReX_INTERP_F.H
Tools/typechecker/typechecker.py
Tutorials/AMR_Adv_C/Source/Adv_F.H

commit b5d3aff3d6afe034dfd27dc0afd40aa7cc1ab8ca
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 5 17:57:36 2017 -0700

    Make WriteAsciiFile include the template parameters in the output.

Src/Particle/AMReX_ParticleContainerI.H

commit 8249a9851ba2ca0dc8644fbea81c5f35adaf275e
Merge: 9a92f979f 6169428f2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri May 5 16:49:25 2017 -0700

    Merging.

commit 07371725c3f7044176378af4063fbacb391c2dc3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 5 16:01:24 2017 -0700

    add missing header

Src/Particle/AMReX_Particles_F.H
Tools/GNUMake/Make.rules

commit 22cbc4bd7feb0c81e7f6034f44d256eda65f7d33
Author: dtgraves <dtgraves@lbl.gov>
Date:   Fri May 5 15:35:56 2017 -0700

    added EBCoarseAverage (with an improved interface from Chombo) which calls a nifty function from MultiFab_Util for the regular grid bits.  It passes its convergence test.

Src/EBAMRTools/AMReX_EBCoarseAverage.H
Src/EBAMRTools/AMReX_EBCoarseAverage.cpp
Src/EBAMRTools/Make.package
Tests/EBAMRTools/README
Tests/EBAMRTools/regression/GNUmakefile
Tests/EBAMRTools/regression/ebCoarseAveTest.cpp
Tests/EBAMRTools/regression/ebcoarave.inputs

commit 021bedb5e41bf577c282b3e952ed9b8b474379ca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 5 15:10:45 2017 -0700

    first pass of typechecker.py

Src/Base/AMReX_SPACE.H
Tools/GNUMake/Make.rules
Tools/typechecker/typechecker.py

commit e906e5528ef5f521a305d3f430dfc9be0bfa4f8a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 5 11:33:30 2017 -0700

    rule for making CPP'd headers

Tools/GNUMake/Make.rules

commit 2c9f2bedfc12bacb79732d226e9ed43c777f8135
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 5 11:32:37 2017 -0700

    rm pycparser

Tools/typechecker/pycparser/LICENSE
Tools/typechecker/pycparser/__init__.py
Tools/typechecker/pycparser/_ast_gen.py
Tools/typechecker/pycparser/_build_tables.py
Tools/typechecker/pycparser/_c_ast.cfg
Tools/typechecker/pycparser/ast_transforms.py
Tools/typechecker/pycparser/c_ast.py
Tools/typechecker/pycparser/c_generator.py
Tools/typechecker/pycparser/c_lexer.py
Tools/typechecker/pycparser/c_parser.py
Tools/typechecker/pycparser/ply/LICENSE
Tools/typechecker/pycparser/ply/__init__.py
Tools/typechecker/pycparser/ply/cpp.py
Tools/typechecker/pycparser/ply/ctokens.py
Tools/typechecker/pycparser/ply/lex.py
Tools/typechecker/pycparser/ply/yacc.py
Tools/typechecker/pycparser/ply/ygen.py
Tools/typechecker/pycparser/plyparser.py

commit fded07ba762f990e6226fda41dec6ba00d56a222
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 5 10:45:52 2017 -0700

    add a script for amrex::Real --> amrex_real

Tools/Migration/amrex_real.sh

commit a29078400d357eb8e17ab840ad6373a7c801f17e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 5 10:44:59 2017 -0700

    amrex::Real --> amrex_real in *_F.H and *_f.H files so that c parser can parse them

MiniApps/MultiGrid_C/COEF_F.H
MiniApps/MultiGrid_C/RHS_F.H
MiniApps/PGAS_SMC/SMC_F.H
Src/Amr/AMReX_MAKESLICE_F.H
Src/Amr/AMReX_PROB_AMR_F.H
Src/Amr/AMReX_SLABSTAT_F.H
Src/AmrCore/AMReX_FLUXREG_F.H
Src/AmrCore/AMReX_INTERP_F.H
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_COORDSYS_F.H
Src/Base/AMReX_MultiFabUtil_F.H
Src/Boundary/AMReX_INTERPBNDRYDATA_F.H
Src/F_BaseLib/MultiFab_C_F.H
Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H
Src/LinearSolvers/C_CellMG/AMReX_LO_F.H
Src/LinearSolvers/C_CellMG/AMReX_LP_F.H
Src/LinearSolvers/C_CellMG/AMReX_MG_F.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H
Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H
Src/Particle/AMReX_Particles_F.H
Tests/LinearSolvers/C_CellMG/COEF_F.H
Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H
Tests/LinearSolvers/C_TensorMG/main_F.H
Tests/LinearSolvers/ComparisonTest/COEF_F.H
Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H
Tools/C_util/Convergence/AVGDOWN_F.H
Tools/C_util/Statistics/AVGDOWN_F.H
Tutorials/AMR_Adv_C/Source/Adv_F.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H
Tutorials/HeatEquation_EX1_C/myfunc_F.H
Tutorials/HeatEquation_EX2_C/myfunc_F.H
Tutorials/MultiGrid_C/COEF_F.H
Tutorials/MultiGrid_C/RHS_F.H
Tutorials/ShortRangeParticles/short_range_F.H

commit 2b12a1210f7185d2356f0ec76260a6a684135d23
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 5 10:35:35 2017 -0700

    more #ifdef __cplusplus

MiniApps/MultiGrid_C/COEF_F.H
MiniApps/MultiGrid_C/RHS_F.H
MiniApps/PGAS_SMC/SMC_F.H
Src/Base/AMReX_BLFort.H
Tests/C_BaseLib/AMRPROFTEST_F.H
Tests/C_BaseLib/TPROFILER_F.H
Tests/LinearSolvers/C_CellMG/COEF_F.H
Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H
Tests/LinearSolvers/ComparisonTest/COEF_F.H
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_F.H
Tutorials/AMR_Adv_C/Source/Adv_F.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H
Tutorials/HeatEquation_EX1_C/myfunc_F.H
Tutorials/HeatEquation_EX2_C/myfunc_F.H
Tutorials/MultiGrid_C/COEF_F.H
Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H
Tutorials/MultiGrid_C/RHS_F.H
Tutorials/ShortRangeParticles/short_range_F.H

commit 0771c3da02bdf5de888da1402de6eaa23e6fbc9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 5 10:18:44 2017 -0700

    wrap extern C around ifdef __cplusplu.  this will allow the headers to be included in C codes and be parsed by a C parser

Src/Amr/AMReX_MAKESLICE_F.H
Src/Amr/AMReX_PROB_AMR_F.H
Src/Amr/AMReX_SLABSTAT_F.H
Src/AmrCore/AMReX_FLUXREG_F.H
Src/AmrCore/AMReX_INTERP_F.H
Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_COORDSYS_F.H
Src/Base/AMReX_MultiFabUtil_F.H
Src/Boundary/AMReX_INTERPBNDRYDATA_F.H
Src/F_BaseLib/MultiFab_C_F.H
Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H
Src/LinearSolvers/C_CellMG/AMReX_LO_F.H
Src/LinearSolvers/C_CellMG/AMReX_LP_F.H
Src/LinearSolvers/C_CellMG/AMReX_MG_F.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H
Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H
Src/Particle/AMReX_Particles_F.H

commit 4a691512cf6847ceb27032fbf95e24046ffe9da4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 5 10:05:16 2017 -0700

    restart typeChecker.py

Tools/GNUMake/Make.defs
Tools/typechecker/typeChecker.py
Tools/typechecker/typechecker.py

commit 6169428f26c4e6d7242febcf8e2dd5eddbe8f3c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 5 11:32:26 2017 -0400

    comment out an OpenMP version assert because of a PGI bug

Src/Base/AMReX.cpp

commit 0d5276927788d2a034a8c9341c1a5f60c0e1ab5d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 5 08:43:40 2017 -0400

    fix compilation with PROF=t

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_prof.f90

commit de0fd9a1484bcc132846f3f7b41af97af0e45144
Merge: 9a7183c46 f4ce1736d
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri May 5 02:47:08 2017 -0400

    Merge branch 'development' into gpu

commit 9a92f979fe58ad0d08b42b86f497667698984a6f
Merge: feabb1cab 1cb66d597
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 4 17:34:40 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit feabb1cab28ee1e33de7d62670ac24bb85723064
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 4 17:34:28 2017 -0700

    have the fillGhosts routine take a number of ghost zones as an argument.

Tutorials/ShortRangeParticles/ShortRangeParticleContainer.H
Tutorials/ShortRangeParticles/ShortRangeParticleContainer.cpp
Tutorials/ShortRangeParticles/main.cpp

commit 15bba93903392cb72839ab1a680b16626302557f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu May 4 17:31:50 2017 -0700

    update the ShortRangeParticle example to show the use of the particle derived type in fortran

Tutorials/ShortRangeParticles/ShortRangeParticleContainer.H
Tutorials/ShortRangeParticles/ShortRangeParticleContainer.cpp
Tutorials/ShortRangeParticles/short_range_2d.f90
Tutorials/ShortRangeParticles/short_range_3d.f90
Tutorials/ShortRangeParticles/short_range_F.H

commit f4ce1736ded06f292b25730ba42d2c89d4902cb3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 4 18:09:33 2017 -0400

    fix AMReX testing

Tools/RegressionTesting/suite.py

commit e2317d93c3eb2e5459d3d875f53ecc5722cfa68c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 4 12:43:01 2017 -0700

    add pycparse license

Tools/typechecker/pycparser/LICENSE

commit 6b18c2424807bf0265e997217bb099ac93c130da
Author: dtgraves <dtgraves@lbl.gov>
Date:   Thu May 4 11:56:41 2017 -0700

    fixed EBFastFR.   amrex::FluxRegister could really use a memory scrub.

Src/AmrCore/AMReX_FluxRegister.cpp
Src/EBAMRTools/AMReX_EBFastFR.H
Src/EBAMRTools/AMReX_EBFastFR.cpp
Src/GeometryShop/AMReX_EBFaceFAB.cpp
Tests/EBAMRTools/regression/fluxRegTest.cpp
Tests/EBAMRTools/regression/fluxreg.inputs
Tests/EBAMRTools/regression/regFluxRegTest.cpp

commit d312eb072b4ad4905d9c937a800c597caa057a9b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 4 11:18:28 2017 -0700

    fix merge

Src/Base/Make.package

commit b1151453172b074c6b47f6fb903658950c1be132
Merge: 02c921186 7f70711fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 4 11:10:58 2017 -0700

    Merge branch 'development' into fortran_check
    
    Conflicts:
            Src/Base/Make.package
            Tools/GNUMake/Make.defs
            Tools/GNUMake/Make.rules

commit 7f70711fe2de193dccee6bc75e8830ed97713a61
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 4 11:06:09 2017 -0700

    minor changes in User's Guide

Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex
Docs/AMReXUsersGuide/Introduction/Introduction.tex

commit 045f0549b93d7a69ab6ca2c36fab8b7a5b208eb3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 4 10:22:52 2017 -0700

    more in .gitignore

Docs/AMReXUsersGuide/.gitignore

commit 44ef0132187bb1a8a6f79df0fbf3cce45f986dfa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 4 09:16:06 2017 -0400

    need iso_c_binding to compile

Src/F_BaseLib/fabio.f90

commit 9a7183c4636b615a90e9a03b7a2f241a48f81f31
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu May 4 04:34:20 2017 -0400

    Add a CUDA compiler option (using nvcc+pgfortran)

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 67e766e859e61fc85b893a190dd4164e022a9cb6
Merge: 0d6b44580 573089aa0
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu May 4 03:16:15 2017 -0400

    Merge branch 'development' into gpu

commit 573089aa0daae5ae5ba72a15306d0b2be54e5f8f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu May 4 02:16:56 2017 -0400

    Use ISO C bindings for timer_c and fabio_c

Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/amrex_fabio_c.f90
Src/F_BaseLib/amrex_timer_c.f90
Src/F_BaseLib/bl_timer.f90
Src/F_BaseLib/fab.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/parallel_stubs.f90
Src/F_BaseLib/timer_c.c

commit b33f3376770e62de0f4bd8cacea8ccdbefcb0e7b
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 3 16:20:08 2017 -0700

    added a couple of clarifying (to me) comments to FluxRegister.H.  EBFastFR still does not work but I am on the case.

Src/AmrCore/AMReX_FLUXREG_2D.F
Src/AmrCore/AMReX_FluxRegister.H
Src/EBAMRTools/AMReX_EBFastFR.H
Src/EBAMRTools/AMReX_EBFastFR.cpp
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Tests/EBAMRTools/regression/fluxRegTest.cpp
Tests/EBAMRTools/regression/fluxreg.inputs
Tests/EBAMRTools/regression/regFluxRegTest.cpp

commit 36a6e20fcc651388d8118ea49a34b0ed239c981f
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 3 14:10:08 2017 -0700

    added all-regular flux register test that also fails.

Tests/EBAMRTools/regression/GNUmakefile
Tests/EBAMRTools/regression/regFluxRegTest.cpp

commit 55944054d3bdb114b4737d48917ebb089f429245
Author: dtgraves <dtgraves@lbl.gov>
Date:   Wed May 3 11:43:59 2017 -0700

    adding README files that list the tests and what they do

Tests/EBAMRTools/README
Tests/GeometryShop/README

commit 0d6b44580c116b53b7955c2e326a8d8fd5724f50
Merge: af364f2ac 636404b57
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed May 3 01:37:09 2017 -0400

    Merge branch 'development' into gpu

commit aa6d70d42a0137cc2a03b0ff4aa3d33d96a9ad55
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue May 2 16:48:52 2017 -0700

    we now have an EB flux register and a test (that fails for now)

Src/EBAMRTools/AMReX_EBFastFR.H
Src/EBAMRTools/AMReX_EBFastFR.cpp
Src/EBAMRTools/AMReX_EBLevelDataOps.H
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Src/EBAMRTools/Make.package
Src/GeometryShop/AMReX_EBFaceFAB.H
Src/GeometryShop/AMReX_EBFaceFAB.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Tests/EBAMRTools/regression/GNUmakefile
Tests/EBAMRTools/regression/fluxRegTest.cpp
Tests/EBAMRTools/regression/fluxreg.inputs

commit 636404b575a44437f3686708143e44d5286250f5
Merge: c6bf22211 873e825ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 2 15:23:32 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit c6bf22211f6745a42d3c35c08b327f279884791e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 2 15:23:21 2017 -0400

    boxlib -> amrex

Tools/F_scripts/makebuildinfo.py

commit 873e825ea58d5617246ea8c83e1f69d4a18d2379
Merge: f3dc5f406 9595c4bf7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 2 15:05:07 2017 -0400

    Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development

commit f3dc5f406789e43f922c142796ca7f563dcf1884
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 2 15:04:36 2017 -0400

    fix the summary table info to be at the start of a line
    close some files that were left openned

Tools/RegressionTesting/regtest.py

commit 9595c4bf7d76873cf9caa0b0d6efdfdc762f2d3f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 2 12:01:03 2017 -0700

    assertion

Src/Base/AMReX_FabArrayBase.cpp

commit 00e0608bb2a5605c978a5f2e5db634597306a650
Merge: 36687bb24 bc274fcf0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue May 2 10:21:02 2017 -0700

    Merge pull request #3 from AMReX-Codes/dtg_branch
    
    Dtg branch

commit bc274fcf073872aef15733be3c54331bab711a13
Author: dtgraves <dtgraves@lbl.gov>
Date:   Tue May 2 10:12:31 2017 -0700

    removing unwanted files

Tests/GeometryShop/regression/Backtrace.rg_0_rl_0
Tests/GeometryShop/regression/bl_prof/bl_call_stats_D_00000
Tests/GeometryShop/regression/bl_prof/bl_call_stats_H
Tests/GeometryShop/regression/bl_prof/bl_call_stats_H_00000
Tests/GeometryShop/regression/bl_prof/bl_comm_prof_D_00000
Tests/GeometryShop/regression/bl_prof/bl_comm_prof_H
Tests/GeometryShop/regression/bl_prof/bl_comm_prof_H_00000
Tests/GeometryShop/regression/bl_prof/bl_prof_D_00000
Tests/GeometryShop/regression/bl_prof/bl_prof_H

commit 36687bb24104eb09ef26911cd0c938f8d936bb17
Merge: 2972ca732 3aaaa52c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 2 13:00:17 2017 -0400

    Merge pull request #4 from WeiqunZhang/weiqun/regtest
    
    fix suite.py

commit 2972ca732feb013ea86eb22009cbe3f1e548a96f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 2 09:18:29 2017 -0700

    AMR_Adv_CF: should use contains not intersects

Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90

commit 7bfbb1d2fcd89fee3d6c0093ed48a98225f68232
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 2 09:17:59 2017 -0700

    amrex_box_module: add contains function

Src/F_Interfaces/Base/AMReX_box_mod.F90

commit 3aaaa52c77643b1db0164ad931235282d952560d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 2 08:59:22 2017 -0700

    fix suite.py

Tools/RegressionTesting/suite.py

commit cf0c02bfec6579c1737ae00dcd21ca632b438e34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 2 06:01:14 2017 -0700

    forgot a new file

Src/Base/AMReX_filcc_mod.F90

commit af364f2acf9b4a859bbfce77c52814135e088ede
Merge: 0b693bcf8 68fe11d4e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue May 2 01:46:32 2017 -0400

    Merge branch 'development' into gpu

commit 68fe11d4e025fd52c920660b3ba57f5bfdbc405d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 1 17:26:26 2017 -0700

    add inputs.physbc

Tutorials/AMR_Adv_CF/Exec/SingleVortex/inputs.physbc

commit 0acc0707761c59ddad986f1f8d709a250129880e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 1 17:24:12 2017 -0700

    amrex_box_module: implement intersects

Src/F_Interfaces/Base/AMReX_box_mod.F90

commit 9267d3755bd54589d726c328bb94ab969bbded91
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 1 16:18:52 2017 -0700

    add amrex_filcc_module and add non-periodic boundaries to AMR_Adv_CF example

Src/Base/AMReX_parmparse_fi.cpp
Src/Base/AMReX_parmparse_mod.F90
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/F_Interfaces/Base/AMReX_base_mod.F90
Src/F_Interfaces/Base/AMReX_box_mod.F90
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Tutorials/AMR_Adv_CF/Source/bc_mod.F90
Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit f5cf7a28ca0a37e9cb80068cdb9a5fb861454582
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 1 13:40:14 2017 -0700

    Physbc module: add geometry

Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp
Src/F_Interfaces/Base/AMReX_FPhysBC.H
Src/F_Interfaces/Base/AMReX_FPhysBC.cpp
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Src/F_Interfaces/Base/AMReX_physbc_fi.cpp
Src/F_Interfaces/Base/AMReX_physbc_mod.F90
Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/fillpatch_mod.F90

commit 8783a3f0c33c7bbe0dd6582382e95378c85fb5be
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon May 1 16:27:57 2017 -0700

    added EBNormalizeByVolumeFraction (catchy name, no?) so we can do the whole conservative and  non-conservative divergence thing.

Src/EBAMRTools/AMReX_EBFastFR.H
Src/EBAMRTools/AMReX_EBFastFR.cpp
Src/GeometryShop/AMReX_EBCellFAB.cpp
Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H
Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp
Src/GeometryShop/Make.package
Tests/GeometryShop/regression/Backtrace.rg_0_rl_0
Tests/GeometryShop/regression/GNUmakefile
Tests/GeometryShop/regression/bl_prof/bl_call_stats_D_00000
Tests/GeometryShop/regression/bl_prof/bl_prof_D_00000
Tests/GeometryShop/regression/bl_prof/bl_prof_H
Tests/GeometryShop/regression/ebnormalizeTest.cpp
Tests/GeometryShop/regression/ebnormtest.inputs

commit 1cb66d597d98e125798976915a6068f892bea5cf
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon May 1 11:08:58 2017 -0700

    update scripts used to compile VARDEN

Tools/F_scripts/makebuildinfo.py

commit b30d64e48efecd6cef486e7ba2234d709eb09c05
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 1 12:29:20 2017 -0400

    allow "source" to also contribute to the compile_string

Tools/RegressionTesting/params.py
Tools/RegressionTesting/suite.py

commit 4356189d5fb905ad7c73e0f3081f8c9d75dc66c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 1 09:25:07 2017 -0700

    give omp critical a name

Src/Particle/AMReX_ParticleI.H

commit cd9ef8b41219dd3427e11de2c0f6adbe87d00583
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Mon May 1 02:31:08 2017 -0400

    Add a hook so that an AmrLevel can force a post-timestep regrid
    
    The motivation for this change is that sometimes, during the course of a coarse
    timestep, the timestep will found to be unstable due to a lack of resolution. In
    this case the coarse level may want to signal that more resolution is required
    immediately (as opposed to waiting for a future regrid), because even a single
    unstable step may cause significant harm to the integrity of the simulation. An
    example is a spurious numerical detonation caused by insufficient resolution in
    a thermonuclear burning region. If this numerically-seeded detonation is detected
    at the end of a timestep, more levels can be added immediately so that the fine
    levels can improve the situation and quench the detonation (since they will
    overwrite the coarse data at the end of the timestep).
    
    Each AmrLevel now has a member variable post_step_regrid. To trigger a regrid
    at the end of a step, but before any fine timesteps would be taken, they only need
    to set this variable to one. At the beginning of every timestep, it will be reset to 0.

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H

commit 539158c220a48cfb9de13d30baff100461616634
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 28 20:48:01 2017 -0700

    add EB to doxygen and move doxygen stuff to its own directory

Docs/Doxygen/doxygen.conf
Docs/Doxygen/main.dox

commit 86f202ffeea0c4b347dff8cb9eb9d50b632a253f
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Apr 28 16:43:53 2017 -0700

    started work on hybrid flux register.  this one should be interesting

Src/EBAMRTools/AMReX_EBFastFR.H
Src/EBAMRTools/AMReX_EBFastFR.cpp

commit c3dac35b1fa68e756e3fdb3813f7fb3cf94eb6d9
Merge: 09c86ec44 b008f5c06
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 28 16:04:08 2017 -0700

    Merge branch 'master' into development

commit b008f5c064f116bcb3a7560b54c329b64ebc90fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 28 15:48:08 2017 -0700

    add a main page

Docs/doxygen.conf
Docs/doxygenmain.dox

commit 09c86ec44517860d3965a8b55e8e5f658c69b233
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 28 14:47:07 2017 -0700

    update migration guide

Docs/Migration/Migration.md

commit 1a28c13a677ff1561bf699eaa5defae74e9b1a47
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 28 14:47:07 2017 -0700

    update migration guide

Docs/Migration/Migration.md

commit c908fd516a9fde900c2fb614ab244cd9e4c01e57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 28 14:28:48 2017 -0700

    simplify helloworld

Tutorials/HelloWorld_C/Make.package
Tutorials/HelloWorld_C/main.cpp
Tutorials/HelloWorld_C/work.f90

commit 04f3465c905072314858d7ac94c02266b752311a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 28 14:25:00 2017 -0700

    start AMReX User's Guide

Docs/AMReXUsersGuide/.gitignore
Docs/AMReXUsersGuide/AMReXUsersGuide.tex
Docs/AMReXUsersGuide/GNUmakefile
Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex
Docs/AMReXUsersGuide/Introduction/Introduction.tex
Docs/AMReXUsersGuide/Preface/Preface.tex
Docs/AMReXUsersGuide/README.md
Docs/AMReXUsersGuide/amrexsymbols.tex

commit a5b189c844054c069cc3b29dc9777ac9f50ab250
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 28 13:53:20 2017 -0700

    rename UsersGuide to BoxLibUsersGuide

Docs/BoxLibUsersGuide/C_AdvancedTopics/C_AdvancedTopics.tex
Docs/BoxLibUsersGuide/F_AdvancedTopics/F_AdvancedTopics.tex
Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example1.eps
Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example1.fig
Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example2.eps
Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example2.fig
Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example3.eps
Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example3.fig
Docs/BoxLibUsersGuide/F_AdvancedTopics/subcycling_algorithm.eps
Docs/BoxLibUsersGuide/GNUmakefile
Docs/BoxLibUsersGuide/GettingStarted/GettingStarted.tex
Docs/BoxLibUsersGuide/GettingStarted/VisIt_2D.eps
Docs/BoxLibUsersGuide/GettingStarted/VisIt_3D.eps
Docs/BoxLibUsersGuide/GettingStarted/edison.run
Docs/BoxLibUsersGuide/GettingStarted/edison_omp.run
Docs/BoxLibUsersGuide/Introduction/AMR.eps
Docs/BoxLibUsersGuide/Introduction/Introduction.tex
Docs/BoxLibUsersGuide/Introduction/boxlib_directory_bw2.eps
Docs/BoxLibUsersGuide/Introduction/castro_scaling.eps
Docs/BoxLibUsersGuide/Introduction/data_loc.odg
Docs/BoxLibUsersGuide/Introduction/data_loc2.eps
Docs/BoxLibUsersGuide/Introduction/index_grid.odg
Docs/BoxLibUsersGuide/Introduction/index_grid2.eps
Docs/BoxLibUsersGuide/Introduction/lmc_scaling.eps
Docs/BoxLibUsersGuide/Introduction/maestro_scaling.eps
Docs/BoxLibUsersGuide/Introduction/varden1.eps.REMOVED.git-id
Docs/BoxLibUsersGuide/Introduction/varden2.eps.REMOVED.git-id
Docs/BoxLibUsersGuide/Introduction/varden3.eps.REMOVED.git-id
Docs/BoxLibUsersGuide/Introduction/varden4.eps.REMOVED.git-id
Docs/BoxLibUsersGuide/LinearSolvers/LinearSolvers.tex
Docs/BoxLibUsersGuide/Preface/Preface.tex
Docs/BoxLibUsersGuide/README
Docs/BoxLibUsersGuide/Regression/test_suite.tex
Docs/BoxLibUsersGuide/Regression/testsuite.eps
Docs/BoxLibUsersGuide/UsersGuide.tex

commit 5f994adf6482bf1acb2b841e1f73a765a86d7388
Merge: b35d80636 943e9fe38
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Fri Apr 28 19:30:30 2017 +0000

    Merged in development (pull request #28)
    
    Development

commit 943e9fe38699a66be19400093076f4566b39fe02
Merge: 473f640a2 7c04defb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 28 12:28:30 2017 -0700

    Merge branch 'master' into development

commit 7c04defb4930150f3ebca0289cdf83f1ffb45774
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 28 12:27:36 2017 -0700

    update copyright notice and license agreement

README.txt
license.txt

commit 473f640a26388d613b8e483e30de3aaa8c938ab9
Merge: 7ad754e31 3384eabe3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 27 16:35:18 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit 3384eabe3b94ebd6b5ebe890acdadae3824db23e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 27 16:21:35 2017 -0700

    print origin and value in addition to the fully expanded value when
    `make print-%` is invoked

Tools/GNUMake/Make.rules

commit 7b0f4cb519fd35fe67b9a7836ca9ae7a3623810b
Merge: 02442b8af 172dd063a
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 27 14:56:58 2017 -0700

    getting Weiqun's fixes to aliasing stuff

commit 02442b8af72d49e1aca0bbd5187f39c0a3387dc3
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 27 14:55:43 2017 -0700

    found the bug that was making PWLFP get the wrong convergence rates.   Looks good now.   On to trying to figure out how to integrate with MultiFab fillpatch

Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp
Tests/EBAMRTools/regression/aggpwlfpTest.cpp

commit 7ad754e31ecd2ca4e0cbec158eee7db2aa06903d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 27 14:55:31 2017 -0700

    Make the C interface to the nodal multigrid solver a bit more general.

Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit a109e0c40c78d595c3a6ff6754fb49008e531e48
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 27 13:55:43 2017 -0700

    another change of a MFIter declaration

Src/GeometryShop/AMReX_EBLevelGrid.cpp

commit 975cba9f821ea7745b0d41439b0015f56a716d23
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 27 13:54:27 2017 -0700

    added fancier static initialization to IntVect::Zero and IntVect::Unit from Chombo

Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp

commit 172dd063ac42507db962e045ff765fd11fdcb70b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 27 13:25:49 2017 -0700

    support amrex::Print() << std::endl

Src/Base/AMReX_Print.H

commit d7ba37fed65f0dd9ce072dc0c31154b2cd83a90d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 27 12:26:21 2017 -0700

    add new FArrayBox constructor that takes a Real*

Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp

commit 21a933c2bc9f07a6597894b668b404fce40c2dc4
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 27 12:00:27 2017 -0700

    some bug fixes improve convergence rate but not quite enough

Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp

commit 41426fc1fd4aa0a69d23c0b662901b9fdba6ee82
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 27 11:54:52 2017 -0700

    apparently using a LayoutData for defining a MFIter makes bad things happen

Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp

commit 503511916f8fd7a0332036c4e096a003cea25dbf
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 27 11:53:55 2017 -0700

    added bounds checking to BaseIVFAB

Src/GeometryShop/AMReX_BaseIVFABI.H

commit 2c54addf5b6d358ece633b14aa9b08e27af96bcb
Merge: 449239cea a3ceaefa2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 27 11:16:29 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit a3ceaefa2965558c48d5f0054ada2019dae501d3
Merge: 6f44a4e6e 0fc48b3a2
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 27 18:16:09 2017 +0000

    Merged in dtg_branch (pull request #27)
    
    Dtg branch--merge to get Ray the dataholders he wants

commit 449239ceace31ca40e220ff2ad2df60527715d16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 27 10:20:10 2017 -0700

    add new MultiFab/FabArray constructors that take non-owning pointers; clean up FabArray StatusType

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/Make.package

commit 6f44a4e6e5af0a5e00abca56078a4e5609eafa15
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 26 17:17:13 2017 -0700

    added random number engine copy

Src/F_BaseLib/bl_random_c.cpp
Src/F_BaseLib/bl_random_f.f90

commit 0fc48b3a2482755c9adb35e0657840fdc2ae94e5
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Apr 26 15:58:31 2017 -0700

    I added EBFluxFAB, IrregFAB and their associated factories.  They pass their a simple test.

Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/AMReX_BaseIVFactory.H
Src/GeometryShop/AMReX_EBFluxFAB.H
Src/GeometryShop/AMReX_EBFluxFAB.cpp
Src/GeometryShop/AMReX_EBFluxFactory.H
Src/GeometryShop/AMReX_EBFluxFactory.cpp
Src/GeometryShop/AMReX_FaceIndex.H
Src/GeometryShop/AMReX_FaceIndex.cpp
Src/GeometryShop/AMReX_IrregFAB.H
Src/GeometryShop/AMReX_IrregFAB.cpp
Src/GeometryShop/AMReX_IrregFABFactory.H
Src/GeometryShop/AMReX_IrregFABFactory.cpp
Src/GeometryShop/AMReX_VolIndex.H
Src/GeometryShop/AMReX_VolIndex.cpp
Src/GeometryShop/Make.package
Tests/EBAMRTools/regression/aggpwlfp.inputs
Tests/EBAMRTools/regression/aggpwlfpTest.cpp
Tests/GeometryShop/regression/Backtrace.rg_0_rl_0
Tests/GeometryShop/regression/GNUmakefile
Tests/GeometryShop/regression/bl_prof/bl_call_stats_D_00000
Tests/GeometryShop/regression/bl_prof/bl_prof_D_00000
Tests/GeometryShop/regression/bl_prof/bl_prof_H
Tests/GeometryShop/regression/dataArith.cpp
Tests/GeometryShop/regression/dataarith.inputs

commit bde177139c6fd18902ac3fdde3e8ff2524a47d01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 26 08:49:46 2017 -0700

    fix shebang

configure

commit 744be16ecda3fd5fe1888c4a82fa411f36891757
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Apr 25 16:26:45 2017 -0700

    Good news: PWL fill patch test works.  Bad news:  convergence rate is wrong.

Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H
Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp
Src/EBAMRTools/AMReX_EBLevelDataOps.H
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Src/EBAMRTools/AMReX_MeshRefine.H
Src/EBAMRTools/AMReX_MeshRefine.cpp
Tests/EBAMRTools/regression/aggpwlfp.inputs
Tests/EBAMRTools/regression/aggpwlfpTest.cpp
Tests/EBAMRTools/regression/sphere.inputs

commit c2e5702721fabf52ca318cc6ce027443a1cdb51e
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Apr 25 12:44:32 2017 -0700

    EBAMRTools again compiles.   I added a bunch of EBLevelDataOps functionality

Src/EBAMRTools/AMReX_EBLevelDataOps.H
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Src/EBAMRTools/AMReX_MeshRefine.H
Src/EBAMRTools/AMReX_MeshRefine.cpp
Src/GeometryShop/AMReX_EBCellFAB.cpp
Tests/EBAMRTools/regression/aggpwlfpTest.cpp

commit 0faf79700e22af9b62bccf0d1646c6325cf2dc30
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Apr 25 12:25:59 2017 -0700

    added IntVect::Zero and IntVect::Unit because TheZeroVector() was pissing me off

Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp

commit 8eccdb3eb503a18e63bcc387a1cb8f7e226bd4fd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 25 09:49:49 2017 -0700

    fix the advection tutorial.

Src/Particle/AMReX_ParticleInit.H

commit e2f885c26d4382c3291778a221221eb5c4fae40b
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Apr 24 16:11:25 2017 -0700

    I ported over a bunch of tools I use to write tests

Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp
Src/EBAMRTools/AMReX_EBLevelDataOps.H
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Src/EBAMRTools/AMReX_MeshRefine.H
Src/EBAMRTools/AMReX_MeshRefine.cpp
Src/EBAMRTools/Make.package
Src/GeometryShop/AMReX_EBCellFAB.H
Src/GeometryShop/AMReX_EBCellFAB.cpp
Tests/EBAMRTools/regression/aggpwlfpTest.cpp

commit 0c7642b61bed921181ef467909fc7ac6c5b21ac3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 24 15:54:05 2017 -0700

    Use the new syntax to get the Real data from the struct-of-arrays.

Src/Particle/AMReX_ParticleContainerI.H

commit 07b87c6db3a0eff345bb8d8d2e4b59a9fe38b100
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 24 15:47:35 2017 -0700

    give the AmrParticleContainer 4 components as well.

Src/AmrCore/AMReX_AmrParticles.H

commit 18175f9c96081f9a91ec7d61b43e9f8e0c4dadb3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 24 10:50:45 2017 -0700

    add some additional accessor methods to StructOfArrays.

Src/Particle/AMReX_Particles.H

commit e371eaf7aba70e290f468a5e99ecdd8c27aca7c2
Merge: 1a036584c 6f8475b22
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 24 09:43:08 2017 -0700

    Merge branch 'integer_soa_data' into development

commit 1a036584ce55d8bb855f9771cb1b012372ba5d7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 24 08:51:58 2017 -0700

    move some rules out of Tools/GNUMake to avoid potential conflicts

GNUmakefile.in
Tools/GNUMake/Make.rules

commit 7cc436205df8c48b7ec9a959ede113b8f72f4736
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 23 12:42:37 2017 -0700

    configure: enforce libamrex and application are consistent on the use of OpenMP

Tools/GNUMake/Make.rules
Tools/libamrex/mkconfig.py

commit b4c585bb6a00415049364771f829a9ce115e140c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 23 12:19:43 2017 -0700

    configure: by default enforce the same compiler is used to build application

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/libamrex/configure.py
Tools/libamrex/mkconfig.py

commit 28e94d3065e7fc30a54b4792bf600c43f2586781
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 23 12:17:29 2017 -0700

    minor tweak

Tutorials/libamrex_C/GNUmakefile

commit 9cdd34b19b3ba30e3a0efd73e4d356289574b41d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 22 22:14:00 2017 -0700

    minor tweak of make

GNUmakefile.in
Tools/GNUMake/Make.rules

commit ef5c301fc233c8a1a13a0273aadc3d6de8b20a24
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 22 21:56:13 2017 -0700

    add a note for linking to C++11 and Fortran libraries

INSTALL

commit f218fd3839b6b78ce95d9e5605e81cb5285039d1
Merge: 8dcb53320 8ba64d97d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 22 21:41:14 2017 -0700

    Merge branch 'libamrex' into development

commit 8ba64d97d986e00982962ccc94c42e35f4f92006
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 22 21:40:31 2017 -0700

    add INSTALL

INSTALL
Tools/libamrex/configure.py

commit 63a2ee02d172961457f6fb3d63de4a381a731c12
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 22 21:19:38 2017 -0700

    add configure

GNUmakefile.in
Tools/libamrex/configure.py
configure

commit 879d84dfd49c201f60ebcd622c406854b3fcdf1b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 22 15:46:16 2017 -0700

    create a directory for libarmex scripts

Tools/GNUMake/Make.defs
Tools/libamrex/mkconfig.py

commit 998544cc3dfd38780e44bce932f371d5b0210b69
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 22 09:07:31 2017 -0700

    An example using libamrex

Tutorials/libamrex_C/GNUmakefile
Tutorials/libamrex_C/MyAmr.H
Tutorials/libamrex_C/MyAmr.cpp
Tutorials/libamrex_C/main.cpp
Tutorials/libamrex_C/myf.f90

commit c18e42c4fd4db87790c6fc22fd6f8661ce23704e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 22 08:24:46 2017 -0700

    install headers and modules

GNUmakefile
Src/Base/Make.package
Tools/C_scripts/mkconfig.py
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 0488479179d38b3fcc5e55143f757476429a1d46
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 21 18:04:45 2017 -0700

    add a top level GNUmakefile for building libamrex

GNUmakefile
Src/Amr/Make.package
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 6f8475b22bc116c9fdccd2e6125e69939d50209c
Merge: de664ee35 8dcb53320
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 21 17:33:29 2017 -0700

    Merging development into integer_soa_data

commit 8dcb53320d203447aebd43a29f988efe97018973
Merge: 77c5698f5 5e5e7f281
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 21 17:19:44 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit 77c5698f56fbcf904117dfb774de223108803ace
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 21 17:19:29 2017 -0700

    Make Reset() return the particle location data.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit be6abd36092827eabb8532c17db6fd12fd13df16
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Apr 21 16:02:08 2017 -0700

    starting to wade into EBLevelDataOps.   I managed to cut out everything I think is redundant and just keep what I think is useful.

Src/EBAMRTools/AMReX_EBLevelDataOps.H
Src/EBAMRTools/AMReX_EBLevelDataOps.cpp
Src/GeometryShop/AMReX_EBCellFAB.H
Src/GeometryShop/AMReX_EBCellFAB.cpp
Src/GeometryShop/AMReX_EBLevelRedist.cpp

commit de664ee357d199a78d5fddeba41c08d33521b00c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 21 15:03:43 2017 -0700

    fix dumb mistake.

Src/Particle/AMReX_ParticleContainerI.H

commit 8982946e952064ad299d9f946c5f41132decd7ac
Merge: 39d1baa03 bf54e3009
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 21 12:57:34 2017 -0700

    Merge branch 'integer_soa_data' of bitbucket.org:berkeleylab/amrex into integer_soa_data

commit 39d1baa03960d5f17641dd088d54d941fd23518f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 21 12:57:13 2017 -0700

    rename these variables.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit c1f8f1589bee174ec4035b7bdea7c22e710b225d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 21 12:52:40 2017 -0700

    reset this to TRUE

Tests/Particles/GNUmakefile

commit bf54e30096df54a61af08e5bc7e8be3f81be1f28
Merge: d4e9f23ba 5e5e7f281
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 21 12:38:01 2017 -0700

    Merge branch 'development' into integer_soa_data

commit d4e9f23bae5d9bdd9c9f697f8349637c6c73ac6a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 21 12:15:18 2017 -0700

    change the struct-of-array interface to make it harder to make mistakes.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Tests/Particles/main.cpp

commit cb59093ddab9e4d7b46e9fc091f14655a4650ccb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 21 10:51:33 2017 -0700

    Fix bug in assert statements.

Src/Particle/AMReX_ParticleContainerI.H

commit 5e5e7f281e433b2b131dc3d867e5546926e0dc51
Merge: 96659ee00 da9993487
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Apr 21 17:17:08 2017 +0000

    Merged in dtg_branch (pull request #25)
    
    Dtg branch
    
    Approved-by: Weiqun Zhang <WeiqunZhang@lbl.gov>

commit da9993487fb78a8d80d5d43839ce1a9130c57f6a
Merge: 38e7177d9 96659ee00
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Apr 21 09:50:42 2017 -0700

    getting the latest from the development branch

commit 96659ee004dbf1ab3b8d0ac1407e8333f14251e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 21 08:58:30 2017 -0700

    add default move constructor to MFIter

Src/Base/AMReX_MFIter.H

commit 3c7459576c24a4dc8664315479bec277f25ad2b6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 20 17:23:14 2017 -0700

    Update test of the particle struct-of-arrays to also test the integer components.

Src/Particle/AMReX_ParticleContainerI.H
Tests/Particles/GNUmakefile
Tests/Particles/main.cpp

commit 724c2db554e40928fdbdf09a1885d9af5052ef67
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 20 17:04:48 2017 -0700

    Add support for integer particle stored in the struct-of-arrays style.

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H

commit 7b816739be5060e457881780992d4d2bf0876bf7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 20 16:19:58 2017 -0700

    add new MFIter constructors that take BoxArray and DistributionMapping

Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp

commit 38e7177d92b47e24a745d826b3f49f9d0de6c905
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 20 15:44:33 2017 -0700

    after some bug fixes, we now have working, single-level redistribution.

Src/EBAMRTools/AMReX_MeshRefine.cpp
Src/GeometryShop/AMReX_BaseIVFactory.H
Src/GeometryShop/AMReX_EBLevelGrid.cpp
Src/GeometryShop/AMReX_EBLevelRedist.cpp
Tests/GeometryShop/regression/Backtrace.rg_0_rl_0
Tests/GeometryShop/regression/GNUmakefile
Tests/GeometryShop/regression/Make.package
Tests/GeometryShop/regression/bl_prof/bl_call_stats_D_00000
Tests/GeometryShop/regression/bl_prof/bl_call_stats_H
Tests/GeometryShop/regression/bl_prof/bl_call_stats_H_00000
Tests/GeometryShop/regression/bl_prof/bl_comm_prof_D_00000
Tests/GeometryShop/regression/bl_prof/bl_comm_prof_H
Tests/GeometryShop/regression/bl_prof/bl_comm_prof_H_00000
Tests/GeometryShop/regression/bl_prof/bl_prof_D_00000
Tests/GeometryShop/regression/bl_prof/bl_prof_H
Tests/GeometryShop/regression/levelRedistTest.cpp
Tests/GeometryShop/regression/levelredist.inputs

commit 095491ed7e2167bf6324104ab623affa9031019b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 20 13:17:17 2017 -0700

    rename the particle template parameters to be more expressive.

Src/AmrCore/AMReX_AmrParticles.H
Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H

commit 6ab7f3b266b0deff9b9f2e55db4a00daf63fc351
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 20 11:31:44 2017 -0700

    Porting over EBLevelRedist was trickier than I thought.   It compiles now.  On to testing

Src/GeometryShop/AMReX_BaseIVFactory.H
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBLevelRedist.H
Src/GeometryShop/AMReX_EBLevelRedist.cpp
Src/GeometryShop/AMReX_IntVectSet.H
Src/GeometryShop/AMReX_IntVectSet.cpp
Src/GeometryShop/AMReX_LayoutData.H
Src/GeometryShop/Make.package

commit d71c1849225f7d52a856f6ca9e7c82e26e045ed1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 19 20:25:19 2017 -0700

    If you restore the random state using more threads than you saved it with, give the RNG a sensible seed on the new threads.

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit 6d4dbaffe72928aad5d4c441c21e10d41fd5fc8d
Merge: c0499c799 31adc1e87
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 19 18:05:23 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit c0499c7994e138f179cd28cfb6cfa54f3faed047
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 19 18:04:50 2017 -0700

    A hopefully more portable way of saving the random state.

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit 638067eacc04fef16412ac3c359873b6545f8945
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 19 17:23:50 2017 -0700

    use critical here instead of atomic capture on older versions of gcc

Src/Particle/AMReX_ParticleI.H

commit 0e18753129b44564f035acc20ba17a61b167bd98
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 19 17:16:18 2017 -0700

    replace the the current implementation of the thread-safe RNG with an array-of-generators, since clang doesn't support thread_local.

Src/Base/AMReX_Utility.cpp

commit 31adc1e875d83d7848994514ce2dbaa70beb2348
Merge: 7e3a47f99 4c863ebc4
Author: Michael  Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Apr 19 23:07:37 2017 +0000

    Merged in mzingale/amrex/development (pull request #24)
    
    add more compilation info to the build info routines

commit 00309aae0f2b65ec2812ed4df17a8c8d8f8e5a0d
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Apr 19 15:58:39 2017 -0700

    RedistStencil now compiles.

Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBLevelGrid.H
Src/GeometryShop/AMReX_EBLevelRedist.H
Src/GeometryShop/AMReX_EBLevelRedist.cpp
Src/GeometryShop/AMReX_RedistStencil.H
Src/GeometryShop/AMReX_RedistStencil.cpp
Src/GeometryShop/Make.package

commit d4ea80795a0809a3199014e1c41956d87939488d
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Apr 19 15:32:36 2017 -0700

    ported over the most important bits of EBArith.   I only kept the bits that did not involve communication.   The full level stuff I will leave to EBLevelDataOps (previously they had a lot of redundant functionality)

Src/GeometryShop/AMReX_EBArith.H
Src/GeometryShop/AMReX_EBArith.cpp

commit 4c863ebc4feef0412d750fa289c9335ab4bc20dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Apr 19 17:50:20 2017 -0400

    clean things up considerably

Tools/C_scripts/makebuildinfo_C.py

commit 7e3a47f99eaf352b2ad867dbc5669fa4cfc0109a
Merge: 39b43d9b6 3e0eb9566
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 19 14:46:51 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit 39b43d9b6d65981a5cc4c245104f22fbecde3438
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 19 14:46:38 2017 -0700

    Break up the short-range particle container into multiple files.

Tutorials/ShortRangeParticles/Make.package
Tutorials/ShortRangeParticles/ShortRangeParticleContainer.H
Tutorials/ShortRangeParticles/ShortRangeParticleContainer.cpp
Tutorials/ShortRangeParticles/main.cpp

commit 70c7845abd8fb0231a09e3b6f9aed4513b59cdc3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Apr 19 17:29:44 2017 -0400

    more compiler options

Tools/C_scripts/AMReX_buildInfo.H
Tools/C_scripts/makebuildinfo_C.py

commit 3e0eb95660f706624ed510e87a2ca341f74585a2
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 19 13:48:10 2017 -0700

    revert last commit - this affects things in codes I wasn't aware of which assumed specifically dimensioned strings

Src/F_BaseLib/fabio.f90

commit b6c330db30c0f83c74eb1068951eac4838f6208f
Merge: 48b399ffb dfdae0292
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 19 13:32:22 2017 -0700

    Merge branch 'development' of https://bitbucket.org/berkeleylab/amrex into development

commit 48b399ffb0b3003d24162a05ea69bf76224d8034
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 19 13:32:07 2017 -0700

    FABIO_MAX_VAR_NAME = 64

Src/F_BaseLib/fabio.f90

commit dfdae0292d1a2a7518d9bc485f7f14dbf4ed8b61
Merge: bf3703667 31c8ec003
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 19 11:05:59 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit bf3703667b9402384f1547c317081c9080f305a6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 19 11:05:45 2017 -0700

    Save and restore the state of the random number generator using an Array of ulongs.

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit 31c8ec00380b17cad8a9d8449e03a17541f7e50c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 18 19:50:43 2017 -0700

    must include BaseFab header in TypeTraits otherwise it may give wrong results if the type is incomplete

Src/Base/AMReX_TypeTraits.H

commit 5ec774f97e4b9592dfd345f44f35491ed47ad3cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 18 17:40:47 2017 -0700

    need to include <random> otherwise gcc 6 won't compile

Src/Particle/AMReX_Particles.H

commit 2c12df1f7b68474298f1ec5f3bde0b5101b79f68
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 18 17:31:27 2017 -0700

    update the dependencies of this particle test, now that additional packages are required.

Tests/Particles/GNUmakefile

commit 27ec5cfa6b54c9209834e9829adde040462c5977
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 18 17:30:31 2017 -0700

    no need to do this now - the random number generator will get different seeds on different threads by default.

Src/Particle/AMReX_ParticleContainerI.H

commit 233dae85ad0401d53f0d085a50599429d035a3d1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 18 16:03:38 2017 -0700

    fix MoveRandom after changes to RNG stuff.

Src/Particle/AMReX_ParticleContainerI.H

commit 1b0805bc8086b349f3ba6a0dad2902ae8182fd72
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 18 12:40:33 2017 -0700

    move the specialization of IsBaseFab into AMReX_TypeTraits

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_TypeTraits.H

commit 2adb6aa3a5e02250c53d97d59e71e398b47afa0f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Apr 18 15:39:05 2017 -0700

    remove AMReX's C++ implemention of the Mersenne twister in favor of the one in C++11.

Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp

commit af6bc0fc45bc5e19b051d059ae82c1c571e337f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 18 10:13:33 2017 -0700

    update cmake

Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 62aef837f9050120a69624feba89bb80ead40f82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 18 10:05:24 2017 -0700

    enable_if a number of FabArray functions that make senses only if FAB is really a BaseFab

Src/Base/AMReX_FabArray.H

commit 84c1bfa1a435e8d80536490ebc686f7b696447f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 18 09:28:23 2017 -0700

    add AMReX_TypeTraits for SFINAE

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_TypeTraits.H

commit 0334bb25179871040a55d9a66b73dc71d8bbabff
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Apr 17 16:08:53 2017 -0700

    started porting over redistribution (on a single level) objects

Src/GeometryShop/AMReX_RedistStencil.H
Src/GeometryShop/AMReX_RedistStencil.cpp

commit 62d69337a15a757e703f17bb318a4fb2f6bed6e8
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Apr 17 14:33:54 2017 -0700

    fixed bug in MeshRefine test.  Seems to work fine now.

Src/GeometryShop/AMReX_EBFluxFAB.H
Tests/EBAMRTools/regression/meshref.inputs
Tests/EBAMRTools/regression/simpleMeshRefine.cpp

commit 6eec2f6f4eb1bd9ddbdeb320244faa2069555aea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 17 13:12:50 2017 -0700

    move MakeType to a new header

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MakeType.H
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit f457a4b9e2f6112d4ca36a8b052b6e5c84ac103d
Merge: 744c58396 c8a30e580
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 17 13:01:23 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit 744c583969fb44b97134faf150a97a4dcae9071b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Apr 17 13:00:55 2017 -0700

    Use the c++11 random number generator here.

Src/Particle/AMReX_ParticleInit.H

commit c8a30e580b8b6332e8fd1a7f802fca1e5c5af37d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 17 11:15:16 2017 -0700

    add new make_alias constructor for MultiFab and iMultiFab

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp

commit 18a90796b9fd760c99d145005b5840ba9ecf9e16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 17 10:54:49 2017 -0700

    add a new FabArray constructor for making alias;  I think it's very confusing to make a deep copy with constructor so make_deep_copy is not support for FabArray

Src/Base/AMReX_FabArray.H

commit 76031a2557bafbbebbb98e051b7c50d20fbb2bec
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Apr 17 10:41:22 2017 -0700

    adding debugging tools so I can figure out what is wrong with AMReX_MeshRefine

Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_EBDebugDump.H
Src/GeometryShop/AMReX_EBDebugOut.H
Src/GeometryShop/AMReX_EBDebugOut.cpp
Src/GeometryShop/AMReX_EBFaceFAB.H
Src/GeometryShop/AMReX_EBFaceFAB.cpp
Src/GeometryShop/AMReX_EBFluxFAB.H
Src/GeometryShop/Make.package

commit 538b248eeceb2879d3f0288e8801f2b8afadb6ef
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Apr 17 10:40:58 2017 -0700

    added face-centered stuff

Src/GeometryShop/AMReX_BaseEBFaceFAB.H
Src/GeometryShop/AMReX_BaseEBFaceFABI.H

commit 2bd57481da6aa3e22b5fae94456d7a98c704b753
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 17 09:45:35 2017 -0700

    add StatusType to FabArray

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.cpp

commit 1a5b2494de358ce883eec1deb5c818283ef0778a
Author: Marc Day <MSDay@lbl.gov>
Date:   Sun Apr 16 22:15:48 2017 -0700

    Partial fix of CMakeLists.txt files - still need to fix mpi

CMakeLists.txt
Tutorials/MultiGrid_C/CMakeLists.txt
Tutorials/MultiGrid_C/main.cpp

commit 58d6e618073703b1acf5934fc828de1184a2abb7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 16 18:49:47 2017 -0700

    new IArrayBox constructor for making alias or deep copy

Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IArrayBox.cpp

commit 64c42dcab1873fba9765654d29313b4efc34d472
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 16 18:36:27 2017 -0700

    new FArrayBox constructor for make alias or deep copy

Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp

commit bcd4adc110e9aacf311c95023ddcf8ea5f9bac68
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sat Apr 15 20:38:26 2017 -0700

    a couple of changes to the InitRandomPerBox routine.

Src/Particle/AMReX_ParticleInit.H

commit 9fb2d3b7ea62c9c38b4aa8e3f275a1f73546cbb0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Apr 15 19:25:25 2017 -0700

    Clarify the comment and error message

Src/Particle/AMReX_ParticleInit.H

commit 6179cfd8ad901b4551bea46a1f76130fb1d6de5b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Apr 15 18:59:20 2017 -0700

    Add a new initialization routine for particles -- InitRandomPerBox --
    which is used when we want the particle distribution to be random
    within a box but we want to be able to replicate the box exactly
    for a scaling study.

Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H

commit 55f8e2a44ad47eb484666615ec2f7927fdc4dfe2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 15 07:56:57 2017 -0700

    mod migration script for IAMR Fortran code

Tools/Migration/step-7-bindc/bindc.sh

commit 43f50eeba4cf44918ed230496ce2981dd82e9ea6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 14 15:50:08 2017 -0700

    ParmParse inputs.

Tutorials/ShortRangeParticles/main.cpp

commit 7c0746edafec5c9b4599b0b8fcb092afbb6b4a46
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 14 14:30:05 2017 -0700

    updating this thing to work in 3D as well.

Tutorials/ShortRangeParticles/main.cpp

commit 1c61d94bb09c3477c00284f62adbbc70fd5e0206
Merge: 6f43405d9 0cc044603
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 14 13:09:46 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit 6f43405d994dd2cdabb35d79feef8a93aea4b62e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 14 13:09:22 2017 -0700

    add 3d versions of fortran routines.

Tutorials/ShortRangeParticles/main.cpp
Tutorials/ShortRangeParticles/short_range_2d.f90
Tutorials/ShortRangeParticles/short_range_3d.f90

commit f18ce7d465a6f2aeb7cfe930f4421724de3fa0cb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 14 12:59:06 2017 -0700

    renaming / reorganization.

Tutorials/ShortRangeParticles/Make.package
Tutorials/ShortRangeParticles/main.cpp
Tutorials/ShortRangeParticles/short_range_2d.f90
Tutorials/ShortRangeParticles/short_range_F.H

commit 68b4efda763b7ddd6e2130875798b41ddcdfc386
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 14 12:55:18 2017 -0700

    removing some now un-needed code.

Tutorials/ShortRangeParticles/main.cpp

commit 163212e803b88c60c3ad5dd4038955b78378d681
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 14 12:48:24 2017 -0700

    move the particle time integration to a fortran subroutine.

Tutorials/ShortRangeParticles/compute_force_2d.f90
Tutorials/ShortRangeParticles/compute_force_F.H
Tutorials/ShortRangeParticles/main.cpp

commit 0cc044603a793f8ff02cdfb967f42879d720f7a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 14 09:48:00 2017 -0700

    new BaseFab constructor that makes either an alias or a deep copy

Src/Base/AMReX_BaseFab.H

commit 2ee64d81b071a0da3e95b92e5952d5f4d6200985
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Apr 14 11:04:34 2017 -0700

    EBIS coarsening issues resolved for now.  BoxArray's ostream operator does seem to have weird integer overflow issues, however.

Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Tests/EBAMRTools/regression/meshref.inputs

commit cd73337237b28678716fb0f248887377d39bcb31
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Apr 14 10:43:48 2017 -0700

    made another destructor virtual to get the compiler to shut up.

Src/Base/AMReX_BaseFab.H

commit 67c6ad040b023e254582ba5fa0b18af81afea7a8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Apr 14 09:52:21 2017 -0700

    more comments.

Tutorials/ShortRangeParticles/main.cpp

commit 613cf90701f8dfb729adc915062be91e2662c9ca
Merge: ed24ddb64 4b0117769
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 13 23:08:37 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit ed24ddb643cfd8525aa76ff04d712ae8abb32c70
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 13 23:08:05 2017 -0700

    MPI communication for ghost particles working now.

Tutorials/ShortRangeParticles/main.cpp

commit 2605bc9eb56d5a8ca4ae87297c3f041690f474f5
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 13 15:39:47 2017 -0700

    did I forgot to add these?

Src/EBAMRTools/AMReX_MeshRefine.H
Src/EBAMRTools/AMReX_MeshRefine.cpp

commit 56f540eed9b9e70db54659835a3bf8a6019ba7a6
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 13 15:39:06 2017 -0700

    made one base constructor virtual to shut the compiler up.   I also coded up a standalone meshrefine and a test from Weiqun's example.   EBIndexSpace coarsening is currently having some problems.

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp
Src/Base/AMReX_IArrayBox.H
Src/EBAMRTools/Make.package
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_IntVectSet.cpp
Tests/EBAMRTools/regression/GNUmakefile
Tests/EBAMRTools/regression/Make.package
Tests/EBAMRTools/regression/meshref.inputs
Tests/EBAMRTools/regression/simpleMeshRefine.cpp

commit bc9c4ae72a77ffbc418852a7f38182c5f12128c9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 13 14:27:20 2017 -0700

    first stab at getting the MPI comm stuff working.

Tutorials/ShortRangeParticles/main.cpp

commit 4b0117769568494638f4432e5cecd748b5a99359
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 13 14:00:43 2017 -0700

    add average_node_to_cellcenter

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_F.H

commit b052343fb4500f3c2b002477dc0a5f6806c68497
Merge: fb73f698e fd037d52e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 13 11:22:08 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit fb73f698e7dcb646c1bc35f254ef86eb3fa2c7cc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Apr 13 11:21:53 2017 -0700

    more functionality for the particle neighbors tutorial. this works in serial now.

Tutorials/ShortRangeParticles/Make.package
Tutorials/ShortRangeParticles/compute_force_2d.f90
Tutorials/ShortRangeParticles/compute_force_F.H
Tutorials/ShortRangeParticles/main.cpp

commit 6ee0ffd10fba4667d8e759989fc5ccf40b047688
Merge: 1e47645d1 fd037d52e
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 13 10:23:23 2017 -0700

    merging with dev branch

commit fd037d52e2df6283bba9218fcecc94c5a92990f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 13 10:20:11 2017 -0700

    fix assertion

Src/AmrCore/AMReX_AmrMesh.H

commit 5afba3ccb0e23951c48fddb378e352ac3121ea2a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 12 23:20:13 2017 -0700

    more work on the ghost particle stuff.

Tutorials/ShortRangeParticles/main.cpp

commit 0a66e5b5073d85438ddda0390e40e899fd20ab7e
Merge: 2ceedce1c 513e1a837
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 12 17:01:16 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit 2ceedce1c370053885fdb5bf814e7d3c2960ed91
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Apr 12 17:00:50 2017 -0700

    Some work towards neighbor computation for particles that see short-range forces.

Src/Particle/AMReX_ParticleContainerI.H
Tutorials/ShortRangeParticles/GNUmakefile
Tutorials/ShortRangeParticles/Make.package
Tutorials/ShortRangeParticles/main.cpp

commit 513e1a837f176c74c4bb0021af71ae24ba263571
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 12 16:07:42 2017 -0700

    Box: remove the lengthy overflow check because I don't think it could happen on exascale machines unless they run Windows

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp

commit 1e47645d1c357ece906bcc91dd576c7ab1a5de8e
Merge: b448f33eb 6d2f47edc
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Apr 12 15:56:15 2017 -0700

    merging to  get new fancier mesh generator

commit 6d2f47edc2218b7b9545f76ae67fd72c0ef963bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 12 15:41:02 2017 -0700

    clean up the MeshRefinement example

Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp
Tutorials/MeshRefinement/main.cpp

commit b448f33eb5ab751cba79fc53f9775c56aa4d7e74
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Apr 12 15:29:34 2017 -0700

    EBAMRTools first tool now compiles.

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H
Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp
Src/GeometryShop/AMReX_AllRegularService.H
Src/GeometryShop/AMReX_AllRegularService.cpp
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_EBCellFAB.H
Src/GeometryShop/AMReX_EBCellFactory.H
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/Make.package
Tests/EBAMRTools/regression/aggpwlfpTest.cpp

commit 76e5ae3414da72a610447f1263c4fb217cdd161a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 12 14:40:10 2017 -0700

    Geometry: allow default coordinates and let passed in paramters take precedence over parmparse parameters

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp

commit 4de535348ee3139d1a9841058a182b36bcd88f9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 12 14:20:31 2017 -0700

    AmrMesh: add some set functions

Src/AmrCore/AMReX_AmrMesh.H

commit cbe7c7950c14d75a3fab5b0b8f06d0ade06ab7cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 12 13:41:17 2017 -0700

    add assertion

Src/Base/AMReX_MFIter.cpp

commit a5af63aae16e382ba1f7210b27ec4e4926ac4695
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 12 13:12:37 2017 -0700

    minor optimization

Src/Base/AMReX_ParmParse.cpp

commit b902b1bc342b8f45b0d3fcf0cbae949b4fb4fdda
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 12 13:09:49 2017 -0700

    move BoxIterator from GeometryShop to Base

Src/Base/AMReX_BoxIterator.H
Src/Base/AMReX_BoxIterator.cpp
Src/Base/AMReX_RealVect.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/GeometryShop/Make.package

commit a3eec0f400417b3fd3a7ed188bee12037dafb164
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 12 12:58:53 2017 -0700

    move RealVect from GeometryShop to Base

Src/Base/AMReX_RealVect.H
Src/Base/AMReX_RealVect.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/GeometryShop/Make.package

commit 2aae191b1487976ca7f685f2dca30a8c0d074018
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Apr 12 11:18:06 2017 -0700

    more fixes to get all the geometryshop tests working again (now with hybrid EBCellFAB)

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseIndex.H
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp

commit 722beb41ce4eb4ecb2b7c3dbeedde9ef01c031f1
Merge: 752935ecf c72c4f118
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Apr 12 11:02:13 2017 -0700

    merging with deveopment branch because I have to add a function to BaseFab

commit 752935ecf1583e2464b3de7e5693e0d8a456d4c4
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Apr 12 11:00:35 2017 -0700

    tweaking test to fit changing API (EBCellFAB is no longer just a wrapper)

Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp

commit 2575c5a8abd5c25847f88dd498b88201f74c216b
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Apr 12 10:30:46 2017 -0700

    changed argument names to make the API less of a lie

Src/GeometryShop/AMReX_EBGraph.H

commit fe27475171a2b667d6856bf0b9ae6a726a25c355
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Apr 12 10:29:56 2017 -0700

    fixed this test to reflect API changes

Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp

commit c72c4f1183a1907284478e6d9baa97b793da36a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 11 16:55:02 2017 -0700

    add clang-analyze and clang-tidy to make

Tools/GNUMake/Make.rules

commit 665a2df80a37e334a6862e48932a75d86dec7f0b
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Apr 11 16:07:40 2017 -0700

    had to put in real EBCellFAB and associated stuff

Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H
Src/GeometryShop/AMReX_BaseEBCellFAB.H
Src/GeometryShop/AMReX_BaseEBCellFABI.H
Src/GeometryShop/AMReX_EBCellFAB.H
Src/GeometryShop/AMReX_EBCellFAB.cpp
Src/GeometryShop/AMReX_EBCellFactory.H
Src/GeometryShop/AMReX_EBCellFactory.cpp

commit d29e5ac5c9311e8fcf9581ed96f6b99a8c0f4882
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 11 13:00:38 2017 -0700

    add llvm

Tools/GNUMake/Make.defs
Tools/GNUMake/comps/llvm.mak

commit dbc1e489a8f7d8c16558077679f6e421575cb4dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 11 12:31:57 2017 -0700

    add some braces

Src/Base/AMReX_ArrayLim.H

commit cfc2de9155acc34bba642b61dc8ff1beca42168f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 11 10:04:31 2017 -0700

    add override

Tutorials/AMR_Adv_C/Source/Adv.H

commit 4e515d6df5513ea33495f12f89c41022fb9bdb0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 11 10:02:14 2017 -0700

    reimplement a few macros so that Clang 4.0.0 is happy.

Src/Base/AMReX_ArrayLim.H

commit b08c564a2fdb90536496027904f5968067a8f0f4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 7 12:59:10 2017 -0700

    add a new AmrMesh constructor

Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit 0b693bcf8be16167ec03832d702c7cf7f14ce047
Merge: 4841df8bb f676319ba
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Mon Apr 10 00:53:27 2017 -0400

    Merge branch 'development' into gpu

commit f676319bafb78a166f43442500421144e6e7111c
Merge: 029b3ec0b 594d3150c
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Fri Apr 7 21:05:48 2017 +0000

    Merged in jrood-nrel/amrex/nrel_intel_make_fix (pull request #23)
    
    Fixing GCC in the make files for NREL machines.
    
    Approved-by: Jon Rood <jon.rood@nrel.gov>

commit 029b3ec0b2452bf6687d40fccd805844c64f3661
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 7 12:53:38 2017 -0700

    need to call some initialization functions in one of the AmrMesh constructor

Src/AmrCore/AMReX_AmrMesh.cpp

commit 594d3150c1e22a9e78c92829c9483467df7b1fba
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Fri Apr 7 10:39:30 2017 -0600

    Fixing GCC in the make files for NREL machines.

Tools/GNUMake/sites/Make.nrel

commit 384b18d58234402d9a3f4e2fe455de7078c0f17d
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Fri Apr 7 10:10:57 2017 -0600

    Fixing GCC in the make files for NREL machines.

Tools/GNUMake/sites/Make.nrel

commit c52fa7fce6bfc0d7fc0962200ec4b27f0b39f6fd
Merge: 1a79b04a4 aeef35681
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 6 15:54:28 2017 -0700

    Merge branch 'development' into dtg_branch

commit 1a79b04a4d13d79d2190e9eeb3a1612c88c2eea4
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Apr 6 15:53:31 2017 -0700

    commit premerge with development branch

Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp
Src/EBAMRTools/Make.package
Src/GeometryShop/AMReX_EBLevelGrid.H
Tests/EBAMRTools/regression/GNUmakefile
Tests/EBAMRTools/regression/Make.package
Tests/EBAMRTools/regression/aggpwlfpTest.cpp
Tests/EBAMRTools/regression/sphere.inputs
Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp

commit aeef3568137d8256743679b93b37c05ea079b650
Merge: 5aaa28e34 c9064cb24
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Thu Apr 6 20:09:05 2017 +0000

    Merged in jrood-nrel/amrex/nrel_intel_make_fix (pull request #21)
    
    Adding Intel compiler compatiblity into make system for NREL machines.
    
    Approved-by: Ray Grout <ray.grout@nrel.gov>

commit c9064cb24d38e9788c7bab4534fe40d081ac1397
Author: Jon Rood <jon.rood@nrel.gov>
Date:   Thu Apr 6 13:59:38 2017 -0600

    Adding Intel compiler compatiblity into make system for NREL machines.

Tools/GNUMake/Make.machines
Tools/GNUMake/sites/Make.nrel

commit 5aaa28e344e14cacd84d9d7539b994c908eb365c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 5 17:12:15 2017 -0700

    MeshRefinement test: write a mf with value set to amr level

Tutorials/MeshRefinement/main.cpp

commit c8430fd0d0304f4083718d651be97ce10ed83004
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 5 17:02:51 2017 -0700

    Add an example showing how to generate Amr meshes for testing

Tutorials/MeshRefinement/GNUmakefile
Tutorials/MeshRefinement/Make.package
Tutorials/MeshRefinement/MyAmr.H
Tutorials/MeshRefinement/MyAmr.cpp
Tutorials/MeshRefinement/main.cpp

commit b1b2507bd2de658b82f669e92d885fd968f98f84
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 5 15:59:12 2017 -0700

    add AmrMesh::SetFinestLevel

Src/AmrCore/AMReX_AmrMesh.H

commit d3d7bc2da2f9598293a1b4b613e8eb89f97b860a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 5 15:16:03 2017 -0700

    add const

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/AmrCore/AMReX_AmrMesh.H

commit 586443e2dbd62c7d5e4e2caf3a4a505bf4724a8b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 5 13:56:36 2017 -0700

    add comments

Src/AmrCore/AMReX_AmrMesh.H

commit 971bba7ef271275f76ff6e896661fa0a706a5fd2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 5 13:42:48 2017 -0700

    make AmrMesh concrete

Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp

commit 49380d0c431c2483cb5e5e9b6cbbcc0d74768e0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 5 10:54:16 2017 -0700

    Split AmrCore into two.  The new AmrMesh class will allow for more flexible grids generation for testing.

Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_AmrMesh.H
Src/AmrCore/AMReX_AmrMesh.cpp
Src/AmrCore/CMakeLists.txt
Src/AmrCore/Make.package

commit c288ddd301e475925d094cab1cce8561479e98ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 4 12:45:21 2017 -0700

    add kiryu to CCSE_MACHINES make

Tools/GNUMake/Make.machines

commit 8d4b41b531fc4d15ad0a7a170b25d4ce6041692a
Merge: ff0b2a1d4 4ded3ea78
Author: Michele Rosso <MRosso@lbl.gov>
Date:   Tue Apr 4 03:38:29 2017 +0000

    Merged in mrosso84/amrex/cmake_build_tools (pull request #20)
    
    Cmake build tools

commit 4ded3ea788a92cc9ae975eebcb5b70ba114b5116
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 3 16:32:03 2017 -0700

    Use plt_compare_diff_grids instead of fcompare for cmake-enabled projects

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py

commit 66666277aec9826f8333a1fb2cf7872a02ba4dfb
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Mon Apr 3 16:15:38 2017 -0700

    Add plt_compare_diff_grids to cmake build

Tools/Postprocessing/F_Src/CMakeLists.txt

commit 8d374be2fba21c601cbeb019c17d76b4032c87e0
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Apr 3 15:45:57 2017 -0700

    As Zhukov said to Eisenhower, If we come to a minefield, our infantry attacks exactly as if it were not there.

Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H
Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp

commit b35d80636cf9e1794b6132e1b72b5ab0b0d3110d
Merge: 072aa45b9 ff0b2a1d4
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Mon Apr 3 17:18:51 2017 +0000

    Merged in development (pull request #19)
    
    AMReX 17.04

commit ff0b2a1d46461a8490b93822829d3463b5148a9c
Merge: 072aa45b9 06fa2462e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 3 10:12:29 2017 -0700

    Merge branch 'development'

commit 06fa2462e01ab556479803c1948c9a48f03f11a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 3 09:55:45 2017 -0700

    Reimplement BoxArray::RefID, DistributionMapping::RefID and
    FabArrayBase::BDKey using std::less for pointer comparison.  This
    fixes the undefined behavior in the old implementation.  In C++11,
    std::less is guaranteed to work for pointers (even if operator < does
    not).

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 26eb7c719ed5a00e8db495c836256e74d73eeb6e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 1 19:05:00 2017 -0700

    have to include MultiFab.H because it's used as template paramter for Array<MultiFab>

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 143a1ea2b773cb10432452ad6f13b9515c1ceb4c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Apr 1 17:13:30 2017 -0700

    Revert the latest revert.

Src/Base/AMReX_MultiFabUtil.H

commit 6e1080826712ca65b351bfa70b78d1f2f964a25f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 1 15:31:52 2017 -0700

    add include back to MulitFabUtil.H

Src/Base/AMReX_MultiFabUtil.H

commit 9ca6775d6dc020ecd9d287dd0d49694d308d9b0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 1 10:57:58 2017 -0700

    add MultiFab::OverlapMask function that counts how many duplicates are at each point; add new versions of norm1 and norm2 that do not double count for nodal data

Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp

commit 8e6e05514a7b4559b8307797b3046e078ed795ab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 1 10:34:36 2017 -0700

    add FabArrayBase::ixType() and other minor changes

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp

commit 3c89d504e1adf590ae92ff0af18cd1a30b908bf4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 16:12:22 2017 -0700

    fix a new bug in BoxArray::minimalBox

Src/Base/AMReX_BoxArray.cpp

commit f90406b9b385d6d90fcd0dcf8d5676358cf57b14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 15:54:56 2017 -0700

    use uint64_t instead of long long in initializing snan

Src/Base/AMReX_MemPool.cpp

commit a4cf7b4c269d3d660f48c6fb03fc9cd4a983a483
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 15:31:07 2017 -0700

    fix some particle initialization functions for 1d and 2d

Src/Particle/AMReX_ParticleInit.H

commit 0c495ecb81d75ef63f7fcf8ae450076980769886
Merge: 9de54a3ba 547254880
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 14:55:03 2017 -0700

    Merge branch 'development' into weiqun/cba

commit 547254880b97351df85b68b64db15de2d41f6de6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 14:53:09 2017 -0700

    add a missing header

Src/Base/AMReX_FabArrayBase.cpp

commit 9de54a3bad4782a6258ba3d8d8c57df46733d13e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 14:08:12 2017 -0700

    fix a new bug

Src/Base/AMReX_BoxArray.cpp

commit f91919a255a00ef3befcf3ee87158812aff0ef07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 13:24:29 2017 -0700

    minor

Src/Amr/AMReX_Amr.cpp

commit 7ad20e59a120fa5cafe4edac1d94c737898e056a
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Mar 31 13:17:56 2017 -0700

    EBLevelGrid and LayoutData now compile.   On to porting the tools that use them

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArrayBase.H
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Src/GeometryShop/AMReX_EBLevelGrid.H
Src/GeometryShop/AMReX_EBLevelGrid.cpp
Src/GeometryShop/AMReX_LayoutData.H
Src/GeometryShop/Make.package

commit dddc3c16cc0a3fab0fed85f38248ca0294dd95e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 13:09:53 2017 -0700

    update FluxRegister for crse_ratio

Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Boundary/AMReX_BndryRegister.cpp
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX1_C/writePlotFile.H
Tutorials/HeatEquation_EX2_C/main.cpp
Tutorials/HeatEquation_EX2_C/writePlotFile.H
Tutorials/PGAS_HEAT/main.cpp
Tutorials/PGAS_HEAT/writePlotFile.H
Tutorials/Tiling_Heat_C/main.cpp
Tutorials/Tiling_Heat_C/writePlotFile.H
Tutorials/WaveEquation_C/main.cpp
Tutorials/WaveEquation_C/writePlotFile.H

commit 8f4238a6ef07850f808b4670bf043a2641c04b1b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 31 11:49:33 2017 -0700

    Oops -- that was the wrong file for plt_compare_diff_grids.f90 -- this one should work.

Tools/Postprocessing/F_Src/GNUmakefile
Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90

commit ebae6e5f6d768297c3745c32eb08c62992099d7d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 31 11:41:59 2017 -0700

    Build plt_compare_diff_grids.f90 instead of fcompare.f90

Tools/Postprocessing/F_Src/CMakeLists.txt

commit 085dbfdc2fe35da7dadafc11a9844ac0683ac082
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 31 11:31:33 2017 -0700

    Add a new file that can be used to compare plotfiles that have the same problem
    domain at each level but that have different grids covering that domain.  This
    is particularly useful for comparing different domain decompositions of the same
    problem

Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90

commit 5696e024b1a9c11b4b736438bb80adb313a5ba01
Merge: dccf46b08 97a1e8c42
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 11:26:46 2017 -0700

    Merge branch 'development' into weiqun/cba

commit dccf46b0819920f91e62fa00a50a362f3d74c2fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 11:25:49 2017 -0700

    update tiling for crse_ratio

Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 3157d643ce085e8dd754e604430490e1d498d35b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 10:29:09 2017 -0700

    update FillBoundary for crse_ratio

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp

commit 0439c72ca2d2dfe18ad7f461be6cb212922a8cc4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 09:58:42 2017 -0700

    more changes due to the addition of crse ratio to BoxArray

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit 97a1e8c420becbbce0dea7e3db93696c25ead689
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 08:35:03 2017 -0700

    add a missing header

Tutorials/MultiGrid_C/writePlotFile.cpp

commit 5996b8338b7cd8f888547f3485da8ce883268632
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 08:31:09 2017 -0700

    fix a typo

Src/F_Interfaces/Base/AMReX_multifab_fi.cpp

commit 405181421ce594ad631adbbf755afc6ff5dbf63d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 31 08:29:26 2017 -0700

    remove a print

Src/Base/AMReX_DistributionMapping.cpp

commit 1d17982f6e64c513e866938caede70e6836dbefc
Merge: a9695369f de7b6d105
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Mar 31 15:25:46 2017 +0000

    Merged in dtg_branch (pull request #16)
    
    eb sort of works so it should be merged

commit a9695369f482d1a5f58707e1caa652b73860b6ad
Merge: 147c45d32 c755cebc6
Author: Michele Rosso <MRosso@lbl.gov>
Date:   Thu Mar 30 23:49:44 2017 +0000

    Merged in mrosso84/amrex/cmake-mpi-build (pull request #18)
    
    Add fextract and fcompare as part of the install

commit 5357ad27176130e0c051785a4183110df0b66766
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 30 16:47:30 2017 -0700

    changes due the addition of crse ratio to BoxArray

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit c755cebc62a5a2b00d8c4388481aabd955a8bd16
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Thu Mar 30 16:04:29 2017 -0700

    Add fextract and fcompare as part of the install

CMakeLists.txt
Tools/Postprocessing/F_Src/CMakeLists.txt

commit d12033413ea953355e53d48df7d7d923d780d2fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 30 14:12:08 2017 -0700

    BoxArray: moved some functions from .H to .cpp

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit a47160506a6b45f843ae213ee618e9740d5de2b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 30 13:48:32 2017 -0700

    Coarsen the boxes in BoxArray::uniqify

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit f527c4d0952b469a1151103b8cbdf3c0dc8fda68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 30 13:00:47 2017 -0700

    rm BoxArray::shiftHalf

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit 2d106b4a8282ab55a2d101f5c9c6f71f7fb5c058
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 30 11:27:18 2017 -0700

    add a special case to IntVect::coarsen

Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp

commit fb5494cdc5bf89a5342014c207fd07f0833545f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 30 10:55:22 2017 -0700

    add crse ratio to BoxArray class

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit de7b6d105c433eefa44743c313fd5a0f8bfe5133
Merge: b6356f234 147c45d32
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Mar 30 10:53:59 2017 -0700

    Merge branch 'development' into dtg_branch

commit b6356f234f829fa1355fcccaed183191d4262e64
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Mar 30 10:53:48 2017 -0700

    committing some temporary stuff so I can merge with development branch

Src/GeometryShop/AMReX_EBLevelGrid.H
Src/GeometryShop/AMReX_EBLevelGrid.cpp

commit b67c5654078c5d690193f0ab7fede006d6f68353
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Mar 30 10:52:30 2017 -0700

    committing some temporary stuff so I can merge with development branch

Tests/GeometryShop/sphereEBISBox/sphere.inputs

commit 77607a636f7dd139ab785fb2e98c681c645b463e
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Mar 30 10:51:52 2017 -0700

    committing some temporary stuff so I can merge with development branch

Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H

commit 8ebc00999c1832d8a74d5747fc220859a8387724
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Mar 30 10:49:23 2017 -0700

    starting adding multi-level EB objects into EBAMRTools layer

Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H
Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp
Src/EBAMRTools/AMReX_EBCoarseAverage.H
Src/EBAMRTools/AMReX_EBCoarseAverage.cpp
Src/EBAMRTools/AMReX_EBPWLFineInterp.H
Src/EBAMRTools/AMReX_EBPWLFineInterp.cpp
Src/EBAMRTools/Make.package

commit 147c45d32513989dd892eef21b4236ee17db2d6c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 29 13:12:05 2017 -0700

    add FabArray::setDomainBndry

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_Geometry.H

commit 3d46ebe92e3595813bcabb429b6c58bb8d1ee1af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 29 12:24:19 2017 -0700

    To avoid confusion, remove nodal flag from FabArray constructor.

Src/AmrCore/AMReX_FluxRegister.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_FabArray.H
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/Particle/AMReX_TracerParticles.cpp
Tutorials/MultiColor_C/main.cpp

commit ae888a2cd71c667c678f8c1bbe8efd17210a1048
Merge: fb86f9728 680a53c4f
Author: Michele Rosso <MRosso@lbl.gov>
Date:   Thu Mar 30 13:27:31 2017 +0000

    Merged in mrosso84/amrex/regtest_fix (pull request #17)
    
    Fix regtest bug for builds using cmake
    
    Approved-by: Michael  Zingale <michael.zingale@stonybrook.edu>

commit fb86f9728bb61668f69350d89df1f54079fb596e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 29 21:05:12 2017 -0700

    make clean: rm dSYM directory

Tools/GNUMake/Make.rules

commit 680a53c4fc35c3545a36fc03cf176124624d5d82
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Mar 29 17:37:25 2017 -0700

    Fix regtest bug for builds using cmake

Tools/RegressionTesting/suite.py

commit c9cad1e7f11e917abc3ddfb92ea8e36c7d430630
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Mar 29 14:27:28 2017 -0700

    one more bug fix

Src/GeometryShop/AMReX_EBISLevel.cpp

commit 09fae1d08e259be05dc8238a43c1aa2ead3d7300
Merge: 7d33c4aef 943815a99
Author: Michele Rosso <MRosso@lbl.gov>
Date:   Wed Mar 29 18:22:36 2017 +0000

    Merged in mrosso84/amrex/cmake-mpi-build (pull request #15)
    
    Cmake mpi build

commit e012bede7b6077a2a72a3f67115520688a082aeb
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Mar 29 10:09:59 2017 -0700

    needed to recompute normals and boundary areas after copies (otherwise they can be wrong at box boundaries)

Src/GeometryShop/AMReX_EBData.cpp

commit aa8b40bf0307c509e92c679410ea4d1b415d7761
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Mar 28 15:46:30 2017 -0700

    after many bug fixes, I got an actual test that uses EBISLayout and EBIndexSpace and everythign to run correctly.

Src/Base/AMReX_Box.H
Src/Base/AMReX_DistributionMapping.cpp
Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp
Tests/GeometryShop/sphereEBISBox/sphere.inputs

commit 1e50e1acd9c6413d0289e600a4c46fdbe884f2f4
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Mar 28 11:41:12 2017 -0700

    this unholy union is proceeding according to our fiendish plan

Src/GeometryShop/AMReX_BaseIVFactory.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_FlatPlateGeom.H
Src/GeometryShop/AMReX_FlatPlateGeom.cpp
Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Tests/GeometryShop/sphereEBISBox/Make.package
Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp

commit e9696c092363bf393eff03fc5cc8c477a4888237
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Mar 27 15:56:08 2017 -0700

    I added a first test for the new classes

Tests/GeometryShop/sphereEBISBox/GNUmakefile
Tests/GeometryShop/sphereEBISBox/Make.package
Tests/GeometryShop/sphereEBISBox/sphere.inputs
Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp

commit d2df4f995b817656843b5377b47f815d570f15e9
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Mar 27 13:04:47 2017 -0700

    everything compiles, off to testing the core stuff

Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.cpp

commit 7d33c4aefdeea6621400b8e9944b772a68c21bcf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 25 11:06:58 2017 -0700

    put temp build directory d/ o/ f/ into tmp_build_dir/

.gitignore
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 54fcf02225f6e8b863d64de616701ebfc262377c
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Mar 24 15:56:48 2017 -0700

    lots of progress but still many compilation errors.

Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBDataFactory.H
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Src/GeometryShop/AMReX_FlatPlateGeom.cpp
Src/GeometryShop/AMReX_GeometryService.H
Src/GeometryShop/AMReX_GeometryService.cpp
Src/GeometryShop/AMReX_SPMD.cpp
Src/GeometryShop/AMReX_VoFIterator.H
Src/GeometryShop/AMReX_VoFIterator.cpp
Src/GeometryShop/Make.package

commit 5456060baaffceb240f5f9f8c654a52bb728225a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 24 13:06:45 2017 -0700

    add num_multifabs back, but wrap them inside BL_MEM_PROFILING

Src/Base/AMReX_MultiFab.cpp

commit 4d28672aa1e94ead342966ad8db9a383681ba812
Merge: bea2d9158 108750a3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 24 13:00:47 2017 -0700

    Merge branch 'dtg_branch' into development

commit 108750a3b537b58d4555ab74dc3eefd17a09eb20
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Mar 24 11:43:02 2017 -0700

    But wait, there's more!  Now EBISLevel has many fewer communication stages in coarsening!  Now how much would you pay?

Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp

commit bea2d915809c28ed6c467b21891a426d2d54424b
Merge: 7dea03d8d a7fb2815a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 24 11:00:07 2017 -0700

    Merge branch 'development' into weiqun/split_fabarray

commit 7dea03d8db7b0d31d773493b9dead96fe8d923cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 24 10:58:12 2017 -0700

    update AmrData

Src/Extern/amrdata/AMReX_AmrData.cpp

commit ce5905ee0110e1d566bbc1bb491962348d227a50
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 24 10:01:09 2017 -0700

    update cmake

Src/Base/CMakeLists.txt

commit a1cd520f7836a264972d744e5e192fc9d1be7d93
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Mar 23 18:51:15 2017 -0700

    redesign of EBISLevel::coarsenVoFs.  Now with fewer temporaries and communications.   Not available in stores.

Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.cpp

commit a7fb2815a4c15addfa143287a33e4803cd7c7164
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 23 17:12:36 2017 -0700

    make mpi-2 happy by const_cast

Src/Base/AMReX_ParallelDescriptor.H

commit b4a390e44763778197a9db4e5439163aee2b490b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 23 16:29:34 2017 -0700

    more on splitting FabArray

Src/Amr/AMReX_StateData.H
Src/Base/AMReX_FACopyDescriptor.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MFCopyDescriptor.H
Src/Base/AMReX_MFCopyDescriptor.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/Make.package

commit 8191d1a4ecda06808c8749ae1b3594170705e4f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 23 13:05:19 2017 -0700

    change how gfortran library is linked

Tools/GNUMake/comps/gnu.mak

commit 0bf2623b554b7f241841aed0f80cdb91fd1fb522
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 23 11:05:30 2017 -0700

    split off MFIter

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MFIter.H
Src/Base/AMReX_MFIter.cpp
Src/Base/Make.package

commit 05302eec84131d986eb6b30939173c8a7406eba1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 23 10:55:42 2017 -0700

    split off FabArrayBase

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArray.cpp
Src/Base/AMReX_FabArrayBase.H
Src/Base/AMReX_FabArrayBase.cpp
Src/Base/Make.package

commit af2844275dc6495906f72a694f7fb94dbfbb329f
Merge: b327acfe1 ab1eb9f66
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Mar 23 10:53:01 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit b327acfe1a8fe7ca174cb9e719e32a08f8278fcb
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Mar 23 10:52:44 2017 -0700

    move the num local tiles function to ParticleContainer.

Src/Particle/AMReX_Particles.H

commit ab1eb9f66d0f7a3f57a0cafefd7222f438c4f3cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 23 09:08:16 2017 -0700

    make: strip the whitespace around DIM to make the make system more robust

Tools/GNUMake/Make.defs

commit e7e59a718f894f0f8b495f65bba4c0464ac65d65
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Mar 22 16:55:43 2017 -0700

    Add a function ParIter to return the total number of tiles.

Src/Particle/AMReX_Particles.H

commit a849417c2ac92c785063bf3ff6b3c09e03bae2fe
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Mar 22 15:03:57 2017 -0700

    still pretty deep in the weeds over here

Src/Base/AMReX_Box.H
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Src/GeometryShop/AMReX_FlatPlateGeom.cpp
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_SPMD.cpp

commit 943815a9944cdd1a172e5a13f098929eb6116ccc
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Mar 22 13:50:55 2017 -0700

    Fix cmake mpi-enabled build.

Tools/CMake/FindCCSE.cmake

commit 82ea10329c5c0b76ea9fdc3fd75c631334f6ed60
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Mar 21 16:16:11 2017 -0700

    slogged my way through EBIndexSpace and EBISLayout--some minor redesign (and some major cleanup) from the Chombo versions

Src/GeometryShop/AMReX_EBDataFactory.H
Src/GeometryShop/AMReX_EBISBox.H
Src/GeometryShop/AMReX_EBISLayout.H
Src/GeometryShop/AMReX_EBISLayout.cpp
Src/GeometryShop/AMReX_EBISLevel.H
Src/GeometryShop/AMReX_EBISLevel.cpp
Src/GeometryShop/AMReX_EBIndexSpace.H
Src/GeometryShop/AMReX_EBIndexSpace.cpp
Src/GeometryShop/AMReX_GeometryService.H
Src/GeometryShop/AMReX_GeometryService.cpp
Src/GeometryShop/AMReX_SlabService.H
Src/GeometryShop/AMReX_SlabService.cpp

commit 77e414d7c946619afd62a7a404285f9eb0bac150
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Mar 21 14:44:34 2017 -0700

    Remove all references to PETSc and X11.

Tools/CMake/FindCCSE.cmake

commit 6f026b24ed9b2e404c66ffaef95cc4ba13a3a7a2
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Mar 21 13:31:51 2017 -0700

    Replace "BOXLIB" with "AMREX" in CMake variables name.

Src/Base/CMakeLists.txt
Src/CMakeLists.txt
Tools/CMake/CCSEOptions.cmake

commit 35561e1f01302d0c7f6daeb377d23bdd49127d8e
Merge: 5aafb61b3 0d4cb177c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 21 13:16:08 2017 -0700

    Merge branch 'fortran_interface' into development

commit 0d4cb177c7bcbc4b00f2093cc642fa91bb39c2e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 21 13:15:30 2017 -0700

    fixe memory leaks

Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/my_amr_mod.F90

commit 7d6cea2729397a2a0212a4252ea2979ee8ff99af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 21 12:47:45 2017 -0700

    fix reflux due grids coveed by fine do not have fluxes computed

Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90

commit 5674cdf80104470a2178a2bc1cbc120492a6c7a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 21 11:17:35 2017 -0700

    tidy

Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90

commit 7cd3779ccfbb396182f4330fb513cad0f5ffea0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 21 11:03:55 2017 -0700

    add octree iterator

Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Src/F_Interfaces/Octree/AMReX_octree_fi.cpp
Src/F_Interfaces/Octree/AMReX_octree_mod.F90
Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs.rt
Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/my_amr_mod.F90

commit 4feee626cd17ea6116eee4a411aec11d063ab4b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 21 08:35:43 2017 -0700

    build octree leaf nodes

Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90
Src/F_Interfaces/Octree/AMReX_octree_fi.cpp
Src/F_Interfaces/Octree/AMReX_octree_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90

commit 5aafb61b3e042a8072898b0095c2e470b5faf61a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 21 08:28:52 2017 -0700

    add a new MFIter::tilebox takes nodal IntVect flag

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArray.cpp

commit d441bd0f3e94755b1ee2a400e55a64d4b7d3c9e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 20 12:48:12 2017 -0700

    add F_Interfaces/Octree

Src/AmrCore/AMReX_AmrCore.cpp
Src/F_Interfaces/Octree/AMReX_octree_fi.cpp
Src/F_Interfaces/Octree/AMReX_octree_mod.F90
Src/F_Interfaces/Octree/Make.package
Tutorials/AMR_Adv_CF_octree/Exec/Make.Adv
Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs.rt
Tutorials/AMR_Adv_CF_octree/Source/fmain.F90

commit 17e7cb92c3a54f362a2b1bba00b587c73ed336cb
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Mar 20 11:00:07 2017 -0700

    EBData, EBISBox, and PolyGeom all compile now.   On to writing more tests.

Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBISBox.cpp
Src/GeometryShop/AMReX_PolyGeom.cpp

commit 02f16e6995a845ee2ab31473fbbb92032cb254c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 20 08:46:43 2017 -0700

    AMR_Adv_CF_octree: no subcycling

Tutorials/AMR_Adv_CF/Source/averagedown_mod.F90
Tutorials/AMR_Adv_CF_octree/Exec/Make.Adv
Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_CF_octree/Source/averagedown_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/compute_dt_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/my_amr_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/plotfile_mod.F90

commit e2199418d91142d5db5a85bc9abaf9ff54c9f84e
Merge: b58e95927 d15eac8e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Mar 17 20:34:23 2017 -0400

    Merge branch 'development' of ssh://bitbucket.org/berkeleylab/AMReX into development

commit b58e95927fcbf68fd4e7bfc8f0f45f9b454adfa7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Mar 17 20:34:14 2017 -0400

    don't need FCOMP for C++ codes

Tools/RegressionTesting/suite.py

commit d15eac8e930b75162ce020556a077c8561a9fe2b
Merge: d59d6343a 7daaee09e
Author: Michele Rosso <MRosso@lbl.gov>
Date:   Fri Mar 17 23:59:58 2017 +0000

    Merged in mrosso84/amrex/cmake-regtest (pull request #14)
    
    Enable AMReX regression testing tools to build using CMake.

commit 40a6543b734f08b5b2c2eee8f45ee0c893139cb6
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Mar 17 16:02:49 2017 -0700

    finished EBData/EBISBox/PolyGeom transition --- still working on getting it all to compile

Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBISBox.H
Src/GeometryShop/AMReX_EBISBox.cpp
Src/GeometryShop/AMReX_PolyGeom.H
Src/GeometryShop/AMReX_PolyGeom.cpp
Src/GeometryShop/Make.package

commit 7daaee09e606e6eb602b21a3ae0e3f56c90f6678
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Wed Mar 15 13:52:59 2017 -0700

    Enable AMReX regression testing tools to build using CMake.

Tools/RegressionTesting/params.py
Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_util.py

commit d3357a446e6750a31ad77c439d89d54306f3fa2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 17 12:35:40 2017 -0700

    start Tutorials/AMR_Adv_CF_octree

Tutorials/AMR_Adv_CF_octree/Exec/Make.Adv
Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/Make.package
Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/Prob.f90
Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/face_velocity_2d.F90
Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs.rt
Tutorials/AMR_Adv_CF_octree/README
Tutorials/AMR_Adv_CF_octree/Source/Make.package
Tutorials/AMR_Adv_CF_octree/Source/Src_2d/Make.package
Tutorials/AMR_Adv_CF_octree/Source/Src_2d/advect_2d_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/Src_2d/compute_flux_2d.f90
Tutorials/AMR_Adv_CF_octree/Source/Src_2d/slope_2d.f90
Tutorials/AMR_Adv_CF_octree/Source/amr_data_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/averagedown_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/bc_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/compute_dt_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/fillpatch_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/fmain.F90
Tutorials/AMR_Adv_CF_octree/Source/initdata.F90
Tutorials/AMR_Adv_CF_octree/Source/my_amr_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/plotfile_mod.F90
Tutorials/AMR_Adv_CF_octree/Source/tagging_mod.F90

commit 3b3d4f198aea3c520cf21aa221f90e09bd871562
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 17 12:12:59 2017 -0700

    allow blocking factor greater than max_grid_size

Src/AmrCore/AMReX_AmrCore.cpp
Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp

commit d59d6343ab570b41793b04964ace57e8584cff80
Merge: 4b66112b5 a6c7e4fa3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 16 14:56:48 2017 -0700

    Merge branch 'fortran_interface' into development

commit a6c7e4fa3bd8e088c638b973742bac4ae7700261
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 16 14:55:57 2017 -0700

    add some assertions to fortran amrcore

Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp

commit f18af0a1d010e8a280463cf14353ce56be89da6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 16 14:55:31 2017 -0700

    assert blocking factor is not too small relative to ref_ratio

Src/AmrCore/AMReX_AmrCore.cpp

commit d02032d38043fe41b2888eafcaa60c470be03c94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 16 13:59:14 2017 -0700

    add string version of amrex::Abort, Warning and Error

Src/Base/AMReX.H
Src/Base/AMReX.cpp

commit 4b66112b5319f8883fc3cdcab965fd2e40bc28d2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Mar 16 09:45:06 2017 -0700

    fixing the Nyx restart test.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleI.H

commit fea84d328e8a0c5a7aab10d7439f6540b36b6f16
Merge: 05f820e07 ff24069df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 16 08:27:34 2017 -0700

    Merge branch 'fortran_interface' into development

commit a2cb8a1c842c3b304561255c2c1ae3d9a383c5ad
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Mar 15 16:06:25 2017 -0700

    progress made on EBData (and I took it out of the make.package in case people want to compile this branch)

Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/Make.package

commit ff24069df64855d28b8198244c23b83abecdc909
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 15 15:03:45 2017 -0700

    cleanup

Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90

commit 13a2a0ee37bc49b9fbecd7d5be5121e01ecbd928
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 15 14:52:43 2017 -0700

    make some variables in fortran geometry static

Src/F_Interfaces/Base/AMReX_geometry_fi.cpp
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90
Tutorials/AMR_Adv_CF/Source/evolve_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 8a60b84b823f1cd9a4a28a3cf88608138496d92c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 15 13:59:20 2017 -0700

    simplify the regrid logic

Tutorials/AMR_Adv_CF/Source/evolve_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp

commit fe43208d22ce1e6884793340649d955a8658c888
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 15 12:22:26 2017 -0700

    comments

Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 05f820e07016ba944d62e703053fa9799ec9d6a4
Author: atmyers <atmyers2@gmail.com>
Date:   Wed Mar 15 12:15:08 2017 -0700

    increment particle version string.

Src/Particle/AMReX_ParticleI.H

commit 8243f3d5f167092f52eda88deb2ae34fd6567d36
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Mar 14 16:13:41 2017 -0700

    starting the long slog of redesigning ebdata

Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/AMReX_EBData.H
Src/GeometryShop/AMReX_EBData.cpp
Src/GeometryShop/AMReX_EBDataVarMacros.H
Src/GeometryShop/Make.package

commit 52e9f2f833fdded272445c205a25fc8f50630732
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 14 16:02:27 2017 -0700

    add Fortran fillcoarsepatch and tweak the test problem to test teh new functionality

Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90
Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90
Tutorials/AMR_Adv_CF/Source/tagging_mod.F90
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp

commit 2ee27b21bf9ca39682fe741e435db63057a8cee2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 14 14:14:06 2017 -0700

    add a new regression test inputs

Tutorials/AMR_Adv_CF/Exec/SingleVortex/inputs.rt

commit afca0741e5248b6a085d18df75cec0131f326769
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 14 14:12:32 2017 -0700

    fix a bug in fortran fillpatch

Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90

commit 6356ffa50e8a0c8a0dedb7b998567891cf7bbbe4
Merge: 608e11bbd 1e22bdbef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 14 13:23:46 2017 -0700

    Merge branch 'fortran_interface' into development

commit 1e22bdbef58fa51a80e1acdfe29b3e647fea8628
Merge: c3e72f638 232da81b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 14 13:23:08 2017 -0700

    Merge branch 'development' into fortran_interface

commit 608e11bbdc713d3098c37caaab44f0b877f06b1d
Merge: 4eff9e1c3 864458fd5
Author: Michele Rosso <MRosso@lbl.gov>
Date:   Tue Mar 14 20:16:28 2017 +0000

    Merged in mrosso84/amrex/cmake-installation-fix (pull request #13)
    
    Fix issue with Tools not being copied to installation dir.

commit 864458fd58b5925af99baabe248e4afa1425c475
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Tue Mar 14 13:09:20 2017 -0700

    Fix issue with Tools not being copied to installation dir.

Src/CMakeLists.txt

commit f0439c248c9b693d9eceba49fe58753cf8982374
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Mar 14 13:08:10 2017 -0700

    sparse data tests pass now

Src/GeometryShop/AMReX_BaseIVFABI.H

commit 4eff9e1c3801598070cd7920005a262399ccd93a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Mar 14 15:27:42 2017 -0400

    PGI explicitly needs libatomic to link

Tools/GNUMake/comps/pgi.mak

commit 1da21811a0b62e6ab20163552c68dbaf45d5ee88
Merge: 232da81b6 48b076b36
Author: Michael  Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Mar 14 16:04:28 2017 +0000

    Merged in mzingale/amrex/development (pull request #8)
    
    some reporting fixes

commit 7b814fa67a4c2d786247a8e9555996df455a007d
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Mar 13 14:29:13 2017 -0700

    got sparse, distributed data test to run to complettion but still failing one of the tests

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_MultiFab.cpp
Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFactory.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_BaseIVFactory.H
Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp

commit 232da81b625c4f33c2aa5178b4ca5304787f8595
Merge: 1c307e220 5bff9218a
Author: Michele Rosso <MRosso@lbl.gov>
Date:   Mon Mar 13 16:44:58 2017 +0000

    Merged in mrosso84/amrex/cmake-regtest (pull request #12)
    
    Fix CMake dependencies issue.

commit 5bff9218aea70da20f8a92b93fcd4a82140dda59
Author: Michele Rosso <mrosso@lbl.gov>
Date:   Fri Mar 10 16:44:35 2017 -0800

    Fix CMake dependencies issue.

Src/Amr/CMakeLists.txt
Src/Boundary/CMakeLists.txt
Src/Extern/amrdata/CMakeLists.txt
Src/F_BaseLib/CMakeLists.txt
Src/Particle/CMakeLists.txt

commit 1c307e220e2601c12000003ba50660b565484eb1
Merge: c7f847d2c e8631de77
Author: Ray Grout <ray.grout@nrel.gov>
Date:   Sat Mar 11 21:40:35 2017 +0000

    Merged in regtest_for_gitlabci (pull request #11)
    
    Adjust regtest script to allow empty branch and return number of failures as exit code

commit e8631de77cb50abab7c059b8edf69ed8e78cef20
Merge: ea53e9028 c7f847d2c
Author: Ray Grout <ray.grout@nrel.gov>
Date:   Sat Mar 11 12:01:30 2017 -0700

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into regtest_for_gitlabci

commit ea53e90283c5ebee1f59af1ed232681c5852bf36
Author: Ray Grout <ray.grout@nrel.gov>
Date:   Sat Mar 11 12:01:07 2017 -0700

    Adjust regtest script to allow empty branch and return number of failures as exit code

Tools/RegressionTesting/regtest.py

commit c7f847d2ce7caff1039da009dbd395af6196fc07
Author: atmyers <atmyers2@gmail.com>
Date:   Sat Mar 11 09:33:24 2017 -0800

    explicitly mark these methods as override.

Src/AmrCore/AMReX_TagBox.H
Src/Base/AMReX_MultiFab.H

commit a1829c85603f81781cef3f384717a40ac6c706c4
Author: atmyers <atmyers2@gmail.com>
Date:   Sat Mar 11 08:20:27 2017 -0800

    fix GetArrayData function.

Src/Particle/AMReX_ParticleContainerI.H

commit 4841df8bbbe92b1c79b91082213d459e17fb7f08
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Mar 11 01:19:57 2017 -0500

    Add a CUDArena memory management system using CUDA UM
    
    CUDA Unified Memory (available for NVIDIA GPUs of the Kepler generation
    or newer) allows a single pointer to point to a region of memory that can
    live either on the CPU or the GPU, and switches back and forth on demand.
    This is done by declaring a managed memory allocation using cudaMallocManaged,
    a drop-in replacement for malloc.
    
    The CUDArena as currently written is a drop-in replacement for BArena.
    
    Credit for the name and original idea belong to Brian Friesen.

Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_CUDArena.H
Src/Base/AMReX_CUDArena.cpp
Src/Base/Make.package

commit 3919163643b2ffad987f368667dc09618cccf0bb
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Mar 11 01:12:37 2017 -0500

    Allow C/C++ builds with nvcc using USE_CUDA
    
    This replaces the CC/CXX executable with nvcc, and sets the nvcc
    host compiler to what was previously set there (based on COMP).

Tools/GNUMake/Make.defs

commit 3c8e997c2e281d85d511552a1b2a92434f6ff003
Merge: 48329b0a4 ba8669a64
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Mar 10 21:43:48 2017 -0800

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit 48329b0a41b880c119589def505112378a90f024
Author: atmyers <atmyers2@gmail.com>
Date:   Fri Mar 10 21:43:37 2017 -0800

    Adding methods for getting the SoA data

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit ba8669a648fcccb440dde7f4238db061a4bbc034
Merge: b57d05636 a3df796ec
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 10 15:43:24 2017 -0800

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit b57d05636864994dfb31fc4e384fd5fc3f6987a5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 10 15:43:09 2017 -0800

    Adding fortran CIC interpolation function.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particle_mod_3d.F90
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_Particles_F.H
Tests/Particles/AssignDensity/main.cpp
Tests/Particles/AssignMultiLevelDensity/inputs
Tests/Particles/AssignMultiLevelDensity/main.cpp

commit a3df796ec9a60f95683884c58cf3d19c555f75a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 10 15:08:59 2017 -0800

    have to initialize the data otherwise it may crash due to fpe

Src/Boundary/AMReX_FabSet.cpp

commit c3e72f6382e029145eadbcff366532542043abb9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 9 16:20:12 2017 -0800

    AMR_Adv_v2: finished reflux

Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Tutorials/AMR_Adv_CF/Source/evolve_mod.F90

commit f2aec04eac26df872c2e9f17c182fe3f6dda55a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 9 14:17:48 2017 -0800

    fix a bug I introduced when FillBoundary was modified a few days ago

Src/Base/AMReX_FabArray.cpp

commit 46b83dbbb5476e649d298793d82f152b8a3c0bc3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 9 14:00:20 2017 -0800

    AMR_Adv_CF: start to add flux register

Tutorials/AMR_Adv_CF/Source/amr_data_mod.F90
Tutorials/AMR_Adv_CF/Source/evolve_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 1e0dd1a5167a6ce1e1a261a4f8a78cfb7947af77
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 9 11:10:38 2017 -0800

    add fluxregister module

Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90
Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90
Src/F_Interfaces/AmrCore/Make.package

commit 36e8da52db69b15cbac8d44c98a40a959f03c979
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 9 10:25:17 2017 -0800

    AMR_Adv_CF runs

Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 4087e3a4347f714a7817f6e471fcb25a178f7788
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 9 10:20:33 2017 -0800

    fix fortran index

Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90

commit 7f09a48e862bbc92145beffa33838684bd6116f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 9 10:11:43 2017 -0800

    refactor fillpatch module

Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90
Tutorials/AMR_Adv_CF/Source/Make.package
Tutorials/AMR_Adv_CF/Source/amr_data_mod.F90
Tutorials/AMR_Adv_CF/Source/bc_mod.F90
Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 362204271ac20a1c1ffd9c88be5914ecf3581360
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 8 18:10:45 2017 -0800

    wip: need to fix circular dependency of fortran modules

Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90
Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90

commit 545425f68c48ffed52780e32c502d2a9c3951bba
Merge: 781c66099 4815f4f02
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Mar 8 15:33:31 2017 -0800

    Merge branch 'development' into dtg_branch

commit 4526bf0663e7b0835aa7e51ceaedb1ec1785517b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 8 14:44:39 2017 -0800

    wip

Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 781c66099728f9aa78c96b7c5c9e8656a8cbbacc
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Mar 8 14:39:13 2017 -0800

    sparse data holders pass single grid test

Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_BaseIVFABI.H
Src/GeometryShop/Make.package
Tests/GeometryShop/sparseDataSingleGrid/GNUmakefile
Tests/GeometryShop/sparseDataSingleGrid/Make.package
Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp
Tests/GeometryShop/sparseDataSingleGrid/sphere.inputs

commit fd52f4cc6885923557e2ac44ec141f084d57fe0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 8 11:53:32 2017 -0800

    add more virtual functions

Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 4815f4f0276590035cfc0dd9c8991b91b63b4db9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 8 10:38:21 2017 -0800

    do a const_cast in make_aliase

Src/Base/AMReX_BaseFab.H

commit 692b8e6ab3ff29d7e82d1d6add587eee58e17dbc
Merge: 5592fb7b5 12f6c1c94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 8 09:59:49 2017 -0800

    Merge branch 'development' into fortran_interface

commit 12f6c1c9405352efb6581695a967a4f3baed57d7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Mar 7 16:39:50 2017 -0800

    More fixes to the build system from Michele Rosso.

Tools/CMake/FindCCSE.cmake

commit 984e95ebbab2f14583eee1ce22a4cd9254686de2
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Mar 7 16:21:23 2017 -0800

    added (as yet still untested) sparse data holders

Src/GeometryShop/AMReX_BaseIFFAB.H
Src/GeometryShop/AMReX_BaseIFFABI.H
Src/GeometryShop/AMReX_BaseIVFAB.H
Src/GeometryShop/AMReX_BaseIVFABI.H

commit 5349fe31bbe23df53931fc66647efcf166d1d6c0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Mar 7 14:41:50 2017 -0800

    Fix CMake build stuff for AMReX.

CMakeLists.txt
Src/Amr/CMakeLists.txt
Src/Base/CMakeLists.txt
Src/CMakeLists.txt

commit 8b3816ac97ce25e17cf875a191906bcbc036db1a
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Mar 7 11:18:52 2017 -0800

    after figuring out that FabArray and LevelData have somewhat different copy semantics, I was able to get FabArray<EBGraph> to behave as advertised

Src/GeometryShop/AMReX_EBGraph.cpp
Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp

commit 0aa8c2a687bb9430c1cdace845da00738dd0a657
Merge: aa20228c6 3a7758da2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Mar 7 11:07:45 2017 -0800

    Merge branch 'development' of https://bitbucket.org/berkeleylab/amrex into development

commit aa20228c6eb35d698218a8ff0827a5191c488ec8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Mar 7 11:07:17 2017 -0800

    Change instances of BoxLib/boxlib/BOXLIB to AMReX/amrex/AMREX.  This occurs only in cmake stuff
    and README*

CMakeLists.txt
Src/CMakeLists.txt
Tools/CMake/AMReX_Version.cmake
Tools/CMake/PreprocessAMReXFortran.cmake
Tools/CMake/PreprocessAMReXFortran90.cmake
Tutorials/README_C
Tutorials/README_F

commit 3a7758da2bd287c4960910b7755fad402c31c501
Merge: 0e3403ff2 5931b3c74
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Mar 6 17:17:18 2017 -0800

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit 0e3403ff229ff60e55b09413953aa5745c6f7e5d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Mar 6 17:15:34 2017 -0800

    Avoid redefined macro warning in AMReX_INTERP_1D.F

Src/AmrCore/AMReX_INTERP_1D.F

commit e23aa58aab899a5c4247de589de5bf1540a91a45
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Mar 6 16:16:25 2017 -0800

    working on distributed graph

Src/Base/AMReX_BaseFab.H
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_SPMD.cpp
Src/GeometryShop/AMReX_SPMDI.H
Tests/GeometryShop/ebgraphDistributed/GNUmakefile
Tests/GeometryShop/ebgraphDistributed/Make.package
Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp
Tests/GeometryShop/ebgraphDistributed/sphere.inputs

commit 5931b3c74b4db252076b8eb6604b6e15c6b0bc47
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 3 21:47:07 2017 -0800

    Capture the return code of the analysis scripts in the test suite.

Tools/RegressionTesting/regtest.py

commit 8a2aa1edae821a9fbc85c682fca148d6d21f5861
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Mar 6 13:54:22 2017 -0800

    porting some changes to the CMake stuff from BoxLib to AMReX.

CMakeLists.txt
Tools/CMake/CCSEOptions.cmake

commit 072aa45b9e3460192de61636babf93e8af4dc525
Merge: a3ae08c4c 99f41bf1e
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Mon Mar 6 17:01:58 2017 +0000

    Merged in development (pull request #9)
    
    Development

commit 99f41bf1e214145d9cd4ac25f25184bda62f63a0
Merge: 73fb9d8cd 6f326d751
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sun Mar 5 10:39:36 2017 -0800

    Merge branch 'development' into particle_refactor

commit 73fb9d8cd6f8273a54c75b60c7d40df774032ff6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 5 07:35:05 2017 -0800

    explicitly mark amrex_deposit_cic public

Src/Particle/AMReX_Particle_mod_3d.F90

commit 33aaf75f2f4641218874fb0cb28c14ddadbc5b68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 5 07:31:36 2017 -0800

    merge SingleLevelWhere into Where

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt

commit 6f326d7511c671fa90544db73e4f7f57891ef486
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 3 17:12:28 2017 -0800

    Add my computer name to the list of CCSE machines.

Tools/GNUMake/Make.machines

commit e503389d12dd0f5df19968211f3b36165110eabf
Merge: 4b3488970 c65ce4960
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 3 17:09:06 2017 -0800

    Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor
    
    merging.

commit 4b34889700a311d7f678435fe8ccf678f31fd04b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 3 17:08:11 2017 -0800

    Move the new deposition stuff to the fortran particle module.

Src/Particle/AMReX_Deposition_F.F90
Src/Particle/AMReX_Deposition_F.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particle_mod_3d.F90
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_Particles_F.H
Src/Particle/Make.package

commit c65ce4960f4c50a29c9ace6faf7b13c057115212
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 3 16:28:16 2017 -0800

    fix an assertion and a static constexpr

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H

commit b8038571f74710d88825db1e1b4f70cd6555d142
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Mar 3 14:52:51 2017 -0800

    added linearization routines to EBGraph.  On to seeing if I can get this to work with FabArray

Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp

commit 218a84d363f9b9382833515f35331a056c54ce0d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 3 12:38:25 2017 -0800

    fixing restart.

Src/Particle/AMReX_ParticleContainerI.H

commit 7b7429d899d14467753a38484869ed53cc34c3ad
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 3 11:10:51 2017 -0800

    Making redistribute work when lev_min = lev_max (needed by virtual particles).

Src/Particle/AMReX_ParticleContainerI.H

commit 96bcdb916871cef729014fbb0421ad8a3498a194
Merge: 3970a4d5f 1c55eaa6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 3 10:54:51 2017 -0800

    Merge branch 'dtg_branch' into development
    
    Conflicts:
            Src/Base/AMReX_FabArray.H

commit 3970a4d5f12251dd77b7940bab55507b9b7b9581
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 3 10:36:20 2017 -0800

    fix conflict

Src/Base/AMReX_FabArray.H

commit b1777f7b192c10030fcfbe6a93c7c5c4f651926b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 3 09:53:13 2017 -0800

    fix FillBoundary's cross option

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArray.cpp

commit 389e2c6d63df3b3ac87a625bdfb32adbf25914fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 3 08:33:23 2017 -0800

    fix a new bug

Src/Base/AMReX_FabArray.H

commit b5122351ce4ba56e89490b30d2f945f5c6556ffe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 2 20:49:06 2017 -0800

    fix some issues copyInter

Src/Base/AMReX_FabArray.H

commit c79184bcf0cc2615d849e406fd38b02bef36fa6f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 2 17:17:59 2017 -0800

    modified FabArray's communication for EB
    
    Conflicts:
            Src/Base/AMReX_FabArray.H

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.f90
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArray.cpp

commit e25c91a4edb5ba9e50500403f4b05438613fcffc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 27 17:12:23 2017 -0800

    forgot a new file in last commit

Src/Base/AMReX_FabFactory.H

commit 5ff3db714c7ca145923c71299547623db86b3dc1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 27 17:09:51 2017 -0800

    add Fab factory; note that dynamic sidecar and FabArrayCopyDescriptor do not work with non-default factory

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 1c55eaa6a8b67a25aee64c73694c3750c0838c1b
Merge: 224379f49 5186175f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 3 09:57:57 2017 -0800

    Merge branch 'weiqun/mpibuffer' into dtg_branch

commit 5186175f8d2387f05cc8133f970233dbd3789a6d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 3 09:53:13 2017 -0800

    fix FillBoundary's cross option

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArray.cpp

commit 68c2790d11a82fe5779aeed91b37bcf78e7d5c7a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 3 08:33:23 2017 -0800

    fix a new bug

Src/Base/AMReX_FabArray.H

commit fd1f437b3ff76047bb43e993d1623ecaa1683e1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 2 20:49:06 2017 -0800

    fix some issues copyInter

Src/Base/AMReX_FabArray.H

commit 2c5625bb49544f47bcf95590a72374ed055d95da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 2 17:17:59 2017 -0800

    modified FabArray's communication for EB

Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.f90
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArray.cpp

commit 224379f498f8cd20c7dac55e7683c9b510c405ec
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Mar 2 15:52:55 2017 -0800

    ebgraph test now also tests coarsening

Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp

commit 7a78a2eba4bb0dfc888289aede7330f7ea8fdc0a
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Mar 2 13:32:03 2017 -0800

    EBGraph passes its first test

Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp

commit 026ece8f12e2bdf7f67e290b73a3d45b52a69e74
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Mar 1 16:12:20 2017 -0800

    added a test for the graph

Tests/GeometryShop/ebgraphSingleGrid/GNUmakefile
Tests/GeometryShop/ebgraphSingleGrid/Make.package
Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp
Tests/GeometryShop/ebgraphSingleGrid/sphere.inputs

commit e0407d1786fea70efec777768c431243b635918d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 1 14:49:49 2017 -0800

    fix container resizing in redistribute

Src/Particle/AMReX_ParticleContainerI.H

commit fc4bb2877bfce1bf0b3d0d65ee6232cac99c86b3
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 1 13:42:51 2017 -0800

    There is no need for a Where() call here.

Src/Particle/AMReX_ParticleContainerI.H

commit 33f920536fbf378f98549abf9eb41edf623fa606
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 1 13:04:55 2017 -0800

    Have AddParticlesAtLevel clear the input container, as before.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit b080f2698a2ddf6619c6e2b47f86ed040ac86633
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 1 12:17:52 2017 -0800

    Check whether we need to resize m_particles in AddParticlesAtLevel()

Src/Particle/AMReX_ParticleContainerI.H

commit 12c054148c0b6765ddcdd7be3e76834fcaeba22a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 1 11:13:10 2017 -0800

    Rename here also.

Src/Particle/AMReX_ParticleContainerI.H

commit c879056e4be253cf0d1e12acd7759b1a44022760
Merge: 38f8bbfef ade2cf8f4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 1 11:11:59 2017 -0800

    Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor
    
    merging.

commit 38f8bbfef69a8b968ee85c9d6e0de36e62501505
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 1 11:11:47 2017 -0800

    forgot to include this file.

Src/Particle/AMReX_ParticleContainerI.H

commit 7201b375c2858eaad42809415ec10aabef7478ed
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 1 11:11:17 2017 -0800

    Give the AddParticlesAtLevel function an nGrow argument.

Src/Particle/AMReX_Particles.H

commit ade2cf8f48bd5a694ff5e534ba60ddb32998172e
Merge: e524336ff 97ea54b96
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 1 11:10:01 2017 -0800

    merging

commit e524336ff43e29032d2e32ab9581fe028206b18a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Mar 1 11:08:23 2017 -0800

    rename SingleLevelWhere and give it a default of 0 grow cells.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 4fc053676157354337948420a36609361b0b9345
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Mar 1 10:15:08 2017 -0800

    I managed to wedge EBGraph into AMReX.  Only missing the parallel communication stuff now.  I can now start testing it.

Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_FaceIndex.H
Src/GeometryShop/AMReX_FaceIndex.cpp
Src/GeometryShop/AMReX_FaceIterator.H
Src/GeometryShop/AMReX_FaceIterator.cpp
Src/GeometryShop/AMReX_SPMD.H
Src/GeometryShop/AMReX_VoFIterator.H
Src/GeometryShop/AMReX_VoFIterator.cpp
Src/GeometryShop/Make.package

commit 97ea54b9606fc0f63e5042634711147b6adedb05
Merge: 615a12dd3 379fe78a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 1 09:23:02 2017 -0800

    Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor
    
    Conflicts:
            Src/Particle/AMReX_ParticleContainerI.H
            Src/Particle/AMReX_ParticleInit.H

commit 615a12dd382293da78d9ad2a66b4f85857b23afe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 1 09:18:25 2017 -0800

    add functions to get/set particle positions

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particle_mod_1d.F90
Src/Particle/AMReX_Particle_mod_2d.F90
Src/Particle/AMReX_Particle_mod_3d.F90
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_Particles_F.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 379fe78a120ed0d8fec949daabc0204b7270909f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 28 18:05:34 2017 -0800

    remove unused variable.

Src/Particle/AMReX_ParticleInit.H

commit 229880b0c5de2196a38365e96e32272052fe7c90
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 28 18:05:08 2017 -0800

    Fix an assertion.

Src/Particle/AMReX_ParticleContainerI.H

commit 0df8cb3caaf9585f0fce67d849a5c2da2326a60a
Merge: d37ae41bd 7e9c88cce
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 28 17:46:28 2017 -0800

    Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor
    
    merging.

commit d37ae41bd83eab5131f9b546ae2e6e311e838a72
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 28 17:27:42 2017 -0800

    update advection tutorial to use the new form of Redistribute()

Tutorials/AMR_Adv_C/Source/Adv.cpp

commit 37f71f072aa4dd3980fd21902a08e2811cbac64f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 28 17:25:34 2017 -0800

    Making the new particle data structures work with Nyx.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit ae376527defd9291de4078e64fe7d62b1b6991fd
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Feb 28 17:23:54 2017 -0800

    Fix a bug in an assert.

Src/Base/AMReX_MultiFabUtil.cpp

commit cdc636747a9deb855ccb2685b558b1b0634bb550
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 28 15:13:53 2017 -0800

    renaming

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit ad3791edda0b3b78354a519bbe336d66527874cf
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Feb 28 14:51:36 2017 -0800

    added more of the components of EBGraph---I had forgotten how complicated this stuff is

Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_GraphNode.H
Src/GeometryShop/AMReX_GraphNode.cpp
Src/GeometryShop/AMReX_SPMD.H
Src/GeometryShop/AMReX_SPMD.cpp
Src/GeometryShop/AMReX_SPMDI.H
Src/GeometryShop/AMReX_VolIndex.H
Src/GeometryShop/AMReX_VolIndex.cpp
Src/GeometryShop/Make.package

commit 7e9c88ccebf5a5fa0ccdddb3ee61160582116d7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 28 13:59:42 2017 -0800

    fix an assertion

Src/Base/AMReX_MultiFabUtil.cpp

commit 4cfeecd9de6139a719ea39cd2de38e313db39c07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 28 13:57:16 2017 -0800

    add some push_back and access functions

Src/Particle/AMReX_Particles.H

commit 48b076b3623ef34f48621f036a52c4aa412d9ad7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 28 10:27:39 2017 -0500

    handle the reporting for when no benchmark is found.  Also don't
    get confused by variable names that start with diff

Tools/RegressionTesting/test_report.py

commit c37619c79941fad2ce79a429bc32e30c8148f8ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 27 17:12:23 2017 -0800

    forgot a new file in last commit

Src/Base/AMReX_FabFactory.H

commit 47b59d49318059f4de9c7db55477bc07ff411110
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 27 17:09:51 2017 -0800

    add Fab factory; note that dynamic sidecar and FabArrayCopyDescriptor do not work with non-default factory

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 33fa4eb4e5cddb10509288f7de132bf2b709a119
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 27 14:12:40 2017 -0800

    minor.

Src/Particle/AMReX_ParticleContainerI.H

commit 7fc361ff7f95988ffa98ffaed27f173c76f21261
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 27 13:52:42 2017 -0800

    Use fancy new helper functions to access the particle data pointer, instead of doing it manually.

Src/Particle/AMReX_ParticleContainerI.H

commit 62d10e42a15e9e5fe0b0454f63500b631111eb97
Merge: 57c0052b8 458f4adc9
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 27 12:22:40 2017 -0800

    merging.

commit 57c0052b83ff4e6040796c58491a91a286d59f22
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 27 12:21:00 2017 -0800

    Also call average_down at the end of AssignDensityFort

Src/Particle/AMReX_ParticleContainerI.H

commit eac127acd756f8af8917c44ab3b31b7fc8ec2d06
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 27 12:20:06 2017 -0800

    An extra sanity check for the sum_fine_to_coarse function.

Src/Base/AMReX_MultiFabUtil.cpp

commit 118201af7495b64f7fd7b793455a0329d8dea5b8
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Feb 27 11:38:33 2017 -0800

    keeping up with the development branch--some fortran stuff had changed names.  Also, fortran declarations need to be in amrex namespace.   Also,  moved some files from test directory to Src/GeometryShop.  Stuff compiles again

Src/GeometryShop/AMReX_AggStencil.H
Src/GeometryShop/AMReX_AggStencilI.H
Src/GeometryShop/AMReX_BaseIndex.H
Src/GeometryShop/AMReX_EBCellFAB.H
Src/GeometryShop/AMReX_EBCellFAB.cpp
Src/GeometryShop/AMReX_EBGraph.H
Src/GeometryShop/AMReX_EBGraph.cpp
Src/GeometryShop/AMReX_FaceIndex.H
Src/GeometryShop/AMReX_FaceIndex.cpp
Src/GeometryShop/AMReX_Stencils.H
Src/GeometryShop/AMReX_Stencils.cpp
Src/GeometryShop/AMReX_VolIndex.H
Src/GeometryShop/AMReX_VolIndex.cpp
Src/GeometryShop/Make.package
Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H
Tests/GeometryShop/stencilTestbed/src/Make.package
Tests/GeometryShop/stencilTestbed/src/lapl_nd.F90
Tests/GeometryShop/stencilTestbed/src/lapl_nd_F.H

commit b0926c9fd72506b56f3e158cb55f16dd239a244b
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Feb 27 10:37:03 2017 -0800

    paring this down to the minimum number of files because I am about to add a bunch more

Src/GeometryShop/AMReX_CellEdge.H
Src/GeometryShop/AMReX_CellEdge.cpp
Src/GeometryShop/AMReX_ComplementIF.H
Src/GeometryShop/AMReX_ComplementIF.cpp
Src/GeometryShop/AMReX_EllipsoidIF.H
Src/GeometryShop/AMReX_EllipsoidIF.cpp
Src/GeometryShop/AMReX_IntersectionIF.H
Src/GeometryShop/AMReX_IntersectionIF.cpp
Src/GeometryShop/AMReX_IrregNode.cpp
Src/GeometryShop/AMReX_LatheIF.H
Src/GeometryShop/AMReX_LatheIF.cpp
Src/GeometryShop/AMReX_TransformIF.H
Src/GeometryShop/AMReX_TransformIF.cpp
Src/GeometryShop/AMReX_UnionIF.H
Src/GeometryShop/AMReX_UnionIF.cpp

commit 458f4adc972eae7e9752f84b779097d91e37e9de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 27 09:11:00 2017 -0800

    add a new IntVect::operator== for comparing IntVect with int, and fix an out of bound problem

Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MultiFabUtil.cpp

commit c2bc83c3a7e78a63d21ba18c4794a941909764f5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 24 16:22:56 2017 -0800

    quick bug fix to TotalNumberOfParticles in parallel.

Src/Particle/AMReX_ParticleContainerI.H

commit 982ae05ccb7b364415e6f39a9e281a24ef61965a
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Feb 24 15:55:02 2017 -0800

    bug fix for flat plate

Src/GeometryShop/AMReX_FlatPlateGeom.cpp

commit 44edd4d479e89cdc58c4ec63cb843d49a1f5db58
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Feb 24 15:10:54 2017 -0800

    got flat plate geometry working as far as I have tested it

Src/GeometryShop/AMReX_FlatPlateGeom.cpp
Tests/GeometryShop/flatPlate/GNUmakefile
Tests/GeometryShop/flatPlate/Make.package
Tests/GeometryShop/flatPlate/flatPlateTest.cpp
Tests/GeometryShop/flatPlate/flatplate.inputs

commit ad4d34fc4b47abaa8f105b33d407b11917762bbe
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 24 13:46:24 2017 -0800

    Also write out the extra integer components.

Src/Particle/AMReX_ParticleContainerI.H

commit 328e173848980ec4560ce930cf2e39518ea93a9e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 24 13:32:25 2017 -0800

    Also write out whether this is a checkpoint format particle file or not.

Src/Particle/AMReX_ParticleContainerI.H

commit 65d9cef9ffdb021442e8f8adebc4ba3a1f25b654
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 24 13:08:52 2017 -0800

    Add ability to specify particle component names for IO.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Tests/Particles/AssignMultiLevelDensity/main.cpp

commit 8fa744dcac7e40efec7aa3e9ad7883571d3125fe
Merge: a3c9800cb 92ec13d40
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 24 10:57:35 2017 -0800

    merging.

commit a3c9800cb748b07a438d4938b0e07381b96ebe8a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 24 10:35:23 2017 -0800

    rewrite the multi-level charge deposition code.

Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Particle/AMReX_Deposition_F.F90
Src/Particle/AMReX_Deposition_F.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Tests/Particles/AssignDensity/GNUmakefile
Tests/Particles/AssignDensity/Make.package
Tests/Particles/AssignDensity/inputs
Tests/Particles/AssignDensity/main.cpp
Tests/Particles/AssignMultiLevelDensity/GNUmakefile
Tests/Particles/AssignMultiLevelDensity/Make.package
Tests/Particles/AssignMultiLevelDensity/inputs
Tests/Particles/AssignMultiLevelDensity/main.cpp
Tutorials/PIC_C/GNUmakefile

commit 02c921186749e46e0b7a3029ed9f66dadf96318d
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Feb 23 23:10:02 2017 -0800

    just used this version to test castro, and no bug was found

Tools/typechecker/typeChecker.py

commit e452ab58bc357bac1416dc944a9f3e340119b703
Merge: 101b039b2 e5e4dbde0
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Feb 23 17:35:15 2017 -0800

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development
    
    merging # the commit.

commit 101b039b25fd294e8512a96458bb0e19da9e5e9c
Author: atmyers <atmyers2@gmail.com>
Date:   Thu Feb 23 17:34:48 2017 -0800

    Fixing a bug in the PIC_C tutorial pointed out by Matthias Frey.

Tutorials/PIC_C/two_level.cpp

commit faf106e858d575368ccd31579eb87b31546ea9e7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 23 17:30:25 2017 -0800

    Fixing a bug in the PIC_C tutorial pointed out by Matthias Frey.

Tutorials/PIC_C/two_level.cpp

commit 4d852e613c7bba4be86f4a1bc94b146d54945eda
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Feb 23 16:11:04 2017 -0800

    made some progress on flat plate goem.  trickier than I thought (story of my life)

Src/GeometryShop/AMReX_FlatPlateGeom.H
Src/GeometryShop/AMReX_FlatPlateGeom.cpp
Src/GeometryShop/Make.package

commit f388df0202457298fd9eed78b38314da83b8bda4
Merge: 9b502a104 e5e4dbde0
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Feb 23 09:08:06 2017 -0800

    Merge branch 'development' into dtg_branch

commit b7683d4fadf3d16ddb33ec5ed9493e1a9b1339c9
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Feb 22 18:42:01 2017 -0800

    type checker can handler C++ input

Tools/typechecker/typeChecker.py

commit 92ec13d407f7df24b262d6b64a4008ca15fa47ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 21 16:59:38 2017 -0800

    Particle: merge two maps into one

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit da9c145bfa7f5ef19e35bd63cbe10d624baf414e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 21 09:45:31 2017 -0800

    no need to reset dummy mulitfab if the boxarray and distribution map do not change

Src/Particle/AMReX_ParticleContainerI.H

commit d9973cd9ee6325e343b36b00c870d56b03f20089
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 21 09:32:54 2017 -0800

    remove the where_already_called flag from Redistribute

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Tutorials/AMR_Adv_C/Source/Adv.cpp

commit d6d965258321f1a991749983730d5765b2d5f315
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 20 10:49:49 2017 -0800

    update AmrParticleContainer

Src/AmrCore/AMReX_AmrParticles.H

commit fb666db52d432cea93cbaa1f75ce8e837a685179
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 20 10:26:29 2017 -0800

    ParticleContainer::GetParticles --> GetAoSMap; add GetSoAMap

Src/Particle/AMReX_Particles.H

commit 0bfa46b9e1946bfe8de6649d9e152670e9bd84b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 20 10:17:26 2017 -0800

    define dummy multifab in resizeData

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit d546c2d1a1b0c811ba1856dd60c4dcc37be28145
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 20 07:52:16 2017 -0800

    add ParticleContainer::MakeMFiter that returns a normal MFIter

Src/Particle/AMReX_Particles.H

commit 77140c59fada962d481985c5389744e33c4dd88b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 20 07:43:57 2017 -0800

    fix typo

Src/Particle/AMReX_Particles.H

commit 0ca667ea8ae2a2c792b4edc4a12d0d9a84b2e060
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 20 07:26:59 2017 -0800

    add a few functions to ParticleContainer for convenience

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 1dda880bf1e7cfe9aff4500b907aba39981fedea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 19 15:43:59 2017 -0800

    ParIter: skip tiles that do not exist in maps

Src/Particle/AMReX_ParIterI.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit 9acaeebf989777b009f805cc964af844b74332af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 19 15:17:02 2017 -0800

    Make sure [] will insert a new item to the map even when SoA has no data, otherwise erase may fail

Src/Particle/AMReX_ParticleContainerI.H

commit 6afd20a2a064e5d3279ee0b58fe5fa2b4203d9c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 19 15:15:09 2017 -0800

    add const to MFIte::isValid()

Src/Base/AMReX_FabArray.H

commit 82ff020a1500ec7d75644d0d50fa76a156f17393
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 19 12:07:56 2017 -0800

    Particle Iterator: rename

Src/Particle/AMReX_Particles.H

commit d73a0df391a5f4bee4a51ba68fb481c63bd5b3a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 19 10:16:47 2017 -0800

    add class ArrayOfStructs

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit 66c37f3887e7311f221512790335f3d9121c77dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 18 16:34:37 2017 -0800

    rm the iterator get functions for a single component to avoid being called repeatedly; one can always get the whole data and access each component. some other minor changes

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit d6fad844e1256a1a755a157e46c9211efc6d7866
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 18 12:40:35 2017 -0800

    add ParIter

Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.H

commit 2214a79bbdce5d253a044ce23d4e38c5f6fa091e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 18 11:32:48 2017 -0800

    add static assertion the size of particle is a multiple of the size of real

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit d0f3c6bf49b19d075817d7dbc25f66f6febbb16f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 18 11:30:37 2017 -0800

    typo

Src/Particle/CMakeLists.txt

commit fd935b99e53e5e2838d06c7e92dbb89e45442391
Merge: 9ed4a3b6c a3b443ac8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 17 16:48:40 2017 -0800

    merging.

commit 9ed4a3b6c6b2f4db9fc76f2361dd4dd3e34a1da2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 17 16:45:05 2017 -0800

    Faster particle deposition routines.

Src/Particle/AMReX_Deposition_F.F90
Src/Particle/AMReX_Deposition_F.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit a3b443ac8bc123d5e62e2d82ee879649916e4818
Merge: 18c195334 e5e4dbde0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 17 15:43:45 2017 -0800

    Merge branch 'development' into particle_refactor

commit e5e4dbde01b51e65b11af19a31674656175295c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 17 15:42:55 2017 -0800

    de-virtualize some BoxArray functions

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit 6636822e84d02e0ca851015e4e328be8cdbd5c41
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 17 14:49:48 2017 -0800

    add amrex::Print::SetPrecision

Src/Base/AMReX_Print.H

commit 18c195334ea85dd706191a6ee399cb229da5581b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 17 14:51:24 2017 -0800

    tweak locateParticle to handle particles right on domain boundary

Src/Particle/AMReX_ParticleContainerI.H

commit 4bd158a8f8eb3f90fa57c451bd0180923bd8cb8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 17 14:49:48 2017 -0800

    add amrex::Print::SetPrecision

Src/Base/AMReX_Print.H

commit 4b7e5e394d5e97ddc4c263ae2779d65d2baf7aaa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 17 13:33:42 2017 -0800

    refactor OK()

Src/Particle/AMReX_ParticleContainerI.H

commit 9a4319c62759d4d279d51aa87c5a24c3200a048e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 17 13:28:22 2017 -0800

    refactor OK and locateParticle

Src/Particle/AMReX_ParticleContainerI.H

commit ca40440e80d9f807990519d1cb98fc772fb7e504
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 17 12:15:18 2017 -0800

    fix SingleLevelGrownWhere

Src/Particle/AMReX_ParticleContainerI.H

commit 34c03b8d227d5d0d0d7c6006563508d1446b57e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 17 10:50:30 2017 -0800

    refactor Where and OK

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit c8070cbb19f8a0ea256718bcd58e864fd929c10b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 17 09:53:21 2017 -0800

    rm single level where

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit ccf00b6a7d2e58da00b4423fd32b2a9097ea81f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 17 08:54:56 2017 -0800

    minor optimization

Src/Particle/AMReX_ParticleContainerI.H

commit adae91af12176b615c1877546d8ac4d3d1dfa16d
Merge: 56ef14662 d76ec1c90
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 16 13:14:22 2017 -0800

    Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor
    
    merging.

commit 56ef1466236bbde99b62e1e286eb7b1c0cd82815
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 16 13:13:59 2017 -0800

    Implementing particle restart for the advection test.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Tutorials/AMR_Adv_C/Source/Adv.H
Tutorials/AMR_Adv_C/Source/Adv_io.cpp

commit d76ec1c9025994427002e8c4cd543af62f1677cf
Merge: 222dcc247 dbfc42d8b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 16 10:50:47 2017 -0800

    Merge branch 'development' into particle_refactor

commit 222dcc247a63b7075a1021c80cc24dae0420c8cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 16 10:19:14 2017 -0800

    make the particle tiling consistent with MFIter tiling

Src/Base/AMReX_FabArray.cpp
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 20dbfcdead7ae61ca7995ea68e95b96bcc883202
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 16 09:29:37 2017 -0800

    optimization of Where

Src/Particle/AMReX_ParticleContainerI.H

commit b424e405a37ff7ac2f19c37c3abd1e65a3eb7e6b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 16 09:34:58 2017 -0800

    also read the extra int information from checkpoint files.

Src/Particle/AMReX_ParticleContainerI.H

commit 5107af27e6d17435a80395bcbbbcb4bcd1b8e363
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 15 20:14:38 2017 -0800

    cleaning up the particle restart routines.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 9b502a104130fb00f4ade65c5f4fa5539d10a9ca
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Feb 15 19:20:55 2017 -0800

    Fix up MSD version of stencil test again.

Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp

commit 3988e9aef5b7b8b4e0ecf0a6e1b6ef0e8ef09544
Merge: aa72f1ef6 46635b718
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 15 17:46:53 2017 -0800

    Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor
    
    merging

commit aa72f1ef67cf501c926011bc5e15300c333fa14e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 15 17:46:25 2017 -0800

    Remove duplicate versions of ReadParticles by using a template function.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 46635b718ef33d095c702b2b1abb6b93acc3a2aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 15 17:01:08 2017 -0800

    need to test for nullptr

Src/Particle/AMReX_ParticleContainerI.H

commit 4f26057b5b8a4a2bfafd1130572c8b253680f55f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 15 16:55:57 2017 -0800

    add dummy multifabs to particle container

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H

commit ca0f86fcd81087dbd256021c346346979922e4f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 15 15:47:37 2017 -0800

    add tilebox and gridbox to particle location data

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 8bedf58e7aaddd832c0da2c9744108683b7dcadd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 15 15:24:46 2017 -0800

    Where: optimization

Src/Particle/AMReX_ParticleContainerI.H

commit 8e8e24de9f9405c7919823cd71b0f8fda9aa8cfa
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 15 16:16:00 2017 -0800

    This reference can't be const, as this function updates the particles.

Src/Particle/AMReX_ParticleContainerI.H

commit dae67a4f7af6c6e2f6b16a2021a7db01975ab7ce
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 15 15:12:48 2017 -0800

    Add the SoA data to the restart routines

Src/Particle/AMReX_ParticleContainerI.H

commit 9e6f661802425365bb28001abf80d014e1ebedcf
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Feb 15 13:00:44 2017 -0800

    Fix the mess I made in the stencilTest folder...still messy, but correct.

Tests/GeometryShop/stencilTestbed/exec/GNUmakefile
Tests/GeometryShop/stencilTestbed/exec/Make.package
Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_2d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_3d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_F.H
Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H

commit 9c95d917caaa6b817f9354bd4c022600a58f99c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 15 11:06:41 2017 -0800

    add a static Initialize function to ParticleContainer

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit daa0585923477eca9f31d60b3f268eb902a5ef44
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 15 10:53:44 2017 -0800

    minor

Src/Particle/AMReX_ParticleContainerI.H

commit 6ac5d1e5d9af665b5ad2cec92a6c072c4f9e27e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 15 10:46:03 2017 -0800

    fix assertion

Src/Particle/AMReX_ParticleContainerI.H

commit 987266663f6ab7c49e8775ef8f84db4061325a0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 15 10:43:13 2017 -0800

    update tutorial because of the interface of Redistribute

Tutorials/AMR_Adv_C/Source/Adv.cpp

commit c7aee617f6bc8becbe4ab0841f10987d764fe012
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 15 10:31:18 2017 -0800

    refactor Redistribute

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 85a49bd07870478abfdee9c79ad57a851be9c54d
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 14 18:43:09 2017 -0800

    Add logic to shift bc interp stencil to avoid extrapolations and more smoothly continue with sign changes of the normal components.  Not sure if this has a direct analogue in 3d yet.

Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90

commit a7fa5dfc782a4d76665e1a9865a1fd2eb4bd051e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 17:29:43 2017 -0800

    fix last commit

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 8fb4e9854356e1effb731f4f525576bdd92f2364
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 17:02:10 2017 -0800

    clean up and add a test for trivally copyable

Src/Particle/AMReX_ParticleContainerI.H

commit 4da2c4583a7a60a1024d10b768bd543d8e5ef5a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 16:56:19 2017 -0800

    Assertion on pointers obtained with c type cast won't work.

Src/Particle/AMReX_ParticleContainerI.H

commit 5364daddf19a98a2870b782e1a0cb57a535832a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 16:48:40 2017 -0800

    minor

Src/Particle/AMReX_ParticleContainerI.H

commit 23de4ae531a3081bcf15f41cdaea69f1a5a43fcf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 15:58:13 2017 -0800

    add where_already_called option to Redistribution

Src/Particle/AMReX_ParticleContainerI.H

commit a85d42dc28ea56c276be37efa46806ee5e1124bd
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 14 15:21:02 2017 -0800

    Nearly trivial hack to stencil

Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp
Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90
Tests/GeometryShop/stencilTestbed/exec/dirichletTest_F.H

commit e68558361c35c040c5e6b77df27d3ddcf5daa61e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 15:06:13 2017 -0800

    remove SoA data too

Src/Particle/AMReX_ParticleContainerI.H

commit af18c48c5fdfa4f745cf4f9f111fc13e3945f9c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 14:56:49 2017 -0800

    remove some duplicated code

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit bdefc0095cb3d82c080f1e580d4b6b258dc244d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 14:28:27 2017 -0800

    some cout --> Print()

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H

commit e480193c7166aa0ab221026b0f9f2374361a84ab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 13:27:13 2017 -0800

    add some optional argument for skipping mpi reduction

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit d8a7866b32ac2ee7276ba2c554d162976313d536
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 13:05:35 2017 -0800

    add some optional argument for skipping mpi reduction

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 323e5c2cdde23b2c03e058cb64c15e4593d29fbf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 12:46:39 2017 -0800

    add SoA to ByteSpread

Src/Particle/AMReX_ParticleContainerI.H

commit 93d8f872e26fb113609ff388b1a2298c515a6a03
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 12:41:08 2017 -0800

    fix a bug: when tiling is on, we may visit a grid multiple times

Src/Particle/AMReX_ParticleContainerI.H

commit a15c1923915b13c361fca3f0388d4690afe59cc3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 12:25:45 2017 -0800

    forgot #ifdef; use unique_ptr

Tutorials/AMR_Adv_C/Source/Adv.H
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/Adv_setup.cpp

commit 2167cbcc40464241e2b8189baa73d4fa60f58cc9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 12:19:13 2017 -0800

    unroll a loop

Src/Particle/AMReX_ParticleContainerI.H

commit bd0838a647be08f8d3cc59d54fb9ecf36e7845b8
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 14 09:49:19 2017 -0800

    Minor mod to stencil test.

Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90

commit 554b81623e2211f71e855aea271d2932b7936de6
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 14 09:46:24 2017 -0800

    Working on EB stencil stuff, pushing WIP

Tests/GeometryShop/stencilTestbed/exec/GNUmakefile
Tests/GeometryShop/stencilTestbed/exec/Make.package
Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp
Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90
Tests/GeometryShop/stencilTestbed/exec/dirichletTest_F.H
Tests/GeometryShop/stencilTestbed/exec/sphere.inputs
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H

commit c0989b8bb41a2dd2770ecd541d30ee42fd257f47
Merge: 065a74b3a 9fb55cee1
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 13 16:29:48 2017 -0800

    Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor
    
    merging.

commit 065a74b3a39d54366be26cc088d3c34c15264d12
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 13 16:29:25 2017 -0800

    remove redundant Where() call

Src/Particle/AMReX_ParticleContainerI.H

commit 9fb55cee131aa0bcd661cdca94e1f89fffb904e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 13 15:46:07 2017 -0800

    take a shortcut in Where

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit 35fbfc60f22b93f866c53036b8970f584f79ac7f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 13 14:33:28 2017 -0800

    Initialize the communicate_comp member properly

Src/Particle/AMReX_Particles.H

commit 5428aad5aab4c87215b6634ad6bc8a9ae838dbdf
Merge: cc966b2f6 c73751ecb
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 13 14:12:36 2017 -0800

    Merging.

commit cc966b2f6460f05b72afd40e731b5bbff20d0dbc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 13 13:57:53 2017 -0800

    Some renaming for clarity.

Src/AmrCore/AMReX_AmrParticles.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H

commit c73751ecbae61818dcbaae2065b0599a4a944c9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 13 13:41:14 2017 -0800

    rm using std::make_pair from headers

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H

commit 90ee02bb1cd74ef7803ddf69418cdccaf889faff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 13 13:02:58 2017 -0800

    use std::vector<bool> instead of built-in array because zero size built-in array is not allowed

Src/Particle/AMReX_Particles.H

commit 1a8f35be36f051a06ead10705baedce8e4fc9582
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 13 12:45:33 2017 -0800

    minor changes for consistence

Src/Particle/AMReX_Particles.H

commit 48d4c8a8b4356ba2514f332ced5390a146def74d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 13 12:43:21 2017 -0800

    use amrex::Array instead of std::vector in some places

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 826fa8674e927a782f6da787180f9d27dd736e9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 13 12:25:17 2017 -0800

    fix omp race conditions

Tutorials/AMR_Adv_C/Source/Adv_advance.cpp

commit e4f34c03519a29bc80b0f4d0b8e04aa36b4eaf4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 13 12:24:41 2017 -0800

    delete particle container

Tutorials/AMR_Adv_C/Source/Adv_setup.cpp

commit 55dbe14ca6828eb755e77952e95662e604039ccc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 13 11:17:04 2017 -0800

    rename to avoid confusion

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArray.cpp

commit 90982cf05f2445d00174e664cbd0c37083d5e316
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 13 10:38:49 2017 -0800

    CoordSys: bcast inv_dx and set default inv_dx to infinity

Src/Base/AMReX_CoordSys.cpp

commit 5592fb7b51f152fdb6689b5e2e640a03b0037c68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 9 21:52:42 2017 -0800

    AMR_Adv_CF: multiple levels without regridding works

Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90
Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90

commit b994d7f62a33e8363bde00ed3237d93a682a3c2f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 9 17:09:15 2017 -0800

    add amrex_bc_types_module and fillpatch from two levels

Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90
Src/F_Interfaces/Base/AMReX_bc_types_mod.F90
Src/F_Interfaces/Base/Make.package

commit 1f37d6f4dd7cf1f5830b780acb039bb55cc20838
Merge: c6a2860bc dbfc42d8b
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Feb 9 16:28:32 2017 -0800

    resolve a confict when merging dev to check_fortran

commit 2cbde3dcecda5c1f31e48bd75ecc80b0511a7592
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 9 15:35:28 2017 -0800

    AMR_Adv_CF: add clear level function

Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90
Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90
Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp
Src/F_Interfaces/AmrCore/Make.package
Src/F_Interfaces/Base/AMReX_base_mod.F90
Src/F_Interfaces/Base/Make.package
Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 4283ccfcb574fd0c1d29a40d121e08ebb19cc7ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 9 15:33:35 2017 -0800

    add amrex_interpolater_module

Src/F_Interfaces/AmrCore/AMReX_interpolater_mod.F90

commit 49cd87ac6c80b1cd9d7c2a3a40436477e4906f1b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 9 13:34:56 2017 -0800

    Also write out the SoA data to the plt files.

Src/Particle/AMReX_ParticleContainerI.H

commit 4598948b0eb952c812d6fdd214b921c3b194b609
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 9 11:38:14 2017 -0800

    Updating the AMR_Adv_C tutorial to optionally use tracer particles.

Tutorials/AMR_Adv_C/Exec/Make.Adv
Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs
Tutorials/AMR_Adv_C/Source/Adv.H
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/Adv_advance.cpp
Tutorials/AMR_Adv_C/Source/Adv_io.cpp

commit 0c3cca12782bfc40fd2cdfa4e1817c551025eaef
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 9 11:37:07 2017 -0800

    Updating the tiled particles to use a pair-indexed map.

Src/AmrCore/AMReX_AmrParticles.H
Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp
Tests/Particles/main.cpp

commit 716858a07ba3a2dae43445186491339840a2cf40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 9 10:53:55 2017 -0800

    AMR_Adv_CF: works for single level now

Src/F_Interfaces/Base/AMReX_box_mod.F90
Tutorials/AMR_Adv_CF/Exec/Make.Adv
Tutorials/AMR_Adv_CF/Source/Src_2d/Make.package
Tutorials/AMR_Adv_CF/Source/Src_2d/advect_2d_mod.F90
Tutorials/AMR_Adv_CF/Source/Src_2d/compute_flux_2d.f90
Tutorials/AMR_Adv_CF/Source/Src_2d/slope_2d.f90
Tutorials/AMR_Adv_CF/Source/evolve_mod.F90

commit cbc0274d5af97069169b6a4356ba09f325697c88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 9 10:14:08 2017 -0800

    fix box type for amrex_mfiter

Src/F_Interfaces/Base/AMReX_box_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 8cc0940db330473c9c8d0502851d3c0de54dbcef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 9 09:52:48 2017 -0800

    AMR_Adv_CF: get face velocity

Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90
Tutorials/AMR_Adv_CF/Source/evolve_mod.F90

commit 3ff7485bbe6f58970bd24994bd8539064ff5a2e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 9 09:40:16 2017 -0800

    simplify amrex_print

Src/F_Interfaces/Base/AMReX_box_fi.cpp
Src/F_Interfaces/Base/AMReX_box_mod.F90
Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_distromap_fi.cpp
Src/F_Interfaces/Base/AMReX_distromap_mod.F90

commit 07082172b850b6ddcccd4ff9c095f5898343a315
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 9 09:30:33 2017 -0800

    add nodal flag to amrex_box

Src/F_Interfaces/Base/AMReX_box_mod.F90

commit 76841906e4cb469b10b4eca9c136895ce342122a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 9 08:56:56 2017 -0800

    clean up by using fab%resize

Src/F_Interfaces/Base/AMReX_box_mod.F90
Src/F_Interfaces/Base/AMReX_fab_mod.F90
Tutorials/AMR_Adv_CF/Exec/SingleVortex/face_velocity_2d.F90
Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90

commit f88cce56f934439f56f87ff1d4628205077da5c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 8 21:05:32 2017 -0800

    more amrex fab procedures

Src/F_Interfaces/Base/AMReX_box_mod.F90
Src/F_Interfaces/Base/AMReX_fab_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 9b71209227cfe56c331c5562c93288e565cfcc6f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 8 17:04:34 2017 -0800

    start amrex_fab_module

Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90
Src/F_Interfaces/Base/AMReX_base_mod.F90
Src/F_Interfaces/Base/AMReX_fab_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Src/F_Interfaces/Base/Make.package
Tutorials/AMR_Adv_CF/Source/evolve_mod.F90

commit 929805eb07b5a5b88b12f0c5b21f0ab8a2be13ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 8 16:50:52 2017 -0800

    add amrex prefix to mempool functions

Src/Base/AMReX.cpp
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_MemPool.H
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_mempool_f.f90
Src/F_BaseLib/boxlib_f.f90
Src/F_BaseLib/fab.f90
Src/F_Interfaces/Base/AMReX_fab_mod.F90

commit 12afca58d02454e1c69c38ed21d76abceca84592
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 8 15:38:29 2017 -0800

    add generic assignment for tagboxarray

Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 19bfe7a683c09f311524b78f6ebe8fabfab9021b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 8 15:32:27 2017 -0800

    define some amrex function interfaces a user code must provide

Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90
Src/F_Interfaces/Base/AMReX_physbc_mod.F90
Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit e5a556bc08c124853289dddf43c62fe148bc8dcf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 8 14:44:06 2017 -0800

    add amrex_fillpatch_single

Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90
Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90
Src/F_Interfaces/AmrCore/Make.package
Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90

commit 7c6e78ed3ca0fed374ca6be5ab9d86f258bf15f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 8 14:12:35 2017 -0800

    add physbc

Src/F_Interfaces/Base/AMReX_FPhysBC.H
Src/F_Interfaces/Base/AMReX_base_mod.F90
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_distromap_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Src/F_Interfaces/Base/AMReX_physbc_fi.cpp
Src/F_Interfaces/Base/AMReX_physbc_mod.F90
Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 544a50fc5a15cbd58519fca17302670d52d86319
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 8 12:49:25 2017 -0800

    rename for consistence

Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90
Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90
Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp
Src/F_Interfaces/AmrCore/Make.package
Tutorials/AMR_Adv_CF/Source/fmain.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 28199fda86e6573058f3c1b22a1929d6c167b153
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 8 12:40:04 2017 -0800

    add AMReX_FPhysBC

Src/F_Interfaces/Base/AMReX_FPhysBC.H
Src/F_Interfaces/Base/AMReX_FPhysBC.cpp
Src/F_Interfaces/Base/AMReX_physbc_fi.cpp
Src/F_Interfaces/Base/AMReX_physbc_mod.F90
Src/F_Interfaces/Base/Make.package
Tutorials/AMR_Adv_CF/Source/Make.package
Tutorials/AMR_Adv_CF/Source/evolve_mod.F90
Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90

commit c6a2860bcce8893bac42f38082bdb627596e9927
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Feb 8 11:56:25 2017 -0800

    update type checker

Tools/typechecker/typeChecker.py

commit 33a304c7c95e45b9136d51aba9f66fede5e8ec61
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Wed Feb 8 11:52:01 2017 -0800

    fix a few fortran headers

Src/AmrCore/AMReX_FLUXREG_F.H
Src/AmrCore/AMReX_INTERP_F.H
Src/Base/AMReX_COORDSYS_F.H
Src/Boundary/AMReX_INTERPBNDRYDATA_F.H

commit 2d68a817ec613db42c6d03d026e09e14fb37e6ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 8 10:21:31 2017 -0800

    call regrid

Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Tutorials/AMR_Adv_CF/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_CF/Source/evolve_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90
Tutorials/AMR_Adv_CF/Source/plotfile_mod.F90

commit af33b94564691d6d76f64eb0e660bd6b9d89ee57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 8 08:54:28 2017 -0800

    change how amrex_mpi_real is initialzied

Src/F_Interfaces/Base/AMReX_parallel_mod.F90

commit 68fbcc9ca7188ddfaf6e797c2e99129e1411f953
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 20:40:55 2017 -0800

    mpi_amrex_real --> amrex_mpi_real

Src/F_Interfaces/Base/AMReX_parallel_mod.F90

commit 63792fc9142d4a830dc540b54c23a9eb34e0fdcb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 17:09:39 2017 -0800

    add recursive timestep function

Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90
Tutorials/AMR_Adv_CF/Source/evolve_mod.F90

commit 172fd516a7b219ae3360768587b910837841a7f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 17:01:18 2017 -0800

    add some parallel reduce functions

Src/F_Interfaces/Base/AMReX_parallel_mod.F90

commit 679cb91d75f20a218976e6d059a6ff00022a6eef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 16:17:38 2017 -0800

    implement compute dt

Src/F_Interfaces/Base/AMReX_base_mod.F90
Src/F_Interfaces/Base/AMReX_box_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Tutorials/AMR_Adv_CF/Exec/SingleVortex/Make.package
Tutorials/AMR_Adv_CF/Exec/SingleVortex/face_velocity_2d.F90
Tutorials/AMR_Adv_CF/Source/Make.package
Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90
Tutorials/AMR_Adv_CF/Source/evolve_mod.F90

commit ce432452203d70b5faeae4cc890021ff97eabcf7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 14:33:23 2017 -0800

    move geometry array into amrex_famrcore module

Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Tutorials/AMR_Adv_CF/Source/averagedown_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90
Tutorials/AMR_Adv_CF/Source/plotfile_mod.F90

commit b8d8223b3e2c2c8e4e9f7aac363a1821b4eef2b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 14:26:59 2017 -0800

    add evolve module

Tutorials/AMR_Adv_CF/Source/Make.package
Tutorials/AMR_Adv_CF/Source/averagedown_mod.F90
Tutorials/AMR_Adv_CF/Source/evolve_mod.F90
Tutorials/AMR_Adv_CF/Source/fmain.F90

commit 5e5cf7c3a90e4a2708e63443daec1b5161d5841b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 14:23:36 2017 -0800

    add missing use module

Src/F_Interfaces/Base/AMReX_box_mod.F90

commit 8c90bec9b98ba578fd741a378638c5497d4559f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 14:22:48 2017 -0800

    add implicit none to interface blocks

Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90
Src/F_Interfaces/Base/AMReX_box_mod.F90
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_distromap_mod.F90
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 84b9272b4dc5386580206d6e7e585052a5c7ec17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 14:17:08 2017 -0800

    add multifabutil module

Src/F_Interfaces/Base/AMReX_base_mod.F90
Src/F_Interfaces/Base/AMReX_multifabutil_fi.cpp
Src/F_Interfaces/Base/AMReX_multifabutil_mod.F90
Src/F_Interfaces/Base/Make.package
Tutorials/AMR_Adv_CF/Source/Make.package
Tutorials/AMR_Adv_CF/Source/initdata.F90

commit e01ca0d84e03347e379a7bf7c5c8e8dbfd85cdfe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 13:48:58 2017 -0800

    write plotfile

Src/Base/AMReX_string_mod.F90
Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Src/F_Interfaces/AmrCore/AMReX_tagbox_fi.cpp
Src/F_Interfaces/Base/AMReX_base_mod.F90
Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp
Src/F_Interfaces/Base/AMReX_plotfile_mod.F90
Src/F_Interfaces/Base/Make.package
Tutorials/AMR_Adv_CF/Source/Make.package
Tutorials/AMR_Adv_CF/Source/error_estimate_mod.F90
Tutorials/AMR_Adv_CF/Source/initdata.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90
Tutorials/AMR_Adv_CF/Source/plotfile_mod.F90
Tutorials/AMR_Adv_CF/Source/tagging_mod.F90

commit b3d799ce2ae5583d265354b66da2a80e5834c356
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 11:10:10 2017 -0800

    finish error estimate module for the example

Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H
Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp
Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Tutorials/AMR_Adv_CF/Source/error_estimate_mod.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 022eb2ad39a3f287ab6f41d8937b1e01bead04eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 10:42:03 2017 -0800

    add getarr and queryarr for int and real

Src/Base/AMReX_parmparse_fi.cpp
Src/Base/AMReX_parmparse_mod.F90

commit dbfc42d8b7069edb55de9aeffeefabcf2ef4cc21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 09:08:13 2017 -0800

    fix extra argument

Src/Base/AMReX_BaseFab_nd.f90

commit 840d36e3fe4228e058fb184207499e42c7d8dbc9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 09:04:43 2017 -0800

    rename amrex_module to amrex_base_module

Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90
Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90
Src/F_Interfaces/Base/AMReX_base_mod.F90
Src/F_Interfaces/Base/AMReX_fi_mod.F90
Src/F_Interfaces/Base/Make.package
Tutorials/HeatEquation_EX1_CF/advance.f90
Tutorials/HeatEquation_EX1_CF/fmain.f90
Tutorials/HeatEquation_EX1_CF/init_phi.f90
Tutorials/HelloWorld_CF/fmain.f90

commit 315d278f5bc39f5ca6c92f286ba3c6132a04caba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 08:56:48 2017 -0800

    add amrex_tagbox_module

Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90
Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90
Src/F_Interfaces/AmrCore/Make.package
Tutorials/AMR_Adv_CF/Source/fmain.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 6dd01b47da73cbbe9039a6d02e92f0b8f35b598e
Author: tannguyen <tannguyen@tannguyens-MacBook-Pro.local>
Date:   Tue Feb 7 03:39:25 2017 -0800

    first version of the static type checker

Tools/typechecker/pycparser/__init__.py
Tools/typechecker/pycparser/_ast_gen.py
Tools/typechecker/pycparser/_build_tables.py
Tools/typechecker/pycparser/_c_ast.cfg
Tools/typechecker/pycparser/ast_transforms.py
Tools/typechecker/pycparser/c_ast.py
Tools/typechecker/pycparser/c_generator.py
Tools/typechecker/pycparser/c_lexer.py
Tools/typechecker/pycparser/c_parser.py
Tools/typechecker/pycparser/ply/LICENSE
Tools/typechecker/pycparser/ply/__init__.py
Tools/typechecker/pycparser/ply/cpp.py
Tools/typechecker/pycparser/ply/ctokens.py
Tools/typechecker/pycparser/ply/lex.py
Tools/typechecker/pycparser/ply/yacc.py
Tools/typechecker/pycparser/ply/ygen.py
Tools/typechecker/pycparser/plyparser.py
Tools/typechecker/typeChecker.py

commit 13e92b846e675b98fea7db8f7dd11ba0fe9fdf63
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 6 17:38:36 2017 -0800

    Don't go through this if tiling is turned off.

Src/Particle/AMReX_ParticleContainerI.H

commit f54486a8011b1ad350d9c6c182c9e08621ef5ce8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 6 16:42:07 2017 -0800

    add imultifab and errorest

Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H
Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Tutorials/AMR_Adv_CF/Source/Make.package
Tutorials/AMR_Adv_CF/Source/error_estimate_mod.F90
Tutorials/AMR_Adv_CF/Source/initdata.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 20eccfa7467dbe7487af5bed4e328b0fabde7e87
Merge: 65577edd0 886c677d8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 6 15:11:22 2017 -0800

    Merge branch 'development' of https://bitbucket.org/berkeleylab/amrex into particle_refactor
    
    merging with development.

commit 886c677d86a58922306470367336aa4947e67e22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 6 15:01:02 2017 -0800

    start to support virtual functions in F_Interface

Src/AmrCore/AMReX_AmrCore.H
Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H
Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp
Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Tutorials/AMR_Adv_CF/Source/initdata.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H

commit 65577edd0fdc2698e41fdd4966ef805869e842c5
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 6 14:52:04 2017 -0800

    Fixing a couple of tiling-related bugs.

Src/Particle/AMReX_ParticleContainerI.H

commit fadd68755cf1e45e63d3ae51c1a2eda841973b9e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 6 13:31:12 2017 -0800

    fix typo

Src/Amr/AMReX_Amr.H

commit 3295fedfcaf4eacd4cc666a97097644ab14b1878
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 6 13:20:20 2017 -0800

    add a few virtual functions to AmrCore

Src/Amr/AMReX_Amr.H
Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp

commit c63ed87b150d211c27d8a1434f55121466d1264c
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 6 12:41:56 2017 -0800

    Adding tiling information to the particle location functions.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 73b40f726b31470f89af25d3997f0cc0f3f0dc54
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 6 11:27:39 2017 -0800

    Moving many of the Particle static methods to the ParticleContainer class instead.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit b443940df7e274a42e20f570ed7fb2c7e211db58
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Feb 6 10:12:20 2017 -0800

    Restructure unpacking the particle data so we don't have to call Where twice.

Src/Particle/AMReX_ParticleContainerI.H
Tests/Particles/test.py

commit f727599fc92060a1b5a197da3a9f3a74afcd9941
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Sun Feb 5 19:15:10 2017 -0800

    Communicate the particle data in one MPI burst instead of two.

Src/Particle/AMReX_ParticleContainerI.H

commit b6c5c08d0426dc6ba652dd469c2ba47e0a92ff2b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 3 21:25:31 2017 -0800

    update amrex_multifab_build

Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 985b0b6ee960d05b64426120519f2d1bad4f4797
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 3 17:14:50 2017 -0800

    build fine levels

Tutorials/AMR_Adv_CF/Source/initdata.F90

commit c79e1d47d2ba80cf6b160659eebed6ea5e2b1c50
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 3 16:33:06 2017 -0800

    add amrex_multifab_write

Src/F_Interfaces/Base/AMReX_fi_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Src/F_Interfaces/Base/AMReX_vismf_fi.cpp
Src/F_Interfaces/Base/Make.package
Tutorials/AMR_Adv_CF/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_Adv_CF/Exec/SingleVortex/Prob.f90
Tutorials/AMR_Adv_CF/Source/initdata.F90

commit 79b3a9a91916d853485f503f6cb153e0f616d74a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 3 16:08:59 2017 -0800

    Have the particle iterator inherit as much as possible from MFITer

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp
Tests/Particles/ParticleIterator/main.cpp

commit a589555de5c5b745640d8f94414e59da185b8dd6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 3 15:57:20 2017 -0800

    Allocating dummy multifabs in the particle container for helping with iteration.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H

commit 2f6849002973ef7770cfe9fd08e1068c5b9ac243
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 3 15:13:28 2017 -0800

    Add amrex_fi_module.  It doesn't do anything now.  But in the future we might do some fortran specific init and finalize stuff

Src/F_Interfaces/Base/AMReX_fi_main.cpp
Src/F_Interfaces/Base/Make.package
Tutorials/AMR_Adv_CF/Source/initdata.F90

commit 752b58f1b8231223652f723615a3f831a42d771f
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 3 15:06:28 2017 -0800

    Adding a couple of useful tile-related methods to MFIter.

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArray.cpp

commit 6d690045b3421d2a7af6cbffb91615ba6cbd7003
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 3 14:56:21 2017 -0800

    make base level

Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Tutorials/AMR_Adv_CF/Source/initdata.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 96ef975de03260fdcc683be70bea81fe6994d9c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 3 13:36:13 2017 -0800

    add some set functions

Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H
Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90

commit 43e7779db5a63e87114e0b43f4fa70f1326fa66d
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 3 11:47:13 2017 -0800

    update main particle test.

Tests/Particles/main.cpp

commit c62060150e651a9a0ad904f7e59542b8ac8c7da1
Merge: 7659ba1b3 da27df5e2
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 3 11:46:15 2017 -0800

    Merge branch 'particle_refactor' of https://bitbucket.org/berkeleylab/amrex into particle_refactor
    
    merging.

commit 7659ba1b3ae45edd9f0ddb0ff2297e68a24061c4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Feb 3 11:44:04 2017 -0800

    Make the_next_id static member data of particle.

Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_Particles.H

commit da27df5e220ed93eb2ed08a0ed54114bade8934d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 3 10:48:54 2017 -0800

    minor

Src/Particle/AMReX_Particles.H

commit efe4ca8363897a6d310449c2c40e11f2c45c3544
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 3 09:48:15 2017 -0800

    fix cpu() and add const & version of some functions

Src/Particle/AMReX_Particles.H

commit 34e08d86fb7e172f9f99e4f3da7cc8d193e89dfb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 3 09:28:52 2017 -0800

    some constexpr

Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_Particles.H

commit 363898f113da1c0737f6e10ba73ee40ff8bb1066
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 3 08:49:35 2017 -0800

    mark some finalization procedures as impure elemental

Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_distromap_mod.F90
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 72898b849c04e62fb0ce9642165605bf56dfa3fc
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 2 17:43:27 2017 -0800

    Allocate the appropriate data structures for the tiling case.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 9b35a9813180b46081561c51ff00aa06e81aa269
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 2 17:04:20 2017 -0800

    need to clear the old level and update finest_level variable

Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Tutorials/AMR_Adv_CF/Source/initdata.F90
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp

commit 16a6c875701c6f6c403dbe1810621d517e8d43f7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 2 16:44:47 2017 -0800

    Replacing the loops in the particle code with ones that use the tiling iterators.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp
Tests/Particles/ParticleIterator/main.cpp

commit 4b94cd59c6e08144958981c8afeebc5930bc2a7d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 2 16:24:26 2017 -0800

    add amrex_print to box, boxarray and distromap modules

Src/Base/AMReX_Print.H
Src/F_Interfaces/Base/AMReX_box_fi.cpp
Src/F_Interfaces/Base/AMReX_box_mod.F90
Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_distromap_fi.cpp
Src/F_Interfaces/Base/AMReX_distromap_mod.F90
Src/F_Interfaces/Base/Make.package
Tutorials/AMR_Adv_CF/Source/initdata.F90

commit f596029bf6f4d67163220255df5c3834347fdfdd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 2 15:13:15 2017 -0800

    add some get functions

Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Src/F_Interfaces/Base/AMReX_box_mod.F90
Src/F_Interfaces/Base/AMReX_geometry_fi.cpp
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Tutorials/AMR_Adv_CF/Source/Make.package
Tutorials/AMR_Adv_CF/Source/fmain.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit ea9b5a4fa05c7f62706504dc3166f52987df2fa7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 2 14:01:44 2017 -0800

    A tiling particle iterator that works in parallel.

Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp
Tests/Particles/ParticleIterator/main.cpp

commit de96be0defaa9ddf3a85433445213de6a3635197
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 2 12:28:47 2017 -0800

    amrex_famr_core: add static data

Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp
Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Tutorials/AMR_Adv_CF/Source/fmain.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit a8b51d679944ce26e80afa0cd267e2102b8cbc9e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 2 11:36:48 2017 -0800

    Some renaming for clarity.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit a918a7074e9f93eac272372fa7fc9849ddf961f0
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Feb 2 11:21:51 2017 -0800

    Some work towards implementing tiling for the Particle Container.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit 2b18516cf891f1a613e1c077611838a5bf2b5e33
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 2 10:52:44 2017 -0800

    add amrex_error_module and call amrex_abort if amrex_mfiter assignment is called

Src/Base/AMReX_error_fi.cpp
Src/Base/AMReX_error_mod.F90
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/F_Interfaces/Base/AMReX_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit f8da60be689898c98d1c05f05adffceb9962f6e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 2 10:14:19 2017 -0800

    define assignment operator for types containing c_ptr

Src/Base/AMReX_parmparse_mod.F90
Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_distromap_mod.F90
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Tutorials/AMR_Adv_CF/Source/fmain.F90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90

commit 9582a62229a77a39963a0dfa38871ea1a87f751b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 1 19:29:02 2017 -0800

    Cleaning up the code a bit with some typedefs.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_Particles.H

commit 5accc7978e088f891672abee59a36258e0bb971a
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 1 19:16:42 2017 -0800

    an iterator for doing tiling with particles and a test.

Tests/Particles/ParticleIterator/GNUmakefile
Tests/Particles/ParticleIterator/Make.package
Tests/Particles/ParticleIterator/main.cpp

commit 75522cc5e984389997749ab416c8756ea6518087
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 1 17:13:42 2017 -0800

    don't need this data structure to store pointers.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H

commit 0d3e6f28defe4a73fc44854c733b97b7ab041dac
Merge: 5e6bccb22 ca7babcd0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 1 17:07:55 2017 -0800

    Merge branch 'development' into fortran_interface

commit ca7babcd0e222bd1685e8639baeb57ea24897820
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 1 17:07:12 2017 -0800

    fix BLBackTrace namespace issue

Src/Base/AMReX_BLBackTrace.H

commit 5e6bccb2249bca3cebdd49bf66e1066839155564
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 1 17:07:12 2017 -0800

    fix BLBackTrace namespace issue

Src/Base/AMReX_BLBackTrace.H

commit 58910c843a438c19e03293aa75c309a1f0fac41f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 1 16:12:32 2017 -0800

    WIP: F_Interfaces/AmrCore

Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H
Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp
Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp
Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90
Src/F_Interfaces/AmrCore/Make.package
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_distromap_mod.F90
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Src/F_Interfaces/Base/AMReX_parallel_mod.F90
Tutorials/AMR_Adv_CF/Exec/Make.Adv
Tutorials/AMR_Adv_CF/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_Adv_CF/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_CF/Source/Make.package
Tutorials/AMR_Adv_CF/Source/fmain.F90
Tutorials/AMR_Adv_CF/Source/fmain.f90
Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90
Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/GNUmakefile

commit 2eb7d1fc2744d72112affdf4123acd8245b92bbf
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Feb 1 16:04:56 2017 -0800

    No longer shift particles silently in add particle / initialization routines.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H

commit 7368263bb9ca8e9528b4cf82d34f6570d1e424f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 1 14:15:22 2017 -0800

    fix HelloWorld_CF

Tools/CompileTesting/compiletesting.py
Tutorials/AMR_Adv_CF/README
Tutorials/HeatEquation_EX1_CF/GNUmakefile
Tutorials/HelloWorld_CF/GNUmakefile
Tutorials/HelloWorld_CF/fmain.f90

commit 28a70d8856458a157812ffc28800a37cd5a51d15
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 31 12:55:28 2017 -0800

    Make communicating SOA data optional.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Tests/Particles/main.cpp

commit a263a5e5f0814872e39b29d032cf0ef65d11b65b
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 31 12:31:06 2017 -0800

    Fix bug in initialization.

Src/Particle/AMReX_ParticleInit.H

commit d713e5d13dfa43119b3c06d07c807d9fdc052417
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 31 12:20:52 2017 -0800

    Don't template on the particle container type. We always use std::vector.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.H

commit 7b4bf85d4c95311d8fb86c69902548334926acaf
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 31 10:25:09 2017 -0800

    Making the SOA particle test use two levels.

Tests/Particles/main.cpp

commit fa47bebcf6b417cdea5adcd8932b76aa7d7ad485
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 30 17:01:22 2017 -0800

    Make this zero by default.

Src/Particle/AMReX_Particles.H

commit 90c97943b4bb0742d7054b2fc9f856169c10c25e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 30 16:45:54 2017 -0800

    Use zero SoA attributes by default.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Tests/Particles/main.cpp
Tests/Particles/test.py

commit d8dc1b9807319faa19347eb6331d00d5708991f7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Mon Jan 30 15:54:07 2017 -0800

    Implementing MPI communication of struct-of-array style particle data and adding a test.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Tests/Particles/GNUmakefile
Tests/Particles/Make.package
Tests/Particles/main.cpp
Tests/Particles/test.py

commit 0b7b9242a56e507050fb7321b385f550b608a943
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 30 14:54:28 2017 -0800

    add --always to git describe as fallback.  some codes may not have tags

Tools/C_scripts/makebuildinfo_C.py

commit c1c6ddd6d44e3a1c23292d8d7177320671ac2de9
Merge: 6b20b325a 6a0622405
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 30 10:33:33 2017 -0800

    Merge branch 'fortran_interface' into development

commit 6a0622405ef62338ee4a1258698410313a7e4ee7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 30 10:32:44 2017 -0800

    set pointer to null after being deleted

Src/F_Interfaces/Base/AMReX_geometry_mod.F90

commit baf070fc95b41c08d5324185341b419b87cad9ca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 30 10:20:10 2017 -0800

    fix gfortran macro

Src/Base/AMReX_parmparse_mod.F90
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_distromap_mod.F90
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 6b20b325a515bf4ae80a3aaf6d0cee25feb3b2d8
Merge: f7e5f72aa 9bf35516a
Author: Michael  Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jan 30 15:40:03 2017 +0000

    Merged in mzingale/amrex/development (pull request #7)
    
    some updates to the Fortran commandline tools

commit 9bf35516aafe7cbfa5225ee1a8303ad1976bb2a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 29 12:01:36 2017 -0500

    extend the `-v` option to take a string of space-separated variable
    to allow for outputing a specific set of variables.  Previously
    it only allowed for a single variable.

Tools/Postprocessing/F_Src/fextract.f90

commit 49becefdce77733efa5ec0477cf698961a5ac96e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 29 12:01:25 2017 -0500

    also output the % of domain covered

Tools/Postprocessing/F_Src/fboxinfo.f90

commit c5649f8d875da8be5ca16ec77606b31e299ab93e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 28 15:37:59 2017 -0800

    add contiguous to Fortran pointers

Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit f7e5f72aadb375d2b872d37bee925bd7240190ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 28 12:54:55 2017 -0800

    clean up

Src/F_Interfaces/Base/AMReX_parallel_fi.cpp
Src/F_Interfaces/Base/Make.package

commit f6798d346ebcf56414caa04509a6cb04404833dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 28 12:50:49 2017 -0800

    add DistributionMapping fortran wrapper

Src/F_Interfaces/Base/AMReX_distromap_fi.cpp
Src/F_Interfaces/Base/AMReX_distromap_mod.F90

commit e434e688e8edc19e60f634d41635683b38867b9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 28 12:48:33 2017 -0800

    forgot to check in a new file

Src/Base/AMReX_omp_mod.F90

commit 27fee08a04a53c427618968b1ab24f2d4ca7694f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 28 12:45:35 2017 -0800

    remove deprecated threadbox.f90

Src/Base/AMReX_threadbox.f90
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 8760d7171a6ff6697d8c3681b6be62d1ed16b36c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 28 12:43:13 2017 -0800

    change the way of passing a c null char array because pgi didn't like it

Src/Base/AMReX_parmparse_mod.F90
Src/Base/AMReX_string_mod.F90

commit e69b28293cd720fee22ee373356bc9a753a8b674
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 28 12:11:00 2017 -0800

    fix macro around final and add destroy calls

Src/Base/AMReX_parmparse_mod.F90
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Tutorials/HeatEquation_EX1_CF/advance.f90
Tutorials/HeatEquation_EX1_CF/fmain.f90
Tutorials/HeatEquation_EX1_CF/init_phi.f90

commit 0666bd6ca6139fe320ca88642ec03eb0445338fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 28 10:41:16 2017 -0800

    turn on finalize for gfortran > 4

Src/Base/AMReX_parmparse_mod.F90
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90

commit 75316f583701b77a59df78931bdf773101aa8147
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 28 10:35:02 2017 -0800

    make F_Interfaces compile again in AMReX

Src/Base/AMReX.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_parmparse_mod.F90
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/F_Interfaces/Base/AMReX_box_mod.F90
Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp
Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_geometry_fi.cpp
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Src/F_Interfaces/Base/AMReX_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Src/F_Interfaces/Base/AMReX_omp_mod.F90
Src/F_Interfaces/Base/AMReX_parallel_fi.cpp
Src/F_Interfaces/Base/AMReX_parallel_mod.F90
Src/F_Interfaces/Base/Make.package
Tutorials/HeatEquation_EX1_CF/GNUmakefile
Tutorials/HeatEquation_EX1_CF/advance.f90
Tutorials/HeatEquation_EX1_CF/fmain.f90
Tutorials/HeatEquation_EX1_CF/init_phi.f90

commit 786e602479a4db3fcfd8f3f81378e755bccd99f8
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 27 22:12:52 2017 -0800

    Provide a more convenient API for working with the new particle class.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit 65bc6900e892335ffe493f2c5c6122f5bd419a81
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 27 16:42:31 2017 -0800

    Splitting the implementation of the particle and particle container classes into seperate files.

Src/Particle/AMReX_ParticleContainerI.H
Src/Particle/AMReX_ParticleI.H
Src/Particle/AMReX_Particles.H
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit eee84c6d71c940bfa2b6ea7508054c69c79ecbe4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 27 16:23:17 2017 -0800

    Removing the full_where option - making this always true.

Src/Particle/AMReX_Particles.H

commit 24db11bc566973aab03672180ac62ca5a544f2f7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 27 16:06:40 2017 -0800

    Remove where_already_called option, since the particles no longer store their cell / level / grid data.

Src/Particle/AMReX_Particles.H

commit 298929198f999b3f287689ce82fb7aa1dd329649
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 27 15:27:40 2017 -0800

    This version gets the same test results as before the refactor, in parallel and on multiple levels.

Src/Particle/AMReX_Particles.H

commit 44c7376d3ebaf88953cf99d20bd940a9a41291d6
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 27 15:15:24 2017 -0800

    make sure to call Where in MoveKick

Src/Particle/AMReX_Particles.H

commit 9bef64a82207cfbe17baf57fb06fb02d6ef80711
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 27 13:00:57 2017 -0800

    Fix bug I just introduced into the MPI communication code.

Src/Particle/AMReX_Particles.H

commit 6f70f3034d3646abb1435d327202b510928ad1ce
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 27 12:40:48 2017 -0800

    Getting rid of the extra arrays in the particle struct.

Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit 1102cd484132207bf57d027a3a47459ef025311a
Merge: 167bdb4c8 634792844
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 27 12:32:45 2017 -0800

    Merge branch 'development' into fortran_interface
    
    Conflicts:
            Src/Amr/AMReX_extrapolater_1d.f90
            Src/Amr/AMReX_extrapolater_2d.f90
            Src/Amr/AMReX_extrapolater_3d.f90
            Src/Base/AMReX_BaseFab_nd.f90
            Src/Base/AMReX_MultiFabUtil_1d.f90
            Src/Base/AMReX_MultiFabUtil_2d.f90
            Src/Base/AMReX_MultiFabUtil_3d.f90
            Src/Base/AMReX_fort_mod.F90
            Src/Base/AMReX_mempool_f.f90
            Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90
            Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90

commit 634792844da4f48e88d9fc994ce60a0cddc1694b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 27 10:34:05 2017 -0800

    migration doc

Docs/Migration/Migration.md

commit 3156c47dbc938c724215827fbec8e621a9360471
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Jan 27 09:47:05 2017 -0800

    Making Particle a POD type.

Src/Particle/AMReX_Particles.H

commit 08681206f872c94685a8c2bd3adc8fa70f630de8
Merge: 88b3b2b01 efca85699
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 26 20:41:31 2017 -0800

    merging.

commit 88b3b2b01bdc613eb22e15c4c250cd47a066ab10
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 26 20:33:17 2017 -0800

    Removing the lev, grid, and cell attributes from the particle class - compute these on the fly instead.

Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit 2e78c3a574ddd681f28978db0aa78cbe5d631b5e
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 26 18:02:36 2017 -0800

    New version of stencil test, stenciTestMSD.cpp that takes a flag compute_geom to either compute or read EB info

Tests/GeometryShop/stencilTestbed/exec/GNUmakefile
Tests/GeometryShop/stencilTestbed/exec/sphere.inputs
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp

commit 1e12306c6dd7722eeeae81251cb1eef0686f12e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 26 16:02:54 2017 -0800

    Real --> amrex::Real

MiniApps/MultiGrid_C/COEF_F.H
MiniApps/MultiGrid_C/RHS_F.H
MiniApps/PGAS_SMC/SMC.H
MiniApps/PGAS_SMC/SMC_F.H
Src/Amr/AMReX_Derive.H
Src/Amr/AMReX_Extrapolater.cpp
Src/Amr/AMReX_MAKESLICE_F.H
Src/Amr/AMReX_PROB_AMR_F.H
Src/Amr/AMReX_SLABSTAT_F.H
Src/Amr/AMReX_SlabStat.H
Src/Amr/AMReX_extrapolater_1d.f90
Src/Amr/AMReX_extrapolater_2d.f90
Src/Amr/AMReX_extrapolater_3d.f90
Src/AmrCore/AMReX_ErrorList.H
Src/AmrCore/AMReX_FLUXREG_F.H
Src/AmrCore/AMReX_INTERP_F.H
Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.f90
Src/Base/AMReX_COORDSYS_F.H
Src/Base/AMReX_MemPool.H
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_REAL.H
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_bl_fort_module.F90
Src/Base/AMReX_fort_mod.F90
Src/Base/AMReX_mempool_f.f90
Src/Base/AMReX_parmparse_fi.cpp
Src/Base/AMReX_parmparse_mod.F90
Src/Base/AMReX_string_mod.F90
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/Boundary/AMReX_INTERPBNDRYDATA_F.H
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/F_BaseLib/MultiFab_C_F.H
Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H
Src/LinearSolvers/C_CellMG/AMReX_LO_F.H
Src/LinearSolvers/C_CellMG/AMReX_LP_F.H
Src/LinearSolvers/C_CellMG/AMReX_MG_F.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H
Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/Particle/AMReX_Particles_F.H
Tests/LinearSolvers/C_CellMG/COEF_F.H
Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H
Tests/LinearSolvers/C_CellMG/MacOpMacDrivers.H
Tests/LinearSolvers/C_CellMG/MacOperator.H
Tests/LinearSolvers/C_TensorMG/main_F.H
Tests/LinearSolvers/ComparisonTest/COEF_F.H
Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H
Tools/C_util/Convergence/AVGDOWN_F.H
Tools/C_util/Statistics/AVGDOWN_F.H
Tutorials/AMR_Adv_C/Source/Adv.H
Tutorials/AMR_Adv_C/Source/Adv_F.H
Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdvBC.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H
Tutorials/HeatEquation_EX1_C/myfunc_F.H
Tutorials/HeatEquation_EX1_C/writePlotFile.H
Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90
Tutorials/HeatEquation_EX2_C/myfunc_F.H
Tutorials/HeatEquation_EX2_C/writePlotFile.H
Tutorials/MultiGrid_C/COEF_F.H
Tutorials/MultiGrid_C/RHS_F.H

commit 167bdb4c8995ffee8a8df998b53a8d55d73d267c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 26 13:31:12 2017 -0800

    more renaming

Src/F_Interfaces/Base/AMReX_boxarray_mod.F90
Src/F_Interfaces/Base/AMReX_boxlib_mod.F90
Src/F_Interfaces/Base/AMReX_fi_main.cpp
Src/F_Interfaces/Base/AMReX_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_mod.F90
Src/F_Interfaces/Base/Make.package

commit a8333b58cb5c19e4a2c57d970671d2a650e03c85
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 26 13:14:33 2017 -0800

    Fix error in template instantiation.

Src/Particle/AMReX_Particles.H

commit 112b26826253a63755cccc787f46ae3a1ffae855
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 26 13:12:16 2017 -0800

    F_Interfaces/BaseLib --> F_Interfaces/Base for consistence

Src/F_Interfaces/Base/AMReX_box_mod.F90
Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp
Src/F_Interfaces/Base/AMReX_boxlib_mod.F90
Src/F_Interfaces/Base/AMReX_fi_main.cpp
Src/F_Interfaces/Base/AMReX_geometry_fi.cpp
Src/F_Interfaces/Base/AMReX_geometry_mod.F90
Src/F_Interfaces/Base/AMReX_multifab_fi.cpp
Src/F_Interfaces/Base/AMReX_omp_mod.F90
Src/F_Interfaces/Base/AMReX_parallel_fi.cpp
Src/F_Interfaces/Base/AMReX_parallel_mod.F90
Src/F_Interfaces/Base/Make.package

commit deac4bab0b001e3e750e6ed0f7c2f62396b2363b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 26 13:11:09 2017 -0800

    add AMReX prefix

Src/F_Interfaces/BaseLib/AMReX_box_mod.F90
Src/F_Interfaces/BaseLib/AMReX_boxarray_fi.cpp
Src/F_Interfaces/BaseLib/AMReX_boxlib_mod.F90
Src/F_Interfaces/BaseLib/AMReX_fi_main.cpp
Src/F_Interfaces/BaseLib/AMReX_geometry_fi.cpp
Src/F_Interfaces/BaseLib/AMReX_geometry_mod.F90
Src/F_Interfaces/BaseLib/AMReX_multifab_fi.cpp
Src/F_Interfaces/BaseLib/AMReX_omp_mod.F90
Src/F_Interfaces/BaseLib/AMReX_parallel_fi.cpp
Src/F_Interfaces/BaseLib/AMReX_parallel_mod.F90
Src/F_Interfaces/BaseLib/Make.package
Src/F_Interfaces/BaseLib/boxarray_mod.f90
Src/F_Interfaces/BaseLib/multifab_mod.f90

commit 9f6e4b59cee44f80b4e860dd229f7ed5b65daac8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 26 12:59:17 2017 -0800

    no longer need bl_space_module

Src/F_Interfaces/BaseLib/Make.package
Src/F_Interfaces/BaseLib/bl_space_mod.F90

commit 5ca90f7a1f51fc34bb24dd8e2692c2263661f269
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 26 12:58:13 2017 -0800

    bl_fort_module --> amrex_fort_module

Src/Amr/AMReX_extrapolater_1d.f90
Src/Amr/AMReX_extrapolater_2d.f90
Src/Amr/AMReX_extrapolater_3d.f90
Src/Base/AMReX_BaseFab_nd.f90
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_fort_mod.F90
Src/Base/AMReX_mempool_f.f90
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90
Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90

commit 975e6198bff5da6b631aafc7bb99471fbec87d08
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 26 12:46:45 2017 -0800

    rm parparse from F_Interfaces because they are now in Base

Src/F_Interfaces/BaseLib/Make.package
Src/F_Interfaces/BaseLib/parmparse_fi.cpp
Src/F_Interfaces/BaseLib/parmparse_mod.f90
Src/F_Interfaces/BaseLib/string_mod.f90

commit 0dccefa3c6fcb5bacfa5ff44f23bef15590f2770
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 26 12:39:04 2017 -0800

    add parmparse to Fortran

Src/Base/AMReX_parmparse_fi.cpp
Src/Base/AMReX_parmparse_mod.F90
Src/Base/AMReX_string_mod.F90
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 9648c4111d35c916e2057edc2e6d352d7e10a671
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Thu Jan 26 12:22:09 2017 -0800

    Precompute the inverse cell spacing for particle binning.

Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_Geometry.cpp
Src/Particle/AMReX_Particles.H

commit efca85699bba03c7c4b6c8f283cbd68ca214214e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 26 09:45:00 2017 -0800

    reorder data layout

Src/Particle/AMReX_Particles.H

commit 1ca8d111c029e3ff34f804abcf625eb0639cc80c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 25 21:13:18 2017 -0800

    fix some tests

Tests/C_BaseLib/tVisMF.cpp
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp

commit 88c8ec9c47ee2d2e5ed5941b654012ebccbed09b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 25 21:04:49 2017 -0800

    replace the timer using gettimeofday with C++ timer

Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Tutorials/HelloWorld_C/main.cpp

commit da215ae2a7b4f730f90396c19bfc900241446985
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 25 16:19:40 2017 -0800

    use constexpr and get rid of if in IntVect::shift_hasher

Src/Base/AMReX_IntVect.H
Src/Base/AMReX_Utility.H

commit 4a71a5110afadbff1ffa78f916dcdbfe2790da44
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jan 25 14:54:45 2017 -0800

    use a typedef to save typing

Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H

commit b550d21702f69e2a070f5e62ebf1c5e5a48425d7
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Wed Jan 25 14:37:19 2017 -0800

    Begin refactor of Particle classes.

Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_Particles.cpp
Src/Particle/AMReX_TracerParticles.cpp
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit ba2580c179c6d98f007d8d0e5abde69ae0fb1730
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 25 14:10:56 2017 -0800

    remove WIN32 macro

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
Src/Base/AMReX.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FPC.cpp
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/timer_c.c
Tests/C_BaseLib/tCArena.cpp
Tests/LinearSolvers/C_TensorMG/testVI.cpp
Tools/CMake/CCSEConfigReport.cmake
Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp
Tools/C_util/ViewMF/MFNorm.cpp
Tools/C_util/ViewMF/checkMFghostcells.cpp
Tools/C_util/ViewMF/main.cpp
Tools/C_util/ViewMF/mfMinMax.cpp
Tools/C_util/ViewMF/viewMF.cpp
Tools/C_util/ViewMF/viewMFcol.cpp
Tools/C_util/ViewMF/viewMFdiffHardWire.cpp
Tools/C_util/WritePlotFile.cpp
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/timer_c.c
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp
Tutorials/MultiFabTests_C/GridMoveTest.cpp
Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp

commit 553fc33e7bbcf2baab0fb8457ae5dc05dbb5a731
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 25 13:49:27 2017 -0800

    remove BL_USE_SETBUF macro

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
Src/Amr/AMReX_Amr.cpp
Src/Base/AMReX_VisMF.cpp
Src/Extern/amrdata/AMReX_AmrData.cpp
Tools/CMake/CCSEOptions.cmake
Tools/C_util/WritePlotFile.cpp
Tools/C_util/dbgTools/crsGrids.cpp
Tools/C_util/dbgTools/intersectGrids.cpp
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp
Tutorials/MultiFabTests_C/GridMoveTest.cpp
Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp

commit 603edd9d2a08cff465169b1035537f8378ecd5ab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 25 12:26:57 2017 -0800

    fix some util tools

Tools/C_util/Convergence/DiffSameDomainRefined.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp

commit 209167abb052c6fa3d0f88d86159d8bc63fd0748
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 24 17:00:12 2017 -0800

    Porting changes to regression test suite forward from BoxLib.

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py

commit fcd6cedbb42ed24c025f968f44b25f4de5cfa02b
Merge: 6096bdf0c 82fa46778
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 23 12:12:17 2017 -0800

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit dda199301eb7d74edbe5b90501770b87940b443a
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jan 23 11:54:47 2017 -0800

    Add access to tileindex in MFIter and use that to cache EB data in stencil test code.

Src/Base/AMReX_FabArray.H
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90

commit 82fa46778526b1969626f1b1d1280236a34b832c
Author: tannguyen <tannguyen@tannguyens-MacBook-Pro.local>
Date:   Sat Jan 21 23:50:15 2017 -0800

    add some more comments

Src/Amr/AMReX_AuxBoundaryData.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BoxArray.H
Src/Boundary/AMReX_BndryData.H
Src/Boundary/AMReX_BndryRegister.H

commit 4ee004f3f18f6011154b65088b02fa1682e19ddb
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Jan 21 22:48:56 2017 -0800

    fix doxygen comments

Src/Amr/AMReX_AuxBoundaryData.H
Src/Base/AMReX_BoxArray.H

commit b3ed2e880be7a0b3513f99db0285b925256bcbf8
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sat Jan 21 22:40:52 2017 -0800

    hide the description of some internal classes

Src/Amr/AMReX_AuxBoundaryData.H
Src/Base/AMReX_BoxArray.H

commit 8e640f341d926962c8fb1877e8ce5918b393a783
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jan 20 18:45:03 2017 -0800

    More minor cleaning of stencil testBench

Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90
Tests/GeometryShop/stencilTestbed/src/AMReX_AggStencilI.H

commit 3d6428e1db97d72dea11e02e8eb0384927096c76
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jan 20 14:27:06 2017 -0800

    Make boundary treatment the same for all the different forms of the stencil operator in the stencelTests

Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp

commit 344e453e1d7969e4b30762150e5fbc71304f3988
Merge: b93233a15 3eb28eced
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jan 20 13:55:03 2017 -0800

    Merge branch 'dtg_branch' of bitbucket.org:berkeleylab/amrex into dtg_branch

commit b93233a154015580a28cd76ebe781195a0c651bf
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jan 20 13:54:50 2017 -0800

    Fix a bug in the irregular stencils for the stencil tests

Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90

commit 3eb28eced9825fc6aefc02047e6d65d8ed4a7596
Merge: 8f6a69575 002bac56f
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Jan 20 12:35:14 2017 -0800

    Merge branch 'development' into dtg_branch

commit 8f6a6957581dd55e8dc2469e736fd95be6092314
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Jan 20 12:34:16 2017 -0800

    added counts

Tests/GeometryShop/stencilTestbed/src/AMReX_AggStencilI.H

commit ebf3fbfe77e5eed3041b0f41713b55f77ff10444
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jan 20 11:11:32 2017 -0800

    Fix up fortran-only stencils in stencil testbed, add nontrivial initial data.

Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H

commit f93494fab7b063fba0e26a2fcdacdfa874fdaddf
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jan 20 10:07:19 2017 -0800

    Remove div by kappa in fortran-only Laplace stencil test.  Minor reformatting.

Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H
Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp

commit c5100ee4cf4c4cfcbff125c14a7c94d8947902c3
Merge: 6dba31f49 ac782e1a1
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 19 20:24:54 2017 -0800

    Merge branch 'dtg_branch' of bitbucket.org:berkeleylab/amrex into dtg_branch

commit 6dba31f498908ab0e7bcc01f736c2021f5b01233
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 19 20:23:55 2017 -0800

    Add Fortran-only version to stencilTest, add some timers... still need to confirm correctness

Tests/GeometryShop/stencilTestbed/exec/GNUmakefile
Tests/GeometryShop/stencilTestbed/exec/Make.package
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90
Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H
Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp

commit 002bac56f7864d70396ba2d7ac860e8b1abce1b3
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Jan 19 19:17:29 2017 -0800

    fix hash func

Src/Base/AMReX_IntVect.H

commit ac782e1a170dfb0851c90aec3affe35124f17c09
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Jan 19 15:52:27 2017 -0800

    ported the regular-kitty-corner-to-covered fix from Pele

Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp

commit d23cb07e63cda8973e65b044369d9bd1ffac6688
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Jan 19 12:32:43 2017 -0800

    hash boxArray

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_IntVect.H

commit d11e68d1b4e54b599390db0667872c897f34c606
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Jan 19 09:53:08 2017 -0800

    bug fix for bug found by Marc

Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp

commit 6096bdf0ca3c2dabda40004bb3e2e362c30bd296
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 18 10:48:39 2017 -0800

    use some C++11 headers and remove some Windows stuff

Src/Base/AMReX.H
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/Extern/amrdata/AMReX_AmrvisConstants.H
Src/F_BaseLib/backtrace_c.cpp
Src/F_BaseLib/f2kgetcl.c

commit 613c04945f47cbc8e13a3ef5ad735755cd7378c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 18 08:57:40 2017 -0800

    add -P to cpp

Tools/GNUMake/Make.rules

commit 650988cb17e2cd01c57d729a8b3923cbb2b88bd8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 17 13:46:19 2017 -0800

    save cpp'd headers containing C binding of Fortran function

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit fcda9b6aa0481b63ff6c936e4d85b31a045011ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 17 12:45:09 2017 -0800

    typo

Src/Base/Make.package

commit dbc907c2c7e9806962b785b9d4213e5733be332e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 17 12:44:13 2017 -0800

    start to tweak the make sytem for fortran call checking

Src/Base/Make.package
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules

commit 0c4e01afa1b56c855761cf5b4d1be76735ae7dcd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 13 16:03:38 2017 -0800

    add a function AmrData to return Distribution Map

Src/Extern/amrdata/AMReX_AmrData.H

commit 877f7219bf9470d1ba84d72d328197d4d6586c8e
Merge: 887ffb391 0911d7f1f
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Fri Jan 13 15:33:36 2017 -0800

    Merged in mzingale/amrex/development (pull request #6)
    
    switch from a hash to describe --tags --dirty

commit 0911d7f1f1c914b71403326d0c601f2a41b76199
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jan 13 18:05:32 2017 -0500

    switch from a hash to describe --tags --dirty to get a more complete
    picture of the state

Tools/C_scripts/makebuildinfo_C.py

commit 887ffb391c62b212b79e4c561f8b8b41f974afd5
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Jan 13 14:08:39 2017 -0800

    fix comments in AMReX_Print.H

Src/Base/AMReX_Print.H

commit 062bb1508af1527ed3af1bbe01844661f93bab5e
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Jan 13 13:56:44 2017 -0800

    add some more comments

Src/Amr/AMReX_Amr.H
Src/AmrCore/AMReX_AmrCore.H
Src/Base/AMReX_Print.H

commit 0b718401826c88b70ed1a064d5581e5ebf4577e3
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Fri Jan 13 00:22:25 2017 -0800

    add more comments in AMReX_FabArray.H

Src/Base/AMReX_FabArray.H

commit 0ab27c3f31ff192d7049c34fc22dde0dfd20f48d
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Jan 12 21:13:30 2017 -0800

    fix a comment

Src/Base/AMReX_FabArray.H

commit 35e8972126fe37fb731580bb045db8320f287565
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Thu Jan 12 19:03:53 2017 -0800

    add comments to functions in AMReX_FabArray.H

Src/Base/AMReX_FabArray.H

commit 3a7c6244abac1b4e148dee5f70060b84321c776c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jan 12 12:44:57 2017 -0500

    switch to unicode by default, since some source files have unicode characters

Tools/F_scripts/dep.py

commit 452702ac8efbc0d943df35fba54124b011215bae
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Jan 11 16:51:06 2017 -0800

    stencil test bed is complete and seems to work for the four cases I have programmed

Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H
Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp
Tests/GeometryShop/stencilTestbed/src/Make.package
Tests/GeometryShop/stencilTestbed/src/lapl_nd.F90
Tests/GeometryShop/stencilTestbed/src/lapl_nd_F.H

commit 073a73846fe3e4608a30b4f7118c586e49e087f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 11 13:28:50 2017 -0800

    add amrex::AllPrint() to save some typing

Src/Base/AMReX_Print.H
Tutorials/HelloWorld_C/main.cpp

commit 3c57b7dbbde231fbe7b9b06c660cc6128f520e94
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Jan 11 11:27:08 2017 -0800

    trying to keep up with the development branch

Src/GeometryShop/AMReX_IntVectSet.H

commit 044a3c9ed654649cabfe95b267b02012d905c40a
Merge: 7d4e7d466 ba0e1919a
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Jan 11 11:22:51 2017 -0800

    Merge branch 'development' into dtg_branch

commit 7d4e7d4668b08f55b6bf3a2e19e348ef5448f8bd
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Jan 11 11:19:33 2017 -0800

    added some files to make.package

Src/GeometryShop/Make.package

commit 14bdcdd246d9b6514bd63e8fd5cd811c5cff90ff
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Jan 11 11:16:08 2017 -0800

    The AggSten everywhere example works now.   On to figuring out how to get AMReX to call fortran

Tests/GeometryShop/stencilTestbed/exec/sphere.inputs
Tests/GeometryShop/stencilTestbed/src/#AMReX_FaceIndex.H#
Tests/GeometryShop/stencilTestbed/src/AMReX_AggStencil.H
Tests/GeometryShop/stencilTestbed/src/AMReX_AggStencilI.H
Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H
Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp

commit ba0e1919ac8e351afd1cda3c92d5cf4ea5292cf3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 16:17:06 2017 -0800

    minor

Src/Base/AMReX_mempool_f.f90

commit 6af03daad2281c00a1d313f7cc8e8a48f9b7a746
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 16:16:00 2017 -0800

    don't have bl_fort_module for Fortran build

Src/Base/AMReX_mempool_f.f90

commit 07a8b0809fd0e8600b42045cca12b5f46ab3ba6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 16:03:25 2017 -0800

    some double precision --> real(c_real)

Src/Amr/AMReX_Extrapolater.cpp
Src/Amr/AMReX_extrapolater_1d.f90
Src/Amr/AMReX_extrapolater_2d.f90
Src/Amr/AMReX_extrapolater_3d.f90
Src/Base/AMReX_MemPool.H
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_mempool_f.f90
Src/F_BaseLib/fab.f90
Src/Particle/AMReX_Particles.H

commit 72cb7ebd4c4971a85bdae0496d467f239c159e53
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Jan 10 16:00:29 2017 -0800

    put initialize and bl_profile_start/stop calls into test so we can get stats

Tests/GeometryShop/stencilTestbed/exec/GNUmakefile
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp

commit 751e6dd6d715a5b6f3d4d1955d509c29dc9d6f23
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Jan 10 15:16:08 2017 -0800

    simplest version of the testbed now runs

Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H
Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.cpp
Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.H
Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.cpp
Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp

commit 1186aefc81c5f0588d8f0ba46f39d51748b776c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 14:56:47 2017 -0800

    std:iota can be used now.

Src/Base/AMReX_FabArray.cpp

commit 1df6d1eb316d8556624f95171d2eb4d145b12b4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 14:46:48 2017 -0800

    removed hack for Cray compiler

Src/Base/AMReX_FArrayBox.cpp

commit c4e43bc8244d24cccaf69074b76f5db7c3c170ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 14:35:12 2017 -0800

    if AMREX_GIT_VERSION is not defined, reutrn Unknown

Src/Base/AMReX.cpp

commit c3be767c8b8cfa7fb18a2ce6c9b3bc97d3f9b6da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 14:26:15 2017 -0800

    add amrex::Version()

Src/Base/AMReX.H
Src/Base/AMReX.cpp
Tools/GNUMake/Make.defs
Tutorials/HelloWorld_C/main.cpp

commit 547329fdfdcf9a51ce7f154c903f05e4aebe5e1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 13:41:35 2017 -0800

    rm BL_USE_ARLIM

Src/Base/AMReX_ArrayLim.H

commit 67422b71ebd8156e8149274eedff95fe1a8b7074
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 12:59:38 2017 -0800

    make_build_info_cpp no longer used

Tools/C_scripts/make_build_info_cpp

commit 10cb06eff33a535956caa761e5d44ef0b9c926f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 12:58:04 2017 -0800

    start to use Print in some places

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AuxBoundaryData.cpp
Src/AmrCore/AMReX_AmrCore.cpp
Src/Base/AMReX.cpp
Src/Base/AMReX_BLPgas.cpp
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxDomain.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.H

commit 1269f2c5d8cea9430cad493d1508f998257f5c7b
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Jan 10 11:22:32 2017 -0800

    got the testbed to compile on this branch

Tests/GeometryShop/stencilTestbed/exec/GNUmakefile
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H
Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.cpp
Tests/GeometryShop/stencilTestbed/src/AMReX_FaceIndex.H
Tests/GeometryShop/stencilTestbed/src/AMReX_FaceIndex.cpp
Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.H
Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.cpp
Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.H
Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp
Tests/GeometryShop/stencilTestbed/src/AMReX_VolIndex.H

commit 570a41b78cbee3cb455324f1bdfe17e95c8b4646
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 11:02:14 2017 -0800

    Revert "Print: change the default to print on all calling processes. To print on IO Process only, do Print(Print::IOProc) << ..."
    
    This reverts commit b5a0461fac5343053d0370a9ac659c6bd39e4126.

Src/Base/AMReX_Print.H
Tutorials/HelloWorld_C/main.cpp

commit b5a0461fac5343053d0370a9ac659c6bd39e4126
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 10:16:05 2017 -0800

    Print: change the default to print on all calling processes. To print on IO Process only, do Print(Print::IOProc) << ...

Src/Base/AMReX_Print.H
Tutorials/HelloWorld_C/main.cpp

commit d0466177c797ea66fb6af660d8b6a6cd4ac5e0b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 09:31:19 2017 -0800

    minor

Src/Particle/AMReX_Particles.H

commit e2f8f317e37ebc11f198e01be01429265bf9d9a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 09:26:13 2017 -0800

    Add amrex::Print.  One can use this to replace
    
      if (ParallelDescriptor::IOProcessor() {
         std::cout << ....;
      }
    
    with
    
      amrex::Print() << ....;
    
    To print on all processes, one can do
    
      amrex::Print(amrex::Print::AllProcs) << ...;
    
    To print on a particular process in a communicator, one can do
    
      amrex::Print(rank_for_print, communicator) << ...;
    
    By default Print uses std::cout.  By it also takes an optional
    std::ostream argument.

Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_Print.H
Src/Base/CMakeLists.txt
Src/Base/Make.package
Tutorials/HelloWorld_C/main.cpp

commit 9ad04f0677844003b2d25f6f879e08469d36428c
Merge: 5ff830e9e 837a31d61
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Jan 9 20:55:44 2017 -0800

    Merge branch 'dtg_branch' of https://bitbucket.org/berkeleylab/amrex into dtg_branch

commit 5ff830e9e8553416fcb7c97ee43c9c034836b8c2
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Jan 9 20:55:14 2017 -0800

    I had the variable names incorrect

Tests/GeometryShop/stencilTestbed/src/Make.package

commit 9aceec28b250c8ff243c45359f9be69de60f0e5b
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Jan 9 20:49:43 2017 -0800

    forgot to add the src directory into the makefile

Tests/GeometryShop/stencilTestbed/exec/GNUmakefile

commit 837a31d61b70006f3f1da3f76f3bc067d1cad61f
Author: Brian VS <bvstraalen@lbl.gov>
Date:   Mon Jan 9 18:17:47 2017 -0800

    needed right std::sqrt

Src/GeometryShop/AMReX_RealVect.H

commit 63a58cfc0b403e36b04094eb0c3d1b799748a6d1
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Jan 9 16:43:06 2017 -0800

    lots of progress on the testbed.  should have it compiling soon.

Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp
Tests/GeometryShop/stencilTestbed/src/#AMReX_FaceIndex.H#
Tests/GeometryShop/stencilTestbed/src/AMReX_BaseIndex.H
Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H
Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.cpp
Tests/GeometryShop/stencilTestbed/src/AMReX_FaceIndex.H
Tests/GeometryShop/stencilTestbed/src/AMReX_FaceIndex.cpp
Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.H
Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.cpp
Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.H
Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp
Tests/GeometryShop/stencilTestbed/src/AMReX_VolIndex.H
Tests/GeometryShop/stencilTestbed/src/AMReX_VolIndex.cpp
Tests/GeometryShop/stencilTestbed/src/Make.package

commit 8bcb720656d9d8856694afa9abb3ea5581fa601f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 9 10:45:19 2017 -0800

    minor

MiniApps/PGAS_SMC/SMC_io.cpp
Src/Amr/AMReX_AmrLevel.cpp
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Tutorials/AMR_Adv_C/Source/main.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/PIC_C/single_level.cpp
Tutorials/PIC_C/two_level.cpp
Tutorials/TwoGrid_PIC_C/main.cpp

commit 8f472a37f61d246efffd8b983144618b96fe77fb
Merge: 57b2b14e9 4b0a24c96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 8 12:31:43 2017 -0800

    Merge branch 'development' into weiqun/development

commit 57b2b14e91ab50bb6d6c11d038947474e2e56891
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 8 12:31:29 2017 -0800

    forward --> move in non-template function

Src/Base/AMReX_MemProfiler.cpp

commit 4b0a24c9602ee31899b6ac8a6cc1f9fe5b88b9e0
Merge: b5dc8f984 f9a653f31
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sun Jan 8 00:20:05 2017 -0800

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit b5dc8f9848ad5c670eea133146cef7fbf6d8a8e6
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sun Jan 8 00:19:31 2017 -0800

    modify comments in BoxArray.H

Src/AmrCore/AMReX_TagBox.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IArrayBox.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.H
Src/F_BaseLib/MemProfiler_f.cpp
Tools/GNUMake/Make.rules

commit 6a486815d4c452d266b42b6d5a7b5b04b8f1d78d
Author: Tan Nguyen <tannguyen@lbl.gov>
Date:   Sun Jan 8 00:11:46 2017 -0800

    modify comments in BoxArray.H

Src/Base/AMReX_BoxArray.H

commit a39d99571d439da770f485c6a1528a481e14d21e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 7 20:27:56 2017 -0800

    removed some Array<unique_pt>

Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BndryRegister.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp

commit b371198da5432a396e8700f35c0276d91a8f0f73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 7 13:04:44 2017 -0800

    explicitly delete some constructors and operator=

Src/Boundary/AMReX_BndryData.H
Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_MacBndry.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H

commit 32fbcd1cb587f14b2bb6e36646202ec5536b27e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 7 12:41:43 2017 -0800

    make Tuple simply a template alias of std:array; add move constructors to FabSet, FluxRegister, BndryRegister, etc.

Src/AmrCore/AMReX_FluxRegister.H
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Tuple.H
Src/Boundary/AMReX_BndryData.H
Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_FabSet.H
Src/Boundary/AMReX_FabSet.cpp
Src/Boundary/AMReX_InterpBndryData.H
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp

commit 4c4e58d8dd5f28810021834ac8df9733d1362f8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 7 10:39:13 2017 -0800

    store MultiMasks in Array

Src/Boundary/AMReX_BndryData.H
Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_MultiMask.H
Src/Boundary/AMReX_MultiMask.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp

commit 63372f9ad042ec5b50d6b28013ccadda07db7732
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 7 08:01:30 2017 -0800

    move constructor for Mask and MultiMask

Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_Mask.cpp
Src/Boundary/AMReX_MultiMask.H

commit f9a653f310d9a04fdbfad5250eac25a885f2bffc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 21:31:42 2017 -0800

    F_BaseLib: fix memory profiling by add using namespace amrex

Src/F_BaseLib/MemProfiler_f.cpp

commit e44c8838ba1f78aa0860ef7813f400d3cd5981b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 17:22:55 2017 -0800

    minor

Src/Base/AMReX_BaseFab.H

commit 830fd8496afd95299858841df76764fd12db916e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 17:13:45 2017 -0800

    add noexcept

Src/Base/AMReX_FabArray.H

commit d28fe6462a0d21f822f2d32a3fc7b641e97803fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 17:04:10 2017 -0800

    add noexcept

Src/AmrCore/AMReX_TagBox.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_IArrayBox.H

commit 6871a060bd0ac1d16f199dc463feab29f6516f37
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 17:02:33 2017 -0800

    add move constructor to MultiFab, iMultiFab, and TagBoxArray

Src/AmrCore/AMReX_TagBox.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_iMultiFab.H

commit 4aaf772eb3aa20c41da1ea4034aec061a492b7ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 16:50:45 2017 -0800

    move constructor for FabArray

Src/Base/AMReX_FabArray.H

commit d1c1922d77ae2e394de54aa0b77966fef4862806
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Fri Jan 6 16:31:07 2017 -0800

    made some slow progress on the testbed

Tests/GeometryShop/stencilTestbed/exec/GNUmakefile
Tests/GeometryShop/stencilTestbed/exec/Make.package
Tests/GeometryShop/stencilTestbed/exec/sphere.inputs
Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp

commit 0445fef74d2652410021dafbfd53ede54183bb1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 15:47:28 2017 -0800

    move constructor for FArrayBox, IArrayBox, and TagBox

Src/AmrCore/AMReX_TagBox.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IArrayBox.cpp

commit 9ff8738dada39b6cd6bc71ca89ee6f692629f6a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 15:30:22 2017 -0800

    BaseFab: add move constructor

Src/Base/AMReX_BaseFab.H

commit 5cbffc50ab946179b760002498b932ed3fb1ebf0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 15:23:14 2017 -0800

    add a BARef constructor taking a single Box

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit 5b118cfe14b0097441bf4044dd64b4178519373d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 15:17:18 2017 -0800

    add explicit to a BoxList ctor taking a single Box, and tidy

Src/Base/AMReX_BoxList.H

commit 56a3de456d4b4ec642bbf5dd975aa1fc8f0ad360
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 15:10:15 2017 -0800

    remove Geometry's copy ctor and dtor to let compilers auto-generate copy and move constructors.

Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp

commit 8dc5518a2e3bbb71471af8d90f402316b6891653
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 15:08:56 2017 -0800

    remove the do-nothing ~CoordSys so that compilers will auto-generate copy and move constructors.

Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp

commit a682ca10938519b23ffc9ac91da56a1c904287e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 14:59:16 2017 -0800

    minor

Tools/GNUMake/Make.rules

commit 6ed9bf87f64ead40e112247dfef47e62fa126a28
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 14:54:17 2017 -0800

    comments on make

Tools/GNUMake/Make.rules

commit 709b31f3d2445051ca06be651bd2d66b3e3a4e6f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 12:50:55 2017 -0800

    change due to IntVect operator<= change

Src/Base/AMReX_BoxArray.cpp

commit f20c924c3c7c04f205033ed56969c54f0cd434db
Merge: 51ddd3039 9826741d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 11:45:47 2017 -0800

    Merge branch 'weiqun/development' of bitbucket.org:WeiqunZhang/amrex into weiqun/development
    
    Conflicts:
            Src/Base/AMReX_Box.cpp

commit 51ddd3039d29045943ec122c5bbb7be0dadebced
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 11:09:09 2017 -0800

    Change the behavior of IntVect::operator< and >.  They now do
    lexicographical comparisons that are suitable for STL.  The per
    component comparison is now done by IntVec::allLT, allLE, allGT, and
    allGE.  We have also removed IntVect::Compare, IntVect::lexLT, and
    IntVect::lexGT for simplicity.

Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp
Src/Particle/AMReX_Particles.H
Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp

commit 9826741d9c6d056de644be4f7c0072dad30bdcf8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 6 11:09:09 2017 -0800

    Change the behavior of IntVect::operator< and >.  They now do
    lexicographical comparisons that are suitable for STL.  The per
    component comparison is now done by IntVec::allLT, allLE, allGT, and
    allGE.  We have also removed IntVect::Compare, IntVect::lexLT, and
    IntVect::lexGT for simplicity.

Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp
Src/Particle/AMReX_Particles.H
Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp

commit 2891e66f727f91d4ff46e73d2097239f8bc3bcc4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 5 16:29:39 2017 -0800

    migration doc

Docs/Migration/Migration.md

commit 177c72624a14da7c7e1ea2ee686ae77f0aedc6d7
Merge: 5bf0d0df9 7de1eb76d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 5 15:25:49 2017 -0800

    Merge branch 'development' into weiqun/development
    
    Conflicts:
            Src/Amr/AMReX_Amr.H
            Src/Amr/AMReX_AmrLevel.H
            Src/Base/AMReX_BoxArray.H
            Src/Base/AMReX_DistributionMapping.H
            Src/Base/AMReX_PList.H
            Src/Base/AMReX_Pointers.H
            Src/Base/AMReX_UseCount.H

commit 5bf0d0df966640e9448166bb31b415fc2f3a2a7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 5 13:48:21 2017 -0800

    rm PList

Src/Base/AMReX_PList.H
Src/Base/CMakeLists.txt

commit 5cddb6f831e34716ec7c93c2dfed33023ebb27c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 5 13:45:43 2017 -0800

    rm UseCount

Src/Base/AMReX_UseCount.H
Src/Base/AMReX_UseCount.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package

commit 31f16a7928663b6cdd22c3cc9ad77a2142b2e537
Merge: 8b764a3e5 7de1eb76d
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Jan 5 10:16:59 2017 -0800

    Merge branch 'development' into dtg_branch

commit 7de1eb76db7136a8c62cd1caab4ba92b6dd620d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 5 08:42:48 2017 -0800

    CompileTesting: Change the default to running a small set of tests; add --full for running the full testing.

Tools/CompileTesting/compiletesting.py

commit 50f15baad9515938776392bfca58c68c7818c30f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 22:12:23 2017 -0800

    add a compile testing script

Tools/CompileTesting/compiletesting.py

commit d4d471c214f6b3f02939751ae42f978df93ab742
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 21:49:43 2017 -0800

    fix comment line

Src/Amr/AMReX_AmrLevel.H

commit e151382b5bf8c1552699918ec52cc875ac0a05b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 21:48:34 2017 -0800

    revert AMReX_iMultiFab.H

Src/Base/AMReX_iMultiFab.H

commit b8851dff629a658b83c01f7416c405f2d8fb06a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 21:46:41 2017 -0800

    remove a duplicated line

Src/Base/AMReX_BaseFab.H

commit e3a78890dbecd97f645eb3cad50db3408aa5494b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 21:43:52 2017 -0800

    fix comment line

Src/Base/AMReX_Pointers.H

commit 7beb273d1dfeeecfeef34a943e4ff3c0ed872472
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 21:40:54 2017 -0800

    Too hard to fix. I am just going to revert to back to a working vesion.  The lost works are comments

Src/Base/AMReX_FabArray.H

commit a47703ee2357fb08c12584ab44eb7d084726233e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 21:32:41 2017 -0800

    fix more merge problems

Src/Base/AMReX_DistributionMapping.H

commit 0d272890be84d1c79e5df7154a2f7ea17c2098d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 21:07:46 2017 -0800

    fix more merge problems

Src/Base/AMReX_DistributionMapping.H

commit b863afebe6b3717cf0c78715a186410c44180153
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 20:41:07 2017 -0800

    fix conflicts from previous merge

Src/Base/AMReX_Box.H
Src/Base/AMReX_FPC.H
Src/Base/AMReX_MultiFab.H

commit 903bf44c20a3e4af4c63686014b689707d6b140d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 20:28:36 2017 -0800

    MultiFab.H no longer exists

Src/Base/MultiFab.H

commit ff07516343a40e9cc426874c4ad61ce669347af9
Author: tannguyen <tannguyen@212.135.3.128.in-addr.dhcp.lbl.gov>
Date:   Wed Jan 4 18:51:43 2017 -0800

    add comments to the amr and amrLevel files

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_AmrLevel.H

commit 60bfa00f832ba5ccfeefcd6a54acb8e80b95a349
Merge: 6df5adb53 5f99dcda0
Author: tannguyen <tannguyen@212.135.3.128.in-addr.dhcp.lbl.gov>
Date:   Wed Jan 4 16:44:17 2017 -0800

    resolved conflit

commit ffc00feb095ecaa9aeaf845998bd1c01f55a185e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 16:32:16 2017 -0800

    make Amr & AmrLevel::derive return std::unique_ptr instead of raw ptr

Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp

commit 6df5adb5311f64b07b4186d817c2e23f4b119f33
Author: tannguyen <tannguyen@212.135.3.128.in-addr.dhcp.lbl.gov>
Date:   Wed Jan 4 16:18:33 2017 -0800

    update header files with comments

Src/Base/AMReX_Arena.H
Src/Base/AMReX_Array.H
Src/Base/AMReX_BArena.H
Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BLPgas.H
Src/Base/AMReX_BLPgas.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxDomain.H
Src/Base/AMReX_BoxLib.H
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FPC.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabConv.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_Looping.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_Orientation.H
Src/Base/AMReX_PList.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParmParse.H
Src/Base/AMReX_Periodicity.H
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_Pointers.H
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_Tuple.H
Src/Base/AMReX_UseCount.H
Src/Base/AMReX_Utility.H
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_ccse-mpi.H
Src/Base/AMReX_iMultiFab.H
Src/Base/MultiFab.H

commit ea3b83fecc1d6a28ca3284a6563ef7c89d759ea0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 16:10:37 2017 -0800

    turn on C++14 for Intel >= 17

Src/Base/AMReX_DistributionMapping.H
Tools/GNUMake/comps/intel.mak

commit 28d704b660ca9157883b1171d5957c5d2ccdaa48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 16:02:47 2017 -0800

    For gcc >= 6, C++14 is on by default.

Src/Base/AMReX_DistributionMapping.H
Tools/GNUMake/comps/gnu.mak

commit 5e8b69d7174e1cceb0e88c825e77f598d00a2b25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 15:52:06 2017 -0800

    fix a bug in last commit

Src/Base/AMReX_FabArray.cpp

commit 90911bbaf9a330ecd16c7dc1429330b8cbc17d25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 15:25:21 2017 -0800

    get rid of the sentinel in DistributionMapping

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_VisMF.cpp
Src/Extern/amrdata/AMReX_AmrData.cpp
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H
Tutorials/MultiFabTests_C/GridMoveTest.cpp
Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp
Tutorials/Sidecar_EX1/DestMFTest.cpp
Tutorials/Sidecar_EX1/NSidecarsTest.cpp

commit 363a6ecd22d9f92e85cabaf236ffc02bea5020dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 13:43:02 2017 -0800

    remove AMReX_Pointers.H

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_Pointers.H
Src/Base/CMakeLists.txt
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H

commit cfbc1319e97a4bba811a8f66363bd7421ff6de8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 13:39:12 2017 -0800

    FArrayBox: use unique_ptr instead of CpClassPtr for RealDescriptor

Src/Base/AMReX_FArrayBox.cpp

commit 464d307b672447fd51a4616567d07019cba9b71d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 13:25:09 2017 -0800

    remove the use of LnPtr and LnClassPtr

Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp

commit cd2483e32c86804d01a211beade18794291d1988
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 13:07:17 2017 -0800

    PhysBCFunct: use std::unique_ptr

Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp

commit 8b764a3e555a29eef638ce20b6080a1f01b49b60
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Wed Jan 4 13:03:09 2017 -0800

    AMReX_GeometryShop now does the right thing with its test once I realized IntVect::operator < is stupid

Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_IntVectSet.H
Src/GeometryShop/AMReX_IntVectSet.cpp
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/Make.package
Tests/GeometryShop/sphere/GNUmakefile
Tests/GeometryShop/sphere/sphere.inputs
Tests/GeometryShop/sphere/sphereTest.cpp

commit fed8befdbd42d4d772b89b802aeac155ae3183c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 12:51:26 2017 -0800

    remove unsafe assertion

Src/Base/AMReX_BoxArray.cpp

commit c2a6e1c45d6ca901745f4955dacc16de8eb1306c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 12:21:43 2017 -0800

    BoxArray::clear() should leave it at a valid state

Src/Base/AMReX_BoxArray.cpp

commit cec55bac927deeb9a02a3bccacc204192d3f8437
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 10:50:56 2017 -0800

    BoxArray: move constructor

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp

commit 43266031df20f08cca78d80fe10ddae4352db90d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 10:44:52 2017 -0800

    BoxArray: use std::shared_ptr

Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_DistributionMapping.H

commit ff3c966b2f589accc7319d5c394137a175cc3dd9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 3 16:16:59 2017 -0800

    DistributionMapping: use std::shared_ptr and add move constructor

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp

commit 2af510e0dcc15eefbd785113183a4bc999d7a85b
Merge: 453976871 5f99dcda0
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Jan 3 15:09:33 2017 -0800

    Merge branch 'development' into dtg_branch

commit 453976871c17b6b6c6ccdce4177107f97b124d76
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Jan 3 15:08:33 2017 -0800

    more paranoid commits

Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_SphereIF.H

commit 07f2b5b24d22be8397af48294b85f661612e6a7d
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Jan 3 15:07:35 2017 -0800

    committing so that I can merge with development changes

Tests/GeometryShop/sphere/sphere.inputs
Tests/GeometryShop/sphere/sphereTest.cpp

commit 5f99dcda0766b80efa0df10d54fa6ee720f2e6b8
Merge: e3b5cfe5d 930e0df61
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 3 14:52:17 2017 -0800

    Merge branch 'weiqun/development' into development

commit e3b5cfe5daa587c72b838882162b65a15c13bd65
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 3 13:30:38 2017 -0800

    typo

Docs/Migration/Migration.md

commit 930e0df61c86638105cc9fd55cead008ed4a0710
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 3 12:59:43 2017 -0800

    comments on dtor, copy-ctor, copy-op=, move-ctor, and move-op=

Src/Base/AMReX_Box.H
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_RealBox.H

commit 571783d0233dcad395653fe2f7821548faf035d1
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Jan 3 11:24:40 2017 -0800

    geometryshop port now compiles.  on to testing.

Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Tests/GeometryShop/sphere/sphereTest.cpp

commit a7c32d886b3e79110fa6dc58d98c14583f751c8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 3 11:01:16 2017 -0800

    add assertion for OpenMP >= 3.1

Src/Base/AMReX.cpp

commit c4c46002f8b1c2fb8c177b8a8eec1e1c5e9167f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 30 13:20:38 2016 -0800

    add explicit to DistributionMapping constructors

Src/Base/AMReX_DistributionMapping.H
Tutorials/MultiFabTests_C/GridMoveTest.cpp

commit 8a9eee1e76eb6efae5a071d4e08a123e272fa972
Merge: dc20767ad 120fa2176
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Fri Dec 30 12:58:11 2016 -0800

    Merged in mzingale/amrex/development (pull request #5)
    
    this fixes an issue when using ⁠⁠-copy_benchmarks⁠⁠ on tests that crashed and did not output

commit 120fa2176aa9595bbafeab7eae6dcdb41a25b44a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Dec 30 10:25:51 2016 -0500

    this fixes an issue when using ⁠⁠-copy_benchmarks⁠⁠ on tests that crashed and did
    not output

Tools/RegressionTesting/regtest.py

commit dc20767ad300a8eb51365075d48b91f342136826
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 29 21:47:01 2016 -0800

    forgot to check in step 5 script

Tools/Migration/step-5-amrex-namespace/amrex-namespace.sh

commit 20fca5b8c39b0a69103c58e47f2f67c58c10e66b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 29 21:44:13 2016 -0800

    update buildInfo

Docs/Migration/Migration.md
Tools/C_scripts/AMReX_buildInfo.H
Tools/C_scripts/makebuildinfo_C.py
Tools/Migration/step-8-deboxlib/deboxlib.sh

commit a75a5b0865acddcc5044e57de74ac787d8b02545
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 29 12:49:33 2016 -0800

    Migration document

Docs/Migration/Migration.md

commit 06209f45b1b0cf523f615a22e8113fb594308c0b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 29 12:16:21 2016 -0800

    more BoxLib --> AMReX

MiniApps/MultiGrid_C/GNUmakefile
Src/Amr/Make.package
Src/Base/AMReX_BLPgas.cpp
Src/Base/AMReX_BLassert.H
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_FPC.H
Src/Base/AMReX_FPC.cpp
Src/Base/AMReX_FabConv.H
Src/Base/AMReX_MemProfiler.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_REAL.H
Src/Base/AMReX_SPACE.H
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Src/Base/Make.package
Src/Boundary/Make.package
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp
Src/Particle/AMReX_Particles.H
Src/Particle/Make.package

commit c3e297304b0ea2d07bd6efc22d2823c517eadeb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 29 11:46:20 2016 -0800

    rm BoxLib version and change ParmParse parameters starting with boxlib. to amrex.

Src/Base/AMReX.cpp

commit 5e89906c138bcac8252037279eefef635663047c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 29 11:36:35 2016 -0800

    AMReX_BoxLib --> AMReX

Docs/Readme.backtrace
Docs/Readme.profiling
Docs/Readme.sidecars
Src/Base/AMReX.H
Src/Base/AMReX.cpp
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_BLassert.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabConv.cpp
Src/Base/AMReX_IArrayBox.cpp
Src/Base/AMReX_IntVect.cpp
Src/Base/AMReX_MemProfiler.cpp
Src/Base/AMReX_Orientation.cpp
Src/Base/AMReX_ParmParse.cpp
Src/Base/AMReX_Pointers.H
Src/Base/AMReX_UseCount.H
Src/Base/AMReX_Utility.cpp
Src/Base/CMakeLists.txt
Src/Base/Make.package
Src/F_Interfaces/BaseLib/main.cpp
Tools/C_util/ViewMF/checkMFghostcells.cpp
Tools/Migration/step-8-deboxlib/deboxlib.sh
Tutorials/AMR_Adv_C_v2/Source/main.cpp
Tutorials/HelloWorld_C/main.cpp
Tutorials/PIC_C/main.cpp
Tutorials/PIC_C/single_level.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/solve_with_f90.cpp
Tutorials/PIC_C/two_level.cpp
Tutorials/Sidecar_EX1/DestMFTest.cpp
Tutorials/Sidecar_EX1/GridMoveTest.cpp
Tutorials/Sidecar_EX1/NSidecarsTest.cpp
Tutorials/Sidecar_EX1/SidecarResizeTest.cpp
Tutorials/Sidecar_EX1/TestRankSets.cpp
Tutorials/Tiling_C/main.cpp
Tutorials/TwoGrid_PIC_C/main.cpp
Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp
Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp

commit 834c983c29a368a973058dc4ad2a03b782242127
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 29 09:04:46 2016 -0800

    add migration step 8 script and rm #include <AMReX_windstd.H>

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AuxBoundaryData.cpp
Src/Amr/AMReX_Derive.cpp
Src/Amr/AMReX_SlabStat.cpp
Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StateDescriptor.cpp
Src/Amr/AMReX_StationData.cpp
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BoxLib.cpp
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabArray.cpp
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_IArrayBox.cpp
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_ParmParse.cpp
Src/Base/AMReX_Utility.H
Src/Base/AMReX_VisMF.cpp
Src/Base/AMReX_ccse-mpi.H
Src/Base/AMReX_iMultiFab.cpp
Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_MacBndry.cpp
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/Extern/amrdata/AMReX_DataServices.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp
Tests/C_BaseLib/tFillFab.cpp
Tests/C_BaseLib/tMF.cpp
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/MKDir/MKDir.cpp
Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp
Tools/C_util/WritePlotFile.cpp
Tools/C_util/dbgTools/crsGrids.cpp
Tools/C_util/dbgTools/intersectGrids.cpp
Tools/Migration/step-8-deboxlib/deboxlib.sh
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp
Tutorials/MultiFabTests_C/GridMoveTest.cpp
Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp

commit 547378a4f0735f72cd443418a88490c19a013e69
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 29 08:40:40 2016 -0800

    remove Base/GNUmakefile and winstd.H

Src/Base/AMReX_winstd.H
Src/Base/CMakeLists.txt
Src/Base/GNUmakefile

commit 358468dc6445f8ee6c4d4602164da7b187a73b25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 28 12:46:49 2016 -0800

    migration document

Docs/Migration/Migration.md

commit 4f908ec54e66a1226af1e883f92807a02d5281e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 28 12:37:46 2016 -0800

    fix typo in migration doc

Docs/Migration/Migration.md

commit 49ad9027bf34e9d2f998fc2dc39f29bed3d645e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 28 12:14:31 2016 -0800

    migration script for bind(c)

Tools/Migration/step-7-bindc/bindc.sh

commit e945029d5c5c7e5c3f89c0ca12beebbc11a07026
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 28 12:13:29 2016 -0800

    fix subroutine probinit

Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90

commit d2c7626e51ffbe5ca48b27ed7c43a5bb8de848af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 28 11:48:00 2016 -0800

    FORT_PROBINIT --> amrex_probinit and remove unused BL_SYNC_RANTABLES

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_PROB_AMR_F.H

commit 6c23c170de61bebe3a71b6befd1977400ebb8d99
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 28 10:56:47 2016 -0800

    remove unused AMReX_FLUSH_F.H

Src/Amr/AMReX_FLUSH_F.H
Src/Amr/CMakeLists.txt

commit 4b9cc72d207f5e28076eb039f18674c89def9cca
Merge: 848985c5c 73e7797d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 28 10:45:39 2016 -0800

    Merge branch 'migration/6-distributionmap' into development

commit 73e7797d5664d6c938b0e0db2cbf5d1bc88b55b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 28 10:45:22 2016 -0800

    some bugs fixed: forgot to pass MFInfo to MultiFab constructor

Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp

commit 848985c5c775ad598389a01434d48a78b7b2c8b2
Merge: 189ae998a dc4639f6d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 28 08:16:54 2016 -0800

    Merge branch 'migration/6-distributionmap' into development

commit dc4639f6d923634554eaa3327189a35070c22da2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 28 08:16:11 2016 -0800

    Set Amr's BoxArray and DistributionMapping in AmrLevel::restart.  This is safer

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp

commit c680d093302f3a8598f0d5df981c39df2c5aa6f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 27 23:21:07 2016 -0800

    make sure FluxRegister, BndryRegister and FabSet::read() functions only read data into predefined objects.

Src/AmrCore/AMReX_FluxRegister.cpp
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_FabSet.cpp

commit 189ae998a8d91816424cd26cf4ba4b623d093efd
Merge: d2abe37a6 ac5f563b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 27 16:39:46 2016 -0800

    Merge branch 'migration/6-distributionmap' into development

commit ac5f563b4f43ba0349b991a3425c2efc5f32f022
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 27 16:39:32 2016 -0800

    typo

Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp

commit d2abe37a6a8a23301fdf3db9b8e5da7d49070432
Merge: a9b5bceae 39cd48bc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 27 13:28:30 2016 -0800

    Merge branch 'migration/6-distributionmap' into development

commit 39cd48bc7416984d013878f7738b7d61cfebb5c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 27 13:28:13 2016 -0800

    minor update to migration document

Docs/Migration/Migration.md

commit 1121f8a863841f7771a7e9e5e666e9476acd7bb2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 27 13:18:45 2016 -0800

    update migration document

Docs/Migration/Migration.md

commit a58f76bfc08fbe59303b337cad64db362caf4ca0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 27 12:02:14 2016 -0800

    update C_TensorMG

Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H
Tests/LinearSolvers/C_TensorMG/testVI.cpp

commit 4a6686d54d6ebe45ffff4474eb0d003c80c132d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 27 08:33:40 2016 -0800

    update more tests

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
MiniApps/MultiGrid_C/main.cpp
MiniApps/PGAS_SMC/SMC_init.cpp
MiniApps/PGAS_SMC/SMC_io.cpp
Tests/C_BaseLib/tFAC.cpp
Tests/C_BaseLib/tFB.cpp
Tests/C_BaseLib/tMFcopy.cpp
Tests/C_BaseLib/tVisMF.cpp
Tests/C_BaseLib/tVisMF2.cpp
Tests/FillBoundaryComparison/main.cpp
Tests/IOBenchmark/IOTest.cpp
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/C_CellMG/main.cpp
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp
Tutorials/TwoGrid_PIC_C/main.cpp
Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp

commit 0e2373f8bd34c1eb7bef87799da244b11d9abdbf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 27 07:39:21 2016 -0800

    update Particles

Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_TracerParticles.cpp
Tutorials/PIC_C/single_level.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/two_level.cpp

commit 4ac6a313f04d3e5240bd9b28228386ff3e4034b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 26 16:56:02 2016 -0800

    update C_CellMG4 and C_to_F_MG

Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp
Tutorials/MultiGrid_C/main.cpp

commit 2d00bd1badaad6d0d8f53370fed531ed658bee20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 26 16:27:16 2016 -0800

    update C_CellMG

Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp
Tutorials/MultiColor_C/main.cpp

commit c32a1d8d61c96b1c6ba2ef614411220fe39ded2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 26 15:38:17 2016 -0800

    update Amr

Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AuxBoundaryData.cpp
Src/Amr/AMReX_Extrapolater.cpp
Src/Amr/AMReX_LevelBld.H
Src/Amr/AMReX_SlabStat.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StationData.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_FabSet.cpp
Tutorials/AMR_Adv_C/Source/Adv.H
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/AdvBld.cpp
Tutorials/AMR_Adv_C/Source/Adv_advance.cpp
Tutorials/AMR_Adv_C/Source/Adv_io.cpp
Tutorials/AMR_Adv_C/Source/main.cpp

commit a9b5bceae07d8ad424e8c02ac88fdbc971219769
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 25 11:47:43 2016 -0800

    uncomment BaseFab::size

Src/Base/AMReX_BaseFab.H

commit 69d0a4b492a6e456ecc8f27570d3dcdee51d9d1b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 25 20:49:39 2016 -0800

    update Boundary and AmrCore

Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/Boundary/AMReX_BndryData.H
Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_FabSet.H
Src/Boundary/AMReX_FabSet.cpp
Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_MacBndry.H
Src/Boundary/AMReX_MacBndry.cpp
Src/Boundary/AMReX_MultiMask.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp

commit 23e84e4850c2b803a8147db655c1df7f72da7a71
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 25 12:18:22 2016 -0800

    modify VisMF::Read to allow predefined MF

Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp

commit 47808ed97b1cd1cc0db9a734f65e9d9413767bab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 25 11:54:30 2016 -0800

    make FabArray::define virtual

Src/Base/AMReX_FabArray.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_iMultiFab.H

commit cef0bc0335c619b3466245770cba1a47ce57b653
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 25 11:47:56 2016 -0800

    fix a number of tutorials

Tutorials/GettingStarted_C/main.cpp
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX2_C/main.cpp
Tutorials/MultiColor_C/main.cpp
Tutorials/MultiFabTests_C/GNUmakefile
Tutorials/MultiFabTests_C/GridMoveTest.cpp
Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp
Tutorials/PGAS_HEAT/main.cpp
Tutorials/Sidecar_EX1/DestMFTest.cpp
Tutorials/Sidecar_EX1/GNUmakefile
Tutorials/Sidecar_EX1/GridMoveTest.cpp
Tutorials/Sidecar_EX1/NSidecarsTest.cpp
Tutorials/Tiling_C/main.cpp
Tutorials/Tiling_Heat_C/main.cpp
Tutorials/WaveEquation_C/main.cpp

commit def31ae0437e539db17060a4d5f298cc2bc98c89
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 25 11:47:43 2016 -0800

    uncomment BaseFab::size

Src/Base/AMReX_BaseFab.H

commit a93ac4024c23bf60e1ee3f24319388f63ec46b29
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 25 08:33:08 2016 -0800

    fix AmrData

Src/Base/AMReX_FabArray.H
Src/Extern/amrdata/AMReX_AmrData.cpp
Tutorials/DataServicesTest0/DataServicesTest0.cpp

commit d43418b463d4ea87a31c5e139c038efe8223493a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 25 07:44:59 2016 -0800

    removed DistributionMapping cache

Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_Utility.cpp

commit d82abdf0c80cc9d526f2c8813ffe5c585ea0c83c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 25 07:26:41 2016 -0800

    DistributionMapping is now a required argument of FabArray and hence MultiFab constructors.

Docs/Migration/Migration.md
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_VisMF.cpp
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp
Tutorials/HelloWorld_C/main.cpp

commit ed4415740ce8eb7e4178030617ead123bd033551
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Dec 22 16:46:20 2016 -0800

    these are too useful to go away

Src/GeometryShop/AMReX_LoHiSide.H
Src/GeometryShop/AMReX_LoHiSide.cpp

commit 484dce6668f330771e4c16e5566fb1ee98be5ff4
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Dec 22 16:45:40 2016 -0800

    more progress toward geometry port

Src/GeometryShop/AMReX_BaseIF.H
Src/GeometryShop/AMReX_BoxIterator.H
Src/GeometryShop/AMReX_BoxIterator.cpp
Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_IrregNode.cpp
Src/GeometryShop/AMReX_LSquares.H
Src/GeometryShop/AMReX_LSquares.cpp
Src/GeometryShop/AMReX_Moments.H
Src/GeometryShop/AMReX_Moments.cpp
Src/GeometryShop/AMReX_PlaneIF.H
Src/GeometryShop/AMReX_PlaneIF.cpp
Src/GeometryShop/AMReX_RealVect.H
Src/GeometryShop/AMReX_RealVect.cpp
Src/GeometryShop/Make.package
Tests/GeometryShop/sphere/GNUmakefile

commit 043f632aca84b810dbdb3e7c4bcb4b980408b9ab
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Dec 22 16:08:34 2016 -0800

    some casts to make stuff compile on our crappy mpi platform

Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_ParallelDescriptor.cpp

commit d9b0b94fffc8ff9dd301a05bdd276ef55ff723b5
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Dec 22 15:29:28 2016 -0800

    adding some files

Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_PlaneIF.H
Src/GeometryShop/AMReX_PlaneIF.cpp
Src/GeometryShop/AMReX_SphereIF.H
Src/GeometryShop/AMReX_SphereIF.cpp
Src/GeometryShop/Make.package
Tests/GeometryShop/sphere/GNUmakefile
Tests/GeometryShop/sphere/sphereTest.cpp

commit 7e2754ef45479ea9293e2386d68bb57b63a87726
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Thu Dec 22 15:26:46 2016 -0800

    making more progress on geometry

Src/GeometryShop/AMReX_HyperPlaneIF.H
Src/GeometryShop/AMReX_HyperPlaneIF.cpp
Src/GeometryShop/AMReX_HyperSphereIF.H
Src/GeometryShop/AMReX_HyperSphereIF.cpp
Tests/GeometryShop/sphere/GNUmakefile
Tests/GeometryShop/sphere/Make.package
Tests/GeometryShop/sphere/sphere.inputs
Tests/GeometryShop/sphere/sphereConvTest.cpp
Tests/GeometryShop/sphere/sphereTest.cpp

commit c5bf39ba316677a0161726ab591f9c67ca57905b
Merge: a53949df8 7f41d2d3f
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Thu Dec 22 10:31:13 2016 -0800

    Merged in mzingale/amrex/zingale/work (pull request #3)
    
    update regtest to AMReX

commit a53949df8869b16d58ee2dda33a2d5588bc23856
Merge: 7664ee2fa 44fb7bc4b
Author: tannguyen <tannguyen@tannguyens-MacBook-Pro.local>
Date:   Wed Dec 21 16:19:45 2016 -0800

    Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development

commit 7664ee2fa04d46d06b8603f36f77f5234fd805db
Author: tannguyen <tannguyen@tannguyens-MacBook-Pro.local>
Date:   Wed Dec 21 16:18:48 2016 -0800

    mark up a few dot H files

Src/Base/AMReX_Arena.H
Src/Base/AMReX_Array.H
Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BaseFab.H

commit 7f41d2d3f70b85edb59a54d56752589bbd0310ef
Merge: ebd67a213 750427c3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Dec 21 14:29:43 2016 -0500

    Merge branch 'development' into zingale/work

commit 44fb7bc4b545221fcbaf2a4e90851778cd79e9d7
Merge: 015c830b3 750427c3f
Author: Michael  Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Dec 21 14:28:34 2016 -0500

    Merged in mzingale/amrex/development (pull request #4)
    
    add --log_file option to the test suite

commit 750427c3f80576ca603a8f12551dd37b37e1cd86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Dec 21 14:22:10 2016 -0500

    add a --log_file option to direct output to a log file (it still
    goes to stdout too)

Tools/RegressionTesting/params.py
Tools/RegressionTesting/test_util.py

commit 29c107ab5ba3267f5762b7c41d5422093e5da7f6
Merge: 56a4f36c3 015c830b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Dec 21 11:26:58 2016 -0500

    Merge branch 'development' of ssh://bitbucket.org/berkeleylab/AMReX into development

commit 015c830b3d03623dcc68f547118c092b39dfadc8
Author: tannguyen <tannguyen@tannguyens-MacBook-Pro.local>
Date:   Tue Dec 20 19:47:38 2016 -0800

    doxygen config file

Docs/doxygen.conf

commit 1d0fddfa150e98bdae745d4088977b24935438e5
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Tue Dec 20 15:35:28 2016 -0800

    lots of progress made here but not quite done

Src/GeometryShop/AMReX_BaseIF.H
Src/GeometryShop/AMReX_BoxIterator.H
Src/GeometryShop/AMReX_BoxIterator.cpp
Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_LSquares.H
Src/GeometryShop/AMReX_LSquares.cpp
Src/GeometryShop/AMReX_Moments.H
Src/GeometryShop/AMReX_Moments.cpp
Src/GeometryShop/AMReX_MultiSphereIF.H
Src/GeometryShop/AMReX_MultiSphereIF.cpp
Src/GeometryShop/AMReX_RealVect.H
Src/GeometryShop/AMReX_RealVect.cpp
Src/GeometryShop/Make.package

commit bdbe733c3f6f3736961e481f13e7f2bd270362c7
Author: Dan Graves <dtgraves@lbl.gov>
Date:   Mon Dec 19 16:21:57 2016 -0800

    starting the geometryshop port in this branch

Src/GeometryShop/AMReX_BaseIF.H
Src/GeometryShop/AMReX_BoxIterator.H
Src/GeometryShop/AMReX_BoxIterator.cpp
Src/GeometryShop/AMReX_CellEdge.H
Src/GeometryShop/AMReX_CellEdge.cpp
Src/GeometryShop/AMReX_ComplementIF.H
Src/GeometryShop/AMReX_ComplementIF.cpp
Src/GeometryShop/AMReX_EllipsoidIF.H
Src/GeometryShop/AMReX_EllipsoidIF.cpp
Src/GeometryShop/AMReX_GeometryShop.H
Src/GeometryShop/AMReX_GeometryShop.cpp
Src/GeometryShop/AMReX_HyperPlaneIF.H
Src/GeometryShop/AMReX_HyperPlaneIF.cpp
Src/GeometryShop/AMReX_HyperSphereIF.H
Src/GeometryShop/AMReX_HyperSphereIF.cpp
Src/GeometryShop/AMReX_IntersectionIF.H
Src/GeometryShop/AMReX_IntersectionIF.cpp
Src/GeometryShop/AMReX_IrregNode.H
Src/GeometryShop/AMReX_IrregNode.cpp
Src/GeometryShop/AMReX_LatheIF.H
Src/GeometryShop/AMReX_LatheIF.cpp
Src/GeometryShop/AMReX_MultiSphereIF.H
Src/GeometryShop/AMReX_MultiSphereIF.cpp
Src/GeometryShop/AMReX_PlaneIF.H
Src/GeometryShop/AMReX_PlaneIF.cpp
Src/GeometryShop/AMReX_RealVect.H
Src/GeometryShop/AMReX_RealVect.cpp
Src/GeometryShop/AMReX_SphereIF.H
Src/GeometryShop/AMReX_SphereIF.cpp
Src/GeometryShop/AMReX_TransformIF.H
Src/GeometryShop/AMReX_TransformIF.cpp
Src/GeometryShop/AMReX_UnionIF.H
Src/GeometryShop/AMReX_UnionIF.cpp
Src/GeometryShop/Make.package

commit ebd67a21377d3e289f6c078251d0d7484a177a3b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Dec 18 20:53:29 2016 -0500

    update ini

Tools/RegressionTesting/AMReX-tests.ini

commit 62b3bbca68e2357578cefc6a7eb5bf4411ff0014
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Dec 18 20:51:56 2016 -0500

    remove old inis

Tools/RegressionTesting/Castro-tests.ini
Tools/RegressionTesting/VARDEN-tests.ini
Tools/RegressionTesting/radiation-tests.ini

commit e18e53ce0bee1baee0e05a93fe3df661c3f251ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Dec 18 20:51:21 2016 -0500

    switch to AMReX

Tools/RegressionTesting/README
Tools/RegressionTesting/example-tests.ini
Tools/RegressionTesting/params.py
Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_util.py

commit 56a4f36c3cc939e93341d56857367f41e53dad04
Merge: 2c64f7aeb 67bfbc308
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Dec 18 20:14:35 2016 -0500

    Merge /home/zingale/temp/AMReX into development

commit 2c64f7aebf4338066da11492ccee52830f263ccf
Merge: 2b2be2c87 a3ae08c4c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Dec 18 20:10:48 2016 -0500

    Merge ssh://bitbucket.org/berkeleylab/AMReX into development

commit 67bfbc30820247bec111616b9174935334f991af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 18 07:15:32 2016 -0800

    fix tests

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
MiniApps/MultiGrid_C/main.cpp
MiniApps/PGAS_SMC/SMC.H
MiniApps/PGAS_SMC/SMC.cpp
MiniApps/PGAS_SMC/SMC_advance.cpp
MiniApps/PGAS_SMC/SMC_init.cpp
MiniApps/PGAS_SMC/SMC_io.cpp
MiniApps/PGAS_SMC/main.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp
Tests/BBIOBenchmark/BBIOTest.cpp
Tests/BBIOBenchmark/BBIOTestDriver.cpp
Tests/C_BaseLib/AMRProfTestBL.cpp
Tests/C_BaseLib/t8BIT.cpp
Tests/C_BaseLib/tBA.cpp
Tests/C_BaseLib/tCArena.cpp
Tests/C_BaseLib/tDM.cpp
Tests/C_BaseLib/tFAC.cpp
Tests/C_BaseLib/tFB.cpp
Tests/C_BaseLib/tFillFab.cpp
Tests/C_BaseLib/tMF.cpp
Tests/C_BaseLib/tMFcopy.cpp
Tests/C_BaseLib/tParmParse.cpp
Tests/C_BaseLib/tProfiler.cpp
Tests/C_BaseLib/tRABcast.cpp
Tests/C_BaseLib/tRan.cpp
Tests/C_BaseLib/tVisMF.cpp
Tests/C_BaseLib/tVisMF2.cpp
Tests/C_BaseLib/tread.cpp
Tests/FillBoundaryComparison/main.cpp
Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/LinearSolvers/C_CellMG/MacOpMacDrivers.H
Tests/LinearSolvers/C_CellMG/MacOperator.H
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/C_CellMG/macprojTest.cpp
Tests/LinearSolvers/C_CellMG/main.cpp
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp
Tests/LinearSolvers/C_TensorMG/testVI.cpp
Tests/LinearSolvers/ComparisonTest/compute_norm.cpp
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp
Tests/LinearSolvers/ComparisonTest/writePlotFile.H
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp
Tests/MKDir/MKDir.cpp

commit c64870ee4c88752e20c17af32163c7a59fed10e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 18 06:41:25 2016 -0800

    put pgas into amrex namespace

Src/Base/AMReX_BLPgas.H

commit 626553905203b7504da8d540917e00a0dc293f54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 18 06:36:26 2016 -0800

    fix some name conflicts in amrdata

Docs/Migration/Migration.md
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/Extern/amrdata/AMReX_DataServices.H
Tutorials/DataServicesTest0/DataServicesTest0.cpp
Tutorials/GettingStarted_C/main.cpp
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX1_C/writePlotFile.H
Tutorials/HeatEquation_EX1_C/writePlotFile.cpp
Tutorials/HeatEquation_EX2_C/main.cpp
Tutorials/HeatEquation_EX2_C/writePlotFile.H
Tutorials/HeatEquation_EX2_C/writePlotFile.cpp
Tutorials/MultiColor_C/main.cpp
Tutorials/MultiFabTests_C/GridMoveTest.cpp
Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp
Tutorials/PGAS_HEAT/main.cpp
Tutorials/PGAS_HEAT/writePlotFile.H
Tutorials/PGAS_HEAT/writePlotFile.cpp
Tutorials/Sidecar_EX1/DestMFTest.cpp
Tutorials/Sidecar_EX1/GridMoveTest.cpp
Tutorials/Sidecar_EX1/InTransitAnalysis.H
Tutorials/Sidecar_EX1/InTransitAnalysis.cpp
Tutorials/Sidecar_EX1/NSidecarsTest.cpp
Tutorials/Sidecar_EX1/SidecarResizeTest.cpp
Tutorials/Sidecar_EX1/TestRankSets.cpp
Tutorials/Tiling_C/main.cpp
Tutorials/Tiling_Heat_C/main.cpp
Tutorials/Tiling_Heat_C/writePlotFile.H
Tutorials/Tiling_Heat_C/writePlotFile.cpp
Tutorials/TwoGrid_PIC_C/main.cpp
Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp
Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp
Tutorials/TwoGrid_PIC_C/split_boxes.cpp
Tutorials/WaveEquation_C/main.cpp
Tutorials/WaveEquation_C/writePlotFile.H
Tutorials/WaveEquation_C/writePlotFile.cpp

commit cdd6f0b6a6804e8934f580333afaf3ddca70e281
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 17 17:15:36 2016 -0800

    add amrex namespace to particle

Src/Particle/AMReX_ParGDB.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_Particles.cpp
Src/Particle/AMReX_TracerParticles.H
Src/Particle/AMReX_TracerParticles.cpp
Tutorials/PIC_C/main.cpp
Tutorials/PIC_C/single_level.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/solve_with_f90.cpp
Tutorials/PIC_C/two_level.cpp

commit 192a50e948a536884c38d6a8dc488949f8a06a16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 17 17:09:30 2016 -0800

    add amrex namespace to linear solvers

Docs/Migration/Migration.md
Src/F_BaseLib/MultiFab_C_F.H
Src/F_BaseLib/MultiFab_C_F.cpp
Src/F_BaseLib/backtrace_c.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_stencil_types.H
Tutorials/MultiGrid_C/main.cpp
Tutorials/MultiGrid_C/writePlotFile.H
Tutorials/MultiGrid_C/writePlotFile.cpp

commit 74133aa3ba71c3c444ea3767b85db3e128ece309
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 17 16:59:49 2016 -0800

    move a few variables in amrex namespace into amrex::system namespace; one of the variables, verbose, was likely to cause conflict when using namespace amrex is used.

Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_BoxLib.H
Src/Base/AMReX_BoxLib.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FabArray.cpp

commit 63fc1748463471622aa6736d97dff93116d755da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 17 15:56:19 2016 -0800

    add namespace to Amr

Docs/Migration/Migration.md
Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AuxBoundaryData.H
Src/Amr/AMReX_AuxBoundaryData.cpp
Src/Amr/AMReX_Derive.H
Src/Amr/AMReX_Derive.cpp
Src/Amr/AMReX_Extrapolater.H
Src/Amr/AMReX_Extrapolater.cpp
Src/Amr/AMReX_LevelBld.H
Src/Amr/AMReX_SlabStat.H
Src/Amr/AMReX_SlabStat.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StateDescriptor.H
Src/Amr/AMReX_StateDescriptor.cpp
Src/Amr/AMReX_StationData.H
Src/Amr/AMReX_StationData.cpp
Tutorials/AMR_Adv_C/Source/Adv.H
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/AdvBld.cpp
Tutorials/AMR_Adv_C/Source/Adv_advance.cpp
Tutorials/AMR_Adv_C/Source/Adv_dt.cpp
Tutorials/AMR_Adv_C/Source/Adv_io.cpp
Tutorials/AMR_Adv_C/Source/Adv_setup.cpp
Tutorials/AMR_Adv_C/Source/main.cpp

commit 408b6e0c53e3a4131ce5223071d27632497c18fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 17 15:14:38 2016 -0800

    add namespace to Boundary and AmrCore

Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_AmrParGDB.H
Src/AmrCore/AMReX_AmrParticles.H
Src/AmrCore/AMReX_Cluster.H
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_ErrorList.H
Src/AmrCore/AMReX_ErrorList.cpp
Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/Boundary/AMReX_BndryData.H
Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_BoundCond.H
Src/Boundary/AMReX_FabSet.H
Src/Boundary/AMReX_FabSet.cpp
Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_MacBndry.H
Src/Boundary/AMReX_MacBndry.cpp
Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_Mask.cpp
Src/Boundary/AMReX_MultiMask.H
Src/Boundary/AMReX_MultiMask.cpp
Src/Extern/amrdata/AMReX_AmrData.H
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/Extern/amrdata/AMReX_AmrvisConstants.H
Src/Extern/amrdata/AMReX_DataServices.H
Src/Extern/amrdata/AMReX_DataServices.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvBC.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp
Tutorials/AMR_Adv_C_v2/Source/main.cpp

commit f968ea1082ae323fecab8d5e77ef46800eb2efbf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 16 15:56:09 2016 -0800

    add namespace to Base

Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_Array.H
Src/Base/AMReX_BArena.H
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCRec.cpp
Src/Base/AMReX_BLBackTrace.H
Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_BLPgas.cpp
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxDomain.H
Src/Base/AMReX_BoxDomain.cpp
Src/Base/AMReX_BoxLib.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FPC.H
Src/Base/AMReX_FPC.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArray.cpp
Src/Base/AMReX_FabConv.H
Src/Base/AMReX_FabConv.cpp
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IArrayBox.cpp
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IndexType.cpp
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp
Src/Base/AMReX_Lazy.H
Src/Base/AMReX_Lazy.cpp
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_MemProfiler.H
Src/Base/AMReX_MemProfiler.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_NFiles.H
Src/Base/AMReX_NFiles.cpp
Src/Base/AMReX_Orientation.H
Src/Base/AMReX_Orientation.cpp
Src/Base/AMReX_PList.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ParmParse.H
Src/Base/AMReX_ParmParse.cpp
Src/Base/AMReX_Periodicity.H
Src/Base/AMReX_Periodicity.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp
Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_Pointers.H
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp
Src/Base/AMReX_Tuple.H
Src/Base/AMReX_UseCount.H
Src/Base/AMReX_UseCount.cpp
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp
Src/Base/AMReX_ccse-mpi.H
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp
Tutorials/HelloWorld_C/main.cpp

commit 18563c0d75bb187e08f4de1ba194843c1f658591
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 16 13:32:07 2016 -0800

    namespace BoxLib --> namespace amrex

Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/Base/AMReX_Arena.H
Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_Box.H
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxDomain.H
Src/Base/AMReX_BoxLib.H
Src/Base/AMReX_BoxLib.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_SPACE.H
Src/Base/AMReX_Utility.H

commit cec98853d5d49ce39432669b6536dda2ce3832d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 16 12:58:01 2016 -0800

    BoxLib:: --> amrex::

Docs/Migration/Migration.md
Docs/Readme.profiling
MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
MiniApps/MultiGrid_C/main.cpp
MiniApps/PGAS_SMC/SMC_io.cpp
MiniApps/PGAS_SMC/main.cpp
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AuxBoundaryData.cpp
Src/Amr/AMReX_Derive.cpp
Src/Amr/AMReX_SlabStat.cpp
Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StationData.cpp
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrCore/AMReX_TagBox.cpp
Src/Base/AMReX_BCRec.cpp
Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_BLPgas.cpp
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_BLassert.H
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxDomain.cpp
Src/Base/AMReX_BoxLib.H
Src/Base/AMReX_BoxLib.cpp
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArray.cpp
Src/Base/AMReX_FabConv.cpp
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_IArrayBox.cpp
Src/Base/AMReX_IndexType.cpp
Src/Base/AMReX_IntVect.cpp
Src/Base/AMReX_MemProfiler.cpp
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_NFiles.H
Src/Base/AMReX_NFiles.cpp
Src/Base/AMReX_Orientation.cpp
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ParmParse.cpp
Src/Base/AMReX_PhysBCFunct.cpp
Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_RealBox.cpp
Src/Base/AMReX_TinyProfiler.cpp
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_VisMF.cpp
Src/Base/AMReX_iMultiFab.cpp
Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_FabSet.H
Src/Boundary/AMReX_FabSet.cpp
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_MacBndry.cpp
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/Extern/amrdata/AMReX_DataServices.cpp
Src/Extern/hpgmg/BL_HPGMG.cpp
Src/F_BaseLib/MultiFab_C_F.cpp
Src/F_Interfaces/BaseLib/main.cpp
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_Particles.cpp
Src/Particle/AMReX_TracerParticles.cpp
Tests/BBIOBenchmark/BBIOTest.cpp
Tests/BBIOBenchmark/BBIOTestDriver.cpp
Tests/C_BaseLib/AMRProfTestBL.cpp
Tests/C_BaseLib/BcastClasses/BcastClasses.cpp
Tests/C_BaseLib/tBA.cpp
Tests/C_BaseLib/tCArena.cpp
Tests/C_BaseLib/tDM.cpp
Tests/C_BaseLib/tDir.cpp
Tests/C_BaseLib/tFAC.cpp
Tests/C_BaseLib/tFB.cpp
Tests/C_BaseLib/tFillFab.cpp
Tests/C_BaseLib/tMF.cpp
Tests/C_BaseLib/tMFcopy.cpp
Tests/C_BaseLib/tParmParse.cpp
Tests/C_BaseLib/tProfiler.cpp
Tests/C_BaseLib/tRABcast.cpp
Tests/C_BaseLib/tRan.cpp
Tests/C_BaseLib/tVisMF.cpp
Tests/C_BaseLib/tVisMF2.cpp
Tests/C_BaseLib/tread.cpp
Tests/FillBoundaryComparison/main.cpp
Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/C_CellMG/macprojTest.cpp
Tests/LinearSolvers/C_CellMG/main.cpp
Tests/LinearSolvers/C_TensorMG/testVI.cpp
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp
Tests/MKDir/MKDir.cpp
Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp
Tools/C_util/Convergence/Add.cpp
Tools/C_util/Convergence/ComputeAmrDataNorms.cpp
Tools/C_util/Convergence/DiffFab.cpp
Tools/C_util/Convergence/DiffSameDomainRefined.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGrid2.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileNormB.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp
Tools/C_util/Statistics/ComputeAmrDataStat.cpp
Tools/C_util/Statistics/PltFileFluxAve.cpp
Tools/C_util/Statistics/PltFileList.cpp
Tools/C_util/Statistics/PltFileStat.cpp
Tools/C_util/Statistics/PltFileXAve.cpp
Tools/C_util/TV_TempWrite.H
Tools/C_util/ViewMF/MFNorm.cpp
Tools/C_util/ViewMF/checkMFghostcells.cpp
Tools/C_util/ViewMF/main.cpp
Tools/C_util/ViewMF/mfMinMax.cpp
Tools/C_util/ViewMF/viewMF.cpp
Tools/C_util/ViewMF/viewMFcol.cpp
Tools/C_util/ViewMF/viewMFdiff.cpp
Tools/C_util/ViewMF/viewMFdiffHardWire.cpp
Tools/C_util/WritePlotFile.cpp
Tools/C_util/dbgTools/crsGrids.cpp
Tools/C_util/dbgTools/intersectGrids.cpp
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/Adv_advance.cpp
Tutorials/AMR_Adv_C/Source/Adv_io.cpp
Tutorials/AMR_Adv_C/Source/main.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp
Tutorials/AMR_Adv_C_v2/Source/main.cpp
Tutorials/DataServicesTest0/DataServicesTest0.cpp
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp
Tutorials/GettingStarted_C/main.cpp
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX1_C/writePlotFile.cpp
Tutorials/HeatEquation_EX2_C/main.cpp
Tutorials/HeatEquation_EX2_C/writePlotFile.cpp
Tutorials/HelloWorld_C/main.cpp
Tutorials/MultiColor_C/main.cpp
Tutorials/MultiFabTests_C/GridMoveTest.cpp
Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp
Tutorials/MultiGrid_C/main.cpp
Tutorials/MultiGrid_C/writePlotFile.cpp
Tutorials/PGAS_HEAT/main.cpp
Tutorials/PGAS_HEAT/writePlotFile.cpp
Tutorials/PIC_C/main.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/solve_with_f90.cpp
Tutorials/PIC_C/two_level.cpp
Tutorials/Sidecar_EX1/DestMFTest.cpp
Tutorials/Sidecar_EX1/GridMoveTest.cpp
Tutorials/Sidecar_EX1/NSidecarsTest.cpp
Tutorials/Sidecar_EX1/SidecarResizeTest.cpp
Tutorials/Sidecar_EX1/TestRankSets.cpp
Tutorials/Tiling_C/main.cpp
Tutorials/Tiling_Heat_C/main.cpp
Tutorials/Tiling_Heat_C/writePlotFile.cpp
Tutorials/TwoGrid_PIC_C/main.cpp
Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp
Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp
Tutorials/WaveEquation_C/main.cpp
Tutorials/WaveEquation_C/writePlotFile.cpp

commit 261d73f46dc56b9a4ca915cc560bac7ce1ef4087
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 16 10:39:36 2016 -0800

    AMReX:: --> amrex::

Docs/Migration/Migration.md
Src/Base/AMReX_Array.H
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp
Tutorials/MultiColor_C/main.cpp
Tutorials/MultiGrid_C/main.cpp
Tutorials/PIC_C/single_level.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/two_level.cpp
Tutorials/TwoGrid_PIC_C/main.cpp
Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp

commit 08f0891a5422221b823d8a8fd7cfac66199c4e7b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 16 09:43:57 2016 -0800

    fix Fortran BoxLib tests too

Src/F_BaseLib/GPackage.mak
Tools/Migration/step-1-amrex_home/amrex_home.sh

commit 8d43b15f138cec47fd1a636365c9c7a84959e8f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 16 09:19:46 2016 -0800

    update migration document and scripts

Docs/Migration/Migration.md
Tools/Migration/step-1-amrex_home/amrex_home.sh
Tools/Migration/step-3-amrex-prefix/amrexprefix.sh
Tools/Migration/step-4-dirname/dirname.sh

commit 5b87f27b1258a3850453d690ad91533d776280ab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 16 09:00:16 2016 -0800

    update make files for the directory name changes

MiniApps/FillBoundary/GNUmakefile
MiniApps/MultiGrid_C/GNUmakefile
MiniApps/PGAS_SMC/GNUmakefile
Src/Amr/Make.package
Src/AmrCore/Make.package
Src/Base/GNUmakefile
Src/Base/Make.package
Src/Boundary/Make.package
Src/CMakeLists.txt
Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/GPackage.mak
Src/Particle/Make.package
Tests/BBIOBenchmark/GNUmakefile
Tests/C_BaseLib/BcastClasses/GNUmakefile
Tests/C_BaseLib/GNUmakefile
Tests/FillBoundaryComparison/GNUmakefile
Tests/IOBenchmark/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile.dumpi
Tests/LinearSolvers/C_TensorMG/GNUmakefile
Tests/LinearSolvers/ComparisonTest/GNUmakefile
Tests/MKDir/GNUmakefile
Tools/C_util/AmrDeriveTecplot/GNUmakefile
Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Statistics/GNUmakefile
Tools/C_util/dbgTools/GNUmakefile
Tools/GNUMake/Make.defs
Tools/GNUMake/Make.rules
Tools/GNUMake/README.md
Tutorials/AMR_Adv_C/Exec/Make.Adv
Tutorials/AMR_Adv_CF/Exec/Make.Adv
Tutorials/AMR_Adv_CF/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_Adv_C_v2/Exec/Make.Adv
Tutorials/DataServicesTest0/GNUmakefile
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile
Tutorials/GettingStarted_C/GNUmakefile
Tutorials/HeatEquation_EX1_C/GNUmakefile
Tutorials/HeatEquation_EX1_CF/GNUmakefile
Tutorials/HeatEquation_EX2_C/GNUmakefile
Tutorials/HelloWorld_C/GNUmakefile
Tutorials/HelloWorld_CF/GNUmakefile
Tutorials/MultiColor_C/GNUmakefile
Tutorials/MultiFabTests_C/GNUmakefile
Tutorials/MultiGrid_C/GNUmakefile
Tutorials/PGAS_HEAT/GNUmakefile
Tutorials/PIC_C/GNUmakefile
Tutorials/Sidecar_EX1/GNUmakefile
Tutorials/Tiling_C/GNUmakefile
Tutorials/Tiling_Heat_C/GNUmakefile
Tutorials/TwoGrid_PIC_C/GNUmakefile
Tutorials/WaveEquation_C/GNUmakefile

commit 3c0d2fcde396c6d656d3359e10f4ec0223251a51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 16 08:53:23 2016 -0800

    shorten directory names

Src/Amr/AMReX_ARRAYLIM_1D.F
Src/Amr/AMReX_ARRAYLIM_2D.F
Src/Amr/AMReX_ARRAYLIM_3D.F
Src/Amr/AMReX_Amr.H
Src/Amr/AMReX_Amr.cpp
Src/Amr/AMReX_AmrLevel.H
Src/Amr/AMReX_AmrLevel.cpp
Src/Amr/AMReX_AuxBoundaryData.H
Src/Amr/AMReX_AuxBoundaryData.cpp
Src/Amr/AMReX_Derive.H
Src/Amr/AMReX_Derive.cpp
Src/Amr/AMReX_Extrapolater.H
Src/Amr/AMReX_Extrapolater.cpp
Src/Amr/AMReX_FLUSH_F.H
Src/Amr/AMReX_LevelBld.H
Src/Amr/AMReX_MAKESLICE_3D.F
Src/Amr/AMReX_MAKESLICE_F.H
Src/Amr/AMReX_PROB_AMR_F.H
Src/Amr/AMReX_SLABSTAT_1D.F
Src/Amr/AMReX_SLABSTAT_2D.F
Src/Amr/AMReX_SLABSTAT_3D.F
Src/Amr/AMReX_SLABSTAT_F.H
Src/Amr/AMReX_SlabStat.H
Src/Amr/AMReX_SlabStat.cpp
Src/Amr/AMReX_StateData.H
Src/Amr/AMReX_StateData.cpp
Src/Amr/AMReX_StateDescriptor.H
Src/Amr/AMReX_StateDescriptor.cpp
Src/Amr/AMReX_StationData.H
Src/Amr/AMReX_StationData.cpp
Src/Amr/AMReX_extrapolater_1d.f90
Src/Amr/AMReX_extrapolater_2d.f90
Src/Amr/AMReX_extrapolater_3d.f90
Src/Amr/CMakeLists.txt
Src/Amr/Make.package
Src/AmrCore/AMReX_AmrCore.H
Src/AmrCore/AMReX_AmrCore.cpp
Src/AmrCore/AMReX_AmrParGDB.H
Src/AmrCore/AMReX_AmrParticles.H
Src/AmrCore/AMReX_Cluster.H
Src/AmrCore/AMReX_Cluster.cpp
Src/AmrCore/AMReX_ErrorList.H
Src/AmrCore/AMReX_ErrorList.cpp
Src/AmrCore/AMReX_FLUXREG_1D.F
Src/AmrCore/AMReX_FLUXREG_2D.F
Src/AmrCore/AMReX_FLUXREG_3D.F
Src/AmrCore/AMReX_FLUXREG_F.H
Src/AmrCore/AMReX_FillPatchUtil.H
Src/AmrCore/AMReX_FillPatchUtil.cpp
Src/AmrCore/AMReX_FluxRegister.H
Src/AmrCore/AMReX_FluxRegister.cpp
Src/AmrCore/AMReX_INTERP_1D.F
Src/AmrCore/AMReX_INTERP_2D.F
Src/AmrCore/AMReX_INTERP_3D.F
Src/AmrCore/AMReX_INTERP_F.H
Src/AmrCore/AMReX_Interpolater.H
Src/AmrCore/AMReX_Interpolater.cpp
Src/AmrCore/AMReX_TagBox.H
Src/AmrCore/AMReX_TagBox.cpp
Src/AmrCore/CMakeLists.txt
Src/AmrCore/Make.package
Src/Base/AMReX_Arena.H
Src/Base/AMReX_Arena.cpp
Src/Base/AMReX_Array.H
Src/Base/AMReX_ArrayLim.H
Src/Base/AMReX_BArena.H
Src/Base/AMReX_BArena.cpp
Src/Base/AMReX_BCRec.H
Src/Base/AMReX_BCRec.cpp
Src/Base/AMReX_BC_TYPES.H
Src/Base/AMReX_BLBackTrace.H
Src/Base/AMReX_BLBackTrace.cpp
Src/Base/AMReX_BLBoxLib_F.f
Src/Base/AMReX_BLFort.H
Src/Base/AMReX_BLParmParse_F.f
Src/Base/AMReX_BLPgas.H
Src/Base/AMReX_BLPgas.cpp
Src/Base/AMReX_BLProfiler.H
Src/Base/AMReX_BLProfiler.cpp
Src/Base/AMReX_BLProfiler_F.f
Src/Base/AMReX_BLassert.H
Src/Base/AMReX_BLutil_F.f
Src/Base/AMReX_BaseFab.H
Src/Base/AMReX_BaseFab.cpp
Src/Base/AMReX_BaseFab_f.H
Src/Base/AMReX_BaseFab_nd.f90
Src/Base/AMReX_Box.H
Src/Base/AMReX_Box.cpp
Src/Base/AMReX_BoxArray.H
Src/Base/AMReX_BoxArray.cpp
Src/Base/AMReX_BoxDomain.H
Src/Base/AMReX_BoxDomain.cpp
Src/Base/AMReX_BoxLib.H
Src/Base/AMReX_BoxLib.cpp
Src/Base/AMReX_BoxList.H
Src/Base/AMReX_BoxList.cpp
Src/Base/AMReX_CArena.H
Src/Base/AMReX_CArena.cpp
Src/Base/AMReX_CONSTANTS.H
Src/Base/AMReX_COORDSYS_1D.F
Src/Base/AMReX_COORDSYS_2D.F
Src/Base/AMReX_COORDSYS_3D.F
Src/Base/AMReX_COORDSYS_F.H
Src/Base/AMReX_CoordSys.H
Src/Base/AMReX_CoordSys.cpp
Src/Base/AMReX_DistributionMapping.H
Src/Base/AMReX_DistributionMapping.cpp
Src/Base/AMReX_FArrayBox.H
Src/Base/AMReX_FArrayBox.cpp
Src/Base/AMReX_FILCC_1D.F
Src/Base/AMReX_FILCC_2D.F
Src/Base/AMReX_FILCC_3D.F
Src/Base/AMReX_FPC.H
Src/Base/AMReX_FPC.cpp
Src/Base/AMReX_FabArray.H
Src/Base/AMReX_FabArray.cpp
Src/Base/AMReX_FabConv.H
Src/Base/AMReX_FabConv.cpp
Src/Base/AMReX_Geometry.H
Src/Base/AMReX_Geometry.cpp
Src/Base/AMReX_IArrayBox.H
Src/Base/AMReX_IArrayBox.cpp
Src/Base/AMReX_IndexType.H
Src/Base/AMReX_IndexType.cpp
Src/Base/AMReX_IntVect.H
Src/Base/AMReX_IntVect.cpp
Src/Base/AMReX_Lazy.H
Src/Base/AMReX_Lazy.cpp
Src/Base/AMReX_Looping.H
Src/Base/AMReX_MemPool.H
Src/Base/AMReX_MemPool.cpp
Src/Base/AMReX_MemProfiler.H
Src/Base/AMReX_MemProfiler.cpp
Src/Base/AMReX_MultiFab.H
Src/Base/AMReX_MultiFab.cpp
Src/Base/AMReX_MultiFabUtil.H
Src/Base/AMReX_MultiFabUtil.cpp
Src/Base/AMReX_MultiFabUtil_1d.f90
Src/Base/AMReX_MultiFabUtil_2d.f90
Src/Base/AMReX_MultiFabUtil_3d.f90
Src/Base/AMReX_MultiFabUtil_F.H
Src/Base/AMReX_NFiles.H
Src/Base/AMReX_NFiles.cpp
Src/Base/AMReX_Orientation.H
Src/Base/AMReX_Orientation.cpp
Src/Base/AMReX_PList.H
Src/Base/AMReX_ParallelDescriptor.H
Src/Base/AMReX_ParallelDescriptor.cpp
Src/Base/AMReX_ParmParse.H
Src/Base/AMReX_ParmParse.cpp
Src/Base/AMReX_Periodicity.H
Src/Base/AMReX_Periodicity.cpp
Src/Base/AMReX_PhysBCFunct.H
Src/Base/AMReX_PhysBCFunct.cpp
Src/Base/AMReX_PlotFileUtil.H
Src/Base/AMReX_PlotFileUtil.cpp
Src/Base/AMReX_Pointers.H
Src/Base/AMReX_REAL.H
Src/Base/AMReX_RealBox.H
Src/Base/AMReX_RealBox.cpp
Src/Base/AMReX_SPACE.H
Src/Base/AMReX_SPACE_F.H
Src/Base/AMReX_TinyProfiler.H
Src/Base/AMReX_TinyProfiler.cpp
Src/Base/AMReX_Tuple.H
Src/Base/AMReX_UseCount.H
Src/Base/AMReX_UseCount.cpp
Src/Base/AMReX_Utility.H
Src/Base/AMReX_Utility.cpp
Src/Base/AMReX_VisMF.H
Src/Base/AMReX_VisMF.cpp
Src/Base/AMReX_bc_types.fi
Src/Base/AMReX_bl_flush.f
Src/Base/AMReX_bl_fort_module.F90
Src/Base/AMReX_ccse-mpi.H
Src/Base/AMReX_iMultiFab.H
Src/Base/AMReX_iMultiFab.cpp
Src/Base/AMReX_mempool_f.f90
Src/Base/AMReX_threadbox.f90
Src/Base/AMReX_winstd.H
Src/Base/CMakeLists.txt
Src/Base/GNUmakefile
Src/Base/GPackage.mak
Src/Base/Make.package
Src/Base/OpenSource.txt
Src/Boundary/AMReX_BndryData.H
Src/Boundary/AMReX_BndryData.cpp
Src/Boundary/AMReX_BndryRegister.H
Src/Boundary/AMReX_BndryRegister.cpp
Src/Boundary/AMReX_BoundCond.H
Src/Boundary/AMReX_FabSet.H
Src/Boundary/AMReX_FabSet.cpp
Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F
Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F
Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F
Src/Boundary/AMReX_INTERPBNDRYDATA_F.H
Src/Boundary/AMReX_InterpBndryData.H
Src/Boundary/AMReX_InterpBndryData.cpp
Src/Boundary/AMReX_LO_BCTYPES.H
Src/Boundary/AMReX_LO_UTIL.F
Src/Boundary/AMReX_MacBndry.H
Src/Boundary/AMReX_MacBndry.cpp
Src/Boundary/AMReX_Mask.H
Src/Boundary/AMReX_Mask.cpp
Src/Boundary/AMReX_MultiMask.H
Src/Boundary/AMReX_MultiMask.cpp
Src/Boundary/CMakeLists.txt
Src/Boundary/Make.package
Src/Boundary/OpenSource.txt
Src/Particle/AMReX_ParGDB.H
Src/Particle/AMReX_ParticleInit.H
Src/Particle/AMReX_Particles.H
Src/Particle/AMReX_Particles.cpp
Src/Particle/AMReX_Particles_1D.F
Src/Particle/AMReX_Particles_2D.F
Src/Particle/AMReX_Particles_3D.F
Src/Particle/AMReX_Particles_F.H
Src/Particle/AMReX_TracerParticles.H
Src/Particle/AMReX_TracerParticles.cpp
Src/Particle/CMakeLists.txt
Src/Particle/Make.package

commit efd5f98217bc71fbfbe672ab2a42386006f1381e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 16 08:48:28 2016 -0800

    rename C_mk to GNUMake

Tools/GNUMake/Make.defs
Tools/GNUMake/Make.local.template
Tools/GNUMake/Make.machines
Tools/GNUMake/Make.rules
Tools/GNUMake/Make.upcxx
Tools/GNUMake/README.md
Tools/GNUMake/comps/cray.mak
Tools/GNUMake/comps/gnu.mak
Tools/GNUMake/comps/intel.mak
Tools/GNUMake/comps/pgi.mak
Tools/GNUMake/packages/Make.hpgmg
Tools/GNUMake/sites/Make.ccse
Tools/GNUMake/sites/Make.nersc
Tools/GNUMake/sites/Make.olcf
Tools/GNUMake/sites/Make.unknown
Tools/GNUMake/tools/Make.vtune

commit 461d92f70c6428c0123e02d1520eb57ba5a8a041
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 16 08:35:21 2016 -0800

    migration script: limit the scope of search and replace for performace

Tools/Migration/step-3-amrex-prefix/amrexprefix.sh

commit f8e7ec860056dd3df00d52a986b8b398b6aefca3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 17:11:34 2016 -0800

    add migration step 3 script

Tools/Migration/step-3-amrex-prefix/amrexprefix.sh

commit 00f52694287ece3a033a021ca2a7257513125aa4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 17:06:32 2016 -0800

    missed a few names

Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H

commit 77ebc80c39f3549f292be4f3f9e9bf5b3a7b563c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 16:39:37 2016 -0800

    remove duplicated AMReX_

Src/C_AMRLib/AMReX_ARRAYLIM_1D.F
Src/C_AMRLib/AMReX_ARRAYLIM_2D.F
Src/C_AMRLib/AMReX_ARRAYLIM_3D.F
Src/C_AMRLib/AMReX_Amr.H
Src/C_AMRLib/AMReX_Amr.cpp
Src/C_AMRLib/AMReX_AmrLevel.H
Src/C_AMRLib/AMReX_AmrLevel.cpp
Src/C_AMRLib/AMReX_AuxBoundaryData.H
Src/C_AMRLib/AMReX_AuxBoundaryData.cpp
Src/C_AMRLib/AMReX_Derive.H
Src/C_AMRLib/AMReX_Derive.cpp
Src/C_AMRLib/AMReX_Extrapolater.H
Src/C_AMRLib/AMReX_Extrapolater.cpp
Src/C_AMRLib/AMReX_FLUSH_F.H
Src/C_AMRLib/AMReX_LevelBld.H
Src/C_AMRLib/AMReX_MAKESLICE_3D.F
Src/C_AMRLib/AMReX_MAKESLICE_F.H
Src/C_AMRLib/AMReX_PROB_AMR_F.H
Src/C_AMRLib/AMReX_SLABSTAT_1D.F
Src/C_AMRLib/AMReX_SLABSTAT_2D.F
Src/C_AMRLib/AMReX_SLABSTAT_3D.F
Src/C_AMRLib/AMReX_SLABSTAT_F.H
Src/C_AMRLib/AMReX_SlabStat.H
Src/C_AMRLib/AMReX_SlabStat.cpp
Src/C_AMRLib/AMReX_StateData.H
Src/C_AMRLib/AMReX_StateData.cpp
Src/C_AMRLib/AMReX_StateDescriptor.H
Src/C_AMRLib/AMReX_StateDescriptor.cpp
Src/C_AMRLib/AMReX_StationData.H
Src/C_AMRLib/AMReX_StationData.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp

commit 8523c2109a8f6a6970317462b8bc00a38d217edf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 16:34:15 2016 -0800

    update Migration document

Docs/Migration/Migration.md

commit f5c1eafe444649460a0ed8ef394e127e284a3b22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 16:29:12 2016 -0800

    add AMReX_ to include

Docs/Readme.backtrace
MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
MiniApps/MultiGrid_C/COEF_3D.F
MiniApps/MultiGrid_C/COEF_F.H
MiniApps/MultiGrid_C/RHS_3D.F
MiniApps/MultiGrid_C/RHS_F.H
MiniApps/MultiGrid_C/main.cpp
MiniApps/PGAS_SMC/SMC.H
MiniApps/PGAS_SMC/SMC.cpp
MiniApps/PGAS_SMC/SMC_F.H
MiniApps/PGAS_SMC/SMC_io.cpp
MiniApps/PGAS_SMC/main.cpp
Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_1D.F
Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_2D.F
Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_3D.F
Src/C_AMRLib/AMReX_AMReX_Amr.H
Src/C_AMRLib/AMReX_AMReX_Amr.cpp
Src/C_AMRLib/AMReX_AMReX_AmrLevel.H
Src/C_AMRLib/AMReX_AMReX_AmrLevel.cpp
Src/C_AMRLib/AMReX_AMReX_AuxBoundaryData.H
Src/C_AMRLib/AMReX_AMReX_AuxBoundaryData.cpp
Src/C_AMRLib/AMReX_AMReX_Derive.H
Src/C_AMRLib/AMReX_AMReX_Derive.cpp
Src/C_AMRLib/AMReX_AMReX_Extrapolater.H
Src/C_AMRLib/AMReX_AMReX_Extrapolater.cpp
Src/C_AMRLib/AMReX_AMReX_LevelBld.H
Src/C_AMRLib/AMReX_AMReX_MAKESLICE_3D.F
Src/C_AMRLib/AMReX_AMReX_SLABSTAT_1D.F
Src/C_AMRLib/AMReX_AMReX_SLABSTAT_2D.F
Src/C_AMRLib/AMReX_AMReX_SLABSTAT_3D.F
Src/C_AMRLib/AMReX_AMReX_SlabStat.H
Src/C_AMRLib/AMReX_AMReX_SlabStat.cpp
Src/C_AMRLib/AMReX_AMReX_StateData.H
Src/C_AMRLib/AMReX_AMReX_StateData.cpp
Src/C_AMRLib/AMReX_AMReX_StateDescriptor.H
Src/C_AMRLib/AMReX_AMReX_StateDescriptor.cpp
Src/C_AMRLib/AMReX_AMReX_StationData.H
Src/C_AMRLib/AMReX_AMReX_StationData.cpp
Src/C_AmrCoreLib/AMReX_AmrCore.H
Src/C_AmrCoreLib/AMReX_AmrCore.cpp
Src/C_AmrCoreLib/AMReX_AmrParGDB.H
Src/C_AmrCoreLib/AMReX_AmrParticles.H
Src/C_AmrCoreLib/AMReX_Cluster.H
Src/C_AmrCoreLib/AMReX_Cluster.cpp
Src/C_AmrCoreLib/AMReX_ErrorList.H
Src/C_AmrCoreLib/AMReX_ErrorList.cpp
Src/C_AmrCoreLib/AMReX_FLUXREG_1D.F
Src/C_AmrCoreLib/AMReX_FLUXREG_2D.F
Src/C_AmrCoreLib/AMReX_FLUXREG_3D.F
Src/C_AmrCoreLib/AMReX_FLUXREG_F.H
Src/C_AmrCoreLib/AMReX_FillPatchUtil.H
Src/C_AmrCoreLib/AMReX_FillPatchUtil.cpp
Src/C_AmrCoreLib/AMReX_FluxRegister.H
Src/C_AmrCoreLib/AMReX_FluxRegister.cpp
Src/C_AmrCoreLib/AMReX_INTERP_1D.F
Src/C_AmrCoreLib/AMReX_INTERP_2D.F
Src/C_AmrCoreLib/AMReX_INTERP_3D.F
Src/C_AmrCoreLib/AMReX_INTERP_F.H
Src/C_AmrCoreLib/AMReX_Interpolater.H
Src/C_AmrCoreLib/AMReX_Interpolater.cpp
Src/C_AmrCoreLib/AMReX_TagBox.H
Src/C_AmrCoreLib/AMReX_TagBox.cpp
Src/C_BaseLib/AMReX_Arena.H
Src/C_BaseLib/AMReX_Arena.cpp
Src/C_BaseLib/AMReX_Array.H
Src/C_BaseLib/AMReX_ArrayLim.H
Src/C_BaseLib/AMReX_BArena.H
Src/C_BaseLib/AMReX_BArena.cpp
Src/C_BaseLib/AMReX_BCRec.H
Src/C_BaseLib/AMReX_BCRec.cpp
Src/C_BaseLib/AMReX_BLBackTrace.cpp
Src/C_BaseLib/AMReX_BLFort.H
Src/C_BaseLib/AMReX_BLPgas.H
Src/C_BaseLib/AMReX_BLPgas.cpp
Src/C_BaseLib/AMReX_BLProfiler.H
Src/C_BaseLib/AMReX_BLProfiler.cpp
Src/C_BaseLib/AMReX_BLassert.H
Src/C_BaseLib/AMReX_BaseFab.H
Src/C_BaseLib/AMReX_BaseFab.cpp
Src/C_BaseLib/AMReX_BaseFab_f.H
Src/C_BaseLib/AMReX_Box.H
Src/C_BaseLib/AMReX_Box.cpp
Src/C_BaseLib/AMReX_BoxArray.H
Src/C_BaseLib/AMReX_BoxArray.cpp
Src/C_BaseLib/AMReX_BoxDomain.H
Src/C_BaseLib/AMReX_BoxDomain.cpp
Src/C_BaseLib/AMReX_BoxLib.H
Src/C_BaseLib/AMReX_BoxLib.cpp
Src/C_BaseLib/AMReX_BoxList.H
Src/C_BaseLib/AMReX_BoxList.cpp
Src/C_BaseLib/AMReX_CArena.H
Src/C_BaseLib/AMReX_CArena.cpp
Src/C_BaseLib/AMReX_CONSTANTS.H
Src/C_BaseLib/AMReX_COORDSYS_1D.F
Src/C_BaseLib/AMReX_COORDSYS_2D.F
Src/C_BaseLib/AMReX_COORDSYS_3D.F
Src/C_BaseLib/AMReX_COORDSYS_F.H
Src/C_BaseLib/AMReX_CoordSys.H
Src/C_BaseLib/AMReX_CoordSys.cpp
Src/C_BaseLib/AMReX_DistributionMapping.H
Src/C_BaseLib/AMReX_DistributionMapping.cpp
Src/C_BaseLib/AMReX_FArrayBox.H
Src/C_BaseLib/AMReX_FArrayBox.cpp
Src/C_BaseLib/AMReX_FILCC_1D.F
Src/C_BaseLib/AMReX_FILCC_2D.F
Src/C_BaseLib/AMReX_FILCC_3D.F
Src/C_BaseLib/AMReX_FPC.H
Src/C_BaseLib/AMReX_FPC.cpp
Src/C_BaseLib/AMReX_FabArray.H
Src/C_BaseLib/AMReX_FabArray.cpp
Src/C_BaseLib/AMReX_FabConv.H
Src/C_BaseLib/AMReX_FabConv.cpp
Src/C_BaseLib/AMReX_Geometry.H
Src/C_BaseLib/AMReX_Geometry.cpp
Src/C_BaseLib/AMReX_IArrayBox.H
Src/C_BaseLib/AMReX_IArrayBox.cpp
Src/C_BaseLib/AMReX_IndexType.H
Src/C_BaseLib/AMReX_IndexType.cpp
Src/C_BaseLib/AMReX_IntVect.H
Src/C_BaseLib/AMReX_IntVect.cpp
Src/C_BaseLib/AMReX_Lazy.cpp
Src/C_BaseLib/AMReX_MemPool.cpp
Src/C_BaseLib/AMReX_MemProfiler.cpp
Src/C_BaseLib/AMReX_MultiFab.H
Src/C_BaseLib/AMReX_MultiFab.cpp
Src/C_BaseLib/AMReX_MultiFabUtil.H
Src/C_BaseLib/AMReX_MultiFabUtil.cpp
Src/C_BaseLib/AMReX_MultiFabUtil_F.H
Src/C_BaseLib/AMReX_NFiles.H
Src/C_BaseLib/AMReX_NFiles.cpp
Src/C_BaseLib/AMReX_Orientation.H
Src/C_BaseLib/AMReX_Orientation.cpp
Src/C_BaseLib/AMReX_ParallelDescriptor.H
Src/C_BaseLib/AMReX_ParallelDescriptor.cpp
Src/C_BaseLib/AMReX_ParmParse.cpp
Src/C_BaseLib/AMReX_Periodicity.H
Src/C_BaseLib/AMReX_Periodicity.cpp
Src/C_BaseLib/AMReX_PhysBCFunct.H
Src/C_BaseLib/AMReX_PhysBCFunct.cpp
Src/C_BaseLib/AMReX_PlotFileUtil.H
Src/C_BaseLib/AMReX_PlotFileUtil.cpp
Src/C_BaseLib/AMReX_Pointers.H
Src/C_BaseLib/AMReX_RealBox.H
Src/C_BaseLib/AMReX_RealBox.cpp
Src/C_BaseLib/AMReX_SPACE_F.H
Src/C_BaseLib/AMReX_TinyProfiler.H
Src/C_BaseLib/AMReX_TinyProfiler.cpp
Src/C_BaseLib/AMReX_Tuple.H
Src/C_BaseLib/AMReX_UseCount.H
Src/C_BaseLib/AMReX_UseCount.cpp
Src/C_BaseLib/AMReX_Utility.H
Src/C_BaseLib/AMReX_Utility.cpp
Src/C_BaseLib/AMReX_VisMF.H
Src/C_BaseLib/AMReX_VisMF.cpp
Src/C_BaseLib/AMReX_ccse-mpi.H
Src/C_BaseLib/AMReX_iMultiFab.H
Src/C_BaseLib/AMReX_iMultiFab.cpp
Src/C_BoundaryLib/AMReX_BndryData.H
Src/C_BoundaryLib/AMReX_BndryData.cpp
Src/C_BoundaryLib/AMReX_BndryRegister.H
Src/C_BoundaryLib/AMReX_BndryRegister.cpp
Src/C_BoundaryLib/AMReX_BoundCond.H
Src/C_BoundaryLib/AMReX_FabSet.H
Src/C_BoundaryLib/AMReX_FabSet.cpp
Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_1D.F
Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_2D.F
Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_3D.F
Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_F.H
Src/C_BoundaryLib/AMReX_InterpBndryData.H
Src/C_BoundaryLib/AMReX_InterpBndryData.cpp
Src/C_BoundaryLib/AMReX_LO_UTIL.F
Src/C_BoundaryLib/AMReX_MacBndry.H
Src/C_BoundaryLib/AMReX_MacBndry.cpp
Src/C_BoundaryLib/AMReX_Mask.H
Src/C_BoundaryLib/AMReX_Mask.cpp
Src/C_BoundaryLib/AMReX_MultiMask.H
Src/C_BoundaryLib/AMReX_MultiMask.cpp
Src/C_ParticleLib/AMReX_ParGDB.H
Src/C_ParticleLib/AMReX_Particles.H
Src/C_ParticleLib/AMReX_Particles.cpp
Src/C_ParticleLib/AMReX_Particles_F.H
Src/C_ParticleLib/AMReX_TracerParticles.H
Src/C_ParticleLib/AMReX_TracerParticles.cpp
Src/Extern/amrdata/AMReX_AmrData.H
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/Extern/amrdata/AMReX_AmrvisConstants.H
Src/Extern/amrdata/AMReX_DataServices.H
Src/Extern/amrdata/AMReX_DataServices.cpp
Src/Extern/amrdata/AMReX_FABUTIL_1D.F
Src/Extern/amrdata/AMReX_FABUTIL_2D.F
Src/Extern/amrdata/AMReX_FABUTIL_3D.F
Src/Extern/hpgmg/BL_HPGMG.H
Src/F_BaseLib/MemProfiler_f.cpp
Src/F_BaseLib/MultiFab_C_F.H
Src/F_BaseLib/backtrace_c.cpp
Src/F_Interfaces/BaseLib/boxarray_fi.cpp
Src/F_Interfaces/BaseLib/geometry_fi.cpp
Src/F_Interfaces/BaseLib/main.cpp
Src/F_Interfaces/BaseLib/multifab_fi.cpp
Src/F_Interfaces/BaseLib/parallel_fi.cpp
Src/F_Interfaces/BaseLib/parmparse_fi.cpp
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H
Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F
Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F
Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H
Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F
Src/LinearSolvers/C_CellMG/AMReX_AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG/AMReX_AMReX_MultiGrid.cpp
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H
Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F
Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F
Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F
Src/LinearSolvers/C_CellMG/AMReX_LO_F.H
Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F
Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F
Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F
Src/LinearSolvers/C_CellMG/AMReX_LP_F.H
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F
Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F
Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F
Src/LinearSolvers/C_CellMG/AMReX_MG_F.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H
Src/LinearSolvers/C_CellMG4/ABec2.H
Src/LinearSolvers/C_CellMG4/ABec2_F.H
Src/LinearSolvers/C_CellMG4/ABec4.H
Src/LinearSolvers/C_CellMG4/ABec4_F.H
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F
Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F
Src/LinearSolvers/C_TensorMG/AMReX_DV_3D1.F
Src/LinearSolvers/C_TensorMG/AMReX_DV_3D2.F
Src/LinearSolvers/C_TensorMG/AMReX_DV_3D3.F
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_2D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_3D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_2D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_3D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp
Src/LinearSolvers/C_TensorMG/DV_2D.mF
Src/LinearSolvers/C_TensorMG/DV_3D1.mF
Src/LinearSolvers/C_TensorMG/DV_3D2.mF
Src/LinearSolvers/C_TensorMG/DV_3D3.mF
Src/LinearSolvers/C_TensorMG/DV_3D4.mF
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp
Tests/BBIOBenchmark/BBIOTest.cpp
Tests/BBIOBenchmark/BBIOTestDriver.cpp
Tests/C_BaseLib/AMRProfTestBL.cpp
Tests/C_BaseLib/BcastClasses/BcastClasses.cpp
Tests/C_BaseLib/t8BIT.cpp
Tests/C_BaseLib/tBA.cpp
Tests/C_BaseLib/tCArena.cpp
Tests/C_BaseLib/tDM.cpp
Tests/C_BaseLib/tDir.cpp
Tests/C_BaseLib/tFAC.cpp
Tests/C_BaseLib/tFB.cpp
Tests/C_BaseLib/tFillFab.cpp
Tests/C_BaseLib/tMF.cpp
Tests/C_BaseLib/tMFcopy.cpp
Tests/C_BaseLib/tParmParse.cpp
Tests/C_BaseLib/tProfiler.cpp
Tests/C_BaseLib/tRABcast.cpp
Tests/C_BaseLib/tRan.cpp
Tests/C_BaseLib/tVisMF.cpp
Tests/C_BaseLib/tVisMF2.cpp
Tests/C_BaseLib/tread.cpp
Tests/FillBoundaryComparison/main.cpp
Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/LinearSolvers/C_CellMG/COEF_2D.F
Tests/LinearSolvers/C_CellMG/COEF_3D.F
Tests/LinearSolvers/C_CellMG/COEF_F.H
Tests/LinearSolvers/C_CellMG/MACOPERATOR_2D.F
Tests/LinearSolvers/C_CellMG/MACOPERATOR_3D.F
Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H
Tests/LinearSolvers/C_CellMG/MACPROJ_2D.F
Tests/LinearSolvers/C_CellMG/MACPROJ_3D.F
Tests/LinearSolvers/C_CellMG/MacOperator.H
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/C_CellMG/macprojTest.cpp
Tests/LinearSolvers/C_CellMG/main.cpp
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp
Tests/LinearSolvers/C_TensorMG/main_2D.F
Tests/LinearSolvers/C_TensorMG/main_3D.F
Tests/LinearSolvers/C_TensorMG/main_F.H
Tests/LinearSolvers/C_TensorMG/testVI.cpp
Tests/LinearSolvers/ComparisonTest/COEF_1D.F
Tests/LinearSolvers/ComparisonTest/COEF_3D.F
Tests/LinearSolvers/ComparisonTest/COEF_F.H
Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_3D.F
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_F.H
Tests/LinearSolvers/ComparisonTest/compute_norm.cpp
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp
Tests/LinearSolvers/ComparisonTest/writePlotFile.H
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp
Tests/MKDir/MKDir.cpp
Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp
Tools/C_util/Convergence/AVGDOWN_2D.F
Tools/C_util/Convergence/AVGDOWN_3D.F
Tools/C_util/Convergence/AVGDOWN_F.H
Tools/C_util/Convergence/Add.cpp
Tools/C_util/Convergence/ComputeAmrDataNorms.H
Tools/C_util/Convergence/ComputeAmrDataNorms.cpp
Tools/C_util/Convergence/DiffFab.cpp
Tools/C_util/Convergence/DiffSameDomainRefined.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGrid2.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileNormB.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp
Tools/C_util/Statistics/AVGDOWN_2D.F
Tools/C_util/Statistics/AVGDOWN_3D.F
Tools/C_util/Statistics/AVGDOWN_F.H
Tools/C_util/Statistics/ComputeAmrDataStat.H
Tools/C_util/Statistics/ComputeAmrDataStat.cpp
Tools/C_util/Statistics/PltFileFluxAve.H
Tools/C_util/Statistics/PltFileFluxAve.cpp
Tools/C_util/Statistics/PltFileList.cpp
Tools/C_util/Statistics/PltFileStat.cpp
Tools/C_util/Statistics/PltFileXAve.H
Tools/C_util/Statistics/PltFileXAve.cpp
Tools/C_util/TV_TempWrite.H
Tools/C_util/ViewMF/MFNorm.cpp
Tools/C_util/ViewMF/checkMFghostcells.cpp
Tools/C_util/ViewMF/main.cpp
Tools/C_util/ViewMF/mfMinMax.cpp
Tools/C_util/ViewMF/viewMF.cpp
Tools/C_util/ViewMF/viewMFcol.cpp
Tools/C_util/ViewMF/viewMFdiff.cpp
Tools/C_util/ViewMF/viewMFdiffHardWire.cpp
Tools/C_util/WritePlotFile.H
Tools/C_util/WritePlotFile.cpp
Tools/C_util/dbgTools/crsGrids.cpp
Tools/C_util/dbgTools/intersectGrids.cpp
Tutorials/AMR_Adv_C/Source/Adv.H
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/AdvBld.cpp
Tutorials/AMR_Adv_C/Source/Adv_F.H
Tutorials/AMR_Adv_C/Source/Adv_io.cpp
Tutorials/AMR_Adv_C/Source/Adv_setup.cpp
Tutorials/AMR_Adv_C/Source/main.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvBC.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H
Tutorials/AMR_Adv_C_v2/Source/main.cpp
Tutorials/DataServicesTest0/DataServicesTest0.cpp
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp
Tutorials/GettingStarted_C/main.cpp
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX1_C/myfunc_F.H
Tutorials/HeatEquation_EX1_C/writePlotFile.H
Tutorials/HeatEquation_EX2_C/FILCC_2D.F
Tutorials/HeatEquation_EX2_C/FILCC_3D.F
Tutorials/HeatEquation_EX2_C/advance_2d.f90
Tutorials/HeatEquation_EX2_C/advance_3d.f90
Tutorials/HeatEquation_EX2_C/main.cpp
Tutorials/HeatEquation_EX2_C/myfunc_F.H
Tutorials/HeatEquation_EX2_C/writePlotFile.H
Tutorials/HelloWorld_C/main.cpp
Tutorials/MultiColor_C/main.cpp
Tutorials/MultiFabTests_C/GridMoveTest.cpp
Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp
Tutorials/MultiGrid_C/COEF_2D.F90
Tutorials/MultiGrid_C/COEF_3D.F90
Tutorials/MultiGrid_C/COEF_F.H
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H
Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F
Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H
Tutorials/MultiGrid_C/RHS_2D.F90
Tutorials/MultiGrid_C/RHS_3D.F90
Tutorials/MultiGrid_C/RHS_F.H
Tutorials/MultiGrid_C/main.cpp
Tutorials/MultiGrid_C/writePlotFile.H
Tutorials/MultiGrid_C/writePlotFile.cpp
Tutorials/PGAS_HEAT/main.cpp
Tutorials/PGAS_HEAT/writePlotFile.H
Tutorials/PGAS_HEAT/writePlotFile.cpp
Tutorials/PIC_C/main.cpp
Tutorials/PIC_C/single_level.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/solve_with_f90.cpp
Tutorials/PIC_C/two_level.cpp
Tutorials/Sidecar_EX1/DestMFTest.cpp
Tutorials/Sidecar_EX1/GridMoveTest.cpp
Tutorials/Sidecar_EX1/InTransitAnalysis.cpp
Tutorials/Sidecar_EX1/NSidecarsTest.cpp
Tutorials/Sidecar_EX1/SidecarResizeTest.cpp
Tutorials/Sidecar_EX1/TestRankSets.cpp
Tutorials/Tiling_C/main.cpp
Tutorials/Tiling_Heat_C/main.cpp
Tutorials/Tiling_Heat_C/writePlotFile.H
Tutorials/Tiling_Heat_C/writePlotFile.cpp
Tutorials/TwoGrid_PIC_C/main.cpp
Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp
Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp
Tutorials/TwoGrid_PIC_C/split_boxes.cpp
Tutorials/WaveEquation_C/main.cpp
Tutorials/WaveEquation_C/writePlotFile.H
Tutorials/WaveEquation_C/writePlotFile.cpp

commit 8b06440262bffbcca2e1d540f638319bba71e304
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 15:34:10 2016 -0800

    rm Tests/F_BaseLib

Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/ball_def.14656
Tests/F_BaseLib/conn_defs
Tests/F_BaseLib/def_knapsack.out
Tests/F_BaseLib/fornberg_weights.f90
Tests/F_BaseLib/inputs.domain
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/makefile
Tests/F_BaseLib/mt19937ar.f90
Tests/F_BaseLib/t_bl_prof.f90
Tests/F_BaseLib/t_bx.f90
Tests/F_BaseLib/t_bxasc.f90
Tests/F_BaseLib/t_cls.f90
Tests/F_BaseLib/t_knapsack.f90
Tests/F_BaseLib/t_main.f90
Tests/F_BaseLib/t_particles.f90

commit beec626d6dd716ea7335c84e48dec4e7d4b48ca1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 15:33:28 2016 -0800

    rm Src/Python

Src/Python/.gitignore
Src/Python/F90/Makefile
Src/Python/F90/README
Src/Python/F90/fboxlib/__init__.py
Src/Python/F90/fboxlib/boxarray.py
Src/Python/F90/fboxlib/fab.py
Src/Python/F90/fboxlib/layout.py
Src/Python/F90/fboxlib/multifab.py
Src/Python/F90/fboxlib/regrid.py
Src/Python/F90/setup.py
Src/Python/F90/src/blobjects.f90
Src/Python/F90/src/blobjects.py
Src/Python/F90/src/boxlib_numpy_c.c
Src/Python/F90/src/boxlib_numpy_f.f90
Src/Python/F90/src/fboxlib.f90
Src/Python/F90/src/fboxlib_c.c
Src/Python/F90/src/make_new_grids.f90
Src/Python/F90/src/regrid.f90
Src/Python/F90/src/tag_boxes.f90
Src/Python/F90/tests/regrid.py
Src/Python/GMakerules.mak
Src/Python/GNUmakefile
Src/Python/GNUmakefile_CXX.mak
Src/Python/GPackage.mak
Src/Python/README
Src/Python/boxlib/__init__.py
Src/Python/boxlib/bl1.py
Src/Python/boxlib/bl2.py
Src/Python/boxlib/bl3.py
Src/Python/contrib/chemSupport.H
Src/Python/contrib/chemSupport.cpp
Src/Python/contrib/support.H
Src/Python/contrib/support.cpp
Src/Python/setup.py
Src/Python/src/boxlib_wrap_1.cpp.REMOVED.git-id
Src/Python/src/boxlib_wrap_2.cpp.REMOVED.git-id
Src/Python/src/boxlib_wrap_3.cpp.REMOVED.git-id
Src/Python/swig/boxlib.i
Src/Python/swig/numpy.i
Src/Python/tests/test-multifab.py

commit 3ab050052e1eaffe0dbca75a356b4dc7de2b66dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 15:32:50 2016 -0800

    add AMReX prefix to file names

Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_1D.F
Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_2D.F
Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_3D.F
Src/C_AMRLib/AMReX_AMReX_Amr.H
Src/C_AMRLib/AMReX_AMReX_Amr.cpp
Src/C_AMRLib/AMReX_AMReX_AmrLevel.H
Src/C_AMRLib/AMReX_AMReX_AmrLevel.cpp
Src/C_AMRLib/AMReX_AMReX_AuxBoundaryData.H
Src/C_AMRLib/AMReX_AMReX_AuxBoundaryData.cpp
Src/C_AMRLib/AMReX_AMReX_Derive.H
Src/C_AMRLib/AMReX_AMReX_Derive.cpp
Src/C_AMRLib/AMReX_AMReX_Extrapolater.H
Src/C_AMRLib/AMReX_AMReX_Extrapolater.cpp
Src/C_AMRLib/AMReX_AMReX_FLUSH_F.H
Src/C_AMRLib/AMReX_AMReX_LevelBld.H
Src/C_AMRLib/AMReX_AMReX_MAKESLICE_3D.F
Src/C_AMRLib/AMReX_AMReX_MAKESLICE_F.H
Src/C_AMRLib/AMReX_AMReX_PROB_AMR_F.H
Src/C_AMRLib/AMReX_AMReX_SLABSTAT_1D.F
Src/C_AMRLib/AMReX_AMReX_SLABSTAT_2D.F
Src/C_AMRLib/AMReX_AMReX_SLABSTAT_3D.F
Src/C_AMRLib/AMReX_AMReX_SLABSTAT_F.H
Src/C_AMRLib/AMReX_AMReX_SlabStat.H
Src/C_AMRLib/AMReX_AMReX_SlabStat.cpp
Src/C_AMRLib/AMReX_AMReX_StateData.H
Src/C_AMRLib/AMReX_AMReX_StateData.cpp
Src/C_AMRLib/AMReX_AMReX_StateDescriptor.H
Src/C_AMRLib/AMReX_AMReX_StateDescriptor.cpp
Src/C_AMRLib/AMReX_AMReX_StationData.H
Src/C_AMRLib/AMReX_AMReX_StationData.cpp
Src/C_AMRLib/AMReX_extrapolater_1d.f90
Src/C_AMRLib/AMReX_extrapolater_2d.f90
Src/C_AMRLib/AMReX_extrapolater_3d.f90
Src/C_AMRLib/CMakeLists.txt
Src/C_AMRLib/Make.package
Src/C_AmrCoreLib/AMReX_AmrCore.H
Src/C_AmrCoreLib/AMReX_AmrCore.cpp
Src/C_AmrCoreLib/AMReX_AmrParGDB.H
Src/C_AmrCoreLib/AMReX_AmrParticles.H
Src/C_AmrCoreLib/AMReX_Cluster.H
Src/C_AmrCoreLib/AMReX_Cluster.cpp
Src/C_AmrCoreLib/AMReX_ErrorList.H
Src/C_AmrCoreLib/AMReX_ErrorList.cpp
Src/C_AmrCoreLib/AMReX_FLUXREG_1D.F
Src/C_AmrCoreLib/AMReX_FLUXREG_2D.F
Src/C_AmrCoreLib/AMReX_FLUXREG_3D.F
Src/C_AmrCoreLib/AMReX_FLUXREG_F.H
Src/C_AmrCoreLib/AMReX_FillPatchUtil.H
Src/C_AmrCoreLib/AMReX_FillPatchUtil.cpp
Src/C_AmrCoreLib/AMReX_FluxRegister.H
Src/C_AmrCoreLib/AMReX_FluxRegister.cpp
Src/C_AmrCoreLib/AMReX_INTERP_1D.F
Src/C_AmrCoreLib/AMReX_INTERP_2D.F
Src/C_AmrCoreLib/AMReX_INTERP_3D.F
Src/C_AmrCoreLib/AMReX_INTERP_F.H
Src/C_AmrCoreLib/AMReX_Interpolater.H
Src/C_AmrCoreLib/AMReX_Interpolater.cpp
Src/C_AmrCoreLib/AMReX_TagBox.H
Src/C_AmrCoreLib/AMReX_TagBox.cpp
Src/C_AmrCoreLib/CMakeLists.txt
Src/C_AmrCoreLib/Make.package
Src/C_BaseLib/AMReX_Arena.H
Src/C_BaseLib/AMReX_Arena.cpp
Src/C_BaseLib/AMReX_Array.H
Src/C_BaseLib/AMReX_ArrayLim.H
Src/C_BaseLib/AMReX_BArena.H
Src/C_BaseLib/AMReX_BArena.cpp
Src/C_BaseLib/AMReX_BCRec.H
Src/C_BaseLib/AMReX_BCRec.cpp
Src/C_BaseLib/AMReX_BC_TYPES.H
Src/C_BaseLib/AMReX_BLBackTrace.H
Src/C_BaseLib/AMReX_BLBackTrace.cpp
Src/C_BaseLib/AMReX_BLBoxLib_F.f
Src/C_BaseLib/AMReX_BLFort.H
Src/C_BaseLib/AMReX_BLParmParse_F.f
Src/C_BaseLib/AMReX_BLPgas.H
Src/C_BaseLib/AMReX_BLPgas.cpp
Src/C_BaseLib/AMReX_BLProfiler.H
Src/C_BaseLib/AMReX_BLProfiler.cpp
Src/C_BaseLib/AMReX_BLProfiler_F.f
Src/C_BaseLib/AMReX_BLassert.H
Src/C_BaseLib/AMReX_BLutil_F.f
Src/C_BaseLib/AMReX_BaseFab.H
Src/C_BaseLib/AMReX_BaseFab.cpp
Src/C_BaseLib/AMReX_BaseFab_f.H
Src/C_BaseLib/AMReX_BaseFab_nd.f90
Src/C_BaseLib/AMReX_Box.H
Src/C_BaseLib/AMReX_Box.cpp
Src/C_BaseLib/AMReX_BoxArray.H
Src/C_BaseLib/AMReX_BoxArray.cpp
Src/C_BaseLib/AMReX_BoxDomain.H
Src/C_BaseLib/AMReX_BoxDomain.cpp
Src/C_BaseLib/AMReX_BoxLib.H
Src/C_BaseLib/AMReX_BoxLib.cpp
Src/C_BaseLib/AMReX_BoxList.H
Src/C_BaseLib/AMReX_BoxList.cpp
Src/C_BaseLib/AMReX_CArena.H
Src/C_BaseLib/AMReX_CArena.cpp
Src/C_BaseLib/AMReX_CONSTANTS.H
Src/C_BaseLib/AMReX_COORDSYS_1D.F
Src/C_BaseLib/AMReX_COORDSYS_2D.F
Src/C_BaseLib/AMReX_COORDSYS_3D.F
Src/C_BaseLib/AMReX_COORDSYS_F.H
Src/C_BaseLib/AMReX_CoordSys.H
Src/C_BaseLib/AMReX_CoordSys.cpp
Src/C_BaseLib/AMReX_DistributionMapping.H
Src/C_BaseLib/AMReX_DistributionMapping.cpp
Src/C_BaseLib/AMReX_FArrayBox.H
Src/C_BaseLib/AMReX_FArrayBox.cpp
Src/C_BaseLib/AMReX_FILCC_1D.F
Src/C_BaseLib/AMReX_FILCC_2D.F
Src/C_BaseLib/AMReX_FILCC_3D.F
Src/C_BaseLib/AMReX_FPC.H
Src/C_BaseLib/AMReX_FPC.cpp
Src/C_BaseLib/AMReX_FabArray.H
Src/C_BaseLib/AMReX_FabArray.cpp
Src/C_BaseLib/AMReX_FabConv.H
Src/C_BaseLib/AMReX_FabConv.cpp
Src/C_BaseLib/AMReX_Geometry.H
Src/C_BaseLib/AMReX_Geometry.cpp
Src/C_BaseLib/AMReX_IArrayBox.H
Src/C_BaseLib/AMReX_IArrayBox.cpp
Src/C_BaseLib/AMReX_IndexType.H
Src/C_BaseLib/AMReX_IndexType.cpp
Src/C_BaseLib/AMReX_IntVect.H
Src/C_BaseLib/AMReX_IntVect.cpp
Src/C_BaseLib/AMReX_Lazy.H
Src/C_BaseLib/AMReX_Lazy.cpp
Src/C_BaseLib/AMReX_Looping.H
Src/C_BaseLib/AMReX_MemPool.H
Src/C_BaseLib/AMReX_MemPool.cpp
Src/C_BaseLib/AMReX_MemProfiler.H
Src/C_BaseLib/AMReX_MemProfiler.cpp
Src/C_BaseLib/AMReX_MultiFab.H
Src/C_BaseLib/AMReX_MultiFab.cpp
Src/C_BaseLib/AMReX_MultiFabUtil.H
Src/C_BaseLib/AMReX_MultiFabUtil.cpp
Src/C_BaseLib/AMReX_MultiFabUtil_1d.f90
Src/C_BaseLib/AMReX_MultiFabUtil_2d.f90
Src/C_BaseLib/AMReX_MultiFabUtil_3d.f90
Src/C_BaseLib/AMReX_MultiFabUtil_F.H
Src/C_BaseLib/AMReX_NFiles.H
Src/C_BaseLib/AMReX_NFiles.cpp
Src/C_BaseLib/AMReX_Orientation.H
Src/C_BaseLib/AMReX_Orientation.cpp
Src/C_BaseLib/AMReX_PList.H
Src/C_BaseLib/AMReX_ParallelDescriptor.H
Src/C_BaseLib/AMReX_ParallelDescriptor.cpp
Src/C_BaseLib/AMReX_ParmParse.H
Src/C_BaseLib/AMReX_ParmParse.cpp
Src/C_BaseLib/AMReX_Periodicity.H
Src/C_BaseLib/AMReX_Periodicity.cpp
Src/C_BaseLib/AMReX_PhysBCFunct.H
Src/C_BaseLib/AMReX_PhysBCFunct.cpp
Src/C_BaseLib/AMReX_PlotFileUtil.H
Src/C_BaseLib/AMReX_PlotFileUtil.cpp
Src/C_BaseLib/AMReX_Pointers.H
Src/C_BaseLib/AMReX_REAL.H
Src/C_BaseLib/AMReX_RealBox.H
Src/C_BaseLib/AMReX_RealBox.cpp
Src/C_BaseLib/AMReX_SPACE.H
Src/C_BaseLib/AMReX_SPACE_F.H
Src/C_BaseLib/AMReX_TinyProfiler.H
Src/C_BaseLib/AMReX_TinyProfiler.cpp
Src/C_BaseLib/AMReX_Tuple.H
Src/C_BaseLib/AMReX_UseCount.H
Src/C_BaseLib/AMReX_UseCount.cpp
Src/C_BaseLib/AMReX_Utility.H
Src/C_BaseLib/AMReX_Utility.cpp
Src/C_BaseLib/AMReX_VisMF.H
Src/C_BaseLib/AMReX_VisMF.cpp
Src/C_BaseLib/AMReX_bc_types.fi
Src/C_BaseLib/AMReX_bl_flush.f
Src/C_BaseLib/AMReX_bl_fort_module.F90
Src/C_BaseLib/AMReX_ccse-mpi.H
Src/C_BaseLib/AMReX_iMultiFab.H
Src/C_BaseLib/AMReX_iMultiFab.cpp
Src/C_BaseLib/AMReX_mempool_f.f90
Src/C_BaseLib/AMReX_threadbox.f90
Src/C_BaseLib/AMReX_winstd.H
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/GPackage.mak
Src/C_BaseLib/Make.package
Src/C_BoundaryLib/AMReX_BndryData.H
Src/C_BoundaryLib/AMReX_BndryData.cpp
Src/C_BoundaryLib/AMReX_BndryRegister.H
Src/C_BoundaryLib/AMReX_BndryRegister.cpp
Src/C_BoundaryLib/AMReX_BoundCond.H
Src/C_BoundaryLib/AMReX_FabSet.H
Src/C_BoundaryLib/AMReX_FabSet.cpp
Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_1D.F
Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_2D.F
Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_3D.F
Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_F.H
Src/C_BoundaryLib/AMReX_InterpBndryData.H
Src/C_BoundaryLib/AMReX_InterpBndryData.cpp
Src/C_BoundaryLib/AMReX_LO_BCTYPES.H
Src/C_BoundaryLib/AMReX_LO_UTIL.F
Src/C_BoundaryLib/AMReX_MacBndry.H
Src/C_BoundaryLib/AMReX_MacBndry.cpp
Src/C_BoundaryLib/AMReX_Mask.H
Src/C_BoundaryLib/AMReX_Mask.cpp
Src/C_BoundaryLib/AMReX_MultiMask.H
Src/C_BoundaryLib/AMReX_MultiMask.cpp
Src/C_BoundaryLib/CMakeLists.txt
Src/C_BoundaryLib/Make.package
Src/C_ParticleLib/AMReX_ParGDB.H
Src/C_ParticleLib/AMReX_ParticleInit.H
Src/C_ParticleLib/AMReX_Particles.H
Src/C_ParticleLib/AMReX_Particles.cpp
Src/C_ParticleLib/AMReX_Particles_1D.F
Src/C_ParticleLib/AMReX_Particles_2D.F
Src/C_ParticleLib/AMReX_Particles_3D.F
Src/C_ParticleLib/AMReX_Particles_F.H
Src/C_ParticleLib/AMReX_TracerParticles.H
Src/C_ParticleLib/AMReX_TracerParticles.cpp
Src/C_ParticleLib/CMakeLists.txt
Src/C_ParticleLib/Make.package
Src/Extern/amrdata/AMReX_AmrData.H
Src/Extern/amrdata/AMReX_AmrData.cpp
Src/Extern/amrdata/AMReX_AmrvisConstants.H
Src/Extern/amrdata/AMReX_DataServices.H
Src/Extern/amrdata/AMReX_DataServices.cpp
Src/Extern/amrdata/AMReX_FABUTIL_1D.F
Src/Extern/amrdata/AMReX_FABUTIL_2D.F
Src/Extern/amrdata/AMReX_FABUTIL_3D.F
Src/Extern/amrdata/CMakeLists.txt
Src/Extern/amrdata/Make.package
Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H
Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F
Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F
Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F
Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H
Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F
Src/LinearSolvers/C_CellMG/AMReX_AMReX_ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_AMReX_CGSolver.cpp
Src/LinearSolvers/C_CellMG/AMReX_AMReX_Laplacian.cpp
Src/LinearSolvers/C_CellMG/AMReX_AMReX_LinOp.cpp
Src/LinearSolvers/C_CellMG/AMReX_AMReX_MultiGrid.cpp
Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H
Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F
Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F
Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F
Src/LinearSolvers/C_CellMG/AMReX_LO_F.H
Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F
Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F
Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F
Src/LinearSolvers/C_CellMG/AMReX_LP_F.H
Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H
Src/LinearSolvers/C_CellMG/AMReX_LinOp.H
Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F
Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F
Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F
Src/LinearSolvers/C_CellMG/AMReX_MG_F.H
Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H
Src/LinearSolvers/C_CellMG/AMReX_lo_bctypes.fi
Src/LinearSolvers/C_CellMG/CMakeLists.txt
Src/LinearSolvers/C_CellMG/Make.package
Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F
Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F
Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F
Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F
Src/LinearSolvers/C_CellMG4/CMakeLists.txt
Src/LinearSolvers/C_CellMG4/Make.package
Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F
Src/LinearSolvers/C_TensorMG/AMReX_DV_3D1.F
Src/LinearSolvers/C_TensorMG/AMReX_DV_3D2.F
Src/LinearSolvers/C_TensorMG/AMReX_DV_3D3.F
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H
Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp
Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H
Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_2D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_3D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_2D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_3D.F
Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H
Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H
Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp
Src/LinearSolvers/C_TensorMG/CMakeLists.txt
Src/LinearSolvers/C_TensorMG/Make.package
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp
Src/LinearSolvers/C_to_F_MG/AMReX_stencil_types.H
Src/LinearSolvers/C_to_F_MG/CMakeLists.txt
Src/LinearSolvers/C_to_F_MG/Make.package

commit f141a37c0f3b8fa4d436292dc157b07f8bf9846c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 14:52:55 2016 -0800

    fix Tensor MG test

Tests/LinearSolvers/C_TensorMG/GNUmakefile
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp
Tests/LinearSolvers/C_TensorMG/main_2D.F
Tests/LinearSolvers/C_TensorMG/main_3D.F
Tests/LinearSolvers/C_TensorMG/main_F.H

commit d12b6d0ea206228857613a3b4d96059b45110d34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 14:52:40 2016 -0800

    rm duplicated source file

Tests/LinearSolvers/C_CellMG/Make.package

commit 59eb9e6e65e1612f7597862348b8c4b5c07cdfa9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 11 16:00:58 2016 -0800

    rm Tests/StencilOrder

Tests/StencilOrder/README
Tests/StencilOrder/program.f90

commit 4031d584790874e7e77003ad23d5c9af1cc846b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 11 15:58:57 2016 -0800

    rm LinearSolvers/F_MG_Old_Nodal_Stencil
    
    Conflicts:
            Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/GNUmakefile

Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/GNUmakefile
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/bc_interp.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_edge_coeffs.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_multi.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_rhs.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/compute_defect.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_2d_1lev
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_2d_2lev
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_3d_1lev
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_3d_2lev
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/init_cell_coeffs.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.2d.nodal.cross
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.2d.nodal.dense
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.3d.nodal.cross
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.3d.nodal.dense
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/itsol.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/main.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/makefile
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/ml_nd.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/ml_solve.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_interface_stencil.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_mg_cpp.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_mg_tower_smoother.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_multi.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_rhs.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_smoothers.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil_apply.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil_fill.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_sync_resid.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/regression
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/t_smoother.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/t_stencil.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/wrapper.f90

commit faafd2cdf45b1111b8cdaf709173a036f77ea5fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 11 08:16:23 2016 -0800

    rm Tutorials/MultiFab_C_F
    
    Conflicts:
            Tutorials/MultiFab_C_F/GNUmakefile
            Tutorials/MultiFab_C_F/main.cpp

Tutorials/MultiFab_C_F/GNUmakefile
Tutorials/MultiFab_C_F/Make.package
Tutorials/MultiFab_C_F/ff.f90
Tutorials/MultiFab_C_F/main.cpp

commit 7da71ecef4d2dadce59d1a76c57dc073f8043abb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 10 11:43:48 2016 -0800

    rm AMR_Trilinos_C
    
    Conflicts:
            Tutorials/AMR_Trilinos_C/GNUmakefile
            Tutorials/AMR_Trilinos_C/Solver.H
            Tutorials/AMR_Trilinos_C/Solver.cpp
            Tutorials/AMR_Trilinos_C/driver.cpp
            Tutorials/AMR_Trilinos_C/writePlotFile.H
            Tutorials/AMR_Trilinos_C/writePlotFile.cpp

Tutorials/AMR_Trilinos_C/GNUmakefile
Tutorials/AMR_Trilinos_C/Make.package
Tutorials/AMR_Trilinos_C/README
Tutorials/AMR_Trilinos_C/Solver.H
Tutorials/AMR_Trilinos_C/Solver.cpp
Tutorials/AMR_Trilinos_C/SolverBoundary.cpp
Tutorials/AMR_Trilinos_C/driver.cpp
Tutorials/AMR_Trilinos_C/inputs
Tutorials/AMR_Trilinos_C/writePlotFile.H
Tutorials/AMR_Trilinos_C/writePlotFile.cpp

commit 8df7abc6a1cf001b0150b1b33ce59f74236c8519
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 14:28:52 2016 -0800

    rm boxlib release notes

ReleaseNotes/release-notes-16.12.1

commit 1809a2d88da8be69a9ef415bf55b10495bf9e42c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 10 10:59:17 2016 -0800

    rm BoxLib ReleaseNotes
    
    Conflicts:
            ReleaseNotes/release-notes-16.11

ReleaseNotes/release-notes-16.04
ReleaseNotes/release-notes-16.05
ReleaseNotes/release-notes-16.06
ReleaseNotes/release-notes-16.07
ReleaseNotes/release-notes-16.08
ReleaseNotes/release-notes-16.09
ReleaseNotes/release-notes-16.10
ReleaseNotes/release-notes-16.11
ReleaseNotes/release-notes-16.12

commit 8473b732c9426724f09228b071c0fe1249619253
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 9 13:18:25 2016 -0800

    rm Extern/gslib

Src/Extern/gslib/CMakeLists.txt
Src/Extern/gslib/acorni.f
Src/Extern/gslib/backtr.f
Src/Extern/gslib/beyond.f
Src/Extern/gslib/blue.f
Src/Extern/gslib/chknam.f
Src/Extern/gslib/chktitle.f
Src/Extern/gslib/cova3.f
Src/Extern/gslib/dlocate.f
Src/Extern/gslib/dpowint.f
Src/Extern/gslib/dsortem.f
Src/Extern/gslib/gauinv.f
Src/Extern/gslib/gcum.f
Src/Extern/gslib/getindx.f
Src/Extern/gslib/getz.f
Src/Extern/gslib/green.f
Src/Extern/gslib/hexa.f
Src/Extern/gslib/ksol.f
Src/Extern/gslib/ktsol.f
Src/Extern/gslib/locate.f
Src/Extern/gslib/nscore.f
Src/Extern/gslib/numtext.f
Src/Extern/gslib/ordrel.f
Src/Extern/gslib/picksupr.f
Src/Extern/gslib/powint.f
Src/Extern/gslib/psfill.f
Src/Extern/gslib/psline.f
Src/Extern/gslib/pstext.f
Src/Extern/gslib/rand.f
Src/Extern/gslib/red.f
Src/Extern/gslib/resc.f
Src/Extern/gslib/scal.f
Src/Extern/gslib/setrot.f
Src/Extern/gslib/setsupr.f
Src/Extern/gslib/sortem.f
Src/Extern/gslib/sqdist.f
Src/Extern/gslib/srchsupr.f
Src/Extern/gslib/strlen.f

commit 7fb882bb494461e29748428ee928e234666073f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 9 13:17:43 2016 -0800

    rm Tutorials/Chemotaxis_F
    
    Conflicts:
            Tutorials/Chemotaxis_F/GNUmakefile

Tutorials/Chemotaxis_F/GNUmakefile
Tutorials/Chemotaxis_F/GPackage.mak
Tutorials/Chemotaxis_F/README
Tutorials/Chemotaxis_F/advance.f90
Tutorials/Chemotaxis_F/chemotaxis.f90
Tutorials/Chemotaxis_F/dtypes.f90
Tutorials/Chemotaxis_F/inputs.mwe
Tutorials/Chemotaxis_F/kernels.f90
Tutorials/Chemotaxis_F/main.f90
Tutorials/Chemotaxis_F/sdcquad.f90
Tutorials/Chemotaxis_F/write_plotfile.f90
Tutorials/README_F

commit 37b08bf93a067a10de98383763998e055f694d6e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 14:25:15 2016 -0800

    add a readme for migration tools

Tools/Migration/README.md

commit efb191d6dfccc065f43914cd1cee2a69af500752
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 14:14:30 2016 -0800

    update migration document for step 2

Docs/Migration/Migration.md

commit 4e7a2295273b5622a27338d98ac76eef21ae0872
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 13:59:14 2016 -0800

    start to use AMReX namespace for new functions

Src/C_BaseLib/Array.H
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp
Tutorials/MultiColor_C/main.cpp
Tutorials/MultiGrid_C/main.cpp
Tutorials/PIC_C/single_level.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/two_level.cpp
Tutorials/TwoGrid_PIC_C/main.cpp
Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp

commit bf56848daacf9b117c26f4e053b34198b5a90df5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 15 09:24:14 2016 -0800

    add the equivalent of PArray::clear()

Src/C_BaseLib/Array.H

commit a3ae08c4cb86800d8b7b3d806e9f30f70ef2ea1d
Merge: 41e78fc3a a858d833e
Author: John Bell <jbbell@lbl.gov>
Date:   Wed Dec 14 15:49:18 2016 -0800

    Merged in license (pull request #2)
    
    fixed copyright

commit a858d833e0d98b37c707982f69c0282cb9c8ce8b
Author: jbb <jbbell@lbl.gov>
Date:   Wed Dec 14 15:48:00 2016 -0800

    fixed copyright

README.txt
license.txt

commit 74a4cccbdd97e96e659e82fba4a964c744178266
Merge: 2b2be2c87 13fe8835e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 14 12:48:56 2016 -0800

    Merge branch 'weiqun/tmp' into migration/2-parray
    
    Conflicts:
            Src/C_AMRLib/Amr.cpp
            Src/C_AMRLib/Make.package

commit 2b2be2c87ed1d1bc2aa968925246dadcb1f39af9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 14 12:24:12 2016 -0800

    start migration document

Docs/Migration/Migration.md
Tools/Migration/step-1-amrex_home/amrex_home.sh

commit c8bef76bd142d6bc24424b91be1e2bfb81bf951d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 14 10:47:59 2016 -0800

    fix compilation of some tests

Tests/FillBoundaryComparison/GNUmakefile
Tutorials/MultiFabTests_C/GNUmakefile
Tutorials/MultiFabTests_C/GridMoveTest.cpp
Tutorials/Tiling_Heat_C/GNUmakefile

commit 99b43c22f5bbe6449b78ea1f2bb667e0bc8fd585
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 14 10:11:09 2016 -0800

    some Fortran BoxLib update

Tools/C_mk/README.md
Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak
Tools/Migration/step-1-amrex_home/amrex_home.sh

commit beebbfc33d266b2c1aeb0fe51441944bf031d917
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 14 09:42:19 2016 -0800

    Migration step 1: replace BOXLIB_HOME with AMREX_HOME

MiniApps/AMR_Adv_Diff_F90/GNUmakefile
MiniApps/FillBoundary/GNUmakefile
MiniApps/MultiGrid_C/GNUmakefile
MiniApps/PGAS_SMC/GNUmakefile
MiniApps/SMC/GNUmakefile
Src/C_AMRLib/Make.package
Src/C_AmrCoreLib/Make.package
Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/Make.package
Src/C_BoundaryLib/Make.package
Src/C_ParticleLib/Make.package
Src/Extern/amrdata/Make.package
Src/Extern/hpgmg/Make.package
Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/unittests/GNUmakefile
Src/LinearSolvers/C_CellMG/Make.package
Src/LinearSolvers/C_CellMG4/Make.package
Src/LinearSolvers/C_TensorMG/Make.package
Src/LinearSolvers/C_to_F_MG/Make.package
Src/LinearSolvers/F_MG/FParallelMG.mak
Tests/BBIOBenchmark/GNUmakefile
Tests/C_BaseLib/BcastClasses/GNUmakefile
Tests/C_BaseLib/GNUmakefile
Tests/F_BaseLib/GNUmakefile
Tests/FillBoundaryComparison/GNUmakefile
Tests/IOBenchmark/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_TensorMG/GNUmakefile
Tests/LinearSolvers/ComparisonTest/GNUmakefile
Tests/LinearSolvers/F_MG/GNUmakefile
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/GNUmakefile
Tests/MKDir/GNUmakefile
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules
Tools/C_mk/packages/Make.hpgmg
Tools/C_util/AmrDeriveTecplot/GNUmakefile
Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Statistics/GNUmakefile
Tools/C_util/ViewMF/GNUmakefile
Tools/C_util/dbgTools/GNUmakefile
Tools/Migration/step-1-amrex_home/amrex_home.sh
Tools/Postprocessing/F_Src/GNUmakefile
Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/GNUmakefile
Tools/Postprocessing/F_Src/MAESTRO_xrb/GNUmakefile
Tools/Postprocessing/F_Src/tutorial/GNUmakefile
Tools/Py_util/GNUmakefile
Tutorials/AMR_Adv_C/Exec/Make.Adv
Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_Adv_CF/Exec/Make.Adv
Tutorials/AMR_Adv_C_v2/Exec/Make.Adv
Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_Adv_F/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_Adv_F/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_Trilinos_C/GNUmakefile
Tutorials/Chemotaxis_F/GNUmakefile
Tutorials/DataServicesTest0/GNUmakefile
Tutorials/Exp_CNS_NoSpec_F/GNUmakefile
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile
Tutorials/GettingStarted_C/GNUmakefile
Tutorials/GettingStarted_F/GNUmakefile
Tutorials/HeatEquation_EX1_C/GNUmakefile
Tutorials/HeatEquation_EX1_CF/GNUmakefile
Tutorials/HeatEquation_EX1_F/GNUmakefile
Tutorials/HeatEquation_EX2_C/GNUmakefile
Tutorials/HeatEquation_EX2_F/GNUmakefile
Tutorials/HeatEquation_EX3_F/GNUmakefile
Tutorials/HeatEquation_EX4_F/GNUmakefile
Tutorials/HeatEquation_EX5_F/GNUmakefile
Tutorials/HelloWorld_C/GNUmakefile
Tutorials/HelloWorld_CF/GNUmakefile
Tutorials/MultiColor_C/GNUmakefile
Tutorials/MultiFabTests_C/GNUmakefile
Tutorials/MultiFab_C_F/GNUmakefile
Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_F/GNUmakefile
Tutorials/PGAS_HEAT/GNUmakefile
Tutorials/PIC_C/GNUmakefile
Tutorials/Random_F/GNUmakefile
Tutorials/Sidecar_EX1/GNUmakefile
Tutorials/Tiling_C/GNUmakefile
Tutorials/Tiling_Heat_C/GNUmakefile
Tutorials/Tiling_Heat_F/GNUmakefile
Tutorials/TwoGrid_PIC_C/GNUmakefile
Tutorials/WaveEquation_C/GNUmakefile
Tutorials/WaveEquation_F/GNUmakefile

commit 41e78fc3a2b459710cd91a54ef91449ecf07e72b
Merge: d4c9fd3bd 816f4e785
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Wed Dec 14 09:01:26 2016 -0800

    Merged in development (pull request #1)
    
    fix 2d addNParticles

commit 816f4e785154c46e00e7d2c9df5cdd00ee55503f
Merge: d4c9fd3bd 6c3216ef5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 14 08:56:45 2016 -0800

    Merge branch 'github-development' into development

commit 6c3216ef5e42c70e36a7e321370132d31d792c7d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 14 08:54:56 2016 -0800

    fix 2d addNParticles

Src/C_ParticleLib/Particles.H

commit d4c9fd3bd93960931e606166de4fd92cd7fc02e0
Merge: f76840cde 38bf06512
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 13 14:46:28 2016 -0800

    Merge branch 'github'

commit f76840cde6807cd4eaddbfc837786b8eb7e87cb4
Merge: 001805229 19f33fb2f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 13 14:46:01 2016 -0800

    Merge branch 'master' into development

commit 38bf065123d5b5cdb179f31d0a07e9d2b939c956
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 13 14:24:13 2016 -0800

    Release 16.12.1

ReleaseNotes/release-notes-16.12.1

commit 4a136ee6fcf098275088aa37a55454d618957535
Merge: 2da8d8d46 bc82627c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 13 13:56:06 2016 -0800

    Merge branch 'master' into development

commit 2da8d8d46e77dfabc4b494f0d38134a889f499f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 13 13:27:09 2016 -0800

    fix generic plotfile writer

Src/C_BaseLib/PlotFileUtil.cpp

commit 3892093c7e819f1307bb6a26fc4c57bc0ae99a9c
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 13 11:40:41 2016 -0800

    fix comment, format.

Src/C_BaseLib/PlotFileUtil.H

commit 685b71d8d2978674db4b7c678b1f6bca101c3242
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 13 11:34:57 2016 -0800

    clarify comment.

Src/C_BaseLib/PlotFileUtil.H

commit 2fd460ef6fbe1b7d010f608f45b38c5e65802b76
Merge: fe6b64049 e99e2a4ac
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 13 11:27:06 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit fe6b640493978e190a89af629108a2f309d1fcfd
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 13 11:26:45 2016 -0800

    fix comments, back.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 3c49247a88861ce4307876df7e52ab4a0e3aaa75
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 13 11:25:04 2016 -0800

    call new function to prebuild directories.

Src/C_AMRLib/Amr.cpp

commit e99e2a4acb1d8eea193787655675ca01a8e4c371
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Dec 12 19:44:12 2016 -0500

    switch from getopt to argparse to get self-help

Tools/C_scripts/makebuildinfo_C.py

commit bc82627c132c68f293c2bf743a39b49dd94e81ac
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 12 16:29:21 2016 -0800

    First pass at addNParticles function in ParticleContainer class.

Src/C_ParticleLib/Particles.H

commit bfd9da39ed4447db3514af16d55c94e7727f8dd0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Dec 12 14:36:05 2016 -0500

    the generic COMP_VERSION variable is used by the build info scripts to
    put the compiler version into job_info

Tools/C_mk/comps/cray.mak
Tools/C_mk/comps/gnu.mak
Tools/C_mk/comps/intel.mak
Tools/C_mk/comps/pgi.mak

commit ed5c4b57936b88ed1ca2cbd2a089726a1f81161d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 9 12:11:19 2016 -0800

    put instruction on how to use addr2line into Backtrace files

Src/C_BaseLib/BLBackTrace.cpp

commit 900a96c50603982308786052fe39d6999b2e8dfe
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 9 12:04:16 2016 -0800

    remove static.

Src/C_BaseLib/PlotFileUtil.H

commit 885f5503c9c89bac8092b417604f8ae0074f5ec1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 9 10:13:40 2016 -0800

    better way to detect Open MPI

Tools/C_mk/sites/Make.unknown

commit 143f53b6149c980b44d3ad0ed27c0acc8fb94068
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 8 16:11:07 2016 -0800

    support for new cartgrid format.

Src/Extern/amrdata/AmrData.H
Src/Extern/amrdata/AmrData.cpp

commit e0ae1df7ef5ae63041f5f724fdcf1933b9450710
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 8 16:01:24 2016 -0800

    functions for generic plotfiles.

Src/C_BaseLib/PlotFileUtil.H
Src/C_BaseLib/PlotFileUtil.cpp

commit 19f33fb2fe15ce449a4cd50ee686e4daf8b2e84b
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 8 15:13:08 2016 -0800

    bitbucketpushtest.

Docs/Notes.io_implementation

commit 0018052297337ea42d75efc3b31c5fb170b4f736
Merge: 632640dd4 a5568940e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Dec 3 16:41:25 2016 -0500

    Merge pull request #16 from nbren12/development
    
    raise error in dep.py if fortran preprocessor fails

commit 632640dd4da4364f719fea58e6b6ac9bb4672090
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 2 15:43:46 2016 -0800

    add support for trapping ABRT.  this allows for backtracing interger overflow with gcc.

Src/C_BaseLib/BLBackTrace.H
Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Utility.cpp

commit c222467f1efdf78f665e7cbd7666a2f2999c3fcb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 2 13:48:26 2016 -0800

    gfortran: in debug mode use 2^31 - 1 as the initial value for integers

Tools/C_mk/comps/gnu.mak

commit 54b703c465160bb53f3e9ffa23ac8343c8239ac7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 2 13:07:59 2016 -0800

    make missing f90.depends an error so that error messages become more helpful

Tools/C_mk/Make.rules
Tutorials/HelloWorld_C/Make.package

commit e8f41712ef7ef4f069e6405b34bd6b3893c7e3b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 2 10:35:33 2016 -0800

    because of pgi compiler issue, have to remove -traceback

Tools/C_mk/comps/pgi.mak

commit 13fe8835ee4fe00e810ff04d3985ab7c6076f28c
Merge: 5e350c37a 650327da6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 2 09:04:37 2016 -0800

    Merge branch 'development' into experimental

commit 650327da65624ee069445b7aed363abaaee8ec2a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 2 09:02:56 2016 -0800

    Release Notes for BoxLib 16.12

ReleaseNotes/release-notes-16.12

commit 9ed9d498f5bd793ffc7571aa885e09288da4a294
Merge: 97142e632 6027b8e4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 2 08:35:31 2016 -0800

    Merge branch 'master' into development

commit 97142e63240f72420bf6268b9a61fc765da1a002
Merge: 3408453ff 753a8362f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Dec 2 01:12:57 2016 -0500

    Merge pull request #18 from BoxLib-Codes/preprocessing
    
    continue if we encounter a module that is not provided

commit 753a8362fb5fc3dd25ff26210c303f02172b94a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Dec 2 01:11:32 2016 -0500

    use a GNU make $(warning...) to report unfound module dependencies.
    We retain the print to stderr too, so we can easily see these by
    simply redirecting stdout if desired

Tools/F_scripts/dep.py

commit f7a062fcf27a6a9599f3f1f4e29705f214e6bce4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 1 20:12:21 2016 -0500

    if we file requests a module that nothing provides then continue
    on to the next.  This was the intended behavior originally, but
    we missed a `continue` statement.  This allows for system-provided
    modules to work without them in the `IGNORES` list.  This fixes
    a bug that Brian ran into

Tools/F_scripts/dep.py

commit 3408453ffec9e03d86ed7ffb945315ae6f728264
Merge: 71ae16382 5b6d179b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 1 20:03:18 2016 -0500

    Merge pull request #17 from BoxLib-Codes/preprocessing
    
    catch dep.py errors and have make abort with an error message

commit 5b6d179b23869864421faad5c2c02cfb5aaa6ce9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 1 19:22:12 2016 -0500

    address Weiqun's PR comments

Tools/F_scripts/dep.py

commit 1bea892e800c6779cbf4ad0447e378ab58c54877
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 1 19:14:43 2016 -0500

    catch dep.py errors and have make abort with an error message
    explaining how to enable debug info in the dependency checking

Tools/C_mk/Make.rules
Tools/F_scripts/dep.py

commit 71ae16382c2bb88f71f943117e78f0204f4491b0
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 1 14:09:42 2016 -0800

    make extra stream flushes the default for now.

Src/C_BaseLib/VisMF.cpp

commit 56a7a8410ab981ce4d1ae57c71fbf53fb9cfedbf
Merge: 6258dfedc 1a6ca1b70
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 1 13:23:17 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 1a6ca1b70184f8f9d9fe8f92f7269e1afbac5e73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 1 12:43:35 2016 -0800

    intel: link with multi-threaded fortran library

Tools/C_mk/comps/intel.mak

commit 171a60c99e0229a7f5ebffe408d8dbe9a26572b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 1 10:14:52 2016 -0800

    delete more potential unsafe functions

Src/C_BaseLib/BCRec.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp

commit b43be2394070fb1db01a79ae213ea1222e6245ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 30 22:22:23 2016 -0800

    move the distribution map check into BL_ASSERT and make sure it does not dereference null ptr

Src/C_BaseLib/FabArray.H

commit a5568940ec947794b6980ba57384bec8c1244dba
Author: Noah D. Brenowitz <nbren12@gmail.com>
Date:   Wed Nov 30 22:45:55 2016 -0500

    remove bash stuff

Tools/F_scripts/dep.py

commit 5df703a4b4646fa6e2eacf42eb520c80bf03be51
Author: Noah D. Brenowitz <nbren12@gmail.com>
Date:   Wed Nov 30 22:37:59 2016 -0500

    raise error if fortran preprocessor fails
    
    Fixes https://github.com/BoxLib-Codes/BoxLib/issues/15

Tools/F_scripts/dep.py

commit 1b3d8de9b629e976f7d447b84d18a5b647e92e5f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 30 17:39:38 2016 -0800

    added flush options to try to fix titan.

Src/C_BaseLib/VisMF.cpp

commit 916d16b10e6c0ff0108665632054454493ac780a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 30 16:10:02 2016 -0800

    more compiler flag tweaks

Tools/C_mk/comps/intel.mak
Tools/C_mk/comps/pgi.mak

commit 6258dfedc718597ec1535e23bdabbef8c08b893d
Merge: 9acde8afc b46d3301b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 30 14:32:13 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 4bd885ea8a157f506c05f51bbe5aa98fce97ddff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 30 14:27:32 2016 -0800

    gcc: trap integer overflow

Tools/C_mk/comps/gnu.mak

commit b46d3301bf9710b04a7e9ebf6e1863d3dc4efcf9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 30 10:14:24 2016 -0800

    fix due to recently deleted functions

Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit e1158a7ebc009df62511bfa07455d5f0d4d4b428
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 30 10:13:30 2016 -0800

    we can now safely inline validbox and fabbox

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit be96a07ed4556d9e65a99ba1469c579196710442
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 30 09:17:17 2016 -0800

    fix make for a test

Tests/C_BaseLib/GNUmakefile

commit 8e6450c9ac0084866fb833c4556739d2450edd78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 30 08:55:47 2016 -0800

    fix a dangling pointer

Src/C_BaseLib/FabArray.H

commit f2fab6992013e10baa735128f9f4d9487bbd1cf1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 30 08:51:00 2016 -0800

    delete functions that return a pointer to internal data of rvalue objects

Src/C_BaseLib/BCRec.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/RealBox.H

commit 9acde8afc7e6c4849ff6a2f11a2839b8990322e5
Merge: 37f8bb599 69b9bc3e3
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 29 10:43:30 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 69b9bc3e3b2dd5e5d6d617d2115ef9f6cafae4cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 28 14:43:33 2016 -0800

    remove duplicated function arguments

Src/F_BaseLib/cc_restriction.f90
Src/F_BaseLib/ml_cc_restriction.f90
Src/LinearSolvers/F_MG/mg.f90

commit 20281549bc84b16e8d417d443df87113d2ec1393
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 28 14:15:10 2016 -0800

    fix memory leak

Src/C_BaseLib/VisMF.cpp

commit cf6dfed17b7f76977596e5a5f1a9c5246a9a0cf9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 13:01:32 2016 -0800

    Don't want to get compile error because of call to 3d routine with lo,hi hardwired to lo(2),hi(2)

Tutorials/GettingStarted_F/work_on_data.f90

commit 6027b8e4c985d1c79b71fcf1cf9d3d09745dd324
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 13:00:05 2016 -0800

    Don't want to get warning about calling 3d routine with lo,hi hardwired to lo(2),hi(2)

Tutorials/GettingStarted_F/work_on_data.f90

commit 39baea948b0506ff3f5dc29fb9b72f083450968e
Merge: 978bea7de 751c9f20c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Mon Nov 28 10:25:40 2016 -0800

    Merge pull request #12 from zingale/development
    
    add USE_GPROF to enable profiling with gprof

commit 751c9f20cd4e74eef64f3cfd8917279612b3e1a4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Nov 28 13:19:15 2016 -0500

    add USE_GPROF to enable profiling with gprof

Tools/C_mk/comps/gnu.mak

commit 978bea7deb298c13de8ef0aaea7c6f47ec7f2d83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Nov 27 18:46:11 2016 -0500

    remove tcsort -- this is not used by anything

Tools/F_mk/GMakedefs.mak
Tools/F_scripts/tcsort.pl

commit a67b52a971f338c07c17f2396fdd56a5583862dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 26 22:42:53 2016 -0500

    isinf --> std::isinf

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 8dc1b3cc2a5718fa43499105797886cbca17545a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 26 17:03:53 2016 -0800

    Intel: -openmp --> -qopenmp for Intel >= 16 because -openmp is deprecated.

Tools/C_mk/comps/intel.mak

commit 760972de2ef309ea0618a3eab79a6bff192bea3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 26 12:32:47 2016 -0800

    Intel: add more checks

Tools/C_mk/comps/intel.mak

commit 1f2e13327aadce6ff7f88417970390e54998c95c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 26 12:06:57 2016 -0800

    PGI: add fpe trap and force implicit none on f90 files

Tools/C_mk/comps/pgi.mak

commit 592e18cd46ceb5f5614ceaa2e9fd724f378b50c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 26 12:06:04 2016 -0800

    GNU: initialize fortran integers to a large bogus number in debug mode

Tools/C_mk/comps/gnu.mak

commit 7cf6fc0e394702544223cc0ec47c3efa3e51938c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 26 11:26:39 2016 -0800

    force implicit none for f90 files with gnu

Tools/C_mk/comps/gnu.mak

commit 5e350c37a8736b77ef6b0cb097399fa5f33c327c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 26 10:57:22 2016 -0800

    typo

Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp

commit 37f8bb5990854b62f336b75873fb8bd11e3a3cbf
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 23 11:42:50 2016 -0800

    fix comments.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit 3354078cb7f8d24402ec90328b85734c4d5db30b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 22 15:53:05 2016 -0800

    mpic++ -> mpicxx because some systems do not seem to have mpic++

Tools/C_mk/sites/Make.unknown

commit 41849f68803e42439dd52e92e128113e4a26c574
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 22 15:03:47 2016 -0800

    amr_level is a unique_ptr

Src/C_AMRLib/Amr.cpp

commit e7166ffc434ac0c8f1087ae2905b194f1b39e8fe
Merge: bf0164576 30e67b677
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 22 14:53:10 2016 -0800

    Merge branch 'development' into experimental
    
    Conflicts:
            Src/C_AMRLib/Amr.cpp
            Src/C_BaseLib/Array.H
            Src/C_BaseLib/CMakeLists.txt
            Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp

commit 30e67b67719a97478e5f54b52c87f5676dcc39c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 22 13:34:22 2016 -0800

    add python version check and force make to exit if requirement is not met

Tools/C_mk/Make.defs

commit 7641739be7759a629c0a7b8ddcce852b47df2167
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 22 11:11:25 2016 -0800

    fix Tutorials/AMR_Adv_C_v2

Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp

commit 827897be87f72ad3eab98b9e19fc8bddac5c8631
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 22 11:11:03 2016 -0800

    std::min -> std::min<int> because Array::size() returns size_t now

Src/C_BaseLib/VisMF.cpp

commit 8ba46f878ef64b979378c528f895f1f94408083a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 17 10:45:54 2016 -0800

    more helpful message

Tools/C_mk/Make.rules

commit 8c617bc3743908bcfdcdc2a5cc8875beea692865
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 15 17:01:10 2016 -0800

    mpif90 -->

Tools/C_mk/sites/Make.unknown

commit ecf80e3d5edea85c95a669a9c69dfbf8d1138860
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 15 16:14:53 2016 -0800

    more intelligent way of adding link flags

Tools/C_mk/sites/Make.unknown

commit 23a79c85bf0c4318599b59e4de34e5dd8e577da4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 12 12:47:43 2016 -0800

    turn on C++11 in F_mk

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/Linux_cray.mak
Tools/F_mk/comps/Linux_intel.mak
Tools/F_mk/comps/Linux_pgi.mak
Tools/F_mk/comps/gfortran.mak

commit dccc134baaed527a21b0f3f35d24b3ad7ec4c575
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 11 13:23:05 2016 -0800

    rm Rose

Tests/RoseTests/CPP/NullTransTest/GNUmakefile
Tests/RoseTests/CPP/NullTransTest/PROB_3D.F
Tests/RoseTests/CPP/NullTransTest/PROB_F.H
Tests/RoseTests/CPP/NullTransTest/README
Tests/RoseTests/CPP/NullTransTest/RoseNullTest.cpp
Tests/RoseTests/F90/Readme
Tests/RoseTests/F90/test1/GNUmakefile
Tests/RoseTests/F90/test1/main.f90
Tests/RoseTests/F90/test2/GNUmakefile
Tests/RoseTests/F90/test2/main.f90
Tests/RoseTests/F90/test3/GNUmakefile
Tests/RoseTests/F90/test3/bc.f90
Tests/RoseTests/F90/test4/GNUmakefile
Tests/RoseTests/F90/test4/main.f90
Tests/RoseTests/F90/test5/GNUmakefile
Tests/RoseTests/F90/test5/main.f90
Tests/RoseTests/F90/test6/GNUmakefile
Tests/RoseTests/F90/test6/main.f90
Tests/RoseTests/F90/test6/omp.f90
Tests/RoseTests/F90/test7/GNUmakefile
Tests/RoseTests/F90/test7/main.f90
Tests/RoseTests/F90/test7/probin.f90
Tests/RoseTests/F90/test7/runtime.f90
Tests/RoseTests/F90/test8/GNUmakefile
Tests/RoseTests/F90/test8/init_data.f90
Tests/RoseTests/F90/test8/main.f90

commit 681af15bd4a30f481fc7cec4fdb1bf7075cf5241
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 11 12:59:41 2016 -0800

    rm C_TowerLib with Marc's permission

Src/C_TowerLib/Layout.H
Src/C_TowerLib/Layout.cpp
Src/C_TowerLib/MFTower.H
Src/C_TowerLib/MFTower.cpp
Src/C_TowerLib/MFTower_2D.F
Src/C_TowerLib/MFTower_3D.F
Src/C_TowerLib/MFTower_F.H
Src/C_TowerLib/Make.package
Tutorials/AMR_PETSc_C/Exec/Make.PETSc
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/.gdbinit
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Make.package
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Prob_2d.f90
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_2lev.dat
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_3lev.dat
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probdata.f90
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probin.2d
Tutorials/AMR_PETSc_C/README
Tutorials/AMR_PETSc_C/Source/Darcy.H
Tutorials/AMR_PETSc_C/Source/Darcy.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES.H
Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES_2D.F
Tutorials/AMR_PETSc_C/Source/DarcySNES_F.H
Tutorials/AMR_PETSc_C/Source/Darcy_2D.f90
Tutorials/AMR_PETSc_C/Source/Darcy_F.H
Tutorials/AMR_PETSc_C/Source/MLBoundary.H
Tutorials/AMR_PETSc_C/Source/MLBoundary.cpp
Tutorials/AMR_PETSc_C/Source/Make.package
Tutorials/AMR_PETSc_C/Source/extern_probin.template
Tutorials/AMR_PETSc_C/Source/interpolate.f90
Tutorials/AMR_PETSc_C/Source/main.cpp
Tutorials/README_C

commit b71f76e806f146bcd6060a31339c01c0149e3015
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 11 12:34:56 2016 -0800

    add a few functions for converting array of (unique) pointers to array of (const) pointers

Src/C_BaseLib/Array.H

commit 1876e60cc7d1035bd5ef752e637cea48bbcc6fcc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 11 12:29:20 2016 -0800

    fix  in make

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit bd7f8cac2849c6ab72b057d57e52f8e637c4af84
Merge: f67819baa 90595472a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 22 10:48:07 2016 -0800

    Merge branch 'before-parray' into dev-exp-make-array
    
    Conflicts:
            Src/C_BaseLib/CMakeLists.txt

commit f67819baab5047372b54c3d7dcd84694005bab8b
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 21 13:24:13 2016 -0800

    fix for ieee_32 rd.

Src/C_BaseLib/VisMF.cpp

commit 6652eff1cae54ba33285ddad5a2d099b54fca5a0
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 18 14:54:22 2016 -0800

    clean up debugging diagnostics.

Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.cpp

commit 902b3cab83a3118b77fd718c678e738d22c42870
Merge: e7adec596 afdef8515
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 18 13:00:50 2016 -0800

    merge fix.

commit e7adec596c6c3cb344947e9cabc3ee9e420cc3d9
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 18 12:57:26 2016 -0800

    output cleanup.

Src/C_BaseLib/VisMF.cpp

commit 974a43b8b0cad35b7411f26ce075c1e441b6dd87
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 18 12:56:33 2016 -0800

    additions to i/o documentation.

Docs/Notes.io_implementation
Docs/Readme.io

commit 85bccb3141ff9792c0635bd4057411e9a61206fe
Merge: ff92fc959 983f9e996
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 18 12:07:28 2016 -0800

    Merge branch 'optio' of https://github.com/BoxLib-Codes/BoxLib into optio

commit 983f9e9965150bc9496251f9facc80b3e20b3528
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 17 16:19:15 2016 -0800

    combine nfiles dependent iterators.

Src/C_BaseLib/BLProfiler.H
Src/C_BaseLib/BLProfiler.cpp

commit bf01645769fa027cba0ebd34fad2c3c9670c7ad4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 17 10:45:54 2016 -0800

    more helpful message

Tools/C_mk/Make.rules

commit a1d408fdce3ac909d25026286f7219e258315293
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 17 10:34:00 2016 -0800

    rm MLSDCAmr

Src/C_AMRLib/MLSDCAmr.H
Src/C_AMRLib/MLSDCAmr.cpp
Src/C_AMRLib/MLSDCAmrEncap.cpp
Src/C_AMRLib/Make.package

commit afdef851547ef67c7b11dd5875bc4f628243b85e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 16 16:56:53 2016 -0800

    bl_avg_eg_to_cc for 2 and 1D

Src/C_BaseLib/MultiFabUtil.cpp
Src/C_BaseLib/MultiFabUtil_1d.f90
Src/C_BaseLib/MultiFabUtil_2d.f90
Src/C_BaseLib/MultiFabUtil_F.H

commit ff92fc9596b901b2b189336d95f79585d2970ca6
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 16 15:33:02 2016 -0800

    fix comment.

Src/C_BaseLib/NFiles.H

commit 192d871d718cf9561077a450bc48ffa6731a878b
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Nov 16 15:16:56 2016 -0800

    Fixup README to use the example-tests.py example file instead of one that no longer exists.

Tools/RegressionTesting/README

commit 4ea2cc82a23c7dbd66c9f2b505425faf784e908f
Merge: 9a5555176 b92a7b290
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Nov 16 16:16:52 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 9a5555176460a69c0e4d216e6c7be346b743e0cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Nov 16 16:16:37 2016 -0500

    add a heavily commented example inputs file

Tools/RegressionTesting/example-tests.ini

commit b92a7b290143e7ae404ca9a8549fa0fdbd14911c
Merge: 467ecfe66 ccef5dc3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 16 09:18:11 2016 -0800

    Merge branch 'fnodalfillpatch' into development

commit 467ecfe66b847cd22d25b46a7664356aafbb7b5c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed Nov 16 01:25:59 2016 -0500

    Fix error message

Src/C_AMRLib/Amr.cpp

commit 52ad8c8e7ec671f16f904158bfd04dbea6f05b17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Nov 15 22:27:14 2016 -0500

    fix the --no_update functionality to work when a repo is specified

Tools/RegressionTesting/regtest.py

commit b4ba5ef36c28a5695d0e760a36799a7de7b145af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 15 17:01:10 2016 -0800

    mpif90 -->

Tools/C_mk/sites/Make.unknown

commit b63792092e40151d194cf1c7979af96c92195611
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 15 16:14:53 2016 -0800

    more intelligent way of adding link flags

Tools/C_mk/sites/Make.unknown

commit 5d458fed043e7ad90f433f2256cdf129101f4448
Merge: f3b6d4bf8 0775508fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Nov 15 18:03:32 2016 -0500

    Merge pull request #11 from jrood-nrel/development
    
    Adding exception handling to a particular shutil.rmtree().

commit 0775508fa9f7628f514e7c2c21e9927c31dbfe85
Author: Jon Rood <jrood@nrel.gov>
Date:   Tue Nov 15 15:59:44 2016 -0700

    Reducing exception to only OSError.

Tools/RegressionTesting/regtest.py

commit b2e47b80c264fdfde6a25a62f7b0a53a98804e30
Author: Jon Rood <jrood@nrel.gov>
Date:   Tue Nov 15 15:12:43 2016 -0700

    Adding exception handling to a particular shutil.rmtree(). Otherwise, this command can cause errors on certain filesystems and the test suite can completely fail before finishing.

Tools/RegressionTesting/regtest.py

commit f07997a1a78e4b4fe04540b51271d68c6ff35ac5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 15 13:20:21 2016 -0800

    fix more int and unsigned comparisons for OPAL because it uses -Werror=sign-compare.

Src/C_ParticleLib/Particles.H

commit f1e283732e322c87dceec6d251ab4b96bcd2ee5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 15 12:12:45 2016 -0800

    typo

Src/C_ParticleLib/Particles.H

commit 428e348abb2b8ff1cb980182e1d0b78187b39a08
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 15 12:12:01 2016 -0800

    fix more int and unsigned comparisons for OPAL because it uses -Werror=sign-compare.

Src/C_ParticleLib/Particles.H

commit 60a7ed700a34840b8c2c56c81bc4a926c78141a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 15 10:33:05 2016 -0800

    fix more int and unsigned comparisons for OPAL because it uses -Werror=sign-compare.

Src/C_ParticleLib/Particles.H

commit 9267833f64a7dd780b652c0739501566e9148977
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 15 09:07:48 2016 -0800

    fix a number of typos; fix a number of int and unsigned comparison for OPAL

Src/C_AMRLib/SlabStat.cpp
Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp
Src/C_BaseLib/FabArray.H
Src/C_ParticleLib/Particles.H
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H

commit 47d19b9966ca602c4582a7c68d15308f3e406c83
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 14 16:17:43 2016 -0800

    more code for nfiles and blprof.

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit b78cfd7e2e8f0e8aef926b0660abaee946535801
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 13 17:29:57 2016 -0800

    fix signature of function average_down_faces

Src/C_BaseLib/MultiFabUtil.cpp

commit d04f8c27393c1b2582c42a9b356126c9d0ec5f7c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 13 10:17:31 2016 -0800

    fix new bug in last commit

Src/C_BaseLib/Array.H

commit 517a53140eb9023a1bae17d00becd09554519347
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 13 08:27:18 2016 -0800

    more consistent style

Src/C_BaseLib/Array.H
Src/C_ParticleLib/Particles.H
Tests/LinearSolvers/ComparisonTest/compute_norm.cpp
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp
Tests/LinearSolvers/ComparisonTest/writePlotFile.H
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp
Tutorials/MultiColor_C/main.cpp
Tutorials/MultiGrid_C/main.cpp
Tutorials/PIC_C/Make.package
Tutorials/PIC_C/single_level.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/solve_with_f90.cpp
Tutorials/PIC_C/solve_with_hpgmg.cpp
Tutorials/PIC_C/two_level.cpp
Tutorials/TwoGrid_PIC_C/main.cpp
Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp
Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp

commit 0392339692680d18e80cc5e0288e0b46f0aa3f6d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 12 12:47:43 2016 -0800

    turn on C++11 in F_mk

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/Linux_cray.mak
Tools/F_mk/comps/Linux_intel.mak
Tools/F_mk/comps/Linux_pgi.mak
Tools/F_mk/comps/gfortran.mak

commit 031940ce20bcaae498f7c7516cb7103794e069cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 12 12:28:49 2016 -0800

    fix tutorials

Tutorials/GettingStarted_C/GNUmakefile
Tutorials/GettingStarted_C/main.cpp
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX2_C/main.cpp
Tutorials/MultiColor_C/main.cpp
Tutorials/MultiFabTests_C/GridMoveTest.cpp
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp
Tutorials/MultiGrid_C/main.cpp
Tutorials/PGAS_HEAT/main.cpp
Tutorials/PIC_C/solve_with_hpgmg.cpp
Tutorials/README_C
Tutorials/Tiling_Heat_C/main.cpp
Tutorials/TwoGrid_PIC_C/main.cpp
Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp
Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp

commit db0b6f16aaed2e6037cfb482b7c6aba6f307d3c5
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 11 17:17:14 2016 -0800

    use NFilesIter for profiling output.

Src/C_BaseLib/BLProfiler.H
Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/NFiles.H

commit e9d92f7ed3824260d09336b02e9c0121674217f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 11 15:14:19 2016 -0800

    fix compilation of a number of tests

Tests/C_BaseLib/GNUmakefile
Tests/FillBoundaryComparison/main.cpp
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/ComparisonTest/compute_norm.cpp
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp
Tests/LinearSolvers/ComparisonTest/writePlotFile.H
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp

commit 04fd580fc0ce3bd1ddb9fe80dd75fb84e3370023
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 11 14:46:04 2016 -0800

    add support for appending nfiles set.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit 47a56e3353dc8dac2874303837fce3ae469a7577
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 11 14:30:00 2016 -0800

    add const

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 52a813079d02d2669315cd1513060ddca47df6b5
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 11 13:30:16 2016 -0800

    output for verbose only, remove unused var.

Src/C_AMRLib/Amr.cpp

commit 84aec263556074f931aae8c6e0b6c991c32cff3c
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 11 13:29:01 2016 -0800

    test for zero grids, output for debug only.

Src/C_BaseLib/NFiles.cpp
Src/C_BaseLib/VisMF.cpp

commit c4ae192af235eb58f707d74f3723ce9fe4f61b35
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 11 13:23:05 2016 -0800

    rm Rose

Tests/RoseTests/CPP/NullTransTest/GNUmakefile
Tests/RoseTests/CPP/NullTransTest/PROB_3D.F
Tests/RoseTests/CPP/NullTransTest/PROB_F.H
Tests/RoseTests/CPP/NullTransTest/README
Tests/RoseTests/CPP/NullTransTest/RoseNullTest.cpp
Tests/RoseTests/F90/Readme
Tests/RoseTests/F90/test1/GNUmakefile
Tests/RoseTests/F90/test1/main.f90
Tests/RoseTests/F90/test2/GNUmakefile
Tests/RoseTests/F90/test2/main.f90
Tests/RoseTests/F90/test3/GNUmakefile
Tests/RoseTests/F90/test3/bc.f90
Tests/RoseTests/F90/test4/GNUmakefile
Tests/RoseTests/F90/test4/main.f90
Tests/RoseTests/F90/test5/GNUmakefile
Tests/RoseTests/F90/test5/main.f90
Tests/RoseTests/F90/test6/GNUmakefile
Tests/RoseTests/F90/test6/main.f90
Tests/RoseTests/F90/test6/omp.f90
Tests/RoseTests/F90/test7/GNUmakefile
Tests/RoseTests/F90/test7/main.f90
Tests/RoseTests/F90/test7/probin.f90
Tests/RoseTests/F90/test7/runtime.f90
Tests/RoseTests/F90/test8/GNUmakefile
Tests/RoseTests/F90/test8/init_data.f90
Tests/RoseTests/F90/test8/main.f90

commit 2a0467c8920b5cc1c08b8dc88553e7b3f46d2519
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 11 12:59:41 2016 -0800

    rm C_TowerLib with Marc's permission

Src/C_TowerLib/Layout.H
Src/C_TowerLib/Layout.cpp
Src/C_TowerLib/MFTower.H
Src/C_TowerLib/MFTower.cpp
Src/C_TowerLib/MFTower_2D.F
Src/C_TowerLib/MFTower_3D.F
Src/C_TowerLib/MFTower_F.H
Src/C_TowerLib/Make.package
Tutorials/AMR_PETSc_C/Exec/Make.PETSc
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/.gdbinit
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Make.package
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Prob_2d.f90
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_2lev.dat
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_3lev.dat
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probdata.f90
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probin.2d
Tutorials/AMR_PETSc_C/README
Tutorials/AMR_PETSc_C/Source/Darcy.H
Tutorials/AMR_PETSc_C/Source/Darcy.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES.H
Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES_2D.F
Tutorials/AMR_PETSc_C/Source/DarcySNES_F.H
Tutorials/AMR_PETSc_C/Source/Darcy_2D.f90
Tutorials/AMR_PETSc_C/Source/Darcy_F.H
Tutorials/AMR_PETSc_C/Source/MLBoundary.H
Tutorials/AMR_PETSc_C/Source/MLBoundary.cpp
Tutorials/AMR_PETSc_C/Source/Make.package
Tutorials/AMR_PETSc_C/Source/extern_probin.template
Tutorials/AMR_PETSc_C/Source/interpolate.f90
Tutorials/AMR_PETSc_C/Source/main.cpp
Tutorials/README_C

commit 9e252f1397e4780329bdf2cac4b76f0d2c9b2976
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 11 12:55:04 2016 -0800

    add const to MultiFabUtil functions

Src/C_BaseLib/MultiFabUtil.H
Src/C_BaseLib/MultiFabUtil.cpp
Src/C_BaseLib/MultiFabUtil_F.H
Tutorials/PIC_C/solve_for_accel.cpp

commit ee0a76a72a141145220b5499998b1c0fb480d3aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 11 12:34:56 2016 -0800

    add a few functions for converting array of (unique) pointers to array of (const) pointers

Src/C_BaseLib/Array.H

commit 08abd3caf3aa3d6f65530198d3861fa1c51e825d
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 11 12:45:40 2016 -0800

    change function name.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit db98ecfcaba24215b00edb3f0578d6d7c1a1baf1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 11 12:29:20 2016 -0800

    fix  in make

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 60283fa6f6b80ccf49f07ea6062121736bee581c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 11 11:33:41 2016 -0800

    rm PArray from ParticleLib and LinearSolver

Src/C_BaseLib/MultiFabUtil.H
Src/C_BaseLib/MultiFabUtil.cpp
Src/C_ParticleLib/Particles.H
Src/C_ParticleLib/TracerParticles.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG4/ABec2.cpp
Src/LinearSolvers/C_CellMG4/ABec4.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Tutorials/MultiGrid_C/main.cpp
Tutorials/PIC_C/single_level.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/solve_with_f90.cpp
Tutorials/PIC_C/two_level.cpp

commit 3ee3b4376103e73c73742e8c7fdc5c53097ce5aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 10 13:46:02 2016 -0800

    remove PArray

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/SlabStat.H
Src/C_AMRLib/SlabStat.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp
Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp
Src/C_AmrCoreLib/AmrCore.cpp
Src/C_AmrCoreLib/ErrorList.H
Src/C_AmrCoreLib/ErrorList.cpp
Src/C_AmrCoreLib/FillPatchUtil.H
Src/C_AmrCoreLib/FillPatchUtil.cpp
Src/C_AmrCoreLib/TagBox.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package
Src/C_BaseLib/MemPool.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/MultiFabUtil.H
Src/C_BaseLib/MultiFabUtil.cpp
Src/C_BaseLib/MultiFabUtil_F.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/iMultiFab.cpp
Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/InterpBndryData.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp

commit f3b6d4bf865bd7815333caf5397e57f54c419056
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Nov 9 19:54:49 2016 -0500

    report for each variable in a plotfile if there is a NaN

Tools/Postprocessing/F_Src/fnan.f90

commit e07e33a627e9c5ec4f8af4c49651e3979d025dd5
Merge: 3bb003f9e e7eba2fc5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Nov 9 19:37:30 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 3bb003f9eedb8d181b9f79d4a4e71997bc969938
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Nov 9 19:37:13 2016 -0500

    add a simple tool to dump data to the screen

Tools/Postprocessing/F_Src/fdump.f90

commit 90595472a6fd20699036524aa0892336491db879
Merge: 1b80c5227 e7eba2fc5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 9 10:27:46 2016 -0800

    Merge branch 'development' into experimental

commit e7eba2fc5fceb6019f1a866e720de365e530b16c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 9 10:27:16 2016 -0800

    use size_t instead of int as loop index in a few places so that OPAL can compile

Src/C_ParticleLib/Particles.H

commit 1b80c5227eeec087b32d948b0b52d430613a1937
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 9 09:37:30 2016 -0800

    use Array instead of vector for consistence and bound checking

Src/C_BaseLib/PlotFileUtil.H
Src/C_BaseLib/PlotFileUtil.cpp

commit d96e70dcfd0f306520f75f99609c42ec407791a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 8 14:43:06 2016 -0800

    rework on the Array class

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Array.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/FabConv.cpp
Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp
Tools/C_mk/Make.defs

commit 96c72c5b55b151eccff5598cbadd4c7857736ed0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 8 14:41:21 2016 -0800

    rm BL_CXX11.H because C++11 is now require; replace BL_OVERRIDE with override

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
Src/C_AMRLib/Amr.H
Src/C_AMRLib/MLSDCAmr.H
Src/C_AMRLib/StateDescriptor.H
Src/C_AmrCoreLib/Interpolater.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BLPgas.cpp
Src/C_BaseLib/BL_CXX11.H
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/CArena.H
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/MemPool.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/PhysBCFunct.H
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/MacBndry.H
Src/C_ParticleLib/Particles.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_TensorMG/DivVis.H
Tests/C_BaseLib/BcastClasses/GNUmakefile
Tests/C_BaseLib/GNUmakefile
Tutorials/AMR_Adv_C/Source/Adv.H
Tutorials/AMR_Adv_C/Source/AdvBld.cpp
Tutorials/AMR_Adv_C_v2/Exec/Make.Adv
Tutorials/MultiFabTests_C/GNUmakefile

commit 11e41eed28cee8818b45dd3c7a2a6566fb7b2ffe
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 8 14:38:23 2016 -0800

    change Array to vector to run with the intel compiler.

Src/C_BaseLib/VisMF.cpp

commit fc67a15c6ac869b04aeed4f9c57e79282d008939
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 8 14:21:30 2016 -0800

    no longer need to specify FCOMP

Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_Trilinos_C/GNUmakefile
Tutorials/HeatEquation_EX1_C/GNUmakefile
Tutorials/HeatEquation_EX2_C/GNUmakefile
Tutorials/HelloWorld_C/GNUmakefile
Tutorials/MultiColor_C/GNUmakefile
Tutorials/MultiFabTests_C/GNUmakefile
Tutorials/MultiGrid_C/GNUmakefile
Tutorials/PGAS_HEAT/GNUmakefile
Tutorials/PIC_C/GNUmakefile
Tutorials/Sidecar_EX1/GNUmakefile
Tutorials/Tiling_C/GNUmakefile
Tutorials/Tiling_Heat_C/GNUmakefile
Tutorials/TwoGrid_PIC_C/GNUmakefile

commit 0f1ada142f095da780e6832dc6a9fd2d6f9ec3c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 8 14:12:28 2016 -0800

    Src/C_AMRLib/Make.package doe not include C_AmrCoreLib anymore

MiniApps/FillBoundary/GNUmakefile
MiniApps/MultiGrid_C/GNUmakefile
Src/C_AMRLib/Make.package
Tests/C_BaseLib/BcastClasses/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/MacOpMacDrivers.H
Tests/LinearSolvers/C_CellMG/MacOperator.H
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/C_TensorMG/GNUmakefile
Tests/LinearSolvers/ComparisonTest/GNUmakefile
Tests/MKDir/GNUmakefile
Tutorials/AMR_Adv_C/Exec/Make.Adv
Tutorials/AMR_PETSc_C/Exec/Make.PETSc
Tutorials/Tiling_Heat_C/GNUmakefile
Tutorials/WaveEquation_C/GNUmakefile

commit cbd753d3269e58e5af7c25a8526ca8009782533e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 8 13:34:44 2016 -0800

    need to pass fincludes into MODDEP

Tools/C_mk/Make.rules

commit 07692755c815b3970e887efdf0f6330f51b4d521
Merge: 693988c97 7271aa170
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 8 12:24:12 2016 -0800

    Merge branch 'development' into experimental
    
    Ray will have to add his make setup back to maybe Tools/C_mk/sites/Make.nrel.
    
    Conflicts:
            Tools/C_mk/Make.Linux
            Tools/C_mk/Make.defs
            Tools/C_mk/Make.mpi

commit 693988c97bda8819ebf80205e1e0686194985b1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 7 17:06:03 2016 -0800

    try to detect mpich or openmpi

Tools/C_mk/sites/Make.unknown

commit 811597575f05d202c8da268e68a10782b2f1807f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 7 16:37:48 2016 -0800

    more on README.md

Tools/C_mk/README.md

commit 62b462d61ffbc22f49a8c86e45982a59bf3c1e75
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 7 16:25:45 2016 -0800

    minor

Tools/C_mk/README.md

commit 2ca7c52d7e09ebc7cf06c2d96447f541c910c046
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 7 16:22:08 2016 -0800

    fix format

Tools/C_mk/README.md

commit 40facdd70b4cf0d61b4765c1feb400c2a550b678
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 7 16:17:57 2016 -0800

    more on README.md for make

Tools/C_mk/Make.defs
Tools/C_mk/README.md

commit 7271aa170436056f61ed76b9ce12b1fe13ddcae2
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Nov 6 18:45:02 2016 -0800

    C_mk: add workaround for compiling C++11 features using Intel compilers at NERSC
    
    This is a known but unfixed Cray bug. The workaround is to force Intel
    compilers to use compatible header files from GCC, specifically from GCC 4.9.3.
    The user can do this by loading the 'gcc/4.9.3' module.

Tools/C_mk/Make.defs

commit 5d4116587ac489ff6b8bd244ba8159117932dab9
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 7 08:16:54 2016 -0800

    C_mk, F_mk: remove Babbage compiler hooks (it has been retired)

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit b8ca62f7c537c3f881313813e249668b1c61dc1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 7 09:14:31 2016 -0800

    MLSDCAmr: restrict --> Restrict to avoid name conflict.  Although restrict is not a C++ keyword and it was used as a member function of class MLSDCAmrLevel, cray compiler is unhappy about it being used because it is a C keyword.

Src/C_AMRLib/MLSDCAmr.H
Src/C_AMRLib/MLSDCAmr.cpp

commit 7a9c305847768730e85ea114a7c394d6338d89ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 6 12:08:51 2016 -0800

    add python to build requirement

Tools/C_mk/README.md

commit de368e7090af91ce40a2621a983d2e90c1d735f4
Merge: 745216615 c10cf9a7e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Nov 5 21:40:01 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 745216615e28fda97cda225f9a5720a75f3d8cfa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Nov 5 21:39:38 2016 -0400

    need to actually pass FPP_DEFINES to the dependency script

Tools/F_mk/GMakerules.mak

commit a20df7d9f49447f650a0a2ff3d55854bd5fc50a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 4 20:12:54 2016 -0400

    do not exit due to compiler mismatch for goals like clean, realclean, etc.

Tools/C_mk/Make.rules
Tools/C_mk/sites/Make.nersc
Tools/C_mk/sites/Make.olcf

commit 63fd17bc896d8d36639e56d9a328dc0aad4e00fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 4 16:39:21 2016 -0700

    removed -fimplicit-none flag because we have some really old Fortran code

Tools/C_mk/comps/gnu.mak

commit 99b28139ae995d81f9e1eea2e22f790f9af3c0cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 4 14:45:25 2016 -0700

    Make.nersc: add -lmpichf90

Tools/C_mk/sites/Make.nersc
Tools/C_mk/sites/Make.olcf

commit 07e9f1825df97cc6b59d817491b107ea424ca59c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 4 12:58:20 2016 -0700

    add intel.mak and Make.vtune

Tools/C_mk/Make.defs
Tools/C_mk/comps/cray.mak
Tools/C_mk/comps/gnu.mak
Tools/C_mk/comps/intel.mak
Tools/C_mk/comps/pgi.mak
Tools/C_mk/tools/Make.vtune

commit 0ac4db369d75c03f49a539c78ce49e863b95149a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 4 11:21:58 2016 -0700

    add Make.nersc and cray.mak

Tools/C_mk/comps/cray.mak
Tools/C_mk/comps/pgi.mak
Tools/C_mk/sites/Make.nersc

commit 7f797916e4f41352c5921b33209d9c36ae18e515
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 4 13:35:11 2016 -0400

    Make.olcf: link to mpichf90

Tools/C_mk/sites/Make.olcf

commit e2ba3f7b1304116698fa6f36a9ac93381c9c354c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 4 10:30:11 2016 -0700

    fix missing $ in gnu.mak

Tools/C_mk/comps/gnu.mak

commit 057adabf2aef9737bcee377520d257b62d474038
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 4 13:11:30 2016 -0400

    rename gcc.mak to gnu.mak to match Cray's convention for naming PrgEnv; add sites/Make.olcf

Tools/C_mk/Make.defs
Tools/C_mk/Make.local.template
Tools/C_mk/comps/gnu.mak
Tools/C_mk/sites/Make.olcf
Tools/C_mk/sites/Make.unknown

commit c352b65091fc2e4ebdf83bf346e448491e1b81e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 3 19:19:27 2016 -0400

    add an example of filter-out in Make.local.template

Tools/C_mk/Make.local.template

commit 1c75381a16ce5ad5ad40b2fd0b7d910e7573dcf7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 3 18:33:50 2016 -0400

    In C++11, isnan and isinf are in std namespace

Src/C_BaseLib/FArrayBox.cpp

commit 11d4d5be73515b06dde315e765bd5c6e093d6a86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 3 18:33:22 2016 -0400

    add pgi.mak

Tools/C_mk/Make.defs
Tools/C_mk/comps/gcc.mak
Tools/C_mk/comps/pgi.mak

commit ceb2e1dd6d571eddc985f05e6aad0799cf65bf6c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 3 17:21:47 2016 -0400

    add Make.unknown

Tools/C_mk/Make.defs
Tools/C_mk/Make.local.template
Tools/C_mk/sites/Make.ccse
Tools/C_mk/sites/Make.unknown

commit 4e84ff39e74aa7a07939b4d437128fe3e10aa530
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 3 13:37:30 2016 -0700

    another typo in README

Tools/C_mk/README.md

commit d054d348f506bda03cf4103df78b855ad1ee6dea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 3 13:34:43 2016 -0700

    typo in README

Tools/C_mk/README.md

commit 08bea853a826f2b07e49860d8456f082a817ee46
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 3 13:27:43 2016 -0700

    new Make system work in progress: gcc and CCSE are done

Tools/C_mk/Make.AIX
Tools/C_mk/Make.CYGWIN_NT
Tools/C_mk/Make.Darwin
Tools/C_mk/Make.FreeBSD
Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.local.template
Tools/C_mk/Make.machines
Tools/C_mk/Make.mpi
Tools/C_mk/Make.rules
Tools/C_mk/Make.upcxx
Tools/C_mk/README.md
Tools/C_mk/comps/gcc.mak
Tools/C_mk/packages/Make.hpgmg
Tools/C_mk/sites/Make.ccse

commit c10cf9a7e70bbbe04c0df806dc4939a3b0926326
Author: Grout <ray.grout@nrel.gov>
Date:   Thu Nov 3 09:22:38 2016 -0600

    Revised Peregrine (NREL) configuration to use intel or gcc toolchains

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit e32cc3c503a6c91aa70cae9674a1d4f34220d5dd
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 2 15:34:12 2016 -0700

    set default header formats.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/VisMF.cpp

commit dc31fcfa6396c0fbaf8be0345b07f27dc46d9fab
Merge: 08425aebd 8360c56b5
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 2 13:36:45 2016 -0700

    fix merge conflicts.

commit c3cd50d6fedf109dce2a35078b1d651d8c8d2ee0
Author: Grout <ray.grout@nrel.gov>
Date:   Wed Nov 2 13:11:20 2016 -0600

    Add makefile defs for Peregrine (NREL cluster)

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 08425aebd7a37e581a70629de60c0610fedd4189
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 2 12:08:34 2016 -0700

    changes to doc and inputs.

Docs/Readme.io
Tests/IOBenchmark/inputs

commit 8360c56b55f66506089cf4d32321f2712191d02d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Nov 2 09:19:51 2016 -0400

    add a runtime_params attribute for a test to override inputs

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py

commit 3dc041cfdca767f52ea606cdb9686994d6800787
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 1 16:37:18 2016 -0700

    simplify file order reads.

Src/C_BaseLib/VisMF.cpp

commit 1ba883e6d99c561ba6d81b7d3d75d5d2d0c662fe
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 1 16:35:41 2016 -0700

    function for items per bin.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit ddd49a238efedf1aa937499c4bbb219dda2d6034
Merge: 54c9457de 6a7cfb954
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Nov 1 12:31:57 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 54c9457de4b623da0eb8a31cc431ca640bf1c334
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Nov 1 12:28:26 2016 -0700

    Intel doesn't seem to define __STDC__ for its Fortran preprocessor,
    so force it to take a particular branch for macro expansion

Src/C_BaseLib/ArrayLim.H

commit 6a7cfb954e1503f242828c06e8eae59016665c1b
Merge: f801a8c0d 20ecaa152
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 1 09:17:51 2016 -0700

    Merge branch 'development'

commit f801a8c0dea4037d7785a71afe2d6a6522002df4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 1 09:17:28 2016 -0700

    Release Notes 16.11

ReleaseNotes/release-notes-16.11

commit 20ecaa152c51b436f8f560ced368daba4aa9ca80
Merge: 71e1cd7e7 b7a3db689
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 1 09:16:50 2016 -0700

    Merge branch 'master' into development

commit ccef5dc3add4bb814b0932b1e84de68c4d1b700f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 31 20:46:15 2016 -0700

    fix a new bug in Fortran fillpatch for face data

Src/F_BaseLib/fillpatch.f90

commit 71e1cd7e78ea5b633e43236d13913c7c0dd8c1ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Oct 31 13:59:36 2016 -0400

    don't require probin -- this will be on the user to ensure it exists

Tools/RegressionTesting/params.py
Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/test_report.py

commit 57bd51ee71d2290e95442b9e92b50baca8756222
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 31 09:11:34 2016 -0700

    fix some new bugs in Fortran fillpatch for face data

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/interp.f90

commit 73f548f64af7516a8ac3aea77d3cc8505b63cb9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 28 14:56:59 2016 -0700

    minor

Src/C_BaseLib/Box.cpp

commit 49b75e5ccfca6175cec4f3bae4ca9e50dd10edd6
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 28 14:48:44 2016 -0700

    optimize sync reads.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 25909ced2abd51d940a6951088ad5e9e450b5461
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 28 10:37:02 2016 -0700

    fillpatch for face data

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/interp.f90

commit 66cb4d5f07e6fb616076d4495db73dcc964a727c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 28 10:35:35 2016 -0700

    add some functions for nodal box coarsening

Src/F_BaseLib/box_f.f90
Src/F_BaseLib/boxarray_f.f90

commit 08cc1ef82edcc462c9e39b2635cdb41fedf3e8c0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 27 16:21:43 2016 -0700

    Last one ...

Tools/RegressionTesting/IAMR-tests.ini

commit 6c9a0ab224d3ad5593108eadd356305ee318c9ac
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 27 15:58:22 2016 -0700

    Remove more app specific regression test files.

Tools/RegressionTesting/LMC-tests.ini
Tools/RegressionTesting/RNS-tests.ini
Tools/RegressionTesting/SMC-tests.ini

commit da41eabd3d23ca78d4e3a58ac9a3d71f4500a6a2
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 27 15:43:39 2016 -0700

    support for non-native format conversions.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 48f21a9f1268ce1af6492c2734a5d092caf9278a
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 27 15:39:37 2016 -0700

    added const.

Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp

commit bb72844266cd2585caf4728341221ad51ee2edb4
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 27 15:38:54 2016 -0700

    correct comments.

Src/C_BaseLib/FArrayBox.H

commit 421bcdd8fae8f03a51ec6eade55f80fcbfff793c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 27 18:37:48 2016 -0400

    move these to the application codes

Tools/RegressionTesting/Castro-SBU-tests.ini
Tools/RegressionTesting/Maestro-tests.ini
Tools/RegressionTesting/Microphysics-tests-pgi.ini
Tools/RegressionTesting/Microphysics-tests.ini

commit b657453bc32310c5e5d04e98f72b119872426c48
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 27 15:26:05 2016 -0700

    Removed Nyx-tests.ini from the regression testing directory.

Tools/RegressionTesting/Nyx-tests.ini

commit 7c232dbda1d65b3c0364ec4864ac63ddb841f4b1
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 26 12:26:21 2016 -0700

    change to a more searchable name.

Src/C_BaseLib/FArrayBox.cpp

commit 75c119ea5ba10b60d292f6e6df9e2a645d406ed7
Author: Grout <ray.grout@nrel.gov>
Date:   Wed Oct 26 08:28:41 2016 -0600

    Fix to make InitOnePerCell work in 2D

Src/C_ParticleLib/ParticleInit.H

commit 38d943e13df8bfb6ee6469d0d157334d41e73a89
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 24 15:33:45 2016 -0700

    make sure grid id is valid

Src/C_ParticleLib/Particles.cpp

commit ed1661ecf453ce9f7fdadd1ca9a6118c7640474d
Merge: 8b9027e09 eb58c46b0
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 24 15:22:28 2016 -0700

    Merge branch 'optio' of https://github.com/BoxLib-Codes/BoxLib into optio

commit 8b9027e09e78b941437792f095adb5911af26fce
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 24 15:21:57 2016 -0700

    dont copy data for single grid combined read, seek fix for persistent streams, secondary sort.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/VisMF.cpp

commit 266526ba2e73a7d7c2caed249de6e1e822269ba4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 24 12:17:17 2016 -0700

    fix typo

Src/C_BaseLib/PlotFileUtil.H
Src/C_BaseLib/PlotFileUtil.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp

commit 0a26ebb18a7547af985faafaafd918b5c6669a8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 24 11:09:57 2016 -0700

    Particles: add functions to clear particle boxarray and distribution map and some other minor changes

Src/C_AmrCoreLib/AmrCore.cpp
Src/C_AmrCoreLib/AmrParGDB.H
Src/C_AmrCoreLib/AmrParticles.H
Src/C_ParticleLib/ParGDB.H
Src/C_ParticleLib/ParticleInit.H
Src/C_ParticleLib/Particles.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp

commit 47918e76854dd49b9a1041d09b4a347b38369f0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 21 20:59:16 2016 -0700

    AMR_Adv_C_v2 tutorial: fix bc in interp

Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp

commit 244df0549da85e73042d8f9bb959e2d515cdaaea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 21 12:27:17 2016 -0700

    AMR_Adv_C_v2 tutorial: iteratively build fine levels in init

Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp

commit 21211ca3dbaa97d9f5d82ccbd776e61d7d28bc49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 21 11:52:46 2016 -0700

    sync up time in post coarse timestep for all levels

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H

commit f17fc95e78225aaf7aa347017e058bda6740f12f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 21 11:50:19 2016 -0700

    AMR_Adv_C_v2 tutorial: put regrid_int, check_int, plot_int, etc. in amr parameter space

Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp

commit d25d213937381b12a183b71771b23b8715d0f2a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 21 09:37:07 2016 -0700

    sync up time in post coarse timestep

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp

commit fca81accb5297e8f02b33d302a41139fd4091825
Merge: f6585ee39 21459f95f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 20 16:43:52 2016 -0700

    Merge branch 'development' into amrcore

commit f6585ee3907461bd821cc984deae0504a6aca981
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 20 16:43:45 2016 -0700

    minor

Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp

commit b7a3db689e02c83ab5804cffaa0ae9b3acdedd17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 20 16:07:36 2016 -0700

    add missing template parameter

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/MultiFab.cpp

commit 21459f95f85876cd2b9c8136e3d1005fcb7e0f40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 20 16:07:36 2016 -0700

    add missing template parameter

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/MultiFab.cpp

commit 301fb50c99f29b743b4d810a6da9b6f635904dc4
Merge: 0706bee8b 42e8f0468
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 20 16:03:18 2016 -0700

    Merge branch 'amrcore' of github.com:BoxLib-Codes/BoxLib into amrcore

commit 42e8f04687c0fdea16c228a270feb60156700dc5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 20 15:06:59 2016 -0700

    Getting the cmake stuff to work ...

Src/CMakeLists.txt

commit 1d5fb27d7515c02e05ffa3749fc0b75a84d9dded
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 20 15:05:50 2016 -0700

    Rename box_camr --> box_camrcore for C_AmrCoreLib.

Src/C_AmrCoreLib/CMakeLists.txt

commit 5d78e92b5813d7562ca541454261f8440eb74b56
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 20 15:00:46 2016 -0700

    We want AmrParticles to depend on AmrCore not Amr

Src/C_AmrCoreLib/AmrParticles.H

commit fc261a8e712a1e57bfd0fa412950202d3678ff7b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 20 14:58:30 2016 -0700

    Add new CMakeLists.txt for C_AmrCoreLIb and modify the ones in C_AMRLib and Source.

Src/CMakeLists.txt
Src/C_AMRLib/CMakeLists.txt
Src/C_AmrCoreLib/CMakeLists.txt

commit 0706bee8b46c0244413433fa4e9c4a285b26bf4f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 20:48:33 2016 -0700

    minor

Src/C_BaseLib/PlotFileUtil.cpp

commit afa5d62ec08618f830bc56fe766d8c8d7e2cc199
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 16:58:10 2016 -0700

    AmrAdv/AmrCore tutorial: write the last plotfile

Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp

commit 0064621bec870ca65702a201b131e2e8bc280525
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 16:43:13 2016 -0700

    pass explicit distributionmap

Src/C_AMRLib/FillPatchUtil.cpp

commit 7b75876a82cc15a83b664558367dc634c6f4a21c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 16:41:46 2016 -0700

    minor

Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp

commit 5f6ad74268a48c7e4a37864af8da3e82e27608c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 16:34:50 2016 -0700

    AmrAdv/AmrCore tutorial: flush distributionmap cache

Src/C_AmrCoreLib/FillPatchUtil.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp

commit b8f4404d0ef76a492df5fc2145d48ab903d505e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 16:15:46 2016 -0700

    AmrAdv/AmrCore tutorial: add regrid

Src/C_AmrCoreLib/AmrCore.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp

commit 89c4e0d6cbb09298cbc2fee1601b32947b61f022
Merge: 04bef474e db6bec872
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 19 17:16:29 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 04bef474ee99a39b3cf984e7eec33e9aa533c6de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 19 17:15:47 2016 -0400

    since there can be many more system-provided modules, don't abort if
    a module is not found, but instead print a warning to STDERR

Tools/F_scripts/dep.py

commit db6bec8722e91854e57c32766c4d7f33df7ed817
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 10:28:55 2016 -0700

    fix a typo

Tools/Release/ppCleanup.py

commit fda957069933072a9edc0eaea3c189cc085cb06b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 10:28:06 2016 -0700

    wip

Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp

commit 8849d4ccf78b46a3a35a451d5ed3aa1a33a4cd86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 09:47:18 2016 -0700

    AmrAdv/AmrCore tutorial: add reflux

Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp

commit e4cbf5007c7257dd628750acb4dc630fcfe3b7d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 09:01:16 2016 -0700

    AmrAdv/AmrCore tutorial: average down in post timestep

Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp

commit 06a364639f91f790ace3e81ba4ecc21ea5b3a5bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 11:37:45 2016 -0400

    fix isinf and isnan for PGI; it looks like PGI pretends to be __GNUC__

Src/C_BaseLib/FArrayBox.cpp

commit d61a0d29fd79d6a8437b57b99ab10b2cd194954d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 17:06:10 2016 -0700

    AmrAdv/AmrCore tutorial: write plotfiles

Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp

commit 14ebd0aaf4a030872b36c2a163a1784c6aee821c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 16:50:39 2016 -0700

    AmrAdv/AmrCore tutorial: add advect Fortran routines

Tutorials/AMR_Adv_C_v2/Exec/Make.Adv
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H
Tutorials/AMR_Adv_C_v2/Source/Src_2d/Adv_2d.f90
Tutorials/AMR_Adv_C_v2/Source/Src_2d/Make.package
Tutorials/AMR_Adv_C_v2/Source/Src_2d/compute_flux_2d.f90
Tutorials/AMR_Adv_C_v2/Source/Src_2d/slope_2d.f90
Tutorials/AMR_Adv_C_v2/Source/Src_3d/Adv_3d.f90
Tutorials/AMR_Adv_C_v2/Source/Src_3d/Make.package
Tutorials/AMR_Adv_C_v2/Source/Src_3d/compute_flux_3d.f90
Tutorials/AMR_Adv_C_v2/Source/Src_3d/slope_3d.f90

commit b273fcb66cca245ecb9da6705380467b06a612f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 16:12:55 2016 -0700

    AmrAdv/AmrCore tutorial: FillPatch

Src/C_BaseLib/PhysBCFunct.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvBC.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp
Tutorials/AMR_Adv_C_v2/Source/Make.package

commit 6fde01d77bd8be674bc4d2aacf2a8b1dae7cefa8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 16:12:32 2016 -0700

    new BaseFab::make_alias function

Src/C_BaseLib/BaseFab.H

commit 83ec549869ad72a9932924299a1881a7531052c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 16:12:32 2016 -0700

    new BaseFab::make_alias function

Src/C_BaseLib/BaseFab.H

commit 0be1ddcbf45e8d7b6a949b3e8ca0c077144a0deb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 13:29:34 2016 -0700

    AmrAdv/AmrCore tutorial: compute dt; set up time stepping

Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp
Tutorials/AMR_Adv_C_v2/Source/main.cpp

commit b4c9ebf3fbad40ffc1c98032a52cb938684c6a5e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 10:46:43 2016 -0700

    AmrAdv/AmrCore tutorial: put tagging parameters in inputs

Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H
Tutorials/AMR_Adv_C_v2/Source/Src_nd/Make.package
Tutorials/AMR_Adv_C_v2/Source/Src_nd/Tagging_nd.f90
Tutorials/AMR_Adv_C_v2/Source/Src_nd/tagging_params.f90

commit dc5d97a5525f3ace538b00c128862204be9128e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 10:29:12 2016 -0700

    AmrAdv/AmrCore tutorial: write plotfile

Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp

commit 58ac3c505a7b1ceb0e03bbb4751377ad1cd8b3f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 10:28:36 2016 -0700

    remove unused variables

Tutorials/AMR_Adv_C_v2/Source/Src_nd/Tagging_nd.f90

commit 4bdf1ed867dd0cfb56ea09e9ad9f6a73f8c45357
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 10:27:40 2016 -0700

    PlotFileUtil: write multi-level plotfile

Src/C_BaseLib/PlotFileUtil.H
Src/C_BaseLib/PlotFileUtil.cpp

commit d1c85af7b3b04a31050afe8354dbd58435261e75
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Oct 17 19:26:43 2016 -0400

    copy the string routines over from Castro

Src/F_Interfaces/BaseLib/parmparse_fi.cpp
Src/F_Interfaces/BaseLib/parmparse_mod.f90

commit ce704fee1c39a8b5b4d75746136647c49b56e502
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 15 22:07:39 2016 -0700

    AmrAdv/AmrCore tutorial: implement ErrorEst

Tutorials/AMR_Adv_C_v2/Exec/Make.Adv
Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H
Tutorials/AMR_Adv_C_v2/Source/Src_nd/Make.package
Tutorials/AMR_Adv_C_v2/Source/Src_nd/Tagging_nd.f90
Tutorials/AMR_Adv_C_v2/Source/Src_nd/tagging_params.f90

commit 7bff01d7ab84f313bd26f4f6ed09588abfdca771
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 15 16:58:50 2016 -0700

    AmrAdv/AmrCore tutorial: build fine grids and init data on fine levels; ErrorEst to be implemented

Src/C_AmrCoreLib/AmrCore.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp

commit a38877815f798d3c0d6326e64ca9696c453683fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 15 11:59:18 2016 -0700

    AmrAdv/AmrCore tutorial: init data on base level

Src/C_AmrCoreLib/AmrCore.H
Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90
Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H
Tutorials/AMR_Adv_C_v2/Source/Make.package

commit f5acabc46f0e56c809bed16a90832718536d8548
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 15 13:16:31 2016 -0400

    change how we record COMP_VERSION and FCOMP_VERSION to be safer for Ubuntu

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit c6b5065dee41ebdb6758ba70635e77b5b9567625
Merge: 1444b7a12 75e72cb60
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 14 15:55:58 2016 -0700

    Merge branch 'development' into amrcore

commit 1444b7a121aeba84853a6afd3281a2cc5a3d1a0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 14 13:36:40 2016 -0700

    start AMR_Adv tutorial based on AmrCoreLib

Src/C_AmrCoreLib/AmrCore.H
Tutorials/AMR_Adv_C_v2/Exec/Make.Adv
Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Make.package
Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90
Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_C_v2/README
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H
Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp
Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp
Tutorials/AMR_Adv_C_v2/Source/Make.package
Tutorials/AMR_Adv_C_v2/Source/main.cpp
Tutorials/README_C

commit a9c7b9490195daa54eb919ddd75d699b852b219f
Merge: eeba6f120 d120ef458
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 14 12:47:04 2016 -0700

    Merge branch 'amrcore' of github.com:BoxLib-Codes/BoxLib into amrcore
    
    Conflicts:
            Src/C_AMRLib/Amr.H
            Src/C_AMRLib/Amr.cpp
            Src/C_AmrCoreLib/AmrCore.H
            Src/C_AmrCoreLib/AmrCore.cpp

commit eeba6f120b3e7ae4f9031bb48cb140d99a91473f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 12 14:22:29 2016 -0700

    move part of the regrid function into AmrCore

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AmrCoreLib/AmrCore.H
Src/C_AmrCoreLib/AmrCore.cpp

commit 75e72cb60780d1b024787cee5b9c9900ee357ed0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 13 16:00:06 2016 -0700

    using std::isinf & std::isnan for GCC >= 5

Src/C_BaseLib/FArrayBox.cpp

commit 4ab1e8b48aa385f68568427e1716fb8ff4238294
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 13 10:42:42 2016 -0700

    Add PlotFileUtil for writing plotfiles; some functions in MultiFabUtil for averaging from face and edge to cell center

Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package
Src/C_BaseLib/MultiFabUtil.H
Src/C_BaseLib/MultiFabUtil.cpp
Src/C_BaseLib/MultiFabUtil_3d.f90
Src/C_BaseLib/PlotFileUtil.H
Src/C_BaseLib/PlotFileUtil.cpp

commit 5640cef897b8492c4699792674369fc3105dfa31
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 13 14:59:52 2016 -0400

    some updates on the suite

Docs/UsersGuide/Regression/test_suite.tex

commit 596212861108711ae600730de1b2342e5a2c06de
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Oct 13 08:32:43 2016 -0700

    Minor mods to README to point user to BoxLib User Guide

Tools/RegressionTesting/README

commit d120ef4587340ff6b3469c1430b5fff70d56990b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 12 14:22:29 2016 -0700

    wip

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AmrCoreLib/AmrCore.H
Src/C_AmrCoreLib/AmrCore.cpp

commit 30964d2bbcb8e9b3423f3039ba7a3b3f91c05187
Merge: f4f6da610 8b48742ed
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Oct 12 17:58:53 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit f4f6da610ba2b3da4c2f0e21a30a2d11f4a2e81c
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Oct 12 17:58:24 2016 -0700

    Add more info in the RegTest README

Tools/RegressionTesting/README

commit 8b48742ed52415a461c78886617fdc4fdc2d7812
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 12 15:14:55 2016 -0700

    cmake update

CMakeLists.txt
Src/C_AMRLib/CMakeLists.txt
Src/C_BaseLib/CMakeLists.txt
Src/C_ParticleLib/CMakeLists.txt
Tools/CMake/CCSEOptions.cmake

commit 2c5f4137a74d7cd3b5d83689c483e8164a16d335
Merge: 748303a9d a218db786
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 12 15:12:13 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 748303a9d9b082b05b43a7365949c58914a63587
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 12 15:11:33 2016 -0700

    fix typo in profiling call.

Src/C_BaseLib/ParallelDescriptor.H

commit eb58c46b0b435215c5c12a5a38d8cc3520469fc0
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 12 15:09:43 2016 -0700

    fix typo in profiling call.

Src/C_BaseLib/ParallelDescriptor.H

commit 75df7175d785f41ade5d817cba22b2fe0b0d66e5
Merge: 76928bb02 a218db786
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 12 12:44:38 2016 -0700

    Merge branch 'development' into amrcore

commit 76928bb020df03b7191ed9cadc5c34d12398ebfc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 12 12:37:21 2016 -0700

    fix particle grids and dmap; move the two grids stuff from AmrLevel to AmrParGDB

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AmrCoreLib/AmrCore.H
Src/C_AmrCoreLib/AmrCore.cpp
Src/C_AmrCoreLib/AmrParGDB.H

commit c4a97398a9741e39e259246dc97a07bb38be4e1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 12 11:02:03 2016 -0700

    remove a number of unused and do-nothing functions

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H

commit a218db786f054652d79c31565a206c4a29824028
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 12 11:16:54 2016 -0400

    hook in preprocessing of the .F90 files -- some code bases need this

Tools/F_mk/GMakerules.mak

commit 0b045054fe2e0135cfb3576516107f4ee71bba34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 12 11:16:43 2016 -0400

    make the use of the f90_preprocessor optional

Tools/F_scripts/dep.py

commit 2c2a8f9bf73cae487bf5ff4bad7174746e2f728e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 12 10:33:20 2016 -0400

    module matching needs to be case-insensitive

Tools/F_scripts/dep.py

commit cce15b1b7ed7402113d2a42a15657969e49b618a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 11 15:57:03 2016 -0700

    AmrCore: finish particles

Src/C_AmrCoreLib/AmrCore.H
Src/C_AmrCoreLib/AmrCore.cpp
Src/C_AmrCoreLib/AmrParGDB.H
Src/C_BaseLib/DistributionMapping.H
Src/C_ParticleLib/ParGDB.H
Src/C_ParticleLib/Particles.H
Tutorials/PIC_C/two_level.cpp
Tutorials/TwoGrid_PIC_C/main.cpp

commit 592d596328ae42a39af3a0a14ebb4707a27fcc35
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 11 16:27:40 2016 -0700

    set checkpoint and plot header versions individually.

Src/C_AMRLib/Amr.cpp

commit a18e79aaf782eaa2e4bcc477874fedac4650e647
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 11 09:05:45 2016 -0700

    move some data from Amr into AmrCore

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AmrCoreLib/AmrCore.H
Src/C_AmrCoreLib/AmrCore.cpp
Src/C_AmrCoreLib/AmrParGDB.H
Src/C_AmrCoreLib/Make.package
Src/C_BaseLib/Geometry.cpp
Src/C_ParticleLib/ParGDB.H

commit 3913650ac383456a3e3bc9396d444f4eb898b222
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 11 14:20:29 2016 -0700

    fix for dss for different nfiles for plots and checkpoints.

Src/C_BaseLib/NFiles.cpp

commit e55d5060b3e48f207a115166fc061e11185ea17a
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 11 13:05:29 2016 -0700

    fix for faminmax header.

Src/C_BaseLib/VisMF.cpp

commit a31b1304fc0c3f1e24c862b107d4bc0fedb3edd1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 11 11:19:10 2016 -0700

    particle: minor

Src/C_ParticleLib/ParticleInit.H
Src/C_ParticleLib/Particles.H

commit 244f7aa6d39b39d3ffccd9bb87d51da0ea33b72d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 11 13:38:00 2016 -0400

    fix dupe

Tools/F_mk/GMakerules.mak

commit 22eeb6c4f68853a4b793e41cd1cc4e01cbb016e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 11 11:12:02 2016 -0400

    capture the return code from dep.py and abort if it was not happy

Tools/F_mk/GMakerules.mak

commit e0ea0d6b38f2a6655d556e94457d86a18108376f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 11 09:48:56 2016 -0400

    clarify where EXT_DIR data lives

Src/C_BaseLib/BC_TYPES.H

commit 4635fe720fed661abd0e2a7843baceb8e0996a94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 11 09:44:58 2016 -0400

    move the F90 BoxLib dependency checking over to the same dep.py
    that we use for C++ builds.  Remove the old perl script.
    
    Note, for F90 BoxLib, we do not preprocess the files before the
    dependency checking.  This is easy to add in, if necessary.
    
    Also remove the old deppairs target -- that does not seem to be
    used anywhere.

Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak
Tools/F_scripts/moddep.pl

commit c2bdeb2eecd1ffe5640eaf915d188758050c3afa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 10 13:37:39 2016 -0700

    move more files from C_AMRLib into C_AmrCoreLib

Src/C_AMRLib/Make.package
Src/C_AmrCoreLib/ErrorList.H
Src/C_AmrCoreLib/ErrorList.cpp
Src/C_AmrCoreLib/FLUXREG_1D.F
Src/C_AmrCoreLib/FLUXREG_2D.F
Src/C_AmrCoreLib/FLUXREG_3D.F
Src/C_AmrCoreLib/FLUXREG_F.H
Src/C_AmrCoreLib/FillPatchUtil.H
Src/C_AmrCoreLib/FillPatchUtil.cpp
Src/C_AmrCoreLib/FluxRegister.H
Src/C_AmrCoreLib/FluxRegister.cpp
Src/C_AmrCoreLib/INTERP_1D.F
Src/C_AmrCoreLib/INTERP_2D.F
Src/C_AmrCoreLib/INTERP_3D.F
Src/C_AmrCoreLib/INTERP_F.H
Src/C_AmrCoreLib/Interpolater.H
Src/C_AmrCoreLib/Interpolater.cpp
Src/C_AmrCoreLib/Make.package
Src/C_AmrCoreLib/TagBox.H
Src/C_AmrCoreLib/TagBox.cpp

commit ee0259aadc9d7dc0a189b585c9b4967e468c4e5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 10 13:13:54 2016 -0700

    start C_AmrCoreLib

Src/C_AMRLib/Make.package
Src/C_AmrCoreLib/AmrParGDB.H
Src/C_AmrCoreLib/AmrParticles.H
Src/C_AmrCoreLib/Cluster.H
Src/C_AmrCoreLib/Cluster.cpp
Src/C_AmrCoreLib/Make.package

commit 074030b29714f7a23769c2edf71c6470112a8e76
Merge: 7c9de23f6 44fdaef52
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Oct 10 15:58:13 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 7c9de23f657018fd8ec21a1c250471933f704b67
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Oct 10 15:58:00 2016 -0400

    allow for no preprocessing if --cpp is not supplied

Tools/F_scripts/dep.py

commit 44fdaef527f32fb24855f4f83e199f8eba1fa5ca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 10 10:44:01 2016 -0700

    Particle: template on container type, vector or deque

Src/C_ParticleLib/AmrParticles.H
Src/C_ParticleLib/ParticleInit.H
Src/C_ParticleLib/Particles.H
Src/C_ParticleLib/TracerParticles.H

commit 95783ae2b2e16b60ca9b257539027a793bffb959
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 10 10:12:01 2016 -0700

    Particle: reimplement removing particles so that we can use either deque or vector

Src/C_ParticleLib/Particles.H

commit 7a563eb4f6bc08b48b111e282907181b50f04b6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 9 21:00:42 2016 -0700

    Particle: send the new int data

Src/C_ParticleLib/Particles.H

commit fd3ad67166c1d2a75679995b0c5b2d5fc62cfcf0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 9 20:29:21 2016 -0700

    Particle: loop fusion

Src/C_ParticleLib/Particles.H

commit 70b1e6dd1f555e740446754b45edccbc59b74809
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 9 13:19:23 2016 -0700

    Particle: fix my recent bug

Src/C_ParticleLib/Particles.H

commit c3e23ed429628b03e4ec4e3160e97d79eb02d62b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 9 13:09:22 2016 -0700

    particle: a comment

Src/C_ParticleLib/Particles.H

commit 2f3f1463d23ae68a604743d2759c662c166f22d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 9 12:48:23 2016 -0700

    Particle: skip PeriodicWhere if not periodic

Src/C_ParticleLib/Particles.cpp

commit 720d0dd92e0a4785703bc152d382cf4747ca8a5c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 8 22:57:56 2016 -0700

    Particles: range for and auto

Src/C_ParticleLib/Particles.H

commit 3e03f970e0269e8b4e2199e14693b6208893aaee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Oct 9 16:21:45 2016 -0400

    skip dependency if a file provides the modules it needs on its own

Tools/F_scripts/dep.py

commit 932bfab3a29822c0bcd573ecd23eeb77df10a1c5
Merge: 052e6da5b 74d3f7181
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 8 19:37:53 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 052e6da5b9fb2d40e58b36c1c7072b0a23607f03
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 8 19:37:13 2016 -0400

    we don't use Solaris anywhere in the make stuff

Tools/C_mk/Make.defs
Tools/C_mk/README.md

commit 74d3f7181618c365b090e87aa4335bbc05bba9ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 8 16:29:24 2016 -0700

    Particles: move a few functions back

Src/C_ParticleLib/Particles.H

commit 06bb8e3471765f6af297b7f317c9032584488f0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 8 15:07:39 2016 -0700

    Particles: move a few functions back so that the tutorials can compile

Src/C_ParticleLib/Particles.H
Tutorials/PIC_C/single_level.cpp
Tutorials/PIC_C/two_level.cpp
Tutorials/TwoGrid_PIC_C/main.cpp

commit 15ab10ee79453e2e41a77bf23e22b846fc66a17f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 8 12:47:01 2016 -0700

    Particles: towards losing weight by moving a lot of stuff into Nyx

Src/C_ParticleLib/AmrParticles.H
Src/C_ParticleLib/Particles.H
Src/C_ParticleLib/Particles.cpp
Src/C_ParticleLib/TracerParticles.H

commit 054273b941f1aa65a5a77c959fbd25484c13bce4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 8 15:12:18 2016 -0400

    remove g77 support

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 82499fedcbd946ee54b72086c91f6c3b72ec8478
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 8 15:07:23 2016 -0400

    fix endit

Tools/C_mk/Make.Linux

commit 68fecd45c828715b4a41332e565d79173212b804
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 8 15:06:53 2016 -0400

    some machine clean-ups

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit bcec425a35fe65fd08a2720d68fff9fd9bc1588a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 8 11:19:58 2016 -0400

    ppCleanup is obsoleted by Release

Tools/ppCleanup/README
Tools/ppCleanup/cleanWords.txt
Tools/ppCleanup/ppCleanup.py

commit 7fa7a5b6a41c496acd79a01774d9537f7bd9b7a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 8 11:18:26 2016 -0400

    darter, lens, alphacluster, and pccluster are no more

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 507720caf254637c8b4c23afb178211849fadc32
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 7 21:43:54 2016 -0700

    Add a new script that does macro cleanup on a directory

Tools/Release/ppCleanupDir.py
Tools/Release/release.py

commit da9a34d46283f831e0e90bff063879eb3490c30e
Merge: 241878fba 4700a1375
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 7 21:36:51 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 4700a1375c674fcd4bc70dd93bd47d62de97eeb0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 7 13:39:43 2016 -0700

    MultiFabUtil average_edge_to_cellcenter

Src/C_BaseLib/MultiFabUtil.H
Src/C_BaseLib/MultiFabUtil.cpp
Src/C_BaseLib/MultiFabUtil_3d.f90
Src/C_BaseLib/MultiFabUtil_F.H

commit 98733f42117e6fe7e0446c2c346c2675a9287874
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 7 12:31:11 2016 -0700

    add particlecontainer default constructor

Src/C_ParticleLib/Particles.H

commit 1ed1e9f3c02da3c7b6f8c408504ce29c035615e6
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 7 11:14:06 2016 -0700

    fixes for serial.

Src/C_BaseLib/NFiles.cpp
Tests/IOBenchmark/IOTest.cpp

commit 10aeaa9759962bab4aca4ca66b56748d3d4d9c5f
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 7 10:36:25 2016 -0700

    fix for serial.

Src/C_BaseLib/NFiles.cpp

commit 241878fba86ad31baa05c1a4db53b958fbdedd85
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 7 12:41:59 2016 -0400

    we don't use the library building features for C++ BoxLib, so remove
    them to make the make stuff clearer and easier to read

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 90b7a3405b2e40892f9b35f7e863e53c1d004621
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 7 12:31:41 2016 -0400

    compressor is a job management script -- it doesn't belong here

Tools/F_scripts/compressor

commit 46024f6bcc4ca6af7aa99f7fae2e1c6861857e43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 7 12:31:28 2016 -0400

    remove coco -- this is not used

Tools/F_scripts/coco/coco.pl
Tools/F_scripts/coco/coco_e.FF
Tools/F_scripts/coco/e1.FF
Tools/F_scripts/coco/e1.II

commit 445307c60b2611bb11965f9e90f2a5cda1db18ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 7 12:31:16 2016 -0400

    require python 2.7 or later

Tools/F_scripts/dep.py

commit 98ec454f9c250d05182b1eb103e9171b87cfc27f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 7 09:35:07 2016 -0400

    add a few comments

Tools/F_scripts/dep.py

commit 1aaab75fcc50cddc4cc5846054d9771a8ba3be4a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 7 08:58:54 2016 -0400

    add some system modules to IGNORES, make things case insensitive

Tools/F_scripts/dep.py

commit 75a27de1c802d81c1e99d21905e3c89272f49506
Merge: 9d1d42292 dc389498f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 20:57:23 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 9d1d42292ef9f5d719aa98ad9826f3c18460c630
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 20:56:57 2016 -0400

    add a readme, remove a very old submission script

Tools/F_scripts/README.md
Tools/F_scripts/dep.py
Tools/F_scripts/ibm_sp_batch.poe

commit dc389498f00cf85b6061511c6c77e6ab5b733c71
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 6 17:08:34 2016 -0700

    Revert "FabArray: always respect the wish of nodal flag"
    
    This reverts commit d14adae93b0fb1e68e5cd2c34255eeaa276ea7f5.

Src/C_BaseLib/FabArray.H

commit e6ea768a6210141252fb3b6566518a73f99614e8
Merge: 9d7e9926b d14adae93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 19:58:20 2016 -0400

    Merge branch 'development' into preprocessing

commit 9d7e9926b574c24378e524a19a97bd4f7950392d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 19:40:32 2016 -0400

    add debugging option, make the "use module" be matched at the start of a line
    (perhaps with some whitespace) and test for key errors

Tools/F_scripts/dep.py

commit d14adae93b0fb1e68e5cd2c34255eeaa276ea7f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 6 16:33:01 2016 -0700

    FabArray: always respect the wish of nodal flag

Src/C_BaseLib/FabArray.H

commit f08029f132f183f27ab29749bc122680e95db9ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 15:16:52 2016 -0400

    pylint + python 3 changes

Tools/F_scripts/dep.py

commit f425f06f45f856d6c048d33dae45b1af7ed071d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 15:00:04 2016 -0400

    a little cleaning

Tools/C_mk/Make.rules

commit 28fe699a768f6b8f958b066e0827f1813af19877
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 14:40:57 2016 -0400

    this seems to work -- .F90 files are now preprocessed for dependency
    checking only (using the new dep.py script to find module dependencies)
    and then these preprocessed files are ignored and the Fortran compiler
    is invoked on the .F90 file itself, doing the preprocessing
    internally.

Tools/C_mk/Make.rules
Tools/F_scripts/dep.py

commit 0707181e3791c21e4bcd6216cb90bac7d78716b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 13:35:17 2016 -0400

    a little cleaning

Tools/F_scripts/dep.py

commit 8c1c9cf88d6f16283dd15e35e79874ad5d880693
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 10:27:30 2016 -0400

    prep for preprocessing

Tools/F_scripts/dep.py

commit 1eeaa041a28227e2d85c2faf501e4e59a15cd89d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 10:05:11 2016 -0400

    make it classy

Tools/F_scripts/dep.py

commit cb218b88af5143b54da6fbe09de31f6332c5af56
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 5 23:04:29 2016 -0400

    add runtime hooks for preprocessing

Tools/F_scripts/dep.py

commit dbc24d223622ae039476c587a82578e3c38a436c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 5 22:46:21 2016 -0400

    remove dupes

Tools/F_scripts/dep.py

commit 0e5f45bac2624cd36a47e706fbb5c29e773604fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 5 22:15:48 2016 -0400

    switch in a python F90 dependency checker
    
    this works for Castro in the current way of doing things.  Needs more testing and
    cleaning, and then needs an option for doing preprocessing

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules
Tools/F_scripts/dep.py

commit df1fcb6e286123c328d661c14104e51299236b9f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 5 17:34:40 2016 -0700

    multiple deciders for chained fabarray reads, clean up ignored messages.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp
Tests/IOBenchmark/IOTest.cpp

commit 19380156a3dc20d516adc6300ab386bc6d32e25e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 5 16:34:13 2016 -0700

    allow BaseFab change box type without changing size

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H

commit fad05dfd8dc92e2372c64baa4abb4afde9317a7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 5 19:17:30 2016 -0400

    add support for OpenACC tests

Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_report.py
Tools/RegressionTesting/test_util.py

commit 67b290a56e40fe0800167e37fb3debbf5f3a6ee3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 5 15:30:30 2016 -0700

    NodalDepositionSingleLevel: the new MultiFab must have the same index type as the MultiFab to be filled

Src/C_ParticleLib/Particles.H

commit 696c9778984b5b6dffe4dbc930ea8df457439c2d
Merge: 2ee1d59bd 244e37fac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 17:08:07 2016 -0700

    Merge branch 'master' into development
    
    Conflicts:
            Src/C_AMRLib/CMakeLists.txt

commit 244e37fac9aadf3e8d0fa3907df1ab760068d085
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 17:07:03 2016 -0700

    cmake

Src/C_AMRLib/CMakeLists.txt

commit 2ee1d59bd8513a95005ab0f2b64f37c0f7f18bdc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 17:01:55 2016 -0700

    cmake

Src/CMakeLists.txt
Src/C_AMRLib/CMakeLists.txt
Src/C_ParticleLib/CMakeLists.txt

commit ef2e74c4e7b6d2b668ec96716432569135336a0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 16:49:13 2016 -0700

    include(PreprocessBoxLibFortran90)

Src/CMakeLists.txt

commit 878b5fdf6015063099a88889588812dcff4c8081
Merge: 0b9f600c8 e6065df1e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 16:30:38 2016 -0700

    Merge branch 'master' into development

commit e6065df1e63aa6319b46d1d9a45c1557f30b38ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 16:30:25 2016 -0700

    typo

Src/C_BaseLib/CMakeLists.txt

commit 0b9f600c899b1d5b07ee846198b7d37c82b1b83c
Merge: e18f31eb9 87eb45695
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 16:29:17 2016 -0700

    Merge branch 'master' into development

commit 87eb456955106a1d16f15be48b5e5effb321cee5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 16:28:42 2016 -0700

    trying to fix cmake; not tested because I don't know how to run cmake

CMakeLists.txt
Src/C_BaseLib/CMakeLists.txt
Tools/CMake/PreprocessBoxLibFortran90.cmake

commit b1262e615076ec8171d8cb117e69cf10a4a0b0d6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 4 07:07:33 2016 -0700

    FILCC* now live in C_BaseLib so remove them from C_AMRLib/CMakeLists.txt

Src/C_AMRLib/CMakeLists.txt

commit e18f31eb9d4ca9aa081952f97908206e27a95a81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 15:50:19 2016 -0700

    clean up

Tutorials/HelloWorld_C/GNUmakefile

commit 2c67a85aab2d9bf781af305ad3f1caaca20a1d97
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 13:23:55 2016 -0700

    move Timestamp function into TracerParticleContainer class

Src/C_ParticleLib/Particles.H
Src/C_ParticleLib/TracerParticles.H
Src/C_ParticleLib/TracerParticles.cpp

commit a9dc8ec1205437c4163ce961f78dcd8dad977d70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 12:26:55 2016 -0700

    move Particle stuff into C_ParticleLib; add TracerParticleContainer; note that cmake needs to be fixed

Src/C_AMRLib/Make.package
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package
Src/C_ParticleLib/AmrParGDB.H
Src/C_ParticleLib/AmrParticles.H
Src/C_ParticleLib/Make.package
Src/C_ParticleLib/ParGDB.H
Src/C_ParticleLib/ParticleInit.H
Src/C_ParticleLib/Particles.H
Src/C_ParticleLib/Particles.cpp
Src/C_ParticleLib/Particles_1D.F
Src/C_ParticleLib/Particles_2D.F
Src/C_ParticleLib/Particles_3D.F
Src/C_ParticleLib/Particles_F.H
Src/C_ParticleLib/TracerParticles.H
Src/C_ParticleLib/TracerParticles.cpp
Tutorials/PIC_C/GNUmakefile
Tutorials/TwoGrid_PIC_C/GNUmakefile

commit d98ee529b7845bb847829fb8a22ac24c5cd481d9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 4 12:57:43 2016 -0700

    Make 1d and 2d versions of NodalDeposition

Src/C_BaseLib/Particles.H

commit 7a27362978142ccbce6eb99dc1e311e3b058e1fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 08:39:31 2016 -0700

    NodalDepositionSingleLevel only works in 3d

Src/C_BaseLib/Particles.H

commit a74bfaa15c1a5c2d9ad1b2d807f05fd994bc8deb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 4 07:07:33 2016 -0700

    FILCC* now live in C_BaseLib so remove them from C_AMRLib/CMakeLists.txt

Src/C_AMRLib/CMakeLists.txt

commit 0773551bbd409590df55a44f8a3ac9e4f9a713a4
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 3 17:30:18 2016 -0700

    name barriers for profiling.

Src/C_BaseLib/VisMF.cpp
Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit c6ebc0f24df89c31d677d615a2d224ecfc3e2e56
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 17:13:05 2016 -0700

    some minor changes

Src/C_BaseLib/Particles.H

commit a8af51e4789163ae0d467824a4c8d695bd90ada1
Merge: 6a471e3cd 7c910574f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 3 16:34:12 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 6a471e3cd68a09f3a059aaad3779f0b90ab1cd61
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 3 16:34:01 2016 -0700

    Add the single level nodal deposition routine here.

Src/C_BaseLib/Particles.H

commit 7c910574f88c13b18d7e83520d37a623c4906eea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 16:30:24 2016 -0700

    elide some mpi reduce

Src/C_BaseLib/Particles.H

commit 5c1c23cb2a16151b3a8c4fa7d1489a7241191138
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 15:04:12 2016 -0700

    Particle: use std::array for Real m_data

Src/C_BaseLib/Particles.H

commit 21bd8e0e5302ace97170397ec7cd2edff982e1f8
Merge: fe75db6f3 2858e4670
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 3 14:51:22 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit fe75db6f3964e254a5eb7d09c6283f3115aa25b0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 3 14:50:58 2016 -0700

    Get rid of everything to do with neutrinos / relativistic mass -- that all now lives in the Nyx repo.

Src/C_BaseLib/Particles.H

commit 7e65d8209ae02153043d7b9adf07b056ee7ed226
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 3 14:21:03 2016 -0700

    added option to provide coordinator processor number to VisMF::Read for chained fabarray reads.

Src/C_BaseLib/NFiles.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 2858e4670d08d9e428ac7f0218c497401b970a88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 14:07:13 2016 -0700

    update function parameter names

Src/C_BaseLib/Particles.H

commit b33cd4865f9c8e035c143a78c8ed5b79cdbf9d64
Merge: 1407161db b740ae256
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 13:58:24 2016 -0700

    Merge branch 'development' into devel-particle
    
    Conflicts:
            Src/C_BaseLib/Particles.H

commit b740ae25687b562e16f0d0c5c16b783c28c37d4b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 3 13:50:23 2016 -0700

    1) Remove the versions of moveKick and moveKickDrift that took normal acceleration vectors on faces (keep the versions
    that use cell-centered accelerations)
    2) Remove movePredict and moveCorrect -- no one is using those.
    3) Remove AssignDensityAndVels -- that now lives in the Nyx repo.
    4) Replace references to "gravity" by references to "acceleration"

Src/C_BaseLib/Particles.H

commit 1407161dba535ad9cfbc7d92abf1f3e65efcdc48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 13:48:03 2016 -0700

    white space

Src/C_BaseLib/Particles.H

commit 24f06a95aa801c781b71140c038a60dd2fb46c25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 12:49:51 2016 -0700

    Add number of intergers to Particle template

Src/C_AMRLib/AmrParticles.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/ParticleInit.H
Src/C_BaseLib/Particles.H
Tools/C_mk/Make.defs

commit 1bfe38b37bdd641cfb2a118fb8b61ab8c5816c95
Merge: ea7e36e57 b78a92494
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Oct 3 09:08:45 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit ea7e36e57db669da0c5cba0f719ee23488bbb639
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Oct 3 09:08:27 2016 -0700

    update readme_'s

Tutorials/GettingStarted_F/main.f90
Tutorials/README_C
Tutorials/README_F

commit b78a92494d2ddba24cf795dbc87a20e43556819f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 08:56:32 2016 -0700

    comment

Src/C_BaseLib/FabArray.cpp

commit d76809be838c705be7e347c3d84df202eb50f015
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 08:54:09 2016 -0700

    Release Notes 16.10

ReleaseNotes/release-notes-16.10

commit 71d026f0528a4f31f69fd44ea99f226703130e63
Merge: 1027df993 4ed405e1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 08:53:20 2016 -0700

    Merge branch 'development'

commit 1027df993c79d61512b46c7a48ba474d338221eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 08:53:16 2016 -0700

    fix a typo

ReleaseNotes/release-notes-16.09

commit 4ed405e1f4338b137397373f4f2d869e31728ae9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 2 16:13:26 2016 -0700

    Move all of the ParticleContainer<N>::InitCosmo... routines out of BoxLib and
    into Nyx because they are specific to cosmological applications

Src/C_BaseLib/ParticleInit.H
Src/C_BaseLib/Particles.H

commit daf7b37ecc4b0279b27b4200aa4a42121b816c96
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 29 16:43:34 2016 -0700

    more preread headers.

Tests/IOBenchmark/IOTest.cpp

commit 49fbfba8927e720cf1c4ce80eac17adaf3ee366d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 29 16:31:21 2016 -0700

    workaround for intel compiler, preread mf headers.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit e9f173c6281e685551ac4b8d0dd75d148cc33ff7
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 28 19:26:54 2016 -0700

    cleanup of C++ tutorials.  start bc documentation

Docs/UsersGuide/C_AdvancedTopics/C_AdvancedTopics.tex
Docs/UsersGuide/F_AdvancedTopics/F_AdvancedTopics.tex
Docs/UsersGuide/GettingStarted/GettingStarted.tex
Docs/UsersGuide/UsersGuide.tex
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX1_C/writePlotFile.H
Tutorials/HeatEquation_EX1_C/writePlotFile.cpp
Tutorials/HeatEquation_EX2_C/main.cpp
Tutorials/HeatEquation_EX2_C/writePlotFile.H
Tutorials/HeatEquation_EX2_C/writePlotFile.cpp

commit 328cadbc9bbf248f54f9a6ba7700fe2ad0a67c15
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 28 18:49:03 2016 -0700

    setup.cpp not needed

Tutorials/HeatEquation_EX2_C/setup.cpp

commit 5e2031cc65c021b8c7752b830d09720070f4748c
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 28 16:08:29 2016 -0700

    implemented dirichlet and neumann conditions in HeatEquation_EX2_C.  Results match HeatEquation_EX2_F

Tutorials/HeatEquation_EX2_C/advance_2d.f90
Tutorials/HeatEquation_EX2_C/advance_3d.f90
Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90
Tutorials/HeatEquation_EX2_C/inputs_2d
Tutorials/HeatEquation_EX2_C/inputs_3d
Tutorials/HeatEquation_EX2_C/main.cpp
Tutorials/HeatEquation_EX2_C/writePlotFile.cpp
Tutorials/HeatEquation_EX2_F/inputs_2d
Tutorials/HeatEquation_EX2_F/inputs_3d

commit 05310503e1dab449c890e2ce1a5b8f0651f669dc
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 28 15:47:49 2016 -0700

    index bugfix in bcs

Tutorials/HeatEquation_EX2_F/advance.f90
Tutorials/HeatEquation_EX3_F/advance.f90
Tutorials/HeatEquation_EX4_F/advance.f90
Tutorials/HeatEquation_EX5_F/advance.f90

commit dc7e29128399b38bb0e0d215ce5c4b6e82c23e2f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 28 15:06:17 2016 -0700

    remove init, more options.

Docs/Readme.io
Src/C_BaseLib/NFiles.cpp
Src/C_BaseLib/VisMF.cpp

commit 9a78426ae796ab24b66c98c0fe3a92aeaa634f34
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 28 14:52:13 2016 -0700

    tests to read and write multiple multifabs.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/IOBenchmark/inputs.dssmf

commit 21bbccd2bce6692e3a3d6a39b56aa0119768cba7
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 28 12:35:47 2016 -0700

    use single write for old format.

Src/C_BaseLib/VisMF.cpp

commit bc376e4d3643be3092ac7313cca575b7d40cfcf4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 16:14:55 2016 -0700

    fix comment

Src/C_BaseLib/Box.H

commit 83d64a9376a71ddc1ee516cf23f7f90faae1d28f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 16:02:28 2016 -0700

    comment

Src/C_BaseLib/Box.H

commit 1b0d35b1de1adaef60d6ebec71913b94f08f1581
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 16:02:19 2016 -0700

    minor

Src/C_BaseLib/BoxArray.cpp

commit ab4cf7286f50f2600fb342df0f32d8fb32f81f56
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 27 15:42:11 2016 -0700

    fix for combined transfer.

Src/C_BaseLib/VisMF.cpp

commit 936a2bae9687459b0cbad6152be18a2da55a2cfc
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 27 15:41:15 2016 -0700

    separate options for plot and checkpoint formats.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 66243a74e51e5d4606e49a52b79e564ed8d8e66d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 08:15:17 2016 -0700

    nodal SumBoundary: forgot to zero out the destination

Src/C_BaseLib/MultiFab.cpp

commit 825ab04f88eae6be8a5db21a0c3c434974b2c6ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 26 22:22:57 2016 -0700

    nodal SumBoundary: fix new bug

Src/C_BaseLib/IntVect.H
Src/C_BaseLib/MultiFab.cpp

commit fea4f4b4532a94843b9bd2aa152008402eb0eaa2
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 26 13:44:30 2016 -0700

    pass in bc(:,:) and domlo/hi into compute_flux

Tutorials/HeatEquation_EX2_C/advance_2d.f90
Tutorials/HeatEquation_EX2_C/advance_3d.f90
Tutorials/HeatEquation_EX2_C/main.cpp
Tutorials/HeatEquation_EX2_C/myfunc_F.H

commit 306094bec387971af24360efd26fd3a19ea1ffd2
Merge: 3eaa5ad09 437479d44
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 26 13:08:33 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 3eaa5ad09aa7905f0c279ebbe0de821c5bd9ce2f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 26 13:06:41 2016 -0700

    starting to put Dirichlet BC's in.
    
    This doesn't work quite right yet, as compute_flux() in advance_xd.f90 needs to know to alter the stencil at the boundary for the EXT_DIR case, where the ghost cell stores the value on the boundary.

Tutorials/HeatEquation_EX2_C/FILCC_2D.F
Tutorials/HeatEquation_EX2_C/FILCC_3D.F
Tutorials/HeatEquation_EX2_C/inputs_2d
Tutorials/HeatEquation_EX2_C/inputs_3d

commit 437479d44dd7403fffe27e9a7673916976c3a997
Merge: 00c872cf2 b3c53e5c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 26 12:06:25 2016 -0700

    Merge branch 'weiqun/SumBoundary' into development

commit b3c53e5c9a696fefb9d719b4d35528d5fc320930
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 26 11:29:01 2016 -0700

    SumBoundary: fix new bug

Src/C_BaseLib/FabArray.H

commit 9165bf3f819a1ae606e8b40c10fd3d72834f2a34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 26 10:08:43 2016 -0700

    make MultiFab::SumBoundary work for nodal

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp

commit 00c872cf2f252d996ec17d352bbfb41002bc27e0
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 26 09:53:43 2016 -0700

    C++ plotfiles now report the time and variable name properly

Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX1_C/writePlotFile.H
Tutorials/HeatEquation_EX1_C/writePlotFile.cpp
Tutorials/HeatEquation_EX2_C/main.cpp
Tutorials/HeatEquation_EX2_C/writePlotFile.H
Tutorials/HeatEquation_EX2_C/writePlotFile.cpp

commit 2ad36906ca8303ba495ed44275de419d853f50e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 26 09:10:38 2016 -0700

    MultiFab::AddProduct that computes dst += src1*src2

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BaseFab_f.H
Src/C_BaseLib/BaseFab_nd.f90
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 233fcc71e7799bde75ef3e06ef0f3f2da1103696
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 26 08:37:50 2016 -0700

    typos

Src/C_BaseLib/IntVect.H

commit eba7a6139ccb5728ebb8874db968e79e9d3f26f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Sep 25 18:16:49 2016 -0400

    add -Mbounds for PGI in debug mode

Tools/C_mk/Make.Linux

commit b3a425a303f4daceb45840806ced762cf61d9d0d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Sep 24 15:19:34 2016 -0700

    Add two more initialization routines for particles to ParticleInit.H

Src/C_BaseLib/ParticleInit.H
Src/C_BaseLib/Particles.H

commit 7bba15f51b5a036a961cea206ff0cd9d83747afb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Sep 24 14:48:43 2016 -0700

    Moved the ParticleContainer::Init... routines into their own file.

Src/C_BaseLib/Make.package
Src/C_BaseLib/ParticleInit.H
Src/C_BaseLib/Particles.H

commit a2b076cc2238a42c81f242dc25c96bd50d5bc0cf
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Sep 23 17:37:21 2016 -0700

    added explicit array shaping to the C++ version and a note in the user's guide

Docs/UsersGuide/GettingStarted/GettingStarted.tex
Tutorials/GettingStarted_C/work_on_data_2d.f90
Tutorials/GettingStarted_C/work_on_data_3d.f90
Tutorials/GettingStarted_F/main.f90

commit 5142f6a914325329c6fc675fd73e54d2786f4dd8
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Sep 23 17:15:34 2016 -0700

    finish updating chapter 2.  looking pretty good now.  next on the list is documenting the first 'advanced' C++ feature: boundary conditions

Docs/UsersGuide/GettingStarted/GettingStarted.tex

commit 479d10d8b3ebf53231691a3cd629f0776d81d445
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Sep 23 16:51:34 2016 -0700

    created a fortran version of the GettingStarted tutorial, and the User's Guide links directly to the source code for a first example

Docs/UsersGuide/GettingStarted/GettingStarted.tex
Tutorials/GettingStarted_F/GNUmakefile
Tutorials/GettingStarted_F/GPackage.mak
Tutorials/GettingStarted_F/main.f90
Tutorials/GettingStarted_F/work_on_data.f90

commit 4d3864d00b830fa5263a3c5965d66a9366b9f8d4
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Sep 23 16:07:01 2016 -0700

    created a new C++ tutorial, "GettingStarted_C", which is basically a 'hello-world' type program that builds multifabs, accesses the multifab data in an f90 routine, and fills interior/periodic boundaries.  Bonus points is that the user's guide now directly links to the source code!  I hope to do the same for fortran90 shortly.

Docs/UsersGuide/GettingStarted/GettingStarted.tex
Docs/UsersGuide/UsersGuide.tex
Tutorials/GettingStarted_C/GNUmakefile
Tutorials/GettingStarted_C/Make.package
Tutorials/GettingStarted_C/main.cpp
Tutorials/GettingStarted_C/work_on_data_2d.f90
Tutorials/GettingStarted_C/work_on_data_3d.f90

commit 8c90f88811d5081265671ea3b010cbb1ab05b18f
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 23 15:18:24 2016 -0700

    added support for precreating plot file level directories.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H

commit 3b7184e0ad66183fd1ca936ea4557b7eadf06802
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 23 15:15:12 2016 -0700

    added io parameters.

Docs/Readme.io

commit fa7ce3765948c74fd69b940050256615f0cfd0d3
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 23 14:09:21 2016 -0700

    sync vismf vars for dsc.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/VisMF.H

commit eda28a3b589f2609e6c1d484714af24868cc1f35
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Sep 23 13:11:28 2016 -0700

    remove the bl_abort statements when using the default EXT_DIR option.  Some codes with mixed inflow + extrapolation (on different faces) boundary conditions rely on EXT_DIR being a null-op

Src/C_BaseLib/FILCC_1D.F
Src/C_BaseLib/FILCC_2D.F
Src/C_BaseLib/FILCC_3D.F
Src/F_BaseLib/multifab_physbc.f90

commit ca1806760a847d94eba9a73275f97f9a38817a8b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Sep 23 12:57:54 2016 -0700

    now FILLCC has EXT_DIR options built in for C++, just like multifab_physbc.f90 for F90
    
    however, both C++ and F90 will now abort if you use EXT_DIR as given - we are forcing users to supply their own Dirichlet values

Src/C_BaseLib/FILCC_1D.F
Src/C_BaseLib/FILCC_2D.F
Src/C_BaseLib/FILCC_3D.F
Src/F_BaseLib/multifab_physbc.f90

commit f073bd7bf9151e0c8edb12b53f85b9619dcf82c4
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 23 12:15:24 2016 -0700

    parmparse inputs, change defaults.

Src/C_BaseLib/VisMF.cpp

commit b293a7cd461657d0dba75cebc6a9b8850db61058
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 23 11:03:11 2016 -0700

    set passed options.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/inputs.dssmf

commit 1895a7d839d465bce0f0e55a9c36e065b86b89b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 22 21:19:15 2016 -0700

    This reverts commit 883a93f4365.  PArray is fundamentally broken, we cannot fix it.  When we switch to C++ 11, we should make PArray be purely non-owning and use Array of smart pointers when we need memory management.  We should also add a PArray constructor that takes Array of smart pointers.

Src/C_BaseLib/PArray.H

commit b8e2b02d90e19da855234d8bc09e5b6a35146a49
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 22 18:12:55 2016 -0700

    Cleaned up Tutorials/PIC_C/GNUmakefile.

Tutorials/PIC_C/GNUmakefile

commit 883a93f4365a6c5a109aadaf76d92abacb533461
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 22 16:06:42 2016 -0700

    add PArray copy assignment operator so that we can assert that the sizes are zero

Src/C_BaseLib/PArray.H

commit 5da212d3f346d0a67479ce1dc9d2fc3b3b42b71d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 22 11:51:57 2016 -0700

    added setting for synchronous reads.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 3ab6ffd79a5d122eb6416d89fe6a7d990421c9d6
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 21 15:21:14 2016 -0700

    minor name changes to user's guide matches tutorial

Docs/UsersGuide/GettingStarted/GettingStarted.tex
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX2_C/main.cpp

commit 8463e3eabaeeb2d99d12a58ae9540e9525381e94
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 21 14:47:07 2016 -0700

    periodic and outflow working in 2d and 3d

Tutorials/HeatEquation_EX2_C/inputs_2d
Tutorials/HeatEquation_EX2_C/inputs_3d

commit 4f32d63b377fafdc35d1aa2fade12451c7203d91
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 21 14:43:08 2016 -0700

    outflow bcs working for HeatEquation_EX2_C

Tutorials/HeatEquation_EX2_C/inputs_2d
Tutorials/HeatEquation_EX2_C/main.cpp

commit 90a34123047fe94ab07031bfd9bc662ff4387b93
Merge: 1e966fa2a 5e80a9cbf
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 21 13:24:01 2016 -0700

    merge fixes.

commit 9f0225a9c44bdea6c2b9ce9a579c14b1eb42c22b
Merge: eec445d27 f6990b16a
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 21 13:17:07 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit eec445d278dbff0f88cb9909d51a274f4ebdc27d
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 21 13:16:18 2016 -0700

    HeatEquation_EX1_C to uses PArray<MultiFab> now for the state and fluxes

Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX2_C/main.cpp

commit aeb5fdfd168a2b29ff05aac2cdc40630101a23bf
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 21 12:57:44 2016 -0700

    updating HeatEquation_EX1_C to more closely match EX2_C.  WIP

Tutorials/HeatEquation_EX1_C/GNUmakefile
Tutorials/HeatEquation_EX1_C/Make.package
Tutorials/HeatEquation_EX1_C/advance_3d.f90
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX1_C/myfunc_F.H
Tutorials/HeatEquation_EX2_C/Make.package
Tutorials/HeatEquation_EX2_C/main.cpp

commit f6990b16a6fdd8712785400726d736312593b6e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 21 09:06:28 2016 -0700

    move User's Guide from Docs/ to Docs/UsersGuide/

Docs/UsersGuide/C_AdvancedTopics/C_AdvancedTopics.tex
Docs/UsersGuide/F_AdvancedTopics/F_AdvancedTopics.tex
Docs/UsersGuide/F_AdvancedTopics/bc_example1.eps
Docs/UsersGuide/F_AdvancedTopics/bc_example1.fig
Docs/UsersGuide/F_AdvancedTopics/bc_example2.eps
Docs/UsersGuide/F_AdvancedTopics/bc_example2.fig
Docs/UsersGuide/F_AdvancedTopics/bc_example3.eps
Docs/UsersGuide/F_AdvancedTopics/bc_example3.fig
Docs/UsersGuide/F_AdvancedTopics/subcycling_algorithm.eps
Docs/UsersGuide/GNUmakefile
Docs/UsersGuide/GettingStarted/GettingStarted.tex
Docs/UsersGuide/GettingStarted/VisIt_2D.eps
Docs/UsersGuide/GettingStarted/VisIt_3D.eps
Docs/UsersGuide/GettingStarted/edison.run
Docs/UsersGuide/GettingStarted/edison_omp.run
Docs/UsersGuide/Introduction/AMR.eps
Docs/UsersGuide/Introduction/Introduction.tex
Docs/UsersGuide/Introduction/boxlib_directory_bw2.eps
Docs/UsersGuide/Introduction/castro_scaling.eps
Docs/UsersGuide/Introduction/data_loc.odg
Docs/UsersGuide/Introduction/data_loc2.eps
Docs/UsersGuide/Introduction/index_grid.odg
Docs/UsersGuide/Introduction/index_grid2.eps
Docs/UsersGuide/Introduction/lmc_scaling.eps
Docs/UsersGuide/Introduction/maestro_scaling.eps
Docs/UsersGuide/Introduction/varden1.eps.REMOVED.git-id
Docs/UsersGuide/Introduction/varden2.eps.REMOVED.git-id
Docs/UsersGuide/Introduction/varden3.eps.REMOVED.git-id
Docs/UsersGuide/Introduction/varden4.eps.REMOVED.git-id
Docs/UsersGuide/LinearSolvers/LinearSolvers.tex
Docs/UsersGuide/Preface/Preface.tex
Docs/UsersGuide/README
Docs/UsersGuide/Regression/test_suite.tex
Docs/UsersGuide/Regression/testsuite.eps
Docs/UsersGuide/UsersGuide.tex

commit 6f5f8d2d1ddc0496b60aafbffc3b821f6ae1006b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 21:08:47 2016 -0700

    PhysBCFunct: for clarity, add empty destructor

Src/C_BaseLib/PhysBCFunct.H

commit e2b9670c0b7d654e2f5cb997b6590a8280ebe58d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 20:53:16 2016 -0700

    HeatEquation_EX2_C: use preprocessing

Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90

commit 2c72ad5b274a4fc59c0dd7f22eb5bf331e52d37a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 17:44:06 2016 -0700

    HeatEquation_EX2_C: fix call filcc

Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90

commit 629f9d65e89d8b3452c534ad5b848c232ee6eaff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 17:27:23 2016 -0700

    HeatEquation_EX2_C: clean up make

Tutorials/HeatEquation_EX2_C/GNUmakefile

commit c5960321fd5b9f6a8f7b62dc2afb028b8867e28f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 17:26:16 2016 -0700

    HeatEquation_EX2_C: almost done except the boundaries are still all periodic

Src/C_BaseLib/PhysBCFunct.H
Src/C_BaseLib/PhysBCFunct.cpp
Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90
Tutorials/HeatEquation_EX2_C/main.cpp

commit f566a0961bf21827b9582192cc97e3996bc10ef1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 16:13:03 2016 -0700

    HeatEquation_EX2_C: move fortran function declarations to a file

Tutorials/HeatEquation_EX2_C/Make.package
Tutorials/HeatEquation_EX2_C/bc_F.H
Tutorials/HeatEquation_EX2_C/main.cpp
Tutorials/HeatEquation_EX2_C/myfunc_F.H

commit 7583d0e264573ac7b4812d048f42dd493c5d037d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 16:07:29 2016 -0700

    simplify bc_fill fortran function

Tutorials/HeatEquation_EX2_C/Make.package
Tutorials/HeatEquation_EX2_C/bc_F.H
Tutorials/HeatEquation_EX2_C/bc_fill_2d.F90
Tutorials/HeatEquation_EX2_C/bc_fill_3d.F90

commit 1e966fa2a3335257411fb4608b78ed7f47b0e6ff
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 20 15:53:13 2016 -0700

    just use sends for now.

Src/C_BaseLib/NFiles.cpp

commit 9626b05a3e62f3628862b385ca5411d64dbe4a30
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 20 15:49:21 2016 -0700

    make stream pointer so intel will compile.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 5e80a9cbff7fa0135c790335ca2ce33f5ae61530
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 15:38:40 2016 -0700

    make PhysBCFunct concrete so that we can use it without StateData; move FILCC to C_BaseLib

Src/C_AMRLib/CMakeLists.txt
Src/C_AMRLib/Make.package
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/FILCC_1D.F
Src/C_BaseLib/FILCC_2D.F
Src/C_BaseLib/FILCC_3D.F
Src/C_BaseLib/Make.package
Src/C_BaseLib/PhysBCFunct.H
Src/C_BaseLib/PhysBCFunct.cpp
Src/C_BaseLib/bc_types.fi

commit 815667c3639c89afc8831e403978ca01befd51db
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 20 15:34:22 2016 -0700

    remove check from timed block, cleanup.

Tests/IOBenchmark/IOTest.cpp

commit b284379472a9d0ca256c22bd5107e75c18865231
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 12:37:22 2016 -0700

    PhysBCFunct --> PhysBCFunctBase and doit --> FillBoundary

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FillPatchUtil.H
Src/C_AMRLib/FillPatchUtil.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/PhysBCFunct.H

commit e759bb23dbe6981b3857a764fc717e6927e676c8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 20 12:12:45 2016 -0700

    We don't actually need C_BndryLib for this example.

Tutorials/HeatEquation_EX1_C/GNUmakefile

commit 42b4d5cfebf6d5021057119019c0c658adec81f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 11:09:30 2016 -0700

    make it compile

Tutorials/HeatEquation_EX2_C/main.cpp

commit fe789ad1326cebe880adea25988fe5697dc4d914
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 08:54:14 2016 -0700

    minor

Tutorials/HeatEquation_EX1_C/GNUmakefile

commit d317c3c6fa404cc693183ac3d06256f3f4c7999b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 08:53:45 2016 -0700

    add default EBASE

Tools/C_mk/Make.defs

commit 0e5e512f27d323ebf30ca702befce854b6f7f15d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 08:37:47 2016 -0700

    simplify GNUmakefile

Tutorials/HeatEquation_EX1_C/GNUmakefile

commit 08bc2fa4d16a1096777294924a113ad06463e82b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 08:37:33 2016 -0700

    move the rule for building executable to the top

Tools/C_mk/Make.rules

commit b327875ccacd642fd818551798ab5e7ebaf1f6eb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 19 21:05:25 2016 -0700

    Making progress but this still doesn't quite work yet ...

Tutorials/HeatEquation_EX2_C/Make.package
Tutorials/HeatEquation_EX2_C/bc_F.H
Tutorials/HeatEquation_EX2_C/bc_fill_2d.F90
Tutorials/HeatEquation_EX2_C/bc_fill_3d.F90
Tutorials/HeatEquation_EX2_C/bcfill_nd.f90
Tutorials/HeatEquation_EX2_C/main.cpp

commit e3cc73088a06c7b72861a4b4dd2b9f343c5d3d3d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 19 20:20:44 2016 -0700

    Move the source file names from GNUmakefile to Make.package

Tutorials/HeatEquation_EX2_C/GNUmakefile
Tutorials/HeatEquation_EX2_C/Make.package

commit 19fce93e8fb498a97ac81303d3e2cca4e8e28ee2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 19 22:18:24 2016 -0400

    use bind(C)

Tutorials/MultiGrid_C/COEF_2D.F
Tutorials/MultiGrid_C/COEF_2D.F90
Tutorials/MultiGrid_C/COEF_3D.F
Tutorials/MultiGrid_C/COEF_3D.F90
Tutorials/MultiGrid_C/COEF_F.H
Tutorials/MultiGrid_C/Make.package
Tutorials/MultiGrid_C/RHS_2D.F
Tutorials/MultiGrid_C/RHS_2D.F90
Tutorials/MultiGrid_C/RHS_3D.F
Tutorials/MultiGrid_C/RHS_3D.F90
Tutorials/MultiGrid_C/RHS_F.H
Tutorials/MultiGrid_C/main.cpp

commit 46aff0c05a9b950860c04d943a639392b738025e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 19 21:31:42 2016 -0400

    use bind(C)

Tutorials/HeatEquation_EX2_C/advance_2d.f90
Tutorials/HeatEquation_EX2_C/advance_3d.f90
Tutorials/HeatEquation_EX2_C/bcfill_nd.f90
Tutorials/HeatEquation_EX2_C/init_phi_2d.f90
Tutorials/HeatEquation_EX2_C/init_phi_3d.f90
Tutorials/HeatEquation_EX2_C/main.cpp

commit 54298f5c2a276e88870a900639ff07ad0947097b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 19 21:16:05 2016 -0400

    add new example

Tutorials/README_C

commit 081fc5bd48646d864c10b05ab2a3333061ee6f72
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 19 21:14:13 2016 -0400

    get this compiling

Tutorials/HeatEquation_EX2_C/GNUmakefile

commit d1f475e00d3c92e3b392eb6edf51ad6a0f29513d
Merge: 26c9fe2c9 71ed949e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 19 20:58:59 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 26c9fe2c91bd2f8659fc4bc598ad28b4c0466dbe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 19 20:58:47 2016 -0400

    use bind(C) for Fortran interfaces

Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob.f90
Tutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/Adv_F.H
Tutorials/AMR_Adv_C/Source/Adv_advance.cpp
Tutorials/AMR_Adv_C/Source/Adv_dt.cpp
Tutorials/AMR_Adv_C/Source/Adv_setup.cpp
Tutorials/AMR_Adv_C/Source/Src_2d/Adv_2d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/Adv_3d.f90
Tutorials/AMR_Adv_C/Source/Src_nd/Adv_nd.f90
Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90
Tutorials/Tiling_Heat_C/advance_3d.f90
Tutorials/Tiling_Heat_C/init_phi_3d.f90
Tutorials/Tiling_Heat_C/main.cpp
Tutorials/WaveEquation_C/advance_2d.f90
Tutorials/WaveEquation_C/advance_3d.f90
Tutorials/WaveEquation_C/init_data_2d.f90
Tutorials/WaveEquation_C/init_data_3d.f90
Tutorials/WaveEquation_C/main.cpp

commit 71ed949e9cfc3ddfe029b0dd5ab500c3eff9ae3f
Merge: f6d608c76 23a1a89e5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 19 17:49:51 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit f6d608c7605e3be2edae7283c68a60025d5d3351
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 19 17:49:18 2016 -0700

    Add a new Tutorial example that demonstrates how to use StateData without Amr or AmrLevel --
    this allows us to introduce boundary conditions in the C++ stuff without being multilevel.

Tutorials/HeatEquation_EX2_C/GNUmakefile
Tutorials/HeatEquation_EX2_C/Make.package
Tutorials/HeatEquation_EX2_C/advance_2d.f90
Tutorials/HeatEquation_EX2_C/advance_3d.f90
Tutorials/HeatEquation_EX2_C/bc_F.H
Tutorials/HeatEquation_EX2_C/bcfill_nd.f90
Tutorials/HeatEquation_EX2_C/init_phi_2d.f90
Tutorials/HeatEquation_EX2_C/init_phi_3d.f90
Tutorials/HeatEquation_EX2_C/inputs_2d
Tutorials/HeatEquation_EX2_C/inputs_3d
Tutorials/HeatEquation_EX2_C/main.cpp
Tutorials/HeatEquation_EX2_C/setup.cpp
Tutorials/HeatEquation_EX2_C/writePlotFile.H
Tutorials/HeatEquation_EX2_C/writePlotFile.cpp

commit 23a1a89e5c1d513969fa16d83fcd3b63d9ab01c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 19 20:30:12 2016 -0400

    use bind(C) to make the Fortran interfaces cleaner

Tutorials/HeatEquation_EX1_C/advance_2d.f90
Tutorials/HeatEquation_EX1_C/advance_3d.f90
Tutorials/HeatEquation_EX1_C/init_phi_2d.f90
Tutorials/HeatEquation_EX1_C/init_phi_3d.f90
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HelloWorld_C/main.cpp
Tutorials/HelloWorld_C/work.f90
Tutorials/README_C
Tutorials/Tiling_C/main.cpp
Tutorials/Tiling_C/work.f90

commit bec03a11125757b7431930bef5830497edb8b74d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 19 17:25:48 2016 -0700

    We don't need C_AMRLib to compile this example.

Tutorials/HeatEquation_EX1_C/GNUmakefile

commit ba276596d78f796054f9798b8fee3e9611e51508
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 19 14:44:41 2016 -0700

    add FluxRegister::ClearInternalBorders

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit a1b58049c9fc5a96ef49a207f7db30a23f33fce6
Merge: 050533067 0e3ef31d6
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 19 12:59:47 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 0505330672fc19e51146690f1d2690dd0f011dbd
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 19 12:59:30 2016 -0700

    update info for running on NERSC

Docs/F_AdvancedTopics/hopper_omp.run
Docs/GettingStarted/GettingStarted.tex
Docs/GettingStarted/edison.run
Docs/GettingStarted/edison_omp.run
Docs/GettingStarted/hopper.run
Docs/UsersGuide.tex

commit d5ecf0f5b68b715f9ee1513087755809a54b487d
Author: vince <vebeckner@lbl.gov>
Date:   Mon Sep 19 12:48:17 2016 -0700

    fix for special case.

Src/C_BaseLib/NFiles.cpp

commit 0e3ef31d62f17ee52374c027a2d4b307b753672f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 19 12:36:20 2016 -0700

    FabSet::plusTo (a MultiFab)

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 5a6f5dcc4b829cfc33e2d8c5daf4dbec4949ac2c
Author: vince <vebeckner@lbl.gov>
Date:   Mon Sep 19 11:49:06 2016 -0700

    another test inputs file.

Tests/IOBenchmark/inputs.dssmf

commit 5e6a8d3dca5b494617dc00791f25f66e673b633f
Author: vince <vebeckner@lbl.gov>
Date:   Mon Sep 19 11:42:31 2016 -0700

    remove implied order.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 638f1743665c75e460a7dff6300363ef170c4ffd
Author: vince <vebeckner@lbl.gov>
Date:   Mon Sep 19 11:39:54 2016 -0700

    check that the written multifab is valid.

Tests/IOBenchmark/IOTest.cpp

commit 168746508383be9427ec1c8dfcf6d6d30931fd3c
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 19 11:20:43 2016 -0700

    cleaning up users guide.  no significant changes yet

Docs/GettingStarted/GettingStarted.tex
Docs/Introduction/Introduction.tex
Docs/Preface/Preface.tex

commit f3bbed524a2d6ba10487fa71b28f71ed7c08a2f7
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 19 09:36:12 2016 -0700

    starting re-org or user's guide.  Move linear solver text into its own chapter, not the introductory material

Docs/GNUmakefile
Docs/GettingStarted/GettingStarted.tex
Docs/LinearSolvers/LinearSolvers.tex
Docs/UsersGuide.tex

commit 6540212ec285653c6d3c3882586782861fcf2e8c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 19 11:58:26 2016 -0400

    finish documenting the tutorials, and list them in an order of complexity

Tutorials/README_C

commit 07d493e1e90ad05ce67a7a2464971033eef4e8ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 19 11:30:24 2016 -0400

    start documenting tutorials

Tutorials/README_C

commit bbf612cf9d0d73d07fa8ec92413036ba4315f6b8
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 15 17:39:00 2016 -0700

    new test flag.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 8bfca64f1ce83238733d51c89a3c7b102ce89da5
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 15 17:38:24 2016 -0700

    fixes for dss offsets.

Src/C_BaseLib/NFiles.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 15d8cc5c321344bde0e26c83292917ed76bb53f8
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 15 14:59:22 2016 -0700

    ifdef for serial.

Src/C_BaseLib/NFiles.cpp

commit c8cd2e329eca650c46c75c81290a7d539dccb840
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 14 17:23:54 2016 -0700

    add option for writing with dynamic set selection.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 12b6cad694eb07dd77340859b3d8af2e0e54b9d4
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 14 17:22:11 2016 -0700

    update test check for nonzero decider.

Tests/IOBenchmark/IOTest.cpp

commit 965e89ce4842f88ae082093939a7b1834cf69ac8
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 14 17:20:36 2016 -0700

    make sure the decider is not in set zero.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit 26ec5295c301683bc86e969e0f84e7e8d9bec083
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 14 14:26:37 2016 -0700

    SetDynamic function instead of constructor.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp
Tests/IOBenchmark/IOTest.cpp

commit 9e537ec5e0cef9ad3cf29269d79e921a0259b3c5
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 14 14:11:01 2016 -0700

    change names to be more correct.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp
Tests/IOBenchmark/IOTest.cpp

commit a276aa69f05040e468ce852db68aa5682aceb0d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 12:41:45 2016 -0700

    remove unused and misspelled variable

Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp

commit b8b234e22db5b06851f15b322d01d009a0a9f449
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 08:57:39 2016 -0700

    use dot product to implement 2-norm

Src/C_BaseLib/MultiFab.cpp

commit 7c47ab7905e174c6852ecaa4b1c78c3ab07d996c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 08:57:16 2016 -0700

    fix typos

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit da6b019f69a6cc0d5e388e2f7168556a82f803bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 17:36:20 2016 -0700

    clean up comments

Src/LinearSolvers/C_CellMG/MG_3D.F

commit a750459bb4c3891961eff0076cb4a7113fd27f8e
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 13 17:26:37 2016 -0700

    more dss support.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit b83a274d34b8c8048fc9f04ceebd59ee14b361dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 16:29:37 2016 -0700

    more omp and tiling in linear solvers

Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit 1665be04d0048f7d924577c80f57c4385eff69b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 16:15:10 2016 -0700

    C_TensorMG: tiling

Src/LinearSolvers/C_TensorMG/MCLO_2D.F
Src/LinearSolvers/C_TensorMG/MCLO_3D.F
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 829337da3d5807bd2a653c78e8e4f7d2e8fe0518
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 16:07:09 2016 -0700

    C_TensorMG: cleanup

Src/LinearSolvers/C_TensorMG/DivVis_F.H

commit 6f8ac889473eddc43d910aa621ce1e84e48fa207
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 13 16:01:46 2016 -0700

    fix the special case.

Src/C_BaseLib/NFiles.cpp

commit 1ddfcb11a698f70a1b3b23f1461bb7da120f28f4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 15:57:36 2016 -0700

    remove FArrayBox::norm functions

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/MultiFab.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit daf027da2a5b7896f25c6afeb0dcc2de85caa512
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 13 15:51:42 2016 -0700

    new iterator tests.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 97adf325b6475af591bcf18b9aa63825265334c1
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 13 15:51:19 2016 -0700

    make the test code into an iterator for dynamic set selection.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit b80c6d83022a61f49362e4612432919f65121c63
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 15:30:33 2016 -0700

    C_TensorMG: remove omp from Fortran subroutines

Src/LinearSolvers/C_TensorMG/DV_3D1.F
Src/LinearSolvers/C_TensorMG/DV_3D2.F
Src/LinearSolvers/C_TensorMG/DV_3D3.F
Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F
Src/LinearSolvers/C_TensorMG/MCLO_3D.F

commit 3f8fd89d802fc9d7247344a96bcd74408ad9a290
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 15:17:18 2016 -0700

    use MulitFab::Xpay in linear solvers

Src/LinearSolvers/C_CellMG/LO_1D.F
Src/LinearSolvers/C_CellMG/LO_2D.F
Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/LO_F.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG4/ABec4.cpp
Src/LinearSolvers/C_TensorMG/DivVis_F.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCLO_2D.F
Src/LinearSolvers/C_TensorMG/MCLO_3D.F
Src/LinearSolvers/C_TensorMG/MCLO_F.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 22fd36f870ccaa86f6a61898b4b7d1dbb1c119c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 15:01:43 2016 -0700

    MultiFab::Xpay and BaseFab::xpay that do y = x + a*y

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BaseFab_f.H
Src/C_BaseLib/BaseFab_nd.f90
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 6b058bbbfb391e384247ce6ff655aef7fa6f5b36
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 14:40:15 2016 -0700

    omp in C_Tensor

Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp

commit dc102e6a4e8c7d6d51727f05768a56a1ce812f7b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 14:34:56 2016 -0700

    omp in MCCGSolver

Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp

commit 924472b312fe755748dd683a3b1fd945636baccd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 14:31:47 2016 -0700

    remove CG_?D.F and use BaseFab and MulitFab functions instead

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/CG_1D.F
Src/LinearSolvers/C_CellMG/CG_2D.F
Src/LinearSolvers/C_CellMG/CG_3D.F
Src/LinearSolvers/C_CellMG/CG_F.H
Src/LinearSolvers/C_CellMG/CMakeLists.txt
Src/LinearSolvers/C_CellMG/Make.package
Src/LinearSolvers/C_CellMG4/CMakeLists.txt
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp

commit 20e5dadb2838cf54960bf6d203930fef5ce7f23c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 14:16:03 2016 -0700

    CGSolver and MCCgSolver: use BaseFab::dot and MultiFab::Dot

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp

commit b5ee4df35b09f668f77752d33629c77161fd4ed7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 14:03:55 2016 -0700

    add MultiFab::Dot and use it in CGSolver

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BaseFab_f.H
Src/C_BaseLib/BaseFab_nd.f90
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 1beb3cb96f9ff97ea33acd2a07e1c208fd40ec7a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 13:22:41 2016 -0700

    CGSolver: use MultiFab::linComb

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit f7bd663498fd5e183e8c5ea92ce843c829616c4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 13:22:16 2016 -0700

    add MultiFab::LinComb

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 1c008a6a82bf6b78edf02d088b4b3810436bd8d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 13:10:38 2016 -0700

    BaseFab: make linInterp call linComb

Src/C_BaseLib/BaseFab.H

commit 03264b71f81c01d961945d7ecf3738f82b55feed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 13:06:48 2016 -0700

    BaseFab: specialize linComb

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BaseFab_f.H
Src/C_BaseLib/BaseFab_nd.f90

commit e4e39cbcae03fe8412dc5877a504154761797a7f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 10:30:47 2016 -0700

    BaseFab: fix new bug

Src/C_BaseLib/BaseFab_nd.f90

commit 744c464d9fdd4b4a08921e70ad642d9e329c2cb8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 10:11:38 2016 -0700

    BaseFab: remove SPECIALIZE_?D.F

Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package
Src/C_BaseLib/SPECIALIZE_1D.F
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H

commit 107afac74d906e1fe324c80ad5109f2fdbd95e22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 10:08:32 2016 -0700

    BaseFab: dimension agnostic minus, mult, divide, and invert

Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BaseFab_f.H
Src/C_BaseLib/BaseFab_nd.f90

commit 3c824ce246476055eafcfd2a09fbff7ff497fe78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 09:53:22 2016 -0700

    BaseFab: dimension agnostic plus

Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BaseFab_f.H
Src/C_BaseLib/BaseFab_nd.f90

commit 781feccde138a46b78a23668d645677c72470376
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 09:40:40 2016 -0700

     BaseFab: dimension agnostic norm

Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BaseFab_f.H
Src/C_BaseLib/BaseFab_nd.f90

commit 5b2704fe7efc1d69ba3d13f740d62be36573869f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 09:25:13 2016 -0700

     BaseFab: dimension agnostic setval

Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BaseFab_f.H
Src/C_BaseLib/BaseFab_nd.f90

commit 19f4f00ec60fe157aad5eb309cb99dfd689078e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 09:05:41 2016 -0700

    BaseFab: dimension agnostic copyfrommem

Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BaseFab_f.H
Src/C_BaseLib/BaseFab_nd.f90

commit 78155fd1d640f54bcf8ff2f69220f6ca7f201ddb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 08:51:40 2016 -0700

    BaseFab: dimension agnostic copy

Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BaseFab_f.H
Src/C_BaseLib/BaseFab_nd.f90

commit 53e21d532c32597498e3013a6a95db70cdfc7681
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 12 13:44:20 2016 -0700

    move fortran saxpy routine to dimension agnostic BaseFab_nd.f90

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BaseFab_f.H
Src/C_BaseLib/BaseFab_nd.f90
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package

commit 6d83ab2ea61681d42160c999c4ae577bfc32db5d
Author: vince <vebeckner@lbl.gov>
Date:   Mon Sep 12 13:21:24 2016 -0700

    test implementation of nfiles dynamic set selection.

Src/C_BaseLib/VisMF.cpp
Tests/IOBenchmark/GNUmakefile
Tests/IOBenchmark/IOTest.cpp

commit f1d86c7f1fe4174c654d7866fd5df028bd858666
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 12 12:30:43 2016 -0700

    add bl_fort_module.F90

Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package
Src/C_BaseLib/bl_fort_module.F90

commit 63fd9ba849da8f2315a34662666810c74182d924
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 12 12:14:12 2016 -0700

    clean up some GNUmakefile

MiniApps/PGAS_SMC/GNUmakefile
Tools/C_mk/Make.defs
Tutorials/AMR_Adv_C/Exec/Make.Adv

commit e2a889500a06a6db3f060edf1e1f74a545fc0239
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 12 11:19:27 2016 -0700

    add vpath %.fi

Tools/C_mk/Make.rules

commit bb2a46c463fec52bfa401a8cb35ba2e6aa444f34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 12 11:10:43 2016 -0700

    set up VPATH_LOCATIONS and INCLUDE_LOCATIONS in various Make.package and add vpath ...  to Make.rules so that the user does not need to do it

Src/C_AMRLib/Make.package
Src/C_BaseLib/Make.package
Src/C_BoundaryLib/Make.package
Src/C_TowerLib/Make.package
Src/Extern/amrdata/Make.package
Src/Extern/hpgmg/Make.package
Src/F_BaseLib/FParallelMG.mak
Src/LinearSolvers/C_CellMG/Make.package
Src/LinearSolvers/C_CellMG4/Make.package
Src/LinearSolvers/C_TensorMG/Make.package
Src/LinearSolvers/C_to_F_MG/Make.package
Src/LinearSolvers/F_MG/FParallelMG.mak
Tools/C_mk/Make.rules

commit 67ab2c4a9e760c277d4d235f71c79c7e94c53e0c
Merge: 676ceecae 67c7ad4a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Sep 11 10:02:50 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 676ceecae61f744e45affc0b18825817d1f2b921
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Sep 11 10:02:37 2016 -0400

    new inputs for the merged castro + radiation

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 67c7ad4a7e6ae8fbd27a62c3b8915378c3548471
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 9 14:52:51 2016 -0700

    omp in TensorMG

Src/LinearSolvers/C_TensorMG/DivVis.cpp

commit 59ea9107416f88ff874d82a8440a92621f37f869
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 9 14:19:32 2016 -0700

    omp in CellMG4

Src/LinearSolvers/C_CellMG4/ABec4.cpp

commit 18c70c6ddd93d10629132f3a78890654b0d904c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 9 13:57:02 2016 -0700

    omp in cg and remove XBLAS stuff

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 0127c59afeb6812cdb37bdd6eae85a8185389aae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 9 13:56:40 2016 -0700

    remove nested omp parallel

Src/LinearSolvers/F_MG/itsol.f90

commit cbfba005668367b3fbec4117a50d41f94f3bc85c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 9 13:43:42 2016 -0700

    fix assertion

Src/C_BaseLib/BoxArray.cpp

commit eb8f20e89c6db6a6747d299bc44857d8e25a1834
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 9 09:45:40 2016 -0700

    use BL_ASSERT for calls to contains_nan

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit eb68c7e79af10cebd47f14d9c62a447556167d74
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 9 09:21:01 2016 -0700

    remove the fast version of contains function from Cluster.cpp and incorporate it into BoxArray class

Src/C_AMRLib/Cluster.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 65d9210e53b0b2cff4bef5caa8a5e6f2631e9498
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 8 17:57:51 2016 -0700

    test implementation of nfiles dynamic set selection.  not complete.

Tests/IOBenchmark/IOTest.cpp

commit 8c66c05e41773870079d88d9475ca7bbe5701afd
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 8 17:39:58 2016 -0700

    more io notes.

Docs/Readme.io

commit 456e76ab2d2085f2b6792103a469dc326653e172
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 8 17:39:27 2016 -0700

    test inputs.

Tests/IOBenchmark/inputs
Tests/IOBenchmark/inputs.dss
Tests/IOBenchmark/inputs.nft

commit dc048754f9b7316ad078a9b53db87e8a33bd9537
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 8 17:38:28 2016 -0700

    test for nfiles dynamic set selection.

Tests/IOBenchmark/IOTestDriver.cpp

commit 935b57e75456d58edd10e40475113631cd212788
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 8 17:13:08 2016 -0700

    cleanup

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp

commit 2ca099c9a9563e63a7a55c01079195bf23f20ab0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 8 17:11:43 2016 -0700

    comment

Src/C_BoundaryLib/BndryData.cpp

commit 1c8832e384b194a2806561dd2390de84dd99845c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 8 17:01:01 2016 -0700

    tiling in FabArray::BuildMask

Src/C_BaseLib/FabArray.H

commit 97e01b756fc4ca247aad7ffd94c6de1536daeb14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 8 16:57:06 2016 -0700

    make MultiMask work with multiple component

Src/C_BoundaryLib/MultiMask.cpp

commit 8bd07844a78c13de7527ee714024dd5c8d0240d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 8 16:51:20 2016 -0700

    fix a new bug in tensor solver

Src/LinearSolvers/C_TensorMG/DivVis.cpp

commit 6791d3c0c6eb8574b1e1c9622877696d33e35c87
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 8 15:05:35 2016 -0700

    added check for total nfiles.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit ce433a91841bf97ee3b5c5f8cc26b7865e754f40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 7 17:05:02 2016 -0700

    update 4th order linear solver to the new Mask

Src/LinearSolvers/C_CellMG4/ABec2.cpp
Src/LinearSolvers/C_CellMG4/ABec4.cpp

commit 3bbae688ff83cfaef47febc545784850d9320184
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 7 16:42:40 2016 -0700

    reimplement Masks used by linear solvers with FabArray

Src/C_BaseLib/FabArray.H
Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp
Src/C_BoundaryLib/MultiMask.H
Src/C_BoundaryLib/MultiMask.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 7bccdb48ce82a63755e6dcfd79950e1a77a54775
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 7 12:19:46 2016 -0700

    settable buffer size, option for synchronous reads.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit c3919dcc839a19aea8da80b97042488b2244161b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 7 12:07:28 2016 -0700

    use buffer size function.

Src/C_AMRLib/Amr.cpp
Src/Extern/amrdata/AmrData.cpp

commit b2fe1d535ff779d78d2a9db3852290476366c9b7
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 7 11:57:27 2016 -0700

    use buffer size function.

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/NFiles.cpp

commit c7f2a90bc1549f3b0627134a1ac9b23741a10c5f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 7 11:55:06 2016 -0700

    use buffer size function.

Src/C_BaseLib/Particles.H

commit cd37c0f560925781eec8cf14b51d07f4de683bbf
Merge: e47e3fb27 d9522a5d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 7 10:02:22 2016 -0700

    Merge branch 'development' into weiqun/multimask

commit d9522a5d2063e6995f3f04b6cac356b233a615aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 7 09:53:14 2016 -0700

    minor

Src/C_BaseLib/BoxArray.cpp

commit 0a142ab0d3da7cca6d9a13160adc6a262d77b736
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 7 09:10:33 2016 -0700

    Cluster: if there is a tie, z-direction has the highest precedence whereas x-direction the lowest.  This is more likely to generate boxes with the longest dimension in x.

Src/C_AMRLib/Cluster.cpp

commit 594e6680c7094867e4702eaca9101b604526e69e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 7 08:36:52 2016 -0700

    clean up fpb

Src/C_BaseLib/BLPgas.H
Src/C_BaseLib/BLPgas.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 2c0b25b21f3fd6f7c4ca73517949ad799136cf04
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 6 15:30:59 2016 -0700

    long seeks and separate tags for reads and signals.

Src/C_BaseLib/VisMF.cpp

commit 3e956e409231d23a90c0176fd4083edcb43ba0a7
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 6 15:28:41 2016 -0700

    updated comment.

Src/C_BaseLib/ParallelDescriptor.H

commit c949ca597470cbc5aa2e5bd8855156e4a1151817
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 6 13:30:30 2016 -0700

    fix the new FabSet::Copy: cannot use MultiFab::Copy

Src/C_BoundaryLib/FabSet.cpp

commit 4dd3dfb6afe70f7b9750d33695c1dbdd81657731
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 6 11:24:52 2016 -0700

    add static local Copy function for FabSet and BndryRegister

Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 342734b40a75296557d85eded35337f2cc4ef43e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 6 11:09:48 2016 -0700

    BoxLib::match: shortcut when BoxArrays are equal (i.e., ==)

Src/C_BaseLib/BoxArray.cpp

commit f919ef4ce409138d029ba7c20bbf4ba05737feb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 6 10:17:17 2016 -0700

    When provided with BoxArray, StateData::restart will use the provided one and make sure it matches the one in the istream.  This helps reduce duplicated BoxArrays.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit 7e7e8c2ce4384a11514a304f8343ac631554c87f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 6 09:51:53 2016 -0700

    add BoxLib::match that returns ture if the boxes returned by operator[] in two BoxArrys match.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 9ad32e2310e22ffdd7a99b9dbaa46a593f144f81
Merge: 098acd48e 495341878
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 5 22:58:04 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 098acd48ea04d9127e68f733266febc57bbea46c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 5 22:57:23 2016 -0400

    add the ability to put the point we slice through at the lower left
    instead of the center of the domain.

Tools/Postprocessing/F_Src/fextract.f90

commit 49534187840c0ccf38473cf9fb1674c8da47c85f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 2 14:56:34 2016 -0700

    FillCoarsePatch: call bc function to fill physical boundaries instead of interploating

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.cpp

commit 8e49c9c3730769bce3095dbf0779299dbbe1f1ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 2 11:09:15 2016 -0700

    minor clean up

Src/C_BaseLib/Geometry.cpp

commit a0117bc0fb1c3fb3850040f6c9fdf52818269342
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 2 11:06:16 2016 -0700

    assertion Geometry::Setup is not called inside omp parallel

Src/C_BaseLib/Geometry.cpp

commit 7af78108e0d24d2c5f68e4296cb330f6c4094f9c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 2 10:50:09 2016 -0700

    rm deprecated Geometry::FillPeriodicBoundary and Geometry::PeriodicCopy

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit ee69a8e2d264555069a48479a47079a9656291b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 1 10:16:49 2016 -0700

    call various Initialize() in BoxLib::Initialize() to ensure thread safety

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/IArrayBox.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/iMultiFab.cpp

commit fa8f135ba0fefb6d639e54c7e31ad07fb4965e38
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 1 08:30:29 2016 -0700

    Release Notes 16.09

ReleaseNotes/release-notes-16.09

commit 79a7b62a6d5a484e404df529d955d99e968fdef5
Merge: d728f4305 1846431b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 1 08:29:30 2016 -0700

    Merge branch 'master' into development
    
    Conflicts:
            Src/C_BaseLib/CMakeLists.txt
            Src/C_BaseLib/FabArray.H

commit 33471615ca3c99ad60779391a4cdcc61af9a165f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 31 15:44:44 2016 -0700

    close persistent streams before each test.

Tests/IOBenchmark/IOTest.cpp

commit 7fe9f4b4cfdf17c1c57e9a6f1783ff247eacb9a8
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 31 14:57:50 2016 -0700

    added more test options.

Tests/IOBenchmark/IOTestDriver.cpp
Tests/IOBenchmark/inputs

commit 2ff75ad886e75e993cde0fe392771bb48ebb99be
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 31 14:56:25 2016 -0700

    implemented persistent streams for reading.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 5e1e78d476313e1de8d6be10325d13766ebb33a1
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 31 14:54:54 2016 -0700

    changed default buffer size.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 99db2b99ffed1106724326495867a60671e6096d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 31 10:54:26 2016 -0700

    changed default buffer size.

Src/C_BaseLib/FabConv.cpp

commit d728f43054ff948f224450d775dd599f1dfc6955
Merge: 053128438 94d3f75f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Aug 31 13:12:21 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 053128438351add4c4a8818d30ba5a0fc1758338
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Aug 31 13:11:59 2016 -0400

    print out zone info for the biggest error zone to make Dr. Katz happy :)

Tools/Postprocessing/F_Src/fcompare.f90

commit 94d3f75f34a52397821b3bccd09affc81e39b01d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 30 20:31:58 2016 -0700

    BoxLib::InterpFromCoarseLevel(): fix box type

Src/C_AMRLib/FillPatchUtil.cpp

commit f107760a8cf2c148c495fadcf41eafcea345b0b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 30 20:23:32 2016 -0700

    fix BoxLib::InterpFromCoarseLevel()

Src/C_AMRLib/FillPatchUtil.cpp

commit 39281f23ba6d347550eaccab25d9722856122ab6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 30 16:47:05 2016 -0700

    add BoxLib::InterpFromCoarseLevel()

Src/C_AMRLib/FillPatchUtil.H
Src/C_AMRLib/FillPatchUtil.cpp

commit 508cf269230cd7cc1dc2ea549c15bc503785de08
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 30 18:06:20 2016 -0400

    Revert "protect FArrayBox::Initialize with omp single because it is not thread safe"
    
    This reverts commit 84a980833b5f781a829691721bbfd117a39d7ba3.

Src/C_BaseLib/FArrayBox.cpp

commit 2e24778a7a03c8bb849ee5dee740307dd82a1e52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 30 17:37:22 2016 -0400

    fix the fix (but I think it's compiler's fault): In MultiFab::Iniitialize, construct a FArrayBox so that the FArrayBox class will be properly initialized.

Src/C_BaseLib/MultiFab.cpp

commit 84a980833b5f781a829691721bbfd117a39d7ba3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 30 16:42:37 2016 -0400

    protect FArrayBox::Initialize with omp single because it is not thread safe

Src/C_BaseLib/FArrayBox.cpp

commit e2671b9ccf2f24eb91d1aa6158c4ea7e0fd36b82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 30 13:14:03 2016 -0400

    Insert flush() between writing header and data to get around a bug (?) on Titan.

Src/C_BaseLib/FArrayBox.cpp

commit ac5110e87663615a7d2e4f929f59faaf0b4cbe1b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 29 15:18:46 2016 -0700

    given a MultiFab filled with weights, make a KnapSack DistributionMapping

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit d907a94a0b5b1328db81e9b4a12cb9876fad7e8e
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 25 18:35:18 2016 -0700

    more support for persistent streams.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit edd6874ff543748e22c98c3abea064d4ea761acb
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 25 18:34:23 2016 -0700

    level directory creation setting.

Src/C_AMRLib/AmrLevel.H

commit eb3207c6f55bc9efc2224fcd9b164caa81468877
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 25 18:33:25 2016 -0700

    add more parmparse options.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit dde3f250d7972d18718ddbcc484fd73f240fc941
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 25 17:41:17 2016 -0700

    because the do_async_sends flag is ignored by FillBoundary now, we should not test that flag in WaitForAsyncSends

Src/C_BaseLib/FabArray.H

commit fbcd8606ebc9136c70e8e9b33effd9db1a7b388b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 25 17:21:59 2016 -0700

    remove calls to BoxLib::fill_boundary because it is deprecated

Tutorials/MultiFab_C_F/main.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp

commit 186b4d3fdc223df74f850f51ecdc348a5f3c7795
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 25 15:53:53 2016 -0700

    more io tasks.

Docs/Readme.io

commit 3187ef9991fdbef345fdda700ad54e4f86862719
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 25 12:24:07 2016 -0700

    check for sufficient memory for single reads and writes.

Src/C_BaseLib/VisMF.cpp

commit c7f5a5291472493b1a4f83826e731a0f164caca1
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 25 11:45:35 2016 -0700

    format, set version for plot files.

Src/C_AMRLib/Amr.cpp

commit e03ab79146f54ad2f91d376a38900f2476a0e0aa
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 24 18:20:01 2016 -0700

    added use single read and write code.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 073b42db47ab3edf92adf59277dd1268c5fe9f7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 24 17:32:35 2016 -0700

    remove Geometry::SumPeriodicBoundary

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit f462bae2a69fed8a0a4e92fa29f879c97468e14b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 24 17:18:28 2016 -0700

    add use single read and write parmparse variables.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 874927e02a18b0c50078bf10c414bde2d74db18e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 24 16:57:09 2016 -0700

    use MulitFab::SumBoundary for periodic boundaries too.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/Particles.H

commit f186de8be9f772579bacdb739c114753ab861889
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 24 16:11:37 2016 -0700

    statedata support for prereading fabarray headers.

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 38a2d3d666b96df44b2c01192969362166112092
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 24 14:46:09 2016 -0700

    fix for in file order.

Src/C_BaseLib/VisMF.cpp

commit 2221e2c49b4af713aa71a911d2572c48bd411b44
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 24 14:43:36 2016 -0700

    fix MemProfiler by casting lambda functions into std::function with the correct type.

Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MemPool.cpp
Src/C_BaseLib/MultiFab.cpp
Src/F_BaseLib/MemProfiler_f.cpp

commit 2b09a9d61e0871ae8182e4d0b877110f5ad1fa74
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 24 13:18:26 2016 -0700

    remove const from return type

Tools/C_scripts/buildInfo.H
Tools/C_scripts/makebuildinfo_C.py

commit 9be851922301f09bf750c156afe497c7b2b12960
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 24 13:11:38 2016 -0700

    Add template argument to BATBase otherwise some compilers are not happy.

Src/C_BaseLib/BoxArray.H
Src/C_BoundaryLib/BndryRegister.cpp

commit a1ac2d1b8d7c6f57f75b479f0ec9bf27e35a2f6f
Merge: 4115c6680 def51899d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 24 12:21:27 2016 -0700

    Merge branch 'development' into weiqun/work
    
    Conflicts:
            Src/C_BaseLib/CMakeLists.txt

commit 1846431b6328e62baceffd5442fde639b68008af
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 24 09:55:48 2016 -0700

    We need to add the line include_directories(${CBOXLIB_INCLUDE_DIRS}) to the CMakeLists.txt so that
    backtrace_c.cpp can find BLBackTrace.H (which is in C_BaseLib).

Src/F_BaseLib/CMakeLists.txt

commit def51899d7369b638c3943d7e2ee2c27b87eac03
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 24 09:55:48 2016 -0700

    We need to add the line include_directories(${CBOXLIB_INCLUDE_DIRS}) to the CMakeLists.txt so that
    backtrace_c.cpp can find BLBackTrace.H (which is in C_BaseLib).

Src/F_BaseLib/CMakeLists.txt

commit 9f1a39e57c2dd14d7fff40f65b40434120e1de1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 24 06:27:05 2016 -0700

    fix assertion: the recvcount and disp vections are insignificant on non-root processes.

Src/C_BaseLib/ParallelDescriptor.H

commit 1051c11958514486d0dc2c3e259e7d4e9098729e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 23 21:57:57 2016 -0700

    TagBoxArray::collate: use the long version of ParallelDescriptor::gatherv to avoid interger overflow.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit f890189d35dc1814ccb848790a7006527c4d0ec8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 23 21:16:45 2016 -0700

    add two version of ParallelDescriptor::gatherv: one takes int as offset and the other takes long.  The int version calls MPI_gatherv.  The long version uses MPI_Irecv and MPI_Send because MPI does not support using long as offset in MPI_gatherv.

Src/C_BaseLib/ParallelDescriptor.H

commit 2ecb4591042c9de7fb491fb26b8b6300cd6e23b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 23 20:56:43 2016 -0700

    add a non-const version of IntVect::getVect

Src/C_BaseLib/IntVect.H

commit 5159303869afc1787d6f8b94a4c8033ce201376a
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 23 15:11:27 2016 -0700

    added option to preread and broadcast all multifab headers to avoid synchronization during restart.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit 4115c6680ea695e2387055fd5e38aa07b57ec309
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 23 12:42:28 2016 -0700

    Extrapolater: should still use masks even after setting all crse cells to zero first because these cells get updated.

Src/C_AMRLib/extrapolater_2d.f90
Src/C_AMRLib/extrapolater_3d.f90

commit cbc3917b26c1141e8be9a9b02312be8c6f4f0f49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 22 17:32:14 2016 -0700

    tidy

Src/C_AMRLib/extrapolater_3d.f90

commit 2f5b7fb401b6fe0f6a194c237f667535c79e06cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 22 17:30:48 2016 -0700

    fix array bound in extraploater

Src/C_AMRLib/extrapolater_3d.f90

commit 18e1ead7cd9301668c762532ac89a58bac8ec0b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 22 17:06:22 2016 -0700

    EnforcePeriodicity cannot use ngrow to decide to skip jFillBoundary_finish

Src/C_BaseLib/FabArray.H

commit a52008b6a1495e16be8aabb34be3c5e30dce00d3
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 22 15:25:18 2016 -0700

    added support for prereading fabarray headers.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 2a1e8b8cb95ca0396f8194f232914b94bd803a3f
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 22 14:41:29 2016 -0700

    restart fixes for new formats.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/VisMF.cpp

commit fb418321fa050f6076e0435f91fd1c254b9cd12d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 22 14:36:47 2016 -0700

    FabArray::EnforcePeriodicity: make sure the source cells are always inside the periodic domain.

Src/C_BaseLib/FabArray.cpp

commit 55e5bcc8993b4c0c15be1417ad31d01c0803ecac
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 22 12:08:03 2016 -0700

    remove old code.

Src/C_AMRLib/Amr.cpp

commit 78fa116b6913ed018afe76e856885d88e30d0666
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 22 11:59:58 2016 -0700

    formatting.

Src/C_AMRLib/StateData.cpp

commit 3a759fb86db7cfa41282dc815b15415ebe4349b0
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 22 11:06:34 2016 -0700

    formatting.

Src/C_AMRLib/Amr.cpp

commit 7b8d0ee54d69c6aebb5025cf7e347b13d11304b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 21 16:41:16 2016 -0700

    FillBoundary: return immediately if there are no ghost cells

Src/C_BaseLib/FabArray.H

commit b6a622a7e61374c8401d0c9a04d54e58387e58cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 21 16:32:51 2016 -0700

    EnforcePeriodicity: return immediately if there is no periodic boundaries

Src/C_BaseLib/FabArray.H

commit c4f1e42a9139699b59bd514ac4633004e31c2aba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 21 16:20:36 2016 -0700

    FabArray::BuildMask: treat ghost cells outside periodic boundaries as normal ghost cells not physical boundary cells

Src/C_BaseLib/FabArray.H

commit 63df991c4d3552a37b42d53b33ba715911a20c93
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 21 16:01:41 2016 -0700

    minor name changes

Src/C_BaseLib/FabArray.H

commit 1b706db90a9830c757bb081218b4d718a236ed99
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 21 15:36:27 2016 -0700

    move iMultiFab::buildMask to FabArray::BuildMask so that it becomes a template

Src/C_AMRLib/Extrapolater.H
Src/C_AMRLib/Extrapolater.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/iMultiFab.H
Src/C_BaseLib/iMultiFab.cpp

commit 7a75f8f43cb51c81128a0f2f07d2954461b909bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 20 12:46:11 2016 -0700

    EnforcePeriodicity: allow ghost cells to be source

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 2326e9378d5a688063b9258bcc1d42338d40eff3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 20 12:14:52 2016 -0700

    Extrapolater: set coarse cells to zero first to ensure there are no NaNs

Src/C_AMRLib/extrapolater_2d.f90
Src/C_AMRLib/extrapolater_3d.f90

commit 6e3f70065843796edde28f6d15b290f6480fea3d
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 19 15:52:28 2016 -0700

    set relative path.

Src/C_BaseLib/VisMF.cpp

commit 079348613d750613bbe887cd731018652c1352b9
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 19 15:51:57 2016 -0700

    option to precreate checkpoint directories to avoid a barrier at each level.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit ad1f88cda9cf03ed8afae154cc0fcdff0fb40a5c
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 19 15:50:18 2016 -0700

    more io notes.

Docs/Readme.io

commit cd5fc721d134d9e1110b018b43fa38a923d9e0ff
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 18 17:56:10 2016 -0700

    add nstreams readers.

Src/C_BaseLib/VisMF.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/IOBenchmark/inputs

commit 4551fda2fb45fc1684a41ef2a3e8db471f95a79e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 18 15:42:48 2016 -0700

    Extrapolater: fix bugs

Src/C_AMRLib/extrapolater_3d.f90

commit 25ea870b1db44d0311a4956b145216b2913ce11b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 18 15:35:50 2016 -0700

    Extrapolater: fix a bug

Src/C_AMRLib/extrapolater_3d.f90

commit 8458b904401b820c01a922c1469a24e8b20470b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 18 15:07:08 2016 -0700

    Extrapolater: fix index bug

Src/C_AMRLib/extrapolater_2d.f90

commit 833b211bc7c5249043191ea8224f4ca1819ca583
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 18 14:54:43 2016 -0700

    let Extrapolater build the mask

Src/C_AMRLib/Extrapolater.H
Src/C_AMRLib/Extrapolater.cpp

commit e06a47b4fa985c642e73bf680995dba966772631
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 18 12:21:59 2016 -0700

    Add Extrapolater to replace IAMR functions for extraploating viscout terms.

Src/C_AMRLib/CMakeLists.txt
Src/C_AMRLib/Extrapolater.H
Src/C_AMRLib/Extrapolater.cpp
Src/C_AMRLib/Make.package
Src/C_AMRLib/extrapolater_1d.f90
Src/C_AMRLib/extrapolater_2d.f90
Src/C_AMRLib/extrapolater_3d.f90
Src/C_BaseLib/iMultiFab.H
Src/C_BaseLib/iMultiFab.cpp

commit 23e80cbef88ea8d8b287324987b5a6841ea6b138
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 18 13:55:23 2016 -0700

    removed diagnostics, added timer.

Src/C_BaseLib/VisMF.cpp

commit 4f61204aa85c431b5a6beab6b592dff652590394
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 18 13:32:41 2016 -0700

    file order fabarray reads.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 1f704f246211b6460112d765cad9aa755acb53b7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 18 11:54:05 2016 -0700

    Update CMakeLists.txt to reflect the fact that Particles* have moved from C_AMRLib to C_BaseLib and
    also to include PhysBCFunct.H and  ParGDB.H in C_BaseLib/CMakeLists.txt

Src/C_AMRLib/CMakeLists.txt
Src/C_BaseLib/CMakeLists.txt

commit 6321906784a339ea1935dc1feb5efbed98d744e6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 18 11:54:05 2016 -0700

    Update CMakeLists.txt to reflect the fact that Particles* have moved from C_AMRLib to C_BaseLib and
    also to include PhysBCFunct.H and  ParGDB.H in C_BaseLib/CMakeLists.txt

Src/C_AMRLib/CMakeLists.txt
Src/C_BaseLib/CMakeLists.txt

commit f8ac7e39679cdad1e889b374e5cf1cae1ae22b14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 16:35:42 2016 -0700

    new function iMultiFab::buildMask

Src/C_BaseLib/iMultiFab.H
Src/C_BaseLib/iMultiFab.cpp

commit 16c3927c1f3dc39b68e9fa15bae587d65f9557d8
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 17 14:35:35 2016 -0700

    changed mf name.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 74f7554c548568a8fe75990d7698f9bb13ade4de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 14:31:09 2016 -0700

    tweak FabArrayBase::TheFB interface

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp

commit 9db6058baa94d53bea869d518a7306591e769bdd
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 17 14:15:41 2016 -0700

    calculate header offsets.

Src/C_BaseLib/VisMF.cpp

commit 02f34b4d0b99ea41a26880769bfaabdbd25a80c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 13:58:59 2016 -0700

    clean up iMultiFab

Src/C_BaseLib/iMultiFab.H
Src/C_BaseLib/iMultiFab.cpp

commit c0379574afdfc8a1b36866b61a98bfc0d33a0829
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 13:50:24 2016 -0700

    FillPeriodicBoundary --> EnforcePeriodicity

Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp

commit 5166b4261be7a55651d6b8b1dbf8fbd5a3acd5d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 13:42:47 2016 -0700

    clean up outdated stuff

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 542ed1977a801196d47bb94e4f9d84a3a149f604
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 13:38:03 2016 -0700

    simplify the way of filling boundary corners

Src/LinearSolvers/C_CellMG4/ABec4.cpp

commit 4d3fa63b672badb254a517ea47b48fd74725d09f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 13:09:36 2016 -0700

    a number of small changes related to FillBoundary interface

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Tests/C_BaseLib/tFB.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/PGAS_HEAT/main.cpp
Tutorials/PIC_C/solve_with_hpgmg.cpp
Tutorials/Tiling_Heat_C/main.cpp

commit bcf79f114f09d8745f445a173b50a20fed679ba6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 12:31:23 2016 -0700

    assertion that FillBoundary's (cell-centered verions) BoxArray is non-overlapping

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 7252e25008c28e13a0e70c504a2c90545856f32b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 12:28:15 2016 -0700

    add BoxLib::convert for BoxArray

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit e82a303c72c53d47cb12d1965b4be5e99a05cc70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 12:14:32 2016 -0700

    add assertion and comments

Src/C_AMRLib/FillPatchUtil.cpp
Src/C_BaseLib/FabArray.cpp

commit 4a6ac101cfdd4b4d2b4663ae4f1ff7f264e7c9bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 11:20:36 2016 -0700

    use FillBoundary for periodic boundaries

MiniApps/PGAS_SMC/SMC_advance.cpp
Src/F_Interfaces/BaseLib/multifab_fi.cpp

commit a3a7b5ef348568d34a98b3a145f7835b5f55161c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 10:56:43 2016 -0700

    fix thread safety for FabArray::EnforcePeriodicity

Src/C_BaseLib/FabArray.cpp

commit 711ab9b37aa7e3c6684826cabd6fbdd0a2248a7e
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 16:59:17 2016 -0700

    removed old test function.

Tests/IOBenchmark/IOTest.cpp

commit d14246c427ef0d2563ab97ecf46ef88c15b7d840
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 16 16:52:34 2016 -0700

    fix bind c name for PGI

MiniApps/PGAS_SMC/chemistry_module.f90
MiniApps/PGAS_SMC/derivative_stencil.f90
MiniApps/PGAS_SMC/init_data.f90
MiniApps/PGAS_SMC/kernels.f90
MiniApps/PGAS_SMC/make_plot.f90
MiniApps/PGAS_SMC/transport_properties.f90
MiniApps/PGAS_SMC/variables.f90

commit 960cb8eaa811c744cbee0740fdea17e192f29a22
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 16:48:43 2016 -0700

    removed debugging diagnostics.

Src/C_BaseLib/VisMF.cpp

commit c9e168b465ed77fe3dbe0881d0ee386e24a54348
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 16:45:25 2016 -0700

    added NFiles.

Src/C_BaseLib/CMakeLists.txt

commit d7158f2b5b436601f075aff96b392c5ec4433d4c
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 16:27:01 2016 -0700

    removed test functions.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 6cc92dc53812ec4467f5ef2a1617c954fce74d7d
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 16:26:28 2016 -0700

    more notes.

Docs/Readme.io

commit 87b105f550ddde355f8617e4b4143b24f0017caf
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 16:21:51 2016 -0700

    consolidate write functions for all formats.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 391aa74f1d4dcb5d7d37fce1f997682da607ae69
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 16:20:40 2016 -0700

    consolidate nfiles write tests for the new formats.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/IOBenchmark/inputs

commit abbe43d1d5d9bcda411c6220c505ee999effc2ad
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 15:06:42 2016 -0700

    calculate offsets for old version without communication.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit ca0dc717542a16b999da8a49419d0dc6a857beba
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 11:20:20 2016 -0700

    change names to be more general.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/IOBenchmark/inputs

commit f1d27e5ba22a2c81c92bd203b35028c3aad888f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 16 07:42:31 2016 -0700

    FabArray::EnforcePeriodicity: use a bool flag instead of a domain box

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/Periodicity.H
Src/C_BaseLib/Periodicity.cpp

commit 1af6129e044a152b35400885e7ac22a86b62accf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 15 23:23:12 2016 -0700

    fix EnforcePeriodicity function

Src/C_BaseLib/FabArray.H

commit e7b92b0c045923e8b92f4e8262219a71f6118c9e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 15 23:14:43 2016 -0700

    FabArray::EnforcePeriodicity()

Src/C_BaseLib/Box.H
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp

commit 4e6bb4697568e76a7e049e2469732a0eb3692bc7
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 15 19:01:44 2016 -0700

    combine write functions.

Tests/IOBenchmark/IOTest.cpp

commit dd00429afcd5913b915863e722ebe6b272fe05bd
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 15 19:01:09 2016 -0700

    combine write functions.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 112e1e110613a147986d793487dacea69994f4c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 15 16:11:27 2016 -0700

    remove FabArrayBase::SetSendTag and SetRecvTag because IAMR SyncRegister no longer needs them

Src/C_BaseLib/FabArray.H

commit 1443ec9fbbb11a11bd7ba99ee91dcf07fad5170d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 12 16:01:12 2016 -0700

    Add an option for setting constant coefficients for a nodal solve.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit b344fcfce73a6ab66b103f415ca19a363bcd6f3f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 12 13:13:33 2016 -0700

    remove nested omp parallel.  they seem to cause some problems.

Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/INTERP_3D.F

commit c7f118dd4e43d9fbcae1b2d1d6458e23f087daf9
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Aug 11 21:45:56 2016 -0700

    Remove last bits of old sidecar implementation. The new stuff doesn't need it.

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.cpp
Src/F_BaseLib/parallel.f90

commit f6a272bf798bcbf9a61aecfa1d85a1833698ca8c
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 9 12:57:01 2016 -0700

    C_mk: add SDE ifdef for using Intel SDE for FLOP counting

Tools/C_mk/Make.defs

commit c55e378b3a60aed3f5c2e0c5d1945e7dd8a9b4f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 11 21:53:48 2016 -0700

    remove unused variable

Src/C_BaseLib/CArena.cpp

commit 5c8d5b840b844bffc4d6fa4530f6e504bb4fe37d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 11 17:22:57 2016 -0700

    native reads, fixes for vis with no min max values in the header.

Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit a285a9e63eebfc72ea7af5916cdcc28a2ba158c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 11 12:40:02 2016 -0700

    Fabset::plusFrom takes Periodicity argument

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit e29258d8bc310b495cfa5d11794b69b195aa10b9
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 10 18:26:54 2016 -0700

    implemented new vismf reads for file order reads.  not finished yet.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 9f4d5b9dc1accc6102279692d17a33ebbdc60320
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 10 18:24:30 2016 -0700

    added consts.

Tests/IOBenchmark/IOTest.cpp

commit eebcb07ef730d0aa1fd189e960ad0414bc964eb3
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 10 16:49:48 2016 -0700

    added functions for reading.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit 4c928c624410d8cc3e1d41bbaa8f8f59fc8e755c
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 10 16:46:23 2016 -0700

    added more inputs.

Tests/IOBenchmark/inputs

commit 45d1cde65c5a42435dcdcac0e843d818a16691f6
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Aug 10 15:45:47 2016 -0700

    you can pass in an optional argument to ml_cc_solve, ok_to_fix_singular=.false. (default true).  If false, the multigrid solver will not subtract off the average of the RHS for singular matrices.  Useful for debugging singular problems if you want to see, e.g., if S integrates to zero for low mach codes, or if total charge integrates to zero for electrostatic potential solves.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_solve.f90

commit 4eaeb90e7f34fafed23a119c38a3b7296d05e102
Merge: fad98e200 ea55a29a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 10 14:23:38 2016 -0700

    Merge branch 'development' into weiqun/work

commit fad98e200146f95ab41029700906ef457b08db7c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 10 13:22:53 2016 -0700

    minor

Src/C_AMRLib/FillPatchUtil.cpp

commit ef16f80d1618c0575189061c54e7b78c35f93ab2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 10 13:06:08 2016 -0700

    add static function Periodicity::NonPeriodic() for clarity

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/Periodicity.H
Src/C_BaseLib/Periodicity.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit b68d5f70cb2b0e85478e13ec351775ba0b157e4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 10 12:55:56 2016 -0700

    use FabArray::copy for periodic copy

Src/C_AMRLib/FillPatchUtil.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit ea55a29a33578330f22ef035b92c85e4bb45befb
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Aug 10 12:51:08 2016 -0700

    call parallel reduce only on elements in an array which are initialized.  Otherwise code would crash

Src/LinearSolvers/F_MG/ml_cc.f90

commit 10592c49d1d92891e37b087a8add0c1762daabdc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 10 12:45:27 2016 -0700

    FabArray::copy does periodic copy too

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 87dfbb82b002258f00467184c1ce089fcdd52f01
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 10 12:31:33 2016 -0700

    more io tests.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/IOBenchmark/inputs

commit b177e928f23aad9b01206243c3d8999b43a35126
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 10 11:11:50 2016 -0700

    FabArray::copy: add a new Periodicity argument

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BoundaryLib/FabSet.cpp

commit d5eda63c2773749b49eb7831db8e010d35c765b2
Merge: 605539b05 44b476d93
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 10 10:53:40 2016 -0700

    Merge branch 'development' into weiqun/work
    
    Conflicts:
            Src/C_BaseLib/FabArray.H

commit 605539b05bd39655a8ae64c59d8fda8981fc4f70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 21:16:33 2016 -0700

    minor optimization

Src/C_BaseLib/FabArray.cpp

commit e5caa196e3abaaef2a6904c50f4428d61c14abb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 18:13:39 2016 -0700

    fix new bug

Src/C_BaseLib/FabArray.cpp

commit 5314a873d329c1a15522b164dc93f52edc6b1407
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 9 17:55:17 2016 -0700

    Needed to move the computation of coeff_sum and coeff_max ahead of
    the singular test on rh -- this meant separating back out the
    parallel reductions.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 6e19e4aa7011ab5f845fe6f4922f192dad6ea9d7
Merge: 9d4ba6d93 44b476d93
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 9 17:42:52 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 9d4ba6d930e36825d2cfabcfb67d5622c83ace6a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 9 17:42:24 2016 -0700

    Impose solvability on rh not res at the start of ml_cc -- we need to
    do this because res is recomputed as rh - L(full_soln) after each cycle.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 7ca723b816fa685ddaf63293dc09c7065f311164
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 9 17:29:50 2016 -0700

    started implementing new FabArray reads.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Tests/IOBenchmark/GNUmakefile

commit 882ee5f1d99d7d357c3cab55c4bddabbda219e47
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 9 17:22:50 2016 -0700

    more io notes.

Docs/Readme.io

commit 44b476d93da6ff76c498ae7d9748f9b68432d853
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 16:13:19 2016 -0700

    update the regtest clean script

Tools/RegressionTesting/reg_test_gc.py

commit 40a069a9c115576ac28c73a5bfa3b14a8a8724ef
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 9 15:47:09 2016 -0700

    first part of code for persistent streams.

Src/C_BaseLib/VisMF.cpp

commit 4113091d52eaf59ded9759d454a41f9e97d8cd0b
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 9 15:45:28 2016 -0700

    more notes.

Docs/Readme.io

commit 916533c55fda7cb87dbc5c6651c5549d035f0b83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 14:37:14 2016 -0700

    fix new bugs

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Periodicity.cpp

commit e9707dc03ed487d58bb4b593eb19ee557c182543
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 14:30:46 2016 -0700

    remove MultiFab::FillBoundary because it blocks FabArray::FillBoundary

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/MultiFabUtil.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG4/ABec4.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 527d8bda4a4245d5815ec4a8fa6e3db02d87bba0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 13:18:42 2016 -0700

    start to use FillBoundary for periodic boundaries

Src/C_AMRLib/FillPatchUtil.cpp
Src/C_BaseLib/MultiFabUtil.cpp
Src/C_TowerLib/Layout.cpp
Src/C_TowerLib/MFTower.cpp

commit 92f2b106d12de0123e1cfc2a2c3bb9cb09882df6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 13:03:57 2016 -0700

    add Geometry::periodicity

Src/C_BaseLib/Geometry.H

commit 65c6a801092778129a3e9ebdcfa3839660dcb744
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 12:58:31 2016 -0700

    tweak FillBoundary interface

Src/C_BaseLib/FabArray.H

commit f49596144b1d83c94b0db2709d7cb1e0702f2f28
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 12:47:07 2016 -0700

    make FabArray::FillBoundary fill periodic boundaries too

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/Periodicity.H
Src/C_BaseLib/Periodicity.cpp

commit 97cb8e9055c1c4a3129ba5ce0640850037adbff7
Merge: 4a3a088ed b3124150e
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 9 11:19:27 2016 -0700

    Merge branch 'VTune_fixes' into development

commit b3124150ed1849afb3ec2a4a8796610a9cd190a9
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 9 11:16:45 2016 -0700

    C_mk: add -DVTUNE and -DITTNOTIFY defines for USE_VTUNE and USE_ITTNOTIFY

Tools/C_mk/Make.defs

commit 83f906ca5b328005fbec310c6daae2e7c2af3ea2
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 9 11:13:11 2016 -0700

    C_mk: move Intel compiler flag "-parallel-source-info=2" into USE_VTUNE

Tools/C_mk/Make.defs

commit a5768416349d5e68219f59ea858a399b913badb2
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 8 16:30:30 2016 -0700

    read tests for raw native format.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit c92069dae5a474938be090cf381bf4b4b1998898
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 8 16:28:44 2016 -0700

    add read functions for raw native format.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 13827e9c36a612a5576e30f34ce3475b62aa6eac
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 8 14:48:21 2016 -0700

    remove BL_VISMF_MSGCHECK code.

Src/C_BaseLib/VisMF.cpp

commit 3e42f57eadb17bb4d4324b6a7ee4a7a4990c9c51
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 8 14:45:31 2016 -0700

    combine write code.

Src/C_BaseLib/VisMF.cpp

commit e2900990f41491d8c3dbd1e50028289000f4b96e
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 8 11:57:00 2016 -0700

    change path

Tests/IOBenchmark/GNUmakefile

commit dcd7dda35cc4480644a943498c97e8ea688b07bc
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 8 11:14:30 2016 -0700

    some cleanup.

Src/C_BaseLib/VisMF.cpp

commit 4a3a088ed95bdc7aa05d178287fd5e03abc6ced0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 8 07:45:59 2016 -0700

    promote FabArrayBase::CpOp to public

Src/C_BaseLib/FabArray.H

commit 17d599cb4d29dce3a3cad3a82909cb3d54e615cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 8 07:29:59 2016 -0700

    Add optional argument Periodicity to FillBoundary

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/Periodicity.H

commit 40d05e139e603429a88641e408ed53af6104c2a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 5 22:40:47 2016 -0700

    fixed a bug in last commit

Src/C_BaseLib/FabArray.H

commit 722aff30ad4af00214a66f5a5437d0e19f9b40fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 5 18:12:23 2016 -0700

    prepare CopyComTag for periodic fill boundary and copy

Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/Periodicity.H

commit 42893ce0b15bca1af865c55e58b54dd9a71344a3
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 5 17:51:51 2016 -0700

    some cleanup.

Src/C_BaseLib/VisMF.cpp

commit 2a95b997581929799950fb46c9640fee37692fd9
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 5 17:13:19 2016 -0700

    more io notes.

Docs/Readme.io

commit 0cafc8b05c975909834135c2d22c087f1b0171fb
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 5 17:12:18 2016 -0700

    update tests for new vismf versions.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit cf3698a600b45ad585a0a618683f00c5132ce16b
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 5 17:11:10 2016 -0700

    new header versions, calc famin famax values.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit dcf49422337ac3315378b49de4a52d57243fa023
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 5 15:14:58 2016 -0700

    add ngrow to FabSet::copyTo

Src/C_AMRLib/FluxRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit dd262ee7b85100a55627c68dd85ec8d911f20ca1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 5 14:48:31 2016 -0700

    FabSet: new version of plusFrom that add two FabSets together

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit af215d7f360f37ecc7d64fb35d4ac3af66b6df89
Merge: f13114f46 b14bfcfd2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 5 14:03:53 2016 -0700

    Merge branch 'development' into weiqun/boxarrayconverter
    
    Conflicts:
            Src/C_BaseLib/FabArray.H

commit f13114f46458cb7280a0f84c478a2ec1b5ba8deb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 5 13:53:23 2016 -0700

    Abort if FabSet::AddProcsToComp is called.

Src/C_BoundaryLib/FabSet.H

commit 7ed4485543cc62954819fd4ab9ae6861601c3bdf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 5 13:20:37 2016 -0700

    indexMap --> indexArray

Src/C_BaseLib/FabArray.cpp

commit c2bc245b13989fd7400d3ebf4212dc46b36f2466
Merge: f8ba5fa0a b14bfcfd2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Aug 4 21:09:46 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit f8ba5fa0aaaa75ff581645636275a90dc1d86f79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Aug 4 21:08:46 2016 -0400

    add another color to the summary pages
    black = test crashed (as determined by backtrace files)
    the compile and crash failures now also show on the summary page
    for the entire run

Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_report.py

commit 68e3ba7becce5b39e0847e30921a67261179978a
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 4 17:27:53 2016 -0700

    filename fix for ungrouped sets for VisMF::Write.

Src/C_BaseLib/VisMF.cpp

commit c5727deb18444972feea77cbb133002f1b447d85
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 4 17:27:09 2016 -0700

    simplify code.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit b14bfcfd215560eead13466dede5b074ed924a50
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 4 17:12:51 2016 -0700

    Changed the behavior of bdryLo and bdryNode (for the lower face) when
    len>1.  With the old code the returned node box is obtained by growing
    inwards.  With the new code the returned node box is obtained by
    growing outwards, just like bdryHi.  Not sure the old one is a bug or
    feature.  Marc and I agree that the old behavior is unexpected and
    undesired.  It should be noted as far as I know these functions have
    never been called with len>1.  For len=1, the results do not change.

Src/C_BaseLib/Box.cpp

commit 764ddea8886ed00014fe2d5462b3614384656303
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 4 16:58:08 2016 -0700

    FabSet: remove aliasing in linComb

Src/C_BoundaryLib/FabSet.cpp

commit 8c3eaaeb734da4c465efbbe3f8d794211230d654
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 4 16:35:38 2016 -0700

    FabSet: reimplement linComb

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 65ca3dc1b70e486625d1ed9baafa9be1bb8ad5d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 4 16:17:44 2016 -0700

    fix linComb that was temporarily disabled because only castro radiation uses it

Src/C_BoundaryLib/FabSet.cpp

commit 2244db057ae01527b5c28df8a8b1a04f3afe3df6
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 4 16:10:35 2016 -0700

    use NFilesIter.

Src/C_BaseLib/VisMF.cpp

commit 574a77fbd4bd4de3535de3b82d139e9faa643ecd
Merge: 80cd11b41 6632bb42a
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 4 15:37:41 2016 -0700

    change mf to FabArray.

commit 807c830360e5352df280f3724de5a2f7419f54f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 4 15:01:48 2016 -0700

    BoxArray: clear hash bin whenever the boxes change

Src/C_BaseLib/BoxArray.cpp

commit e1dd2e43466c5064d6d0e351a1f4c4a64e43dff2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 4 14:33:59 2016 -0700

    remove calls to clear_hash_bin()

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/FabArray.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 851c3b65914693ca60e2598dc08bb02c96b80447
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 4 14:17:41 2016 -0700

    clean up BoxArray::intersections functions

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/Particles.H
Src/C_BaseLib/Particles.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 88f6b087a0e16b09013a8e195e193b6f85f22317
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 4 13:47:29 2016 -0700

    minor tweak of TINY_PROFILE in make

Tools/C_mk/Make.defs

commit 6632bb42a0d739e8bf8db9c60fce76ebfed65033
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 4 13:09:07 2016 -0700

    fixec calls to bl_fortran_set_nprocs_sidecar

Src/C_BaseLib/ParallelDescriptor.cpp

commit 0710e73cb5d20d87de4cfb5f9f7d12e1d7c5fa0b
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 4 13:07:53 2016 -0700

    allocate arrays for set_nprocs_sidecar.  needs some error checking.

Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit 27b4e17953bdff9d6ff3cde7783c2586fb803748
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 2 15:00:02 2016 -0700

    add optional no_assertion argument to a number of functions in FabArray because they might get called in situations the assertion for BDKey fails

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 80cd11b41f1bddf9ad950a2db63944b66c608a5a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 3 15:52:49 2016 -0700

    more notes.

Docs/Readme.io

commit 84de84e5240cc1277785eb973e870abde0eb2ed5
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 3 15:52:03 2016 -0700

    move remove out of timed block.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit f2fdf17541bad805166b86e98408126ac87df3cb
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Aug 3 17:46:40 2016 -0400

    Tutorials: write correct number of component names in plotfile header in writePlotFile()
    
    The plotfile header file should list the same number of component names as
    there are components. This was already done correctly in a few versions of
    writePlotFile() in other tutorials, but not in these.

Tutorials/HeatEquation_EX1_C/writePlotFile.cpp
Tutorials/PGAS_HEAT/writePlotFile.cpp
Tutorials/Tiling_Heat_C/writePlotFile.cpp

commit 0bb103fd15f41ed78d948af3fcedb1fbd7deb11b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 3 14:06:37 2016 -0700

    Also want to change the comments in HeatEquation_EX*F/main.f90

Tutorials/HeatEquation_EX2_F/main.f90
Tutorials/HeatEquation_EX3_F/main.f90
Tutorials/HeatEquation_EX4_F/main.f90

commit 8cba628f0e2e266c550d60f4c5200cf7ed863629
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 3 14:05:22 2016 -0700

    Analogous changes to those just made in the other HeatEquation_EX*F

Tutorials/HeatEquation_EX5_F/define_bc_tower.f90
Tutorials/HeatEquation_EX5_F/inputs-rt
Tutorials/HeatEquation_EX5_F/inputs-rt-expl
Tutorials/HeatEquation_EX5_F/inputs-rt-impl
Tutorials/HeatEquation_EX5_F/inputs_2d
Tutorials/HeatEquation_EX5_F/inputs_3d
Tutorials/HeatEquation_EX5_F/main.f90
Tutorials/HeatEquation_EX5_F/multifab_physbc.f90

commit 1681fbec12c3391242db4d1a86527990271e7a07
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 3 13:54:31 2016 -0700

    Analogous changes in HeatEquation_EX4_F to the most recent changes in HE*2_F and HE*3_F

Tutorials/HeatEquation_EX4_F/define_bc_tower.f90
Tutorials/HeatEquation_EX4_F/inputs_2d
Tutorials/HeatEquation_EX4_F/inputs_3d
Tutorials/HeatEquation_EX4_F/multifab_physbc.f90

commit ab6091d9a5e4bba9c131b86084e7e7098ad8f829
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 3 13:51:17 2016 -0700

    Update HeatEquation_EX2_F and HeatEquation_EX3_F so that we include local versions
    of define_bc_tower.f90 and multifab_physbc.f90 so that we can allow for a larger
    range of bc types in the inputs files and so that it more clear where to set the
    Dirichlet values of phi if we are using INLET.

Tutorials/HeatEquation_EX2_F/define_bc_tower.f90
Tutorials/HeatEquation_EX2_F/inputs_2d
Tutorials/HeatEquation_EX2_F/inputs_3d
Tutorials/HeatEquation_EX2_F/multifab_physbc.f90
Tutorials/HeatEquation_EX3_F/define_bc_tower.f90
Tutorials/HeatEquation_EX3_F/inputs_2d
Tutorials/HeatEquation_EX3_F/inputs_3d
Tutorials/HeatEquation_EX3_F/multifab_physbc.f90

commit 456be8632638281620b4c04eb0a6997df2e80d32
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 2 23:28:08 2016 -0700

    fix bounding box bug in the new BoxArray intersection function

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp

commit a5757e2f18afd2b596e4af1b19fff6352a8ea6f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 2 15:00:02 2016 -0700

    add optional no_assertion argument to a number of functions in FabArray because they might get called in situations the assertion for BDKey fails

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 675942631a297fb6510b32c808e4b0154d1671b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 2 15:00:02 2016 -0700

    add optional no_assertion argument to a number of functions in FabArray because they might get called in situations the assertion for BDKey fails

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 0f1f4480c2d13f2258c357a0c565233ccf1f0b1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 2 14:38:57 2016 -0700

    assertion and minor cleanup

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit a0dfd42a3fe6ff66e1d0bcc3997c3ecfe9f3af95
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Aug 2 10:13:27 2016 -0400

    fix benchmade link

Tools/RegressionTesting/test_report.py

commit 899c2732ff5bdf155e904e8959f50d48ad98eb75
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 1 16:18:49 2016 -0700

    forgot the header.

Src/C_BaseLib/VisMF.H

commit b36219cb22bdf6157fecc4a40bc641b8fbeb9a0b
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 1 16:14:59 2016 -0700

    test remove nfiles.

Tests/IOBenchmark/IOTest.cpp

commit cf18248aba427c8956da832a7398ce555c081416
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 1 16:14:33 2016 -0700

    tweak set groups.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit 551579d7704886ff0a025f785ffc27d58c6879b5
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 1 16:13:42 2016 -0700

    added function to remove nfiles.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 0ddfbfb7d35cab80134827d295f9f39c8a1098fa
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 1 12:23:12 2016 -0700

    test group set option.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit fe997f010ce7d3a4e85995c327f331829588ccc1
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 1 12:22:56 2016 -0700

    propagate group set option.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 6f21c30aebc81107ddb81d0d1646fcc9ec33787f
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 1 12:22:15 2016 -0700

    added option to group sets.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit 1455716cd3fda7b69e70ba5d4fefb5376ddfa7d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 1 07:26:59 2016 -0700

    Release Notes 16.08

ReleaseNotes/release-notes-16.08

commit 88371d5d0696e5e84a91a92b4f727d806b79bf35
Merge: fdaefde95 b6f3ba865
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 31 15:07:46 2016 -0700

    Merge branch 'development'
    
    Conflicts:
            Src/C_BaseLib/FabArray.H

commit a40563883d951a5a8e976c43c47e02b0516deae8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 31 07:15:24 2016 -0700

    BoxArray: In some special cases, the internal reference counted cell-center boxes may look empty.

Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.cpp

commit a350a9a98db208faa6bb995c0caabb7dd18544a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 30 22:12:32 2016 -0700

    FabSet::periodicCopyTo

Src/C_AMRLib/FluxRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit c9225927f71508795f82ee0dc60ddb428a1e7d4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 30 16:49:29 2016 -0700

    use doi (domain of influence) in BoxArray intersection

Src/C_BaseLib/Box.H
Src/C_BaseLib/BoxArray.cpp

commit 163b553d468d5b80aee26a7861b6209cf1d8c2e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 30 13:47:53 2016 -0700

    BoxArray Transformer: add doi (domain of influence)

Src/C_BaseLib/BoxArray.H
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit f5c756b6bba9dcb42f8595624c3932c3368426e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 30 10:38:00 2016 -0700

    Revert "refactor BoxArray Transformer"
    
    This reverts commit 02ff0022cf98f0ab2a443e28ba29a6b89472b9a0.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit 02ff0022cf98f0ab2a443e28ba29a6b89472b9a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 30 08:21:48 2016 -0700

    refactor BoxArray Transformer

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit 1686b08a45cb0a9e2de03938c4b0dcce1fceecf4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 29 23:03:53 2016 -0700

    FabSet::copyTo interface

Src/C_AMRLib/FluxRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 7c93dd62c33f7012d3889e9584bc8b10622fd91e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 29 22:40:41 2016 -0700

    update CPC due to that type plus reference key is no longer sufficient for BoxArray comparison

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 94c339dc61b76f816dcdff76ebbd5b6e5ca92741
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 29 18:13:44 2016 -0700

    WIP: FabSet copy wip

Src/C_BaseLib/FabArray.H
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 23c2f3c81fda672eace5daa9408e58782c6e41fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 29 17:44:05 2016 -0700

    WIP: more clean up of FabSet

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 83826fc05eea9959646d170f52d7555e818bd66e
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 29 16:48:15 2016 -0700

    updated readme.

Tests/IOBenchmark/README

commit 234d36b8adcfa1e5ff6c2bb3c29ee63430b7c4bd
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 29 16:42:35 2016 -0700

    command line option for writeminmax.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 0b621ffb1477e97d9c50362230089cea4a4a956c
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 29 16:27:35 2016 -0700

    calc offsets without communication, option to write minmax.

Src/C_BaseLib/VisMF.cpp

commit e195c63b318fb366f335dfe8bb8d2816ccf62292
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 29 16:26:29 2016 -0700

    util function, enforce proc range.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit 40ff35c308716308503e3c4ae4f1c677f7661323
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 29 16:10:34 2016 -0700

    add a new version of FabSet::setVal

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 46ce3dc9c7d4ad66d65fc6916171fe188a1b10ac
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 29 14:22:35 2016 -0700

    added stream buffer option.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit b4eb8c717891bd7c0b9d06b118ad75bdcf53363d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 29 11:24:45 2016 -0700

    WIP: get it to compile be commenting out a lot of codes in FabSet

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit b6f3ba865d0007beb998d647aa67f44ee4db6998
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 29 10:16:46 2016 -0400

    testnew.py -> regtest.py

Docs/Regression/test_suite.tex

commit c6447196eed5992bc39693acd355adf3314897aa
Merge: 3259e717e 47fde68ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 29 10:11:34 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 3259e717e029e92463d0e1dceaac429a95dec366
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 29 10:11:18 2016 -0400

    remove the older suite -- use regtest.py now

Tools/RegressionTesting/testnew.py

commit 47fde68ec62a7b133f1ec9d6e0665c30a0bb3d82
Merge: e2e6629e2 ee11b4c50
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 29 09:44:42 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit e2e6629e2dee415480c5b5760d7c39111aa7874c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 29 09:44:30 2016 -0400

    update to point to regtest.py

Tools/RegressionTesting/README

commit 143417ba2c6862db6ca524f9175225021e9d2e84
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 28 22:11:33 2016 -0700

    WIP: reimplement FabSet with MultiFab as member instead of base class;  this allows more control over hiding MulitFab methods from FabSet

Src/C_AMRLib/FluxRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit a4995648adddd1b56a517b4c274a84ca0db40cec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 28 21:04:09 2016 -0700

    define BndryRegister with BoxArray with special transformer

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit 9b66aef73b366db891dc38dd1e25f9d0c2923540
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 28 17:22:21 2016 -0700

    continue write raw native wirtes.

Src/C_BaseLib/VisMF.cpp
Tests/IOBenchmark/GNUmakefile

commit 6da270eb466ffc113a778eefc019848f82949510
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 28 16:54:13 2016 -0700

    test write minmax to raw native mf.

Tests/IOBenchmark/IOTest.cpp

commit 65662ac3ff673891d8a25ea6e2a955d7f0b90c53
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 28 16:24:51 2016 -0700

    add option to write fab minmax to the data.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 137e5e2f48a57d4760efedf676fe970c219426a1
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 28 16:04:52 2016 -0700

    added comments and an example.

Src/C_BaseLib/NFiles.H

commit 78d3141718b93f6e08fc1666cda25e33c50b19aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 28 15:02:15 2016 -0700

    BoxArray: add transformer that transforms internally stored and possibly shared boxes into boxes of the public interface

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 7019df10602b1e404f1c920f108c6da110bd8775
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 28 14:04:14 2016 -0700

    change defaults.

Src/C_AMRLib/AmrLevel.H

commit ee11b4c50529bc9412f64342039ac1d2efdc5568
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 28 13:00:54 2016 -0400

    a little cleaning

Tools/RegressionTesting/test_report.py
Tools/RegressionTesting/test_util.py

commit a93c26d4dcc713a01b420163d87ecc61494bc17d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 28 12:39:19 2016 -0400

    highlight a compilation failure in a different color (purple) than
    regular failure (comparison)

Tools/RegressionTesting/test_report.py

commit cbf5937014593f813d94b105b98552e9aa374d6f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 28 11:31:57 2016 -0400

    fix stderr output when we aren't sending it to its own file

Tools/RegressionTesting/test_util.py

commit fdaefde950254111540718baf3933148baddf5b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 27 22:43:53 2016 -0700

    add libquadmath

Tools/C_mk/Make.defs

commit 09be8c41cc1d2de838d8696c884e99dda952349c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 27 22:43:53 2016 -0700

    add libquadmath

Tools/C_mk/Make.defs

commit 6b186be99eace20291c4f29eaeeadabbc86cbebb
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 27 17:19:15 2016 -0700

    test functions for VisMF::WriteRawNative.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 9bac42bfb0d354220d53a9ca91c26145961da16e
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 27 17:18:33 2016 -0700

    added WriteRawNative function.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit ab0015bc2b6cece92a715e04ddb4027790212334
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 27 17:17:32 2016 -0700

    added file name functions.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit a6ebbe8dbd0bc77e2abb167c93669367cb8b7915
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Jul 27 13:30:10 2016 -0700

    C_mk: add some extra compiler flags when using VTune
    
    This adds support for the GNUmakefile options USE_VTUNE and USE_ITTNOTIFY when
    using the Intel compilers. USE_VTUNE adds some extra debugging output during
    compilation which allows VTune to resolve more information about the code
    during profilng, while USE_ITTNOTIFY provides support for manual code
    instrumentation with VTune to profile only certain regions instead of the
    entire thing.

Tools/C_mk/Make.defs

commit 4551bcf5a908fab61f93f8a7d38da49af067304d
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Jul 7 13:15:31 2016 -0700

    C_mk, HPGMG: rename DUNLIMIT_FMG_VCYCLES -> DUNLIMIT_FMG_ITERATIONS
    
    Sam renamed this in HPGMG so we need to follow suit in our compilation scripts.

Tools/C_mk/Make.defs

commit 73674a94704e010d8a427257a11459fe05d073e9
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 27 12:12:27 2016 -0700

    change how default, some cleanup.

Src/C_AMRLib/Amr.cpp

commit 77be0ced915d86a197f6fee294f42b12e6967f25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 27 07:07:49 2016 -0700

    fix assertion

Src/C_BaseLib/Geometry.cpp

commit 2eac7f1ddc93149a2ffb910eca791e5e9a4dfa97
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 26 22:28:52 2016 -0700

    explicit

Src/C_BaseLib/BoxArray.H

commit 9318856692b74e851e88b07aa1ce0a7416eb467c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 26 21:02:46 2016 -0700

    reimplement fillperiodicboundary cache using boxarray-distributionmap key

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit c974b138d4dbb4984a943d25f76d674b8d61f991
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 26 16:12:45 2016 -0700

    clean up FB

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 205ef3b3c0cc6288893be664eb4f80926b6e9ce5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 26 15:06:33 2016 -0700

    reimplement parallel copy cache using boxarray-distributionmap key

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit d9c0c3b647cf7158f0ee83096a3844d974e4442d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 26 10:55:13 2016 -0700

    MemPool: static_assert

Src/C_BaseLib/MemPool.cpp

commit 7dd68040cba6f108e3aca24905e2d5094c4be5fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 26 07:51:00 2016 -0700

    reimplement fillboundary cache using boxarray-distributionmap key

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp

commit 891ff3b1ce41942567d5760309c5e1c0fe372e7a
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 26 17:55:19 2016 -0700

    packaged nfiles writing.

Src/C_BaseLib/Make.package
Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp
Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit ca8de6591fbc41d831576e392f43116a69959f0e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jul 26 14:57:44 2016 -0700

    Enable us to call fourth_order interpolation without having to define the
    stencil_width to 2 independently -- affects multifab_fill_ghost_cells and fillpatch.
    
    Also fix the fourth_order_interp routine so that it can fill some but not all fine
    cells in a coarse cell.

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/interp.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 9a135acc413e314278d7d130d372b5689a6a0368
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 26 14:44:12 2016 -0700

    limit buffer size.

Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabConv.cpp

commit 14e7404b56a493175f5a1f58c19e56379f7706f7
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 26 13:01:32 2016 -0700

    added directory creation tests.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 2af3056c664f185099925540f94f224656889596
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 26 12:58:00 2016 -0700

    updated UtilCreateDirectory

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit aa34f5afc8ff47c6f29566caec35e0a13b9af3fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 25 15:53:54 2016 -0700

    fix tilearray memory profiling counter

Src/F_BaseLib/layout.f90

commit ab9359bcddec42aa559e088dba6ad75465d5cd4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 25 15:48:56 2016 -0700

    nullify fortran pointer in bl_deallocate

Src/C_BaseLib/mempool_f.f90

commit fd6b92bd8da33099757b0be76d479542223ebef4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 25 15:10:33 2016 -0700

    use constexpr

Src/C_BaseLib/MemProfiler.cpp

commit 0aeeac80408e4f9c34bcf249e9aac4252c937cc0
Merge: 21d7ae832 c4bba0063
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 25 14:50:33 2016 -0700

    Merge branch 'development' into weiqun/coarsenboxarray
    
    Conflicts:
            Src/C_BaseLib/BoxArray.H
            Src/C_BaseLib/BoxArray.cpp

commit c4bba00639df0a32bde27b809b0f033280642bf1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 25 14:41:49 2016 -0700

    MEM_PROFILE: keep track of the number of BoxArrays and MultiFabs

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/MemProfiler.H
Src/C_BaseLib/MemProfiler.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 21d7ae832362585f2d473954f4be6af3a9fcdd78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 24 18:57:48 2016 -0700

    update because BoxArray::define(const BoxArray&) is gone

Tests/LinearSolvers/ComparisonTest/main.cpp

commit 4490ba0903fea6beba177c5cd97786fd37ca8a29
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 24 17:35:17 2016 -0700

    cache coarse BoxArrays

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/Pointers.H

commit 2bd66e6c577ae8b1641c95512f852bc66ddbb5f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 24 17:33:22 2016 -0400

    'make file_locations' will printout where in the VPATH each source file is found
    as well as indicate which files are not found

Tools/C_mk/Make.rules

commit 320ff827777a7ea8e0e26c9b711699a60f4e9bb8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 24 17:26:58 2016 -0400

    'make file_locations' will output where each source file is found by make
    this will also indicate which files make cannot find

Tools/F_mk/GMakerules.mak

commit 516f9ba39b58704ad5ec67d52f19eadc1d91b4c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 24 17:23:39 2016 -0400

    a useful tool for makefile debugging -- this script will print out
    where files are found in the vpath and which files are not in the
    vpath

Tools/F_scripts/find_files_vpath.py

commit 773fd439ea740c235c517584eb493f3f40980bfc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 23 12:55:15 2016 -0700

    remove BoxArray::define(const BoxArray& bs) because it is equivalent to the assignmeent operator

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit d0e40ebb741ecf047b9e59361c681baf51f2f6ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 23 11:14:17 2016 -0700

    use BoxArray assignment operator instead of define function because I plan to remove the define fucntion

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/FabArray.H
Src/C_BoundaryLib/BndryRegister.cpp

commit ab110a98a847378b94c26ae891118e77d96ca933
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 23 07:33:28 2016 -0700

    make ~FabArrayBase just in case

Src/C_BaseLib/FabArray.H

commit 32c412616f1274b91ec08f265a5f5562889f0e16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 22 17:03:04 2016 -0700

    virtualize a few functions in FabArray and make VisMF a class for FabArray<FArrayBox> instead of MultiFab

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 7300dab04b8257f2dd7f1447d195de95c69e4782
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 22 14:29:40 2016 -0700

    added dir tests.

Tests/MKDir/MKDir.cpp

commit 4d060fa0ca4bfe4c664880ea9738e45189425692
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 21 16:30:16 2016 -0700

    code cleanup.

Src/C_BaseLib/VisMF.cpp

commit e47e3fb27cc5c0bd1b1c7637330ad4318221b167
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 21 14:45:00 2016 -0700

    wip

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/MultiMask.H
Src/C_BoundaryLib/MultiMask.cpp

commit a4fd02c25bc3136f709da80471847ba012e101ce
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 21 14:33:22 2016 -0700

    some code cleanup.

Src/C_BaseLib/FArrayBox.cpp

commit f0e99d9f53eb8edc5669485392b527d567fc4721
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 21 12:58:12 2016 -0700

    start MultiMask class

Src/C_BoundaryLib/CMakeLists.txt
Src/C_BoundaryLib/Make.package
Src/C_BoundaryLib/MultiMask.H
Src/C_BoundaryLib/MultiMask.cpp

commit f159374cc1a4936151afbf73a248181536f50bb2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 21 12:48:04 2016 -0700

    add alloc and shared as optional arguments to Mask class in preparation for new MultiMask class

Src/C_BoundaryLib/Mask.H
Src/C_BoundaryLib/Mask.cpp

commit 74e9f3d86e739460aec3ea0ba5722438629fc03f
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 21 12:38:27 2016 -0700

    added functions to set buffer sizes.

Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp

commit 866cb3b29f70d78b5c2d9dac369568e306085044
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 21 11:14:30 2016 -0700

    remove edge_restriction.f90 because all its functions are already duplicated in cc_restrition_module and the edge restriction functions are called by functions in ml_cc_restriction_module (since there is no ml_edge_restriction_module

Src/F_BaseLib/CMakeLists.txt
Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/edge_restriction.f90
Src/F_BaseLib/ml_cc_restriction.f90
Src/LinearSolvers/F_MG/FParallelMG.mak

commit 506def2a25948116dc92e879fb39a1c29b9eab43
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 21 11:14:01 2016 -0700

    added test files and io doc.

Docs/Readme.io
Tests/C_BaseLib/AMRPROFTEST_F.H
Tests/C_BaseLib/AMRProfTestBL.cpp
Tests/C_BaseLib/tRABcast.cpp
Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp

commit 9d70923d5dfdeafc7cfd9f6b66dce0cfd76f36ac
Merge: ecd7d5f12 65d1c17ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 21 12:28:13 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit ecd7d5f12e044e7637b9495d446288f43672b2b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 21 12:27:53 2016 -0400

    move the return code logic to _after_ we do zone info

Tools/Postprocessing/F_Src/fcompare.f90

commit 65d1c17ae5e0bcf680de584cc028efbb8e7e9c89
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 20 16:46:53 2016 -0700

    remove the word grok.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit d7e20b171fa062b10615400d18039642f20070b4
Merge: 890ffa4a9 946125444
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 20 19:33:46 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 946125444910245cadbac69dab90194e6b3569cd
Merge: e7db6b28e 0fb71cf83
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 20 12:39:20 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit e7db6b28e8ec5e8fab51434057fc4ba79c222bc5
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 20 12:39:15 2016 -0700

    remove profile call.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 0fb71cf836f7440c7b26ddaa8355cdfec48719e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 17 14:13:04 2016 -0400

    the microphysics suite inputs

Tools/RegressionTesting/Microphysics-tests-pgi.ini
Tools/RegressionTesting/Microphysics-tests.ini

commit 9aaf8fd58a7878331a6c70f9aab47ee1f12b4f34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 17 13:07:59 2016 -0400

    detect variable mismatch in comparison

Tools/RegressionTesting/test_report.py

commit 9dace46a53f7924281fcc738460728e85476666f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 17 12:28:40 2016 -0400

    return error code if there are different / missing variables in
    the plotfiles

Tools/Postprocessing/F_Src/fcompare.f90

commit 890ffa4a97a5c130b56bd4cb675d95a764d94255
Merge: c4f76ab2f c05ad7f7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 14 10:03:17 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit c05ad7f7f2e1064d637c8d60043c6e45f25fdcfc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 13 13:42:15 2016 -0700

    tweak Fortran make system to support codes relying on the programs variable

Tools/F_mk/GMakerules.mak
Tools/Postprocessing/F_Src/GNUmakefile

commit 25242ae06013165a07bc80af80bb1b7e5141a9a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 13 12:51:32 2016 -0700

    Fortran random: add more static_assert

Src/F_BaseLib/bl_random_c.cpp

commit 6eb28b7b6c0e4e8a8bac2cefa6fccb1630eee746
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 12 18:30:01 2016 -0700

    Fortran random: add single precision

Src/F_BaseLib/bl_random_c.cpp

commit ba3e7d3568e056cf5987dc05bff2f472ffc27446
Merge: 8a4270773 00dbb2d78
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 12 16:33:44 2016 -0700

    refix name change.

commit c4a1fadd3ecd22b9dbba39ddd2b8176ba8358164
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 12 16:10:48 2016 -0700

    promote IndexMap() and localindex() to public so that some codes can use

Src/C_BaseLib/FabArray.H

commit 00dbb2d78d170ee314146c97d382d391fb4ecf5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 12 16:10:48 2016 -0700

    promote IndexMap() and localindex() to public so that some codes can use

Src/C_BaseLib/FabArray.H

commit 8a427077355b0c94ec1e9f24660852c804dbfe5a
Merge: c210f8bfb 2c360a04b
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 12 16:03:09 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit c210f8bfb581f4ae7654641a419401a795b8fecf
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 12 15:59:38 2016 -0700

    add a default real function.

Src/C_AMRLib/LevelBld.H

commit 2290151b05c40fb3706bd8a024c51b061d686541
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 12 15:41:32 2016 -0700

    dont free the comm from fortran for intransit.

Src/C_BaseLib/BoxLib.cpp

commit fab1628430f7934766a9365c05c1b1686c773eee
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 12 14:32:32 2016 -0700

    flush another cache for MoveFabs.

Src/C_BaseLib/FabArray.H

commit 56cca713393e8366dbd7ea9dc4f5ee4fcd28911a
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 12 14:28:03 2016 -0700

    flush another cache for MoveFabs.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit e82f50a64c1bcd77787393f1dd41c153512e1bef
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 12 14:26:08 2016 -0700

    remove unused vars.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/FillPatchUtil.cpp

commit c4f76ab2f61bbe7533436f6c435d6faaa0e38037
Merge: e5cfdc37d 2c360a04b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 12 14:55:37 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit dab6ce481f7a17bab90f465934162cd2c24b8eff
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 11 14:07:46 2016 -0700

    merge fix.

Src/C_AMRLib/Amr.cpp

commit 2c360a04b643a378831acba2ec72ad037a890384
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 11 14:02:55 2016 -0700

    Fortran random: allow using FluctHydro/HydroGrid distribution

Src/F_BaseLib/bl_random_c.cpp
Src/F_BaseLib/bl_random_f.f90

commit 1448aa9da18a5c945017298c35a2bc199185ccc5
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 11 13:33:32 2016 -0700

    fix for serial.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 04b0ae9716c36aa9c1264e1c164a947537c1b012
Merge: fcaef3d35 e194b5995
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 11 12:19:05 2016 -0700

    merge fix.

commit e5cfdc37dfc750edca8939ed065d832dd3b33467
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jul 11 09:55:21 2016 -0400

    minor formatting

Tools/RegressionTesting/test_report.py
Tools/RegressionTesting/test_util.py

commit acb2b01d1f921ed17aa32babb842aaf35c65430f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jul 11 09:48:46 2016 -0400

    replace redefined name

Tools/RegressionTesting/regtest.py

commit fcaef3d358e76bac55e075f552564d7294bf47c1
Merge: 664efb5f5 61d4401a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 10 16:59:48 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 664efb5f5350363edec0bf21feb0d3f1fad77376
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 10 16:59:21 2016 -0400

    a little cleaning

Tools/RegressionTesting/test_report.py
Tools/RegressionTesting/test_util.py

commit 61d4401a2660becc3f59ce11bd2925a46c629098
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 10 12:01:08 2016 -0400

    a little more PEP-8

Tools/RegressionTesting/params.py
Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/repo.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_report.py
Tools/RegressionTesting/test_util.py

commit ba7b56589e98d73b26868ac3d523691f44dd8c3f
Merge: bcf16ec7f 3f0c5a64f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 10 11:55:47 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit bcf16ec7f8842738bbb7a131095a13b3c21ed1ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 10 11:55:32 2016 -0400

    use is to compare to None

Tools/RegressionTesting/regtest.py

commit 3f0c5a64f070e5ad233007b2f6a070e654fde294
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 10 11:51:20 2016 -0400

    actually check whether the user-specified compareFile exists

Tools/RegressionTesting/regtest.py

commit 7bac53b6c6b262878deb33cef10d09b1fa13854a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 9 19:53:01 2016 -0400

    rely on the return code from fcompare to determine if the comparison
    was successful

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_report.py

commit e0417dc5a19cec8f6a6550d40c6a75038d600782
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 9 15:08:17 2016 -0400

    explicitly send return codes of success or failure

Tools/Postprocessing/F_Src/fcompare.f90

commit 797a236127ca5555e7375c36cdcda8eee03d1c75
Merge: 8b2e6296f 08ec9292b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 9 14:55:58 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 8b2e6296fa37a41b149d13bc9a6f9142b55950a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 9 14:55:41 2016 -0400

    two new functions for sending return codes from Fortran

Src/F_BaseLib/system_util_c.c

commit 08ec9292bbb31a7ca64352cef9901a917bddb126
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Jul 9 14:49:44 2016 -0400

    Write a plotfile on demand with plot_and_continue

Src/C_AMRLib/Amr.cpp

commit bc467c27d62634b407d5c2290b0fa964817b52ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 9 13:27:41 2016 -0400

    use the return code to determine if compilation was successful
    
    consolodate the main copying code

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_report.py

commit 8c7d0064bbd56d96b3ea785f33c7378a82bc8b17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 9 12:55:31 2016 -0400

    no really, .pyc

.gitignore

commit cc794366b19e3c06c1fa54907f4b739f0f6087a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 9 12:55:04 2016 -0400

    add .pyc

.gitignore

commit 720e31371c35cacdfcaf78ec50b00e84179db739
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 9 12:27:47 2016 -0400

    use the return code from make to determine if the tools built

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py

commit e194b599510623d799c3ac623ad72e86be8a3592
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 8 17:47:36 2016 -0700

    copy more vars for comp resize.

Src/C_AMRLib/Amr.cpp

commit a79be09935b32be56c6fde68886ee763b552af24
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 8 17:17:30 2016 -0700

    IBM compiler does not like 'using FabArray::setVal' because FabArray is templated.

Src/C_AMRLib/TagBox.H

commit a116d261e1c2c39348ec026de7aa972070cbd597
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jul 8 15:59:11 2016 -0700

    Copy autogen files into repo as well...a bad idea that these were added in the first place...

Src/Python/boxlib/bl1.py
Src/Python/boxlib/bl2.py
Src/Python/boxlib/bl3.py
Src/Python/src/boxlib_wrap_1.cpp.REMOVED.git-id
Src/Python/src/boxlib_wrap_2.cpp.REMOVED.git-id
Src/Python/src/boxlib_wrap_3.cpp.REMOVED.git-id

commit 64b5350f74346749fc507cc7453f352f5ab5b95e
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jul 8 15:55:46 2016 -0700

    Remove interface to mf->fab function from swig i file

Src/Python/swig/boxlib.i

commit ceaa7dbe83dea3d32101e14f75e6eba1931896f8
Merge: c2d5e9090 4f366a1e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 8 18:37:18 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit fbf09d2389f3ec25460e2b8636eb2c01ad6cf842
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 8 15:23:54 2016 -0700

    some changes for sidecars and teams.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/ParallelDescriptor.cpp

commit f005a4654b5a5c09f8440c66821095f5260649d7
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 8 15:21:12 2016 -0700

    remove test output.

Tutorials/Sidecar_EX1/NSidecarsTest.cpp

commit ff870b9ecf3cb8a827d72cebbaac5a79163267df
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 8 15:20:28 2016 -0700

    option to print unique set.

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 4f366a1e8adca1f6b4dbd8384d6d0c0adcfd6360
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 8 13:31:12 2016 -0700

    added serial initializations.

Src/C_BaseLib/ParallelDescriptor.cpp

commit a9b53226adc108deb1930bf8e782b06a565520b0
Merge: 19e9b5993 5d9d854a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 8 10:40:13 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 19e9b59932d2ffcb9da8a93e8d5d0e77e01da06b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 8 10:38:45 2016 -0400

    don't process _parameters until we ask for a net or eos

Tools/Postprocessing/F_Src/GNUmakefile

commit 5d9d854a5a5d82248b7e7a490462b24313e6d76c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 8 07:35:08 2016 -0700

    fix make

Tools/Postprocessing/F_Src/GNUmakefile

commit 2b1e20486dae3f2eb8fbdf776b59a63e620e5697
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 8 07:22:24 2016 -0700

    fixed a typo

Tools/F_mk/GMakedefs.mak

commit c977f137a8cbc62b749bbe37e3bb0459a32c3317
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 7 16:13:41 2016 -0700

    add F_mk/Readme and some minor tweaks

Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak
Tools/F_mk/Readme

commit 5aebced28e910b96ecc71eab6c0cdc4942e1025e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 7 12:13:56 2016 -0700

    Make: -include Make.local allowing users to reset variables; add ccache and f90cache to speed up compilation

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules
Tools/F_mk/GMakedefs.mak

commit e5c2586179e00a9164a03a68b15426e4b7826681
Merge: 998e6153a 27acb1c23
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 6 22:09:35 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 998e6153afe58a243b44c29a638159a7b11de580
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 6 22:09:11 2016 -0400

    split stdout/err and save stderr from the run, if present

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_report.py
Tools/RegressionTesting/test_util.py

commit c2d5e90908eaa0d841ae9624b5b84caa0569405e
Merge: 66b6b4326 27acb1c23
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 6 18:45:49 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 27acb1c235718ce05a6f7e9e91790e04833a1399
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 6 16:45:56 2016 -0400

    copy -> move for executable

Tools/RegressionTesting/regtest.py

commit 09beea8211ad90c9454161139a6ecbb6f802986e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 6 09:57:45 2016 -0400

    clean-up memory to quiet memory sanitizer

Tools/Postprocessing/F_Src/fcompare.f90

commit 66b6b4326854bfc478d4ca8a382a6d18bfded99e
Merge: d9d9d208f 41f180385
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 5 18:48:33 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit d9d9d208f209d8fea4f2394b3e9e30de2514ef3c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 5 18:48:24 2016 -0400

    remove trailing blanks

Tools/RegressionTesting/suite.py

commit 41f18038583cc6c1779728ab83e820bb8583f500
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 5 13:52:26 2016 -0400

    add a warning if we are running on a non-default branch

Tools/RegressionTesting/regtest.py

commit 50248a43a0e8971344e5b292d373a54aea27c41b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 5 07:00:43 2016 -0700

    Release Notes 16.07

ReleaseNotes/release-notes-16.07

commit 5176359566ae51b52926682e0ae8a969c3dae6f0
Merge: d975c9b24 67df9e613
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 5 06:59:44 2016 -0700

    Merge branch 'development'

commit 67df9e613a7403df7e879122259a73a7aef0aee8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jul 4 21:56:37 2016 -0400

    add an indicator if we are running on a non-default branch + bug fix
    
    now we add an '*' next to the date on the master page if any of the git
    repos are not on "suite.default_branch".  This helps delineate the
    normal tests from those we run occassionally on feature branches.
    
    Also fix a crash if we ran with only self-tests (no output file
    is ever defined)

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_report.py

commit 2f5bfbf7bb0b97effcc0b4bc8fadc2e2b1f304d2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jul 4 13:05:02 2016 -0400

    remove legacy comma warning

Tools/Postprocessing/F_Src/fcompare.f90

commit 5a46b3f376822177f6e3c9f608cbba7c2b292974
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jul 4 12:51:25 2016 -0400

    fcompare no longer needs --infile1/2

Tools/RegressionTesting/regtest.py

commit 9e202fcb36e2113176ba047e60b25b3b53c62918
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 28 21:44:56 2016 -0700

    Only test skewed for the current level

Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90

commit a7e81bdc1bafcfc30c7d6a336f3a54539b9d143f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 28 14:09:09 2016 -0700

    Turn off tiling for skewed stencil

Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90
Src/LinearSolvers/F_MG/cc_smoothers.f90

commit e33ded935a32211dfc05df536a0235c72dd80d65
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 28 11:04:42 2016 -0700

    function to turn on fpe trapping in Fortran BoxLib

Src/F_BaseLib/backtrace_c.cpp
Src/F_BaseLib/backtrace_f.f90

commit d5ce692a406ce5da64b862f22f439f1645a50463
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 28 10:51:07 2016 -0700

    indentation

Tutorials/Tiling_Heat_F/advance.f90

commit 57776ec86d9e60940a8a766f710cda6ab46c1869
Merge: 922a2af85 f50fb564e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 28 14:02:53 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 922a2af85a0f75219ef5d4d596e71180af98bd5c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 28 14:02:40 2016 -0400

    latest version

Tools/RegressionTesting/Maestro-tests.ini

commit f50fb564ed2f4eb88d85e78947a65e4b58383901
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 28 14:00:45 2016 -0400

    latest version

Tools/RegressionTesting/Castro-SBU-tests.ini

commit c69903ea01d329f6dcd4d444f47f9b9e609d5f9c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 27 19:29:06 2016 -0400

    removed my accidental changes in makefile

Tools/C_mk/Make.mpi

commit a575b1b933d528acf69cd57cd21a28eda84c6331
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 27 19:28:10 2016 -0400

    fix typo

Tools/RegressionTesting/suite.py

commit 1e62439b37e07eb322db5793b99659cdc43b582a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 27 19:13:53 2016 -0400

    use subroutine instead of function to get around a gcc 6.1.1 bug

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90
Tools/C_mk/Make.mpi

commit bf6ea460193dd4961d4c03246fbd3a1c3104682c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 27 15:46:09 2016 -0400

    remove some debug prints

Tools/F_scripts/write_probin.py

commit ee2eab864dac38654137fcf7a85a0e5311ace36d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 27 15:40:48 2016 -0400

    sanitize apostrophes in the slack

Tools/RegressionTesting/suite.py

commit a1706641f1962c30ec062e877f10dbf1aaf20dd6
Merge: 9a4c92f64 1896a06f0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 27 15:39:04 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 9a4c92f643de4bdbd87db4d3eeadaf57413c4be3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 27 15:38:54 2016 -0400

    add future

Tools/RegressionTesting/suite.py

commit 1896a06f03798d05a76028ebc8dcb9acd8dce4e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 27 11:24:06 2016 -0700

    missed omp end parallel

Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90

commit a81c1319d28b9b1e57168361109c9a349edded63
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 27 11:18:50 2016 -0700

    turn off tiling for 1d and 2d because they are not ready; fix MS_SMOOTHER_EFF_RB

Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90

commit 599a72f719b760b082591fe406e99c0759b037e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 27 11:10:26 2016 -0700

    turn off tiling for 1d, 2d and nodal because they are not ready

Src/LinearSolvers/F_MG/mg.f90

commit 4df3d5abf31e3226cbc029760517759a1389bbc0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 27 10:01:26 2016 -0400

    using std::isinf for __GNUC__ >= 6

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 3df3891af93548eedf34ba7e4529df7a4fd70539
Merge: ea0e54dfc 03087b72c
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jun 26 17:10:15 2016 -0700

    Merge branch 'fix_tiled_CC_F_MG_2D' into development

commit ea0e54dfc4bdbb963d709bdd8acd06aa78640738
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jun 26 11:56:32 2016 -0700

    C_BaseLib: make Box::isSquare() always return false in 1-D

Src/C_BaseLib/Box.cpp

commit 03087b72c3b364b3b5d2f7e470d56005653ea0cf
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jun 26 12:01:24 2016 -0700

    F_MG: set dim of tile box indicies "tlo" and "thi" to mgt%dim
    
    In commit 59ab377 ("F_MG: tile the cell-centered restriction") I hard-coded the
    dimension of tlo and thi to 3, anticipating that tiling will only benefit 3-D
    problems and not so much 2-D. However this breaks 2-D problems which need to
    use Fortran multigrid, so instead we set the dim of tlo and thi to whatever dim
    is set to in the mgt object.

Src/LinearSolvers/F_MG/mg.f90

commit febaf8efab78f3f311d10d839b3dd1afa33d5264
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jun 26 10:12:40 2016 -0400

    got g++ 6.1, we need use std::isnan and std::isinf

Src/C_BaseLib/FArrayBox.cpp

commit 370db4549cd018832c7e093082e50f5f529ed316
Merge: b70dd38fa c5c5312c4
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jun 24 16:47:38 2016 -0700

    Merge branch 'weiqun/random' into development

commit c5c5312c486fa42a331e6dfeb7ad4519805fa6ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 24 16:34:26 2016 -0700

    fix pmask in ml_layout

Src/F_BaseLib/ml_layout.f90

commit b70dd38faa4758ee54d3b2ad40df485fb9a827b1
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jun 24 14:55:39 2016 -0700

    F_MG: add line wraps to long OpenMP directive
    
    The Cray compiler quits when encountering OpenMP directives with line lengths
    with > 128 characters.

Src/LinearSolvers/F_MG/mg.f90

commit e834d18786d81ca206a1943fcd3540c4106f4e7a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 24 14:30:15 2016 -0700

    Fortran random: in restore, destroy first if the ptr is already associated.

Src/F_BaseLib/bl_random_f.f90

commit 58c6d2dad696021971bd82cc73a1645d2b3df1ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 24 13:39:38 2016 -0700

    add initialization flag to IArrayBox.cpp

Src/C_BaseLib/IArrayBox.cpp

commit 495a0275459322abb81a2f76e7829633adaa5618
Merge: 7b3d70d36 59e72db9f
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jun 24 10:55:47 2016 -0700

    Merge branch 'tile_MultiGrid_C_tutorial' into development
    
    These commits add tiling to setup_rhs() and setup_coeffs() in the MultiGrid_C
    tutorial. These are just initialization routines specific to this tutorial and
    thus the speedup from these commits does not benefit any other BoxLib code.

commit 7b3d70d36424c7d517e38fee50ca0c448a7a2d73
Merge: cf971954d 06e1efb38
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jun 24 10:52:01 2016 -0700

    Merge branch 'tile_CC_F_MG' into development
    
    These commits add OpenMP tiling to the cell-centered GSRB smooths and
    restrictions in F_MG. The prolongation is not as simple as replacing the
    nfabs() loop with a next_tile() loop so that will be done in a different series
    of commits.
    
    Using the MultiGrid_C tutorial with a 512^3 grid decomposed into 8 256^3 boxes,
    these changes yield a roughly 8% speedup on both Ivy Bridge (using 2 MPI x 12
    OpenMP) and pre-production Knights Landing (using 1 MPI x 64 OpenMP).

commit 06e1efb38bf9db5c9a853962f8f1fe200daa03b7
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Jun 23 22:34:47 2016 -0700

    F_MG: tile the cell-centered restriction

Src/F_BaseLib/cc_restriction.f90
Src/F_BaseLib/ml_cc_restriction.f90
Src/LinearSolvers/F_MG/mg.f90

commit 3449e68be4e1e9e7c5d2301564f0043b5827979e
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Jun 23 22:32:32 2016 -0700

    F_MG: tile the cell-centered GSRB smoothers

Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90
Src/LinearSolvers/F_MG/cc_smoothers.f90

commit cf971954d51d9e2f64fed8b782dc7deffc022ad7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Jun 23 21:50:15 2016 -0400

    Add dimension agnostic version of BL_FORT_IFAB_ARG

Src/C_BaseLib/BLFort.H

commit 59e72db9fcd69af01682686d6066989fb80ec203
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Jun 22 17:23:46 2016 -0700

    Tutorials: tile setup_rhs() in MultiGrid_C

Tutorials/MultiGrid_C/main.cpp

commit 10e9f5929f2761e195816b5afecda6a7f73332d2
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Jun 22 17:22:40 2016 -0700

    Tutorials: tile setup_coeffs() in MultiGrid_C

Tutorials/MultiGrid_C/main.cpp

commit 2af8c8ad5f8bed0a2cc7fd93f3c54e7ce972a17f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 22 14:34:51 2016 -0700

    fixes for merge.

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp

commit 7217dc28864b2d95d608c0051b3908dc52a32d40
Merge: 27fd748f3 b874f10fc
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 22 14:15:09 2016 -0700

    fixed merge conflicts.

commit 5f26211bca2dfe1417c9e6954e4abe9bacf4199f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 22 13:24:18 2016 -0700

    Fortran random: consistent names

Src/F_BaseLib/bl_random_f.f90
Tutorials/Random_F/main.f90

commit 635abc30a74c8d5834f59db4463d5818a4b0fb21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 22 12:13:13 2016 -0700

    Fortran random: minor cleanup

Src/F_BaseLib/bl_random_c.cpp

commit ca0877e908a22f79abedb3965279813e552b73fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 22 11:05:16 2016 -0700

    Fortran random: refactor

Src/F_BaseLib/bl_random_c.H
Src/F_BaseLib/bl_random_c.cpp

commit 6916538e8c9e4e3a2454a83afa3b9ff3f2264dc8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 22 07:36:24 2016 -0700

    Fortran random: template save and restore

Src/F_BaseLib/bl_random_c.H
Src/F_BaseLib/bl_random_c.cpp

commit c28104f21c5d558b1b34f7ad6cd4c21cb42e7283
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 22 06:55:19 2016 -0700

    Fortran random: minor

Src/F_BaseLib/bl_random_c.H

commit b874f10fc1ed9744e410b8a1e13b85932049ce99
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 21 22:46:54 2016 -0400

    fix the zone_info functionality
    
    we were not resetting the current zone error

Tools/Postprocessing/F_Src/fcompare.f90

commit dce720e6482d4d524088bcffe42c4779999edd87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 21 22:25:54 2016 -0400

    remove "use f2kcli" -- our compilers support the F2003 command line stuff
    
    that module was a compatibilty-layer module for codes before Fortran 2003
    was commonplace

Tools/Postprocessing/F_Src/CASTRO_radiation/fgaussianpulse.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/flgt_frnt1d.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/fradshock.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/fradsource.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/fradsphere.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/frhdshocktube.f90
Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90
Tools/Postprocessing/F_Src/MAESTRO_tests/fgaussianpulse.f90
Tools/Postprocessing/F_Src/MAESTRO_tests/fmlcompare.f90
Tools/Postprocessing/F_Src/MAESTRO_tests/fmlconverge.f90
Tools/Postprocessing/F_Src/MAESTRO_tests/fnorm.f90
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/feint.f90
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo.f90
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fwdconvect.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/fad_excess.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/fconv_slopes.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/frates.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/fspec_total_mass.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/fspeciesmass.f90
Tools/Postprocessing/F_Src/faverage.f90
Tools/Postprocessing/F_Src/fboxinfo.f90
Tools/Postprocessing/F_Src/fcoarsen.f90
Tools/Postprocessing/F_Src/fcompare.f90
Tools/Postprocessing/F_Src/fdumpdata2d.f90
Tools/Postprocessing/F_Src/fextract.f90
Tools/Postprocessing/F_Src/fextrema.f90
Tools/Postprocessing/F_Src/ffdcompare.f90
Tools/Postprocessing/F_Src/fintgvar2d.f90
Tools/Postprocessing/F_Src/fsnapshot2d.f90
Tools/Postprocessing/F_Src/fsnapshot3d.f90
Tools/Postprocessing/F_Src/ftime.f90
Tools/Postprocessing/F_Src/fvarnames.f90
Tools/Postprocessing/F_Src/old_flame/fbubble_position.f90
Tools/Postprocessing/F_Src/old_flame/fbubble_position_3d.f90
Tools/Postprocessing/F_Src/old_flame/fcusp.f90
Tools/Postprocessing/F_Src/old_flame/fcylflame.f90
Tools/Postprocessing/F_Src/old_flame/fflamelength.f90
Tools/Postprocessing/F_Src/old_flame/finteg.f90
Tools/Postprocessing/F_Src/old_flame/fturbkin.f90
Tools/Postprocessing/F_Src/old_flame/fwidth.f90
Tools/Postprocessing/F_Src/tutorial/fspeciesmass2d.f90
Tools/Postprocessing/F_Src/tutorial/fwrite2d.f90

commit f5fea3b1d04273fb0ea232b11cde3deee4aa3508
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 21 15:53:46 2016 -0700

    Fortran random: clean up

Src/F_BaseLib/bl_random_c.H
Src/F_BaseLib/bl_random_c.cpp

commit 6e8a29b09cc6574e4b0698c4c34de2f9771c58cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 21 15:41:58 2016 -0700

    Fortran random: update tutorial

Tutorials/Random_F/main.f90

commit e373d15a9f28d02677fc2998323dd3d8c3f65391
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 21 15:40:05 2016 -0700

    Fortran random: remove change_distribution

Src/F_BaseLib/bl_random_f.f90

commit 0965ad5f880aba1cfb49e2b4d1bc58dd7ad8a4ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 21 15:32:21 2016 -0700

    Fortran random: separate engine from distribution just like C++ standard

Src/F_BaseLib/bl_random_c.H
Src/F_BaseLib/bl_random_c.cpp
Src/F_BaseLib/bl_random_f.f90
Tutorials/Random_F/main.f90

commit 27fd748f3a74d6d435980ae70244da396d931cde
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jun 21 13:57:18 2016 -0700

    add new test to makefile.

Tutorials/Sidecar_EX1/GNUmakefile
Tutorials/Sidecar_EX1/Make.package

commit 25310bc471cc3b4999f7eb93b6a85a02e62d3477
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 21 16:41:39 2016 -0400

    remove debug print

Tools/F_scripts/write_probin.py

commit 95b0faf8f1898ce06603ad16f5aa79eea29c30aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 21 16:40:32 2016 -0400

    fix priorities

Tools/F_scripts/write_probin.py

commit 558017cc88efb0cff9aca1038fdbbad3a92729c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 21 12:58:44 2016 -0400

    add some help

Tools/F_scripts/findparams.py

commit 5499ea061248be39d996bbe0d3bd9650d6229159
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 20 21:38:46 2016 -0400

    some cleaning -- no change in functionality

Tools/F_scripts/write_probin.py

commit 37eb0206073a53e68136b6e1f9ac15f1e83f1c80
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 20 14:35:44 2016 -0700

    remove extra MultiFabUtil.H and .cpp.

Src/C_BaseLib/Make.package

commit 5e122194f4045ecb18f18d20fcd32d45ecadbae0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 20 13:40:26 2016 -0700

    FabArrayBase::FPC --> FabArrayBase::FPinfo to avoid confusion with class FPC

Src/C_AMRLib/FillPatchUtil.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit d2223259d0e3f46d8ac951418596a63926eb42e5
Merge: efc4e29b2 0ba5886de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 20 18:58:41 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit efc4e29b2a5a8eb7444dac31d187b2f2b11ce645
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 20 18:57:47 2016 -0400

    add the ability to inspect the zone where the largest error (for a given variable)
    is set

Tools/Postprocessing/F_Src/fcompare.f90

commit 44604c533d3b615abfe69b8c5e82f962ffd26f22
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jun 20 15:30:10 2016 -0700

    add check for ranks moving both from and to comp during sidecar resize.  this is currently disallowed.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Tutorials/Sidecar_EX1/TestRankSets.cpp

commit d975c9b241e08760771e0867cdba1afc94559351
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 20 14:35:44 2016 -0700

    remove extra MultiFabUtil.H and .cpp.

Src/C_BaseLib/Make.package

commit 0ba5886de5ed733f9c3deb0f95e31c7b96ed34da
Merge: ca3cbb644 ee6aa25a0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jun 18 16:20:19 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit ca3cbb644603395a66a917eeb923b375823f3192
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jun 18 16:20:02 2016 -0400

    only consider the base name of the aux files when copying

Tools/RegressionTesting/regtest.py

commit ee6aa25a085b6dc07976359063c65dd6a738aba0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 16 15:15:45 2016 -0700

    GCC option for fsantizer

Tools/F_mk/comps/gfortran.mak

commit 7836266d70e05004152e4372265dbc9e68f9433e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 16 15:15:12 2016 -0700

    Fortran BoxLib: respect do_init_fabs parameter

Src/F_BaseLib/fab.f90

commit 575d22c038041f09c8962454ea6e8897dbb12afe
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 16 14:12:15 2016 -0700

    added file to test resizing sidecars with disallowed rank sets.

Tutorials/Sidecar_EX1/TestRankSets.cpp

commit 32f55632ba6f10a7289b7c5b3cc2c48caae8247d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 16 12:29:19 2016 -0700

    random sidecar ranks test.

Tutorials/Sidecar_EX1/NSidecarsTest.cpp

commit fb1041e9e06d33939cfcc0747534b1d23ee5132a
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 16 12:26:56 2016 -0700

    clarified comments.

Src/C_BaseLib/Utility.H

commit 7423e78268790314060294e52657186103440187
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 15 19:52:16 2016 -0400

    this scripts are obsolete
    
    things should be switched over to to the python version, makebuildinfo.py
    See Maestro's GMakestro.mak and the rule for build_info.py for an
    example of using that.

Tools/F_scripts/make_build_info
Tools/F_scripts/make_build_info2

commit fa74cc7ffaeae809a185c0561f39b6664c9a90fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 15 19:51:46 2016 -0400

    clean this up and switch to argparse
    
    this now requires python 2.7 or later

Tools/F_scripts/makebuildinfo.py

commit 57448b122d08df477237dcf0479b26aaed1fdda9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 15 10:58:51 2016 -0400

    port the job_info_field3 stuff over
    
    from this point forward, new features will only go into regtest.py and co,
    testnew.py will not be updated with new features

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_report.py

commit 41682fa34d0447660366943f77dff08b48886fe1
Merge: 291c76e93 a6e7aa4d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 15 10:37:30 2016 -0400

    Merge branch 'master' into development

commit 291c76e93edc04c02fb704acfed7842233dc6555
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 13 16:36:14 2016 -0700

    if generating a random seed, print out the seed

Src/F_BaseLib/bl_random_f.f90

commit f6618caee69ea1e717189e5e0fae3e67d2b41ae1
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 13 15:18:00 2016 -0700

    seed verbosity

Src/F_BaseLib/bl_random_f.f90

commit 062fb7c01c42e8b01b6c8a87fc3662d1583845b1
Merge: ac92fa0fd 47be9e054
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 13 14:04:49 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit ac92fa0fd61828bd1a72d7e9e0442232c05447d5
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 13 14:04:32 2016 -0700

    print out the random seed info

Src/F_BaseLib/bl_random_f.f90

commit 47be9e0545183e93bd7c778253e804bb9cb1b152
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 13 13:07:26 2016 -0700

    Fix spelling in comment.

Tutorials/PIC_C/solve_with_f90.cpp

commit a6e7aa4d64b2b0e1126c9468f8ec360eae0d61d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 13 16:01:05 2016 -0400

    add 3rd job_info field + allow for bigger name length in tables

Tools/RegressionTesting/testnew.py

commit 2aa52b1b303fe30169d4bf028d3d5f8dcc1f6b5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 13 10:55:05 2016 -0700

    OpenMP is very picky.  Have to use it < end() instead of the idomatic it != end() as the for loop predicate.

Src/C_BaseLib/Particles.H

commit d6a86a5991e92fc3cabfd724d5d309172091e232
Merge: 7e552ef3f ca636444e
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 13 10:37:16 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 7e552ef3f3fba4842443452f98318d60b4fde465
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 13 10:35:56 2016 -0700

    mpi settings for laptop

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit ca636444e485c3356395a9801e5c87d2f54ddaa7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 13 13:31:09 2016 -0400

    saner default -- for 1 plotfile, give each var its own line

Tools/Postprocessing/F_Src/fextrema.f90

commit 47722fdee3b6e91d8e3de44fe256c61d0cbec339
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 13 09:13:30 2016 -0400

    add integrator

Tools/F_scripts/makebuildinfo.py

commit bbdd424b3748bc8ab94e306a67a6365bb5175af5
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Jun 11 23:35:19 2016 -0400

    Add Cray compiler version variables to C_mk

Tools/C_mk/Make.Linux

commit c57e7b420101f312d51ec1de1615dda3a75cf69d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jun 11 16:45:43 2016 -0400

    the stub version of parallel_tag needs reset

Src/F_BaseLib/parallel_stubs.f90

commit 7db522defa12fc8a7d6cdcff1b4287e719b5b80e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Jun 11 11:38:33 2016 -0400

    Permit disabling of forced plotfile on checkpoint
    
    Presently the code writes a plotfile when we force a checkpoint with
    the dump_and_stop or dump_and_continue capability. We can now disable
    this behavior by setting amr.write_plotfile_with_checkpoint = 0.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit f55ace29319a65f1715a64f7524172a6a606f0bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 10 16:45:02 2016 -0700

    Fortran BoxLib: reset mpi tag after fancy bottom solve

Src/F_BaseLib/parallel.f90
Src/LinearSolvers/F_MG/mg.f90

commit 8ee7b179236913cec2dbd478c9e3672ee07f4752
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 10 12:21:13 2016 -0700

    new mpi location for naphta.

Tools/C_mk/Make.mpi

commit 09c2f644a0483c6497d53ed4dffe80c67e50f7d3
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 10 12:19:07 2016 -0700

    more testing of multiple sidecars.

Tutorials/Sidecar_EX1/NSidecarsTest.cpp

commit 865abcb54ba22c92339d773d119a5e0fba5dab72
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 10 12:18:20 2016 -0700

    added commBoth, removed default whichSidecar.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 6f9b83efbb0aa52815325b64c2a81ea2be156a61
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 10 12:11:46 2016 -0700

    more documentation.

Docs/Readme.sidecars

commit e3770d3a1ef8a73e0f6bc76c9e43672e6a9da402
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 10 11:39:25 2016 -0700

    add copyInter support for multiple sidecars.

Src/C_BaseLib/FabArray.H

commit 2d3d113c24d000254b03c9af06969fb95d23ac7f
Merge: bd8cf0336 18a6f6353
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jun 10 09:26:59 2016 -0700

    Merge branch 'particle_threading' into development
    
    These commits slightly change the way OpenMP parallelizes over particles to
    improve thread scaling when using a small number of boxes with a large number
    of threads per MPI process.

commit 18a6f63530dbda4d7a18e1b5893adb7f5ed9f8ef
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jun 10 09:12:52 2016 -0700

    ParticleContainer: add TODO about tiling over grid loop in AssignCellDensitySingleLevel()

Src/C_BaseLib/Particles.H

commit d533b9885a697b222c3aca07f23f101cf1e63750
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jun 10 09:11:36 2016 -0700

    ParticleContainer: add comment suffix to #endif for NEUTRINO_PARTICLES for clarity

Src/C_BaseLib/Particles.H

commit 864f23c237e467f17536b1063aa826e56f894af6
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Jun 9 18:37:21 2016 -0700

    ParticleContainer: move OpenMP parallel region from grid loop to PBox loop in AssignCellDensitySingleLevel()
    
    If the OpenMP region parallelizes over grids, and if we have a small number of
    large grids and a large number of OpenMP threads (which is the typical Nyx use
    case), then this routine scales extremely poorly. So instead we parallelize
    threads over PBoxes within each grid, which leads to much better thread
    scaling.

Src/C_BaseLib/Particles.H

commit 4225a1539fbc41c09495aa6680e1466a3036bbb0
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 9 16:34:01 2016 -0700

    update for multiple sidecars.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 2dcff9ff20712f7674ac3ab10ca67fad31f6728b
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 9 16:33:34 2016 -0700

    update for multiple sidecars.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 2231b5073fb51340cfaae5fc63f502e690bca375
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 9 16:03:29 2016 -0700

    remove send to sidecar function.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit e1ad1a19cb3e8d229d957172c99ae884d96b9a30
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 9 15:56:34 2016 -0700

    remove SendMultiFabToSidecars function, use FabArray::copyInter instead.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit bd8cf03364268d971b3a4275674d16f22c93d225
Merge: 2fa49bc30 49dc5dcaa
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Jun 9 18:13:14 2016 -0400

    Merge upsteam 'development' into Adam's local 'development'

commit 2fa49bc30e13e4b458c9c12fddc8d993cb6e8f0b
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Jun 9 18:09:00 2016 -0400

    Add a comment to particle_where noting it sets particle properties.
    
    I found this to be quite unexpected, so I wanted to document in the code that
    particle_where doesn't just indicate a particle's position is valid within the
    grid heirarchy but also sets a found particle's level, grid, and cell properties.

Src/F_BaseLib/particles_f.f90

commit 7ce049c8d637ea1e12f08ebc98dc10b3a6acef52
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 8 13:44:37 2016 -0700

    include both local and global ranks in filename.

Src/C_BaseLib/BLBackTrace.cpp

commit 358810991db833b0dce1d42cc379a3537c8ce94c
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jun 7 16:47:54 2016 -0700

    started documenting the sidecars.

Docs/Readme.sidecars

commit 49dc5dcaa1a625fae52739f176df482df7656a19
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 7 16:30:29 2016 -0700

    Put in error statement if we try to call create_umac_grown
    with factor 4 refinement since we don't currently support that

Src/F_BaseLib/create_umac_grown.f90

commit 7e810b7f5c3e3d64e88169ad7d62b72293582b72
Merge: de1bf457d 11de56b7f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 7 15:08:43 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit de1bf457d7d0c943cb22545a5841dac6d9ace52d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 7 15:08:27 2016 -0700

    Oops -- was printing the wrong times in my print statement!

Tutorials/PIC_C/single_level.cpp

commit 11de56b7f28d01c7b6d08ade45728edc98c4a0a1
Merge: 430ad9eab 635d53bab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 7 14:24:29 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 430ad9eab276a5afe5e08b8432603ec4e156082e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 7 14:23:23 2016 -0400

    add a module flexibilty way of specifying build components
    
    now you can use --module to send in key=value for the different
    components, e.g., as:
    
    "EOS=helmeos NETWORK=triple_alpha"
    
    and get them through the module name and value functions

Tools/C_scripts/buildInfo.H
Tools/C_scripts/makebuildinfo_C.py

commit 635d53bab94d3e349b477d0a1f60913a469782f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 6 21:24:40 2016 -0700

    make sure mpi tags in Fortran and C++ do not overlap

Src/F_BaseLib/parallel.f90

commit 6ae39b1cbba98b26e31e69709d454035f81a9708
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 6 17:06:04 2016 -0700

    Fortran BoxLib: add a function that returns mpi tag just like C++ BoxLib; don't call mpi_wait unless the size mpi statuses is greater than 0

Src/F_BaseLib/multifab_f.f90
Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit 1959ba3515fcc837ee7be144a949ff4a06e8b703
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jun 6 17:04:24 2016 -0700

    write proc number to abort message.

Src/C_BaseLib/BoxLib.cpp

commit 99e591e3af14891118b14cfbec67e378e137e206
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jun 6 15:33:51 2016 -0700

    write proc number to abort message.

Src/C_BaseLib/BoxLib.cpp

commit df8d49d1ea3b73038eb66ec7c64992b8a29f3273
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 4 13:34:06 2016 -0700

    Release Notes 16.06

ReleaseNotes/release-notes-16.06

commit a22746e2d58fe747fee2a1d7c4db3674d569e9ff
Merge: e2d57c490 aa91fe863
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 4 12:54:54 2016 -0700

    Merge branch 'development'
    
    Conflicts:
            Tools/C_mk/Make.defs

commit aa91fe863d1926941b2702a74b42f10941a3811c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jun 3 21:00:31 2016 -0400

    remove ALCF intrepid and all bits of Intel < 13

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 40cadff396baaea8f7d031744172be0f9b342084
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jun 3 20:24:37 2016 -0400

    remove OSF1 and Intel 11,12 support -- they're old

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/Linux_intel.mak
Tools/F_mk/comps/osf1.mak

commit 9e68577ebeb1a0728e08eaacab8fd7d549486f7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jun 3 16:26:37 2016 -0700

    define intel versions so they appear in job_info

Tools/C_mk/Make.defs

commit 0a966798c78ec96d0c73383d5567c1a811ad0345
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 2 22:17:50 2016 -0700

    PIC_C: fix memory leak

Tutorials/PIC_C/single_level.cpp
Tutorials/PIC_C/two_level.cpp

commit 07d0da75ee0113e51f236f294e83bfa7c8435acf
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 2 18:31:07 2016 -0700

    This verison of PIC_C is designed for doing timing studies.  There is also now an inputs file
    rather than hard-wiring the size of the problem into main.cpp

Tutorials/PIC_C/GNUmakefile
Tutorials/PIC_C/Make.package
Tutorials/PIC_C/README
Tutorials/PIC_C/inputs
Tutorials/PIC_C/main.cpp
Tutorials/PIC_C/single_level.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/solve_with_f90.cpp
Tutorials/PIC_C/two_level.cpp

commit 0ab81b7c8f10e2c9d75cb9ee2080a4220eb996ca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 2 09:50:58 2016 -0700

    Make: option to use fsanitizer for debug build too

Tools/C_mk/Make.defs

commit efb2ac48ac758eb23d42ee4a9e3d16c4c9a2638f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 1 22:39:35 2016 -0400

    some cleaning

Tools/RegressionTesting/test_report.py

commit b068d158ec9a49e6e7e69c215365eaa8732d455b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 1 22:39:27 2016 -0400

    simplify run()

Tools/RegressionTesting/test_util.py

commit 688bf010224d985411e8f0b1ad7aacb543c9a26d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 1 21:09:53 2016 -0400

    clean up the warnings

Tools/RegressionTesting/params.py
Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_util.py

commit 5fe08a729c75c362b66c97386eb3fa249f179144
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 1 20:33:31 2016 -0400

    a little more clean-up

Tools/RegressionTesting/regtest.py

commit bcb607e70de2f211080aeaa31f56e666100684c2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 1 19:47:31 2016 -0400

    more refactoring

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_util.py

commit 0f062c84ebdd442365d6f88b90ec37253f11ece1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 1 15:19:11 2016 -0400

    start of some refactoring
    
    split up the main test suite into separate files to make it
    easier to maintain.  regtest.py is now the entrypoint.

Tools/RegressionTesting/params.py
Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/repo.py
Tools/RegressionTesting/suite.py
Tools/RegressionTesting/test_report.py
Tools/RegressionTesting/test_util.py

commit e707f9246dcb05b376665225c990a4df59eb41eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 31 10:55:16 2016 -0700

    Fortran bl_random: use 0 as a special flag for using random device to generate a seed

Src/F_BaseLib/bl_random_c.cpp
Src/F_BaseLib/bl_random_f.f90

commit 04f68f9dc5bb7a7c818e32fdd495dc5d68ab2998
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 31 12:34:43 2016 -0400

    need to rename job_info when copying to the web dir
    
    this prevents job_info from being overwritten by the next test

Tools/RegressionTesting/testnew.py

commit a8e385293e0381c8110be1ad3ae7beb66d2316d8
Merge: 0106641af c9b620ff0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 31 12:29:41 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit c9b620ff03ab4335623cda458a9b3d0e43e33454
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 30 20:44:45 2016 -0700

    MultiColor_C: minor

Tutorials/MultiColor_C/main.cpp

commit 7d9f9450b154f54048bbd2c4b4da61a309dfc8f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 30 18:10:12 2016 -0700

    MultiColor_C test: add a ne fortran file

Tutorials/MultiColor_C/ff.f90

commit 3a988c180de88aa3605e60789c92cc2ce6a28d0b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 30 18:09:24 2016 -0700

    Color C_CellMG

Src/C_BoundaryLib/BndryRegister.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Tutorials/MultiColor_C/Make.package
Tutorials/MultiColor_C/inputs
Tutorials/MultiColor_C/main.cpp

commit 38f219f94977fbfd6eeaa51b91d1769b768a0569
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 30 16:29:26 2016 -0700

    color InterpBndry and MacBndry

Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp
Src/C_BoundaryLib/MacBndry.H
Src/C_BoundaryLib/MacBndry.cpp

commit 44c822616e84db1a01acbcb8bb29c09ced9ead6e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 30 13:38:31 2016 -0700

    color BndryData

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp

commit 638afa32a9b69ea8a5d5ad9fd8c6c74c759ccc21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 30 13:28:44 2016 -0700

    color BndryRegister

Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit 66b4fd2109a259d30e92445724071e6945b1c615
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 30 11:27:16 2016 -0400

    if a restart test produces backtraces -- abort
    
    previously we didn't look for backtraces on the first run of
    a restart test.  Now we do and abort if they are produced.

Tools/RegressionTesting/testnew.py

commit 0106641af906ade6e6f7d576753f0ecd6611f7f4
Merge: b2c6cd8ee 83a3b07c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun May 29 22:28:59 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 83a3b07c766a1079a6aa6bfdb0f3edbcdeb913f2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 29 22:17:06 2016 -0400

    Turn off PGI Fortran debug symbols if using OpenACC

Tools/C_mk/Make.Linux

commit 71d56153f5c8ec88f6af32256150c17116cf5739
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 29 17:30:02 2016 -0700

    Color FabSet

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 240d4253bdf045bfda790c7cda0154e79e0a3cb1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 29 09:59:13 2016 -0700

    Fortran bl_random: more assertion and make sure no duplicates in parallel seeds

Src/F_BaseLib/bl_random_c.cpp

commit e0ef836bd726fa81d9a85482df7bd4ff783955b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 29 09:47:45 2016 -0700

    Fortran bl_random: assert seed >0

Src/F_BaseLib/bl_random_f.f90

commit 79321e07d4190113f999dd9b3eec8d9e564bf3a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 28 23:20:38 2016 -0700

    Fortran bl_random: Use random numbers instead of seed_seq as parallel seed.  The latter has a high chance of collision.

Src/F_BaseLib/bl_random_c.cpp

commit 57df48650326f5d7d0fe2396fe7fbfab5c45b51f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 21:58:06 2016 -0400

    fix formatting of the job_info summary fields

Tools/RegressionTesting/testnew.py

commit a8b80ef2f1f7fc6a6a47fc8243043dcd0bb067f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 21:11:07 2016 -0400

    if we produce backtraces, we fail

Tools/RegressionTesting/testnew.py

commit b2c6cd8ee764879e390d97128ade7ad8fc361686
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 20:32:17 2016 -0400

    shorten some headings

Tools/RegressionTesting/testnew.py

commit 1f4fac74fbe0d889667dd23bef36621cc4a0dc1d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 18:58:19 2016 -0400

    initialize the job_info fields

Tools/RegressionTesting/testnew.py

commit d34eb8f5a037fe6a2f6dabec4777afbaa906fe8d
Merge: 51c29633e 76414711a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 16:02:43 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 51c29633e2e79700b7345ab7796c43e3d6f00ea4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 16:02:22 2016 -0400

    cleaning + copy job_info to web output

Tools/RegressionTesting/testnew.py

commit 76414711acec9c8e3b9b91b737e67bc8aeca3ec8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 14:56:34 2016 -0400

    update prototypes

Tools/C_scripts/buildInfo.H

commit 5356f2ed7f03d5f3c6af362fb64d5954cddc553c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 14:41:42 2016 -0400

    hook in the compiler versions
    
    Note: we cannot quote the shell output because we quote it when passing
    to the makebuildinfo_C.py routine, and trouble ensues.
    
    Also make the names consistent

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_scripts/makebuildinfo_C.py

commit 38a1b17cbcf3a4577357c7ccff486137ba85e23e
Merge: 4548bc602 e765dd946
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 14:27:26 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 4548bc6023416e1899d1da035e8e8c1f79976a0c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 14:27:01 2016 -0400

    add FCOMP_VERSION and CCOMP_VERSION for gfortran and PGI
    
    THis mirrors the F_mk stuff

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit e765dd946cf9c795421559dd7b12877fc12580be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 13:43:59 2016 -0400

    robustify the summary table

Tools/RegressionTesting/Maestro-tests.ini
Tools/RegressionTesting/testnew.py

commit 9a38dc70452c73e0b48a3de52343ec83e6dacf0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 27 21:46:51 2016 -0700

    Fortran bl_random: minor tweak

Src/F_BaseLib/bl_random_c.cpp

commit acc76ed2e8a6d73ccd5aa2d60e375ccb5ac4e5ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 27 21:41:27 2016 -0400

    updated test file

Tools/RegressionTesting/Castro-SBU-tests.ini

commit a0c76cb74d7f3cd43224b600cda500925e52831d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 27 21:36:01 2016 -0400

    add custom fields to the summary table
    
    Now we can define special fields to appear in the suite summary table.
    These fields should appear in the job_info file, and we split on
    a ":", and store the result in the table (we also remove anything
    before the last "/" to handle paths)

Tools/RegressionTesting/testnew.py

commit 4142c040f5d58975e3929a109bfdb2ecba57df64
Merge: a0f155b9c 2ed6e324b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 27 20:03:20 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit a0f155b9cef645fd5390297b48955ff6debf0c58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 27 20:02:44 2016 -0400

    add network, EOS, and conductivity for easy parsing in the test suite

Tools/F_scripts/makebuildinfo.py

commit 2ed6e324b5bfc2dc529447cf5e0523202e348442
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 27 17:01:06 2016 -0700

    Fortran bl_random: add bl_rng_change_distribution for poisson and binomial

Src/F_BaseLib/bl_random_c.H
Src/F_BaseLib/bl_random_c.cpp
Src/F_BaseLib/bl_random_f.f90
Tutorials/Random_F/main.f90

commit 3e50d6d40f34ef90557552434921f8d62233ca70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 27 16:17:48 2016 -0700

    Fortran bl_random: add binomial

Src/F_BaseLib/bl_random_c.H
Src/F_BaseLib/bl_random_c.cpp
Src/F_BaseLib/bl_random_f.f90
Tutorials/Random_F/main.f90

commit e7fd43d0cfe8dff6f79d056fcba73b3d5c622b50
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 27 15:55:15 2016 -0700

    Fortran bl_random: add poisson

Src/F_BaseLib/bl_random_c.cpp
Src/F_BaseLib/bl_random_f.f90
Tutorials/Random_F/main.f90

commit 7db735dc6e3c534edacc86fb162d4f95ec909cd8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 27 15:40:52 2016 -0700

    forgot to add a file

Src/F_BaseLib/bl_random_c.H

commit 0de91cb6d82c86e90ccdca6f3fb0382f25cae980
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 27 15:19:02 2016 -0700

    Fortran: use C++11's random number generators

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_random_c.cpp
Src/F_BaseLib/bl_random_f.f90
Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/Linux_cray.mak
Tools/F_mk/comps/Linux_intel.mak
Tools/F_mk/comps/Linux_pgi.mak
Tools/F_mk/comps/gfortran.mak
Tutorials/Random_F/GNUmakefile
Tutorials/Random_F/GPackage.mak
Tutorials/Random_F/main.f90

commit 2c06bb2e97b315077928b053f4420bfb3e268a3d
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 26 17:34:43 2016 -0700

    working test code with three sidecars.

Tutorials/Sidecar_EX1/GNUmakefile
Tutorials/Sidecar_EX1/NSidecarsTest.cpp

commit 2cceba7532eee61f2363ed99908dcc4054ace6e9
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 26 17:30:15 2016 -0700

    fix for multiple sidecars.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 0486cf2016e3c1beed026ddf4d50d83c27b73ccc
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 26 17:29:17 2016 -0700

    added more error checking.

Src/C_BaseLib/ParallelDescriptor.H

commit 19ef58bf58fd61966962bce9596e5e1e76ba6c76
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 26 14:48:05 2016 -0700

    added function for which sidecar.

Src/C_BaseLib/ParallelDescriptor.H

commit 54f16b5ba5e3556047238b5427ed2ce9fb64260a
Merge: cadc60886 4612d963b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 26 12:07:07 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit cadc6088693d77361b87fb652c7b956975e9de03
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 26 12:06:52 2016 -0400

    make this work with python3

Tools/C_scripts/makebuildinfo_C.py

commit 4612d963bc02915df9a7d5cf28b5c81ecad3b156
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 25 22:24:55 2016 -0400

    The write_probin script now has a hook for updating GPU data

Tools/F_scripts/write_probin.py

commit b4500698df7b502d5341a53ee393d995009a9d27
Author: vince <vebeckner@lbl.gov>
Date:   Wed May 25 13:20:16 2016 -0700

    free extra groups.

Src/C_BaseLib/ParallelDescriptor.cpp

commit aa384a7e488320c3aa24151eebacd07ce2824c55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 25 13:27:08 2016 -0400

    add FPP_DEFINES for .F90 preprocessing

Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak

commit b9366981a1b768bd87463d4ae48eb090bc356278
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 25 13:01:49 2016 -0400

    no need to have 2 copies of moddep.pl
    
    The C++ build now uses the version in the F_scripts

Tools/C_mk/Make.defs
Tools/C_scripts/moddep.pl

commit 4b4b1cf80ead03e92305ad5f0a0f9200e1e844d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 25 12:45:36 2016 -0400

    sync up with the version in C_scripts

Tools/F_scripts/moddep.pl

commit 92b0fd4c86c48b28648da3084eace9192ae82ea6
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 25 11:49:42 2016 -0400

    Conditionally disable -g on PGI when using OpenACC

Tools/F_mk/comps/Linux_pgi.mak

commit 846d028af506dda96cf5677ee2915c5661745155
Merge: f6b8f86d6 8a2be1b6f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 25 11:42:37 2016 -0400

    Merge branch 'development' into openacc

commit 8a2be1b6faca30b71c0c913ef51864b36d52f88f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 25 11:16:41 2016 -0400

    add support for .F90 files -- these will be preprocessed.  We adopt the
    convention that the Fortran compiler is smart enough to handle the
    preprocessing, recognizing the .F90 (caps) means preprocess

Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak

commit b733abc82324bba5f9ad133f78e8f564ea44128a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 25 11:15:28 2016 -0400

    make the Fortran dependency script recognize .F90 too

Tools/F_scripts/moddep.pl

commit 5fae1c1bfad5becf17c53c21be54fb4e73b6452e
Merge: c3a2342df fa7d358d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 25 10:40:59 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit c3a2342dfc6c82a1071a0fa3b91f1e52138c2949
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 25 10:40:37 2016 -0400

    fix the permissions so this is executable so 'make doc' works

Tools/F_scripts/f90doc/f90doc

commit fa7d358d17d2cf5c79d36f5b7080ce15b34fb47b
Merge: b41da6f56 36e123746
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 25 07:04:45 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development
    
    Conflicts:
            Src/F_BaseLib/ml_nd_restriction.f90

commit b41da6f56faec60c25ce75cdb561901aba5a5992
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 25 07:03:25 2016 -0700

    Oops -- should have removed mp_crse, mp_fine

Src/F_BaseLib/ml_nd_restriction.f90

commit 36e123746ad04ff043aef2e8ac8179e3a599174b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 25 08:40:46 2016 -0400

    fix the OMP here

Src/F_BaseLib/ml_nd_restriction.f90

commit 388e6900303025a525a1124c1362b35ee263c542
Merge: 85494791d 6d91ad6f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 24 20:42:45 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 85494791dc8990e52af384eb509a24d6d0a96b42
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 24 20:42:22 2016 -0400

    cause why not ... define FIVE12TH and FIVE32ND

Src/F_BaseLib/bl_constants.f90

commit ec9bc9ae5627fa5d4af31beaa8a62557eddf22d0
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 16:13:07 2016 -0700

    added a new test.

Tutorials/Sidecar_EX1/NSidecarsTest.cpp

commit 8f0cd72f3948c321f1558f5260a376d50eb78818
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 16:12:47 2016 -0700

    added a new test.

Tutorials/Sidecar_EX1/Make.package

commit 1f07d0048595dc8c355d557069752501d0742bfe
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 16:12:23 2016 -0700

    update test for latest boxlib dsc.

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit 07a07b992421d2703b1dd9cd4ac722026eb226b2
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 16:11:37 2016 -0700

    fix group free for zero sidecars.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 6d91ad6f8401e5b91866a376ed628cfaf54070c4
Merge: 944b6f7fc beb27117f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 24 15:26:30 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 944b6f7fc2f292d424484565dd43d105d8d270ab
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 24 15:26:11 2016 -0700

    Add nodal injection (in addition to nodal restriction)

Src/F_BaseLib/ml_nd_restriction.f90
Src/F_BaseLib/nodal_restriction.f90

commit 7e4d1c9ca1ee553199c3b47d8195991bd653a9a7
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 14:21:35 2016 -0700

    fix for serial.

Src/C_BaseLib/ParallelDescriptor.cpp

commit cd24478d22b46b9c3038dca5f97fb01947ab7e2c
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 14:11:18 2016 -0700

    default arg.

Src/C_BaseLib/ParallelDescriptor.H

commit ea9c5153ad65f237ca6b97fb24bfda4db0a1629d
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 13:58:30 2016 -0700

    fix for zero sidecars.

Src/C_BaseLib/ParallelDescriptor.H

commit 12bec56ccb4525cb09252a5c0a7011c8554beba8
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 13:45:15 2016 -0700

    additions for multiple sidecars.  fortran interface needs testing.

Src/F_BaseLib/parallel.f90

commit 3019826768e39d16fedc906fc7313ad66c77fee8
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 13:44:17 2016 -0700

    additions for multiple sidecars.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit beb27117f6960445928789a179760e9e31186f12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 24 14:35:45 2016 -0400

    fix convert_type wrapper for None

Tools/RegressionTesting/testnew.py

commit 148865d1711564e0a82182f2314786e55bcb0db8
Merge: 3ac02be02 272987f15
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 24 14:32:10 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 3ac02be02873029cf8553da648bf36c37626f349
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 24 14:31:58 2016 -0400

    a little clean-up

Tools/RegressionTesting/testnew.py

commit 272987f151e40156339162249d164520f3a94d09
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 24 11:01:42 2016 -0400

    gracefully handle the "grids don't match" error from fcompare

Tools/RegressionTesting/testnew.py

commit fd4a01e133556f61d78e3f38990ada8f70595f30
Merge: a37b66cbf dea56bcbe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun May 22 16:39:23 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit dea56bcbea105c1c1b99610c96df71e435509f4a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 20 22:56:01 2016 -0700

    a multi-color test

Tutorials/MultiColor_C/GNUmakefile
Tutorials/MultiColor_C/Make.package
Tutorials/MultiColor_C/inputs
Tutorials/MultiColor_C/main.cpp

commit 8f46ca6a3f8e15e4447988565a0165c60b308c7f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 20 17:14:55 2016 -0700

    fix non-parallel build

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ccse-mpi.H

commit 3887750f2dc4cb6843dd5d23ccfd1df2815d089b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 20 16:51:34 2016 -0700

    make reduce work with color

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/iMultiFab.cpp

commit 7be4e57e09dda03fb2e68016e65b1314f7ee124b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 20 13:49:13 2016 -0700

    update SeqNum functions for multi-color

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 1731e5f6e8af6ff50cd28b54ca559ce73cfce46d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 19 21:52:18 2016 -0700

    operator<< for ParallelDescriptor::Color

Src/C_BaseLib/ParallelDescriptor.H

commit bc90c129a9dfbc43a80b4ae0106243d97b6f5ba0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 19 21:15:33 2016 -0700

    DistributionMapping: finished coloring

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 79868ff52604d884dbde0f4f404179b9302b7bcd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 19 10:56:41 2016 -0700

    DistributionMapping: use color as part of the key

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit be247b8267b3c6eaf78435a45c18ff38290cbf22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 19 10:34:59 2016 -0700

    replace int type color with ParallelDescriptor::Color class for type safety

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 3f3da43f251dfdfbc33844955ef97085ec780ec4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 19 07:13:36 2016 -0700

    remove useless 'explicit'

Src/C_BaseLib/BLBackTrace.H
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 2e5cda993b1cf0258cb5ff4f55f33c8933a8fed8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 18 22:30:44 2016 -0700

    start sub-communicators controlled by boxlib.ncolors

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Tutorials/MultiGrid_C/GNUmakefile

commit 04409561fe724d6cdb5554129c02b38760f8cfb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 20 17:01:19 2016 -0700

    clean up an unused template for parallel reduce

Src/C_BaseLib/ParallelDescriptor.H

commit e2d57c49096b07211bf4dd8cc42d6bac2ed4f8de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 20 11:21:42 2016 -0700

    update make for CCSE machines because of new MPI installation

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 6568e0f28bb6662a0cc46bc98c0a281e33c587e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 20 10:38:15 2016 -0700

    update make for battra and baragon

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit b0747b1dd7036a03549c3f896ce89adbdd944c03
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 20 11:21:42 2016 -0700

    update make for CCSE machines because of new MPI installation

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 43b64bc6fe1aedb093ad808b485dd5d22ca17a54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 20 10:38:15 2016 -0700

    update make for battra and baragon

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit ec60aab8754353bbd93ffe52c14772375457122e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu May 19 19:51:30 2016 -0400

    Permit disabling of PGI OpenACC

Tools/C_mk/Make.Linux

commit b902d7e224d536ac69d5cefed3d979e1f58eb1cd
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 19 14:58:13 2016 -0700

    additions for multiple sidecars, check bl_fortran_set_nprocs_sidecar.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 840c9703c61af757f3891157cf0710948d52afaf
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 19 14:56:56 2016 -0700

    fixes for multiple sidecars.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit b84ed6de5ac93e8984732cefe152a347fe2940fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 19 08:24:11 2016 -0700

    fix bug in my last commit

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 4b0428572e32b554992c0c7a3f1db7d62a348641
Author: vince <vebeckner@lbl.gov>
Date:   Wed May 18 18:00:04 2016 -0700

    dont need arrays for sidecar groups or comm.  made simple interface function for one sidecar case.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit c5f27284fd10c6a5eb9457add642e37e721ff5dd
Author: vince <vebeckner@lbl.gov>
Date:   Wed May 18 16:03:46 2016 -0700

    update NProcsSidecar for multiple sidecars.

Src/C_BaseLib/ParallelDescriptor.H

commit 3b38b6860c4946b6b48126f0f28824fd77103d4c
Author: vince <vebeckner@lbl.gov>
Date:   Wed May 18 15:43:36 2016 -0700

    update SetNProcsSidecars to support multiple sidecars.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 77e7c135e0b0803c9aaa98ddf551483946c8817a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 18 13:36:55 2016 -0700

    MultiFab::norm0 add nghost optional argument

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/iMultiFab.H
Src/C_BaseLib/iMultiFab.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit cdde4241d2f66a60724e616596e57099f6721f75
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 17 12:25:10 2016 -0700

    typo

Src/C_BaseLib/ParallelDescriptor.H

commit 527cc3142fe6fe38bacb0b74bd731af58ed23223
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 17 12:19:02 2016 -0700

    runtime parameter team.reduce

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 5974164d2cf1e5c98e45ada3b2b495fe9b6c414a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 17 12:05:39 2016 -0700

    keep track of UPC++ and MPI mode

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 035f9e67aa71c1b104136bee3e3f8150921ad5f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 16 17:01:45 2016 -0700

    Reduce: do team reduce first, then team lead reduce, and finally team bcast

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit f74a9b55f6544afc303d44a13dfcbf24838814c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 16 15:06:38 2016 -0700

    Team: create team lead communicator

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit f25f95ccda7910e510ae0663fb02155220ea2344
Author: vince <vebeckner@lbl.gov>
Date:   Mon May 16 14:04:43 2016 -0700

    updated error string and comments.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 2b7ef6580dcbf8b3b6671a0baa635798be2ef779
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 16 12:24:13 2016 -0700

    FMultiGrid: add const

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp

commit 3ab188637b03480eed831e6510890fa78e76dcc0
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 12 12:19:21 2016 -0700

    only print error messages if abortOnError.  these may
    not be errors during transient states.

Src/C_BaseLib/FabArray.H

commit ea0144aab5ed938d1c509d1ac53ad9593ff5c38b
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 12 12:14:32 2016 -0700

    removed cout.

Src/C_AMRLib/Amr.cpp

commit a37b66cbf3bd9bcc8d8d3215391bbcee8bf92ef8
Merge: 6476208b6 17e50770e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 11 22:24:33 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 17e50770ef916d91d324daf51939b57e92260c40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 11 12:42:15 2016 -0700

    Array: removed the disallowed copy assignment so that C++11 compilers could auto-generate move constructor and move assignment

Src/C_BaseLib/Array.H

commit 1e24aa1edfdf82e74c2608179fbb53d965e64940
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 11 12:18:46 2016 -0700

    tweak IntVect comparison functions to make it consistent with Fortran convention.

Src/C_BaseLib/IntVect.cpp

commit f0b2b23be39f1a0198f17662a06d58a84637986f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 10 20:50:30 2016 -0700

    FillPatch: turn off omp for nodal.  This is actually a benign race.

Src/C_AMRLib/FillPatchUtil.cpp

commit 1baf471049e34c07eb251de3ba0543ce237ee2dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 10 20:35:05 2016 -0700

    FillBoundary: avoid writing to valid region

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H

commit a77390fd2427f49d397679bfcfdd6b275deae0b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 10 15:57:53 2016 -0700

    FillPeriodicBoundary: avoid writing to valid regions

Src/C_BaseLib/Geometry.cpp

commit e1222ac52f525b6d288d049b7878a10c1fb9c8a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 10 10:38:03 2016 -0700

    add BoxLib::shift function returning a shifted box

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp

commit cbd5b06167af862532482a1996a8f24c1e40d540
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 9 21:48:48 2016 -0700

    FluxRegister: make it behave exactly the same as before

Src/C_AMRLib/FLUXREG_1D.F
Src/C_AMRLib/FLUXREG_2D.F
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/FLUXREG_F.H
Src/C_AMRLib/FluxRegister.cpp

commit f6b8f86d64db4b69529a2e8750ad66887d8d54f0
Merge: 9c65a5314 dd098ef6a
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon May 9 18:35:11 2016 -0400

    Merge branch 'development' into openacc

commit dabc831daa1908f574dad1e1af0ec46742c1dacc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 9 14:07:19 2016 -0700

    baragon makefile

Tools/C_mk/Make.defs

commit dd098ef6a1ced34f33200683764d2559ebe0ffee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun May 8 18:55:09 2016 -0400

    some more OpenACC PGI flags

Tools/C_mk/Make.Linux

commit 6784f980b15a639e67079a89ce2715dc2647383b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 7 17:33:24 2016 -0700

    update make for baragon

Tools/C_mk/Make.defs

commit 309e0d67b47a29d6650ed916a4e39ea4674d3fdd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 7 07:15:33 2016 -0700

    fix some minor data race

Src/C_BaseLib/MemPool.cpp

commit 9d110831c4a50535669d348f1ecb89bf857f1120
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 7 07:06:00 2016 -0700

    add MultiFab::Saxpy

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 35e3004e237746c85dc8433372b8e10d9cfe0a21
Author: vince <vebeckner@lbl.gov>
Date:   Fri May 6 15:29:09 2016 -0700

    dont abort on CheckFAPointers.

Src/C_AMRLib/Amr.cpp

commit 3511de3304c399a058fdf5265aec18d2ff802ea8
Author: vince <vebeckner@lbl.gov>
Date:   Fri May 6 15:17:28 2016 -0700

    added option to not abort on errors in CheckFAPointers.

Src/C_BaseLib/FabArray.H

commit c345b712953743445e6117415594ce4fe03a2b82
Author: vince <vebeckner@lbl.gov>
Date:   Fri May 6 13:36:17 2016 -0700

    cleanup diagnostics.

Src/C_BaseLib/FabArray.H

commit 02b8e4d1e06996e1fd1026c1fe2e46c0d3c182c1
Author: vince <vebeckner@lbl.gov>
Date:   Fri May 6 13:35:21 2016 -0700

    add call to fabarray internal check.

Src/C_AMRLib/Amr.cpp

commit b7574101b7ac590130ec5e5c3c6c7cc324b80cf5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 6 08:57:33 2016 -0700

    add source ghost cell option to periodicCopy

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 44d47f14c43f85a55cc6897f37460c0b3629523e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 6 08:44:27 2016 -0700

    fix a new bug: need to update BD key

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit d69e618d3d60fa4bce70ecb946394f6e91f7df36
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 5 23:14:28 2016 -0700

    use ADD instead of COPY in mapPeriodic

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 1ce4d9b3c9e5b1fc2fd5c3988221d15d3a5c3d76
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 5 22:19:51 2016 -0700

    simplify TagBoxArray::mapPeriodic

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit fcd065353d70235ddf3353ab922f1afe8cb2b685
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 5 17:07:26 2016 -0700

    fix logic in new BoxArray::complement

Src/C_BaseLib/BoxArray.cpp

commit 7749d3177f417a32ecfac33723ac65202a43d88a
Merge: dab69d918 8fd5701a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 5 14:38:37 2016 -0700

    Merge branch 'development' into weiqun/complement

commit 8fd5701a66ae9f4c03f6801bd41a1e59cdc89125
Merge: 0b280a511 9bafaf848
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 5 14:01:39 2016 -0700

    Merge branch 'new_reflux' into development

commit 9bafaf848264140c99460dc2857fe5d8f74a7ffa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 5 13:23:54 2016 -0700

    clean up

Src/C_AMRLib/FluxRegister.cpp

commit 0b280a511e61401c3180f07c0b71750d4fd44227
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 5 15:35:58 2016 -0400

    output more usage defails

Tools/Postprocessing/F_Src/fcompare.f90
Tools/Postprocessing/F_Src/ffdcompare.f90

commit bbc8d63134affec16bfd7c07d9f52699483350e1
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 5 12:35:30 2016 -0700

    another check for data integrity.

Src/C_BaseLib/FabArray.H

commit dab69d918dbe49bc4dada116d382ea935e8755a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 5 11:18:48 2016 -0700

    new complement list

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FabArray.cpp

commit c68acd5493f30e4e7362906cb9588080d37fb4e4
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 5 01:57:54 2016 -0400

    Update the probin script to handle OpenACC declarations

Tools/F_scripts/write_probin.py

commit 431d9473dab20a84a0459de3f715c865d86a4588
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 18:12:50 2016 -0700

    fix some errors in last commit

Src/C_AMRLib/FLUXREG_3D.F

commit baa75c4c884d5b5015ba56b0ac80694ed346e367
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 18:10:29 2016 -0700

    FluxRegister: no longer use CollectData

Src/C_AMRLib/FLUXREG_1D.F
Src/C_AMRLib/FLUXREG_2D.F
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/FLUXREG_F.H
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp
Src/C_BoundaryLib/FabSet.H

commit b4fb6d2af795f8821057102b84c341c7e70de001
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 15:15:42 2016 -0700

    omp in FluxRegister

Src/C_AMRLib/FluxRegister.cpp

commit c7c482b68e356407186ddedac9c2a040e4304362
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 13:53:26 2016 -0700

    omp in BndryRegister

Src/C_BoundaryLib/BndryRegister.cpp

commit e52c2a9e3c2047a1be76379295fa0956da0f0c0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 12:46:34 2016 -0700

    comment

Src/C_BoundaryLib/FabSet.cpp

commit ed19ae38e5a7ab09d9dd33741621d3be07b6c82b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 12:19:44 2016 -0700

    Switch FillCoarsePatch to using the new FillPatch

Src/C_AMRLib/AmrLevel.cpp

commit 9bdd5c92c67bfe0b14ffce18229bfafaa81194b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 11:24:08 2016 -0700

    fix the new FillCoarsePatch

Src/C_AMRLib/AmrLevel.cpp

commit fedf1b3cc13e15ee2cdf552301fa4d92d65f3936
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 10:40:14 2016 -0700

    If the boxarray for a level does not change during regrid, assign the previous boxarray to the current to avoid making a duplicate with the same boxes but different reference id.  This will help preserve caches associated with the previous boxarray.

Src/C_AMRLib/Amr.cpp

commit 490297221f3280a0fe3a621c9bf334e4bdb030cf
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 4 12:50:44 2016 -0400

    Use pgcc for compiling C code with PGI

Tools/C_mk/Make.Linux

commit 6fcc0a6559044bb88c05e38093f0d1b6221d52a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 3 17:54:48 2016 -0700

    FillPatchIterator: switch to the point-to-point version.  This may break some regression tests with nodal data and periodic boundaries.

Src/C_AMRLib/AmrLevel.cpp

commit bcd94568cac51df183eb0e7aa97a5904e4abece8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 3 14:58:36 2016 -0700

    FillCoarsePatch: optimization

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FillPatchUtil.H
Src/C_AMRLib/FillPatchUtil.cpp

commit ba982ad9c2e1181402864781599923dc68ea2754
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 3 12:20:56 2016 -0700

    mpi_require.

Src/C_BaseLib/FabArray.H

commit 2660a1fb2efde53033ba0b56cd1cf5b4859d74f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 3 12:06:22 2016 -0700

    FillPatchCache: fix a bug

Src/C_BaseLib/FabArray.cpp

commit 3bf953ce5e9c1e2fadfa689811ef99f713e00e32
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 3 09:19:39 2016 -0700

    FillPatch: optimization

Src/C_AMRLib/FillPatchUtil.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 764e0e6c5035e08187e42fc6fe8052b44fd736eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 3 08:29:36 2016 -0700

    FillPatchCache: fix some bugs

Src/C_AMRLib/FillPatchUtil.cpp
Src/C_BaseLib/FabArray.cpp

commit 53996ab05263e6b53ed127d4441b39f40da8d467
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 2 16:53:22 2016 -0700

    FillPatch cache stats

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 6476208b66d7b6d8ad1fc3757051a2cd0e765520
Merge: 8be09b4be 026785fcf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 2 19:15:30 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 1cf641ee4bf3703788bb988236399634994f154d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 2 15:36:45 2016 -0700

    FillPatch cache

Src/C_AMRLib/FillPatchUtil.cpp
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/StateData.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 026785fcf05b52b7ee44b7f36bbb6d7a9bd8fb0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 2 10:40:50 2016 -0700

    Release Notes 16.05

ReleaseNotes/release-notes-16.05

commit 494152762e8ec62f679d0be0996495e4a68c7a2b
Merge: ae86a6f79 68d33340c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 2 10:13:10 2016 -0700

    Merge branch 'master' into development

commit ae86a6f79d7e3cbdd0194ff5f12d7930865e6fd3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 30 13:37:45 2016 -0700

    add ghost cell option to PeriodicCopy

Src/C_AMRLib/FillPatchUtil.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 90e2ac171379792ecc5ef1dfa101cf93dddbba2b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 29 18:34:44 2016 -0700

    fix leastuseteam forUSE_MPI=FALSE

Src/C_BaseLib/DistributionMapping.cpp

commit 5a2f9635d7299e91ed8da1c39cd3e4ecd2fbb008
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 29 17:48:24 2016 -0700

    clean up unused CPC constructor

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 52c8d0f75ebd53462850b1fda2f5bd5522b2b7c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 29 17:21:34 2016 -0700

    fix a bug in paralle copy to ghost cells

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 0cebc798e10de83d8d39efb1849f8d0888d374d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 29 15:23:22 2016 -0700

    new runtime parameter DistributionMapping.node_size that allows knapsack within a node and SFC at the node level

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 2577ca57b59e31203d0bbe30dc472348aed3779e
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 29 15:09:27 2016 -0700

    const refs.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 8b3f69a9a80c10640919eadca457978aa6b52fc9
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 29 15:08:36 2016 -0700

    const refs.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 7f8cde7146d9d94251f4184e82edf647f891d867
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 29 15:08:07 2016 -0700

    const refs.

Src/C_BaseLib/FabArray.H

commit dddd2886c4530854feafab08a674e32ad0c11def
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 29 15:07:17 2016 -0700

    delete dm cache.

Src/C_AMRLib/Amr.cpp

commit e667b6085b6fccb9dd4ad3bd080a5f6d2ae1759d
Merge: 45a34fec7 7cde88b0b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 29 10:35:59 2016 -0700

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit 7cde88b0bdbf2a49a1bb4667cd97e55703084025
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 29 10:05:30 2016 -0700

    Profiling reduce

Src/C_BaseLib/ParallelDescriptor.cpp

commit ec970ab1e3ed8f90f134fd03164599315244325f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 29 10:03:50 2016 -0700

    TinyProfiler: setfill

Src/C_BaseLib/TinyProfiler.cpp

commit d11048d2f5f968b3438646f18bbd1e15421d2435
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Apr 28 12:42:45 2016 -0700

    Tutorials: revert changes to inputs file in MultiGrid_C
    
    Commit 49f3551 ("4th order in progress...") changed some default values
    of the "inputs" file. This changes them back.

Tutorials/MultiGrid_C/inputs

commit 9c65a531443c372694aa0c18cdea8acee180d2d0
Merge: 9aea7776e 4a228c2f9
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Tue Apr 26 15:26:44 2016 -0400

    Merge branch 'development' into openacc

commit 9aea7776ed84da8ea706618875e89560888cf371
Merge: 4d61f3b26 0086b0e30
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Tue Apr 26 15:26:32 2016 -0400

    Merge branch 'openacc' of ssh://github.com/BoxLib-Codes/BoxLib into openacc

commit 8be09b4be1c6f4120e731e1e09376f5a56d22083
Merge: 3945a6862 4a228c2f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Apr 25 18:05:08 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit babde0d9467ba2637ec090bd10901f67107fd855
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 25 12:59:25 2016 -0700

    delete distmap cache function.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 45a34fec7e4420476be85c77354bfaea8ed794b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 25 12:32:18 2016 -0700

    Start Tutorials/AMR_Adv_CF

Tutorials/AMR_Adv_C/README
Tutorials/AMR_Adv_CF/Exec/Make.Adv
Tutorials/AMR_Adv_CF/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_Adv_CF/Exec/SingleVortex/Make.package
Tutorials/AMR_Adv_CF/Exec/SingleVortex/Prob.f90
Tutorials/AMR_Adv_CF/README
Tutorials/AMR_Adv_CF/Source/Make.package
Tutorials/AMR_Adv_CF/Source/fmain.f90

commit 4a228c2f92cc1232fc7fbc95d4d187b5064cf354
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 25 11:18:46 2016 -0700

    runtime parameter boxlib.use_collectdata=1; to use the new fillpatch, set it to 0.

Src/C_AMRLib/AmrLevel.cpp

commit ce5a99f4bc10c3ccf03ce7614f1a5dadc5e8f44f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 25 11:09:56 2016 -0700

    move FillPatchUtil to C_AMRLib

Src/C_AMRLib/CMakeLists.txt
Src/C_AMRLib/FillPatchUtil.H
Src/C_AMRLib/FillPatchUtil.cpp
Src/C_AMRLib/Make.package
Src/C_BaseLib/Make.package

commit cb4d2cd5c1b1e1a5c293cbc5bbbece16d77217bf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 25 11:01:26 2016 -0700

    Revert "move Interpolator from AMRLib to BaseLib"
    
    This reverts commit 4a0cc8dc9c792ee7bce1b8075f63046641384919.

Src/C_AMRLib/ARRAYLIM_1D.F
Src/C_AMRLib/ARRAYLIM_2D.F
Src/C_AMRLib/ARRAYLIM_3D.F
Src/C_AMRLib/CMakeLists.txt
Src/C_AMRLib/INTERP_1D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/Make.package
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package

commit beaf399e077cf9c41462e8560c0127695e477811
Merge: eaf418958 2f24be4fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 25 10:23:26 2016 -0700

    Merge branch 'development' into fp2
    
    Conflicts:
            Src/C_BaseLib/Geometry.H

commit 2f24be4fcbc3ba2f87206c96a7de2f8e4c0e9cc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 25 09:54:21 2016 -0700

    Tutorials: heat equation sovler using the Fortran interfaces of C++ BoxLib

Src/F_Interfaces/BaseLib/multifab_mod.f90
Tutorials/HeatEquation_EX1_CF/Make.package
Tutorials/HeatEquation_EX1_CF/advance.f90
Tutorials/HeatEquation_EX1_CF/fmain.f90
Tutorials/HeatEquation_EX1_CF/inputs

commit e807a2467a22e238c1fd3284050cee61561bb8ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 24 21:32:38 2016 -0700

    FI: add optional nodal argument to multifab_build

Src/F_Interfaces/BaseLib/boxlib_mod.f90
Src/F_Interfaces/BaseLib/multifab_fi.cpp
Src/F_Interfaces/BaseLib/multifab_mod.f90

commit 4e13031086119185fe6cfc55dd3247ce632b2093
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 24 16:33:59 2016 -0700

    FI: add fill boundary

Src/F_Interfaces/BaseLib/multifab_fi.cpp
Src/F_Interfaces/BaseLib/multifab_mod.f90
Tutorials/HeatEquation_EX1_CF/Make.package
Tutorials/HeatEquation_EX1_CF/fmain.f90
Tutorials/HeatEquation_EX1_CF/init_phi.f90

commit cf6ad5015bea82c4a25648e62f66d8c4477ae13b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 24 15:20:43 2016 -0700

    FI: rename baselib module to boxlib module

Src/F_Interfaces/BaseLib/Make.package
Src/F_Interfaces/BaseLib/baselib_mod.f90
Src/F_Interfaces/BaseLib/geometry_mod.f90
Tutorials/HelloWorld_CF/fmain.f90

commit 0ddcbf3f2925308d4c8e5d9cababb4253d98fc81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 24 14:56:41 2016 -0700

    FI: start heat equation

Tutorials/HeatEquation_EX1_CF/GNUmakefile
Tutorials/HeatEquation_EX1_CF/Make.package
Tutorials/HeatEquation_EX1_CF/fmain.f90
Tutorials/HeatEquation_EX1_CF/inputs

commit fad1d7432f730b00009c0c34af37a0cd5b8ec4fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 24 14:56:10 2016 -0700

    FI: geometry module

Src/F_Interfaces/BaseLib/Make.package
Src/F_Interfaces/BaseLib/baselib_mod.f90
Src/F_Interfaces/BaseLib/geometry_fi.cpp
Src/F_Interfaces/BaseLib/geometry_mod.f90
Src/F_Interfaces/BaseLib/multifab_mod.f90

commit 2c8aa8a445995439eee1083512455c76c8144af6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 24 11:15:03 2016 -0700

    FI: ParmParse module

Src/F_Interfaces/BaseLib/Make.package
Src/F_Interfaces/BaseLib/baselib_mod.f90
Src/F_Interfaces/BaseLib/boxarray_mod.f90
Src/F_Interfaces/BaseLib/multifab_mod.f90
Src/F_Interfaces/BaseLib/parmparse_fi.cpp
Src/F_Interfaces/BaseLib/parmparse_mod.f90
Src/F_Interfaces/BaseLib/string_mod.f90
Tutorials/HelloWorld_CF/GNUmakefile

commit aaf93a1b75c8e67e3b8e706bfb583e5d3219173c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 24 06:54:24 2016 -0700

    FI: add string module

Src/F_Interfaces/BaseLib/Make.package
Src/F_Interfaces/BaseLib/omp_mod.F90
Src/F_Interfaces/BaseLib/string_mod.f90

commit 273dfa5e61c7673cc56055f7512863d830899905
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 24 06:42:32 2016 -0700

    FI: prefer default intent

Src/F_Interfaces/BaseLib/boxarray_mod.f90
Src/F_Interfaces/BaseLib/multifab_mod.f90

commit 50ad5d08702d0a9c010a8e6782401520c59818ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 23 22:42:43 2016 -0700

    FI: intent(out) => intent(inout) to avoid a strange gfortran behavior.  gfortran 5.2 calls destructor on threadprivate mfiter when OMP is used.  What's even worse is it does not initialize threadprivate mfiter properly, resulting in error in the initial destructor.

Src/F_Interfaces/BaseLib/boxarray_mod.f90
Src/F_Interfaces/BaseLib/multifab_mod.f90

commit bb0afe1c8ded916c99b11d4652ccb79ed2f4414b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 23 22:11:11 2016 -0700

    FI: parallel and omp module

Src/C_BaseLib/BoxLib.cpp
Src/F_Interfaces/BaseLib/Make.package
Src/F_Interfaces/BaseLib/baselib_mod.f90
Src/F_Interfaces/BaseLib/boxarray_fi.cpp
Src/F_Interfaces/BaseLib/boxarray_mod.f90
Src/F_Interfaces/BaseLib/main.cpp
Src/F_Interfaces/BaseLib/multifab_fi.cpp
Src/F_Interfaces/BaseLib/multifab_mod.f90
Src/F_Interfaces/BaseLib/parallel_fi.cpp
Src/F_Interfaces/BaseLib/parallel_mod.F90
Tutorials/HelloWorld_CF/fmain.f90

commit 3945a6862af29c53a417eb31d53fad0420051271
Merge: 8981ec7f2 c4b27c49d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Apr 23 17:47:54 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 2ca626ad4041101a3f315aca4491c53bcb1ad317
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 23 14:05:36 2016 -0700

    FI: more works

Src/F_Interfaces/BaseLib/boxarray_fi.cpp
Src/F_Interfaces/BaseLib/boxarray_mod.f90
Src/F_Interfaces/BaseLib/multifab_fi.cpp
Src/F_Interfaces/BaseLib/multifab_mod.f90
Tutorials/HelloWorld_CF/GNUmakefile
Tutorials/HelloWorld_CF/fmain.f90

commit 103f9004de9e8966fe04a4a8fcb0c10eea4a95a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 23 07:13:35 2016 -0700

    FI: remove fab because Fortran pointer is kind of like fab

Src/F_Interfaces/BaseLib/Make.package
Src/F_Interfaces/BaseLib/baselib_mod.f90
Src/F_Interfaces/BaseLib/fab_mod.f90
Src/F_Interfaces/BaseLib/multifab_mod.f90
Tutorials/HelloWorld_CF/fmain.f90

commit c4b27c49d5cb641a341d3971cccf247780871fea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 23 00:12:26 2016 -0700

    Start F_Interfaces/BaseLib that provides Fortran interfaces to C++ BoxLib

Src/F_Interfaces/BaseLib/Make.package
Src/F_Interfaces/BaseLib/baselib_mod.f90
Src/F_Interfaces/BaseLib/bl_space_mod.F90
Src/F_Interfaces/BaseLib/box_mod.f90
Src/F_Interfaces/BaseLib/boxarray_fi.cpp
Src/F_Interfaces/BaseLib/boxarray_mod.f90
Src/F_Interfaces/BaseLib/fab_mod.f90
Src/F_Interfaces/BaseLib/main.cpp
Src/F_Interfaces/BaseLib/multifab_fi.cpp
Src/F_Interfaces/BaseLib/multifab_mod.f90
Tutorials/HelloWorld_CF/GNUmakefile
Tutorials/HelloWorld_CF/Make.package
Tutorials/HelloWorld_CF/fmain.f90

commit eaf418958ea0464de6381743182a400c9b3e4d87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 22 14:44:33 2016 -0700

    minor changes in profiling

Src/C_AMRLib/AmrLevel.cpp

commit 69609251d09767df2487d9887192b0a114b39b2a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 22 14:40:26 2016 -0700

    make echo-x will print out the value of x

Tools/C_mk/Make.rules

commit e6a7d34a8c8846566ffe1d73cc27c934d9d8582b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 22 12:32:00 2016 -0700

    fix periodiccopy when the periodic length is very very short (say <= 4 cells)

Src/C_BaseLib/Geometry.H

commit e9438b1f1bb3c5c712f3622bd0b81738d5e1dd77
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Apr 22 10:01:37 2016 -0400

    add navigation links to the top of the test result page

Tools/RegressionTesting/testnew.py

commit d7e9242410dab629ee35c5ac403d42e4418e4e79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 22:29:38 2016 -0700

    more general periodic copy

Src/C_BaseLib/Box.H
Src/C_BaseLib/Geometry.H

commit 522f2cb6a5fef6676ab4b20e6ff77964e77ac195
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 17:57:36 2016 -0700

    BoxArray: need to update type after constructing from boxlist

Src/C_BaseLib/BoxArray.cpp

commit 7b3fe3feeae926b8f95430fa34efd3126740d88e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 21:41:31 2016 -0700

    fillpatch: clean up

Src/C_BaseLib/FillPatchUtil.cpp

commit bf029c4a4cdde16cc941ed0693646e72bbf63c36
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 21:36:45 2016 -0700

    periodic copy: bug fix

Src/C_BaseLib/Geometry.H

commit 07f3511ae33d266bae0163a9dc5b2199650a8510
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 17:57:36 2016 -0700

    BoxArray: need to update type after constructing from boxlist

Src/C_BaseLib/BoxArray.cpp

commit cfdae6f6f9f2143e1a3d29eba5a771237ed6141e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 16:45:05 2016 -0700

    new periodic copy: remove empty boxes from list

Src/C_BaseLib/Geometry.H

commit 046e8edaa04fea58aaded0f77644fada16487776
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 16:39:44 2016 -0700

    profiling two levels fillpatch

Src/C_BaseLib/FillPatchUtil.cpp

commit 1ccda614d4894ee26a26284c6f7012fa24de5a69
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 16:39:07 2016 -0700

    fix the new periodic copy

Src/C_BaseLib/Geometry.H

commit 61a3449aacb03fc5a344e9b09104bda01f066c05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 13:36:29 2016 -0700

    change default blocking factor from 2 to 8

Src/C_AMRLib/Amr.cpp

commit 9f680585366f627c2d5a6cfb1b9eee8e9295f71f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 13:33:14 2016 -0700

    new two levels fillpatch

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/Box.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FillPatchUtil.H
Src/C_BaseLib/FillPatchUtil.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Interpolater.cpp

commit 60e7f67b5276fa100909d4bd2edd16c00dd775a4
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 20 18:11:04 2016 -0700

    cleanup.

Src/C_BaseLib/ParallelDescriptor.cpp

commit e402a0a9be3fb62818222e2d8934717deb3212a0
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 20 18:08:35 2016 -0700

    redistribute particles when resizing sidecars.

Src/C_AMRLib/Amr.cpp

commit 95af6e8c4e21fa474e09a77fe3f8c6bcc11dd632
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 20 18:07:44 2016 -0700

    syncronize sequence numbers across groups.

Src/C_BaseLib/FabArray.H

commit 4a0cc8dc9c792ee7bce1b8075f63046641384919
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 20 14:17:21 2016 -0700

    move Interpolator from AMRLib to BaseLib

Src/C_AMRLib/CMakeLists.txt
Src/C_AMRLib/Make.package
Src/C_BaseLib/ARRAYLIM_1D.F
Src/C_BaseLib/ARRAYLIM_2D.F
Src/C_BaseLib/ARRAYLIM_3D.F
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/INTERP_1D.F
Src/C_BaseLib/INTERP_2D.F
Src/C_BaseLib/INTERP_3D.F
Src/C_BaseLib/INTERP_F.H
Src/C_BaseLib/Interpolater.H
Src/C_BaseLib/Interpolater.cpp
Src/C_BaseLib/Make.package

commit 0591fe7fbd15a7c99b1254ae8ba670a47d330c11
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 20 11:14:33 2016 -0700

    single level fillpatch: parallel copy ghost cells too

Src/C_BaseLib/FillPatchUtil.cpp

commit a8d4b16db8d3639eb97c5ef1a06fe0e0b36f54ca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 20 11:07:04 2016 -0700

    single level fillpatch: support the case source and destination have different BoxArrays

Src/C_BaseLib/FillPatchUtil.cpp

commit 052bd63f1b72ae199462cf1f6726866696469383
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 20 10:43:45 2016 -0700

    derive: fix box type and ghost

Src/C_AMRLib/AmrLevel.cpp

commit 52d65c9f1b9d744ecaf655fc0ecc24a59ca362e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 19 17:59:37 2016 -0700

    new fillpatch: fix single level fillpatch

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/FillPatchUtil.H
Src/C_BaseLib/FillPatchUtil.cpp
Src/C_BaseLib/PhysBCFunct.H

commit 998e2c9f2b9cba7e8fae8b52a39401d5ee321a46
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 19 15:38:29 2016 -0700

    new fillpatch: omp

Src/C_AMRLib/StateData.cpp

commit 06a4967f67129232501dcd9ce13c5f82d31f20e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 19 15:37:46 2016 -0700

    new fillpatch: linear interp in time for level 0

Src/C_BaseLib/FillPatchUtil.cpp

commit b61b04a5fb76c7bc5f6214e422b4d1f8492ce496
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 19 14:41:33 2016 -0700

    new fillpatch: add profiler and rm debug statements

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/FillPatchUtil.cpp

commit 9011c00bd7ba9463a6eb75fc7747bf1f31631ae2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 19 14:06:50 2016 -0700

    new fillpatch: use it on level 0

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/FillPatchUtil.H
Src/C_BaseLib/FillPatchUtil.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/PhysBCFunct.H

commit 3d6b2e583a99ccf7b2319f78f6402f3e6819c393
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 18 14:56:50 2016 -0700

    TinyProfiler: avg % --> max %

Src/C_BaseLib/TinyProfiler.cpp

commit 391f47018275e261ae480a6350482798deeeb7a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 18 14:53:35 2016 -0700

    TinyProfiler: avoid finalizing twice

Src/C_BaseLib/TinyProfiler.cpp

commit 5c93a309c459d55a8bba6a6132e551fb6a151989
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 18 11:12:30 2016 -0700

    remove diagnostic.

Src/C_BaseLib/FabArray.H

commit 8981ec7f28875a388cb3a003c0d4309eac9095a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Apr 16 21:35:30 2016 -0400

    make this python3-aware

Tools/F_scripts/findparams.py

commit 084fa8c6229664a79703d43e0563d77e4a574a56
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 15 18:11:59 2016 -0700

    resolve Fab_noallocate fabarrays for MoveAllFabs.

Src/C_BaseLib/FabArray.H

commit 56d6b3ff6d339e2a9a81658eab04474d3825d7a1
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 15 12:08:12 2016 -0700

    removed reduction.

Src/C_BaseLib/FabArray.H

commit 05451ff4bc15b92349ed40e0feaec526a81e1388
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 14 16:04:26 2016 -0700

    fix for nyx.

Src/C_AMRLib/Amr.cpp

commit 06ab5cf4a2f0f7d98e34e4d07e5ee710a76cffc1
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 14 15:07:06 2016 -0700

    remove temporary diagnostics.

Src/C_BaseLib/FabArray.H

commit 1fb06310c257d713dc4d6618fdff0f3bda3d638e
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 14 14:25:24 2016 -0700

    implemented BroadcastBoundaryPointList.

Src/C_AMRLib/Amr.cpp

commit 841c268b879325e7e2904c7d50f02011328694f9
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 14 14:23:46 2016 -0700

    implemented BroadcastBoundaryPointList.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit b9186ea0650625a66bde5f0ae39005f6f516f124
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 13 17:38:33 2016 -0700

    TinyProfiler: fixed pop

Src/C_BaseLib/TinyProfiler.cpp

commit 8f322ea3e84fabd4d3b325ee3df5ded2eaa14a58
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 13 17:15:57 2016 -0700

    TinyProfiler: fix OMP

Src/C_BaseLib/TinyProfiler.cpp

commit c064aa8b944848a8ba9f17b3061829141de5adf8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 13 16:45:29 2016 -0700

    TinyProfiler: warning about improperly nested timers

Src/C_BaseLib/TinyProfiler.H
Src/C_BaseLib/TinyProfiler.cpp

commit ea8557b66393ada3cc3daa35a29ba0c1e99024b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 13 14:54:55 2016 -0700

    TinyProfiler: fix inclusive time by keeping track of the depth of the call tree

Src/C_BaseLib/TinyProfiler.H
Src/C_BaseLib/TinyProfiler.cpp

commit d5f8f40cd1e32d8f21b4e647f808a97d54b4cb37
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 13 13:59:18 2016 -0700

    TinyProfiler: a tiny profiler that only supports a tiny fraction of what BLProfiler can offer.  It does not need postprocessing.  It shows inclusive and exclusive times.

Src/C_BaseLib/BLProfiler.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/TinyProfiler.H
Src/C_BaseLib/TinyProfiler.cpp
Tools/C_mk/Make.defs

commit e24b668e5a098a0186c920868b35a9dfa964edd4
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 13 12:57:25 2016 -0700

    remove diagnostic.

Src/C_BaseLib/Geometry.cpp

commit c7222ed50bf32ccc9c26cdceb828f43393952ec3
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Apr 13 12:12:32 2016 -0700

    C_scripts: squash warning about "hdf5" module

Tools/C_scripts/moddep.pl

commit dc921e1adb071cc85323e6c43c01eb8193128a96
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Apr 13 10:37:00 2016 -0700

    C_scripts: squash warning about "iso_fortran_env" module

Tools/C_scripts/moddep.pl

commit a1c258184cacc4e850cbcb7f2864d88aafb4dc90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 12 14:37:52 2016 -0700

    update comments

Src/C_AMRLib/Interpolater.cpp

commit 18d2631868bbbe5c22a123fa8fc02e9037236d2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 17:56:45 2016 -0700

    remove unused variable

Src/C_AMRLib/AmrLevel.cpp

commit c3afed492981aa86f0f2dd7c929c0d33e36d4863
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 17:55:23 2016 -0700

    FillBoundary: timer

Src/C_BaseLib/FabArray.H

commit b18d982e59b2abe3d8deac5471858c47024d40c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 17:53:15 2016 -0700

    add fixediter option to MultiGrid_C tutorial

Tutorials/MultiGrid_C/main.cpp

commit d7b3bb0aa995717abe3ee0974418a2ca64305263
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 17:46:50 2016 -0700

    comment out the mpi-3 fix recommended by NERSC

Tools/C_mk/Make.Linux

commit aef7569d0fe4006a4abd90cef3358c4b17dd66df
Merge: ec0c5ec3a ec5fae567
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 16:29:10 2016 -0700

    Merge branch 'development' into pgas
    
    Conflicts:
            Tools/C_mk/Make.defs

commit 68d33340c25dd12815dee7f2f618679d68befe3f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 15:42:12 2016 -0700

    release-notes-16.04

ReleaseNotes/release-notes-16.04

commit 519ff1b68b76095057645ee5650d2063ddf4a901
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 11 15:33:26 2016 -0700

    fixes for nyx.

Src/C_AMRLib/Amr.cpp

commit ec5fae567fe6417c9d5d307ac11528c978ed267c
Merge: 28a724a62 9bc778cab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 14:38:33 2016 -0700

    Merge branch 'master' into development

commit 52c150536fa71e6af45475e3b798aee388481da9
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 8 13:49:50 2016 -0700

    clean up proximity maps.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 1d104764b522c6d9b019029ab43f69b26eae7dae
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 6 16:59:27 2016 -0700

    additions for nyx dynamic sidecars.

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/F_BaseLib/parallel.f90

commit fc144bb833aeaccb53e893d6ea294d3201b725e0
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 6 16:45:39 2016 -0700

    stubs for dynamic sidecars support.

Src/F_BaseLib/parallel_stubs.f90

commit cb9b44744fe33e9b2e5c18a6d40dfcdbed476722
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 6 16:06:57 2016 -0700

    fix for non-mpi.

Src/C_BaseLib/BoxArray.cpp

commit d5b3b21ca5aeea3b204abba421ba82a259891657
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 6 16:04:27 2016 -0700

    fix for non-mpi.

Src/C_BaseLib/FabArray.H

commit 56a351116326662af0ecea8c1ffa75b9e92eb27b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 6 14:38:54 2016 -0700

    remove old SidecarProcess.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 28a724a62aadf9ef2221fb852cc37977a230da34
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 6 10:56:37 2016 -0700

    utility from Aleks that writes the contents of a 2d plotfile into a text file, one line per data point

Tools/Postprocessing/F_Src/GNUmakefile
Tools/Postprocessing/F_Src/fwritecontents2d.f90

commit 43c0142c1244b00ba5296234c910a21560578439
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 6 10:49:18 2016 -0700

    works for all ref ratios now as long as the cells you are averaging down are on the same grid

Tools/Postprocessing/F_Src/fcoarsen.f90

commit f517721af8dfbafa24fca37e8355a26b57e759bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 6 09:41:24 2016 -0700

    fine_flx now starts at level 1, not level 2.

Tutorials/HeatEquation_EX5_F/advance.f90

commit a0a51ec257e84f36d4d943037ce825f5e616a8a7
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 14:45:51 2016 -0700

    get dx for plotfile write correct

Tools/Postprocessing/F_Src/fcoarsen.f90

commit cbc4ff25c76b3acea8e2040371cc35d57082b126
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 14:08:27 2016 -0700

    updates from Aleks - add coarsening factor input

Tools/Postprocessing/F_Src/fcoarsen.f90

commit 881dddfdb189cf5cca8fb5aef9d81e157b61d63b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 13:22:24 2016 -0700

    turn back on 3d coarsening of plotfiles

Tools/Postprocessing/F_Src/fcoarsen.f90

commit 4dd7a312cb41580d9d93ab4b9f9d5c98cea0ac4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 5 13:19:18 2016 -0700

    add fcompiler option to f2py

Tools/Py_util/GNUmakefile

commit 551c0b366bbf61872073b71d502bea78c3db0597
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 12:58:33 2016 -0700

    revert accidental commit

Tools/C_util/Convergence/GNUmakefile

commit c8ba7ddeb07f3712bc0558912ca60e7680964a55
Merge: 668ab17e8 31532a042
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 12:57:14 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 668ab17e89ee742fdd3aa6e2e87721cb15fa70ed
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 12:57:00 2016 -0700

    forgot to add file

Tools/Postprocessing/F_Src/fcoarsen.f90

commit 31532a0421791226551b6690d0528ff2d83fb221
Merge: 30add196f dd726272c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Apr 5 12:39:25 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 30add196f04a23dd90cd48c8c4a55ae27ebb475d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Apr 5 12:38:42 2016 -0700

    The flux we pass into the F90 interface (in ml_solve.f90)
    for cell-centered solves now starts at the base level of the
    solve, not one level higher.

Src/LinearSolvers/F_MG/ml_solve.f90

commit dd726272c245081ac7b22bcf452c9d79f498aa88
Merge: 37304cb0a ead716f18
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 12:23:21 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 37304cb0a8d0b228e1e5faf856ca21eb24e83c83
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 12:22:44 2016 -0700

    utility that reads in a single level plotfile and writes out a coarsened plotfile (rr=2)

Tools/C_util/Convergence/GNUmakefile
Tools/Postprocessing/F_Src/GNUmakefile

commit 339194b1243c7fcc293182aa1d8a658f0de29fbe
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 4 17:21:51 2016 -0700

    check return of getcwd.

Src/C_BaseLib/BoxLib.cpp

commit ead716f182f1ef42f2433a7f48a05302a331dce0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Apr 4 16:35:49 2016 -0700

    Add the option in the F90 interfaces to the cell-centered solver to have the base level
    have Dirichletboundary conditions at a distance away from the boundary, not just at the
    boundary.  You make this happen by passing in base_level > 1 and crse_ratio = the ratio
    of dx between the coarsest level of the solve to the coarser AMR level outside the solve.

Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/ml_solve.f90

commit 16bb6abd221a9a3f32d09677579b09e62735aa89
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 4 12:05:19 2016 -0700

    fix for particles.

Src/C_AMRLib/AmrLevel.cpp

commit 007b26e2b9fd2564d16ea82827db1f084b654bfc
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Apr 1 23:00:33 2016 -0700

    Use gnu99 instead of c99 if using GNU compilers

Tools/C_mk/Make.defs

commit 4bda470332551ec0d5e8c463ce4f25373e9b4720
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Apr 1 16:37:58 2016 -0700

    Add USERSuffix to optionsSuffix to allow generalized suffix creation in app build.  Should probably move app-specific suffix defs out of BoxLib....someday

Tools/C_mk/Make.defs

commit 0086b0e30847905818f0d2cca4f00b015e5970f4
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Fri Apr 1 18:18:41 2016 -0400

    Get PGI compilation working for OpenACC on titan

Tools/F_mk/comps/Linux_pgi.mak

commit 5cafbde658c219bf5c2767d2d9dd23cf2a04a04e
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 31 17:35:27 2016 -0700

    fix for copyInter sidecar tutorial.

Src/C_BaseLib/FabArray.H

commit a7f81840d8786ad1f422a2db4b8586208bd53cdb
Merge: 338053321 25bc646d3
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 31 17:06:29 2016 -0700

    merge with master.

commit cbb8426e43b6d6b60902f762ffad28a61cc686f0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 31 15:29:15 2016 -0700

    Fix another typo in the latest changes to create_umac_grown.

Src/F_BaseLib/create_umac_grown.f90

commit 130cd0e32df5c30b99bd0b118254feda93c6176e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 31 14:45:01 2016 -0700

    Fix some oops from previous commit.

Src/F_BaseLib/create_umac_grown.f90

commit ef453bcb0ffd4653845df30423d6120d5245b31a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 31 14:07:19 2016 -0700

    Allow for factor 4 as well as factor 2 interpolation in create_umac_grown.

Src/F_BaseLib/create_umac_grown.f90

commit 9bc778cab7654e83e0e22267aca476f9f10f3d86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 30 16:02:34 2016 -0700

    try to fix CMake for F_BaseLib; not tested because I don't even know how to use CMake

Src/F_BaseLib/CMakeLists.txt

commit 0b5ade1a306ea5caaaf64431bb6afa205a6f4e7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 30 16:02:34 2016 -0700

    try to fix CMake for F_BaseLib; not tested because I don't even know how to use CMake

Src/F_BaseLib/CMakeLists.txt

commit 5da4cbe59dfd4a2cc7842ba9e1d7aa815ba99b1c
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Mar 30 16:02:19 2016 -0400

    Use Cray compiler wrappers, even for PGI, on Titan

Tools/F_mk/comps/Linux_pgi.mak

commit 4f1128d1bbd13066824801f1e51f401ede951d98
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Mar 30 15:32:40 2016 -0400

    For now, GPUs can't handle PGI's -gopt.  Debug symbols break it with
    internal compiler errors.

Tools/F_mk/comps/Linux_pgi.mak

commit fa9a5e9a5c967aea2c5d57a2b589dbbc98a0e58d
Merge: f1bae6c06 be70088b6
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Mar 30 15:31:00 2016 -0400

    Merge branch 'development' into openacc

commit f1bae6c065f2a21159e1f56933fd1a7d4b43c522
Merge: a4f3315c8 0d55d1400
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Mar 30 15:30:04 2016 -0400

    Merge branch 'openacc' of ssh://github.com/BoxLib-Codes/BoxLib into openacc

commit a4f3315c842a5e74c2c2d722f2fc928438fbeb61
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Mar 30 15:29:52 2016 -0400

    fix indent

Tools/F_mk/comps/Linux_cray.mak

commit ec0c5ec3a449cc4123c9f8d80ed5cb1aeb1f470a
Merge: 2f685a2ea 595b9e272
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 30 09:12:45 2016 -0700

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit 595b9e272f0dc9b2464bdb9e8d3063634227f155
Merge: dd7694793 be70088b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 29 12:56:00 2016 -0700

    Merge branch 'development' into pgas

commit dd7694793f6ffddcc4f813ddd7db3748c98ef030
Merge: 2c3460136 25bc646d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 29 12:55:29 2016 -0700

    Merge branch 'development' into pgas

commit be70088b68aaf725d5b85303df147cfa260250cd
Author: Regression Tester <ccse.lbl@gmail.com>
Date:   Tue Mar 29 11:02:48 2016 -0700

    regression test: option to use valgrind, --with_valgrind

Tools/RegressionTesting/testnew.py

commit 636e9d7e759cc881d9987ab9d107cf567295d90b
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Tue Mar 29 10:56:24 2016 -0700

    battra F_mk

Tools/F_mk/GMakeMPI.mak

commit a8747a8f403dc949144ca05805eb356cf226acc7
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Tue Mar 29 10:30:22 2016 -0700

    battra: use rpath so that we do not need to bother with LD_LIBRARY_PATH

Tools/C_mk/Make.mpi

commit 1d6d554cb01b552eceb2a2b8e39f413dccd93bfb
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Tue Mar 29 10:25:21 2016 -0700

    battra: option to use valgrind friendly build of mpich at /usr/local

Tools/C_mk/Make.mpi

commit 9d0057bc1a6b7981abe334c9e00daea649f2b24f
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Mar 28 15:38:47 2016 -0700

    Remove ifdefd code to set space-varying bcs.  Was a remnant of debugging, and was incorrect anyway.

Tutorials/MultiGrid_C/main.cpp

commit 5b7c6fddce7586546624ccb88cdaaa843f10ccb2
Merge: dff697efd f22e9c951
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon Mar 28 14:06:18 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit dff697efd60f69cc06fa544a2a47915638d8668e
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon Mar 28 14:06:12 2016 -0400

    Add 5/6 to bl_constants

Src/F_BaseLib/bl_constants.f90

commit f22e9c95174e974901abfff583a926e382803a58
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 25 17:21:34 2016 -0700

    bndry_reg: fix a bug when the fine level has a single box and covers the entire non-periodic domain

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90

commit 2f685a2ead420c8816aeb13e8a65b5a956ef9b33
Merge: 2c3460136 25bc646d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 25 14:48:08 2016 -0700

    Merge branch 'development' into pgas

commit 338053321ece9bde683c3816648177227c43c0cb
Merge: 7e506d608 00d985aaf
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 25 12:46:05 2016 -0700

    Merge branch 'master' into dynamicsidecars

commit 7e506d60832131211c218853f3a5ba1f6f7d6535
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 25 12:40:27 2016 -0700

    premerge cleanup.

Src/C_BaseLib/FabArray.cpp

commit 6a84beefa0c1c370c4ed0ff1b3cde382c84f5ea7
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 25 12:38:23 2016 -0700

    added more profiling.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 905ddefee29e911fa48afee05d9f4840039a6e9b
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 25 12:37:53 2016 -0700

    premerge cleanup.

Src/C_AMRLib/Amr.cpp

commit 2c3460136fe3e57624ca32164d0ccc62ed80e40d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 24 15:59:15 2016 -0700

    PGAS_SMC: should use NTeams()

MiniApps/PGAS_SMC/SMC_init.cpp

commit 0b900065c59572d876f19746c5d18ceb0c405261
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 24 15:52:24 2016 -0700

    PGAS_SMC: change defaults

MiniApps/PGAS_SMC/SMC.cpp

commit b24fbf7f89765f095c6bd42b6cd9578ad418314d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 24 15:47:01 2016 -0700

    PGAS_SMC: chop box into small pieces so that each process has at least one box

MiniApps/PGAS_SMC/SMC_init.cpp

commit d91396251a95daa9639414721eb9b509e7bc467c
Author: vince <vebeckner@lbl.gov>
Date:   Tue Mar 22 11:56:38 2016 -0700

    add periodic to output.

Src/C_BaseLib/Geometry.cpp

commit 25bc646d3b3221c73eed13b8984dc08a206a9927
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Mar 22 07:48:26 2016 -0400

    fix typo

Tools/RegressionTesting/testnew.py

commit feb07da5ecfdf7bc5f70e0791a73ca33f7542544
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Mar 21 12:34:13 2016 -0700

    C_mk, F_mk: add optimization reports for Cray compilers

Tools/C_mk/Make.Linux
Tools/F_mk/comps/Linux_cray.mak

commit 5043fc17d745196ed3c0cc5ef52a524de3b67e3d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 21 13:14:35 2016 -0700

    update make for baragon

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit a2f5cd338c071f75af165c386567683067f928dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 21 13:14:08 2016 -0700

    free MPI_group

Src/C_BaseLib/ParallelDescriptor.cpp

commit b893afea3a9e5bdc24f03849f63bce638c76c6ed
Merge: 2b0e17567 ea548ddb7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Mar 21 10:54:13 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 2b0e175678d2004d5425448f9ddb3e6f5a8ef52d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Mar 21 10:53:58 2016 -0400

    some slack cleaning

Tools/RegressionTesting/testnew.py

commit 4763a9a66f59ff423e9f49ee7023c51e749a313b
Merge: 637267ee4 ea548ddb7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 18 14:23:51 2016 -0700

    Merge branch 'development' into pgas

commit 637267ee4d245fa318923d6cacf180e45022df0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 18 14:22:11 2016 -0700

    add upcxx::barrier() before MPI reduce

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Tests/FillBoundaryComparison/main.cpp
Tutorials/PGAS_HEAT/main.cpp

commit e5d2d979e387b530ff79acfc54c87ef13277b415
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 18 13:10:51 2016 -0700

    code cleanup.

Src/C_AMRLib/Particles.H

commit ea548ddb72c25761a7c283919d66ba2aafa84f1e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 18 12:26:43 2016 -0700

    add 'class' because extended friend syntax is a C++11 feature

Src/C_BaseLib/Box.H

commit 8313e58ae4af5f2e501057f3bb372428c4807eeb
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 17 16:52:52 2016 -0700

    added profiling, cleanup.

Src/C_AMRLib/Particles.H

commit 1e510bf82081617f54c0b703c7885bf486a1de19
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Thu Mar 17 16:51:57 2016 -0700

    Bug fix restricted_build

Src/F_BaseLib/ml_boxarray.f90
Src/F_BaseLib/ml_layout.f90

commit 8d4d04df36347cd299d172dd8ea0550bac0ff567
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Thu Mar 17 16:50:21 2016 -0700

    Add varan machine

Tools/F_mk/GMakeMPI.mak

commit ead9a714b43cf8569c0af3a9c560f25ad0a50217
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 17 16:48:09 2016 -0700

    added profiling, cleanup.

Src/C_AMRLib/Particles.H

commit fa4af7f32615b41bdfe91ed7bca18bc087f4ceb4
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 17 16:47:17 2016 -0700

    added profiling, cleanup.

Src/C_AMRLib/Particles.H

commit 909e7e8a9a7eea1ce98502468870eb64d1eee8e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 17 16:24:55 2016 -0700

    new functions for doing shallow copies of ml_layout and ml_boxarray

Src/F_BaseLib/ml_boxarray.f90
Src/F_BaseLib/ml_layout.f90

commit 7975af61d884191cb29d390b145a3c11b24c31a5
Merge: b51578985 03cd46912
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 17 14:19:10 2016 -0700

    Merge branch 'development' into pgas
    
    Conflicts:
            Src/C_BaseLib/Make.package
            Tools/C_mk/Make.defs

commit 789f30b3c8f025b47346ac03b3c9b6e98fcb78bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 17 12:36:25 2016 -0700

    fix a memory leak: must call MPI_Wait to free resources even when we know for sure the messages have been sucessfully sent.

Src/C_BaseLib/FabArray.H

commit 03cd46912bc239a3e108cb2e69d3cf06ccc6ee0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 17 12:36:25 2016 -0700

    fix a memory leak: must call MPI_Wait to free resources even when we know for sure the messages have been sucessfully sent.

Src/C_BaseLib/FabArray.H

commit 18a336cb34231b6313d24b2de149a5c2e17f3ecc
Merge: 2e0fe7dff 641f7a30c
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Mar 17 10:22:44 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 641f7a30caf9711b8f41673a590f48a87c5e9d84
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 17 08:41:01 2016 -0700

    box_f: avoid using Huge(1) because it can cause integer overflow

Src/F_BaseLib/box_f.f90

commit 6e7b4f5056fe101b6b651773649556ef8ccc37b4
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Mar 16 21:34:14 2016 -0700

    Add def for BL_PROFILE_VAR_NS when PROFILE=FALSE

Src/C_BaseLib/BLProfiler.H

commit 2e0fe7dffb4a1a94b068c8a482fca297340065b2
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Mar 16 21:34:14 2016 -0700

    Add def for BL_PROFILE_VAR_NS when PROFILE=FALSE

Src/C_BaseLib/BLProfiler.H

commit 1070b4a7ef4bb74fd8b923d7a83fce5d9670315a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 16 13:08:17 2016 -0700

    add section for start/stop.

Docs/Readme.profiling

commit 627c0da3deab3a6f527b774b3c8060f9981a2192
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 16 12:23:36 2016 -0700

    fort profiling fixes.

Src/LinearSolvers/F_MG/mg.f90

commit f346af596126467f7d048aad673199c7c5f332ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 16 10:37:26 2016 -0700

    make: rm *.mod that could be left over because of wrong PrgEnv

Tools/C_mk/Make.rules

commit 5fca605fafa7e45ca2ffe922c7e64134d1109e2f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 16 10:35:15 2016 -0700

    MemProfiler: add VmSize

Src/C_BaseLib/MemProfiler.cpp

commit b515789854f39d6d702a9e888fb11f6f76d47602
Author: yzheng <yzheng@lbl.gov>
Date:   Wed Mar 16 09:24:42 2016 -0700

    Add UPC++ version of CollectData, which needs the latest version of UPC++

Src/C_BaseLib/BLPgas.H
Src/C_BaseLib/BLPgas.cpp
Src/C_BaseLib/FabArray.H

commit 876bdb37ab934e094368e3094788de0522ceb7e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 22:02:50 2016 -0700

    reduce max # of copyassoc to 25

Src/F_BaseLib/layout.f90

commit 2b90e6b42092fff4bb18994afa59e13e3d82cd05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 22:01:21 2016 -0700

    MemProfiler: fix an index

Src/C_BaseLib/MemProfiler.cpp

commit 414660c9d5f755f88f0bac0acfb8235b4b55bfba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 21:13:00 2016 -0700

    decrement copyassoc_cnt

Src/F_BaseLib/layout.f90

commit 389c26451c837462b9cdb83a89d030eefbd5815e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 20:40:15 2016 -0700

    cleanup

Src/F_BaseLib/memprof.f90

commit 25b2da7dd46109b793350d497e4b9cf523129fa7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 18:13:12 2016 -0700

    MemProfiler: add data form /proc/pid/status

Src/C_BaseLib/MemProfiler.cpp

commit 2ed380df68b69804e18d5a08dc008f9874f2aee3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 17:07:22 2016 -0700

    add a header that Intel complains about missing

Src/C_BaseLib/MemProfiler.cpp

commit eeec9d0cae54887e75553405da6408182daba48c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 16:31:34 2016 -0700

    flush fortran copyassoc after regrid

Src/C_AMRLib/Amr.cpp
Src/LinearSolvers/F_MG/FParallelMG.mak

commit 9d2cc00e51a13ef005b098a4231e64ddb8ddd1dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 16:18:39 2016 -0700

    add the new counters to MemProfiler

Src/F_BaseLib/MemProfiler_f.cpp
Src/F_BaseLib/memprof.f90

commit 63c9931a3432da2a116841991db3b737cdf647a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 16:05:47 2016 -0700

    layout: add more memory counters

Src/F_BaseLib/layout.f90

commit f67526abeab5fb19329e304a592142c75cc5b669
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 15:18:39 2016 -0700

    better estimates of memory cost of fortran data structures

Src/F_BaseLib/box_f.f90
Src/F_BaseLib/layout.f90

commit 76557b5e7f1a838fb934b13673a358dd0d410938
Author: vince <vebeckner@lbl.gov>
Date:   Tue Mar 15 14:26:00 2016 -0700

    use max_level for size.

Src/C_AMRLib/Amr.cpp

commit a5c4b7079cb3d7f13c7dc78c612cf31008db06da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 13:28:44 2016 -0700

    remove gcc-2

Tools/C_mk/Make.defs

commit 807d9343ac842dce702b79f13f2db3691f92e6f3
Author: vince <vebeckner@lbl.gov>
Date:   Tue Mar 15 12:25:05 2016 -0700

    some cleanup.

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit 3f3997aa9bc0f7381200ad4e3e275fa4595b20e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 12:23:44 2016 -0700

    fix an uninitialized value that affects the memory usage counter

Src/F_BaseLib/layout.f90

commit 9ffc3909d615a4a6c9fc57d1666caf4b8359a4a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 12:17:06 2016 -0700

    cleanup

Src/F_BaseLib/layout.f90

commit b0399d2c273cfcfa3ff96c0ad336663f24d0dc7d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 10:13:35 2016 -0700

    Fortran copyassoc: change the max # allowed

Src/F_BaseLib/layout.f90

commit 17c99bf3d188fb85f8f86072873251d00dc89a37
Author: vince <vebeckner@lbl.gov>
Date:   Mon Mar 14 18:36:56 2016 -0700

    added test to copy from sidecars to comp.

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit 194b4ae0ec778cc178f9bb3e109379282dfab5ac
Author: vince <vebeckner@lbl.gov>
Date:   Mon Mar 14 18:34:03 2016 -0700

    allow copy from sidecars to comp.

Src/C_BaseLib/FabArray.H

commit ddee2168f7c21bdfebe6b1df1a1618305642137d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 18:32:18 2016 -0700

    MemProfiler: minor mistake

Src/F_BaseLib/layout.f90

commit 6c6fc2018fcb0c949c4f0433d5e2cf66bb04206c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 18:26:01 2016 -0700

    MemProfiler: add fortran copyassoc and boxassoc

Src/F_BaseLib/MemProfiler_f.cpp
Src/F_BaseLib/layout.f90
Src/F_BaseLib/memprof.f90

commit f5bef54bb3826ae2d588846a41924ec6e74b0977
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 17:50:00 2016 -0700

    MemProfiler: skip print if high water mark is zero

Src/C_BaseLib/MemProfiler.cpp

commit e6e236ac5d1ae8b7f6b4806ce9631995641ee792
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 17:47:03 2016 -0700

    MemProfiler: fortran boxarray

Src/F_BaseLib/MemProfiler_f.cpp
Src/F_BaseLib/boxarray_f.f90
Src/F_BaseLib/memprof.f90

commit b8d3576528a12b9dd1f3572b69102fb61cb7a490
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 17:29:15 2016 -0700

    MemProfiler: add fortran fab

Src/C_BaseLib/BoxLib.cpp
Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/MemProfiler_f.H
Src/F_BaseLib/MemProfiler_f.cpp
Src/F_BaseLib/memprof.f90
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit f917a50ea3fac3d1de2036901567fd7197c42378
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 17:27:38 2016 -0700

    MemProfiler: sort the output

Src/C_BaseLib/MemProfiler.cpp

commit a8d4f898862cc159f7062d4ef420ff64bd7670d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 15:59:23 2016 -0700

    MemProfile: add cached memory

Src/C_BaseLib/MemProfiler.cpp

commit 094ecdfb7422a1ff559ab4d6503c9e72cb7ea6c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 15:25:00 2016 -0700

    MemProfiler: use sysinfo instead of sysconf so that we can get memory used by buffers; we still don't have know about cached memory unless we are going to read /proc/meminfo directly.

Src/C_BaseLib/MemProfiler.cpp

commit 5d9f0c60fc31295ddb255db44ec6987333b6f218
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 11:24:57 2016 -0700

    BoxArray: do nothing if size does not change in maxSize(); cleanup

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit a2a213589f87d39fb0eb834a8bf210f1e578ffde
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 10:36:19 2016 -0700

    fix a new bug in BoxArray I introduced yesterday

Src/C_BaseLib/BoxArray.cpp

commit 6ff4e17447fc6f4cc09988bd866c25bdd210a959
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Mar 14 09:44:31 2016 -0700

    C_mk: remove explicit "-lmpich" flag from link line on Edison/Cori
    
    The Cray wrappers resolve MPICH for us automatically, so we don't need to link
    this by hand. Also, Chris Daley discovered that using this link flag overwrites
    Darshan's MPI_Init() call with the native MPICH MPI_Init(), which means Darshan
    can't collect I/O profiling data for any BoxLib code.

Tools/C_mk/Make.mpi

commit f98fac1014cc49c7c886e78ea5641bd00480a0a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 13 20:55:18 2016 -0700

    MemProfiler: fix BoxArray::removeOverlap

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit ae8a3e6a872f46a09fe2a458871183d1c96b21fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 13 16:58:51 2016 -0700

    MemProfiler: optimization

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit 2cf3638280bf236b6b94e5f510a99c550bbc5cdc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 13 16:13:49 2016 -0700

    MemProfiler: save the log in a file

Src/C_BaseLib/MemProfiler.H
Src/C_BaseLib/MemProfiler.cpp

commit 34c48606a1743e6ceeb7ace6e417f102434cb9ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 13 12:58:45 2016 -0700

    MemProfiler: pretty

Src/C_BaseLib/MemProfiler.cpp

commit 46b23adcf0dee9d594181660d43fb726ae1d4036
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 13 09:08:21 2016 -0700

    BoxArray MemProfiler: split box and cache data

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit bfae3d52bffee45a8480c2c63d1ea781565b01fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 13 09:03:21 2016 -0700

    MemProfiler: Copy and FillBoundary

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit e3821a8904d8b12be96c3a92f4e30b610db9f84f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 12 22:52:58 2016 -0800

    MemProfile: TileArrayCache

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 530bbce8f456e186bb3826679950a40691270e46
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 12 21:37:13 2016 -0800

    MemProfiler: Geometry

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit eb14d2c6315ad7ab1487d7b0a39397e4f9608323
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 12 18:47:28 2016 -0800

    Geometry & FabArray: use the new memory counting function.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit a026b8233a830ae1b71f9f19f736ad6070035bc4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 12 17:56:48 2016 -0800

    move memory counting functions into Utility.H

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/MemProfiler.H
Src/C_BaseLib/MemProfiler.cpp
Src/C_BaseLib/Utility.H

commit 68ce984235fe1a56cccab82bac2402f80b357d44
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 12 17:21:58 2016 -0800

    MemProfiler: replace templates with specialized codes

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/MemProfiler.H
Src/C_BaseLib/MemProfiler.cpp

commit 273b709ad561ecc2bd8475dc0c7f50258d2cf866
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 12 16:24:04 2016 -0800

    MemProfiler: BoxArray and bytesOf for map

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/MemProfiler.H
Src/C_BaseLib/MemProfiler.cpp

commit eb7dae20524a0dd7fc885bbc0463afa2aed90edd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 12 11:09:28 2016 -0800

    MemProfiler: minor

Src/C_BaseLib/MemProfiler.cpp

commit fc1e667925759eafc22ebdef61093c9e10eb95b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 12 11:08:52 2016 -0800

    MemProfiler: bytesOf function for std::vector and Array

Src/C_BaseLib/MemProfiler.H

commit 344f80674e52f06a05cc8a7018993982d5a00ed5
Author: yzheng <yzheng@lbl.gov>
Date:   Fri Mar 11 22:49:07 2016 -0800

    Use map instead of unordered_map in BLPgas because unordered_map would cause some linking errors when using the Intel compilers with a recent version of GCC (4.8 or newer) on Cray XC systems

Src/C_BaseLib/BLPgas.cpp

commit 915b89752d05a173e7ea5212a8747798e753bb45
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 11 21:28:45 2016 -0800

    MemProfiler: cleanup

Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/MemProfiler.H
Src/C_BaseLib/MemProfiler.cpp

commit 8ff5f6aee2e30ca7fcadb9fd0ec7ff72a9b48d76
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 11 17:15:31 2016 -0800

    MemProfiler: when adding, make sure the name does not exist

Src/C_BaseLib/MemProfiler.H
Src/C_BaseLib/MemProfiler.cpp

commit d4de32dc34099df1cfb219a88f28ec4e1ae87691
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 11 17:02:24 2016 -0800

    Memory Profiler: first pass

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/MemPool.cpp
Src/C_BaseLib/MemProfiler.H
Src/C_BaseLib/MemProfiler.cpp
Tools/C_mk/Make.defs

commit fe6a8c807958b52a1a63c90c838401d1fc909c7a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Mar 11 19:44:40 2016 -0500

    latest inputs file -- this has the slack integration

Tools/RegressionTesting/Maestro-tests.ini

commit 292f634879e7be26825e17db7900a33a1490fac6
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 11 15:55:05 2016 -0800

    changed inputs.

Tutorials/Sidecar_EX1/inputs_sc

commit 81fabc8235ae7b1b6ec0cfcda6daf35054144d95
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 11 15:54:16 2016 -0800

    added several tests for shifted and grown multifab copies.

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit 5b306ab00d0e6617b581cbec1db0c2cb762d316d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Mar 11 18:00:00 2016 -0500

    add slack integration using webhooks.  Now, if you define the
    slack parameters it will post to the slack channel when the suite
    starts and post again when the suite ends, reporting the number
    of failures

Tools/RegressionTesting/testnew.py

commit 714364b805528a8c932c616cbfd14e0b20b1b3c1
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 11 14:34:56 2016 -0800

    reenable assertions, add more error checking.

Src/C_BaseLib/FabArray.H

commit 5922501e13efac28c3ca13f11612956f4cb61c7e
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 11 13:57:42 2016 -0800

    remove unused variables.

Src/C_BaseLib/Geometry.cpp

commit 47509c6e05ca3361b167fddc15d88e18b8b5658d
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 11 13:57:25 2016 -0800

    FabArray::copyInter seems to work.  needs more testing.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit e727a5ba523aa74d086e12cb7c1e1ee0e13d9be1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Mar 10 22:04:18 2016 -0500

    fix formatting when variables are not present

Tools/RegressionTesting/testnew.py

commit f0e9c409c5314f9f756a3265629f0a941fcbead4
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 10 18:37:33 2016 -0800

    testing the new FabArray::copyInter.

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit 1397954f21caf1808c9f7737b1b003d5c757dddd
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 10 18:33:46 2016 -0800

    copyInter function, TheCPC that takes IndexMaps, not yet complete.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 935772a0b37fb14169c8c7bb8d3a6c1b10ff9dfb
Merge: 850cacf9a 72cc2fea7
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 10 18:13:09 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 850cacf9a778644042a8ca60d3700bf89f58560d
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 10 18:12:32 2016 -0800

    added a routine to do a nodal sum and nodal volume, weighting faces, edges, and corners appropriately

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/nodal_sum.f90

commit d6a13d8242b048e3e5353f893cc207de73b2b859
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 10 14:05:46 2016 -0800

    buildTileArray: fix reordering

Src/C_BaseLib/FabArray.cpp

commit cb2ce1fd359e70660d779a54cffe82e4e215c9c3
Merge: 26051f44c 72cc2fea7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 10 10:58:32 2016 -0800

    Merge branch 'development' into pgas

commit 72cc2fea7ecf1f164e478596069d664d04c1bd2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 10 10:58:12 2016 -0800

    FillBoundary: remove empty messages in case of cross=true

Src/C_BaseLib/FabArray.cpp

commit e3828378d5c1523f8665c71740d135693eb5ea0f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 9 18:30:20 2016 -0800

    sync translated dist maps to all procs.

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit 26051f44c099fd8812c533b2c9bc17ad6dd9bf7f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 9 16:25:36 2016 -0800

    have to make some changes due to how Intel compiler handles C++11

Src/C_BaseLib/FabArray.cpp

commit c1b0ca0c93c51dcabd62caca37334492891886cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 9 16:15:04 2016 -0800

    add headers

Src/C_BaseLib/FabArray.cpp

commit 788825914b4791e3cf02fc8b48abae39769e96b4
Merge: 1054284a7 8de6aaaaa
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 9 16:06:31 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 1054284a7ade16e06a10d56d6a39bed9fa84d8ea
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 9 16:06:03 2016 -0800

    Need to define nlevs based on the mgt, not on the array of multifabs.

Src/LinearSolvers/F_MG/nodal_enforce_dirichlet_rhs.f90

commit 41f72b95ce18fa95350400e05c230c7c1706ede1
Merge: 887a14968 a5ba1ff38
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 9 15:44:49 2016 -0800

    resolve confilicts.

commit 6abf9813b37b594ec78ffd10db9847fa201d0b1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 9 15:43:37 2016 -0800

    make sure that each team worker is more likely to work on its own fabs

Src/C_BaseLib/FabArray.cpp

commit 887a149681d38852f535d20c021667e4d896d19f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 9 15:17:13 2016 -0800

    copy setup test.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Particles.H
Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/Utility.H
Tools/C_mk/Make.defs
Tutorials/Sidecar_EX1/DestMFTest.cpp
Tutorials/Sidecar_EX1/GNUmakefile
Tutorials/Sidecar_EX1/GridMoveTest.cpp
Tutorials/Sidecar_EX1/inputs_sc

commit a5ba1ff38b825123bd0313b0c04520d1fa6b97c4
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Mar 9 15:07:57 2016 -0800

    DestMFTest: add extra code showing how to translate DistributionMappings between groups

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit 6ea0b1d2da5f1f7c8520b5698b082f092ee4c0fe
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Mar 9 15:05:46 2016 -0800

    DistributionMapping: add static function TranslateProcMap()
    
    This function translates the processor map from a DistributionMapping on
    one MPI group into a map on another group. It currently does not set the
    sentinel rank, so this must be done manually after the call to this
    function.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit cd00a8d2c93c97eb107483bcd0514fd41880c1a5
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Mar 9 15:05:07 2016 -0800

    DestMFTest: add buzzard wings around cases to prevent variable cross-initialization

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit af438f0f526865b74bd244f5b43fb893bd8f997a
Merge: 6c4549897 8de6aaaaa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 9 14:05:38 2016 -0800

    Merge branch 'development' into pgas

commit 8de6aaaaac2c8775d0b5224b0cd2b88c2d80da01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 9 14:02:42 2016 -0800

    Renaming.  C++ standard says, "Each name that contains a double
    underscore (__) or begins with an underscore followed by an uppercase
    letter (2.11) is reserved to the implementation for any use."

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/FabConv.cpp
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit 6ddc23702d4b5642c7eeb1645afe6f8e1eef3e9b
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Mar 9 13:11:13 2016 -0800

    BoxArray: use new BoxArray serialization functions to reduce # of Bcasts()

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Tutorials/Sidecar_EX1/DestMFTest.cpp

commit be2e713ea19450336b1e71d1e99c37642b340f56
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Mar 9 12:59:00 2016 -0800

    BoxArray: split SendBoxArrayToSidecars() into SendBoxArray() and RecvBoxArray()
    
    Originally SendBoxArrayToSidecars() had separate logic for senders and
    receivers internally, but this was confusing because receiving processes
    would still call "SendBoxArrayToSidecars()" so it looked like they were
    actually sending something. Splitting this into two functions brings it
    more in line with point-to-point MPI function names.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Tutorials/Sidecar_EX1/DestMFTest.cpp

commit 43952b66a979bcc73d9a2f11bccdf909450935fe
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 9 12:42:21 2016 -0800

    Oops -- in ml_layout restricted build, only define ref ratio up to max_levs-1, not max_levs.

Src/F_BaseLib/ml_layout.f90

commit 6c45498970709477f630831c6b4c16d436e10f65
Merge: b042813a2 ab80cc4b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 9 11:29:10 2016 -0800

    Merge branch 'development' into pgas

commit ddd126aadb987361d5773753ac662fd6e5074100
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Mar 9 11:24:43 2016 -0800

    Sidecars_EX1: add Marc's new test code for moving MultiFabs

Tutorials/Sidecar_EX1/DestMFTest.cpp
Tutorials/Sidecar_EX1/GNUmakefile
Tutorials/Sidecar_EX1/Make.package

commit ab80cc4b11569c4a3a6c4d5e4e871edb3800f476
Merge: 972ef2703 4fea8a5bc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 9 11:21:19 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 4fea8a5bcf7a456bb214a8e89ab75e6a94646a6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 9 11:06:32 2016 -0800

    Remove BLMap because (1) C++11 enhanced the thread safety of std::map
    (2) BLMap does not play well with FabArray in shared memory.

Src/C_BaseLib/BLMap.H
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG4/ABec2.cpp
Src/LinearSolvers/C_CellMG4/ABec4.cpp

commit 972ef27039f7461ecb124b8faf088abc26d71438
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 9 10:33:40 2016 -0800

    Fix typo in comment in Tutorials/Tiling_C/main.cpp

Tutorials/Tiling_C/main.cpp

commit 15cb8a2a05cd05e56c02793a74ba23af538c4313
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 9 10:25:10 2016 -0800

    Add a new version restricted build to ml_layout that takes a minimum and maximum
    level rather than just a new nlevs.

Src/F_BaseLib/ml_layout.f90

commit b042813a2eecfe11830c780e6c06770cb3ad5eb1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 9 09:43:48 2016 -0800

    minor

Src/C_BaseLib/Box.H
Src/C_BaseLib/FabArray.H

commit dea250cdae45074123c56c2eb1da25fa1d5e80ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 8 18:29:52 2016 -0800

    MultiGrid_C: put the main body into a scope so that local MultiFabs are destroyed before MPI_Finalize is called.

Tutorials/MultiGrid_C/main.cpp

commit 5a9675e20d582f20c100d93c6771ff4216690ac0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 8 11:24:01 2016 -0800

    fix typo

Src/C_BaseLib/BLPgas.cpp
Tools/C_mk/Make.Linux

commit c0074be37baf873b78a33c6d293a73382687927b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 8 11:20:29 2016 -0800

    TagBox::coarsen: disable OMP when team size is greater than 1

Src/C_AMRLib/TagBox.cpp

commit 7430796982d9c8dd6eb2e15197951e0ab2108f38
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 8 08:36:37 2016 -0800

    BLPgas::alloc: proctect against zero or negative size

Src/C_BaseLib/BLPgas.cpp

commit 9c249eceaa31a53fa9bd86fc45d8d885b0323d11
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 7 18:11:28 2016 -0800

    0 --> nullptr

Src/C_BaseLib/FabArray.H

commit 2d838063425a036c49848316e397b37674793125
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 7 17:06:09 2016 -0800

    FabArray::AllocFabs: for upc++, allocate one big chunk of memory for the whole mulitfab just like what we do now in mpi

Src/C_BaseLib/FabArray.H

commit 0b1178317fac19b31fd5f54c4264e7e21f2755e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 7 16:13:07 2016 -0800

    FabArray: move shared memory stuff into a struct

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp

commit 14f10b196116412cedb61cdbecae19ace179c28f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 7 15:18:04 2016 -0800

    MPI-3 shared memory: rewrite AllocFabs to reduce the number of shared memory allocation.  There is a limit of 1024 sysv segments on Cori and Edison.

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 804372860060af4cfda01006811eec05107afbe2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 7 10:36:48 2016 -0800

    BaseFab: remove swap function because it is used and it could be unsafe in shared memory model

Src/C_BaseLib/BaseFab.H

commit 9dc2fcb0e98fc6b99a2c0dd353827309f67694d2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Mar 5 01:52:23 2016 -0500

    Print out a more informative message if we crash because the user's Python is too old to support the print() command used in write_probin.py.

Tools/F_scripts/write_probin.py

commit 754bbd5c893a51503b140dd5f4c1b36f7a9e836d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 4 21:30:55 2016 -0800

    Set MPI_Info for MPI_Win_allocate_shared to alloc_shared_noncontig

Src/C_BaseLib/BaseFab.H

commit 91763d71e42297fda7b970da74ef083e050ca2ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 4 17:20:53 2016 -0800

    Cray supports C++11 now.

Tools/C_mk/Make.Linux

commit 3a46158bfe1e5d6f9c55b5ec411d0442a7657ae1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 4 17:20:53 2016 -0800

    Cray supports C++11 now.

Tools/C_mk/Make.Linux

commit b324ba1f8f8d9c511aa5a3916378e3c23495ef15
Merge: 9cf221489 c24eca0ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 4 17:09:05 2016 -0800

    Merge branch 'development' into pgas

commit c24eca0ef9c389bbcd550edca9cc0841963c03a0
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Mar 4 16:28:46 2016 -0800

    C_mk: turn off debug symbols for optimized code with Cray compilers
    
    Using "-g" or "-G2" significantly reduces code performance, even with "-O2". So
    disable all debug symbols to get the fastest code.

Tools/C_mk/Make.Linux

commit 9f76fcf7b77330806be6b841de4d1ef7895b6059
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 4 16:16:38 2016 -0800

    use new broadcast functions.

Src/C_AMRLib/Amr.cpp

commit 9cf221489afe3bf41ad5746337b613cb6404aec2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 4 16:09:00 2016 -0800

    fix LAZY for team

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit c65ef7a279513f5ade5ad070ce72941bba9584fb
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 4 16:03:09 2016 -0800

    move some code.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit a1e92c4d7db6d53ee484b0ad3a4e535c8b4032a6
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Mar 4 15:20:05 2016 -0800

    C_mk: remove "-debug all" from Intel compiler flags on Edison and Cori
    
    This flag emits the same debug information as "-g", which we already use, so
    it's unnecessary.
    
    This partially reverts commit 4c2d110.

Tools/C_mk/Make.defs

commit 1a05a04247bd9cd6997c1a05f49c9f7b4159c957
Merge: c56c58399 d413a1297
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Mar 4 14:51:54 2016 -0800

    Merge branch 'compiler_flag_fixes' into development
    
    This merge fixes a few logic bugs in Make.defs related to selecting Intel
    compiler flags on Edison, Cori, and Babbage at NERSC.

commit d413a1297c56eda9a632d92c165e5d44d3e09982
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Mar 4 14:34:49 2016 -0800

    C_mk: add back "-fp-model source" to Intel compiler flags on Edison, Intel, and Cori

Tools/C_mk/Make.defs

commit a9620fbf588f85b02f418cc5603e9149aba6e819
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Mar 4 14:33:05 2016 -0800

    C_mk: removed another "else" from "if Edison then" clause when selecting Intel compiler flags

Tools/C_mk/Make.defs

commit d2827f4544ed47ad424014cdb78a0c041c914f0d
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Mar 3 13:27:11 2016 -0800

    C_mk: add "-parallel-source-info=2" and "-debug all" to Intel compiler flags on Edison and Cori
    
    These emit more complete debug information than is emitted by default, which is
    useful when running VTune and other profiling tools on optimized code.

Tools/C_mk/Make.defs

commit bc57f2501f493c2b9b622c8f9b449e4fda0e572f
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Mar 4 14:22:58 2016 -0800

    C_mk: remove "else" from "if Edison then ..." clause when setting Intel compiler flags

Tools/C_mk/Make.defs

commit 31cb043a8aa3e331e888a178ab5df0b13ab87f98
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Mar 4 13:44:35 2016 -0800

    C_mk: remove "-xHost" flag from Intel compiler flags on Edison and Cori
    
    The Cray compiler wrappers for the Intel compilers already contain the correct
    instruction set flags for both architectures ("-xCORE-AVX-I" on Edison and
    "-xCORE-AVX2" on Cori). Furthermore, "-xHost" uses the optimal instruction set
    on the architecture which hosts the compiler, which may be different than that
    of the compute nodes.
    
    This commit partially reverts commit 0088bae.

Tools/C_mk/Make.defs

commit 2d433a00877390e965b72df964363ebbdee52e6b
Merge: 2e1d5e7b3 c56c58399
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 3 17:31:49 2016 -0800

    Merge branch 'development' into pgas

commit c56c583991314898db94d1c3c5ccf48810b1d600
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 3 17:31:33 2016 -0800

    disable SIGFPE trapping by default because vectorized codes with if statement may have invalid floating point operations whose results are eventually masked out.

Src/C_BaseLib/BoxLib.cpp
Src/F_BaseLib/backtrace_c.cpp

commit 99f1edbdae7b013913dc602535581656c91f8255
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 3 14:03:32 2016 -0800

    fix for starting with zero sidecar procs.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 3de11e270bef67fae2f4a0854c731b97273792bc
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 2 17:20:57 2016 -0800

    allow nSidecarProcs == 0

Src/C_BaseLib/ParallelDescriptor.cpp

commit a7fb11e08ee4db4ba22ec3453bfb09b88b7c16d0
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 2 16:58:43 2016 -0800

    allow nSidecarProcs == 0

Src/C_AMRLib/Amr.cpp

commit 5f88b7fac111bf7336e4ba537404db910518c57a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 2 14:27:09 2016 -0800

    some cleanup.

Src/C_AMRLib/Amr.cpp

commit 1e657ecc0e457ece3885358a4369876ff94c9dc4
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 2 14:21:53 2016 -0800

    first fully working version of dynamic sidecars.

Src/C_AMRLib/LevelBld.H
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp

commit 185c0007a575ac33e9a03e9bd43b4cc69174dbe2
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 2 14:10:55 2016 -0800

    some cleanup.

Src/C_AMRLib/AmrLevel.cpp

commit 2e1d5e7b38ff71f89b9614d80fb752e594503ca4
Merge: 3a2e06532 531048693
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 2 13:40:29 2016 -0800

    Merge branch 'development' into pgas

commit 5310486939f299b418c86621094b7a47ca5ff291
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 2 13:39:49 2016 -0800

    explicitly add noinline attribute for gcc

Src/C_BaseLib/FabArray.cpp

commit 3a2e065328be3c97a2be5aa184b3ab03a5b0c09f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 2 13:39:49 2016 -0800

    explicitly add noinline attribute for gcc

Src/C_BaseLib/FabArray.cpp

commit e3332b5746ca4f371737ad4ca118964b13562cb3
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 2 13:39:18 2016 -0800

    reinitialize fortran data for new procs.

Src/C_AMRLib/Amr.cpp

commit 03760ca5ebafeeab3013caa81d23843d7380dd67
Merge: ec2b900a6 592f571d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 2 13:32:14 2016 -0800

    Merge branch 'development' into pgas
    
    Conflicts:
            Src/C_BaseLib/FabArray.H
            Src/C_BaseLib/FabArray.cpp

commit ec2b900a64d9c0b5954dd8f9e4bdf19ad927f557
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 2 13:19:45 2016 -0800

    minor

Src/C_BaseLib/FabArray.H

commit 592f571d86017595ef4ab2176034d91163b54d83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 2 16:13:31 2016 -0500

    For whatever reason, gcc sometimes doesn't like some functions live in FabArray.H, unless '-fno-inline' is used.  Moving them to .cpp file seems to solve the problem.  And we can maybe remove the -fno-line from makefile.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Tools/C_mk/Make.defs

commit 629ee12207c402460da1f4bac32a29f78c78b5ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 1 14:15:34 2016 -0800

    read into MultiFab directly so that it works with shared memory

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit b2eb10a748a678334f9f3640a4f6acf39f21a3f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 1 12:58:35 2016 -0800

    define ownership even if fabs are not allocated so that mfite could work on empty multifabs

Src/C_BaseLib/FabArray.H

commit b61bb3f9d4bc85a60855c2907603a7efd78c33a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 1 12:15:40 2016 -0800

    avoid setFab because it does not work with the new MFIter

Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/Geometry.cpp

commit c4bd91fd5c1f89b97b0debb0179f98f09ef27fa7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 18:02:27 2016 -0800

    MemoryBarrier: add omp barrier before upcxx and mpi barrier; only master thread calls upcxx or mpi barrier

Src/C_BaseLib/ParallelDescriptor.H

commit 6fdf1a1fd547d47432d6c54426ad070b0184d0c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 17:27:01 2016 -0800

    MFGhostIter: support for team and thread

Src/C_BaseLib/FabArray.cpp

commit 9a3071d27f1ba29e867d17ea2f6b1a6c3afb1fb0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 17:06:49 2016 -0800

    minor

Src/C_BaseLib/ParallelDescriptor.H

commit 91b1c63802a05be53b54f9aeab03ce19901df167
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 17:05:10 2016 -0800

    team_for: rework on support for OMP

Src/C_BaseLib/ParallelDescriptor.H

commit 60a210b5e777374644f6c967982e0bc1e1c0e3a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 16:44:38 2016 -0800

    MFIter: support both team and thread

Src/C_BaseLib/FabArray.cpp

commit 8f4028c4f0796c074a1ba1ced4dbd2c6955f2bcf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 15:53:20 2016 -0800

    team_for: support for OMP

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 93969202cadd1301000896002831319cb3c5ed30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 15:21:34 2016 -0800

    Don't call free if not allocated

Src/C_BaseLib/Geometry.H

commit 2f5a1367d98e9c8f9efb566f675a0de994a671b2
Merge: 39b984e3c cde9f65b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 15:01:58 2016 -0800

    Merge branch 'development' into pgas
    
    Conflicts:
            Src/C_BaseLib/BoxLib.cpp
            Src/C_BaseLib/ParallelDescriptor.cpp

commit cde9f65b17c1b23cd86fc0ec4c792132b4e39f85
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 14:39:19 2016 -0800

    fix BL_AMRPROF

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.cpp

commit 39b984e3cbc1cac317842c26c2d7db4395cb5583
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 14:20:04 2016 -0800

    make mpi onesided a runtime parameter mpi.onesided

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Tests/FillBoundaryComparison/main.cpp
Tools/C_mk/Make.defs
Tutorials/PGAS_HEAT/GNUmakefile
Tutorials/PGAS_HEAT/inputs_3d

commit ad9a6269d6a6e5b8364d7beef9c6f50aaa148162
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 29 13:27:39 2016 -0800

    setVect function for broadcasts.

Src/C_AMRLib/BCRec.H

commit 033d947eedea191d33c39ca624a70988a4d9acee
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 29 13:15:07 2016 -0800

    broadcast bcrec.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit b1e76f31c44811589e7024e1a0ad51d2305516fb
Merge: d051b491e 3923a7587
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 10:52:13 2016 -0800

    Merge branch 'development' into pgas

commit 3923a758730de62d20bd17464a7259a9558037fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 10:51:03 2016 -0800

    removed an unsafe omp parallel I recently added

Src/C_AMRLib/TagBox.cpp

commit d051b491e29a260ea4838701ce54661362b668e5
Merge: 9fdf952c2 6eec68f52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 10:24:47 2016 -0800

    Merge branch 'development' into pgas
    
    Conflicts:
            Src/C_BaseLib/ParallelDescriptor.H

commit 6eec68f52e178529833f2e72625392f5f31c791a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 28 12:31:40 2016 -0800

    BoxLib::Error and Abort: call BLBackTrace::handler instead of calling ParallelDescriptor::Abort directly so that it can be backtraced

Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.cpp

commit cf6b90c76a5676d5536395583f3ffa557357b02d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 21:09:05 2016 -0800

    ParallelDescriptor: clean up CommData, which is no longer used in CollectData

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 9fdf952c22b53194d899877566e6870d4dfd3d22
Merge: 5d69deb13 1185cd97b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 18:14:39 2016 -0800

    Merge branch 'development' into pgas
    
    Conflicts:
            Src/C_AMRLib/AmrLevel.cpp
            Src/C_BaseLib/FabArray.H

commit 1185cd97badecbd47a4622bb171273521040affc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 18:04:50 2016 -0800

    protect IndexMap() function and thus preventing raw loops

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/FabArray.H
Src/C_BoundaryLib/FabSet.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG4/ABec2.cpp
Src/LinearSolvers/C_CellMG4/ABec4.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 5d69deb1354ff73bc6cfc304e492d475d0498ffd
Merge: fae165980 77528856b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 16:50:39 2016 -0800

    Merge branch 'development' into pgas

commit 77528856b9514f91f49b91205c434f812a47eba0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 16:50:27 2016 -0800

    remove deprecated functions

Src/C_AMRLib/FluxRegister.cpp

commit fae165980b897f6de4c1eb4a63f801c75e0c502a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 16:16:06 2016 -0800

    remove the owneronly flag and make owneronly the default when tiling is off

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/VisMF.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 7bc1502d89a893763cd4f1231f7d2a55e650df74
Merge: 4b1340616 2c82e57ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 13:07:45 2016 -0800

    Merge branch 'development' into pgas
    
    Conflicts:
            Src/C_AMRLib/TagBox.H
            Src/C_AMRLib/TagBox.cpp

commit 2c82e57ff91eec775176d1af3a181a020ed0f83b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 13:04:44 2016 -0800

    FillPatchIteratorHelper does not need to derive from MFIter

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 09aee65084bbdef356e281d58fab2857f5123cdb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 12:57:37 2016 -0800

    TagBox: sync up with pgas branch

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 4b1340616f0f99f764bcf71bd6e2b9b793e417de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 12:43:35 2016 -0800

    Fix TagBox for team

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit a933003921e8198411b1748ef4e2f7f617d5ef55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 09:50:02 2016 -0800

    minor

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/FabArray.H

commit e5819f55bf71388216b2ee25cac6717d2ed1e9eb
Merge: 223eb19b9 d6a1727d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 25 16:27:18 2016 -0800

    Merge branch 'development' into pgas

commit d6a1727d77d35862a08756f29af1cc02e8af1c72
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 25 16:22:45 2016 -0800

    rename the fabarray to fab copy function to copyTo and optimize it a bit

Src/C_BaseLib/FabArray.H

commit 1a164d187db1c24175639570d7e9e745d98e85ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 25 16:21:06 2016 -0800

    add BoxCommHelper that helps communicating boxes

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp

commit d070a4114b37da526b5fb0747dd77254d8f6efad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 25 10:45:11 2016 -0800

    remove some unused and potentially unsafe and inefficient functions

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit d0da8697d2452c8208c4acdce066bc08a657ab03
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 18:25:41 2016 -0800

    remove some deprecated functions

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 223eb19b9a02f5fa00920a240fa2667f8d3be9db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 18:17:29 2016 -0800

    Owner only in the parallel linComb

Src/C_BoundaryLib/FabSet.cpp

commit 03eb336694a3151a619a0b01c86b907a60dfc161
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 24 18:14:06 2016 -0800

    added min rank to random range map.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 9a9786c24f9c68c23d584a73d82a1b924675c3e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 17:47:40 2016 -0800

    update FabSetIter constructor interface

Src/C_BoundaryLib/FabSet.H

commit 241fe0c5dcf7f8242cd362108709964d3279ed52
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 24 17:07:51 2016 -0800

    added grid redistribution.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 15ad3a488c7fd934e17efe16e72bfa588dad58c8
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 24 17:06:20 2016 -0800

    more broadcast variables.

Src/C_BaseLib/MultiFab.cpp

commit ad1ff2a3ca225ca87025357fefa7729006c76453
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 24 17:05:52 2016 -0800

    more broadcast variables.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 502fe417f8d2f90280ecff5db9a65157a4e2ac06
Merge: 8fdd438df c7c9c3ce3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 15:24:13 2016 -0800

    Merge branch 'development' into pgas

commit c7c9c3ce31dd2e8d909305eaa7816f2f79fa130a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 15:23:54 2016 -0800

    use quiet nans as initial values of some fabs

Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/BndryRegister.cpp

commit 8fdd438df042d43d6a2bd974436893b17a5cf83b
Merge: 7b5f54fb8 843a7d007
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 15:15:05 2016 -0800

    Merge branch 'development' into pgas

commit 843a7d007f919e791bedda791d0fc6e8b47e39cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 15:14:41 2016 -0800

    No need to use bogus values since in debug and test modes farraybox is filled with snan

Src/C_BaseLib/MultiFab.cpp

commit 7b5f54fb8b77772628a1a2a7577ef726532ffb58
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 15:10:12 2016 -0800

    comment

Src/C_BaseLib/FabArray.H

commit 3bc61f504ff6562509b77c85a95313b19fffced8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 14:57:13 2016 -0800

    Insert a memory barrier at the end of FillPatchIterator.  Switch to MFIter in FillCoarsePatch

Src/C_AMRLib/AmrLevel.cpp

commit 22dc9f8c6fad9f466722edb9708b01049f07ea07
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Feb 24 14:25:07 2016 -0800

    C_AMRLib: change "include 'omp_lib.h'" to "use omp_lib"
    
    The IBM XL Fortran compiler does not support omp_lib.h. Also that header often
    includes non-standard OpenMP functions. Using the "omp_lib" module is standard
    and is supported by all compilers.

Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/INTERP_3D.F

commit e65919dc28d4d0035626e349429bc341a7ab218d
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Feb 16 15:09:33 2016 -0800

    MultiFab: update comment on using SendMultiFabToSidecars()

Src/C_BaseLib/MultiFab.cpp

commit c7760cffa8fa9f318132a96e040663cce05230b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 14:14:27 2016 -0800

    FillPatchIterator: owner only in fill()

Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/FabArray.H

commit a038bee4db5589e6cdc6691708accfaf01813c65
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 24 14:00:37 2016 -0800

    added more vars to broadcast.

Src/C_AMRLib/Amr.cpp

commit 433770ebca0798b4dee806d4dde38d44068e04b8
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Feb 24 10:00:19 2016 -0800

    MultiFab::SendMultiFabToSidecars: remove redundant check for Box indices in a procmap
    
    This check always returns true, so remove it.

Src/C_BaseLib/MultiFab.cpp

commit 71376fb7dda44ef16b10e2ecc9ba674e0746c515
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Dec 21 10:45:32 2015 -0800

    C_mk: update library locations for new custom-built versions of GCC and MPICH on orga

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit 82db2b742b67dd7c96a65b6990b42d74474c7155
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 23 22:32:56 2016 -0800

    first pass of new fillpatch that avoid a mpi_alltoallv

Src/C_BaseLib/FabArray.H

commit bb7c48c02ae7581716f36dd6c9d1aafd0ec5a052
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 12:22:06 2016 -0800

    BaseFab::swap: swap those new meta data too

Src/C_BaseLib/BaseFab.H

commit ef2baa91da745530e34ac49e7c57406813e9d8c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 12:20:06 2016 -0800

    TagBox: should use local index instead of global index

Src/C_AMRLib/TagBox.cpp

commit 57bbfadec737aa1984e09e38d6ddbd4ef6ee4fc6
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 24 11:29:30 2016 -0800

    moved data declarations out of function area.

Src/C_AMRLib/Amr.H

commit cf14dc4f149845e1985e67db072557263ca3e5ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 10:52:37 2016 -0800

    BaseFab: need to give empty BaseFab's shared_memory variable an initial value, otherwise resize function will be using uninitialized shared_memory

Src/C_BaseLib/BaseFab.H

commit fe5c7e75d6358236a2d0ff5cd75efecf6f84120a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 24 10:35:37 2016 -0800

    handle zero size intvects.

Src/C_AMRLib/Amr.cpp

commit 13805647b5ba850cfa37d4680fff7b96f79ea8e8
Merge: 4212b32ae cdcef2aca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 09:52:20 2016 -0800

    Merge branch 'new_fillpatch' into pgas

commit cdcef2acabad8b5ed93eed7a68f2ebada727bf6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 23 22:32:56 2016 -0800

    first pass of new fillpatch that avoid a mpi_alltoallv

Src/C_BaseLib/FabArray.H

commit c40daaa6e2e89e3e71e623387fd911f9184496d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 23 10:46:17 2016 -0500

    now that xrb_simple has a different default network, explicitly
    compile in rprox

Tools/RegressionTesting/Maestro-tests.ini

commit 1744bfd6096b21c09a3905903392f32f26320e87
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 22 15:32:42 2016 -0800

    pass flag to add distmap to cache on broadcast.

Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 1cdf7600d61aab6fc251a3100a758f28a8e18d77
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 22 15:15:10 2016 -0800

    whichProc option for CacheStats.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 075753a124f85d9f59e95e77e2d79acf04e037e0
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 22 15:09:01 2016 -0800

    option to add map to cache when defining with Array<int>.

Src/C_AMRLib/ErrorList.H
Src/C_BaseLib/FabArray.H

commit 1ab47e74bf852c2ca7a2e8cfe1cf896e1d3c69e4
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 22 15:07:07 2016 -0800

    option to add map to cache when defining with Array<int>.

Src/C_BaseLib/Utility.cpp

commit 4cc39a847435426649e06e5c11aa71552bbc832c
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 22 15:05:30 2016 -0800

    option to add map to cache when defining with Array<int>.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit c3860b584f0d1248762717294d1bf3e11e1c1180
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 22 15:04:43 2016 -0800

    code cleanup.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/StateData.cpp

commit 4212b32ae18d5f4bc0569749130e679027feb5d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 22 12:24:51 2016 -0800

    comments

Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/FabArray.H

commit 928a0f3a9c1280f375cfdd230f9e9d0a7f27b8de
Merge: ac91482ac 8a67db181
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 22 12:20:33 2016 -0800

    Merge branch 'development' into pgas

commit 8a67db1811d1b08d5a83e2df72f55a99817012e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 19 18:02:14 2016 -0800

    use quiet nan as safe bogus value

Src/C_BoundaryLib/BndryRegister.cpp

commit 18b182e0ed890980336aaf10eac41a0954c771ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 19 17:51:42 2016 -0800

    no longer need to set special bogus values in DEBUG because it is done in constructor of fab now

Src/C_AMRLib/AmrLevel.cpp

commit 3815f42e34b658db7d750f9ebc127586e1e511fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 19 17:23:17 2016 -0800

    tidy

Src/C_AMRLib/AmrLevel.cpp

commit ac91482ac4472996213d5027d1e0b734a267acb2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 19 16:04:07 2016 -0800

    DistributionMapping: Support for team in KnapSack

Src/C_BaseLib/DistributionMapping.cpp

commit a83baaf8ce9ed49662f4b18e1c433c5c378d593a
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 19 15:31:32 2016 -0800

    set dmid for new procs.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/Utility.cpp

commit c48b5c3b920cf8be6f626fcd4c9066f1c88f2991
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 19 15:07:59 2016 -0800

    DistributionMapping: Support for team in RoundRobin

Src/C_BaseLib/DistributionMapping.cpp

commit 8b249d1b626fd2b5158f92d838494fc8a16598ba
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 19 13:56:02 2016 -0800

    print allocatedFAPtrs, remove unused maps.

Src/C_BaseLib/FabArray.H

commit 25001d29d7a8858aee4b3006072362205aa71582
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 19 13:38:41 2016 -0800

    MPI one-sided FabArray::copy

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 90fef1bbfdec95fa30d28d2929ffae04f9e5704b
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Feb 18 18:15:45 2016 -0800

    Uptick tag

Tools/CMake/BoxLib_Version.cmake

commit cda2e3959c26a3e358e7ec22482867ad7eca6c9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 16 16:42:38 2016 -0800

    add Team support in CPC

Src/C_BaseLib/FabArray.cpp

commit ab6a0ace1db7c8bdfa5363381626fd257c0485dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 16 15:43:05 2016 -0800

    UPC++ in FabArray::copy

Src/C_BaseLib/BLPgas.H
Src/C_BaseLib/BLPgas.cpp
Src/C_BaseLib/FabArray.H

commit f712e88202fcf00d62daf16764fb58b7ffe448dd
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Feb 17 10:26:08 2016 +1100

    Initial changes for building on Australian machines

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 2d91b7b7da9c8d9567b78d3af2969065f4f94646
Merge: a432ea430 3f6b1f2e2
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Feb 17 08:40:30 2016 +1100

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit a432ea43010737ddd5ca173026530c933cc1d631
Author: Marcus Day <msday@FyrHead.ad.unsw.edu.au>
Date:   Wed Feb 17 08:39:20 2016 +1100

    PGI doesnt know about fegetexcept

Src/F_BaseLib/backtrace_c.cpp

commit ce45bed0f852d21fb3a95a5fddabeaac99ff77a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 16 13:30:55 2016 -0800

    WIP for TagBox with team

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit c7aa17d20c126a20a65865904165e1b371043a16
Merge: d6c094516 3f6b1f2e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 16 12:40:09 2016 -0800

    Merge branch 'development' into pgas
    
    Conflicts:
            Src/C_BaseLib/BoxLib.cpp
            Src/C_BaseLib/FArrayBox.cpp

commit 3f6b1f2e24f797a901bfa3bf2b353bf9ac2f2b6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 16 07:10:19 2016 -0800

    Following up on parent commit, Fortran also likes to print 1.d99 as 0.1+100, so change the upper bound to 1.d98

Src/F_BaseLib/multifab_physbc_edgevel.f90
Tools/Postprocessing/F_Src/fcompare.f90

commit e032c7884f126e5f8a54578697b6401d937c599a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 16 09:56:25 2016 -0500

    protect the prints at the high-end too -- if the error is larger than
    1.d99, make it 1.d99, this avoids Fortran's habit of dropping the 'E'
    in the asci representation of numbers with 3-digit exponents.

Tools/Postprocessing/F_Src/fcompare.f90

commit c0865fc52313efafbab2e96dcdf8e5584a814638
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 15 16:02:47 2016 -0500

    Turn on floating point exception trapping for PGI 16 and later

Src/C_BaseLib/BoxLib.cpp
Src/F_BaseLib/backtrace_c.cpp

commit 6381cbed7c0da85a8eee2e4f6aa56708131735e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 15 11:40:57 2016 -0800

    Fortran fab build: skip memory allocation if box is empty.

Src/F_BaseLib/fab.f90

commit dbdddf360200722c5b0108f4e1e970bf04d2ea50
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Mon Feb 15 13:09:50 2016 -0500

    Only print warnings if we're on I/O processor

Src/C_AMRLib/Amr.cpp

commit 5c936eb4fce1adb9cab66da64f074b09fce321dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Feb 14 20:59:46 2016 -0500

    some png tweaks

Tools/RegressionTesting/testnew.py

commit 0129205b3fc28dd5b23131b8d316f825a6ef9738
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Feb 13 20:16:42 2016 -0500

    Add two new member functions to StateData: copyOld and copyNew. These copy the old_data and new_data from a source StateData to a destination StateData, and set the time levels correspondingly. Additionally, add a static function StateData::Initialize. Given a StateData generated using the default constructor, set it up with the same characteristics as a source StateData object and do a deep copy of the data.

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit 964d37ef684689c00d7481ca29838fb1f8a8a248
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 18:55:06 2016 -0500

    fix a few uninitialized vars

Tools/RegressionTesting/testnew.py

commit a491534655e93072e9b8571fcb38f99ad6b2cb53
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 18:17:14 2016 -0500

    remove report_test_failure -- we can get that functionality from
    report_single_test now, with a failure_msg

Tools/RegressionTesting/testnew.py

commit 04bc9cd0f6e3ee5e237985666a43050f901dd31a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 15:53:22 2016 -0500

    store the backtrace when we have failures during the benchmark creation

Tools/RegressionTesting/testnew.py

commit 7cf175b38d6b472fc3b7d974b6a80b7c4509afd7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 15:21:52 2016 -0500

    more error reporting

Tools/RegressionTesting/testnew.py

commit 46b5e7da7d112bc53356a3e0cf0429fbb46f1e30
Merge: 88d6287cf e501287f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 15:16:36 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 88d6287cf579bf0fea5dab3271c7f07d538bc594
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 15:16:29 2016 -0500

    some failure reporting

Tools/RegressionTesting/testnew.py

commit e501287f8192cb6b7b16a7423b44ece7bdf6b39b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 14:52:19 2016 -0500

    clean up some error messages

Tools/RegressionTesting/testnew.py

commit 27132492f897683ba8216a8596592f19876187cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 11:46:18 2016 -0500

    fix the early abort test report for restart tests, and also fix
    the wallclock time.

Tools/RegressionTesting/testnew.py

commit 3ea7eb06d572422f658e91f10d7ca776a3388b60
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 09:54:36 2016 -0500

    remove some print debugs

Tools/F_scripts/write_probin.py

commit 0a507bcfd779aca7a688e2a7332a267842c65321
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 12 21:50:01 2016 -0800

    Cray: use -G2 instead of -g for ndebug build

Tools/C_mk/Make.Linux
Tools/F_mk/comps/Linux_cray.mak

commit f7f53910cf051376e05bebe0b4eeb216f86700c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 13 00:31:43 2016 -0500

    PGI: use -gopt instead of -g for ndebug build

Tools/C_mk/Make.Linux
Tools/F_mk/comps/Linux_pgi.mak

commit d6222c9c43c19d2af2ef8505726f0a4e89f51f11
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Feb 12 18:35:31 2016 -0500

    this isn't used anywhere

Tools/C_mk/Make.bgl

commit 2fb19d50eec7246821549f8bee260019dd062011
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Feb 12 18:17:43 2016 -0500

    remove carver

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit 552f30ed7fc889328ec9881cfc06baa3522c0992
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 12 12:48:12 2016 -0800

    no longer define BL_TESTING when DEBUG=TRUE to avoid confusion

Src/F_BaseLib/backtrace_c.cpp
Tools/C_mk/Make.defs
Tools/F_mk/GMakedefs.mak

commit a10a8b8784774fa8b3d99cfc7be29588c4113e27
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 12 12:38:23 2016 -0800

    Linear Solver: set full_soln corner cells to quiet nans

Src/F_BaseLib/backtrace_c.cpp
Src/F_BaseLib/backtrace_f.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit 3a2dcf2cb5d8cabd770c07665c2280fe3a6b3b2d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Feb 12 15:10:19 2016 -0500

    for the PGI compilers, we need to compile the C++ source with -O1
    instead of -O.  This eliminates some global optimizations.  There
    is a compiler error that manifests itself at link time when we compile
    ParmParse.cpp with -O.

Tools/C_mk/Make.Linux

commit 1416cf3c710b4e01b7650ee1ba39c32c68c9c6c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Feb 12 14:07:02 2016 -0500

    Carver is no more

Tools/F_mk/GMakeMPI.mak

commit 03857d40bb5b32be8636479cf5a82892437a44f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Feb 12 12:44:18 2016 -0500

    update for PGI 16.1+ -- pgCC no longer exists.  We now use pgc++.
    Also, we can use just -pgf90libs to get the F90 stuff linked

Tools/C_mk/Make.Linux

commit e96d71240e4ce3444cab07f3186c69c03f0b8652
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 11 23:01:01 2016 -0800

    do not need to avoid PGI in getting exception flags

Src/F_BaseLib/backtrace_c.cpp

commit 31b0a97f4565ab5f279d16017cadbb99f0a5f6e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 11 22:52:49 2016 -0800

    minor tweak of get_fpe_trap()

Src/F_BaseLib/backtrace_c.cpp

commit 3d217f714581f94d11224a528dea661641574557
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 11 22:43:01 2016 -0800

    remove debug print statements

Src/LinearSolvers/F_MG/ml_cc.f90

commit 221b06018c71f95dc5403e6ac218d140a03c0c32
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 11 22:04:10 2016 -0800

    define BL_TESTING when DEBUG=TRUE

Src/F_BaseLib/fab.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Tools/C_mk/Make.defs

commit 259ddcc7059a827c55674e6f7ea9742baf5de402
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 11 18:19:40 2016 -0800

    disable the new code because it does not work.

Src/LinearSolvers/F_MG/ml_cc.f90

commit ad880fff1c4cc9c0a8aad18ec9dac1c7d9258560
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 11 18:13:38 2016 -0800

    Setting corner cells in linear solver: do not set on the first level

Src/LinearSolvers/F_MG/ml_cc.f90

commit 70c35851b62b4720b183d5bade843c54c444140c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 11 18:03:55 2016 -0800

    add get_fpe_trap function; when it returns true, we need to set some corner ghost cells to valid values in linear solver to avoid being trapped by floating point exception

Src/C_BaseLib/BoxLib.cpp
Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/backtrace_c.cpp
Src/F_BaseLib/backtrace_f.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit 3a42f2e0247cb9b2e3dcb8d0c32b3284e4dbd7a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 11 16:57:07 2016 -0800

    add new function mulitfab_set_corner to set corner cells not used in cross stencils;  in linear solver call it on full_soln when cross stencil is used.

Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab_f.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit 92791b4f142a3e0e946ff5b9b4440032ab9cf9f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Feb 11 13:53:17 2016 -0500

    for PGI 16.1, we need -pgc++libs instead of -pgcpplibs on the link
    line (and it should have always been an option, not a library, so
    I switch the make variable for this).
    
    This should hopefully still work on the 15.x compilers, since we
    are now using pgc++

Tools/F_mk/comps/Linux_pgi.mak

commit 043f4041359da8fa0db89fd303be75f4688bc4cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Feb 11 13:27:00 2016 -0500

    as of PGI 16.1, pgCC no longer exists.  The new C++ compiler is pgc++

Tools/F_mk/comps/Linux_pgi.mak

commit e01083a483aaaccdc64dc3d52e7111b0f56c890c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 10 20:08:26 2016 -0500

    we have both compareFile and outputFile -- they serve slightly
    different purposes.  Document that better and make copy_benchmarks
    know about outputFiles

Tools/RegressionTesting/testnew.py

commit 39164ade4bcd0ea6f114f423476c496778b6a695
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Feb 10 14:00:05 2016 -0800

    Add godzilla into the make system

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 9b71f603e825978cd7e57cf44ce4c4a7f3c1798e
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Feb 10 13:54:12 2016 -0800

    Remove my debugging line in the GNUmakefile

Tutorials/MultiGrid_C/GNUmakefile

commit ab4541b1dbdd336c2119811bb45f2178015a76d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 10 12:27:25 2016 -0800

    finally fixed my new bug in INTERPER_3D

Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F

commit 8923c439ed820e7c4c6df49878b46dc0b97da180
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 10 15:23:18 2016 -0500

    fix boxlib-only runs

Tools/RegressionTesting/testnew.py

commit ae06c1140c1693800f69c7b5d0bb0d6dbe92db1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 10 10:32:23 2016 -0800

    latest regression test inputs files

Tools/RegressionTesting/BoxLib-tests.ini
Tools/RegressionTesting/Castro-tests.ini
Tools/RegressionTesting/IAMR-tests.ini
Tools/RegressionTesting/LMC-tests.ini
Tools/RegressionTesting/Nyx-tests.ini
Tools/RegressionTesting/RNS-tests.ini
Tools/RegressionTesting/SMC-tests.ini
Tools/RegressionTesting/VARDEN-tests.ini

commit b2d668e4ce4ba42a0db6101dee6d03376c01470d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 10 09:58:14 2016 -0800

    fix a bug in my last commit: accidentally deleted a line

Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F

commit fcd0aa599febf4bcad719dcca928d962737f5e18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 9 15:25:54 2016 -0800

    avoid nans

Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F

commit 5eb0aaf148b47240498cc586dd2dae199bc6d438
Merge: 1e4d77a75 a880371e1
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 9 13:56:38 2016 -0800

    Merge branch 'development' into 4thOrderMG

commit 1e4d77a7500b08c1b593d82de91eea940e6ee11f
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 9 13:56:08 2016 -0800

    Change default

Tutorials/MultiGrid_C/GNUmakefile

commit 1e6bd7e55f927a35de9f9b4ec8db60cfa922ce4c
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 9 13:51:37 2016 -0800

    Final junk

Tutorials/MultiGrid_C/main.cpp

commit a880371e16e7aed5d641602f532adb8bf56729fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 9 12:50:05 2016 -0800

    avoid copying nans

Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit e49f73f7dbe77f741d2b1b41539d964ffcaed238
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 9 11:56:30 2016 -0500

    fix the backtrace links

Tools/RegressionTesting/testnew.py

commit 1cf2b8d024cc29ff4682d7f11ab36f2a2a4dd214
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 9 10:48:43 2016 -0500

    fix name clashing on the backtrace files

Tools/RegressionTesting/testnew.py

commit 2f568e98327e2ac907285129dae02213c673a840
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Feb 8 19:33:43 2016 -0800

    Fix 3D bug in 4th order boundary stencil, remove some debugging output

Src/LinearSolvers/C_CellMG4/ABec4.cpp
Src/LinearSolvers/C_CellMG4/ABec4_3D.F

commit 114f47cf764afb70d6b7a38462ad60928c193c27
Merge: 8f5080f88 2690108c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Feb 8 21:08:33 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 8f5080f8827732bfe12c1f26b9d1198efde2238f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Feb 8 21:08:21 2016 -0500

    add support for copying and posting the Backtrace files

Tools/RegressionTesting/testnew.py

commit 2690108c7187d5f97aa2c7d60fb5351dc20683a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Feb 8 20:17:53 2016 -0500

    enable TEST=TRUE in the tests

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 8c883521a4e42cdf9f01d61afb631f69a883e6b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Feb 8 19:58:39 2016 -0500

    split C and F add stuff.  Now we have:
    add_to_f_make_line
    add_to_c_make_line
    
    update the Maestro suite to run with TEST=t

Tools/RegressionTesting/Maestro-tests.ini
Tools/RegressionTesting/testnew.py

commit 3e692512afd348ad7d1d9f4e2247d474608b9870
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Feb 8 16:56:02 2016 -0800

    4th order in progress...

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_CellMG4/ABec2.H
Src/LinearSolvers/C_CellMG4/ABec2.cpp
Src/LinearSolvers/C_CellMG4/ABec2_3D.F
Src/LinearSolvers/C_CellMG4/ABec2_F.H
Src/LinearSolvers/C_CellMG4/ABec4.H
Src/LinearSolvers/C_CellMG4/ABec4.cpp
Src/LinearSolvers/C_CellMG4/ABec4_2D.F
Src/LinearSolvers/C_CellMG4/ABec4_3D.F
Src/LinearSolvers/C_CellMG4/ABec4_F.H
Tutorials/MultiGrid_C/COEF_3D.F
Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_C/inputs
Tutorials/MultiGrid_C/main.cpp

commit 0698fc3fdb3f7dd037f8dde5ac25923bc65b3181
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Feb 8 19:50:12 2016 -0500

    add support for a global line to add to the make command

Tools/RegressionTesting/testnew.py

commit 899434b5e57f1c4a3421f8bc77d7aa45d3387772
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 8 14:28:54 2016 -0800

    put abort_fortranboxlib back to module and add a c name for it

Src/F_BaseLib/backtrace_f.f90

commit 4e53bda9e8d36a730d4dea36cb2fd7492d5c608d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 8 14:14:40 2016 -0800

    disable SIGFPE trapping for PGI

Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.cpp
Src/F_BaseLib/backtrace_c.cpp

commit f5b57f9a837742c87f96d4262f8a0258cf0bb604
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 8 13:40:47 2016 -0800

    To make PGI happy, define _GNU_SOURCE for PGI on Linux

Src/C_BaseLib/BLBackTrace.cpp

commit b6baf8f4466f50b7f9917694dc3f402372e7e609
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 8 13:22:19 2016 -0800

    To make PGI happy, define _GNU_SOURCE for PGI on Linux and move subroutine abort_fortranboxlib out of module.

Src/F_BaseLib/backtrace_c.cpp
Src/F_BaseLib/backtrace_f.f90

commit 70d93ffb64d19accca48ef31bbba70f8afcf0b0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 7 16:24:16 2016 -0800

    Backtrace: fix calling handler from Linear Solver in C++ BoxLib codes

Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/backtrace_c.cpp

commit 4bcf94b9bbc087c2f61560d0c310088a0060ba5c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 7 13:16:59 2016 -0800

    add write_to_stderr_without_buffering to BoxLib namespace

Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp

commit 65d7876800389509e641145d3b76f93860d0d471
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 7 12:17:02 2016 -0800

    update Readme.backtrace

Docs/Readme.backtrace

commit 8205184b8e7da4b19fde1d51dfc2c570696f6dce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 7 10:46:50 2016 -0800

    Backtrace: remove SIGTERM because MPI_Abort might use it; cleanup

Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.cpp
Src/F_BaseLib/backtrace_c.cpp
Src/F_BaseLib/bl_error.f90

commit 3f808881e3a0ab4a745938f407bff50ae18dbe81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 7 00:41:57 2016 -0800

    Fortran BoxLib: define BL_TESTING in DEBUG mode

Tools/F_mk/GMakedefs.mak

commit 711872bb7e20e3d156ca559315e4f5c8ecf9c8d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 7 00:36:29 2016 -0800

    Backtrace: remove SIGABRT from backtrace because that's abort sends

Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.cpp
Src/F_BaseLib/backtrace_c.cpp

commit 790436c5dbc76d157ceaf277d6dd64dab398a890
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 7 00:13:43 2016 -0800

    Fortran BoxLib: remove the old backtrace

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_error_backtrace.f90
Src/F_BaseLib/bl_prof_backtrace.f90

commit 792a1d6f22f5db2722bb262583d21c433c23a11f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 7 00:10:02 2016 -0800

    Fortran BoxLib bl_error: call backtrace before abort

Src/F_BaseLib/backtrace_c.cpp
Src/F_BaseLib/bl_error.f90

commit 646c382e998ed5d2fc10fe0a225d2a10bbf687dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 6 23:51:09 2016 -0800

    Fortran fab: if DEBUG or TEST, initialize fab to snan.

Src/F_BaseLib/fab.f90

commit 74115054adbbe913c60cd8bf9ab94ddf2bc23ac4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 6 22:56:00 2016 -0800

    Define BL_TESTING when BACKTRACE=TRUE

Tools/C_mk/Make.defs

commit 376f74696c252f0032d7f53d9f1d6fbafe2f2a4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 6 22:53:25 2016 -0800

    Move the setting of snan from FArrayBox to MemPool so that the bl_allocated array can use it and Fortran BoxLib can use it.

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/MemPool.H
Src/C_BaseLib/MemPool.cpp
Src/C_BaseLib/mempool_f.f90

commit d74b08026581e6f3610e854cf6c1164ab66bed22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 6 20:43:48 2016 -0800

    add -g to get useful information out of backtrace

Tools/C_mk/Make.Linux
Tools/F_mk/comps/Linux_cray.mak
Tools/F_mk/comps/Linux_intel.mak
Tools/F_mk/comps/Linux_pgi.mak
Tools/F_mk/comps/gfortran.mak
Tools/F_mk/comps/osf1.mak

commit 9f6f773a269399fc5c31a1a1fa2011b3a4c3efb6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 6 19:44:00 2016 -0800

    add handler for SIGABGT

Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.cpp
Src/F_BaseLib/backtrace_c.cpp

commit 4efb0d3ab4d7a674fe640942169bf5c6f314f3f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 6 19:33:21 2016 -0800

    Backtrace in Fortran BoxLib: we now backtrace segfault in Fortran BoxLib. TEST=t or empty is added to the make system.  Its purpose is similar to TEST in C++ BoxLib.

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/backtrace_c.cpp
Src/F_BaseLib/backtrace_f.f90
Src/F_BaseLib/boxlib_f.f90
Tools/F_mk/GMakedefs.mak

commit 7e7e1a0aa246d7de71d8ad731a5b859e22e10d28
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 6 19:30:33 2016 -0800

    Add TEST=TRUE or FALSE to the make system.  If TEST=TRUE, floating point execeptions will be trapped and MultiFabs will be initialized to snan.

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FArrayBox.cpp
Tools/C_mk/Make.defs

commit a25e2d4eb2c404aa656130a93c6859d32d3edc45
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 6 19:21:24 2016 -0800

    getcwd should work on any non-windows machines, so move it out of __linux__.

Src/C_BaseLib/BoxLib.cpp
Tutorials/Tiling_Heat_F/inputs_2d

commit a4563bbeca87ab458c23bd7ab03b62d7ccd3138e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 5 18:13:52 2016 -0800

    New runtime parameter fab.init_snan=0 or 1.  The default is 0 when DEBUG=FALSE and 1 when DEBUG=TRUE.  This controls initializing Fabs to snan.  Note that one still needs to set boxlib.fpe_trap_invalid to trap snans.

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp

commit dbd011dc8c90b35099e3ce79aa83290cd0ae1f79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 5 16:08:21 2016 -0800

    Turn on the backtracing of segfault, interruption and assertion by default; Floating point exceptions are trapped when DEBUG=TRUE, and they can be turned on or off by runtime parameters, boxlib.fpe_trap_invalid, boxlib.fpe_trap_zero and boxlib.fpe_overflow.

Src/C_BaseLib/BLBackTrace.H
Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp

commit ea64f0db0a1a74b4c7abb492a49f9dbc0b6bd440
Merge: e02c9a0c7 88b06ad12
Author: vince <vebeckner@lbl.gov>
Date:   Thu Feb 4 17:51:42 2016 -0800

    Merge branch 'master' into development

commit 88b06ad1218519f40c366269bcafe72c6330d02f
Author: vince <vebeckner@lbl.gov>
Date:   Thu Feb 4 16:46:19 2016 -0800

    i/o tests for the burst buffer.  the read part needs to be finished.

Tests/BBIOBenchmark/BBIOTest.cpp
Tests/BBIOBenchmark/BBIOTestDriver.cpp
Tests/BBIOBenchmark/GNUmakefile
Tests/BBIOBenchmark/README

commit e02c9a0c722f2ad5f37462396dbdee7429168f1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 3 15:53:04 2016 -0500

    add priority to runtime parameters.  When two parameters are encountered
    with the same name, the value corresponding to the highest priority one
    will be kept.
    
    Also, a lot of source code cleaning a la PEP-8

Tools/F_scripts/write_probin.py

commit d6c094516688675c80d4fb02492f29e47b8227a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 17:47:56 2016 -0800

    In simple test codes, MultiFabs are still alive after MPI_Finalize()
    has been called.  The dtor of BaseFab calls MPI functions when MPI
    shared memory is used.  To avoid MPI complaining, we explicitly
    destroy these MultiFabs before BoxLib::Finalize().

Tests/FillBoundaryComparison/main.cpp
Tutorials/PGAS_HEAT/main.cpp

commit f6a1784ee64c54ac00521819ae2605aa0ffb37b6
Merge: 8459104cc a15566d94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 17:22:31 2016 -0800

    Merge branch 'development' into pgas

commit 8459104cc2083720099a628d19800190b70e45b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 17:22:04 2016 -0800

    clean up FillPeriodicBoundary

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 117ce93901657658553fc9d83f150cde4182cb74
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 16:18:14 2016 -0800

    clean up FillBoundary

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 5c471e41f7d4f54fc7ec72a9d86d94b44e00aa30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 14:27:21 2016 -0800

    call MPI_Group_free to free the groups

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 0a7a0a05b56d05251ed35310a81f86da7bcd0195
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 14:11:37 2016 -0800

    clean up

Src/C_BaseLib/FabArray.H

commit 062777023c8110ea28a550365064206f07189b96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 13:26:27 2016 -0800

    test-mpi3: write and read

Tutorials/PGAS_HEAT/test-mpi3/main.cpp

commit c12784bb0c8a7685fb3e69430d64581de7d38c07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 13:25:43 2016 -0800

    fix a typo

Src/C_BaseLib/BaseFab.H

commit bf457302fe6503eeb8fbd67dece91d2c59516df2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 12:20:23 2016 -0800

    fix typo

Src/C_BaseLib/FabArray.H

commit 4e90efbf9d70a669c559cd811b73c57324799c36
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 12:19:04 2016 -0800

    minor change for consistence

Src/C_BaseLib/Geometry.H

commit d4f9a16997947408cc029b6f0efd2fa11ae61d19
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 12:18:50 2016 -0800

    another BL_USE_UPCXX --> BL_USE_TEAM

Src/C_BaseLib/FabArray.cpp

commit a8db3dad656594d7581c882174da20b048c97041
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 11:23:13 2016 -0800

    MFIter: BL_USE_UPCXX --> BL_USE_TEAM because of MPI3 team

Src/C_BaseLib/FabArray.cpp

commit ad7406acba7bdc8c4111d883026b7a3ba60488e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 11:22:22 2016 -0800

    add more Memory Barriers

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 7ad50ec3f434f9a8dcf04a0fafcb34cc4969aa42
Merge: 85a7fec83 a15566d94
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 2 10:45:59 2016 -0800

    Merge in process, mg tutorial does not yet build

commit 85a7fec83b3b19230840d1d2d3c8afc0c08085a4
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 2 10:23:49 2016 -0800

    Finish up 4th order implementation

Src/LinearSolvers/C_CellMG4/ABec2.cpp
Src/LinearSolvers/C_CellMG4/ABec2_2D.F
Src/LinearSolvers/C_CellMG4/ABec2_3D.F
Src/LinearSolvers/C_CellMG4/ABec2_F.H
Src/LinearSolvers/C_CellMG4/ABec4.cpp
Src/LinearSolvers/C_CellMG4/ABec4_2D.F
Src/LinearSolvers/C_CellMG4/ABec4_F.H
Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_C/main.cpp

commit 2fda6f06179cdf004f5c598d47ab52a8aafa0ea2
Author: Yili Zheng <yzheng@lbl.gov>
Date:   Mon Feb 1 20:44:14 2016 -0800

    Minor fix of test-mpi3

Tutorials/PGAS_HEAT/test-mpi3/main.cpp

commit a99fd904e360c1a8c6ca233c0af7d2a633c41599
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 20:07:49 2016 -0800

    no need to allocate a MPI_Win in the initialization of team; remove MPI calls in the dtor of team

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 1aa777395bbd2d327648581a94d8f0e5299406a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 19:57:23 2016 -0800

    need to pass T** to MPI_Qin_allocate_shared

Src/C_BaseLib/BaseFab.H

commit 308e48cbf3b18836e59a57604bc712576dee6395
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 19:56:33 2016 -0800

    update ifdef

Src/C_BaseLib/Geometry.H

commit cdaf982af7a3f49c25ef57d4fba5009caef48184
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 17:34:45 2016 -0800

    testing mpi3 shared memory

Tutorials/PGAS_HEAT/test-mpi3/main.cpp

commit adec17b0fc8ec7284637a979ca0e0dc347cdb17d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 16:09:52 2016 -0800

    fix ifdef

Src/C_BaseLib/DistributionMapping.cpp

commit 45bc25dab0f8ae872cfe0a4af029e150ef83b5d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 15:49:48 2016 -0800

    rename the memory barrier

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/ParallelDescriptor.H

commit 3e49e3bd12d98ecfb961545983eeff4391077954
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 1 15:38:42 2016 -0800

    sync sequence number.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 6754588978144b12ca1001bb733a15c65d76e632
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 1 15:04:45 2016 -0800

    braces.

Src/C_BaseLib/VisMF.cpp

commit 185e249e5521bb6a3642e0303ec7b5422b43917c
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 1 15:02:37 2016 -0800

    reset noutfiles.

Src/C_AMRLib/Amr.cpp

commit 3dde7aa2c4be28755de71663014bfddfe68ef682
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 14:45:47 2016 -0800

    fix MFIter::OwnerOnly and NoSharing

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit cbce8adc5d85fad4ccdeec2dfb4e4f88023816b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 12:44:14 2016 -0800

    add MPI3 team

Src/C_BaseLib/BLPgas.H
Src/C_BaseLib/BLPgas.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/IArrayBox.H
Src/C_BaseLib/IArrayBox.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/UArena.H
Src/C_BaseLib/UArena.cpp
Tools/C_mk/Make.defs

commit b658304a8546ba4c56fb0c3166e276d1363366bf
Merge: 8a79a498c 67280d532
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 12:41:09 2016 -0800

    Merge branch 'mpi-onesided' into pgas

commit 67280d5323d0f7f5d58ce983198ac03876964a7b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 09:07:39 2016 -0800

    should be MPI_Group instead of MPI_Comm

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit a15566d9458ea3a780b333609907c532b2d82bf2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 09:02:03 2016 -0800

    fix assertion when DEBUG=FALSE

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 631d6036e9cb5d43c43ae4a25c6408e3acdffdc8
Merge: 5ee53014c 3a1bcbe1e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 31 20:36:28 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 76d138b1b460b0bb6d06aeb48ae6a037e24ca216
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 29 19:05:03 2016 -0800

    sync sequence numbers.

Src/C_AMRLib/Amr.cpp

commit 4c9192a9c4a673e8330edf34b38783e6af72efc8
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 29 19:04:52 2016 -0800

    sync sequence numbers.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit c75bb371be62c016cdd5116abf4a8f246f130079
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 29 16:56:53 2016 -0800

    more code for the dynamic sidecars.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/Utility.cpp

commit 3a1bcbe1ea5a8c497fe1d90501aace993b154eb3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 29 12:16:53 2016 -0800

    Remove unused variables.

Src/C_BaseLib/Particles.H

commit cd9ce2a2b644a28cc508f7d9fa0861a3f4d2a5ea
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 29 11:36:02 2016 -0800

    some name changes.

Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.H

commit 2ce1eb75bfb321d5ad1269e29f1f696c4f04f0f3
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 29 11:35:08 2016 -0800

    also bcast coordsys.

Src/C_BaseLib/Geometry.cpp

commit 535987a60ce7424d37cbf2ac073af97c12346e13
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 29 11:33:34 2016 -0800

    some name changes.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 9faed6b583f34cacbc4cdfd6be78585b87f183f7
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 29 11:30:54 2016 -0800

    sync distributionmap caches.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 83cd97f994517268882c1d73fc1329e83d0bb14e
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 29 11:29:59 2016 -0800

    some name changes.

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 8a79a498c5ee9f838cb56d42afa4f7a401f66210
Merge: ec30c0ae9 38cf0d0de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 28 14:49:46 2016 -0800

    Merge branch 'development' into pgas

commit bba796a8412e0d894227f5f1cb140f2533e0c41c
Merge: df3c57ca0 38cf0d0de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 28 14:49:15 2016 -0800

    Merge branch 'development' into mpi-onesided

commit 38cf0d0debead77ecf5f8d04a94bd6c8f45f75bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 28 14:02:31 2016 -0800

    Particles: fix array index

Src/C_BaseLib/Particles.H

commit 7a5fe83656469f642c201bcb2ff9523f49e91b38
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 28 13:52:15 2016 -0800

    TwoGridPIC: add min_grid_size, the smallest box size we can have

Tutorials/TwoGrid_PIC_C/main.cpp
Tutorials/TwoGrid_PIC_C/split_boxes.cpp

commit b3d3388d60ebd68b923f98cb73b577aac81bebe2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 28 13:44:18 2016 -0800

    Particles: add ParticleBoxArray() and ParticleDistributionMap() to container class

Src/C_BaseLib/Particles.H

commit 2fc9ba34c71f8f3ab53d2872f0acf74b8179979e
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 28 11:54:34 2016 -0800

    func name changes.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit bb3fe9d1a6330207b1181cdd0c0079fdc322d5c7
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 28 11:54:13 2016 -0800

    func name changes.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit eb63aca2eb0810ff46450479ed315245bec48f28
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 28 11:50:39 2016 -0800

    func name changes.

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit 8d52b8fc90a82cb6128ea15531ff9c72c93d9f36
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 28 11:16:51 2016 -0800

    some cleanup.

Src/C_AMRLib/TagBox.cpp

commit 49a09958e952ac4ca432434b1e68e7ee7114c006
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 28 11:15:51 2016 -0800

    some cleanup.

Src/C_AMRLib/StateData.cpp

commit 1869d9441039c305952fb81d8eb6439017d8f2f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 28 11:11:57 2016 -0800

    MemPool: minor clean up

Src/C_BaseLib/MemPool.cpp

commit 11047f90f7f468932d4a224fd8060014b1c5ec60
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 28 10:57:03 2016 -0800

    turn off printing various cache statistics by default; to turn it on, use boxlib.v=1

Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit 428fa49af4b21585d60db6aa21da9df610c5abfc
Merge: c3822ac5a 177e881fb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 27 16:48:47 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit c3822ac5acb19c125cc15d39e0c881415aa4d824
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 27 16:46:08 2016 -0800

    This version checks the actual new efficiency instead of just the approximate efficiency
    and re-distributes the grid if need be.

Tutorials/TwoGrid_PIC_C/main.cpp
Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp
Tutorials/TwoGrid_PIC_C/split_boxes.cpp

commit 0cfffcd4ca8badd1c887a9da105ab66750a2a42d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 27 16:02:58 2016 -0800

    tests for broadcasting and (un)serializing classes.

Tests/C_BaseLib/BcastClasses/BcastClasses.cpp

commit 669a4ebe7ee24afa7c2d989b2812cded38747e80
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 27 16:02:01 2016 -0800

    (un)serializeboxarray.

Src/C_BaseLib/BoxArray.cpp
Tests/C_BaseLib/BcastClasses/GNUmakefile

commit ec30c0ae98035ec22e3f2fd0f8e612658f925e5c
Merge: df3c57ca0 177e881fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 27 13:19:22 2016 -0800

    Merge branch 'development' into pgas

commit df3c57ca00856e2347f369327d746474468ddec1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 27 13:03:15 2016 -0800

    not possible to have zero size message in the communication tags

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 177e881fb065a6c91730f62624bc17407127aa8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 27 12:35:16 2016 -0800

    Particles: replace ParticlesOnSameGrids with OnSameGrids that always does the comparison.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/AmrParGDB.H
Src/C_BaseLib/ParGDB.H
Src/C_BaseLib/Particles.H

commit f7cfcc7b9d9c17878c73e63ef658d1fbdee46feb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 27 11:11:43 2016 -0800

    BoxArray: new CellEqual function that returns true if the two BoxArrays are equal in enclosed cells.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit cdd5110058c80e8cb62f9224fa228fd21e61d0c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 27 06:20:03 2016 -0800

    fix omp problem due to recent renaming

Src/C_BaseLib/Particles.H

commit 33d744c4ec7b79b83d49cf5b459490a59d8ef487
Merge: bab6fb8d8 085a5baae
Author: hongzhang shan <hshan@lbl.gov>
Date:   Wed Jan 27 00:17:55 2016 -0800

    one more timer

commit bab6fb8d8f3ab48bd77bc9a6a35b55213972b279
Author: hongzhang shan <hshan@lbl.gov>
Date:   Tue Jan 26 22:33:31 2016 -0800

    add profiling info

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Tests/FillBoundaryComparison/main.cpp

commit 02388659895e941516e055cd47e3e003c65a8f82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 26 21:24:33 2016 -0800

    fix AdvectWithUmac: (1) since umac is not cell-centered, we should not compare its boxarray with particle boxarray; (2) when we need to build new umac, we should build face-centered mf, not cell-centered

Src/C_BaseLib/Particles.H

commit 881bb52604688ef922f5c5deb25e10aa1d69e198
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 26 21:15:53 2016 -0800

    TwoGrid PIC: leave the original ba untouched and fix a memory leak

Tutorials/TwoGrid_PIC_C/main.cpp

commit d99f1ad2a50a7758bc27f8e959b58d5fc571e7c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 26 21:14:21 2016 -0800

    new MultiFab using Particle BoxArray should also use Particle DistributionMap

Src/C_BaseLib/Particles.H

commit ddbc06f4f1b460a66f2f321b7fa73bbc90118bfc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 26 20:33:43 2016 -0800

    store a copy of Geometry, DistributionMapping & BoxArray in non-Amr particle containers

Src/C_BaseLib/ParGDB.H

commit 085a5baaeed2d132f1c9fa29dedf401fb6a5d077
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 26 16:24:39 2016 -0800

    remove a barrier

Src/C_BaseLib/FabArray.H

commit 83d6a97766435dd5759bec3bd383cf6a770040bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 26 16:23:41 2016 -0800

    fix typo

Src/C_BaseLib/FabArray.H

commit 0e12224689f34e30f4dd12f8b01e81e44bca7a0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 26 16:22:30 2016 -0800

    fix a new bug; forgot that the address of vector element can be invalidate by push_back

Src/C_BaseLib/FabArray.H

commit e2903a9ceaa36dd6760506a4365cfd3a8a3ec8ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 26 15:37:27 2016 -0800

    Add recv_disp as a member of FabArray so that it is still alive when we exit from FillBoundary_nowai_MPI_Onesided, because it is possible that the sender has not received (or even posted recv for) the address stored in recv_disp yet.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 96ee39eadd524720b941779d8c13855b3cea64b9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 26 14:22:13 2016 -0800

    Add a new Tutorial which uses a different boxArray for the particles than for the multigrid solve.
    This uses functions stolen from SedonaBox that split up boxes if they have a disproportionate share
    of the cost.

Tutorials/TwoGrid_PIC_C/GNUmakefile
Tutorials/TwoGrid_PIC_C/Make.package
Tutorials/TwoGrid_PIC_C/main.cpp
Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp
Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp
Tutorials/TwoGrid_PIC_C/split_boxes.cpp

commit 559ab6550b00a3d906028ea7094623bcececb046
Merge: 9b2e497d3 832ad1e5e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 26 14:15:16 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 9b2e497d315c9b0695abcac3dfe0453a496f77a5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 26 14:13:05 2016 -0800

    1) Put in placeholder for AssignDensity for nodal multifabs -- not fully implemented yet.
    2) Enforce that mf in AssignDensitySingleLevel must have at least one ghost cell or we will lost part
       of the contribution of a particle near a fine-fine boundary!
    3) Replace the "ParticlesOnSameGrids" flag by the actual test since that flag may not be set correctly
       when we are not calling it with an AMR.
    4) Add NumberOfParticlesOnGrid so that we can count and return the number of particles per grid to use as
       a work estimate for load balancing.

Src/C_BaseLib/Particles.H

commit 832ad1e5e52a429dde9d3e531f790a76fda34616
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jan 26 13:10:46 2016 -0800

    Add NumGrow as function to LinOp

Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 8e694605ead59b1b8338d5b41b3786f2e3f277a0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 25 17:11:56 2016 -0800

    Let us use the "set" command to reassign a pointer within a PArray if
    PArrayManage is not true (i.e. PArrayNoManage is true)

Src/C_BaseLib/PArray.H

commit 74b9f54e6b37e88c769c27526769d8f3ba5a2757
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jan 25 15:21:59 2016 -0800

    broadcast functions.

Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp

commit 492df6d2a214d92ebfdd530e2b2757c5e0ddeb04
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 25 10:52:30 2016 -0800

    Particles: add SetParticleBoxArray function to set a new Particle
    BoxArray for non-Amr particle containers.  For Amr particle
    containers, users should set the Particle BoxArray in AmrLevel.

Src/C_AMRLib/AmrParGDB.H
Src/C_BaseLib/ParGDB.H
Src/C_BaseLib/Particles.H

commit cb06bf66dba5af0c0eadd7f8e7520e94a7b51f13
Author: hongzhang shan <hshan@lbl.gov>
Date:   Sun Jan 24 18:06:03 2016 -0800

    remove 0 size messages, maybe not necessary

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit c4ec0862716f6e60abfe285f6b8000189beaf97d
Author: hongzhang shan <hshan@lbl.gov>
Date:   Sun Jan 24 15:52:08 2016 -0800

    fix isend error

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 5ee53014c8d3836a4f8c8db93242aee075043a6e
Merge: 823a15878 58e3d531b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jan 22 19:39:13 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit ca38b66bc0339fdcca610cffc2262ad2d0a025af
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 22 15:16:41 2016 -0800

    USleep function.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 74ef2185b5cd79dc6aa953cb7d7f04c847e74c2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 21 17:34:07 2016 -0800

    fixed assertion and a similar 'reserve' bug in Geometry

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 394a522444f9cda8c0597df69390d3ad4947474e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 21 17:10:31 2016 -0800

    Calling reserve is not enough for send_disp. Need to actually allocate space by calling resize.

Src/C_BaseLib/FabArray.H

commit 58e3d531b12ecfa19b88759f2f9b54161334f889
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 21 15:52:57 2016 -0800

    Change itsol_CG_Solve --> itsol_cg_solve to be consistent with the declaration
    at the top.

Src/LinearSolvers/F_MG/itsol.f90

commit 183ad7c30a9cd89c7cbddc7ebde70ccf3b21b1ed
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 21 14:43:56 2016 -0800

    In itsol_CG_solve: removing the diagonalization and calling the preconditioner earlier
    dramatically reduces the number of CG iterations needed.

Src/LinearSolvers/F_MG/itsol.f90

commit 671fb0c664bd49f080be2c732a0eea6d2cef602f
Merge: 6aaaaf457 3c8bea4e8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 21 14:28:19 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 2da45fd18e309073eb0e5324e229aad62a6c4671
Author: hongzhang shan <hshan@lbl.gov>
Date:   Wed Jan 20 18:36:14 2016 -0800

    with finish function

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 3c8bea4e8610a1533b486f52781f5d7831821cef
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 20 17:32:44 2016 -0800

    the makefile.

Tutorials/DataServicesTest0/GNUmakefile

commit ff3d4e049c4fd5945d9511bb82158233ad6462d6
Author: Hongzhang Shan <hshan@lbl.gov>
Date:   Wed Jan 20 17:19:57 2016 -0800

    add finish functions

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 2ae22ce8d6dad00713dd0bdf7326989f4b09374b
Merge: 896eaf6de 3d9629f1a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 20 17:14:41 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 896eaf6de91e2a0cb8caa722172e7902d95ca903
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 20 17:02:35 2016 -0800

    A simple tutorial for DataServices and AmrData.

Tutorials/DataServicesTest0/DataServicesTest0.cpp

commit 3d9629f1a9d60aa148be257346b4c2468465553f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 20 17:01:17 2016 -0800

    fix a recent bug in FillPeriodicBoundary; it affected a special case in which there is a small box (size <= ngrow) near the corner of periodic and non-periodic boundary

Src/C_BaseLib/Geometry.cpp

commit 6aaaaf4575215ab31bf7c7b0fe437fa39159b819
Merge: 1a6024a2d ac054721f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 20 10:59:42 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit ac054721f1eee9bdf9e5c669af336a3782397bca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jan 20 11:19:42 2016 -0500

    add plot of rad sphere

Tools/RegressionTesting/Castro-SBU-tests.ini

commit a842ab87d5e1077b9325ee5b85eedbf2911df6fa
Author: hongzhang shan <hshan@lbl.gov>
Date:   Wed Jan 20 03:24:52 2016 -0800

    version 1

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit ab93588364efa75ff17f4e2c4f8547ebe87dc8dd
Author: hongzhang shan <hshan@lbl.gov>
Date:   Tue Jan 19 17:46:09 2016 -0800

    fix compiling error and process

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Tools/C_mk/Make.defs
Tutorials/PGAS_HEAT/GNUmakefile

commit b0ae3e0f69a8a7faa67c164d652330bf0657518a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 19 16:48:37 2016 -0800

    relax an assertion in average_face_to_cellcenter for Castro Gravity where the cell-centered grad phi has 3 components independent of dimsionality

Src/C_BaseLib/MultiFabUtil.cpp

commit 6cc218095771aa18063eedafe80a3073d8bac6c1
Author: Hongzhang Shan <hshan@lbl.gov>
Date:   Tue Jan 19 15:50:11 2016 -0800

    follow interface from main.cpp

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 1a6024a2dfbea4c846f72fc311b91c6c3e27c2ba
Merge: 56efa4699 0092bb3b0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 19 12:06:31 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 0092bb3b053e7278b7ce59a669c79d57a7c32f81
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jan 19 12:17:55 2016 -0500

    use the Agg backend so that we can do plots when backgrounded

Tools/RegressionTesting/testnew.py

commit 0aa9734db0d3af35fe27f5e9928db67136803206
Author: Hongzhang Shan <hshan@lbl.gov>
Date:   Tue Jan 19 01:59:40 2016 -0800

    add onesided BL_USE_MPI_ONESIDED

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 823a1587829f57a7fb6e867c55bb2659cb0e25e0
Merge: e09da8844 f9d784e66
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jan 18 13:27:17 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit f9d784e66639eee774f4f5503e71f6f4d492a9c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 17 16:47:51 2016 -0500

    use font-awesome

Tools/RegressionTesting/testnew.py

commit da6c5e2dfecd67f784feb0ed4af2acec21be109b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 17 14:45:54 2016 -0500

    add timing plots

Tools/RegressionTesting/testnew.py

commit f5d980710cae4b46f65e5d4f285104f6af718cf5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 17 13:09:24 2016 -0500

    fix complete_report_from_crash and isolate the code that parses all
    completed runs and tests to be a method of Suite

Tools/RegressionTesting/testnew.py

commit e09da8844abaff718c72fb88c87573b95825bdce
Merge: c659fa7d9 1531accdc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 17 12:04:58 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 1531accdc87dd6d358aea785ba47f034eeb74e37
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 16 15:16:09 2016 -0800

    more interfaces to bl_allocate

Src/C_BaseLib/mempool_f.f90

commit c659fa7d9dc894bdb7ee1cbeae0a8a27ed9fd1d3
Merge: 0a6b64b78 df708547d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jan 15 09:37:48 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 27107ca70b785f46696b12aa9e1272e9879b3fce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 13 09:07:16 2016 -0800

    Just like PostRcvs, no need to pass in RcvTags in PostRcvs_PGAS

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 2daa5d50cee4b18022a75007f033c19b879742d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 13 08:59:09 2016 -0800

    fix the merge

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 8bf9c3ca82c7462c0cef5fadaf916d009a01ae1d
Merge: ef8cdde00 df708547d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 13 08:47:12 2016 -0800

    merge

commit df708547dce1dafffc9a379d7d12c3a604e22523
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 13 08:31:39 2016 -0800

    PostRcvs: no need to pass in RcvTags

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit d9f54ad3a7bef9817d20c9925622d4e24dc635af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 12 16:50:11 2016 -0800

    add FabArrayBase::empty()

Src/C_BaseLib/FabArray.H

commit f743c4dd8cb42490d10df5d322f31f4cbe551f5c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 12 12:29:10 2016 -0800

    add AdvectWithUcc that advects particles with cell-centered velocity

Src/C_BaseLib/Particles.H

commit 6007bc38586d7d510bc4eaaf5e01eab1a16e3868
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 12 11:30:14 2016 -0800

    AdvectWithUmac: fix boundary

Src/C_BaseLib/Particles.H

commit c4f06fa2a0a13070257282ce9abf09be058720e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 11 18:12:48 2016 -0800

    remove an assertion

Src/C_BaseLib/Particles.H

commit e692ad4387f42446acd32edf598bc960b5719b00
Merge: 06c5c31c1 719157e94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 10 15:31:24 2016 -0500

    Merge branch 'development' into preprocessing

commit 719157e9434dedc94fd2d83d312142e517472a02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 8 10:11:19 2016 -0800

    Revert this for now because IAMR's SyncRegister actually needs these
    functions.  Will need to fix SyncRegister.
    
    This reverts commit 4652df14803966b5be882529bd3720b9783b4b2f.

Src/C_BaseLib/FabArray.H

commit cb6eb363c105b863b9fb1204be4b75c704147abb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 8 10:07:14 2016 -0800

    fix bug in my recent change to SumPeriodicBoundary

Src/C_BaseLib/Geometry.cpp

commit 5473fc1381dfc3afac0699ae8e1417d2378998a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 8 10:05:36 2016 -0800

    fix bug in my recent change to SumPeriodicBoundary

Src/C_BaseLib/Geometry.cpp

commit 1f38b0f5c269be2f9f9a26aa6034a0ad46b152c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 21:10:46 2016 -0800

    add comments and tweak Geometry::FPB::Operator<

Src/C_BaseLib/Geometry.H

commit 9a68c8e2ee50f0721b023c6035170fd6914e134c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 20:54:09 2016 -0800

    comments

Src/C_BaseLib/FabArray.H

commit 4652df14803966b5be882529bd3720b9783b4b2f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 17:29:11 2016 -0800

    no longer needed

Src/C_BaseLib/FabArray.H

commit 2720761a2a5613dc5139ec7d84093e827427de45
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 17:28:11 2016 -0800

    Optimization of SumPeriodicBoundary by reusing the FillPeriodicBoundary cache

Src/C_BaseLib/Geometry.cpp

commit 25946aa27dcb8ac7a4ea3f5b180cc4dcb0affc51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 15:57:47 2016 -0800

    readablity

Src/C_BaseLib/MultiFab.cpp

commit ef8cdde00efdd66813f547aaced587700fdc5ffa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 12:34:37 2016 -0800

    minor clean up

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 0cb90507526c0524d9d887bd407a30677ddf8b02
Merge: d229cb414 a4dc8a8fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 11:16:19 2016 -0800

    Merge branch 'development' into pgas

commit d229cb414ecd7ea00c2bce9306825892bbfb9a21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 11:16:03 2016 -0800

    remove the option to break messages into smaller pieces

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H

commit 0332ff2f97a887d822529e316d0a7257afd33944
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 6 18:08:16 2016 -0800

    remove team sender and receiver because it does not perform

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 425090c0aa278c55b724c02de7a8d6573d36aa07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 6 17:01:52 2016 -0800

    started MPI-3 team

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Tools/C_mk/Make.defs

commit a4dc8a8fbadf24aca4d2f67be5e725d15a5d4cc8
Author: Changho Kim <changhokim@lbl.gov>
Date:   Wed Jan 6 14:44:49 2016 -0800

    f90 codes do now work on cori.

Tools/F_mk/GMakeMPI.mak

commit d80168e13faf878995c1653b83ed761c6fadd6d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 6 13:46:44 2016 -0800

    TagBox: add optional alloc argument because of its base class BaseFab

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 35879beb87f08af0de9b10455ca328ef6b786c9f
Merge: 605b9fece 68d3922cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 6 12:58:13 2016 -0800

    Merge branch 'development' into pgas
    
    Conflicts:
            Src/C_BaseLib/FabArray.cpp
            Src/C_BaseLib/Geometry.cpp

commit 68d3922cda50e1cf2aff2e05a9bf880931aef910
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 6 12:19:59 2016 -0800

    new way of thread safety check in FillBoundary, FillPeriodicBoundary and parallel copy

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit a2c73b73ec2cde9a7a3897b6ab3f2fd27a15499f
Merge: f3c631554 f7714e0cd
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 5 18:59:38 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit f3c631554695373019424d0ba97cf240e8e85493
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 5 18:58:58 2016 -0800

    plug memory leak in multifab_sum_boundary_c

Src/F_BaseLib/multifab_f.f90

commit f7714e0cd190f39e0173639276fd53381af0d5e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 5 16:39:35 2016 -0800

    FabArray::shift: need to update BoxArray-DistributionMap key.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 8a710b199fbbd54dcc95c8243dc7c80744801be1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jan 5 19:25:53 2016 -0500

    update usage

Tools/Postprocessing/F_Src/fextrema.f90

commit a0120dc11993a523b41838926d88fa3b3f3e4339
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 5 15:37:09 2016 -0800

    clean up

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 605b9fece733ada8283d7eaa9a4cd5f7d073405a
Merge: 183f00038 dfcc6a7cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 5 15:08:12 2016 -0800

    Merge branch 'development' into pgas
    
    Conflicts:
            Src/C_BaseLib/FabArray.cpp
            Src/C_BaseLib/Geometry.H
            Src/C_BaseLib/Geometry.cpp

commit dfcc6a7cfccae1653f47f7239fd1b4b9d0b42961
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 5 13:22:01 2016 -0800

    new functions that copy from periodically shifted MultiFab to another MultiFab.  This is useful for restriction of nodal/edge/face MultiFabs

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 899476117aee60139983234fe558c65e9fe3ba65
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jan 5 13:21:11 2016 -0800

    call bndryreg function.

Src/C_AMRLib/FluxRegister.cpp

commit 0a6b64b781d65f895719badfce08257a8790ac31
Merge: 06c5c31c1 a6fb893a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jan 5 10:45:14 2016 -0500

    Merge branch 'development' into preprocessing

commit 06c5c31c10b4c256d18b14b1533752aa3643fb10
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 4 21:17:04 2016 -0800

    comment out rules for F90 and add VPATH for preprocessed F90

Tools/C_mk/Make.rules

commit a6fb893a8791ca762675f78839298683d1a09d5e
Merge: 6df1d6123 e5d6d0811
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jan 4 19:12:50 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 6df1d61239a5d0eb9d1b7dcc2360088194f7be7c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jan 4 19:12:40 2016 -0500

    new source format

Tools/RegressionTesting/Maestro-tests.ini

commit e5d6d08117e165310858dbe9ff5b2b4f664db8a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jan 4 19:11:23 2016 -0500

    add the Detonation test

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 56efa4699d795047231d8bb643a6b648d18e2266
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jan 4 15:33:33 2016 -0800

    Replace FillPeriodicBoundary by fill_boundary so we fill grad_phi on all ghost cells,
    not just periodic boundaries.

Tutorials/PIC_C/solve_for_accel.cpp

commit 33afb449cc0641308b8a79f58d7a940b9b9c1f46
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jan 4 14:15:51 2016 -0500

    remove Intel compilers version 5 to 9.1 -- they are all more than 10 years old

Tools/C_mk/Make.defs

commit b803db0d09f0b4cb385ac73ea106de7a29c9234a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jan 4 11:30:35 2016 -0500

    remove unneeded clause -- this now seems to work.  The F90 files are
    preprocessed before the dependency checking is done.  This eliminates
    spurrious warnings from the moddep script about modules that are
    ifdef-ed out not being found.  Note: in your code's makefile, you
    need to add:
    
    $(f77TempDir)
    
    to the
    
    vpath %.f90
    
    line

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 4a52f8b71bf950a5e7254ee87e87f086b7d5d039
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jan 4 09:59:58 2016 -0500

    some work to get F90 preprocessed before the dependency checking

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit b32dcaea66b74586a1aea225d3d9793a13eb614f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 3 22:08:03 2016 -0500

    remove homer

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit a19e8547b3327243e07489f83ca983cf7c7190d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 3 16:39:26 2016 -0800

    PArray: add a new function to make it easy for PArray to be used in the 'resource acquisition is initialization' idiom.

Src/C_BaseLib/PArray.H

commit ae7f7562074df81a430da97e601bd673ff0dc095
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 2 20:51:36 2016 -0800

    Remove the SumPeriodicBoundary that takes two mfs.  I don't think it is used in any codes now.  This will allows further optimization of the remaining version of SumPeriodicBoundary.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit f35790bd55c1b9b9f75cefb33bffaf835f8db150
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 2 13:52:46 2016 -0800

    optimize box-box intersection for FillPeriodicBoundary

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit f40f445cbb4ea0979cec51dd29d074496f47de06
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 2 13:52:00 2016 -0800

    keep boxarray hash

Src/C_BaseLib/FabArray.cpp

commit 0590d8e3e53a6a8d205c714d523be96f5b0bff86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 2 08:19:15 2016 -0800

    comments on filling periodic boundary

Src/C_BaseLib/Geometry.H

commit b6866b351d993845df1dec00f77f4f253e4b4646
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 26 20:28:40 2015 -0800

    minor optimization

Src/C_BaseLib/FabArray.cpp

commit 63ecba7946da70c0e3772bf56fa5726799f1ab62
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 26 20:28:09 2015 -0800

    make it more readable

Src/F_BaseLib/layout.f90

commit 35c6f4865a266ef486c4bfa77109c8df32d4f0b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jan 2 16:34:07 2016 -0500

    fix the make_realclean -- we need to be careful about whehter any
    build strings are None

Tools/RegressionTesting/testnew.py

commit 947fce5138fc723edd435d95cfe48cdf78f4002d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jan 2 12:53:46 2016 -0500

    update to the new format + rad and wdmerger tests

Tools/RegressionTesting/Castro-SBU-tests.ini

commit e39edd3bcde1e1c3fae9a3cbd422afe2412616d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jan 2 12:51:57 2016 -0500

    change the way source repos are defined -- they now all have their own
    block in the inputs file.  See
    
    ./testnew.py -h
    
    for a description.  This change makes it a lot easier to support
    multiple sources and define the desired branch for each.

Tools/RegressionTesting/testnew.py

commit d9b2c3b3c7a098bf6b0e419eaac6dbc2c4d5a80b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 26 13:46:52 2015 -0800

    tiling in local copy

Src/C_BaseLib/FabArray.cpp

commit 67223b9ef823c18acae5e6563698b0de68faa87e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 26 12:40:34 2015 -0800

    optimize box-box intersection for parallel copy

Src/C_BaseLib/FabArray.cpp

commit 0d0961e45be36e3a7e52a965371178267c8d5c68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 26 11:59:59 2015 -0800

    fix thread safety in FillPeriodicboundary

Src/C_BaseLib/Geometry.cpp

commit 16a9fdb825eb16a21c9279f82c9716bb96967a7d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 25 21:18:16 2015 -0800

    have to make sure the intersection box is not empty

Src/C_BaseLib/FabArray.cpp

commit ff6644806212005d2caaf772276df7b6c1199032
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 25 20:57:32 2015 -0800

    revert some changes in the last commit because of IAMR

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit 6cc40c84f1114fa2f44bd425810ce38f4ea56a86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 25 17:33:04 2015 -0800

    optimize box-box intersection for Fillboundary

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit 8a9b8b1862fed5fd4ded12895f823e6e2b287f41
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed Dec 23 02:37:22 2015 -0500

    Change the logic for amr.check_per so that it is analogous to amr.plot_per: we write a checkpoint at the first timestep *after* the interval has passed, whereas before we wrote a checkpoint at the timestep *before* we got to the interval.

Src/C_AMRLib/Amr.cpp

commit 59d8a4ee5c955ed27c63e41e2bcc80c7da4b6b8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 21 20:30:54 2015 -0800

    Fortran layout: clean box hash to save memory

Src/F_BaseLib/layout.f90
Src/F_BaseLib/ml_nd_restriction.f90

commit a3b65b36cfc13a11451db7c9249ee181aa915da6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 21 17:09:46 2015 -0800

    tidy

Src/F_BaseLib/layout.f90
Src/F_BaseLib/ml_nd_restriction.f90

commit 8f8389382968d70aabec60e349a98a376d4a2421
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 21 13:12:52 2015 -0800

    removed some temporary layouts

Src/F_BaseLib/ml_nd_restriction.f90

commit 3a9437c64b61b45cca46abbb0793d15ce1238aae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 21 12:37:48 2015 -0800

    Fortran layout: get rid of temporary layouts since now layout box intersector can handle nodal and ghost cells.

Src/F_BaseLib/layout.f90

commit 5d21ab1d9b96faf43e8bea9f6e0190f709122474
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 21 11:21:11 2015 -0800

    Fortran Box Intersector: make it work for nodal and ghost cell

Src/F_BaseLib/layout.f90

commit b7d77a8140641fce54e3d9f2ccbbe7ae56bdcf01
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Dec 19 14:17:02 2015 -0500

    Fix incorrect query for small_plot_file_root

Src/C_AMRLib/Amr.cpp

commit a17dcabc1105035a0a18c28ec85b5c8b661b9e2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 18 15:46:15 2015 -0800

    move the setup of signal handler after MPI_Init

Src/C_BaseLib/BoxLib.cpp

commit b8a9d07d298ca6df4776a389ae212936394c67b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 18 15:35:14 2015 -0800

    move the saving of the executable name after MPI_Init has a chance to propgate argv to all processes

Src/C_BaseLib/BoxLib.cpp

commit 9b22133d37da4fc7b8bc460319e17d54b90bccce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 17 17:52:05 2015 -0800

    Particle: Use midpoint instead of predictor/corrector to advance particles with mac velocity.  This requires only one instead of two ghost cells.

Src/C_BaseLib/Particles.H

commit 578acd0096c148426601b60849942c674fefbffb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 17 17:19:19 2015 -0800

    make the output more readable

Src/C_BaseLib/BoxLib.cpp

commit a6a8b59799ee930de9425f42027259c9bb637c4b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 17 15:50:03 2015 -0800

    Add is_nodal() test for MultiFab so we can easily test if a MultiFab is fully nodal or not.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/MultiFabUtil.cpp

commit 3b6ed54e8af6ca0b5027642aef97746a7cae6e0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 16 12:14:34 2015 -0800

    Particle: change the minimal number of ghost cells of mac velocity from 2 to 1 in assertion

Src/C_BaseLib/Particles.H

commit 2902ffa331b1394226a567f158d66da7a3ee7b07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 16 09:13:48 2015 -0800

    tidy backtrace

Src/C_BaseLib/BoxLib.cpp

commit 80b907900f28a3d75128907fe15592839f802668
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 15 16:51:06 2015 -0800

    print out more comments about addr2line

Src/C_BaseLib/BoxLib.cpp

commit 1cbc5366b04068ca84042c9181b9b411a18dea27
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 15 16:21:14 2015 -0800

    Particles: fix a memory leak in AdvectWithUmac

Src/C_BaseLib/Particles.H

commit 3154f138bdbd1331668cfe0589a95d384abb6a81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 15 16:07:51 2015 -0800

    clean up

Src/C_BaseLib/BoxLib.cpp

commit 3fcb3593c57026fd6ef0169953f8563320ca0e14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 15 16:04:47 2015 -0800

    For backtracing, use addr2line, if available, to print out function names and line numbers

Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Tools/C_mk/Make.defs

commit 54534d33558192da21d937aeb95cdbad6f6568a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 15 14:03:51 2015 -0800

    mfiter: allow growntilebox to have negative ng

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 57e0fc9efe9c3c60e1ba9e51cea3a31f2111fe37
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 18:37:29 2015 -0800

    MakeSidecarsSmaller function.

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 593d43b3bd7e351f131f5e2267a41a6904463f7d
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 17:08:05 2015 -0800

    promote MultiFab::MakeSidecarsSmaller

Src/C_BoundaryLib/FabSet.H

commit c355f897b89427c8fd24b0540f195fceb7285a80
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 17:05:01 2015 -0800

    MakeSidecarsSmaller function.

Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit fea6672ebeedf0101f8c3b75944e4668a586574f
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 17:04:19 2015 -0800

    lock allocated fabarray pointers.

Src/C_BaseLib/FabArray.H

commit 349042ca0158f7fb37b64a1d0179d4bc53497c11
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 17:03:06 2015 -0800

    MakeSidecarsSmaller function.

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit b6a350c3c2d5624cf3652902dbdbe49930f5beec
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 17:02:39 2015 -0800

    multifab movement.

Src/C_AMRLib/StateData.cpp

commit a36771b6960f2b3011a127f8a2dac572eb2cc74a
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 17:01:29 2015 -0800

    lock allocated fabarray pointers.

Src/C_AMRLib/Amr.cpp

commit 53f2d5a9015bc98d9a79c25996d24680d9c0b21b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Dec 14 19:04:54 2015 -0500

    no more hopper

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 183f00038caa3df9ae677839fe846543b7d6a9f7
Merge: ff3987e85 b6e44c2f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 14 11:24:19 2015 -0800

    Merge branch 'development' into pgas

commit b6e44c2f2ede1fc9694a77a86c007fe9f08a3152
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 14 11:23:11 2015 -0800

    cleanup

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit ff3987e8536b2e0906187574fe35cacab343d6f7
Merge: 9d483e825 cc3bc8c97
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 14 11:06:58 2015 -0800

    Merge branch 'development' into pgas
    
    Conflicts:
            Src/C_BaseLib/FabArray.cpp
            Src/C_BaseLib/Geometry.H

commit cc3bc8c979b0f65a181dd37245758b407b377f4f
Merge: 5dcefeef4 8e1389994
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Dec 14 11:45:53 2015 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 5dcefeef4dce679760e23a8c4dae2590b4d7489b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Dec 14 11:45:44 2015 -0500

    goodbye hopper

Tools/F_mk/GMakeMPI.mak

commit 8e1389994802bf9f118a82f9fd7fda690e32f178
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 13 16:14:00 2015 -0800

    clean up

Src/C_BaseLib/FabArray.H

commit 95e34c1153c628734c1d5b343f8023944baefe1d
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Dec 11 08:21:10 2015 -0800

    add gojira and kumonga to DEFAULT_MACHINES

Tools/F_mk/GMakeMPI.mak

commit 2a316b63d05f107d8ce2a0f894b52d9fed53292a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 10 20:58:43 2015 -0500

    simplify a lot of entries in GMakeMPI.mak -- all these machines were doing
    the same thing, so we use a GNU make findstring() to simplify them.

Tools/F_mk/GMakeMPI.mak

commit 0acf5ad73ad2b76346883b74550caf63dc531114
Merge: 784dd19a6 c7e881f1d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 10 17:18:12 2015 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 784dd19a6bb9c2d0ae31e17d7d42e0b4c5a14779
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 10 17:17:58 2015 -0500

    update the build_info.f90 to allow for no modules

Tools/F_scripts/makebuildinfo.py

commit c7e881f1d0a8a928d3d4f058498a1edd9eba3e0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 10 12:35:24 2015 -0800

    use the new BoxArray intersect functions

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/Particles.H
Src/C_BoundaryLib/FabSet.cpp

commit 5a65941fd946714322592a2ec678c15d6e205040
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 10 12:29:48 2015 -0800

    fillpatch: remove the ngrow hack

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/AuxBoundaryData.H
Src/C_AMRLib/AuxBoundaryData.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit baa115c268e94db694f842fa44a06c076dbd3f61
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 10 11:20:59 2015 -0800

    Parallel copy: using the new BoxArray intersect function

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit b9cfd782facfb87cac3b22b390ba09ef0fd4e746
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 10 11:07:01 2015 -0800

    BoxArray: add ng argument to intersect functions.  using it, we don't need to create temporary boxarrays in parallel copy

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 0867a7a5725e59cfac4830b514c5e16d07821387
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 10 12:40:16 2015 -0500

    shut-up the iso_c_binding warning

Tools/C_scripts/moddep.pl

commit ff3ba9b99be38edb37eb92bb6cefa2a34f2e6deb
Merge: 68f86948e 023ea8de3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 10 12:26:26 2015 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 68f86948e7fd5d460799c47bcb3868888b2af3ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 10 12:26:13 2015 -0500

    homer no longer exists

Tools/C_mk/Make.defs

commit 023ea8de37c959853c7f495bf76741310460c96c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 10 12:17:45 2015 -0500

    inlining of C++ doesn't work with GCC 5 and the recent BoxArray stuff.  Disable it
    for now until gcc is fixe.d

Tools/C_mk/Make.defs

commit caf810434369cc7ab293505bf7275ab0fe9787db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 9 20:44:32 2015 -0800

    fix typo

Src/C_BaseLib/BoxArray.cpp

commit 4863c43c18be91260d57e14e9091f843cce659d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 9 18:04:22 2015 -0800

    Since BoxArray has index type now, we can use it insetead of the type of Box 0 in the array

Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_TowerLib/MFTower.cpp
Src/Extern/amrdata/AmrData.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Tools/C_util/WritePlotFile.cpp
Tutorials/AMR_PETSc_C/Source/Darcy.cpp

commit af38aa5c36bf971470ab966b3722189670af2a85
Author: vince <vebeckner@lbl.gov>
Date:   Wed Dec 9 16:27:27 2015 -0800

    broadcast array function.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit b3c80f60954af1c0c3591544b7424b04ed3221e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 9 14:00:12 2015 -0800

    BoxArray:
        Add index type to BoxArray.  This allows nodal and cell-centers
        BoxArrays share the same reference, which is now always stored as
        cell-centered boxes.  Because of the change, the operator[] now
        returns Box on demand instead of const Box&.
    
    MFIter:
        Because of the changes in BoxArray, the tile arrays now always
        store cell-centered boxes.  This will construct a nodal box
        on-demand.
    
    A number of other changes have to be made due to that BoxArray no
    longer provides a const_iterator and the change in return type of
    operator[].

Src/C_AMRLib/AmrLevel.H
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 55457294e743076643b629bcd53f74716b822fc2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 9 10:10:35 2015 -0800

    IndexType: functions testing cell or node given a direction

Src/C_BaseLib/IndexType.H

commit e1ba175d98faa92ddaa8f556009e20b9a5a59e6e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 9 09:54:40 2015 -0800

    Box: add convert more functions and remove a const

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp

commit e7f680cfc9fe08c932c78d28e8230d5af3170bf0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 3 15:47:12 2015 -0800

    add distributin mapping to cache even if it's a single process run so that the reference id could work

Src/C_BaseLib/DistributionMapping.cpp

commit 9d483e825022bde6de7e85824dadbaa5397f0cf3
Merge: 8008487a8 788ced409
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 9 09:39:14 2015 -0800

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit 4d61f3b2658d60d09104f2e65459c36d2334ba4e
Merge: 0d55d1400 9f4ac2bf9
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Tue Dec 8 21:17:26 2015 -0500

    Merge branch 'development' into openacc

commit 3bf956694166255636357cee24e0f92d37143524
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 8 18:03:45 2015 -0800

    more broadcast functions.

Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 58d662713377a35b154b2f85e52ac514fcf9d522
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 8 16:27:37 2015 -0800

    added virtual destructor.

Src/C_BaseLib/MultiFab.H

commit c0553172c7b260d5cab0e0f6d96665492183bc6b
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 8 16:26:49 2015 -0800

    replaced code with broadcast functions.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.cpp

commit afd810c3eaaddd4e8b484d0577c0f000e8231f60
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 8 16:05:16 2015 -0800

    functions to broadcast boxes and boxarrays.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit e6532ea692e9a81be081b6b3a7666919ad93e6e2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Dec 8 16:01:32 2015 -0500

    Add a small plotfile functionality to C++ BoxLib. The small plotfile is very similar to a normal plotfile, but it can be output at a different rate using amr.small_plot_int and amr.small_plot_per. The major difference is that it only accepts state variables, and you have to manually specify each one using amr.small_plot_vars. This is designed for output of a small number of variables at a high rate, for purposes like making movies of your simulations. Unlike the plotfile functionality, this is not implemented as a pure virtual function, so it is not required for derived classes of AmrLevels to implement this functionality.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 9f4ac2bf95d9816866f0d1b77f7525275d1afb48
Merge: 4050be6c2 ea6c230c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Dec 8 12:55:40 2015 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 4050be6c25cd60494d9b4e647c34b1ccf441515f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Dec 8 12:55:23 2015 -0500

    fix the flags for .F90 preprocessing with Linux

Tools/C_mk/Make.Linux

commit bd8b4a788739a047285b8de8307bb9c5a0d8f1aa
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 7 18:28:52 2015 -0800

    added undefined strategy.

Src/C_BaseLib/DistributionMapping.H

commit a33501326da628c33fbd7fea9535e25c89840aa5
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 7 17:56:04 2015 -0800

    functions for making the sidecars smaller.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit faaa06ba223bd8d5334b5096263fba0ef7a69be3
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 7 16:35:46 2015 -0800

    FabArray pointer locks, mpi only sections.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit ea6c230c01a9da80433adb6ad582444b0e0b2b11
Merge: dae4872dc 3f6191b0b
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 7 14:11:29 2015 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit dae4872dc6bbfdfb2534aa636cc438c6c451437f
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 7 14:11:09 2015 -0800

    added machine support for syrah.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 3f6191b0b7e0ef4112f13550813ccb5ebbca5cd8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 4 15:51:22 2015 -0800

    add optional argument to FillCoarsePatch to allow copy into ghost cells

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 9d6c1945320632d5971eaf5b9d2e197d0af0610d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 4 15:45:42 2015 -0800

    copy from FabArray to fab: allow copying from the ghost regions

Src/C_BaseLib/FabArray.H

commit bc51aba591d3cae4661bb2e16286e750083e609a
Author: Gunther H. Weber <GHWeber@lbl.gov>
Date:   Thu Dec 3 18:32:56 2015 -0800

    Fix building with BL_NO_FORT for VisIt

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/Make.package

commit 1176fbc5363d9af2a788121aad70f3f5b4e778ac
Author: Gunther H. Weber <GHWeber@lbl.gov>
Date:   Wed Dec 2 17:05:15 2015 -0800

    Added BL_CXX11.H to CMakeList.txt

Src/C_BaseLib/CMakeLists.txt

commit 8e15ff8f354c0a3ae7a0337616bc1c4145ce821f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 2 14:33:06 2015 -0800

    Copy Cache stats

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 158bbca81a2cccb90bb6980a353d0b31d5ce5b70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 2 14:15:09 2015 -0800

    tidy

Src/C_BaseLib/FabArray.H

commit 3031712e5213c4f50f3b486d84efb325b9201f17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 2 14:04:06 2015 -0800

    Fill Boundary Cache stats

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit f0b5f31d1ee31dfae530043358ec6c3ff19625f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 2 13:08:28 2015 -0800

    rework on cache stats

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 771f00d76da181bd724b18c5485f07fd6e8110a2
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Dec 2 14:11:22 2015 -0800

    Fixup CMakeLists.txt to reflect that BCRec and BC_TYPES.H moved from C_AMRLib to C_BaseLib

Src/C_AMRLib/CMakeLists.txt
Src/C_BaseLib/CMakeLists.txt

commit a1fdef04640f7b9379d7473d35f710ed120b2f57
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Dec 2 13:19:51 2015 -0500

    hack in support for branches for the extra build directories

Tools/RegressionTesting/testnew.py

commit 788ced4092422574486032fe38094a9777ca2b41
Merge: b4ac11c33 06b284237
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 21:31:30 2015 -0800

    Merge branch 'development' into pgas

commit 06b284237ab5482b1ab7d2ff3afa393a816e5c1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 21:28:55 2015 -0800

    TileArrayCache: improve print()

Src/C_BaseLib/FabArray.H

commit b4ac11c333eaa6f17dd2d8c56181a9ef72789213
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 21:28:55 2015 -0800

    TileArrayCache: improve print()

Src/C_BaseLib/FabArray.H

commit 498622edf79fb96582b61ee86db77ef259814862
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 21:27:38 2015 -0800

    PGAS_SMC: limit the scope of SMC for more accurate stats

MiniApps/PGAS_SMC/main.cpp

commit 1615c5f5d5b39d768b81ca68a8e09221a1c8c4f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 20:50:11 2015 -0800

    MFGhostIter: need to set various indices

Src/C_BaseLib/FabArray.cpp

commit a87bf7df09c6592fad8079f0a0e172c49488296f
Merge: ca8613895 f07eb3a0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 20:45:47 2015 -0800

    Merge branch 'development' into pgas

commit f07eb3a0d298e17639de8c9eddb46424627b539f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 20:45:07 2015 -0800

    TileArrayCache: tidy

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 0a2825aa0a96633ff063708607b5714fb22b037d
Merge: b32fc6c79 5353151f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 17:56:06 2015 -0800

    Merge branch 'tilearraycache' into development

commit 8008487a892e090954a095afe55227a44c454c45
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 17:18:20 2015 -0800

    PGAS_SMC: change defaults

MiniApps/PGAS_SMC/SMC.cpp

commit ca8613895a7bac176d886cdbda682ece8f448824
Merge: f094d8fff 5353151f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 17:06:40 2015 -0800

    Merge branch 'tilearraycache' into pgas

commit 5353151f2f2d9899449841c4fa659a40f23c9c6c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 17:06:33 2015 -0800

    FabArray stats: don't need to use long long because long is 8 bytes on 64-bit Unix systems.

Src/C_BaseLib/FabArray.H

commit f094d8fff21c11f91e83d577293d15c065ef111a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 17:03:24 2015 -0800

    fixed MFGhostIter

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 732385539c824bedd12c37ce2e59f9b522f74539
Merge: 285066cf5 ab8483356
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 16:34:39 2015 -0800

    Merge branch 'tilearraycache' into pgas
    
    Conflicts:
            Src/C_BaseLib/FabArray.H
            Src/C_BaseLib/FabArray.cpp

commit ab8483356897c7fe2522e609c7f2509e70bf634c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 16:21:54 2015 -0800

    tidy

Src/C_BaseLib/FabArray.H

commit b707cd204d7f4dba0be92295909f6a3c7bed4b0b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 15:09:28 2015 -0800

    FabArray: stats

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit b57ffaab5dc36d25dba6e77af34936862da6cd38
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 14:40:54 2015 -0800

    TileArray: add stats

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit f29903ea3fc4be9308534d978023af159a75f324
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 10:54:18 2015 -0800

    new MFIter ctor taking TileArray ptr

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 9e8dfeb300ece8be4c19067b663b8ccde650e0fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 10:42:51 2015 -0800

    add MFIter dtor

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 6b32e86ba1f7163ae1dd5a14e7c6239ea6782234
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 10:40:53 2015 -0800

    cleanup

Src/C_BaseLib/FabArray.cpp

commit 85aac227e6c2bca6d6892d2ea651e39877355dbf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 10:30:29 2015 -0800

    TileArray: use pointer instead of reference in MFIter so that we can pass null ptr; use omp critical instead of single.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit d6361e789be8c4bac1517c84aa661c1e77de8566
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 30 16:33:42 2015 -0800

    FabArray: if it is never defined, do not need erase tile array

Src/C_BaseLib/FabArray.H

commit b32fc6c79f415acc49118b9b3387e04c88d10fba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 30 16:10:04 2015 -0800

    more regression tests inputs

Tutorials/MultiGrid_C/inputs-rt-c-neu
Tutorials/MultiGrid_C/inputs-rt-c-ord2
Tutorials/MultiGrid_C/inputs-rt-c-ord3
Tutorials/MultiGrid_C/inputs-rt-f-neu
Tutorials/MultiGrid_C/inputs-rt-f-ord2
Tutorials/MultiGrid_C/inputs-rt-f-ord3

commit ecb829d2c1102d9914b490b03674f161e465d329
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 30 15:49:10 2015 -0800

    Tutorials/MultiGrid_C: fix contradictory comments about Dirichlet boundary order in HPGMG

Tutorials/MultiGrid_C/inputs

commit 9956c1e74f9df135d03f943ca84f96d436b4910d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 30 15:45:56 2015 -0800

    Linear Solvers Comparison Test: add maxorder parameter and new inputs for regression tests

Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord2
Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord3
Tests/LinearSolvers/ComparisonTest/inputs.3d
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp

commit 4bc5612d19a8cfff83d4f90b74d20caeeef8dc83
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 30 15:39:56 2015 -0800

    MultiFab: remove my inexplicable const_cast<> for getVect() pointers in MPI buffers in SendMultiFabToSidecars()
    
    I don't know what I was thinking here. Using const_cast<> sometimes
    sends nonsense data to the sidecars.

Src/C_BaseLib/MultiFab.cpp

commit dd26f41339d1a5b2ac9ff9d7a5a113de6113c2c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 30 15:37:17 2015 -0800

    MultiGrid_C Tutorial: add inputs for new regression tests

Tutorials/MultiGrid_C/inputs-rt-c-ord2
Tutorials/MultiGrid_C/inputs-rt-c-ord3
Tutorials/MultiGrid_C/inputs-rt-f-ord2
Tutorials/MultiGrid_C/inputs-rt-f-ord3

commit 7fd00753ae4c11cb2d49a1827a497f9a8f78bab8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 30 15:32:10 2015 -0800

    MultiGrid_C Tutorial: rename mg.stencil_order to mg.maxorder

Tutorials/MultiGrid_C/inputs
Tutorials/MultiGrid_C/main.cpp

commit 285066cf50add11d0d4b2033eedb7d8316d482e5
Merge: cf38ae82e 1aa6ecc57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 30 14:56:53 2015 -0800

    Merge branch 'tilearraycache' into pgas
    
    Haven't fixed all conflicts yet!
    
    Conflicts:
            Src/C_BaseLib/FabArray.H
            Src/C_BaseLib/FabArray.cpp

commit b007518b7c098748609da04b268f34c8e305e090
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 30 13:58:27 2015 -0800

    Tutorials/MultiGrid_C: set default Dirichlet boundary condition order to 2 in inputs file
    
    HPGMG uses 2nd-order Dirichlet boundary conditions, so use that by
    default in the BoxLib solvers so that all 3 solutions match.

Tutorials/MultiGrid_C/inputs

commit 5cf2f8e4167e7e85485e8cec9b57267aafd14785
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 30 13:57:13 2015 -0800

    Tutorials/MultiGrid_C: enable writing numerical solution plotfiles by default in inputs file

Tutorials/MultiGrid_C/inputs

commit 5a643f29d01553e0568070e2d8b5d4fb94379176
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 30 13:56:27 2015 -0800

    Tutorials/MultiGrid_C: disable calculation of norms by default in inputs file

Tutorials/MultiGrid_C/inputs

commit f4ad864897310fe415f74c5c6b44c4e9654efe76
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 30 13:30:43 2015 -0800

    We can now pass mg.stencil_order in through the inputs file
    to be used to set the max_order for the F90 solver through a set_maxorder call.
    Note that the "orders" must match (2 and 2, or 3 and 3) for the F90 and C++
    solvers to give the same solution with Dirichlet boundaries.

Tutorials/MultiGrid_C/inputs
Tutorials/MultiGrid_C/main.cpp

commit b09cfdd0185265179d0840813e12fec7ddd2c15f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 30 13:29:55 2015 -0800

    Typo in comment.

Tutorials/MultiGrid_C/RHS_3D.F

commit e344d99ae60dd6d477b9fc802659d371b8f5a763
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 30 13:29:38 2015 -0800

    Formatting changes so these are easier to read.

Tutorials/MultiGrid_C/COEF_2D.F
Tutorials/MultiGrid_C/RHS_3D.F

commit 40a33b507e7973b495a643aaa71accc570e3b0d8
Merge: 246801c3f 7ff8d7729
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 30 13:29:13 2015 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 246801c3fe07cb46aa21bd6adf0fed244d1bf57f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 30 13:28:26 2015 -0800

    We previously had the same RHS and the same exact solution in 2D and 3D.
    However, this is not analytically correct.
    We have modified the RHS in 2D so that it gives the 2D solution with the same
    magnitude as the 3D solution.

Tutorials/MultiGrid_C/RHS_2D.F

commit 1aa6ecc577a957a1170cba4ea1079c319e0b48a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 30 13:26:49 2015 -0800

    TileArray: fix typo

Src/C_BaseLib/FabArray.cpp

commit 7ff8d772985e03b7447af9f34f9c14ef1d86008a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Nov 30 16:23:02 2015 -0500

    also fix fab_bind  for 2-d w/ ghost-cells

Src/F_BaseLib/plotfile.f90

commit 04dfa2f13bf1118893540ea9324dd6c4c243d847
Merge: 60a736faf a62fdc7ec
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 30 13:07:38 2015 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 60a736fafb8fd07dd932ff71a0de1b5b1df1db78
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 30 13:07:10 2015 -0800

    Test on whether lo(3) = hi(3) -- if that is true then the data is really 2D so
    doesn't have ghost cells in the third direction.

Src/F_BaseLib/plotfile.f90

commit a62fdc7ece80703697377da1526c3f9f53d04c02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 30 12:40:12 2015 -0800

    AMR_Adv: add some comments

Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_2d

commit 43ddf535035e69665e91a099b3a16b15f7865485
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 30 12:33:10 2015 -0800

    for each level advance, make sure we are not violating cfl since the time step is based on the velocity at t^n

Tutorials/AMR_Adv_F/Source/advance.f90

commit f0ca002a945640c7f5cf9640dfb0bcc5a456a321
Merge: 95bd7b9de 19bf855b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 30 11:24:10 2015 -0800

    Merge branch 'development' into tilearraycache

commit 19bf855b52170d76970f4420c8706b2973011123
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 30 11:22:10 2015 -0800

    AMR_Adv: change cfl to 0.7 for the single vortext problem

Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_2d
Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_3d

commit 95bd7b9de74b6b10aff49d3aaf58d55274f17d5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 30 10:34:01 2015 -0800

    FabArray: add some assertion making sure BoxArray and DistributionMapping do not change

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit b02682e5fc2483f88030ad823aad23d15cb985a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 29 17:51:59 2015 -0800

    FabArray & MFIter: cache tile array and use cached tile array in MFIter

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit b0bafa6b05e3a6ef660a9503e07e24d4e2315463
Merge: 52dd14195 e99811ca8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Nov 29 17:26:07 2015 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 52dd141954b02da46fad00990b6b201db2a33656
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Nov 29 17:25:49 2015 -0800

    See previous comments.

Tutorials/MultiGrid_C/inputs

commit c62d4cc48178c0442d23eeef358f9c86b2e63343
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Nov 29 17:24:28 2015 -0800

    1) We only need a single inputs file for 2d and 3d.
    2) Change the tolerance from 1e-6 to 1e-10
    3) Set the maxorder for the BoxLib_C solver to be 3 in the inputs file.  The
    default is 2, but if we set maxorder = 3 then the Cpp results match the F90 results.

Tutorials/MultiGrid_C/inputs
Tutorials/MultiGrid_C/inputs.f90.3d

commit f888a541df46bbec1ad0b42a248dc3790d694a5f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Nov 29 17:23:53 2015 -0800

    Have the default be not to test HPGMG.

Tutorials/MultiGrid_C/GNUmakefile

commit 132bafaa4c50157953202af85692e1fbae356d3c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Nov 29 17:23:32 2015 -0800

    Fix typo in comment.

Tutorials/MultiGrid_C/COEF_2D.F
Tutorials/MultiGrid_C/COEF_3D.F

commit 1c6797fe49d55c691bd62ec4f3d2675dbb387377
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 29 07:57:42 2015 -0800

    DistributionMapping: ID

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 0ebdadf5de7ee771484802880f52ec66a4657b52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 29 07:50:40 2015 -0800

    BoxArray: ID

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit cf38ae82e1897a63f39892da98b9930cc153e8d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 27 20:12:00 2015 -0800

    PGAS_SMC: tiling

MiniApps/PGAS_SMC/SMC_advance.cpp

commit c7e2880444134dd3b06c8db0ce9caed823b52e3f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 27 20:11:43 2015 -0800

    MFGhostIter: update for UPC++

Src/C_BaseLib/FabArray.cpp

commit eefef6d670e5914ed88e59500f3e2a0b3313f93b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 27 15:14:05 2015 -0800

    PGAS_SMC: change default

MiniApps/PGAS_SMC/SMC.cpp

commit fc5813eb89355957d714253810b1f3a3383a3bba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 27 12:15:16 2015 -0800

    PGAS_SMC: replication for weak scaling

MiniApps/PGAS_SMC/SMC.cpp
MiniApps/PGAS_SMC/init_data.f90

commit ac081902d4b6abfa264b203a07ed54ee8ee1fc6f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 27 07:40:53 2015 -0800

    PGAS_SMC: make max_grid_size a vector

MiniApps/PGAS_SMC/SMC.H
MiniApps/PGAS_SMC/SMC.cpp
MiniApps/PGAS_SMC/SMC_init.cpp

commit 048de281ed1e129c8b843593cf9448d5b0039c4b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 26 15:53:39 2015 -0800

    fix a bug and tidy

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/ParallelDescriptor.H

commit e99811ca8b3e2d1b78224fe6a9701282d5756383
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Nov 26 09:37:50 2015 -0500

    Only print out a warning on the I/O processor.

Src/C_AMRLib/Amr.cpp

commit b31c071bdfb7ccee76a6d520c665d1e8ef5be107
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 24 18:13:15 2015 -0800

    add Team Free consisting of processes not involved in remote communication and use it for local copy in Fill Boundary

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/ParallelDescriptor.H

commit 873e0b44ef666823f72230774504aa95de07a8b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 24 16:35:28 2015 -0800

    finished team message aggregation for periodic boundary

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 2a584940b01af4a91b4e1dbd60709c4c31c9947a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 24 16:15:23 2015 -0800

    fixed bug

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/ParallelDescriptor.H

commit 47cedbbe192e4b9ad4e4db11ba89acef9728ca31
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 24 16:15:14 2015 -0800

    added override

Src/C_BaseLib/UArena.H

commit b98bf0b9abef2c2109e9d0ed1ba7427f64a7154d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 24 15:28:34 2015 -0800

    various message aggregation methods

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 7f43742bce66e998e3354ef32b57c2a5249053c7
Merge: 8584d1f53 099d18a6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 24 13:47:31 2015 -0800

    Merge branch 'development' into pgas
    
    Conflicts:
            Src/C_BaseLib/Make.package

commit 8584d1f53fe9884c595ce7a5fc24de5af14a6dce
Merge: ecd8c9e1d 116c55100
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 24 13:44:23 2015 -0800

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit 099d18a6abc98a7feb787bc394559fd545e10630
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 24 11:14:11 2015 -0800

    Geometry: new versions of GetVolume and GetFaceArea

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 307b2b48965a8b6a323344585f4310958583b05e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 24 11:07:32 2015 -0800

    added edge boxarrays and nodal boxarray to AmrLevel. note that they are built on demand

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 92999a79a6b98f26cdde90c8b981d76337645b3d
Merge: 2b1393e37 032226613
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Nov 24 13:19:08 2015 -0800

    Merge branch 'hpgmg_updates' into development
    
    This merge adds recent changes Sam made to the HPGMG code base, as well
    as significant reorganization of the HPGMG hooks in BoxLib.
    Specifically, the hooks (both headers and source files) have moved from
    MultiFab.{H,cpp} to Src/Extern/hpgmg/BL_HPGMG.{H,cpp}.

commit 032226613bf95ae182ab5ef1adddf1f2fc97f651
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Nov 24 13:12:26 2015 -0800

    Tutorials, C_mk: move all HPGMG compile hooks from GNUmakefile into Make.defs
    
    This way we don't have to define the compile hooks in every GNUmakefile
    separately.

Tools/C_mk/Make.defs
Tutorials/MultiGrid_C/GNUmakefile

commit 57b115f1d508751f5cb82a01229604edaf991c11
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Nov 24 12:20:59 2015 -0800

    MultiFab, HPGMG, Extern: move hooks for HPGMG from MultiFab to Extern

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/Extern/hpgmg/BL_HPGMG.H
Src/Extern/hpgmg/BL_HPGMG.cpp
Src/Extern/hpgmg/Make.package
Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_C/main.cpp

commit cba4dca2e67e78859133ff7da2b0b7677e846ad4
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Nov 19 09:21:03 2015 -0800

    MultiFab, HPGMG: fix weird comment text alignment

Src/C_BaseLib/MultiFab.cpp

commit c17675e1a2544abdf7e39ec69631736540250a1a
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Nov 19 09:20:09 2015 -0800

    MultiFab, HPGMG: misc. fixes which mirror Sam's most recent changes in HPGMG

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit a99cb982810c0ce579f138d9a537c84044782c72
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Nov 18 16:25:11 2015 -0800

    MultiFab, HPGMG: minor fixes to boundary condition logic in MultiFab::CreateHPGMGLevel()

Src/C_BaseLib/MultiFab.cpp

commit 3b0e2a8d4f8c4a6f454121dea52e60e5ba76a513
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Nov 18 16:14:43 2015 -0800

    MultiFab, HPGMG: in MultiFab::CreateHPGMGLevel(), iterate the MFIter until we find one that's valid

Src/C_BaseLib/MultiFab.cpp

commit 2b1393e37f1ea2b027cda5a47c36342b77b5c4cf
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 23 15:38:52 2015 -0800

    Geometry: split retrieval of Box index int array into 2 steps in SendGeometryToSidecars()
    
    Doing Box.type().getVect() yields nonsense numbers. So instead we save
    the IntVect from type() as a temporary variable and then get the int
    array from it as a separate step.

Src/C_BaseLib/Geometry.cpp

commit b52c56864bd4346c239496d3fc7e3aff961fbaa8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 23 16:13:36 2015 -0800

    AMR_Adv_C: added override

Tutorials/AMR_Adv_C/Source/Adv.H
Tutorials/AMR_Adv_C/Source/AdvBld.cpp

commit 8df6d4ac202aaa47229a0180ec137a9ed9af33ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 23 15:52:17 2015 -0800

    omp clean up

Src/F_BaseLib/multifab_f.f90

commit 43d74e1d641135c4d9e9842352a9eb6e7724fc75
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 23 14:15:17 2015 -0800

    added a new header file for C++ 11 stuff and added BL_OVERRIDE (which is preprocessed to override or space depending on BL_USE_CXX11) to overriding virtual functions.  This can help virtual function sugnature mismatch bugs at compile time

Src/C_AMRLib/AmrParGDB.H
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/MLSDCAmr.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BL_CXX11.H
Src/C_BaseLib/CArena.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/Particles.H
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/MacBndry.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_TensorMG/DivVis.H

commit 89d3b258c49c65346dc2aa7f821d0dcaff71c48a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 23 11:18:02 2015 -0800

    replaced omp critical with reduction

Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/iMultiFab.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp

commit 2f94661009f3c3b9109db80f6bf69025fcd03acb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 23 11:12:15 2015 -0800

    replaced omp critical with omp atomic

Src/F_BaseLib/bl_mem_stat.f90

commit ea66c657a05e894b806dcf182f0f11d266c3b3ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 23 10:49:25 2015 -0800

    replaced an omp critical with omp atomic

Src/C_BaseLib/Particles.cpp

commit 9f8f15d05f07a7aa43cf082a1e059a78e34c4aa1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 20 06:01:48 2015 -0800

    Revert "bndry_reg: save have_periodic_bloxes when doing rr_build"
    
    This reverts commit d24ee97bffc1fb31c4e2bddc2d8716907e17592a.

Src/F_BaseLib/bndry_reg.f90

commit d24ee97bffc1fb31c4e2bddc2d8716907e17592a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 19 12:57:59 2015 -0800

    bndry_reg: save have_periodic_bloxes when doing rr_build

Src/F_BaseLib/bndry_reg.f90

commit f6c4252dc40dde801d0006cdace787b536f515b3
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 18 18:28:53 2015 -0800

    better names for allocated fabarray pointers.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 3af0aed911027df67c278e9b074eaf90cac6c0de
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 18 18:28:11 2015 -0800

    more support for dynamic sidecars.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.cpp

commit ebfc7439aa20a9330808df59dc194c5ea696760a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 18 18:26:43 2015 -0800

    vectSize function.

Src/C_AMRLib/BCRec.H

commit af96d9ebaaa9fe83011cb670a71852110aee52a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 18 14:45:51 2015 -0800

    RegressionTesting: rm reg_test_blame because it does work well and updated reg_test_gc

Tools/RegressionTesting/reg_test_blame.py
Tools/RegressionTesting/reg_test_gc.py

commit 97afe8f4c557087d872209e24871ae27c22fe54c
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 18 14:31:38 2015 -0800

    added virtual.

Src/C_AMRLib/AmrLevel.H

commit 8efd455ebe54e4d71efb8b438a7bf81c25679b77
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 18 14:31:12 2015 -0800

    duplicate the initial comm in case it is world.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 31b0137169ed6c4ea0960b35fe1e85cae6397035
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 18 13:32:01 2015 -0800

    Fixed a bug in bndry_reg_copy.  The mf source usually has only one ghost cell, whereas the bndry_reg can have two cell beyond periodic boundary.  Thank Ashish Pathak for pointing this out to us.

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit c1fd7c673c0272d103d83218eaaf613feb939d82
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Nov 18 08:37:51 2015 -0500

    allow test_suite to take a string of arguments to parse -- this allows
    it to be callable by other routines more easily

Tools/RegressionTesting/testnew.py

commit 7005add17b38eb29ed8095b90fa051c9a5bc08e0
Merge: 2e31681d2 b6dbb1f46
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Nov 17 20:54:10 2015 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 7b25368d9e427718215234787537c1ae640ace47
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 17 17:52:01 2015 -0800

    more sidecar copies on resize.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit 2e31681d24be8e04297c5dbb2d8c8bbdf2747757
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Nov 17 20:28:45 2015 -0500

    clean up the parsing

Tools/RegressionTesting/testnew.py

commit b6dbb1f46cc7573f0bd857adf4a1989d47ebb937
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 17 15:56:34 2015 -0800

    AMR_Adv_C: check CFL violation

Tutorials/AMR_Adv_C/Source/Src_2d/Adv_2d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/Adv_3d.f90

commit 4cda92cd6966374f69e76da8f59961b107a90b09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 17 15:34:47 2015 -0800

    AMR_Adv_F: fixed omp

Tutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90

commit f82cf35e262fae7663af92a8c99defb074136eb1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 17 15:22:17 2015 -0800

    AMR_Adv_C: added change_max for dt

Tutorials/AMR_Adv_C/Source/Adv_dt.cpp

commit 9856b802eed4e5a426dc379fec53e1b4d9547891
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 17 14:40:33 2015 -0800

    AMR_Adv_C: updated SingleVortex

Tutorials/AMR_Adv_C/Exec/SingleVortex/ACT_advection_2d.f90
Tutorials/AMR_Adv_C/Exec/SingleVortex/Make.package
Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob.f90
Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob_2d.f90
Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob_3d.f90
Tutorials/AMR_Adv_C/Exec/SingleVortex/amrvis.defaults
Tutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_2d.f90
Tutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_3d.f90
Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs
Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.2d
Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.3d
Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.rt
Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.rt.3d
Tutorials/AMR_Adv_C/Exec/SingleVortex/probdata.f90
Tutorials/AMR_Adv_C/Exec/SingleVortex/probin
Tutorials/AMR_Adv_C/Exec/SingleVortex/probin.2d
Tutorials/AMR_Adv_C/Exec/SingleVortex/probin.3d
Tutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90

commit f714db5a352d84ff0354c54fb1a7e91aa72c7d27
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 17 13:52:45 2015 -0800

    AMR_Adv_C: fixed 3d bug in scaling the flux

Tutorials/AMR_Adv_C/Source/Src_3d/Adv_3d.f90

commit 407d9eb04b4b998d1a80dc186ec5abbed829a03b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 17 13:47:53 2015 -0800

    AMR_Adv_C: fixed tagging

Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs
Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90
Tutorials/AMR_Adv_C/Source/Src_nd/tagging_params.f90

commit 769b7ef051b82ce93c98d710c341b7b355810629
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 17 13:11:44 2015 -0800

    AMR_Adv_C: made the 2d consistent with AMR_Adv_F

Tutorials/AMR_Adv_C/Source/Src_2d/Adv_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/Make.package
Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/compute_flux_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/trace_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/trans_2d.f90

commit 5abbee36319ed58930c9e7b30a709143e3d2a8db
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 17 13:00:25 2015 -0800

    cleanup temporary arrays

Tutorials/AMR_Adv_F/Source/compute_flux.f90

commit f6c7fcb77aba8a03802435db8ce20e96026680ef
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 17 12:50:45 2015 -0800

    change flux convention to positive (and flipped flux register sign convention)

Tutorials/AMR_Adv_F/Source/advance.f90
Tutorials/AMR_Adv_F/Source/compute_flux.f90
Tutorials/AMR_Adv_F/Source/update_phi.f90

commit f72be23e6a1853122ff78bc13e798c07967e9142
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 17 12:44:42 2015 -0800

    AMR_Adv_C: finished 3d

Tutorials/AMR_Adv_C/Source/Adv_dt.cpp
Tutorials/AMR_Adv_C/Source/Src_3d/Adv_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/Make.package
Tutorials/AMR_Adv_C/Source/Src_3d/compute_flux_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/slope_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/trace_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/trans_3d.f90

commit d262215ba524e7765f57ba03d91dae27e7f38886
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 16 17:28:29 2015 -0800

    AMR_Adv_C: clean up

Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs
Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/ACT_advection_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/Derive_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/EstDt_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/Make.package
Tutorials/AMR_Adv_C/Source/Src_3d/React_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/Tagging_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/bc_fill_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/ext_src_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/fill_diff_coeff_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/slope_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/trace_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/trans_3d.f90

commit 078f62d8015baf60a03b183ba7eefb58ea35a623
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 17 10:17:05 2015 -0800

    Go back to the tagging that actually sees the phi blob.

Tutorials/AMR_Adv_F/Source/tag_boxes.f90

commit 28c0337c92fd8281b049f925bf0104769151595a
Merge: e43e7e847 67255e7be
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 17 10:15:12 2015 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 67255e7be651affe8d86b5969ffe4840c079de19
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 17 08:11:25 2015 -0800

    fixed crash issue when nlevs .ne. max_levs based on refinement criteria.
    the compute_dt routine was looping over max_levs, not nlevs

Tutorials/AMR_Adv_F/Source/main.f90

commit 180075a4b537ea5c7d38b9c1610539a37a6cc60f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 17 08:06:36 2015 -0800

    move bubble to center of domain in 3d

Tutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90

commit e43e7e84736667cb508be26605328d9ea21add43
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 16 18:45:23 2015 -0800

    Fix this GNUmakefile

Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile

commit 63da40e5d6fc707348318659b87cb918a211b784
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 16 18:44:25 2015 -0800

    1) Renamed KotheRiderExample --> SingleVortex in AMR_Adv_C.
    2) Copied tag_boxes.f90 into AMR_Adv_F/Source directory so it is easy to see how to set the refinement criteria.

Tutorials/AMR_Adv_C/Exec/SingleVortex/ACT_advection_2d.f90
Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_Adv_C/Exec/SingleVortex/Make.package
Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob_2d.f90
Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob_3d.f90
Tutorials/AMR_Adv_C/Exec/SingleVortex/amrvis.defaults
Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.2d
Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.3d
Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.rt
Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.rt.3d
Tutorials/AMR_Adv_C/Exec/SingleVortex/probdata.f90
Tutorials/AMR_Adv_C/Exec/SingleVortex/probin.2d
Tutorials/AMR_Adv_C/Exec/SingleVortex/probin.3d
Tutorials/AMR_Adv_F/Source/GPackage.mak
Tutorials/AMR_Adv_F/Source/tag_boxes.f90

commit 93033267392a8378baa4854a0045de5dc0b0162c
Merge: fdfabd90f 8db125192
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 16 18:10:23 2015 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit fdfabd90f985ca063ec14689c2afaa25be90f1f2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 16 18:09:21 2015 -0800

    1) Add computation of dt based on time-n velocity at every coarse timestep.
    2) Move the routines to set the velocity and initialize phi into the Exec/problem directories.
    3) Set do_subcycling = T in the inputs files.

Tutorials/AMR_Adv_F/Exec/SingleVortex/GNUmakefile
Tutorials/AMR_Adv_F/Exec/SingleVortex/GPackage.mak
Tutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90
Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_2d
Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_3d
Tutorials/AMR_Adv_F/Exec/SingleVortex/set_velocity.f90
Tutorials/AMR_Adv_F/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_Adv_F/Exec/UniformVelocity/GPackage.mak
Tutorials/AMR_Adv_F/Exec/UniformVelocity/init_phi.f90
Tutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_2d
Tutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_3d
Tutorials/AMR_Adv_F/Exec/UniformVelocity/set_velocity.f90
Tutorials/AMR_Adv_F/Source/GPackage.mak
Tutorials/AMR_Adv_F/Source/advance.f90
Tutorials/AMR_Adv_F/Source/main.f90
Tutorials/AMR_Adv_F/Source/slope.f90

commit 9b7b26c3913e5533438b7407f1334952b3f33f86
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 16 17:42:18 2015 -0800

    consolidate geometry broadcast functions.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp

commit c50ad5ad2bf2af65a8374577bdd53750eb108647
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 16 17:41:14 2015 -0800

    consolidate geometry broadcast functions.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 8db1251923ad630867b2cbccce03ea51f7bda80f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 16 16:45:12 2015 -0800

    AMR_Adv_C: fixed a bug in 2d slope.  The 2D C++ version works now.

Tutorials/AMR_Adv_C/Source/Src_2d/slope_2d.f90

commit 95290f2767d87d0354ec866a4f396f8606455bc5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 16 16:44:25 2015 -0800

    AMR_Adv: make the initial model consistent

Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90
Tutorials/AMR_Adv_F/Source/init_phi.f90

commit ef961ea5f3636ba341629fc27cc809d3d63a4286
Merge: 4d41f8d55 904372936
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 16 16:43:04 2015 -0800

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit 9043729361342c9ebd9119b2336b6678f3d180df
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 16 16:34:56 2015 -0800

    Update the README_F to correctly describe AMR_Adv_F

Tutorials/README_F

commit 8c63a4bf16aa47339a6294794672b4210c59b598
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 16:18:13 2015 -0800

    cleanup only.  2d and 3d check out 2nd order for cfl=0.9

Tutorials/AMR_Adv_F/Source/compute_flux.f90

commit 8bca80a4e4b8a6ecc5f7b6a2675b0f9f60e79d16
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 15:26:29 2015 -0800

    3d advection complete.  convergence testing underway

Tutorials/AMR_Adv_F/Source/compute_flux.f90
Tutorials/AMR_Adv_F/Source/init_phi.f90

commit 4d41f8d55e1b71392b0e6d9d8fee3a9f6717dfc9
Merge: f9e0ecff6 e8b4b1d5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 16 13:43:44 2015 -0800

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit e8b4b1d5b5e24b5d8c0c184dc96b9181ba835c04
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 12:54:37 2015 -0800

    constant velocity test case.  cfl enabled (assumes umax=1).  stop_time enabled

Tutorials/AMR_Adv_F/Exec/inputs_2d
Tutorials/AMR_Adv_F/Exec/inputs_3d
Tutorials/AMR_Adv_F/Source/compute_velocity.f90
Tutorials/AMR_Adv_F/Source/init_phi.f90
Tutorials/AMR_Adv_F/Source/main.f90

commit 87673af99b4d6135c10fd72d13e06dced6af66a7
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 12:49:43 2015 -0800

    get compute_flux compiling again

Tutorials/AMR_Adv_F/Source/compute_flux.f90

commit e9798ccbe4825ba9b6b76815c8d28215835cee73
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 12:42:12 2015 -0800

    updates so we can start comparing F90 and C

Tutorials/AMR_Adv_F/Source/compute_flux.f90

commit f9e0ecff66d5c7720e36fe8ef18e718cdbec6009
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 16 12:32:51 2015 -0800

    AMR_Adv_C: updated assuming div(u)=0

Tutorials/AMR_Adv_C/Source/Src_2d/Make.package
Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/flux_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/trace_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/trans_2d.f90

commit 7616567e20283a10946d6644cca140b2534f6a78
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 11:26:44 2015 -0800

    start 3d flux routine - WIP

Tutorials/AMR_Adv_F/Source/compute_flux.f90

commit 1c6316c8f8c74e489f7107e42e4213b3c1176f21
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 11:26:33 2015 -0800

    3d init match 2d init

Tutorials/AMR_Adv_F/Source/init_phi.f90

commit a9c60ddc9f250f807cba396dcbfc4cc2f23bbfbc
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 11:08:44 2015 -0800

    code clean up

Tutorials/AMR_Adv_F/Source/GPackage.mak
Tutorials/AMR_Adv_F/Source/compute_flux.f90
Tutorials/AMR_Adv_F/Source/main.f90
Tutorials/AMR_Adv_F/Source/prob.f90

commit b2184636f0b4c60b3b82d908c316c15263f3df4a
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 11:03:02 2015 -0800

    clean up boundary conditions

Tutorials/AMR_Adv_F/Source/advance.f90
Tutorials/AMR_Adv_F/Source/compute_flux.f90

commit 82e34a8abf981d76a2646d2b30758e2bfc7332f7
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 10:59:34 2015 -0800

    3d velocity field with w=1 and inputs file

Tutorials/AMR_Adv_F/Exec/inputs_3d
Tutorials/AMR_Adv_F/Source/compute_velocity.f90

commit f802afe45f6d3693443b973b19144e118f5b05d6
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 10:36:20 2015 -0800

    fixed hdtdx scalining / units bug

Tutorials/AMR_Adv_F/Source/compute_flux.f90

commit 929658eda69d6155395e36a6f0a627003556fa31
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 10:23:19 2015 -0800

    get rid of abs(u) < eps cases.  confusing and not needed since this is just conservative scalar advection

Tutorials/AMR_Adv_F/Source/compute_flux.f90

commit 204f914306c5fc9da33d7ad7a24b3f75d4d2c613
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 10:09:19 2015 -0800

    2d advection complete.  assumes div(u)=0.  does the tracing in convective form, then forms the final fluxes in conservative form

Tutorials/AMR_Adv_F/Source/compute_flux.f90

commit 747744cc5adb043ce5dbbc7dc2838fcdabaeb438
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 08:25:53 2015 -0800

    2d cross terms incorporated.  runs now at cfl=0.9.  3d not written yet

Tutorials/AMR_Adv_F/Source/compute_flux.f90
Tutorials/AMR_Adv_F/Source/main.f90

commit 10eec4ca3d9bc4e91065c300cdeba86407414c49
Merge: 03181f43f 33bb9d939
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 07:35:04 2015 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 33bb9d939a571be9175eab51af7a7601f21f54c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 15 15:49:07 2015 -0800

    AMR_Adv_C: write final checkpoint and plotfile

Tutorials/AMR_Adv_C/Source/main.cpp

commit 4f266fdbe066803209785200f6a2156103a4fa24
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 15 11:37:00 2015 -0800

    AMR_Adv_C: minor

Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs

commit d41ee00aefd4606db80d6669cb3262a382c2eda3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 15 11:29:09 2015 -0800

    AMR_Adv_C: change the default max_grid_size to 64

Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs

commit 3ca6624c1730c9ab7ff22fa03c93eaf22e2f831f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 15 11:27:12 2015 -0800

    AMR_Adv_C: tweak initial model

Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs
Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin

commit 2a10b1f87efbbdf2e62aa28f70840bab309daf5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 15 11:20:47 2015 -0800

    AMR_Adv_2d: added missing piece in transx

Tutorials/AMR_Adv_C/Source/Src_2d/trans_2d.f90

commit 35825534806f66e3c588b11277766f0315e72b49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 15 11:19:28 2015 -0800

    AMR_Adv_2d: fixed some comments

Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90

commit 9137c1402007c2e9a203da469046dac538bb5c14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 15 11:14:43 2015 -0800

    AMR_Adv_2d: removed hard coded eps

Tutorials/AMR_Adv_C/Source/Src_2d/flux_2d.f90

commit de7b85c902a9b5af4711094f30d32dd51b7cc834
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 15 10:22:59 2015 -0800

    AMR_Adv_C: use contiguous

Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/slope_2d.f90

commit 7d51f713428d1c56a7a28eb8d99b88203b0f5005
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 15 10:20:28 2015 -0800

    AMR_Adv_C: minor

Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90

commit b482e83ccceb5c81832e354f4a59575b159068e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 15 10:18:16 2015 -0800

    AMR_Adv_C: added tagging

Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90

commit 9b98051d1f90d10f75a43f2f2a7d082b3dcd6f81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 15 10:04:06 2015 -0800

    AMR_Adv_C: clean up

Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/Adv_advance.cpp
Tutorials/AMR_Adv_C/Source/Adv_dt.cpp

commit 2b09377dde647b2e154edef0b937435f981c46be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 14 20:10:49 2015 -0800

    AMR_Adv_C: edge --> face

Tutorials/AMR_Adv_C/Exec/UniformVelocity/Make.package
Tutorials/AMR_Adv_C/Exec/UniformVelocity/face_velocity_2d.f90
Tutorials/AMR_Adv_C/Source/Adv_F.H
Tutorials/AMR_Adv_C/Source/Adv_advance.cpp
Tutorials/AMR_Adv_C/Source/Adv_dt.cpp

commit 6fc141d3d785819617d7026a2a56621643837cf4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 14 20:05:21 2015 -0800

    AMR_Adv_C: 2d finished not checked

Tutorials/AMR_Adv_C/Source/Adv_F.H
Tutorials/AMR_Adv_C/Source/Adv_advance.cpp
Tutorials/AMR_Adv_C/Source/Src_2d/Make.package
Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/advection_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/flux_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/slope_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/trace_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/trans_2d.f90

commit a06451214ddbb7803a1448bc893355f5f73a8b90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 22:04:31 2015 -0800

    AMR_Adv_C: WIP

Tutorials/AMR_Adv_C/Source/Src_2d/Make.package
Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/advection_2d.f90

commit 66e22afa070bde2aaa8fcd2ff1a8789388afd8ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 21:11:54 2015 -0800

    AMR_Adv_C: rm some files

Tutorials/AMR_Adv_C/Exec/Make.Adv
Tutorials/AMR_Adv_C/Source/Src_2d/Derive_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/EstDt_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/Make.package
Tutorials/AMR_Adv_C/Source/Src_2d/Tagging_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/advection_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/bc_fill_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/ext_src_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/fill_diff_coeff_2d.f90

commit ebe971fd5987532111d6622f13c85da0150d2f5c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 21:06:13 2015 -0800

    AMR_Adv_C: compute dt

Tutorials/AMR_Adv_C/Exec/UniformVelocity/Make.package
Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/edge_velocity_2d.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/probdata.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/Adv_F.H
Tutorials/AMR_Adv_C/Source/Adv_advance.cpp
Tutorials/AMR_Adv_C/Source/Adv_dt.cpp
Tutorials/AMR_Adv_C/Source/Adv_setup.cpp
Tutorials/AMR_Adv_C/Source/Make.package
Tutorials/AMR_Adv_C/Source/Src_nd/Adv_nd.f90
Tutorials/AMR_Adv_C/Source/Src_nd/Make.package
Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90
Tutorials/AMR_Adv_C/Source/Src_nd/tagging_params.f90

commit e5a310aa8a1f67225d1f717b6f8a27cf402fe801
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 18:07:22 2015 -0800

    AMR_Adv_C: remvoed prob_hi from initdata

Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/Adv_F.H

commit 6eee1fcd04fb74e95a17bdbb7cda0c6c465b5b20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 17:56:22 2015 -0800

    AMR_Adv_C: fixed boundary function

Tutorials/AMR_Adv_C/Source/Adv_F.H
Tutorials/AMR_Adv_C/Source/Adv_setup.cpp

commit 03181f43ff75adb1e7a95ce596a3230c06ffbb5f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 13 17:52:46 2015 -0800

    now computing velocity and half-time for both subcycling and non-subcycling cases

Tutorials/AMR_Adv_F/Exec/GNUmakefile
Tutorials/AMR_Adv_F/Source/advance.f90
Tutorials/AMR_Adv_F/Source/compute_velocity.f90
Tutorials/AMR_Adv_F/Source/main.f90

commit f01c12a2f8a11c99661e7b3c40eb7694fcba2c4a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 17:38:54 2015 -0800

    AMR_Adv_C: clean up headers

Tutorials/AMR_Adv_C/Source/Adv.H
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/AdvBld.cpp
Tutorials/AMR_Adv_C/Source/main.cpp

commit ebdd2e241e2685f25b3de61781796ce785b13ed8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 17:32:18 2015 -0800

    AMR_Adv_C: removed area and volume

Tutorials/AMR_Adv_C/Source/Adv.H
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/Adv_advance.cpp
Tutorials/AMR_Adv_C/Source/Adv_io.cpp

commit 32229724c33bbeff9ffa144704dd8329ea5a1621
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 17:24:22 2015 -0800

    AMR_Adv_C: clean up Adv::advance

Tutorials/AMR_Adv_C/Source/Adv_advance.cpp

commit be1f4ba73a128991a2186b9bf2819f95d2740082
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 16:44:23 2015 -0800

    AMR_Adv_C: fixed 2d initdata

Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90

commit 2eb3ee01fdcff49912c7d2f72d7e9aa9b80a44fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 16:39:40 2015 -0800

    AMR_Adv_C: fixed initdata

Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/Adv_F.H
Tutorials/AMR_Adv_F/Source/init_phi.f90

commit fbe65f1f4e01a64bcba6f84d3be06e8b730c4979
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 16:24:01 2015 -0800

    AMR_Adv_C: WIP

Tutorials/AMR_Adv_C/Exec/Make.Adv
Tutorials/AMR_Adv_C/Exec/UniformVelocity/Make.package
Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob_2d.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob_3d.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/amrvis.defaults
Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs
Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.3d
Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.rt
Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.rt.3d
Tutorials/AMR_Adv_C/Exec/UniformVelocity/probdata.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin
Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin.2d
Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin.3d
Tutorials/AMR_Adv_C/Source/Adv.H
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/AdvBld.cpp
Tutorials/AMR_Adv_C/Source/Adv_F.H
Tutorials/AMR_Adv_C/Source/Adv_advance.cpp
Tutorials/AMR_Adv_C/Source/Adv_error.cpp
Tutorials/AMR_Adv_C/Source/Adv_io.cpp
Tutorials/AMR_Adv_C/Source/Adv_nd.f90
Tutorials/AMR_Adv_C/Source/Adv_setup.cpp
Tutorials/AMR_Adv_C/Source/Derive_F.H
Tutorials/AMR_Adv_C/Source/Make.package
Tutorials/AMR_Adv_C/Source/Src_2d/MGutils_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/Make.package
Tutorials/AMR_Adv_C/Source/extern_probin.template
Tutorials/AMR_Adv_C/Source/main.cpp
Tutorials/AMR_Adv_C/Source/meth_params.f90
Tutorials/AMR_Adv_C/Source/prob_params.f90

commit 695e46938675616f6a8798e335e2f48b6b967ee6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 11:25:13 2015 -0800

    AMR_Adv_C: rm diffusion

Tutorials/AMR_Adv_C/Source/ADR_diffusion.cpp
Tutorials/AMR_Adv_C/Source/Diffusion.H
Tutorials/AMR_Adv_C/Source/Diffusion.cpp
Tutorials/AMR_Adv_C/Source/Make.package

commit c3b5e58c0578e71e853e0678b9744bf0a8324c14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 11:24:12 2015 -0800

    AMR_Adv_C: ADR --> Adv

Tutorials/AMR_Adv_C/Source/Adv.H
Tutorials/AMR_Adv_C/Source/Adv.cpp
Tutorials/AMR_Adv_C/Source/AdvBld.cpp
Tutorials/AMR_Adv_C/Source/Adv_F.H
Tutorials/AMR_Adv_C/Source/Adv_advance.cpp
Tutorials/AMR_Adv_C/Source/Adv_error.cpp
Tutorials/AMR_Adv_C/Source/Adv_nd.f90
Tutorials/AMR_Adv_C/Source/Adv_setup.cpp
Tutorials/AMR_Adv_C/Source/Make.package

commit 25249f697431acbab39f2407bd8c6b985c6a6446
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 11:21:06 2015 -0800

    AMR_Adv_C: updated make

Tutorials/AMR_Adv_C/Exec/Make.Adv
Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile

commit cf65996939e5bc833e3d85fc076b381985af9966
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 11:09:46 2015 -0800

    AMR_Adv_C: updated README

Tutorials/AMR_Adv_C/README

commit 394ac1acedc82f760e97fc2601794c9e9f2855da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 11:09:30 2015 -0800

    AMR_Adv_C: renamed file

Tutorials/AMR_Adv_C/Exec/Make.Adv

commit 21e3aab8d95e1182bfc7e69ff7f124895cd364bb
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 13 15:57:32 2015 -0800

    more progress on test problem

Tutorials/AMR_Adv_F/Exec/GNUmakefile
Tutorials/AMR_Adv_F/Exec/inputs_2d
Tutorials/AMR_Adv_F/Source/advance.f90
Tutorials/AMR_Adv_F/Source/compute_flux.f90
Tutorials/AMR_Adv_F/Source/compute_velocity.f90
Tutorials/AMR_Adv_F/Source/init_phi.f90
Tutorials/AMR_Adv_F/Source/main.f90
Tutorials/AMR_Adv_F/Source/update_phi.f90

commit d919852804852a2934c9d5a6c7e2415209a633d3
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 13 14:47:36 2015 -0800

    compute_velocity routine... need to fold it into subcycling case properly (so it uses most current time)

Tutorials/AMR_Adv_F/Source/GPackage.mak
Tutorials/AMR_Adv_F/Source/advance.f90
Tutorials/AMR_Adv_F/Source/compute_velocity.f90
Tutorials/AMR_Adv_F/Source/main.f90

commit 58ed60504e65e790618635b234389adc68f88935
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 13 12:53:46 2015 -0800

    comments, initialize fluxes to zero now that the diffusive fluxes are gone

Tutorials/AMR_Adv_F/Source/compute_flux.f90
Tutorials/AMR_Adv_F/Source/main.f90

commit 0a46e496beb72381dac242714eb4d078495da7d9
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 13 12:27:56 2015 -0800

    clean up namelist and inputs file

Tutorials/AMR_Adv_F/Exec/inputs_2d
Tutorials/AMR_Adv_F/Exec/inputs_3d
Tutorials/AMR_Adv_F/Source/init_phi.f90
Tutorials/AMR_Adv_F/Source/main.f90

commit 5e464e214a2d758950d0957a3d69d79dea11ae44
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 13 11:11:57 2015 -0800

    remove redundant inputs file

Tutorials/AMR_Adv_F/Exec/inputs-rt

commit 0268805e6577403e74a7ceb90e5ac9249d17cea5
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 13 11:07:48 2015 -0800

    remove some diffusion stuff
    
    re-org directories to make it look like the C version

Tutorials/AMR_Adv_F/Exec/GNUmakefile
Tutorials/AMR_Adv_F/Exec/inputs-rt
Tutorials/AMR_Adv_F/Exec/inputs_2d
Tutorials/AMR_Adv_F/Exec/inputs_3d
Tutorials/AMR_Adv_F/Source/GPackage.mak
Tutorials/AMR_Adv_F/Source/advance.f90
Tutorials/AMR_Adv_F/Source/compute_flux.f90
Tutorials/AMR_Adv_F/Source/init_phi.f90
Tutorials/AMR_Adv_F/Source/main.f90
Tutorials/AMR_Adv_F/Source/prob.f90
Tutorials/AMR_Adv_F/Source/slope.f90
Tutorials/AMR_Adv_F/Source/update_phi.f90
Tutorials/AMR_Adv_F/Source/write_plotfile.f90

commit 58ce648ecae9364653481ad592a663b9a61389cc
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 13 11:01:55 2015 -0800

    new amr advection examples from Ann's latest commit

Tutorials/AMR_Adv_C/Exec/KotheRiderExample/ACT_advection_2d.f90
Tutorials/AMR_Adv_C/Exec/KotheRiderExample/GNUmakefile
Tutorials/AMR_Adv_C/Exec/KotheRiderExample/Make.package
Tutorials/AMR_Adv_C/Exec/KotheRiderExample/Prob_2d.f90
Tutorials/AMR_Adv_C/Exec/KotheRiderExample/Prob_3d.f90
Tutorials/AMR_Adv_C/Exec/KotheRiderExample/amrvis.defaults
Tutorials/AMR_Adv_C/Exec/KotheRiderExample/inputs.2d
Tutorials/AMR_Adv_C/Exec/KotheRiderExample/inputs.3d
Tutorials/AMR_Adv_C/Exec/KotheRiderExample/inputs.rt
Tutorials/AMR_Adv_C/Exec/KotheRiderExample/inputs.rt.3d
Tutorials/AMR_Adv_C/Exec/KotheRiderExample/probdata.f90
Tutorials/AMR_Adv_C/Exec/KotheRiderExample/probin.2d
Tutorials/AMR_Adv_C/Exec/KotheRiderExample/probin.3d
Tutorials/AMR_Adv_C/Exec/Make.ADR
Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_Adv_C/Exec/UniformVelocity/Make.package
Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob_2d.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob_3d.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/amrvis.defaults
Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.3d
Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.rt
Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.rt.3d
Tutorials/AMR_Adv_C/Exec/UniformVelocity/probdata.f90
Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin.2d
Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin.3d
Tutorials/AMR_Adv_C/README
Tutorials/AMR_Adv_C/Source/ADR.H
Tutorials/AMR_Adv_C/Source/ADR.cpp
Tutorials/AMR_Adv_C/Source/ADRBld.cpp
Tutorials/AMR_Adv_C/Source/ADR_F.H
Tutorials/AMR_Adv_C/Source/ADR_advance.cpp
Tutorials/AMR_Adv_C/Source/ADR_diffusion.cpp
Tutorials/AMR_Adv_C/Source/ADR_error.cpp
Tutorials/AMR_Adv_C/Source/ADR_nd.f90
Tutorials/AMR_Adv_C/Source/ADR_setup.cpp
Tutorials/AMR_Adv_C/Source/Derive_F.H
Tutorials/AMR_Adv_C/Source/Diffusion.H
Tutorials/AMR_Adv_C/Source/Diffusion.cpp
Tutorials/AMR_Adv_C/Source/Make.package
Tutorials/AMR_Adv_C/Source/Src_2d/ACT_advection_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/Derive_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/EstDt_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/MGutils_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/Make.package
Tutorials/AMR_Adv_C/Source/Src_2d/Tagging_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/bc_fill_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/ext_src_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/fill_diff_coeff_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/slope_2d.f90
Tutorials/AMR_Adv_C/Source/Src_2d/trace_2d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/ACT_advection_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/Derive_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/EstDt_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/Make.package
Tutorials/AMR_Adv_C/Source/Src_3d/React_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/Tagging_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/bc_fill_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/ext_src_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/fill_diff_coeff_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/slope_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/trace_3d.f90
Tutorials/AMR_Adv_C/Source/Src_3d/trans_3d.f90
Tutorials/AMR_Adv_C/Source/extern_probin.template
Tutorials/AMR_Adv_C/Source/main.cpp
Tutorials/AMR_Adv_C/Source/meth_params.f90
Tutorials/AMR_Adv_C/Source/prob_params.f90
Tutorials/AMR_Adv_F/GNUmakefile
Tutorials/AMR_Adv_F/GPackage.mak
Tutorials/AMR_Adv_F/advance.f90
Tutorials/AMR_Adv_F/compute_flux.f90
Tutorials/AMR_Adv_F/init_phi.f90
Tutorials/AMR_Adv_F/inputs-rt
Tutorials/AMR_Adv_F/inputs_2d
Tutorials/AMR_Adv_F/inputs_3d
Tutorials/AMR_Adv_F/main.f90
Tutorials/AMR_Adv_F/prob.f90
Tutorials/AMR_Adv_F/slope.f90
Tutorials/AMR_Adv_F/update_phi.f90
Tutorials/AMR_Adv_F/write_plotfile.f90
Tutorials/AMR_Advection_C/Exec/Make.ADR
Tutorials/AMR_Advection_C/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_Advection_C/Exec/UniformVelocity/Make.package
Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_2d.f90
Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_3d.f90
Tutorials/AMR_Advection_C/Exec/UniformVelocity/amrvis.defaults
Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.3d
Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt
Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt.3d
Tutorials/AMR_Advection_C/Exec/UniformVelocity/probdata.f90
Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.2d
Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.3d
Tutorials/AMR_Advection_C/README
Tutorials/AMR_Advection_C/Source/ADR.H
Tutorials/AMR_Advection_C/Source/ADR.cpp
Tutorials/AMR_Advection_C/Source/ADRBld.cpp
Tutorials/AMR_Advection_C/Source/ADR_F.H
Tutorials/AMR_Advection_C/Source/ADR_advance.cpp
Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp
Tutorials/AMR_Advection_C/Source/ADR_error.cpp
Tutorials/AMR_Advection_C/Source/ADR_nd.f90
Tutorials/AMR_Advection_C/Source/ADR_react.cpp
Tutorials/AMR_Advection_C/Source/ADR_setup.cpp
Tutorials/AMR_Advection_C/Source/Derive_F.H
Tutorials/AMR_Advection_C/Source/Diffusion.H
Tutorials/AMR_Advection_C/Source/Diffusion.cpp
Tutorials/AMR_Advection_C/Source/Make.package
Tutorials/AMR_Advection_C/Source/Src_2d/ACT_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/ACT_sums_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/Derive_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/EstDt_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/MGutils_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/Make.package
Tutorials/AMR_Advection_C/Source/Src_2d/React_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/Tagging_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/bc_fill_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/ext_src_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/fill_diff_coeff_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/trans_2d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/ACT_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/ACT_sums_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/Derive_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/EstDt_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/Make.package
Tutorials/AMR_Advection_C/Source/Src_3d/React_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/Tagging_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/bc_fill_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/ext_src_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/fill_diff_coeff_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/slope_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90
Tutorials/AMR_Advection_C/Source/burner.f90
Tutorials/AMR_Advection_C/Source/extern_probin.template
Tutorials/AMR_Advection_C/Source/main.cpp
Tutorials/AMR_Advection_C/Source/meth_params.f90
Tutorials/AMR_Advection_C/Source/network.f90
Tutorials/AMR_Advection_C/Source/prob_params.f90
Tutorials/AMR_Advection_C/Source/sum_integrated_quantities.cpp

commit 6371c9584c5e5b18b889b85dc2f8552416bdc4b8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 13 10:17:13 2015 -0800

    Add new Tutorial example -- AMR_Adv_Diff_C

Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/ACT_advection_2d.f90
Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/GNUmakefile
Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/Make.package
Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/Prob_2d.f90
Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/Prob_3d.f90
Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/amrvis.defaults
Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/inputs.2d
Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/inputs.3d
Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/inputs.rt
Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/inputs.rt.3d
Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/probdata.f90
Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/probin.2d
Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/probin.3d
Tutorials/AMR_Adv_Diff_C/Exec/Make.ADR
Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/Make.package
Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/Prob_2d.f90
Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/Prob_3d.f90
Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/amrvis.defaults
Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/inputs.3d
Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/inputs.rt
Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/inputs.rt.3d
Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/probdata.f90
Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/probin.2d
Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/probin.3d
Tutorials/AMR_Adv_Diff_C/README
Tutorials/AMR_Adv_Diff_C/Source/ADR.H
Tutorials/AMR_Adv_Diff_C/Source/ADR.cpp
Tutorials/AMR_Adv_Diff_C/Source/ADRBld.cpp
Tutorials/AMR_Adv_Diff_C/Source/ADR_F.H
Tutorials/AMR_Adv_Diff_C/Source/ADR_advance.cpp
Tutorials/AMR_Adv_Diff_C/Source/ADR_diffusion.cpp
Tutorials/AMR_Adv_Diff_C/Source/ADR_error.cpp
Tutorials/AMR_Adv_Diff_C/Source/ADR_nd.f90
Tutorials/AMR_Adv_Diff_C/Source/ADR_setup.cpp
Tutorials/AMR_Adv_Diff_C/Source/Derive_F.H
Tutorials/AMR_Adv_Diff_C/Source/Diffusion.H
Tutorials/AMR_Adv_Diff_C/Source/Diffusion.cpp
Tutorials/AMR_Adv_Diff_C/Source/Make.package
Tutorials/AMR_Adv_Diff_C/Source/Src_2d/ACT_advection_2d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_2d/Derive_2d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_2d/EstDt_2d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_2d/MGutils_2d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_2d/Make.package
Tutorials/AMR_Adv_Diff_C/Source/Src_2d/Tagging_2d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_2d/bc_fill_2d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_2d/ext_src_2d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_2d/fill_diff_coeff_2d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_2d/slope_2d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_2d/trace_2d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_3d/ACT_advection_3d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_3d/Derive_3d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_3d/EstDt_3d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_3d/Make.package
Tutorials/AMR_Adv_Diff_C/Source/Src_3d/React_3d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_3d/Tagging_3d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_3d/bc_fill_3d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_3d/ext_src_3d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_3d/fill_diff_coeff_3d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_3d/slope_3d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_3d/trace_3d.f90
Tutorials/AMR_Adv_Diff_C/Source/Src_3d/trans_3d.f90
Tutorials/AMR_Adv_Diff_C/Source/extern_probin.template
Tutorials/AMR_Adv_Diff_C/Source/main.cpp
Tutorials/AMR_Adv_Diff_C/Source/meth_params.f90
Tutorials/AMR_Adv_Diff_C/Source/prob_params.f90

commit ac37c9e19a869a0a914a311d52f0f4305339991d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 12 17:55:25 2015 -0800

    added function to broadcast a geometry.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit e8c686e4395304f3be53f40fe2f9eb7c911a76f1
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 12 17:54:05 2015 -0800

    added function for serialized box size.

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp

commit cc082d5127f4b2565f16df9bbd4c9b67c17ed6fc
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 12 17:52:40 2015 -0800

    added function to send data to procs moved from the sidecars into comp.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 648268ef45ed7b6ddb92677db1056e72f0709aef
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 12 17:52:05 2015 -0800

    added function to send data to procs moved from the sidecars into comp.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 116c55100f391a893bbbd4cfe2450dc25a848de7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 12 16:04:58 2015 -0800

    added a barrier after we finish advance

Tutorials/PGAS_HEAT/main.cpp

commit 9427c6884923c29f2f8796f04939657c9c945998
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 12 11:16:44 2015 -0800

    added switch default.

Src/C_BaseLib/CoordSys.cpp

commit f033a4ddf5eecdd2a0e99caac62301763ab1a62c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 12 11:16:20 2015 -0800

    added more barriers when we switch between MPI and UPC++

Tests/FillBoundaryComparison/main.cpp

commit 2c5faba058e6b9327d4f325300329856491717b3
Merge: d77ca089e cd2e7a17f
Author: yzheng <yzheng@lbl.gov>
Date:   Thu Nov 12 07:58:44 2015 -0800

    Add a barrier before switching from UPC++ to MPI

commit ecd8c9e1dd45de4f89e76a1bae9ac282204da79a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 11 16:24:18 2015 -0800

    renamed parameter upcxx_team_size to team.size and added new parameter team.aggregate_message to control how to aggregate team messages

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 07064552212a55f66121e1438eac194748d52671
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 11 14:28:32 2015 -0800

    change the default of comm_num_pieces to 1; it does not seem to help on cori

Src/C_BaseLib/FabArray.cpp

commit 0e55d132706fab9995d07a000da199e8c03e01f4
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Nov 11 11:08:22 2015 -0800

    a separate version of fabio_ml_multifab_write_d that works when the input multifab is a single-level, non-array

Src/F_BaseLib/fabio.f90

commit cd2e7a17ff39b6388f74de70fa3391815602c00e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 14:45:05 2015 -0800

    MFIter: fixed the no sharing flag

Src/C_BaseLib/FabArray.cpp

commit 8edfe1e293d5594cf0dbca684a1cbd2d6641703b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 14:42:27 2015 -0800

    auto: fixed Intel complaints

Src/C_BaseLib/FabArray.H

commit 4cd7b9cfeb08d1dfa242b546261d5fffdc558209
Merge: 44525e9c9 1535d1bfa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 14:32:16 2015 -0800

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit 1535d1bfa2c195afc64edf6076ca7405d9ecfc22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 14:28:40 2015 -0800

    UArena: check nullptr

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/UArena.cpp

commit c78f4ad5e4e6a52691b5d240fdbac681564a9d39
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 13:47:49 2015 -0800

    UPC++: use auto since we are using C++11.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 004d378b29c6472d01ee2fb4a646438907a1a6cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 13:31:25 2015 -0800

    updated local copy in fill periodic boundaries

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 24dd2888b62ea71802f1c84bc5e3454a53e764b1
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Nov 10 13:28:02 2015 -0800

    C_BaseLib, F_BaseLib: don't try to free MPI_COMM_WORLD in parallel_finalize()
    
    In commit 18fc260 ("C_BaseLib, F_BaseLib: free only the "local" MPI
    communicator when calling parallel_finalize() from C++ code") I added the
    "local" communicator as an argument to bl_fortran_mpi_comm_free() and
    parallel_finalize(). This works fine if MPI_COMM_WORLD has been split, i.e., if
    one is using sidecars, because then only the newly formed communicator gets
    freed. But if not using sidecars, then the code tries to free MPI_COMM_WORLD,
    which causes MPI to abort with an error.
    
    To fix this, we remove the communicator argument from
    bl_fortran_mpi_comm_free() and put it instead in a new function
    bl_fortran_sidecar_mpi_comm_free(). If the IN_TRANSIT preprocessor macro is
    *not* defined, then we have only one communicator (MPI_COMM_WORLD), and we call
    bl_fortran_mpi_comm_free() with no arguments; this restores the original
    behavior before commit 18fc260. If the macro *is* defined, then we have
    multiple communicators, and we call bl_fortran_sidecar_mpi_comm_free() instead.

Src/C_BaseLib/BoxLib.cpp
Src/F_BaseLib/parallel.f90

commit b69dc94a61a15fbb52b0bf29f4e8d1be0e84b5df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 12:55:43 2015 -0800

    UPC++ team: added implicit team barrier in fillboundary and MFIter

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/ParallelDescriptor.H
Tutorials/PGAS_HEAT/main.cpp

commit 8a830122d3145b0c1b864b4f2e06857bb117d610
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 11:21:01 2015 -0800

    FillBoundary: use local copy for communication inside team

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 1face51b5f0769584446c466fa5ed5050879ed1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 11:08:51 2015 -0800

    DistributionMapping: use team_for

Src/C_BaseLib/DistributionMapping.cpp

commit e563ded7585f1da1d68e344e65923cdc2cb766a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 11:08:11 2015 -0800

    ParallelDescriptor: another type of team_for

Src/C_BaseLib/ParallelDescriptor.H

commit 7b5d6a138c445d43b4a05ef2ce88c0b5e3957b82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 10:49:17 2015 -0800

    BLPgas: renamed DEBUG to UPCXX_DEBUG

Src/C_BaseLib/BLPgas.cpp

commit e889ae98358b532c7ff0bbf3ab96d37ab73a6716
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 10:48:29 2015 -0800

    ParallelDescriptor: added team_range and team_for

Src/C_BaseLib/ParallelDescriptor.H

commit fde7bee8570161bf587deff4bec94afea2621903
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 9 16:45:54 2015 -0800

    low memory option for writing particles.

Src/C_BaseLib/Particles.H

commit 74c632365ad970e620d6cbaae96b71056a52ad98
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 9 15:06:50 2015 -0800

    PGAS_HEAT: added a number of barriers

Tutorials/PGAS_HEAT/main.cpp

commit 9192e76c02f7167e275980f22a7b787d1776c1cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 9 15:05:58 2015 -0800

    added UPC++ team barrier.

Src/C_BaseLib/ParallelDescriptor.H

commit b70ba8e7175c9c69d51b753d08d4cfaed11b1745
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 9 13:20:06 2015 -0800

    updated VisMF::Write for UPC++ team

Src/C_BaseLib/VisMF.cpp

commit deb5a85702fd31e4b87e28d2fc52e1d8c8b9a703
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 9 13:07:13 2015 -0800

    rewrote AllocFabs using the new team distribution map

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/UArena.cpp

commit 957aa4a6c05a5c4e0baa3a146250852ff7396f89
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 9 12:48:24 2015 -0800

    C_BaseLib, F_BaseLib: free only the "local" MPI communicator when calling parallel_finalize() from C++ code
    
    When running C++/F90 codes with multiple communicators (i.e., with
    sidecars), the code will crash on BoxLib::Finalize() because
    in parallel_finalize() the sidecars are trying to free the "compute"
    communicator. So now we supply the "local" communicator as an argument
    to parallel_finalize().

Src/C_BaseLib/BoxLib.cpp
Src/F_BaseLib/parallel.f90

commit 562e992f098923b25bd4c0dee2912931b6a6ecbe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 9 12:23:07 2015 -0800

    DistributionMapping: add LeastUsedTeams and for SFC split the works among teams first and then inside teams

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit e1cce37c7f368aa54127205eeee2a272a3af3a01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 7 20:06:45 2015 -0800

    MFIter: new owner_only flag

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit dcb2b373b80a0b344c4315778beeb265c9ad549d
Merge: 4456e5920 4aa1c64f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 7 10:05:35 2015 -0800

    Merge branch 'development' into pgas

commit 4aa1c64f3d520eb8b1359cc85818ec7030d5d7fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 7 10:05:15 2015 -0800

    MFIter: use bitfield flags

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit 4456e59209d7c58d274abe72d5543cad5ca9125e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 6 20:24:10 2015 -0800

    added fab ownership

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H

commit ca436aeb511d07e517a80b70ae10c1761c4ec221
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 6 19:58:40 2015 -0800

    Added an Arena for UPC++

Src/C_BaseLib/BArena.cpp
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/UArena.H
Src/C_BaseLib/UArena.cpp

commit c1068028d948d1fd7854181cf92ce779d7d0c016
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 6 17:14:00 2015 -0800

    first pass of UPC++ team

Src/C_BaseLib/BArena.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/IArrayBox.H
Src/C_BaseLib/IArrayBox.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Tutorials/PGAS_HEAT/GNUmakefile

commit e5c357123b04d6be5576da8aacca57d110070bb0
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 6 16:26:36 2015 -0800

    return coord type as an int (esp. for mpi)

Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp

commit 9ff1b0a0a9701888fb47a3dd5851e537f1ae0a58
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 6 16:01:53 2015 -0800

    check for correct array size.

Src/C_BaseLib/Box.cpp

commit 53c4ce1cb6e8943b5043db68995ef501128e206a
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 6 16:01:12 2015 -0800

    fixed comment.

Src/C_BaseLib/FabArray.H

commit 956a6e9a76fd0e3a79e40acd6c06b51099eb6363
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 6 16:00:49 2015 -0800

    (un)serialize functions for boxarray.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit d2c1a3221f889b381971860c2fa767b4d01a4da2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 6 11:56:16 2015 -0800

    BoxLib/Tutorials/AMR_Adv_Diff_F: Put higher order slopes into algorithm -- now there is a separate slope
    routine which is called from compute_fluxes.  There are still no transverse derivatives though.

Tutorials/AMR_Adv_Diff_F/GPackage.mak
Tutorials/AMR_Adv_Diff_F/compute_flux.f90
Tutorials/AMR_Adv_Diff_F/slope.f90

commit d77ca089e61f98a0923fe3e4cee8900b5dc94a16
Merge: 904d803b4 f6889d7c9
Author: yzheng <yzheng@lbl.gov>
Date:   Fri Nov 6 09:56:17 2015 -0800

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit 905d1a56fb057e87cfc61cc7137e3f2ff74fa94d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 6 09:02:38 2015 -0800

    Don't need interpolate.f90 in this example.

Tutorials/AMR_Advection_C/Source/Make.package
Tutorials/AMR_Advection_C/Source/interpolate.f90

commit ff72c305085a4721d25b2c6e4951d634cb69c0a8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 6 07:35:54 2015 -0800

    Clean up of Tutorials/AMR_Advection_C code --
    1) Convert to use BoxLib::average_down(...
    2) Clean out unused "nspec"

Tutorials/AMR_Advection_C/Source/ADR.cpp
Tutorials/AMR_Advection_C/Source/ADR_F.H
Tutorials/AMR_Advection_C/Source/Src_2d/ACT_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/trans_2d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/ACT_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90

commit 506981603255e6a4a0dd389e1408c17e2780a6e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Nov 5 22:49:32 2015 -0500

    don't print a warning about visualization if we are making benchmarks

Tools/RegressionTesting/testnew.py

commit 70062e3bd69da2ab6e8b276a7f5f2d7602fd22cd
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 5 16:03:51 2015 -0800

    parmparse setting for particles.particles_nfiles.

Src/C_BaseLib/Particles.H

commit f6889d7c925e0fbeb69ac232ae24fc1b513e9c3a
Merge: 759ae876d 079c2cb02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 5 10:52:36 2015 -0800

    Merge branch 'development' into pgas
    
    Conflicts:
            Src/C_BaseLib/BoxLib.cpp
            Src/C_BaseLib/Make.package

commit 079c2cb0293b0901471ff5c8c2a674417ff574f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 5 10:02:49 2015 -0800

    PIC tutorial: update to the FMultiGrid function name

Tutorials/PIC_C/solve_with_f90.cpp

commit de846815af572c9edec8b53f6198fd11d8ab3694
Merge: cd72ddc8d df9792908
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 5 09:51:16 2015 -0800

    Merge branch 'development' into new_particle

commit cd72ddc8d4a21a8175740d75f01442647e0146ef
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 5 03:11:09 2015 -0800

    Add versions of BoxLib::average_down that take an int rather than an IntVect
    for the refinement ratio.

Src/C_BaseLib/MultiFabUtil.H
Src/C_BaseLib/MultiFabUtil.cpp

commit a7486a693755a54909bf28bf599019873b2c2778
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 5 03:09:41 2015 -0800

    This version does a level-0-then-level-1 solve as well as a multilevel 0-1 solve.
    It compiles and runs with the latest versions of BoxLib::new_particle branch.

Tutorials/PIC_C/main.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/solve_with_f90.cpp
Tutorials/PIC_C/solve_with_hpgmg.cpp

commit 53cd9bcab749ba3e005f5de1bc0b5b1845a70d9e
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 4 16:13:49 2015 -0800

    added functions to (un)serialize arrays of strings.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 3654493612818c8822b14ab3d8c84da82f1cad0d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 4 14:53:36 2015 -0800

    proc numbers for all.

Src/C_BaseLib/ParallelDescriptor.H

commit 72077db2ba84c25c45fbf459cf6649a2895b5855
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 4 14:52:42 2015 -0800

    (un)serialize box functions for communicating boxes.

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp

commit 2810d4e9fb82be4fba285bdecab0ae761c2f0068
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 3 15:37:01 2015 -0800

    random multilevel distribution map for testing the sidecars.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 071dad7fecfad3f64592ba1c5f4855209c5bca25
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 3 15:35:36 2015 -0800

    added function to increase the number of processes in a sidecar.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 9ab7b1c582ce3b575dc6c0118b6d0c40f62c256f
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 3 15:34:02 2015 -0800

    added a few diagnostics for dynamic sidecar development.

Src/C_BaseLib/FabArray.H

commit df979290812e1558e844239a1ff58e55a5556f04
Merge: 184fa1934 13a755cd6
Author: Regression Tester <ccse.lbl@gmail.com>
Date:   Tue Nov 3 12:21:16 2015 -0800

    Merge branch 'master' into development

commit 184fa193482b42403c44168d7d26bbdb56bbbae8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 2 16:27:42 2015 -0800

    FMultiGrid: renamed get_grad_phi back to get_fluxes because the latter is more accurate.

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp
Tutorials/MultiGrid_C/main.cpp

commit 075caf7ef6c672cba446bea34c9da4ec2d6ee028
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 2 16:03:08 2015 -0800

    fixed comments thanks to Ashish Pathak of Umass Dartmouth

Tutorials/HeatEquation_EX5_F/advance.f90

commit 1693e7f5b8c7983326a35e6224b4e49ebd5c9b1c
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 2 15:27:46 2015 -0800

    Revert "IntVect: move static variables returned by TheDimensionVector() to anonymous namespace"
    
    This reverts commit 7d380196bce8148af7544b5920af5ab01f0d059d.

Src/C_BaseLib/IntVect.cpp

commit f2e038351720492583c8120cf0f31adbea1660a6
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 2 15:27:45 2015 -0800

    Revert "IntVect: move all remaining static variable declarations to anonymous namespace"
    
    This reverts commit eb4ea0d9b111bc2b5debb5199e09b12a418a4721.

Src/C_BaseLib/IntVect.cpp

commit 0bb3b85e865bcd7d829f734aacd8549fb9a2ef02
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 2 15:27:44 2015 -0800

    Revert "Box: move static variable "Unit" (returned by TheUnitBox()) to anonymous namespace"
    
    This reverts commit 87f50a2d86e8a6bd6d71afeaf238bc277fe20d43.

Src/C_BaseLib/Box.cpp

commit 540445d64641d4ba4e4d9309100b572bae925a7b
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 2 15:27:41 2015 -0800

    Revert "IndexType: move static variables "Cell" and "Node" to anonymous namespace"
    
    This reverts commit 685ad5b30fbff794d69017051fb06f5addcb1401.

Src/C_BaseLib/IndexType.cpp

commit 685ad5b30fbff794d69017051fb06f5addcb1401
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 2 15:04:19 2015 -0800

    IndexType: move static variables "Cell" and "Node" to anonymous namespace

Src/C_BaseLib/IndexType.cpp

commit 87f50a2d86e8a6bd6d71afeaf238bc277fe20d43
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 2 15:02:47 2015 -0800

    Box: move static variable "Unit" (returned by TheUnitBox()) to anonymous namespace

Src/C_BaseLib/Box.cpp

commit eb4ea0d9b111bc2b5debb5199e09b12a418a4721
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 2 15:01:03 2015 -0800

    IntVect: move all remaining static variable declarations to anonymous namespace

Src/C_BaseLib/IntVect.cpp

commit 7d380196bce8148af7544b5920af5ab01f0d059d
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 2 14:33:51 2015 -0800

    IntVect: move static variables returned by TheDimensionVector() to anonymous namespace
    
    This renders unnecessary (and partially reverts) the changes made in
    commit 3f16894 ("IntVect: added braces around cases of
    TheDimensionVector"). In C++11 the "static" qualifier is no longer
    necessary because variable declarations in anonymous namespaces are
    guaranteed to have internal linkage. However, in C++03, without the
    "static" qualifier they have external linkage.

Src/C_BaseLib/IntVect.cpp

commit 1dafc8239c6af1a87b3440dd68560dc8cab54872
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 2 14:41:21 2015 -0800

    MultiFabUtil: fixed bug in my last commit

Src/C_BaseLib/MultiFabUtil.cpp

commit 78fafee5a832476c2e5e3dd848243b18478dc5b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 2 13:50:08 2015 -0800

    FMultiFab: use crse mf to construct MFIter

Src/C_BaseLib/MultiFabUtil.cpp
Src/C_BaseLib/MultiFabUtil_1d.f90
Src/C_BaseLib/MultiFabUtil_2d.f90
Src/C_BaseLib/MultiFabUtil_3d.f90
Src/C_BaseLib/MultiFabUtil_F.H

commit 572837c5de4ebe615d09c63f6a447a11b3f1d241
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 2 11:27:26 2015 -0800

    MultiFabUtil: thread safety

Src/C_BaseLib/MultiFabUtil.cpp

commit a2fe131d50b6f09a009ccb94d6250041db4447ac
Merge: 4bb03b719 2f8c5eaff
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 2 11:25:43 2015 -0800

    Merge branch 'development' into new_particle

commit b10952cf76e7de85701ab7d632ff90654b52be05
Merge: 31cd7af4c 2f8c5eaff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Nov 2 14:25:35 2015 -0500

    Merge branch 'development' into plotfile_ghost

commit 31cd7af4c222484e247cd2e22fd718d8075b00bb
Merge: ca512a4fd 492754ab9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Nov 2 14:25:05 2015 -0500

    Merge branch 'development' into plotfile_ghost

commit ca512a4fdf48ab89711610af597aae3abf217a13
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 2 11:10:43 2015 -0800

    Revert to writing the plotfiles with ghost cells -- the fcompare routine in Tools/PostProcessing/F_src
    is now able to handle plotfiles with ghost cells.

Tutorials/MultiGrid_C/writePlotFile.cpp

commit 2f8c5eaffcce8663752731f8c9004e2e237ae3a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 2 09:56:05 2015 -0800

    MultiFabUtil: Removed bl_constants_module because it is in F_BaseLib, not C_BaseLib.  Some codes may not include F_BaseLib.

Src/C_BaseLib/MultiFabUtil_1d.f90
Src/C_BaseLib/MultiFabUtil_2d.f90
Src/C_BaseLib/MultiFabUtil_3d.f90

commit 13a755cd6c7806f59a6a1c33c08d40ffbaa72d9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 1 19:36:27 2015 -0800

    fixed a bug in regrid.f90 thanks to Ashish Pathak of Umass Dartmouth

Src/F_BaseLib/regrid.f90
Src/Python/F90/src/regrid.f90

commit 492754ab96a8285668931a02683aa613063c1093
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 1 19:43:14 2015 -0800

    Make: flags for using fsanitizer with gcc

Tools/C_mk/Make.defs

commit 0378f7f1319e887828a55e6f31638b7cb533afea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 1 19:41:36 2015 -0800

    C_CellMG: return immediately if the initial residual is already zero.  this could happen for species diffusion when certain species is initially zero everywhere.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit c3a68fe8fb19099ab601e59a7adc506be1902c5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 1 19:36:27 2015 -0800

    fixed a bug in regrid.f90 thanks to Ashish Pathak of Umass Dartmouth

Src/F_BaseLib/regrid.f90
Src/Python/F90/src/regrid.f90

commit e699ab9c81c30ea5e40d6bc22b80cd6553ddbbff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Nov 1 17:46:02 2015 -0500

    copy the diffDir if we do copy_benchmarks

Tools/RegressionTesting/testnew.py

commit a52461f53902541acc182dcac5b4feef682966c2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Nov 1 12:49:08 2015 -0800

    Have two separate versions of BoxLib::average_down -- one which uses
    volume weighting and one which does not.

Src/C_BaseLib/MultiFabUtil.H
Src/C_BaseLib/MultiFabUtil.cpp
Src/C_BaseLib/MultiFabUtil_1d.f90
Src/C_BaseLib/MultiFabUtil_2d.f90
Src/C_BaseLib/MultiFabUtil_F.H

commit 4299b1c5219acc01986bcaacd7139fd846457e93
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Nov 1 11:17:47 2015 -0800

    Use tileboxes in BoxLib::average_down, and fix an indexing error
    in MultiFabUtil_*d.f90

Src/C_BaseLib/MultiFabUtil.cpp
Src/C_BaseLib/MultiFabUtil_1d.f90
Src/C_BaseLib/MultiFabUtil_2d.f90
Src/C_BaseLib/MultiFabUtil_3d.f90

commit dcf421d200602e3c6fea145fd7f92e92703b1209
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 31 18:39:09 2015 -0400

    lots of compilation fixes

Src/C_BaseLib/MultiFabUtil_1d.f90

commit 13513ef41d0e723be0116f883fba8fa09407e1eb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 30 15:44:21 2015 -0700

    Add the average down routines to 1d and 2d.

Src/C_BaseLib/MultiFabUtil_1d.f90
Src/C_BaseLib/MultiFabUtil_2d.f90

commit 9e3990349c71ab0781cb11cccdc108231aa31006
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 30 15:16:15 2015 -0700

    MultiFabUtil: fixed function arguments

Src/C_BaseLib/MultiFabUtil.cpp

commit fe62e3fd13777b57b1d5ca0d7b6dc9edd980a0f3
Merge: 404abd0c8 0932040bc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 30 15:02:21 2015 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 404abd0c80c9b6d899b36f8415b473221b1a0b90
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 30 15:01:48 2015 -0700

    Put in first pass at generic routine in BoxLib namespace that averages a fine MultiFab onto
    a coarse MultiFab without having to be owned by an AmrLevel.

Src/C_BaseLib/MultiFabUtil.H
Src/C_BaseLib/MultiFabUtil.cpp
Src/C_BaseLib/MultiFabUtil_3d.f90
Src/C_BaseLib/MultiFabUtil_F.H

commit 0932040bc99f96e4dc65357997f5feec38a47f78
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Oct 30 13:13:16 2015 -0700

    Update system for OSX 10.11.1

Tools/C_mk/Make.Darwin
Tools/C_mk/Make.mpi

commit 2ecabc668cc171d984493667b782bdd25263c15b
Merge: 0102f402c b326eb957
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Oct 30 13:08:06 2015 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 0102f402ce96017b58e2a61b04f4256d6bc89ace
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Oct 30 13:04:50 2015 -0700

    Remove question make from define of CC and CXX if USE_GNU in Make.defs because make defaults CC=cc before anything else.  On Linux machines, CC then gets redefined explicitly.  On Darwin it does not, and the USE_GNU bit fails to set CC and CXX as it should.

Tools/C_mk/Make.defs

commit b326eb957ef4210b607fe6a19f86281cdc066e2f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 30 12:50:51 2015 -0700

    FMultiGrid: added mac projection

Src/C_BoundaryLib/MacBndry.H
Src/C_BoundaryLib/MacBndry.cpp
Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp

commit 4bb03b719af108738e00c6c27c5a5b7919d03f02
Merge: f776c3d00 ec1bffbd6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 30 10:19:11 2015 -0700

    Merge branch 'development' into new_particle

commit f776c3d0084a2b69db48c6e8a2659e593cb28a58
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 30 10:18:28 2015 -0700

    Latest versions ... still not soup yet.

Tutorials/PIC_C/main.cpp
Tutorials/PIC_C/solve_for_accel.cpp

commit a067b5bb71e22358baa9f3bf907d6947a9c1fcbd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 29 17:26:14 2015 -0700

    This verison of Particles.H actually compiles after the latest change.

Src/C_BaseLib/Particles.H

commit eb54c104b4bdfaac88a3743687eef9e59f86ca5a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 29 17:24:03 2015 -0700

    Modify ParticleContainer::InitRandom so that it can take an optional RealBox argument
    which allows you to constrain the particles to lie within a rectangular region.

Src/C_BaseLib/Particles.H

commit 49e667e45874bb857157317951fc7fdc04ea1d81
Merge: 94fd6c861 445e5a566
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 29 16:52:29 2015 -0700

    Merge branch 'new_particle' of ssh://github.com/BoxLib-Codes/BoxLib into new_particle

commit ec1bffbd6839c870319a907df58a501ffa852ac5
Merge: d6025300e d1a24616b
Author: Changho Kim <changhokim@lbl.gov>
Date:   Thu Oct 29 13:24:32 2015 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit d6025300e0625a2b3db127b19b7224863d7c2bd5
Author: Changho Kim <changhokim@lbl.gov>
Date:   Thu Oct 29 13:14:50 2015 -0700

    new utility added
    
    !! fdumpdata2d generates plain-text-formatted data files from plotfiles.
    !!
    !! usage: fdumpdata2d --pf (pfs) [--var (vars)] [--lev (levs)] [--separate]
    !!        where (pfs) = list of plotfiles,
    !!              (vars) = list of variables,
    !!              (levs) = list of levels,
    !!              --var, --lev, --seprate are optional.

Tools/Postprocessing/F_Src/GNUmakefile
Tools/Postprocessing/F_Src/fdumpdata2d.f90

commit d1a24616b2fdd6c4405464a1ce270d9c81a189fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 29 16:12:08 2015 -0400

    missing contiue

Tools/RegressionTesting/testnew.py

commit a9f7d1be0e21e099e8b425808ff566c833511990
Merge: 25ffc60e4 be1efa629
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 29 15:59:15 2015 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 25ffc60e4538ac767be94643e2a6ac0c4a6c6175
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 29 15:59:07 2015 -0400

    fix the output of the diff

Tools/RegressionTesting/testnew.py

commit 445e5a566734d91cb2f197bfb5dab321b443de66
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 29 12:58:17 2015 -0700

    PIC tutorial: use FMultiGrid

Tutorials/PIC_C/solve_with_f90.cpp

commit f9af5106972cef6776a712a623d6e754f1401d5d
Merge: 6498f8a85 be1efa629
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 29 12:57:25 2015 -0700

    Merge branch 'development' into new_particle

commit be1efa629f9390dba81f1fed55f3778eb6d74977
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 29 12:57:05 2015 -0700

    FMultiGrid: minor tweak

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp

commit 6498f8a852577998506af9e6e9ef102c9c9b2cfe
Merge: 0c02e2b65 6f9753b09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 29 10:48:32 2015 -0700

    Merge branch 'development' into new_particle
    
    Conflicts:
            Tutorials/MultiGrid_C/main.cpp

commit 9046bd671d748b44f9ad0b1df0d1556054dfad7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 28 20:06:39 2015 -0400

    replace lbound() and ubound() with lo and hi, since these are
    safer in the presence of ghost cells

Tools/Postprocessing/F_Src/CASTRO_radiation/fgaussianpulse.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/flgt_frnt1d.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/fradshock.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/fradsphere.f90
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/feint.f90
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fwdconvect.f90

commit 78ac9c418fecb357ce7e589afe1f8724822d403e
Merge: 7724c23d1 0bb054e13
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 28 19:23:07 2015 -0400

    Merge branch 'development' into plotfile_ghost

commit 7724c23d1d9c408237d2fdb0caaa8ce6c9f74b33
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 28 19:00:36 2015 -0400

    get ghost cell support in here -- the size now refers to the size on
    disk, including ghost cells.  There should be no difference at all
    for plotfiles without ghost cells

Src/F_BaseLib/plotfile.f90

commit ab87088f846f93be074d2d8987bd5198db2bca12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 28 19:00:13 2015 -0400

    this works with ghost cells now

Tools/Postprocessing/F_Src/fcompare.f90

commit 6f9753b09aa9b8385871279f66078325c0b36ea9
Merge: c4beaabf3 0bb054e13
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 28 14:19:23 2015 -0700

    Merge branch 'development' into ctof

commit c4beaabf3b29ff7e467961307444e811ef8ac54b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 28 14:17:54 2015 -0700

    capability of sharing a multifab from C++ to Fortran without copying the data

Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/MultiFab_C_F.H
Src/F_BaseLib/MultiFab_C_F.cpp
Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab_c.f90
Tutorials/MultiFab_C_F/GNUmakefile
Tutorials/MultiFab_C_F/Make.package
Tutorials/MultiFab_C_F/ff.f90
Tutorials/MultiFab_C_F/main.cpp

commit 3037300d094af598d034a06804d9231227ff553e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 28 13:07:55 2015 -0700

    moved the stuff that starts mpi for fortran form mgt_solver to c++ boxlib init function

Src/C_BaseLib/BoxLib.cpp
Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/parallel.f90
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 0bb054e13d30bfe7230560f84df7f750333e4e04
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Oct 27 10:51:08 2015 -0700

    Tutorials: add "beta" to argument list of solve_with_HPGMG() in MultiGrid_C
    
    HPGMG internally calculates beta at cell faces from the cell-centered beta
    MultiFab because BoxLib and HPGMG store cell face data in very different ways.
    It's much easier to do the averaging by hand than it is to translate array
    indices.
    
    However, in order to be consistent with the sign conventions of the other
    solvers, we want to calculate grad(Phi) in the same way that they do. So we use
    an AbecLaplacian to calculate the gradients. But AbecLaplacian needs the beta
    at cell faces, not cell centers. So we add beta to the arguments list.
    
    This also fixes a compile-time error if running this tutorial with HPGMG: the
    variable "abec_operator" was never declared.

Tutorials/MultiGrid_C/main.cpp

commit 4bad12766203a47cbc7f94c2895116bec3af75d9
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Oct 26 23:00:43 2015 +0000

    C_BaseLib: remove "__LP64__" preprocessor macro from list of macros describing long pointers
    
    This macro does not uniquely describe long pointers. It leads to compile-time
    errors on Mira (BG/Q) because many variables in FPC.cpp are duplicately
    declared, since both "__ppc__" and "__LP64__" are defined.
    
    This removal should (hopefully) not affect any architectures we run on, since
    at least one of the other macros should be defined.

Src/C_BaseLib/FPC.cpp

commit 1e36c50889063fb0f3f5785d7acc5b304cd094dd
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Oct 20 23:21:34 2015 +0000

    F_MG: include "get_dim()" explicitly from multifab_module in ml_prolongation.f90
    
    The XL Fortran compiler on Mira complains about being unable to find this
    function.

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 3f0b48be6b93765ed00d7f6cd85860810f4a2d7a
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Oct 20 23:20:19 2015 +0000

    C_BaseLib: add FORT_FASTSAXPY definition to SPECIALIZE_F.H for BL_FORT_USE_LOWERCASE
    
    Found this bug when trying to compile the MultiGrid_C tutorial with the XL
    compilers on Mira.

Src/C_BaseLib/SPECIALIZE_F.H

commit fcb28d436ca44c07847b2aaa821f3ad0d251f775
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Oct 15 22:07:14 2015 +0000

    IntVect: added braces around cases of TheDimensionVector
    
    Cases share scope, so without braces the variables declared in the different
    cases percolate down through the entire switch statement.  This can lead to
    uninitialized variables if a particular case is skipped. Adding braces around
    each case creates a unique scope for each of these variables, which protects
    against this possibility.  The IBM XL compiler caught this error.

Src/C_BaseLib/IntVect.cpp

commit 0f550e3b297341c86ae224d3a6287c2840594dd0
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Oct 15 21:56:55 2015 +0000

    C_mk, F_mk: add support for IBM XL compilers on Mira, the BlueGene/Q at ALCF

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/bgq.mak

commit 08c4f5da2561c273ff65d8ea549e88caab481bd0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 27 10:14:34 2015 -0700

    AMR_Advection_C Tutorial: consolidate diffusion code

Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp
Tutorials/AMR_Advection_C/Source/Diffusion.H
Tutorials/AMR_Advection_C/Source/Diffusion.cpp

commit c4cf10e981dd6e7ded363150488b9ba25832b7cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 27 10:14:01 2015 -0700

    FMultiGRid: added functions for diffusion operator

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H

commit 94fd6c861223492c3578333a10db7dfd0bed6b59
Merge: 50d7b90ee 8aecad560
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 27 10:09:40 2015 -0700

    Merge branch 'development' into new_particle

commit 8aecad560000021e10e75866a5f2def1a33a2e5b
Merge: 4990cf45b ba093b337
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 27 09:45:38 2015 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 4990cf45bf2c7a25f3ea1a414ed4e561a712f116
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 27 09:45:17 2015 -0700

    added 1d file.  some subroutines now working yet.

Src/Extern/amrdata/FABUTIL_1D.F

commit ba093b337c58b0006d32cad511a29243641dfe8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 17:28:43 2015 -0700

    AMR_Advection_C Tutorial: use FMultiGrid

Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp
Tutorials/AMR_Advection_C/Source/Diffusion.H
Tutorials/AMR_Advection_C/Source/Diffusion.cpp

commit 0b342a7edbf73455578452730b9b394d3d651a84
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 17:26:47 2015 -0700

    FMultiGrid: added applyop functions

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp

commit 49055091ce52307d5690f8e2f5bc2ea9573d0f57
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 26 17:01:06 2015 -0700

    dont use the word signal.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 045793488c2ac63be8cfd2968f1d44121dbe32f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 16:25:18 2015 -0700

    update Linear Solver Comparison Test to use FMultiGrid

Tests/LinearSolvers/ComparisonTest/COEF_1D.F
Tests/LinearSolvers/ComparisonTest/COEF_3D.F
Tests/LinearSolvers/ComparisonTest/COEF_F.H
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp

commit 5d0a945bf8e3e5e593f7077dce56659cafa57d5a
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 26 16:00:10 2015 -0700

    make safer data broadcasts.

Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit 679f0220773816f3e809bdcb206076576c3c5b3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 15:32:31 2015 -0700

    minor cleanup

Src/C_BaseLib/MultiFabUtil.cpp

commit 82c75eeac3b76e6e6759194d1af6773a7fe02846
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 14:09:59 2015 -0700

    MultiGrid Tutorial: use FMultiGrid instead of MGT_Solver directly

Tutorials/MultiGrid_C/main.cpp

commit 0f0ca5aa97fc660ef48a0cbd1f135f4fdcc0c289
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 14:01:02 2015 -0700

    FMultiGrid: make the interface consistent with C++ ABecLaplacian class

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp

commit 8cbee5677d4c395e8c09741532ac0e43f0b699c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 13:50:59 2015 -0700

    MultiGrid Tutorial: use the new BoxLib::average_face_to_cell_center function and use PArray for bcoeffs

Tutorials/MultiGrid_C/COEF_2D.F
Tutorials/MultiGrid_C/COEF_3D.F
Tutorials/MultiGrid_C/COEF_F.H
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp
Tutorials/MultiGrid_C/main.cpp

commit 500cca1ab3b1a9a47657409e862cc9910672250e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 13:45:09 2015 -0700

    C_CellMG: added a new function that takes PArray as b coeffs

Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp

commit 2e0feccdd375b92ad690582d5a86f77d553d0f73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 13:43:52 2015 -0700

    added a new function that averages from cell-centered to face MultiFabs

Src/C_BaseLib/MultiFabUtil.H
Src/C_BaseLib/MultiFabUtil.cpp
Src/C_BaseLib/MultiFabUtil_1d.f90
Src/C_BaseLib/MultiFabUtil_2d.f90
Src/C_BaseLib/MultiFabUtil_3d.f90
Src/C_BaseLib/MultiFabUtil_F.H

commit 9e5fe738252c46730c2014b5146b6fa8892f33c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 12:40:21 2015 -0700

    MultiGrid Tutorial: removed unnecessary ghost cells

Tutorials/MultiGrid_C/main.cpp

commit 911002caba28a8a6de39a03404fedcfcd0683b5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 11:25:36 2015 -0700

    update HyperABecLap that has been broken for 3 years due to changes in BndryData

Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp

commit 6b9b91bddf52a1191527aaa79c73b3d28c343c53
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 10:18:56 2015 -0700

    FMultiGrid: cleanup

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp

commit ec4803b32a99de323053402cf5ccde094b729b72
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Oct 26 10:47:44 2015 -0400

    fix the build git hash stuff

Tools/C_scripts/makebuildinfo_C.py

commit 1cb1499f3090343d4276aea2f83c10bc0ac246da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 25 18:04:50 2015 -0700

    FMultiGrid: make it more general

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 9776f06aa763c9813f4499412e8e2fa3b9806b4b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 25 16:06:22 2015 -0700

    FMultiGrid: bug fix

Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp

commit 72f602a63c9aa045fc0a46a40c0d2ebf75c418ba
Merge: a149254f4 a4211e592
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 24 22:12:38 2015 -0700

    Merge branch 'development' into mlcc

commit a149254f481447999a8b786e07b6dd63349e9399
Merge: 83e3c9408 5fa4d44a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 24 22:11:52 2015 -0700

    Merge branch 'development' into mlcc

commit 83e3c94085a0003a54702a57e80a8edbaae78e98
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 24 22:10:41 2015 -0700

    minor

Src/C_AMRLib/Amr.cpp

commit 605ecaa9dcc22d9270ef46647831d71a0ae66e07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 24 20:42:05 2015 -0700

    fixed comments

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H

commit 6a066990ed5422fdb423ccf40e2e4094937d6b7c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 24 20:10:46 2015 -0700

    FMultiFab: comments and minor tweak

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp

commit 22cb6f69edf0ed75b2b4c40736f201a5e39c7afa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 23 17:35:49 2015 -0700

    FMultiGrid: refactor

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp

commit 50d7b90ee0bc8f29deee6bb6dadcde366e3e2d7e
Merge: 0c02e2b65 a4211e592
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 23 17:15:53 2015 -0700

    Merge branch 'development' into new_particle

commit a4211e592c887c11634594c283390928fe03623f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 23 17:14:47 2015 -0700

    In Tutorials/MultiGrid_C, I hard-wired the new grad_phi stuff for BL_SPACEDIM = 3.
    This generalizes it to work for BL_SPACEDIM = 2 or 3.

Tutorials/MultiGrid_C/main.cpp

commit 0c02e2b658d5fd00e9409620485c67ab28630d9f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 23 17:14:47 2015 -0700

    In Tutorials/MultiGrid_C, I hard-wired the new grad_phi stuff for BL_SPACEDIM = 3.
    This generalizes it to work for BL_SPACEDIM = 2 or 3.

Tutorials/MultiGrid_C/main.cpp

commit 6fd99675fbca026568931c98b7ebecd423cc85aa
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 23 17:12:17 2015 -0700

    Since the C++ MultiGrid solver uses only V-cycles, we want to hard-wire piecewise constant,
    not piecewise linear interpolation -- the PC interpolation works better for V-cycles while the
    piecewise linear works better for F-cycles.

Src/LinearSolvers/C_CellMG/MG_2D.F
Src/LinearSolvers/C_CellMG/MG_3D.F

commit cf2652fb873d655dbde0a95f198c7807198b366f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 23 17:12:17 2015 -0700

    Since the C++ MultiGrid solver uses only V-cycles, we want to hard-wire piecewise constant,
    not piecewise linear interpolation -- the PC interpolation works better for V-cycles while the
    piecewise linear works better for F-cycles.

Src/LinearSolvers/C_CellMG/MG_2D.F
Src/LinearSolvers/C_CellMG/MG_3D.F

commit 2c02483923caead5987f7809852540c6e9541a61
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 23 16:42:53 2015 -0400

    more safely get the box indicies

Tools/Postprocessing/F_Src/tutorial/fspeciesmass2d.f90

commit b6a4247f6a1b6202604c27c6f817381c774b1b0d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 23 16:33:56 2015 -0400

    eliminate lbound/ubound

Tools/Postprocessing/F_Src/fsnapshot3d.f90

commit 5d0a2eda64c231e47f33f71bde009e324defe507
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 23 16:28:26 2015 -0400

    remove lbound/ubound

Tools/Postprocessing/F_Src/fextract.f90

commit e0bbe775156bee51889250c654cc089a51cdf6ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 23 16:21:16 2015 -0400

    add get_pbox

Src/F_BaseLib/plotfile.f90

commit db3ba7ddce57e3bc10cb5c671a8130b2843fdb8b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 22 22:13:57 2015 -0700

    Remove excess print statements from Particles.H

Src/C_BaseLib/Particles.H

commit e91e2ecaef08dacc9be6e88863317e3c3b3d7e6c
Merge: 8d76fb01b 5fa4d44a4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 22 22:13:36 2015 -0700

    Merge branch 'development' into new_particle

commit 00e46f979f1219ef7aed2968ea0f96a7d411197e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 22 21:52:32 2015 -0700

    PArray: removed isConstPointer

Src/C_BaseLib/PArray.H

commit 5fa4d44a4b99814bbed60222e5a21f8d9e81d934
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 22 17:11:53 2015 -0700

    After we compute the solution, use the operator to return the face-based fluxes, then
    average those onto cell centers using BoxLib::average_face_to_cellcenter and write
    the cell-centered gphi out into a plotfile just like we write out the solution.
    
    This allows us to test the gradient routines as well as the solver itself.

Tutorials/MultiGrid_C/main.cpp

commit 8d76fb01b6ecc957c9dfa7bbdd9e8fef963038fc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 22 17:11:53 2015 -0700

    After we compute the solution, use the operator to return the face-based fluxes, then
    average those onto cell centers using BoxLib::average_face_to_cellcenter and write
    the cell-centered gphi out into a plotfile just like we write out the solution.
    
    This allows us to test the gradient routines as well as the solver itself.

Tutorials/MultiGrid_C/main.cpp

commit ff114ff8198fd025bbf43554ef704424dd4b8505
Merge: a1d31f5ff c60315a6d
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Thu Oct 22 19:16:31 2015 -0400

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit bd223eaae91b79ac20b8c79ee112933dd08d3ad0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 22 15:08:37 2015 -0700

    FMultiGrid: more functions

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp

commit 6a9bcaa8cbb34062a4b050f6d8de1d7acdc0ecb7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 16:20:43 2015 -0400

    replace lbound and ubound with lwb and upb on the boxes -- this will
    be safe when we deal with ghostcells

Tools/Postprocessing/F_Src/faverage.f90

commit c78af9314f58d91de38ea24bf75b3e61baf33aed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 21 21:59:33 2015 -0700

    first pass of MultiLevelMultiGrid

Src/LinearSolvers/C_to_F_MG/CMakeLists.txt
Src/LinearSolvers/C_to_F_MG/FMultiGrid.H
Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp
Src/LinearSolvers/C_to_F_MG/Make.package

commit 0d55d1400434a1bc6752f5b3e9f247ab78be851b
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Oct 22 15:12:25 2015 -0400

    Add ACC flags to fortran mk

Tools/F_mk/comps/Linux_pgi.mak

commit e92c35f6c981d4b4fe7b9fe3443662c96551b028
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Oct 22 15:00:04 2015 -0400

    Start adding ACC to PGI build

Tools/F_mk/comps/Linux_pgi.mak

commit 4ddab485628015ba9909f8150aff545e9da9f7fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 14:34:05 2015 -0400

    some notes along the way

Tools/Postprocessing/F_Src/TODO_GHOST

commit 3fb9899d31bc1596632eb666c7888f4878a34cd0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 14:21:57 2015 -0400

    more simplification + add the --ghost (or -g) option -- it doesn't
    really work yet...

Tools/Postprocessing/F_Src/fcompare.f90

commit 794d7dfd9e1eafbe1f1c2582c623a82ef6a03ce6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 14:09:51 2015 -0400

    remove unused lo and hi

Tools/Postprocessing/F_Src/fcompare.f90

commit 4764009accee9e7a9bdf7002b4211f6b5cb005b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 14:06:12 2015 -0400

    use box_equal() to simplify some stuff

Tools/Postprocessing/F_Src/fcompare.f90

commit 0cde5f7b94758c5c2e67292d38798fbca8d204bc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 13:56:51 2015 -0400

    use volume(get_pbox) in the isnan check

Tools/Postprocessing/F_Src/fcompare.f90

commit 005782ff8c19963beacf3600a78a3b22c17db70b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 13:44:15 2015 -0400

    more work on getting ghostcells into plotfile.f90

Src/F_BaseLib/plotfile.f90

commit c60315a6d3e12bf2551e8456ee680d9aeccd5a05
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 13:02:11 2015 -0400

    some comments on what else to do to get the ghost cells to work

Src/F_BaseLib/plotfile.f90

commit 476160da71e581c6b00f8a07cf1ba13f7f292252
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 12:49:37 2015 -0400

    store ng and create a physical box (%pbx) for each of the fabs in the grid
    hierarchy -- this is to help out with supporting ghostcells in the plotfiles...

Src/F_BaseLib/plotfile.f90

commit 0154618f88ae0ffbe61b34c3ab3e519265e2a1de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 10:48:54 2015 -0400

    check the number of ghostcells in the header and abort if it is not 0
    (for now)

Src/F_BaseLib/plotfile.f90

commit 5f6d84e3a85ded8ab73e643df22a7ad82f8b95d7
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 21 17:58:54 2015 -0700

    Made loop to test multiple sidecar sizes.

Tutorials/Sidecar_EX1/SidecarResizeTest.cpp

commit b67748e3235d4c46ef92556cc7ba95b68e4be135
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 21 17:34:56 2015 -0700

    Support for dynamic sidecars.

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.cpp

commit 248a0c9cf1b3a87855ec867247cb5f8e0042b59b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 21 17:23:51 2015 -0700

    resize to zero at the end.

Tutorials/Sidecar_EX1/SidecarResizeTest.cpp

commit 1b2413b3baf57a2d9dbc3fecac27c2375e7bf35b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 21 17:21:05 2015 -0700

    test with two sizes.

Tutorials/Sidecar_EX1/SidecarResizeTest.cpp

commit dfd041715d346ed82a17c83798829a47780c3fb5
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 21 16:39:59 2015 -0700

    sidecar resize test.

Tutorials/Sidecar_EX1/GNUmakefile
Tutorials/Sidecar_EX1/Make.package
Tutorials/Sidecar_EX1/SidecarResizeTest.cpp
Tutorials/Sidecar_EX1/inputs_sc

commit 4f9e90edc62609e70847d7c5c75b98e0c45b97ae
Merge: 4f7a8b4d4 635bea4a0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 15:00:18 2015 -0700

    Merge branch 'development' into new_particle

commit 635bea4a061458c9ba2f14097dc0cea28d52c7b9
Merge: 7743c84a7 cce7df1d3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 14:58:39 2015 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 7743c84a763dc56cfa01fffe3c71a4730dc8dd02
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 14:57:38 2015 -0700

    Write the plotfile with 0 ghost cells, otherwise fcompare will misinterpret the arrays.

Tutorials/MultiGrid_C/writePlotFile.cpp

commit 4f7a8b4d42c2b7c02e4fe0e6e240ee73e0e9d182
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 14:57:38 2015 -0700

    Write the plotfile with 0 ghost cells, otherwise fcompare will misinterpret the arrays.

Tutorials/MultiGrid_C/writePlotFile.cpp

commit a1d31f5ffd0f7d24e2881cf003d5dbdddd883b52
Merge: 5dacecd61 cce7df1d3
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Wed Oct 21 17:23:01 2015 -0400

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit cce7df1d353ce8049928101f76679bcc2bd2621a
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Oct 21 13:17:24 2015 -0700

    Tutorials: add MPI communicator argument in call to MGBuild() in MultiGrid_C when building with HPGMG

Tutorials/MultiGrid_C/main.cpp

commit 5dacecd61c324c02782c09fd5264e7e60f7b62f3
Merge: 81473c26c 83a7ce0e0
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Wed Oct 21 16:05:52 2015 -0400

    Merge branch 'master' into development

commit b91f298e7c8f3c242d1abc8969d985fdf33b9f44
Merge: 7d4e2155c 81473c26c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 13:03:50 2015 -0700

    Merge branch 'development' into new_particle

commit 81473c26c909802df8bd727b1608e4e39e07e5f6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 12:44:58 2015 -0700

    Modify the C++ solver in MultiGrid.{H,cpp} in order to correctly compute and use the initial residual.
    There was an issue before when a non-zero initial guess was passed in.   This is now closer to the
    decision-making in the F90 solver.

Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 83a7ce0e09afcb551150100ad922d76aade67934
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Wed Oct 21 16:01:34 2015 -0400

    add support for my mac

Tools/F_mk/GMakeMPI.mak

commit 26816e65cc5f626f8c9996e33b3a1ffba742b3bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 21 15:55:31 2015 -0400

    when we do the first --make_benchmarks, the test on get_last_run() fails,
    but it isn't needed there (it is only needed for copy_benchmarks).  Now
    we return None in this case.

Tools/RegressionTesting/testnew.py

commit 7d4e2155cbc2568b320dcf78440e7aac53e63106
Merge: 9c243b8e3 e699a84a1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 12:55:10 2015 -0700

    Merge branch 'new_particle' of ssh://github.com/BoxLib-Codes/BoxLib into new_particle

commit 9c243b8e3fbfda75c4fa748b355618b9be6d0667
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 12:44:58 2015 -0700

    Modify the C++ solver in MultiGrid.{H,cpp} in order to correctly compute and use the initial residual.
    There was an issue before when a non-zero initial guess was passed in.   This is now closer to the
    decision-making in the F90 solver.

Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit e699a84a1726ec4e67aeedce4060737f097b3483
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 21 11:10:10 2015 -0700

    use Array instead of PArray in constructing ParGDB

Src/C_BaseLib/ParGDB.H
Src/C_BaseLib/Particles.H
Tutorials/PIC_C/main.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/solve_with_f90.cpp

commit 8c6c54f33974864ef6f294278f2d241f2db2d3ad
Merge: 4c39e0b27 4595d98e7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 10:40:15 2015 -0700

    Merge branch 'new_particle' of ssh://github.com/BoxLib-Codes/BoxLib into new_particle

commit 4c39e0b2762ff0c23be4166b593e3e88a4acdf46
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 10:39:52 2015 -0700

    Get rid of all the extra print statements in Particles.cpp

Src/C_BaseLib/Particles.cpp

commit 1715a9c223ec50bf584716781bbf6a713bbfb66f
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 19 11:10:37 2015 -0700

    code cleanup.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 0364348453fb1452f820b16f3831081b0edf6f73
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 16 17:00:33 2015 -0700

    moved group and comm initialization to SetNProcsSidecar function.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 657f7cff85415123e2a390605846f872894c7e13
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 16 15:28:52 2015 -0700

    fixed comment.

Src/C_BaseLib/Utility.H

commit 988e219d66f9c64316094438b12ce7edb28bd339
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 13 13:51:25 2015 -0700

    comments.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 1c9058403d946106d37b200113c2ce7d5c4d697c
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 13 13:47:55 2015 -0700

    comments.

Src/C_BaseLib/ParallelDescriptor.H

commit 6edd3cd4e600908ee914c75aeec6d2167a80a3dc
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 13 13:35:37 2015 -0700

    comments.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 4595d98e7e7130122cc7c2efee4e7a042eb1770f
Merge: c7bcd6b17 9e2e4d8d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 21 10:27:42 2015 -0700

    Merge branch 'development' into new_particle
    
    Conflicts:
            Src/C_BaseLib/Make.package

commit 9e2e4d8d685832d468b936a5a59d3ffe0a242920
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 21 10:25:07 2015 -0700

    BoxArray: added a new define function

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit c7bcd6b17e33e4f6b28ec27a54bc03c63d154f68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 20 16:53:02 2015 -0700

    only the I/O processor needs to do I/O

Tutorials/PIC_C/solve_for_accel.cpp

commit 3be6fa84225b6bae47eda7b0c4caf96593582ee8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 20 16:41:52 2015 -0700

    bug fixes in PIC tutorial

Tutorials/PIC_C/main.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/solve_with_f90.cpp

commit d971d2b046bed6e72d2c528e15e11468d467d95b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 20 16:40:13 2015 -0700

    Particles: tweak constructors

Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParGDB.H
Src/C_BaseLib/Particles.H

commit cd772d17dfd27bec5faa7d71f22a78f83cfa6df2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 20 16:38:59 2015 -0700

    BACKTRACE: don't have to sleep if there is only on processor

Src/C_BaseLib/BLBackTrace.cpp

commit a55ad14811a5d15ea0ce9e72baa2170617269b05
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 20 13:01:48 2015 -0700

    This is my latest version of the PIC_C tutorial code and the changes in the Particle
    stuff needed to accomodate a multilevel box array coming into ParGDB.

Src/C_BaseLib/ParGDB.H
Src/C_BaseLib/Particles.H
Src/C_BaseLib/Particles.cpp
Tutorials/PIC_C/main.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/solve_with_f90.cpp
Tutorials/PIC_C/work.f90

commit dc820ec80abe1322697b1d86fa3e5fb559e9b0df
Author: Changho Kim <changhokim@lbl.gov>
Date:   Tue Oct 20 09:49:55 2015 -0700

    new utility to integrate a variable

Tools/Postprocessing/F_Src/GNUmakefile
Tools/Postprocessing/F_Src/fintgvar2d.f90

commit 7f13c91daa38670cf5a15561c93efdd9f2e366b3
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Tue Oct 20 11:02:35 2015 -0400

    At the moment on OLCF machines, pgclibs does not work, so use libstdc++

Tools/F_mk/comps/Linux_pgi.mak

commit fa96b7a1792f3939bdecffeb277b664df5b54151
Merge: a15b0f280 b66ae3553
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Mon Oct 19 13:05:31 2015 -0400

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit a15b0f280b454f0936fd0944888b92cb548ccc4e
Author: Chris Malone <csep23@chester-login1.ccs.ornl.gov>
Date:   Mon Oct 19 12:57:03 2015 -0400

    add support for fortran chester for development

Tools/F_mk/GMakeMPI.mak

commit b66ae3553ee5921e39f942c6791cb4d7a1c1ba92
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Mon Oct 19 12:25:18 2015 -0400

    Add C_mk definition for Chester (XK7) development system at OLCF.

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 2e1bbccb97822a9fd7fa9a9202a15c982343d1c8
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Sep 3 10:09:33 2015 -0700

    C_BaseLib: glorious re-design of the sidecar interface (again)
    
    This is our glorious new interface to the sidecars. It obviates the need
    for abstract base "callback" analysis classes and replaces them with
    void pointers to blackbox functions. This allows the user to write
    arbitrary analysis workflows, rather than requiring her to define
    Initialize(), DoAnalysis(), and Finalize() functions, as was required
    with the previous interface.
    
    Marc Day was responsible for most of this work. I just did some
    peripheral cleaning afterwards.

Src/C_BaseLib/Analysis.H
Src/C_BaseLib/Analysis.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Tutorials/Sidecar_EX1/GridMoveTest.cpp
Tutorials/Sidecar_EX1/InTransitAnalysis.H
Tutorials/Sidecar_EX1/InTransitAnalysis.cpp

commit a9099f8612b3de985e939797658c0399a93d19bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 15 16:20:00 2015 -0700

    BACKTRACE: catch SIGTERM

Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.cpp

commit 44525e9c9f643e786e6bd5324bd6391016d75d72
Merge: 759ae876d 490a8f18a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 15 11:15:03 2015 -0700

    Merge branch 'development' into pgas

commit 490a8f18a3656a604350c5ba89124e72dd957410
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 14 15:13:04 2015 -0700

    added flags for gcc thread sanitizer

Tools/C_mk/Make.defs

commit 389309984c4483833c060322996852b67c7565e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 14 14:29:28 2015 -0700

    turned the just disabled omp back on and put it inside ifdef CRSEGRNDOMP, which has already been used to indicate derive functions are thread safe

Src/C_AMRLib/AmrLevel.cpp

commit 81cf6cba44fe604d91c1cc051a49a01eb408b40a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 14 14:00:02 2015 -0700

    disable omp in FillPatchIterator::Initialize for some LMC problems

Src/C_AMRLib/AmrLevel.cpp

commit 845c81dc82e6f85dd99287cc5f0ad118b8cf84cc
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Oct 14 12:27:34 2015 -0700

    Fixed bug in looping for 3D MFTower fortran

Src/C_TowerLib/MFTower_3D.F

commit 055be40a94de1fb78ab6a9eb2efde39e3338e511
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 13 14:29:15 2015 -0700

    This version of Tutorials/PIC_C works with either the F90 or the HPGMG solver.

Tutorials/PIC_C/GNUmakefile
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/solve_with_hpgmg.cpp

commit 23217ada81f0442f2e683844fe5945936e6fe948
Merge: 55158595c ca65bbfe4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 13 13:04:43 2015 -0700

    Merge branch 'new_particle' of https://github.com/BoxLib-Codes/BoxLib into new_particle

commit ca65bbfe49487a375f1fde1c5fac562ef815e3d6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 13 12:57:37 2015 -0700

    Updated files for Tutorials/PIC_C.

Tutorials/PIC_C/Make.package
Tutorials/PIC_C/main.cpp
Tutorials/PIC_C/solve_for_accel.cpp
Tutorials/PIC_C/solve_with_f90.cpp
Tutorials/PIC_C/solve_with_hpgmg.cpp

commit 55158595c7db3bba15897a325a4fbaf436e77ebe
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 13 11:37:22 2015 -0700

    Starting to add the option for HPGMG to Tutorials/PIC_C.

Tutorials/PIC_C/GNUmakefile
Tutorials/PIC_C/Make.package
Tutorials/PIC_C/main.cpp
Tutorials/PIC_C/solve_with_f90.cpp
Tutorials/PIC_C/solve_with_hpgmg.cpp

commit 00d985aaf05c744317fb2e082e64b4822e95a43d
Merge: 331baee1f 835e67628
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 13 10:41:37 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit 6581cef6833fd9ecdb355b5a4b1386b88cb6e7db
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 13 10:33:15 2015 -0700

    More changes to make the Particle stuff not require anything in C_AMRLib.
      * move BCRec* and BC_TYPES.H from C_AMRLib to C_BaseLib
      * add a "sum" function to MultiFab that sums up the values over all the valid region (analogous to the FArrayBox sum)
      * update the PIC_C Tutorial code so it actually computes the acceleration of each particle

Src/C_AMRLib/Make.package
Src/C_BaseLib/BCRec.H
Src/C_BaseLib/BCRec.cpp
Src/C_BaseLib/BC_TYPES.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Tutorials/PIC_C/GNUmakefile
Tutorials/PIC_C/main.cpp

commit 4cd9d4f0d91e2ede2b55d45235d9dbf8698cf391
Merge: fce0e5fda 9f4d2a5b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 22:16:40 2015 -0700

    Merge branch 'new_particle' of github.com:BoxLib-Codes/BoxLib into new_particle
    
    Conflicts:
            Tutorials/PIC_C/GNUmakefile
            Tutorials/PIC_C/Make.package
            Tutorials/PIC_C/main.cpp

commit fce0e5fda81476d4b8374c11c1cff1ee140f8280
Merge: a84648782 006b5377d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 22:08:58 2015 -0700

    Merge branch 'PIC_Tutorial' into new_particle

commit 9f4d2a5b7dd89a1cb12dd93f0777d427b9c884a6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 11 22:06:02 2015 -0700

    Add AssignDensity

Tutorials/PIC_C/main.cpp

commit a84648782a5812618ff5c94592dc1394f8b93779
Merge: f39a10247 835e67628
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 22:05:14 2015 -0700

    Merge branch 'development' into new_particle
    
    Conflicts:
            Src/C_BaseLib/Particles.H
            Src/C_BaseLib/Particles.cpp

commit 5290f89c4eaae0e1b44faa916b30e46ed8e009a9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 11 22:01:20 2015 -0700

    Make this work without creating an AMR object.

Tutorials/PIC_C/GNUmakefile
Tutorials/PIC_C/Make.package
Tutorials/PIC_C/main.cpp

commit 608f61cc7a40d418fbfc2993c582148d3cedafec
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 11 22:00:48 2015 -0700

    Fix for new gdb stuff.

Src/C_BaseLib/Particles.H

commit f39a102475b088067b9b5a91ba89021aca8371d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 20:59:55 2015 -0700

    Particle: forgot a new file

Src/C_BaseLib/ParGDB.H

commit 0838241061893fab67eb8103de03e86057709117
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 20:55:37 2015 -0700

    moved Amr independent particle files to C_BaseLib

Src/C_AMRLib/Make.package
Src/C_AMRLib/ParGDB.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/Particles.H
Src/C_BaseLib/Particles.cpp
Src/C_BaseLib/Particles_1D.F
Src/C_BaseLib/Particles_2D.F
Src/C_BaseLib/Particles_3D.F
Src/C_BaseLib/Particles_F.H

commit 02452016ffa0ab25f894b632eecfc11e3f5a9409
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 20:49:38 2015 -0700

    Particle: created AmrParticleContainer and some other minor tweak

Src/C_AMRLib/AmrParticles.H
Src/C_AMRLib/Make.package
Src/C_AMRLib/ParGDB.H
Src/C_AMRLib/Particles.H

commit 0ab40db5f324e6c908e31844d9ec96ae518a723e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 20:02:09 2015 -0700

    Particle: forgot to wrap particle stuff inside ifdef USE_PARTICLES

Src/C_AMRLib/Amr.cpp

commit 96e6d8fa4482e1c0c677008d83a5790698bdee05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 19:05:59 2015 -0700

    more on the Amr independent particle

Src/C_AMRLib/ParGDB.H

commit 21539354b75fba38093dca9e66d1d5055c63d401
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 18:34:07 2015 -0700

    Particle: removed multiFab function, we can always build a tmp MF without allocating data.

Src/C_AMRLib/AmrParGDB.H
Src/C_AMRLib/ParGDB.H
Src/C_AMRLib/Particles.H

commit 351183c6fd9dcc89022985603af09c389ddba10f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 16:42:59 2015 -0700

    forgor two new files

Src/C_AMRLib/AmrParGDB.H
Src/C_AMRLib/ParGDB.H

commit c1f87e887b2314cf4ed253aa764febeaecdc9039
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 16:30:41 2015 -0700

    make particles class independent of Amr class

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Make.package
Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 835e67628f63709ca1d56470a56ec105ca81e8ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Oct 11 19:17:03 2015 -0400

    take care of the case where the source is not under git-control

Tools/C_scripts/makebuildinfo_C.py

commit ad0226c79a54e3f5a8f1c3dc935f1b5c1f2041dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Oct 11 19:12:15 2015 -0400

    put a try...except clause around the git stuff, just in case
    a user isn't using git-controlled source

Tools/F_scripts/makebuildinfo.py

commit 006b5377d6a38615451ae9e8078be49a0f05f9e4
Merge: ae22878fd d98e15cc4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 11 15:44:46 2015 -0700

    Merge branch 'development' into PIC_Tutorial

commit d98e15cc4a273bb88dfa78952c356e6b7b60ac3f
Merge: 87a94ac5b 2233dabba
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 11 15:22:03 2015 -0700

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit 87a94ac5be33bbf3611a3d83100f05db3f9abe58
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 11 15:21:47 2015 -0700

    Fix a comment so that it is now correct.

Src/C_AMRLib/AmrLevel.H

commit 2233dabba7f4193b8775e9ab2e7d232204859203
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Oct 11 09:53:30 2015 -0700

    C_mk: added manual link to libmpichf90.a on Cori when linking code with F90 MPI calls using the C++ linker

Tools/C_mk/Make.mpi

commit fcec8cb676c85f0fc4f7ae18581ef1cf8867e325
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Oct 11 09:07:56 2015 -0700

    C_mk: added basic Makefile compiler flags for Intel compiler on Cori

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit c56a206be0faf809dffdcc9b95bba7a563f18d13
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Oct 11 09:01:34 2015 -0700

    ParallelDescriptor: added timer output showing how long sidecars wait for next data set

Src/C_BaseLib/ParallelDescriptor.cpp

commit 9b960bfe9ba7867d6dff06f80a14a8d264b433b7
Merge: 1ca2077c1 8ec2943b0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 9 19:39:54 2015 -0700

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit 1ca2077c16b02a5d143ce6555750bf09ddc8f66b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 9 19:39:33 2015 -0700

    Pass geom instead of amr when possible.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 8ec2943b02e3b5aef0bfd60f5e60cba4fe42c331
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 9 17:17:06 2015 -0700

    SFC: Fixed a bug affecting efficiency

Src/C_BaseLib/DistributionMapping.cpp
Src/F_BaseLib/knapsack.f90

commit 532bb3718aa9839c11eb925a843ef1b016b3ba39
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 9 17:13:01 2015 -0700

    Nodal solver: Fixed a problem in my commit dba46939.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 4f1c4212c3390d54cc920a9a8bf55666c4ec36f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 9 16:18:16 2015 -0700

    BACKTRACE: update Readme

Docs/Readme.backtrace

commit e54c7e4264f3daa1b9d1dec1296271b31e57590f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 9 15:48:02 2015 -0700

    BACKTRACE: output to files instead stdout and stderr

Src/C_BaseLib/BLBackTrace.cpp

commit 1f77d00a6eea985634434c33a024a68467205d1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 9 14:08:31 2015 -0700

    some minor cleanups in F_MG

Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/nodal_divu.f90

commit e9b3d27260653e82a2a00421e397d971b2f047be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 9 14:07:21 2015 -0700

    BACKTRACE: capture user interrupt too

Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.cpp

commit 4413df0f52fb90ac85731048e6f0f33309255231
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 9 14:06:00 2015 -0700

    MGT_Solver: avoid omp critical if we can

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 0f3f148d1edb3f4f927542bc90eba7716b7ab09e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 9 14:02:41 2015 -0700

    add verbose to MGT_Solver

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 30bc5e20e0c16d197a21646894ff3505c86add4a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 9 13:44:10 2015 -0700

    fixed a bug

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit ae22878fd230743212bc23f0ff1baf792289cf6f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 9 09:25:05 2015 -0700

    Latest...

Tutorials/PIC_C/GNUmakefile
Tutorials/PIC_C/Make.package
Tutorials/PIC_C/main.cpp

commit 244ced706c8f047a34107f3c0217fbf57ade48f0
Merge: 60a196bfe 788ce6db4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 9 11:32:59 2015 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 60a196bfef388175949ff5e8854ebd69aa16bc06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 9 11:31:21 2015 -0400

    this now works with python3

Tools/F_scripts/makebuildinfo.py

commit 788ce6db4065c49ff28fe9470c81b372cf8d8a3e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 8 22:33:49 2015 -0400

    more python3 fixes (__cmp__ is replaced by __lt__ for comparing)

Tools/RegressionTesting/testnew.py

commit 1eae17153aeca77687b03e590929a0a06055f3b7
Merge: b2c955e85 8c7a38b53
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 8 22:22:29 2015 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit b2c955e85e268ab30f416967f53cd54c29d33023
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 8 22:22:01 2015 -0400

    .keys() is an iterator in python3, so convert it to a list

Tools/RegressionTesting/testnew.py

commit 8c7a38b53fd1e68648d65c2d1a2e4cb32b5e7c02
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 8 22:07:54 2015 -0400

    start of a port to python 3 -- this handles the prints now.  We also have a
    new Log() object to make it easier to capture and format the output.  Finally,
    fix a bug in the copy_benchmarks option when we are dealing with problems
    that define specific benchmark files instead of the last plotfile

Tools/RegressionTesting/testnew.py

commit c74e210f98194e01f4894028d13fcbc78f03bd87
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 8 13:45:39 2015 -0700

    fix for 1d amrvis.

Src/Extern/amrdata/AmrData.cpp

commit 1fb2a38708dcbcfdc464e1e37b3287385003d713
Merge: 5d4204e79 71e9c3963
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 8 12:25:05 2015 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 5d4204e79fc112dc737b01da4fa712d9d26abef0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 8 12:22:48 2015 -0400

    start of restructing the log into a class so we can control its output

Tools/RegressionTesting/testnew.py

commit 71e9c396316cca8595dcd7f0359eb025f94fb8d4
Merge: e6e0f69b5 a1219e8d3
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 7 15:57:45 2015 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit a1219e8d3da8d5f9c4214bce9a008c03fe74e749
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 7 09:34:01 2015 -0400

    use 2 digits when the level > 10 in the header.  This fix was
    contributed by Ryan Houim via e-mail.

Src/F_BaseLib/fabio.f90

commit 4d51da07e68cdf694cd5844d944e7a8f268d396c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 6 14:59:33 2015 -0700

    These are my first attempt at a PIC tutorial.

Tutorials/PIC_C/GNUmakefile
Tutorials/PIC_C/Make.package
Tutorials/PIC_C/main.cpp
Tutorials/PIC_C/work.f90

commit 759ae876d5bb9beed92fbdd607aca6af92857966
Merge: c20eb5d89 4561e8c9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 6 14:51:08 2015 -0700

    Merge branch 'development' into pgas

commit e6e0f69b5f91fa2a9de75fed1dcd6b105bb6f73e
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 5 13:33:16 2015 -0700

    define constant for 1d.

Src/Extern/amrdata/AmrvisConstants.H

commit 4561e8c9d64336f4632f0cb0ea50e5dd7fe08eaa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Oct 5 12:01:32 2015 -0400

    we were appending to the changelog, not writing a new one.  This caused
    it to get big, and not be very useful.  Now run() takes an outfile_mode

Tools/RegressionTesting/testnew.py

commit c79143ca31564e206a2ec2e13595c6c1186d01a2
Merge: 988353b88 6df9d5fba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 5 08:58:58 2015 -0700

    Merge branch 'poisson' into development

commit 988353b888b6f9520404f4196c66351062fa81b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 3 11:45:33 2015 -0700

    make BoxArray::boxList possible for return value optimization (RVO)

Src/C_BaseLib/BoxArray.cpp

commit e683a6638b2fcea1be57e96fdaf5263630ed2e84
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 3 11:26:48 2015 -0700

    removed a number of const's so that the compiler can do 'copy elision'

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/Orientation.H

commit 32316a4a2a5c70ea9200156c2e1e6853df19cca7
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 2 16:50:37 2015 -0700

    quiet compiler warnings.

Src/Extern/amrdata/DataServices.cpp

commit 3e01b5ff1e4a817cd8d1a96005c56bab2e05752d
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 2 16:48:14 2015 -0700

    only print for special debug.

Src/C_BaseLib/FabArray.H

commit d0972d8158df2d52d38f68ef7b724dce4d76e522
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 2 16:47:39 2015 -0700

    quiet compiler warnings.

Src/Extern/amrdata/DataServices.cpp

commit 6df9d5fba63bd3bf18e200668178e53ab2e0e797
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 2 15:34:47 2015 -0700

    bottom solver: use the simple stencil for interior boxes in the case of constant coefficients

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/stencil_util.f90

commit 5f914db12c031a990f02611d4dc09de85b682cfc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 1 20:30:34 2015 -0700

    F_MG: fixed a new bug in my last commit optimizing box intersection

Src/LinearSolvers/F_MG/cc_stencil.f90

commit a5360f755396e884f86dd971450b67b381d55e15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 1 18:19:47 2015 -0700

    optimization in stencil_set_bc

Src/LinearSolvers/F_MG/cc_stencil.f90

commit c5389fa13a0fcee5870fffbe411e9d9795bcc2b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 1 18:08:15 2015 -0700

    fixed bug in stencil_norm and stencil_set_bc in periodic case

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 9ca0c94addf2aac0aa0165c9b13197d7883b68d6
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 30 15:12:38 2015 -0700

    cxx11 setting.

Tutorials/MultiFabTests_C/GNUmakefile

commit 07a86bfa765bd674a8bd6854b5cd50b3490e902a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 30 15:10:41 2015 -0700

    added profiling to tFB.

Tests/C_BaseLib/tFB.cpp

commit 8ab60177f20e49c13ba51c50718696be69a9a9b2
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 30 15:09:55 2015 -0700

    cxx11 setting.

Tests/C_BaseLib/GNUmakefile

commit 37ef49d7cdd4f4ca42cef88355f57b166cced6c8
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 30 15:08:17 2015 -0700

    more tests for the profiler.

Tests/C_BaseLib/tProfiler.cpp

commit 03d6fe316bb3266951b17bf75dce30e7e8e16207
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 30 14:57:01 2015 -0700

    set n files for profiler, add comm names if not already called.

Src/C_BaseLib/BLProfiler.H
Src/C_BaseLib/BLProfiler.cpp

commit 85d2730fcf1c54e264aa77e0b72396d95324a303
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Sep 30 08:41:51 2015 -0400

    fix NDEBUG -- it is the opposite of what people expect it should be

Tools/RegressionTesting/testnew.py

commit 974fc2fc1be3875ce8ba9aac4462eb7013a26833
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Sep 27 09:58:53 2015 -0400

    some more cleaning

Tools/RegressionTesting/testnew.py

commit 04a69c16585289cd7b3f3619e776550e48ea2cb3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 25 13:27:49 2015 -0700

    changed makefile for babbage

Tools/C_mk/Make.Linux
Tools/F_mk/comps/Linux_intel.mak

commit 90665fb2928b439a0f594e19b5483d4d1e7a43f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 25 12:39:52 2015 -0700

    use relative path for BOXLIB_HOME since these tutorials are inside BOXLIB_HOME already

MiniApps/AMR_Adv_Diff_F90/GNUmakefile
Tutorials/AMR_Adv_Diff_F/GNUmakefile
Tutorials/HeatEquation_EX1_C/GNUmakefile
Tutorials/HeatEquation_EX1_F/GNUmakefile
Tutorials/HeatEquation_EX2_F/GNUmakefile
Tutorials/HeatEquation_EX3_F/GNUmakefile
Tutorials/HeatEquation_EX4_F/GNUmakefile
Tutorials/HeatEquation_EX5_F/GNUmakefile
Tutorials/MultiGrid_F/GNUmakefile
Tutorials/Tiling_Heat_C/GNUmakefile
Tutorials/Tiling_Heat_F/GNUmakefile
Tutorials/WaveEquation_C/GNUmakefile
Tutorials/WaveEquation_F/GNUmakefile

commit d945af5fa443614dd4ac3440ea2aaa73901861c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 25 15:34:27 2015 -0400

    a little more reorg

Tools/RegressionTesting/testnew.py

commit 92e0b986cbed7e5d7b96d695f1e8c20e63fb1040
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 25 12:31:31 2015 -0700

    F_MG: fixed name conflicts

Src/LinearSolvers/F_MG/cc_stencil.f90

commit c20eb5d89612e4b3452558c144e0c5024ae396b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 25 11:10:56 2015 -0700

    added a new fill boundary test

Tests/FillBoundaryComparison/GNUmakefile
Tests/FillBoundaryComparison/Make.package
Tests/FillBoundaryComparison/ba.max
Tests/FillBoundaryComparison/main.cpp

commit 96e83f7651e1671512cfcbfa43601b7325fc846c
Merge: 9589733b4 3943e34c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 25 10:55:04 2015 -0700

    Merge branch 'development' into pgas
    
    Conflicts:
            Src/C_BaseLib/FabArray.cpp

commit 3943e34c8d10a3e530f5e0fd71e0a8d7c0b70c39
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 25 12:41:43 2015 -0400

    remove systemCall entirely in favor of run()

Tools/RegressionTesting/testnew.py

commit 6ea366ce151af8887b10d339dd75713e52aa8268
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 25 10:47:45 2015 -0400

    default the normal direction to 1

Tools/Postprocessing/F_Src/fsnapshot3d.f90

commit 9f4d4803103cfc9f4051db5f7a8e3a723acd5d9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 24 16:56:28 2015 -0700

    Linear solver: for systems with constant coefficients, use simple stencils for interior boxes

Src/F_BaseLib/fab.f90
Src/LinearSolvers/F_MG/CMakeLists.txt
Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_interface_stencil.f90
Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/coarsen_coeffs.f90
Src/LinearSolvers/F_MG/compute_defect.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/stencil_util.f90

commit a452cf1902a214dd9d804097e10ff6e78c18c253
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 24 21:27:31 2015 -0400

    fix some more missing close(), switch a lot of open's to 'with open as'

Tools/RegressionTesting/testnew.py

commit 39cf52a1fd4635dab1f4349c79663d97d70f194d
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 24 17:58:53 2015 -0700

    More typos in CMakeLists.txt

Src/C_BaseLib/CMakeLists.txt

commit 4881edaa811478e011e0b867280725f4f7b224da
Merge: be13a7cfc 1ac3c074e
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 24 17:01:31 2015 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit be13a7cfc78f9dc13d3a11d951e8003b707dbf30
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 24 17:01:25 2015 -0700

    Fix typo in CMakeLists.txt and uptick release number

Src/C_BaseLib/CMakeLists.txt
Tools/CMake/BoxLib_Version.cmake

commit 1ac3c074e1359ece42be01d69e297cd6e5f53fc3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 24 19:49:31 2015 -0400

    remove quotes from the branch name when creating the suite status file

Tools/RegressionTesting/testnew.py

commit 88f36e83f4e3d281a81f16553ec66d0353e7c328
Merge: 4bc8778f9 6b35f83cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 24 16:57:29 2015 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 4bc8778f96420ee40bad456b55206f0faa1a30e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 24 16:57:06 2015 -0400

    fix the deletion of TEST_RUN if it doesn't already exist

Tools/RegressionTesting/testnew.py

commit 6b35f83cf6640fd6cb7849c36c329bf6bb7c91ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 24 16:51:01 2015 -0400

    clean up the compiling of the various tools -- no longer copy them
    to the run directory either

Tools/RegressionTesting/testnew.py

commit 37f78e1d51943f6539ef1a5352bc2ad36a13e4c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 24 14:53:08 2015 -0400

    fix an unclosed file.  Add the branch name to the test run status file

Tools/RegressionTesting/testnew.py

commit 9ded947220941fe7ce9c46f36aebc46c09b8c6b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Sep 23 21:25:31 2015 -0400

    fix the web output directory

Tools/RegressionTesting/testnew.py

commit 5c2da5479fd919911f79463356d393a7a75f171a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Sep 23 20:38:14 2015 -0400

    first cut at an easily parsable status for a run

Tools/RegressionTesting/testnew.py

commit 89ab39d25457c4ce3dcd46644caf3267c5343cec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Sep 23 15:39:29 2015 -0400

    restructure all of the git logic.  Now there is a Repo class that has
    the methods for updates, change log, etc., and knows where the repo
    is, what the current hash is, etc.  This allows us to simply loop over
    all the repos in the suite.repos dictionary and greatly simplify code.

Tools/RegressionTesting/testnew.py

commit a02aa83a9c14fd263ba9b2166d5d90926b491d31
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Sep 23 10:42:28 2015 -0400

    bold heading in list of git info

Tools/RegressionTesting/testnew.py

commit 7e73d966a1572f67688ad0cb5b2cbc557b57df81
Merge: 55f01c0d6 d29cf8e3d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 22 20:24:51 2015 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 55f01c0d69576ce0eff052962104beb6208b3554
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 22 20:24:15 2015 -0400

    add libstdc++ to get around an import error -- not sure why this is pulling
    in the C++ boxlib though...

Tools/Py_util/GNUmakefile

commit d29cf8e3d789376c959b792d095a2c3c86855d78
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 22 19:14:02 2015 -0400

    updated version of our test suite inputs

Tools/RegressionTesting/Maestro-tests.ini

commit 3728f5947777bd6b6f0742ae22a18ef97165abcb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 22 19:10:45 2015 -0400

    default to the development branch

Tools/RegressionTesting/testnew.py

commit 331baee1f65c9ebbadc40bbeefd1b015b7b3e050
Merge: 9bb17854c 85d30d4fd
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 22 15:46:15 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit 85d30d4fd7fb773b96eab6b9ecf56f4efe60bb19
Merge: 485c09fab 7aa2dcc4e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Sep 22 11:41:52 2015 -0400

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit 485c09fab63263ddd30e252cf1f8b4cd91f072dd
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Sep 22 11:37:25 2015 -0400

    Add a dimension-agnostic version of the error function.

Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/ErrorList.cpp

commit 7aa2dcc4e8c765aa1a5dba9c20160a8579a58dcf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 21 16:32:41 2015 -0700

    OMP ml_interface

Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit d6376c86bcbdf1198bed17c3e1bbcc66b680f479
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 21 12:55:25 2015 -0700

    Revert "save a multifab build and copy" because the nodal solver
    relies on that the ghost cells of amr_coeffs are filled with zero.
    
    This reverts commit 0a1b902aafafb0121ca00fd53a6b0332ca9ae153.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 685dcfb73a0e8aaddbb9b6d4bf37e1a016091a6d
Merge: 0a1b902aa 863795b86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 21 12:08:41 2015 -0700

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit 863795b86b76373652553adc9ed0d9f4114c1246
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 21 14:27:41 2015 -0400

    simplify convert_type

Tools/RegressionTesting/testnew.py

commit 0a1b902aafafb0121ca00fd53a6b0332ca9ae153
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 21 11:27:29 2015 -0700

    save a multifab build and copy

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit b0240dcc55cba9717e8e2e739525f6ea7a917eee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 21 11:23:37 2015 -0700

    MGT_Solver: rewrote the cell-centered coeffs stuff in a hopefully less confusing way that is also consistent with the approach in nodal solver

Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 891c3e06c996b0a860afa3b637ed8bfd88c6dc3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 21 09:41:01 2015 -0400

    fix the OMP stuff in the run()

Tools/RegressionTesting/testnew.py

commit 6aefe5d0afa5cbf4503677540e6d215ac57bb340
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 18 15:39:19 2015 -0700

    MGT_Solver: removed unused applybc function and two unnecessary FillBoundary

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 57c87bbb145fbb9ff2da5c6ff18b371536344cd4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 18 13:52:54 2015 -0700

    more coarse-grained OMP in MGT_Solver

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 4f5b11840cb2f7a5efaed938c40ab4671f09c8f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 18 13:49:13 2015 -0700

    add more nodal functions to MFIter

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/F_BaseLib/multifab_f.f90

commit fd627cd44894798e946cc1e2290703e98aec4079
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Sep 19 23:02:07 2015 -0400

    store the diff command

Tools/RegressionTesting/testnew.py

commit fa74a390fb25ea4f7ef16b55965dba23162e7f8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Sep 19 22:32:43 2015 -0400

    switch the diff over to run()

Tools/RegressionTesting/testnew.py

commit 430adb224b6c0c317f758f02fa1c64f988402e8e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Sep 19 22:14:54 2015 -0400

    switch to using subprocess.Popen() to run the tests instead of os.system().  THis is
    safer, and allows us to capture the stdout/err and return code.  Note: for OMP, we need
    to pass a dictoionary of environment variables.

Tools/RegressionTesting/testnew.py

commit 4e9a6578cfafebf0852584212214daf844aa7946
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 17 17:03:03 2015 -0700

    tiling in nodal MGT_Solver

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 9bb17854c7e0255ca10b387fc039d4530ba69588
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 17 15:11:24 2015 -0700

    added profiling.

Tests/C_BaseLib/tFB.cpp

commit 5714a6beec4b5eccf2503a1fb7d08b85e7a8b9dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 17 15:06:39 2015 -0700

    added assertion

Src/C_BaseLib/PArray.H

commit ae87e3777b6085784ecbf6d7cb0b4a066f42adfa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 17 13:49:44 2015 -0700

    fixed assertion

Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tutorials/MultiGrid_C/main.cpp

commit a422e4d8a28c372fe985b2b640f1cf257cf639e7
Merge: 0400519cf a16c81433
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 17 11:35:47 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit 0400519cf27408a64150d67da6cbdfe6808eb605
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 17 11:31:14 2015 -0700

    unique set.

Tutorials/MultiFabTests_C/GridMoveTest.cpp

commit a16c81433509066dd5b282b7e94ca909c4143090
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 16 17:31:38 2015 -0700

    fixed a typo

Src/C_BaseLib/IntVect.cpp

commit 6ad510156ef4f259505a6f0fcdc6faf2cf2891cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 16 16:56:42 2015 -0700

    clean up MGT_Solver

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tutorials/AMR_Advection_C/Source/Diffusion.cpp
Tutorials/MultiGrid_C/main.cpp

commit 520c6434749db26a65314200a121b896fd6c0c41
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 16 16:14:36 2015 -0700

    Added a member function that takes a const * and removes the const.  use it with care.

Src/C_BaseLib/PArray.H

commit e6ec0dc17a5d195bc92ad388fd4c23a62e7613c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 16 14:06:27 2015 -0700

    added IntVect::TheDimensionVector for convenience

Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp

commit 8d729f7e5b81d1e2a53a87a84977778df46c2c20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 16 13:40:08 2015 -0700

    optional nodal argument for MultiFab and FabArray constructors

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit d1c10399a44acf8ec34d71283e4b24cb7ccb4921
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 15 18:23:44 2015 -0700

    tiling in cc MGT_Solver

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 0195828a1d966b318ffe2c0b8391c837120981c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 14 12:52:45 2015 -0700

    In tiled tab_boxes, only the current tile should be touched.

Src/F_BaseLib/tag_boxes.f90

commit 767dd2f81febd02cac07a7e6e60972aa559f5ae3
Merge: cd069a744 39fbaa885
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Mon Sep 14 15:38:45 2015 -0400

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit cd069a744a0e626ec4af26a2a7cff6ecbd341e23
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Mon Sep 14 15:38:41 2015 -0400

    Add a function to StateData that accepts a pointer to a new MultiFab and replaces the old_data or new_data with it, then deletes the old copy of old_data or new_data.

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit 39fbaa8856d5e6006ffd098f8e1b92038457d03c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 14 11:10:31 2015 -0700

    fixed a new bug in tag_boxes

Src/F_BaseLib/tag_boxes.f90

commit c4c37e2e545e5f73b64cd8c88d35b36f6f16aa27
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 14 12:10:46 2015 -0400

    need to define last_run earlier

Tools/RegressionTesting/testnew.py

commit e7718fc28e2fc0b4e76173e997e6f91bd938edab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 12 12:14:01 2015 -0700

    modified Cray C++ compiler option to make it work with a C99 feature we use.

Tools/C_mk/Make.Linux

commit 3b22c203b891570124bcbb4bf2a8a510b0c02611
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 12 11:25:03 2015 -0700

    tweak flags for .F90 files

Tools/C_mk/Make.rules

commit cc6593854fd918ae6b1515f92cbbb2c0ada09810
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Sep 12 02:45:14 2015 -0400

    Don't actually need a separate FILCC_ND.F file to do dimension agnostic boundary filling

Src/C_AMRLib/FILCC_ND.F
Src/C_AMRLib/Make.package
Src/C_AMRLib/StateDescriptor.cpp

commit 98d1ed502703c87b4f2e4a925333f54fa822c92b
Merge: 86b047fe5 eb53dada2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri Sep 11 23:53:13 2015 -0400

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit 86b047fe555cd2892d80addb42f89e3fc75492c7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri Sep 11 23:53:09 2015 -0400

    Dimension agnostic boundary fill routine

Src/C_AMRLib/FILCC_ND.F
Src/C_AMRLib/Make.package
Src/C_AMRLib/StateDescriptor.cpp

commit eb53dada2a4f8a8d7c4d4617c072e9135080b46a
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Sep 11 13:43:04 2015 -0700

    MultiFab: use local communicator with HPGMG instead of MPI_COMM_WORLD
    
    This lets us use the HPGMG solver in runs where we have multiple MPI
    groups/communicators.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 97fc24ba900968b6ddbbb2d7580810f7595f5893
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Sep 10 13:05:52 2015 -0700

    MultiFab: remove commented-out debugging print statement during HPGMG run

Src/C_BaseLib/MultiFab.cpp

commit b1263b6f9ce833ab0c860686c5d3be0936b57a19
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Sep 10 13:05:17 2015 -0700

    MultiFab: minor clean up of status output during HPGMG runs

Src/C_BaseLib/MultiFab.cpp

commit 430a2c2f187ba27cbb7c35c3b828741e00a32765
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Sep 8 15:40:47 2015 -0700

    C_mk: added compile-time options for smoothing behavior of HPGMG

Tools/C_mk/Make.defs

commit 204dc717e1f752f3e2d9cb2de4a37c849d4ae56f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 11 10:33:10 2015 -0700

    tiling in tag_boxes

Src/F_BaseLib/tag_boxes.f90

commit 78c1b2fbc3241f35836597a51a47917271fb4f5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 11 10:24:04 2015 -0700

    added omp paralle do

Src/F_BaseLib/multifab_physbc_edgevel.f90

commit f92d73be340fb2f2732126b6c0517c3c520a692d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 11 10:06:45 2015 -0400

    fix a bug in calling list for reportSingleTest

Tools/RegressionTesting/testnew.py

commit 46e0e1f7f74a6a4eae9b7dc518343ecc000192ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 10 21:16:30 2015 -0700

    trap floating-point exceptions in BACKTRACE

Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.cpp

commit 7f4015c86b663e53c219674694ceafd242ca9f12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 10 20:02:32 2015 -0400

    define FCOMP_VERSION for intel so we can get the compiler version in the
    job_info files

Tools/F_mk/comps/Linux_intel.mak

commit 11953d442a9de0eb01189b7b9291a1d9511885a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 10 16:21:32 2015 -0400

    fix a few bugs

Tools/RegressionTesting/testnew.py

commit 94246bc6b30c72ba7f08cc523fbe391b33742111
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 10 15:58:34 2015 -0400

    a little more cleaning

Tools/RegressionTesting/testnew.py

commit 9cc0c1af0c38ca54b4b17db69773f59ec2b2a2cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 10 12:34:02 2015 -0400

    centralize the logic of how we select the tests to run into a
    method of the suite object.

Tools/RegressionTesting/testnew.py

commit c0633e5f7bb5ce77a55d2311721149097a081c4e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 10 11:59:34 2015 -0400

    let the HTMLTable take a list of div elements

Tools/RegressionTesting/testnew.py

commit a0fa9a873024c5f4d6a3a27445e85573170f016b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 10 11:03:31 2015 -0400

    fix missing ]

Tools/RegressionTesting/testnew.py

commit 93b7456c65b78445c90045a27262e2c80063d817
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 10 10:20:43 2015 -0400

    fix the handling of NaNs present in the compare table

Tools/RegressionTesting/testnew.py

commit 148701c600d8b6378455eeaa9b9b8508f58241d4
Merge: 9360b4be8 acd1b8a1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 9 21:03:30 2015 -0700

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit 9360b4be8229a61678456c1b3526e6d34717a637
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 9 16:55:09 2015 -0700

    tiling in nodal restriction

Src/F_BaseLib/ml_nd_restriction.f90
Src/F_BaseLib/nodal_restriction.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90

commit acd1b8a1d8d3bdb24fbd109b3f5cba2ba04ea8d0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Sep 9 20:39:34 2015 -0400

    be careful -- if a test did not produce any output and we used
    --copy_benchmarks, then there it can erase the entire
    benchmark directory (d'oh).  This is fixed now by checking
    that the last plotfile found is not ""

Tools/RegressionTesting/testnew.py

commit ad85a4e4da615e75ec4d9bef0d64de58ae4073f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 9 10:59:16 2015 -0700

    reduced number of parallel reduce

Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/multifab_f.f90

commit bb7dc4f2cb7c7c65fc49877c14c07789c1d0b394
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Sep 9 10:47:56 2015 -0400

    add a copy_benchmarks functionality -- this does what make_benchmarks + redo_failed
    does, without rerunning any tests -- it simply copies all the benchmarks from
    the last runs that failed.

Tools/RegressionTesting/testnew.py

commit 9589733b4d55237aa9343e8f0d91af2977f97ef3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 8 16:34:07 2015 -0700

    Split MPI calls in FillBoundary and FillPeriodicBoundary into multiple pieces.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H

commit e8a659fef488788087bb19d3766e2a6fb6c53550
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 8 13:12:03 2015 -0400

    some css tweaks

Tools/RegressionTesting/testnew.py

commit d699f0e647384291cad5491ae9ea46586fd4b518
Merge: 3df1493aa d0a252915
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 8 09:58:47 2015 -0700

    Merge branch 'master' into pgas
    
    Conflicts:
            Tools/C_mk/Make.defs

commit d0a25291552cad8554271de1e0c4c2f8ddccb493
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 8 12:54:58 2015 -0400

    use a new HTMLList() object to make the single test output more readable

Tools/RegressionTesting/testnew.py

commit 64ca8c3dd90cb0c55686dd24ea1df01492bc7361
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 8 09:42:32 2015 -0400

    fix ordering of hash and branch in output

Tools/RegressionTesting/testnew.py

commit 5783b8e293997d60cf384f6789994406272e86a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 4 15:08:20 2015 -0700

    Added next_tile function that also returns current fab index.  Using next_tile instead of more_tile is recommended.

MiniApps/SMC/advance.f90
MiniApps/SMC/init_data.f90
Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/ml_cc_restriction.f90
Src/F_BaseLib/multifab_f.f90
Tutorials/Tiling_Heat_F/advance.f90

commit ac351708d870211189cfaaac08d2cc1e4e7b9155
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 4 14:46:51 2015 -0700

    more tiling

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/ml_cc_restriction.f90

commit 9a546c6f2b10cc6de920373e6c44185bf6cf5792
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Sep 6 20:49:34 2015 -0400

    print the branch and hash for the code on the summary page

Tools/RegressionTesting/testnew.py

commit 8cbbc5e55650a2216597062392b5af30888ebac9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 5 14:23:07 2015 -0700

    always include sstream

Src/C_BaseLib/BLBackTrace.H

commit 00a829d55a1cedeec1b750f78c5ef8e933d812f5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 4 17:23:22 2015 -0700

    Don't include bl_constants_module since that lives on F90 side.

Src/C_BaseLib/MultiFabUtil_2d.f90
Src/C_BaseLib/MultiFabUtil_3d.f90

commit 2a6b23af902f4c05f5c34bec0e7b9fc423d1a02d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 4 17:02:26 2015 -0700

    Add the functionality to average down face-based MultiFabs as long as the crse BoxArray is a coarsened
    version of the fine BoxArray.

Src/C_BaseLib/MultiFabUtil.H
Src/C_BaseLib/MultiFabUtil.cpp
Src/C_BaseLib/MultiFabUtil_1d.f90
Src/C_BaseLib/MultiFabUtil_2d.f90
Src/C_BaseLib/MultiFabUtil_3d.f90
Src/C_BaseLib/MultiFabUtil_F.H

commit 5205f255d9a32dcb06db10f55e00c60aad20591b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 4 13:45:23 2015 -0700

    command line option for sending no email when regression tests fail

Tools/RegressionTesting/testnew.py

commit b91a875aebb398af34355d00c3a0cd84fbc5a14a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 4 13:19:19 2015 -0700

    a bit of hack to get consistent answer with OMP

Src/F_BaseLib/multifab_f.f90

commit debdf669d12937bf1b1dbbb70aed110c7d1e53e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 4 11:57:56 2015 -0700

    minor changes that can cause roundoff errors

Src/F_BaseLib/multifab_f.f90

commit 904d803b483ab48834b60c39977c42ad81065a6e
Author: yzheng <yzheng@lbl.gov>
Date:   Fri Sep 4 11:08:23 2015 -0700

    Make async slightly more efficient without the need of reply

Src/C_BaseLib/BLPgas.cpp

commit 7d2b445bb1168391c96f1846f2d072d689bcbceb
Merge: ce4f203b0 3df1493aa
Author: yzheng <yzheng@lbl.gov>
Date:   Fri Sep 4 11:05:09 2015 -0700

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit 94f012e97bba08a6db6aa5a6782fe3c15392b071
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 4 11:03:41 2015 -0400

    fix a link + pretty up some CSS

Tools/RegressionTesting/testnew.py

commit 580d3e436cab2feab6ab8750d83140550624b4e2
Merge: 6f95411c9 7f42a9ab8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 4 10:01:36 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit 6f95411c9b7aae340c33a3b640baff402030ab64
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 4 10:01:16 2015 -0400

    switch the test run overview talbe to HTMLTable

Tools/RegressionTesting/testnew.py

commit 7f42a9ab8319cd8fb5e64d6df987618f9a881ba3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 4 09:28:36 2015 -0400

    wrong indentation in the MPI call

Tools/RegressionTesting/testnew.py

commit da0f3db8cae6fce289f0ffccb9a69b9a2059af28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 4 08:27:55 2015 -0400

    catch when boxes don't match in fcompare

Tools/RegressionTesting/testnew.py

commit 62f9a373360a9bdfb829488e8ceff652abbc1a1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 3 20:53:44 2015 -0700

    tiling

Src/C_BaseLib/MultiFabUtil.cpp

commit 51e0397b80e4d6008d860faad5b04ed9743c2957
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Sep 3 23:38:33 2015 -0400

    Fix minor bug in assertion

Src/C_BaseLib/MultiFabUtil.cpp

commit c2396538bce911835532675d67b865eb964f53e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 3 21:17:33 2015 -0400

    a bit more restructuring -- moving things into the suite class

Tools/RegressionTesting/testnew.py

commit 78f64921acfce03f9476f29141d9341460ecae64
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 3 16:11:53 2015 -0700

    save local index in communication and local copy descriptors to avoid repeated calls to local_index

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90
Src/LinearSolvers/F_MG/nodal_interface_stencil.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_interface_stencil.f90

commit 2b2d1c34095d126f7d40e5b9092db4106c1317c0
Merge: 2381d1f32 fab266b5c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 3 14:47:27 2015 -0700

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit fab266b5c6d851b26552f3aaade1693c0061e5fc
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Sep 3 13:15:59 2015 -0700

    C_mk: updated Makefile flags for HPGMG to allow both pure V-cycles and pure F-cycles

Tools/C_mk/Make.defs
Tutorials/MultiGrid_C/GNUmakefile

commit 2381d1f32a50c7ebecfeb2f51128f729080ae391
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 3 13:08:17 2015 -0700

    Added a few new utility functions to BoxLib namespace.

Src/C_AMRLib/AmrLevel.H
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package
Src/C_BaseLib/MultiFabUtil.H
Src/C_BaseLib/MultiFabUtil.cpp
Src/C_BaseLib/MultiFabUtil_1d.f90
Src/C_BaseLib/MultiFabUtil_2d.f90
Src/C_BaseLib/MultiFabUtil_3d.f90
Src/C_BaseLib/MultiFabUtil_F.H

commit 51b28936fe593c710004e7c7a10dd7221cb05dd4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 3 09:57:49 2015 -0400

    start of what will become some basic unit tests -- nothing to see
    here now.

Src/F_BaseLib/unittests/GNUmakefile
Src/F_BaseLib/unittests/gr0_3d.1level
Src/F_BaseLib/unittests/tests.f90

commit 25d97ca2bf344f54394abfbba2b58e510dca9402
Merge: 7cabf2fa2 b63875baf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 3 09:57:35 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit 3df1493aa128c9cfd7527beaab91f8ed77017324
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 2 20:40:23 2015 -0400

    added bl_profiler

MiniApps/PGAS_SMC/main.cpp

commit b63875bafbab0bd618a0a89b36fe73f053a66833
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 2 10:44:38 2015 -0700

    minor bug: used optional argument without checking

Src/F_BaseLib/make_new_grids.f90

commit cc3f5dce464410f00e3af47ad3a2ebc56c234892
Merge: 62159ed0c ff0ab2af9
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Sep 1 16:13:26 2015 -0700

    Merge branch 'port_hpgmg'
    
    This series of commits adds the ability to call the HPGMG multigrid
    solver written by Sam Williams. It is designed to be more or less a
    drop-in replacement for the in-house multigrid solver. There are a few
    caveats to using it, however:
    
      1.) It is single-level only. No AMR.
      2.) It is not nodal.
      3.) It requires a cubic domain with cubic boxes.
      4.) It does not support Neumann boundary conditions. Only periodic or
          Dirichlet.
    
    In addition, the version of HPGMG which Sam maintains will not work with
    this. You must use my "port" of it, which contains the necessary hooks.

commit ff0ab2af993f633409b38395db30dea5ab99565b
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Sep 1 14:21:55 2015 -0700

    MultiGrid_C: add HPGMG as an example multigrid solver in the tutorial

Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_C/README
Tutorials/MultiGrid_C/main.cpp

commit bf78f385ccd893b0037b61410719aadbbc97d283
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Sep 1 12:29:38 2015 -0700

    MultiFab: add static functions and hooks for using the HPGMG linear solver

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Tools/C_mk/Make.defs

commit 67e538a29045a64c9ac95460d0fa09c232c7089f
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Sep 1 12:17:21 2015 -0700

    Box: add static function isSquare()
    
    Checks that a Box is square (or cubic in 3-D). This is a convenient function to
    have when using the HPGMG solver, which requires cubic Boxes.

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp

commit 62159ed0c9f62b0acca61eb28570c93ee0d529da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 1 17:46:04 2015 -0700

    fixed intel compiler macro in last commit

Src/C_BaseLib/BLBackTrace.H

commit b3e63dbc2eb263d32c4980131b4e17d341a8f2ca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 1 17:44:51 2015 -0700

    Cannot get threadprivate static class memeber work in Cray and Intel, so let's turn it off.  Note that this would not cause race conditions unless we use BL_BACKTRACE_PUSH and POP for debugging. In that case, we have to use gcc.

Src/C_BaseLib/BLBackTrace.H

commit be48bd18ef98e6f5aacc3607bcf3c03434bc1b3d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 1 17:38:58 2015 -0700

    option to turn on assertion if compiled with USE_ASSERTION=TRUE enven when DEBUG is FALSE.

Src/C_BaseLib/BLassert.H
Tools/C_mk/Make.defs

commit 74210f40657801d2afb961f1da477624a67682ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 1 17:24:38 2015 -0700

    added -g to Cray

Tools/C_mk/Make.Linux

commit 7cabf2fa24208783db5360fcd20470a2a4f8bf47
Merge: 932ca949c 766af0030
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 1 19:35:39 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit 932ca949cdd90833839c5577c819dc74b6466fd4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 1 19:35:15 2015 -0400

    change multifab_equal to a function and check the layouts

Src/F_BaseLib/multifab_f.f90

commit f9bef06ec97c27c76412cf21f0057036b24ad506
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 1 14:19:46 2015 -0700

    make Intel compiler happy

MiniApps/PGAS_SMC/SMC_advance.cpp

commit 766af00305c49fb746293f9df25625a4efecaad1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 1 11:21:00 2015 -0700

    Finished tiling in multifab_f.  Roundoff errors are expected because this commit changes the order of sum.

Src/F_BaseLib/multifab_f.f90

commit 8edc219f6ee9dc4b3f6fea1f895684c55a8489d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 1 10:25:04 2015 -0700

    added an assertion in mfiter

Src/F_BaseLib/bl_error.f90
Src/F_BaseLib/multifab_f.f90

commit 88b1c8d723628e2433d420ebe718b2d852cb0a0e
Merge: e2e9fd784 de4c922c2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 1 12:05:09 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit de4c922c2bbb9724f5efeaeec0d19a5517d5d9e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 1 12:00:24 2015 -0400

    if there is no png file produced, then skip the copy

Tools/RegressionTesting/testnew.py

commit e2e9fd784bf181a4bcd23c3563560ace54c44085
Merge: 2153858be 2a93890bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 1 11:50:05 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit 2153858bec97c2f4f969fe628aed2ca39c768f00
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 1 11:49:56 2015 -0400

    add an equal method

Src/F_BaseLib/multifab_f.f90

commit 2a93890bf79989ddded14c9d8f83416f4db3f6bf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 1 08:30:27 2015 -0700

    fixed a new bug: forgot to build mfiter

Src/F_BaseLib/multifab_f.f90

commit cb4507ae0569f594e5fece158a142e9c11a448b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 31 17:44:20 2015 -0700

    more tiling in multifab_f

Src/F_BaseLib/multifab_f.f90

commit 0d7799486e32063af89e483b7f5689c6a36a52ba
Merge: b326f8e33 925293f5d
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 31 17:19:02 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit b326f8e336ab2ee0b5cf6fb6f67e133468c3de77
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 31 17:18:59 2015 -0700

    some code cleanup.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/FabArray.H

commit 737460393b340568891459c569a9c542c0608f66
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 31 16:02:54 2015 -0700

    Fixed a very old in multifab_div_s_c.  Fortunately, I don't think it
    is ever used by any codes.

Src/F_BaseLib/multifab_f.f90

commit 925293f5dea714816c7dcf1f37f391118201e456
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 29 23:41:43 2015 -0700

    fixed a new omp bug and cleanup

Src/F_BaseLib/multifab_f.f90

commit 3a61fb4611958792a536d7e586d20d5830cf7b3f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 29 22:30:54 2015 -0700

    fixed typo

Src/F_BaseLib/multifab_f.f90

commit b8717d8f14d73d0071772651adf2c3173d660f63
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 29 22:15:21 2015 -0700

    more tiling and forgot to build mfiter

Src/F_BaseLib/multifab_f.f90

commit 97e6bec7794cf2c230e0da4414ccde13ff8ad38f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 29 21:53:48 2015 -0700

    Multifab_fab_copy is serial only and I oon't think any codes are it, so it is removed.  If it turns out some codes need to call it, we should implement a parallel version.

Src/F_BaseLib/multifab_f.f90

commit 7fb914a180ca380d9c328e964461b879c95f70b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 29 21:46:48 2015 -0700

    tiling in multifab_min

Src/F_BaseLib/multifab_f.f90

commit 27606743940d5b0c455c0c29c569ac9b48602a59
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 29 21:37:02 2015 -0700

    tiling in multifab_val and removed allow_empty argument because mfiter skips empty box already

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_f.f90

commit f2726b8b2dc312f763baa65b980bd9876cda61fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 29 21:06:55 2015 -0700

    It shouldn't be fab's responsibility to check if the caller passes in a box in fab_max_val and fab_min_val.  Also note that in practice only the multifab module is supposed to call fab_max_val and fab_min_val.

Src/F_BaseLib/fab.f90

commit 520816116d581a1bacfd494b9c0e5a65dc3ef881
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 28 17:01:48 2015 -0700

    more tiling

Src/F_BaseLib/multifab_f.f90

commit be38cd9128f13a1f019d4c8322dc167305f0c888
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 28 16:54:48 2015 -0700

    no longer need to test empty box because mfiter will not hand out an empty box

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_f.f90

commit 76924f077532784446baa5dd4c56d815ad23c770
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 28 16:52:02 2015 -0700

    handle empty box in mfiter

Src/F_BaseLib/layout.f90

commit 0b12c3377131cbb9732f1606b08ed25de1e4ebbd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 28 16:18:13 2015 -0700

    tiling and omp in multifab_f

Src/F_BaseLib/multifab_f.f90

commit a8647e336dac8d6eaa8f513e354f84f5a819988a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 28 15:16:32 2015 -0700

    removed omp in fab.f90 because we are going to do it in multifab_f.f90

Src/F_BaseLib/fab.f90

commit ce4f203b0c05d2293fca73845ed03eb54047d2b5
Merge: 6b979ae3a 6d8e6311c
Author: yzheng <yzheng@lbl.gov>
Date:   Sat Aug 29 15:55:46 2015 -0700

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit bc5d1ae30f26a43344f3a6d3e4b3a279d4209ec7
Merge: e197ff7d0 f4dbf9dee
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Aug 29 01:51:10 2015 -0400

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit e197ff7d0f5d38bee579509ca9a33b7465b212fe
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Aug 29 01:51:07 2015 -0400

    Add a DIMENSION_AGNOSTIC variable to the makefile/defines; we'll use it in some cases for determining whether to call dimension agnostic Fortran functions. Also add a dimension agnostic version of the boundary function routines, similar to how we did this for the derive class.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Make.package
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp
Tools/C_mk/Make.defs

commit f4dbf9dee534a23dcd4d8899a6a943b7e7ed8c9b
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Aug 28 15:45:09 2015 -0700

    ParallelDescriptor: put include of Analysis.H inside IN_TRANSIT ifdef

Src/C_BaseLib/ParallelDescriptor.cpp

commit 37f9e57f977342049c3bf06b8dcc3b7841fefcdc
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Aug 28 15:42:52 2015 -0700

    F_BaseLib: derive world_group communicator from m_comm instead of MPI_COMM_WORLD in parallel_create_communicator()
    
    This routine ultimately just wants the "parent" communicator from which to
    build sub-communicators. It shouldn't care whether the parent communicator is
    actually MPI_COMM_WORLD or anything else.

Src/F_BaseLib/parallel.f90

commit 6d8e6311ccf6aa5bb71a5031b142cf57d0ac3e79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 28 13:15:31 2015 -0700

    split FillPeriodicBoundary_finish into two versions: MPI and UPCXX

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 75f268c744479802e9ef6c494801cdb81293d9ad
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Aug 28 12:10:16 2015 -0700

    F_BaseLib: change parent communicator from MPI_COMM_WORLD to m_comm in parallel_create_communicator()
    
    Using MPI_COMM_WORLD breaks code which uses more than one MPI group. "m_comm"
    should be the correct pseudo-global communicator anyway, so this should work
    for any number of MPI groups.

Src/F_BaseLib/parallel.f90

commit dc5e1a915d1ee2ebec1eec096435f5faf0a5e6b5
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Aug 28 10:44:27 2015 -0700

    F_BaseLib: remove assignment of m_comm to MPI_COMM_WORLD in parallel_finalize()
    
    This breaks the multigrid solver when running with the sidecars because the
    solver invokes many MPI collective routines which hang due to this.

Src/F_BaseLib/parallel.f90

commit f6c070e69e6169ffeee0c55a2d31cbbdaa3f076f
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Aug 28 09:24:57 2015 -0700

    ParallelDescriptor: move creation of InTransitAnalysis variable outside if/else section in SidecarProcess()
    
    Every type of analysis will use an InTransitAnalysis object, so rather than
    duplicating this line in every if/else case, just do it once at the beginning.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 99496596a8b2702446ccaebf9e159b59486f47c4
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Aug 28 07:21:37 2015 -0700

    ParallelDescriptor: break out of while() loop immediately after sidecars receive quit signal

Src/C_BaseLib/ParallelDescriptor.cpp

commit 309f0e4fee068b0fb916bf5c965a752a62a68215
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Aug 28 07:16:18 2015 -0700

    ParallelDescriptor: use automatic allocation instead of new[] and delete[] in SidecarProcess()
    
    There's no reason to use pointers and allocate objects by hand. Let them come
    into and go out of scope automatically.

Src/C_BaseLib/ParallelDescriptor.cpp

commit b5f83b75fce4cfcbc790940f6e62b74ea95daee4
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Aug 28 07:06:16 2015 -0700

    ParallelDescriptor: move sidecar completion message outside the signal if/else section
    
    This way we don't have to duplicate that message inside every if/else case.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 4497ff5c4ca1a8bde5a85b1ba65c4695a5ca860f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 27 17:13:41 2015 -0700

    split FillBoundary_finish into two versions: MPI and UPCXX

Src/C_BaseLib/FabArray.H

commit 6b979ae3a6cec0e76a244305d1d05a00849f392f
Merge: 99f9ddfbd 7cb292106
Author: yzheng <yzheng@lbl.gov>
Date:   Thu Aug 27 16:42:55 2015 -0700

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit 99f9ddfbdac2f03eefa76e7d95c7a2fd42e8b03f
Author: yzheng <yzheng@lbl.gov>
Date:   Thu Aug 27 16:42:52 2015 -0700

    Use UPC++ barrier for the UPC++ version

MiniApps/PGAS_SMC/SMC.cpp

commit 49224fb30b9e2e4f7d4eb4d834a0f03e55a9a508
Merge: 7cb292106 60ff15d3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 27 16:24:34 2015 -0700

    Merge branch 'master' into pgas

commit 7cb292106971b9624e2e2d1af5a94831a8636649
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 27 15:22:44 2015 -0700

    tweak the output of timing results

MiniApps/PGAS_SMC/SMC.cpp

commit 60ff15d3e566e8c49c5d986de7bb1a236a9af60a
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Aug 27 14:37:23 2015 -0700

    Geometry: add forgotten assignment of is_periodic in SendGeometryToSidecars()

Src/C_BaseLib/Geometry.cpp

commit b2c37a6b21ae0dc11942daeaf35591254af3f0dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 27 12:43:48 2015 -0700

    PGAS_SMC: use blocking fill boundary when overlap is false

MiniApps/PGAS_SMC/SMC_advance.cpp

commit d02a4c821f89b57a2caed54e24cf8a690cbb6079
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 27 12:43:06 2015 -0700

    blocking fill boundary function can also use upc++ now

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.cpp

commit 1c867275bb1466b8072259816f9a92286269556b
Author: yzheng <yzheng@lbl.gov>
Date:   Thu Aug 27 10:28:53 2015 -0700

    Poll UPC++ progress engine more aggressivelly right after making send requests

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 7766022a50a9beb61406d628769506cf80e0d555
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Aug 27 09:37:19 2015 -0400

    fix the fix -- keep 0.0 if that is printed :)

Tools/Postprocessing/F_Src/fcompare.f90

commit 2581e79f9561a339470f514bf0acd06d08f77f87
Merge: 93df2931f e94d7fd85
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Aug 27 09:16:15 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit 93df2931f2201c134a2fd14015ea920b5021ed44
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Aug 27 09:15:16 2015 -0400

    Fortran prints numbers with 3-digit exponents without the 'E' (i.e., 0.3979676757-175)
    Python/C don't know how to interpret this.  Now we floor things with 1.d-99

Tools/Postprocessing/F_Src/fcompare.f90

commit e4c3989431184471cdae26bd6209a2e0240fcf95
Merge: 901ee7de1 e94d7fd85
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 26 15:05:06 2015 -0700

    Merge branch 'master' into pgas
    
    Conflicts:
            Src/C_BaseLib/BoxLib.cpp

commit e94d7fd859abc65dcf42982704eef6fe271608ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 26 15:02:46 2015 -0700

    trying to keep x-direction long in creating box list of the compliment of a box in another

Src/C_BaseLib/BoxList.cpp
Src/F_BaseLib/list_box.f90

commit 901ee7de184d9d3a75bef58e2e322322a721df8a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 26 14:58:28 2015 -0700

    adjusted timers

MiniApps/PGAS_SMC/SMC.H
MiniApps/PGAS_SMC/SMC.cpp
MiniApps/PGAS_SMC/SMC_advance.cpp

commit d0bc0708570d7dace9b5a1322cf21f3eaa3a0bf6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 26 11:03:53 2015 -0700

    PGAS_SMC: use the same initial guess for T

MiniApps/PGAS_SMC/make_plot.f90

commit d82efe1d18c59aad082bef64a4784088f06fabda
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 26 11:01:53 2015 -0700

    PGAS_SMC: changed the default max_grid_size

MiniApps/PGAS_SMC/SMC.cpp

commit 3a4332fbba81aec4f26bf908db79009ff7a245ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 26 10:25:50 2015 -0700

    tidy

MiniApps/PGAS_SMC/SMC.cpp

commit 4e8f5888e1770352fa74a8f14e732e7213fe763b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 26 10:19:50 2015 -0700

    added some timers and some minor changes

MiniApps/PGAS_SMC/SMC.H
MiniApps/PGAS_SMC/SMC.cpp
MiniApps/PGAS_SMC/SMC_advance.cpp

commit bccdc7dc0015c2a4dd76fd4943d49cc548d15d7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 25 17:31:04 2015 -0700

    first version of PGAS_SMC

MiniApps/PGAS_SMC/Make.package
MiniApps/PGAS_SMC/SMC.H
MiniApps/PGAS_SMC/SMC.cpp
MiniApps/PGAS_SMC/SMC_F.H
MiniApps/PGAS_SMC/SMC_advance.cpp
MiniApps/PGAS_SMC/SMC_init.cpp
MiniApps/PGAS_SMC/SMC_io.cpp
MiniApps/PGAS_SMC/init_data.f90
MiniApps/PGAS_SMC/kernels.f90
MiniApps/PGAS_SMC/make_plot.f90
MiniApps/PGAS_SMC/transport_properties.f90
MiniApps/PGAS_SMC/variables.f90

commit d4e367a55050efae1e736fc5a8fd3451a1069c6f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 25 17:29:41 2015 -0700

    added MFGhostIter that iterates over ghost cells only

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 0a991ff34e0c307ce17ab0db6d80bf46d29fc39c
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 25 16:21:49 2015 -0700

    Analysis: started adding virtual Initialize() stubs for different kinds of analysis classes
    
    Different types of analyses require different types of input data, and
    at some point the compiler must know *something* about which data an
    analysis class requires. But we don't want to put the entire analysis
    code into BoxLib itself. Since we can't have virtual constructors, the
    compromise is to enumerate all the possible input sets via unique,
    virtual Initialize() stubs. BoxLib will not invoke a callback to
    Initialize() because it doesn't know which one to use. So the analysis
    class itself invokes its own Initialize(), and BoxLib will then invoke
    DoAnalysis() and Finalize(), since it is much easier to implement those
    functions for any analysis class with no arguments.

Src/C_BaseLib/Analysis.H
Src/C_BaseLib/ParallelDescriptor.cpp
Tutorials/Sidecar_EX1/InTransitAnalysis.H
Tutorials/Sidecar_EX1/InTransitAnalysis.cpp

commit cea925810acdc4c9a0a525ded7da38208081b910
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 25 15:57:08 2015 -0700

    Analysis: created namespace "Analysis" and moved most stuff there from ParallelDescriptor

Src/C_BaseLib/Analysis.H
Src/C_BaseLib/Analysis.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Tutorials/Sidecar_EX1/GridMoveTest.cpp

commit e4605fffaf60dd27b8a711627b34db2f2e49e1d6
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 25 15:41:16 2015 -0700

    Analysis: renamed generic class "Analysis" to "AnalysisContainer"

Src/C_BaseLib/Analysis.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 31c1a6f37aeef00a012e1e4b521f0c2c45249d15
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 25 14:26:56 2015 -0700

    ParallelDescriptor: compactify pointer allocation syntax in SidecarProcess()

Src/C_BaseLib/ParallelDescriptor.cpp

commit cfe2e9de9429e07a8cb79c75ac48e409d1620371
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 25 13:19:09 2015 -0700

    fixed typos

Src/C_BaseLib/BLPgas.H
Src/C_BaseLib/BLPgas.cpp

commit e4409f6f263bfd64a20e05165fc4fdd99d4d9e27
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 25 12:49:39 2015 -0700

    Tutorials: added #ifdef IN_TRANSIT to relevant parts of Sidecar_EX1
    
    We want the code to run with or without sidecars. It's just that if you
    don't use the sidecars in this example, the code doesn't do anything
    interesting.

Tutorials/Sidecar_EX1/GridMoveTest.cpp

commit 739741677e63e1188d9a1855ae075c84c63caeee
Author: Amir Kamil <akamil@lbl.gov>
Date:   Tue Aug 25 15:38:01 2015 -0400

    Split Send interface into Send and Request.

Src/C_BaseLib/BLPgas.H
Src/C_BaseLib/BLPgas.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 8aee68f63a835d923e6da21600acd28a3da6c6f6
Merge: 18ebf70e9 114f37dba
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 25 12:35:07 2015 -0700

    Merge branch 'add_sidecar_analysis'
    
    With these commits we return to a signal-based system for interacting
    with the sidecar MPI group. We have also moved to a callback-based
    system for performing the analysis so that the process of "registering"
    and executing a user-defined analysis routine with the sidecars can
    remain fairly generic.

commit 114f37dbab8aacbc0ad12249cd02c4a1cf253da5
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 25 11:29:06 2015 -0700

    Tutorials: removed Sidecar_EX2 example since Sidecar_EX1 has the same features

Tutorials/Sidecar_EX2/GNUmakefile
Tutorials/Sidecar_EX2/InSituAnalysis.H
Tutorials/Sidecar_EX2/InSituAnalysis.cpp
Tutorials/Sidecar_EX2/Make.package
Tutorials/Sidecar_EX2/inputs_3d
Tutorials/Sidecar_EX2/main.cpp

commit 1b7d57d31ac7abcc63f93e72b37b6742ff4442d8
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 25 09:13:48 2015 -0700

    Sidecars: changed sidecar implementation back to signal-based, and updated Sidecar_EX1 tutorial accordingly

Src/C_BaseLib/Analysis.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Tutorials/Sidecar_EX1/GNUmakefile
Tutorials/Sidecar_EX1/GridMoveTest.cpp
Tutorials/Sidecar_EX1/InTransitAnalysis.H
Tutorials/Sidecar_EX1/InTransitAnalysis.cpp
Tutorials/Sidecar_EX1/Make.package

commit a183b158447201bd5bccc4eb54f0be26ce0e78e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 24 17:23:27 2015 -0700

    flesh out PGAS_SMC

MiniApps/PGAS_SMC/Exec/ToyFlame/GNUmakefile
MiniApps/PGAS_SMC/Exec/ToyFlame/Make.package
MiniApps/PGAS_SMC/Exec/ToyFlame/Prob_3d.f90
MiniApps/PGAS_SMC/GNUmakefile
MiniApps/PGAS_SMC/LiDryer.c
MiniApps/PGAS_SMC/Make.package
MiniApps/PGAS_SMC/SMC.H
MiniApps/PGAS_SMC/SMC.cpp
MiniApps/PGAS_SMC/SMC_F.H
MiniApps/PGAS_SMC/SMC_advance.cpp
MiniApps/PGAS_SMC/SMC_init.cpp
MiniApps/PGAS_SMC/SMC_io.cpp
MiniApps/PGAS_SMC/Source/Make.package
MiniApps/PGAS_SMC/Source/SMC.H
MiniApps/PGAS_SMC/Source/SMC.cpp
MiniApps/PGAS_SMC/Source/SMCBld.cpp
MiniApps/PGAS_SMC/Source/SMC_advance.cpp
MiniApps/PGAS_SMC/Source/SMC_io.cpp
MiniApps/PGAS_SMC/Source/SMC_setup.cpp
MiniApps/PGAS_SMC/Source/main.cpp
MiniApps/PGAS_SMC/chemistry_module.f90
MiniApps/PGAS_SMC/derivative_stencil.f90
MiniApps/PGAS_SMC/init_data.f90
MiniApps/PGAS_SMC/main.cpp
MiniApps/PGAS_SMC/variables.f90

commit 18ebf70e9591773a3fe5905ba027ec37db725fc1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 22 23:33:02 2015 -0700

    align memory arena allocation to 16 bytes

Src/C_BaseLib/Arena.H
Src/C_BaseLib/Arena.cpp
Src/C_BaseLib/CArena.cpp

commit 49f13ec43c94465041661c837e941ada4aa7c3d7
Author: yzheng <yzheng@lbl.gov>
Date:   Sat Aug 22 15:45:33 2015 -0700

    Update BLPgas.cpp to use the latest version of UPC++ signaling put interface

Src/C_BaseLib/BLPgas.cpp

commit 92f4d995f0f95c601fb5aa2f7df00f304e10e001
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 21 17:08:25 2015 -0700

    fixed wrong index

Src/LinearSolvers/F_MG/cc_stencil_apply.f90

commit 8efc771a9fd8d20505eecab983776560835f2689
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 21 17:07:49 2015 -0700

    build edge multifab for flux instead of cell-centered with ghsot cells

Src/LinearSolvers/F_MG/cc_mg_cpp.f90

commit a0dfedfe903c8d0c74398af5544baf2c71fe5f1f
Merge: dbe86f9db 54d54ff99
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Aug 21 10:26:09 2015 -0700

    Merge branch 'sidecar_improvements'
    
    This adds a few new static functions for sending various objects to the
    sidecars processes, and cleans up a few things as well.

commit 54d54ff9916cbe00a96a820aa3be595f4cfd01c6
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Aug 12 12:51:38 2015 -0700

    MultiFab: change memcpy() to std::memcpy() in SendMultiFabToSidecars()
    
    memcpy() is a C function. To be consistent let's use the C++ version in
    STL.

Src/C_BaseLib/MultiFab.cpp

commit 074413902d21664e9c8553c9957fde9cffae1942
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Aug 12 12:04:18 2015 -0700

    MultiFab: changed separate MPI_ROOT/MPI_PROC_NULL Bcast()s to a single Bcast()

Src/C_BaseLib/MultiFab.cpp

commit 91f8dbfc631369e8f0aab51abb222a9301bfe0a0
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Aug 12 12:03:42 2015 -0700

    Geometry: changed separate MPI_ROOT/MPI_PROC_NULL Bcast()s to a single Bcast()

Src/C_BaseLib/Geometry.cpp

commit e9c4513ba13a6de93904286e6dc435b48239e7a2
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Aug 12 12:02:43 2015 -0700

    DistributionMapping: changed separate MPI_ROOT/MPI_PROC_NULL Bcast()s to a single Bcast()

Src/C_BaseLib/DistributionMapping.cpp

commit 03c9f99baa1323d00ddfde11e36b471733ffba4a
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Aug 12 12:01:48 2015 -0700

    BoxArray: changed separate MPI_ROOT/MPI_PROC_NULL Bcast()s to a single Bcast()

Src/C_BaseLib/BoxArray.cpp

commit 4bb5f8295cfed8938d487ce43dfe9dfc5fde5328
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 11 13:49:15 2015 -0700

    BoxArray, Geometry, MultiFab: change regular cast to const_cast in Bcast()
    
    The buffer in a Bcast() must not be a const, but some functions return
    consts. So const_cast them to be non-const wen we do the Bcast(). It's
    not pretty but it works.

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit aef3549b3064257e3241072ada11910289875202
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 11 13:06:59 2015 -0700

    DistributionMapping: add static function SendDistributionMappingToSidecars()
    
    When we move distributed data sets between the compute and MPI groups we
    send the FAB data using point-to-point communication, so each MPI group
    needs to know the distribution of FABs on the other group so that it
    knows who to Send() and Recv() from.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 3f45184dad6d20f7dbfc5cf1a3d7c971f69106dc
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 11 11:15:03 2015 -0700

    DistributionMapping: added define() to build a DM out of an Array<int>
    
    This is useful if a DM is initialized with the default constructor and
    one wants to populate with a plain ol' array of ints.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 32755003c7aa4172d11bdbe41fe07c4fd255f7d6
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 11 09:49:29 2015 -0700

    BoxArray: added static function SendBoxArrayToSidecars()
    
    This clones a BoxArray onto the sidecar MPI group.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit fa379456cd67662cdb2b7352f824d40fecf869ca
Merge: bb64f9c64 dbe86f9db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 19 17:53:36 2015 -0700

    Merge branch 'master' into pgas
    
    Conflicts:
            Src/C_BaseLib/FabArray.H
            Src/C_BaseLib/Make.package
            Tools/C_mk/Make.defs

commit dbe86f9dbb5a98c138d71217de169c88cf9f8237
Merge: d0f43cea6 6ba81d4e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 19 17:45:47 2015 -0700

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit d0f43cea62fa715083aee665f3968c8cb1b14515
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 19 17:22:47 2015 -0700

    clean up MGT_Sover

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tutorials/MultiGrid_C/main.cpp

commit 6ba81d4e361d2bc8f1147a31172d1b26e1bcf7a0
Merge: 2c822c57a 9123c7cb7
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Aug 19 16:01:40 2015 -0700

    Merge branch 'add_analysis_abstract_base_class'
    
    This provides an abstract base class "Analysis" for doing data analysis
    during BoxLib simulations. It also provides a simple example of in-situ
    data processing executed on the sidecars. The actual analysis routines
    themselves must be provided by the user.

commit 9123c7cb74adff8c30e8eac3ab3b9574dd053994
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Aug 19 12:45:01 2015 -0700

    Tutorials: added example "Sidecar_EX2" demonstrating use of Analysis class on sidecars

Tutorials/Sidecar_EX2/GNUmakefile
Tutorials/Sidecar_EX2/InSituAnalysis.H
Tutorials/Sidecar_EX2/InSituAnalysis.cpp
Tutorials/Sidecar_EX2/Make.package
Tutorials/Sidecar_EX2/inputs_3d
Tutorials/Sidecar_EX2/main.cpp

commit 9c041ec4a52e69414631ac2069129f3c63651231
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Aug 19 12:24:30 2015 -0700

    C_BaseLib: added abstract base class "Analysis"
    
    This class provides a platform for the user to do data analysis during
    BoxLib simulations. A class derived from Analysis should contain both
    functionality for doing the analysis itself, as well as storage for the
    results.

Src/C_BaseLib/Analysis.H
Src/C_BaseLib/Make.package

commit 2c822c57a3530b463a59ef9b875bcc585417e661
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 18 15:39:40 2015 -0700

    C_mk: added missing "-mmic" flag for compiling Fortran files on MIC in debug mode

Tools/C_mk/Make.Linux

commit bb64f9c64c254e431dcbc84e400125b5fa209bbe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 18 17:37:03 2015 -0700

    started PGAS_SMC

MiniApps/PGAS_SMC/Exec/Make.SMC
MiniApps/PGAS_SMC/Exec/ToyFlame/GNUmakefile
MiniApps/PGAS_SMC/Exec/ToyFlame/Make.package
MiniApps/PGAS_SMC/Exec/ToyFlame/Prob_3d.f90
MiniApps/PGAS_SMC/Source/Make.package
MiniApps/PGAS_SMC/Source/SMC.H
MiniApps/PGAS_SMC/Source/SMC.cpp
MiniApps/PGAS_SMC/Source/SMCBld.cpp
MiniApps/PGAS_SMC/Source/SMC_advance.cpp
MiniApps/PGAS_SMC/Source/SMC_io.cpp
MiniApps/PGAS_SMC/Source/SMC_setup.cpp
MiniApps/PGAS_SMC/Source/main.cpp

commit aea6d0134be2bfe6eb87a89615b1c48e0d06115e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Aug 18 09:55:56 2015 -0400

    add a subtitle to the main test page

Tools/RegressionTesting/testnew.py

commit 54914befc12ddf0960a12c992c7d961d5d29eb6c
Author: Yili Zheng <yzheng@lbl.gov>
Date:   Mon Aug 17 22:34:36 2015 -0700

    Rewrite the PGAS version to use non-blocking signaling put and event-based point-to-point synchronization; thus removing the need of global barriers

Src/C_BaseLib/BLPgas.H
Src/C_BaseLib/BLPgas.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 285eaa1f15b3ebff5bf4e090562ff82b3738af1e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Aug 17 16:02:19 2015 -0400

    turn off inlining for pure PGI -- this generates an internal compiler error
    for knapsack.f90.  Also drop down to -O2.  This brings us more in line with
    what we use on the Cray's when we come in via the ftn wrapper.

Tools/F_mk/comps/Linux_pgi.mak

commit 8056e83ef5ef4b27472ac7328bb67de571bbc066
Merge: 0f9f73299 1247255a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Aug 17 15:04:58 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit 0f9f73299607056c7bf3fcefe4363f6bfffeb34e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Aug 17 15:04:45 2015 -0400

    get the compiler version working for pure PGI

Tools/F_mk/comps/Linux_pgi.mak

commit 1247255a2fe037844fcb5a3e7b2ee2a2614765c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Aug 17 13:48:11 2015 -0400

    make the tol 1.e-6 for highlighting

Tools/RegressionTesting/testnew.py

commit 43e5351103c978400a1712c5051c8736118497e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Aug 17 13:31:39 2015 -0400

    new test comparison table with highlighting

Tools/RegressionTesting/testnew.py

commit c0e3244b73427e2bf30dc6e764e108c6e3650976
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Aug 17 10:53:31 2015 -0400

    close an HTML header

Tools/RegressionTesting/testnew.py

commit cb6fc77310f6c7d6d69300e9075804db04dcaa6c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Aug 15 18:56:04 2015 -0400

    update comment

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 8262c309a796a54591c1083f5345ab421b9db03c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 15 08:36:41 2015 -0700

    Enable mgt.cycle_type = MG_FVCycle in nodal as well.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 09271dc8359284a38c83b711734f069246922424
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 14 13:59:10 2015 -0700

    1) Add the functionality to do 1 F-cycle followed by V-cycles
    2) Force the interpolation to be piecewise constant for V-cycles and piecewise linear for F-cycles,
       regardless of the input values.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 00450cd94822fe557d70f7578efbd60f6859d0b8
Merge: 881163a88 a54624c9e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 14 10:29:43 2015 -0700

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit 881163a8849150da239844c2adae2115aeddce3a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 14 10:28:24 2015 -0700

    Add another cycle type -- MG_FVCycle -- which is 1 F cycle followed by V cycles

Src/LinearSolvers/F_MG/mg_tower.f90

commit a54624c9e828f9b5de38f5bdd82abce2a2b63547
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 13 11:32:21 2015 -0700

    fixed periodic boundary and a local index bug

Src/F_BaseLib/bndry_reg.f90

commit 7bfaa02c267e9b102f2f5fbd4f443a07127341be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 13 06:45:39 2015 -0700

    delete removed variable 'id' from omp private

Src/F_BaseLib/bndry_reg.f90

commit d583e5c50ded96627ab5ffde5c97d73ec41542ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 12 22:37:45 2015 -0700

    avoid covered coarse cells in ml_interp_bcs; in order to to do that, mask is built in bndry register

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/ml_nd.f90

commit 29e2fa82c4af54cb150e94d033ad91a9e10df6ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 12 11:11:27 2015 -0700

    print more information

Src/LinearSolvers/F_MG/ml_cc.f90

commit 942d9df692368d7c26436ea160bcf364d4986a63
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Aug 13 16:14:23 2015 -0500

    Make Titan consistent with other Cray machines we're using by adding -lmpichf90.

Tools/C_mk/Make.mpi

commit 26f6fe4c55e04ae054feb8fa9ba75f2d81e0b1ff
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 13 13:27:21 2015 -0700

    Oops -- committed the wrong expression for the stencil.  Now works with Dirichlet as well as periodic.

Src/LinearSolvers/C_CellMG/ABec_3D.F

commit b570e08d17135f36e61e65556e5ec2f497d4ac16
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 13 13:00:08 2015 -0700

    I have modified the 3D GSRB relaxation to use an over-relaxation factor of 1.15.  This makes it the same
    as the smoother used in the F90 solver, and seems to consistently reduce the number of V-cycles needed.

Src/LinearSolvers/C_CellMG/ABec_3D.F

commit 42647c0490242453ad02fac7cc5b3951857edfb8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 11 11:37:55 2015 -0700

    use std::pair<int, FAB *> instead of std::make_pair<int, FAB *> because the latter does not work in C++11 due to template type deduction rules

Src/C_BaseLib/FabArray.H

commit b276dfbe0d520044c4dc6bdd5bc807d72dfe9514
Merge: 9b377ff08 8c5156991
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 10 17:43:43 2015 -0700

    Merge branch 'weiqun'

commit 9b377ff086a0d113237f85dfece53ae57158c133
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 10 17:43:35 2015 -0700

    allocate at lease 1 element if asked size is zero

Src/C_BaseLib/mempool_f.f90

commit 2bee6466f85ee2353959aea178cb6cd02c2ad5d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 10 17:17:52 2015 -0700

    fixed bugs in vector_i function that has never been used

Src/F_BaseLib/vector_i.f90

commit ad307f80f9387b2a66935d7ac1aea418ea1b5f73
Merge: e75f50d1d 0d6131fee
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 10 12:58:10 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit e75f50d1d8c8bb5b9aba45407132cb3ee79004ef
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 10 12:57:33 2015 -0700

    code cleanup.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Utility.cpp

commit 0d6131fee9bbeb6f9bae7540fad4ca76106552f3
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Aug 10 11:24:49 2015 -0700

    MultiFab: clean up SendMultiFabToSidecars() interface
    
    Now the only argument to MultiFab::SendMultiFabToSidecars() is a
    MultiFab pointer. In the Compute group this will point to a MultiFab
    with actual data filled in, whereas in the Sidecar group this will point
    to a MultiFab which is allocated but uninitialized prior to this
    function call.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Tutorials/Sidecar_EX1/GridMoveTest.cpp

commit bf56ef46b7aac0d249a593f5838aafc22cff278a
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Aug 10 11:02:34 2015 -0700

    Geometry: clean up SendGeometryToSidecars() interface
    
    Now the only argument to Geometry::SendGeometryToSidecars() is a Geometry
    pointer. In the Compute group this will point to a Geometry with actual data
    filled in, whereas in the Sidecar group this will point to a Geometry which is
    allocated but uninitialized prior to this function call.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Tutorials/Sidecar_EX1/GridMoveTest.cpp

commit 84d0e64a6783c3f7e57a7628596599aab44c8c23
Merge: 76b6e96f2 0a20a9d80
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 10 11:03:06 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit 8c5156991340aa926ccbcff863a3751060d8842f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 10 10:59:04 2015 -0700

    Avoided allocating temporary multifab in multifab parallel copy

Src/F_BaseLib/multifab_f.f90

commit 16f369c9bf8a848eb491e40b37579bdd7f2e58a9
Author: Yili Zheng <yzheng@lbl.gov>
Date:   Fri Aug 7 15:13:35 2015 -0700

    Added SeqNum (tag) matching in BLPgas::Send; Changed map to multimap; Use unordered_multimap if C++11 is available; Enabled non-blocking UPC++ code in Geometry.H

Src/C_BaseLib/BLPgas.cpp
Src/C_BaseLib/Geometry.H

commit 484aef11bd079d28f6af420f6ac8318468ffa969
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 6 14:57:48 2015 -0700

    fixed typo

Src/C_BaseLib/Geometry.H

commit eb5a660942118aef1c9e4779d4e7b532259407d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 6 14:38:27 2015 -0700

    nonblocking version of FillPeriodicBoundary

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Tutorials/PGAS_HEAT/main.cpp

commit b7f2e33fd4d6bb6862c3c9c8b7e349b12ffc1d4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 6 11:15:57 2015 -0700

    moved pgas send into new files

Src/C_BaseLib/BLPgas.H
Src/C_BaseLib/BLPgas.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Make.package

commit 3f516f87ca49dee750ee02221b816969932e8617
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 5 12:36:50 2015 -0700

    added USE_UPCXX to makefile

Tools/C_mk/Make.defs
Tools/C_mk/Make.upcxx
Tutorials/PGAS_HEAT/GNUmakefile

commit d6f4ef7b44c2f664e2ac7253aae6a3a2a4fca13b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 5 12:22:33 2015 -0700

    fixed merge

Src/C_BaseLib/BoxLib.cpp

commit 1e18ae957fe083f09a35977ea59e1c80453d020f
Merge: 02dfda140 0a20a9d80
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 5 10:37:11 2015 -0700

    Merge branch 'master' into pgas

commit 0a20a9d80f2554bacc537ca394063c3699fe8520
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 5 06:42:16 2015 -0700

    fixed undefined reference to 'boxarray_build'.

Src/F_BaseLib/fabio.f90

commit b1316b8e65f6dbed07367550eabbe02329399617
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 4 18:08:48 2015 -0700

    minor change for consistence; note that nboxes(tagboxes%la) is the same as nfabs(tagboxes) because tagboxes is a special mf that has all fabs on io processor.

Src/F_BaseLib/cluster_f.f90

commit 845a173c4c1505c87ee7af6d4fa6fdb7a8ebbcb7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 4 17:16:55 2015 -0700

    simplify parallel copy in bndry_reg

Src/F_BaseLib/bndry_reg.f90

commit a5950023951a6f268d39d5e6dc7573cdbc4ba046
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 4 17:02:03 2015 -0700

    added omp parallel do in bndry_reg

Src/F_BaseLib/bndry_reg.f90

commit 292cbd1baf7cf4b741909ee02de42641830f3b57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 4 15:52:56 2015 -0700

    use bl_allocate in vector_i module

Src/F_BaseLib/vector_i.f90

commit f045f1ee6ed9c231478b96ba1342f3def0c7101f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 4 15:46:33 2015 -0700

    replaced a lot of generic calls with explicit calls so that grep and etags can work properly.

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/boxarray_f.f90
Src/F_BaseLib/cluster_f.f90
Src/F_BaseLib/create_umac_grown.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/make_new_grids.f90
Src/F_BaseLib/ml_boxarray.f90
Src/F_BaseLib/ml_cc_restriction.f90
Src/F_BaseLib/ml_layout.f90
Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/ml_nd_restriction.f90
Src/F_BaseLib/multifab_f.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90
Src/F_BaseLib/nodal_stencil_bc.f90
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/nodal_applyop.f90
Src/LinearSolvers/F_MG/nodal_mask.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 81ebd286281a1d33237bd2bd0634ade3b74ef888
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Aug 4 15:32:15 2015 -0700

    Fix the PyTools GNUmakefile for C++, and bump the tag number

Tools/CMake/BoxLib_Version.cmake
Tools/Py_util/GNUmakefile

commit 76b6e96f2320992378b252eb26a1fe51a805595f
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 4 12:15:36 2015 -0700

    itac suffix.

Tools/C_mk/Make.defs

commit 8e0907150a89f81ef4b97915a705ffdbb8bf4fae
Merge: 50205de55 5e5409fae
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 4 12:14:07 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit 02dfda14016d7649565371720471a7b0d7d1ec30
Merge: 36c11c695 5e5409fae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 3 18:18:56 2015 -0700

    Merge branch 'master' into pgas
    
    Conflicts:
            Src/C_BaseLib/BoxLib.cpp

commit 5e5409faedac02787bcaabde9d4b3936e135260e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 3 18:11:15 2015 -0700

    Set HOST in Fortran BoxLib's make system if it is not defined.

Tools/F_mk/GMakedefs.mak

commit 36c11c69562c23a16bdc3e8f11213bbffae4ede5
Author: Yili Zheng <yzheng@lbl.gov>
Date:   Mon Aug 3 13:02:49 2015 -0700

    Add the first UPC++ version

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 976abbd5c3cabc93ec3b235962a9c07fd5d4c009
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 3 11:18:34 2015 -0700

    update url in users's guide and test mailing list

Docs/Introduction/Introduction.tex

commit c0ee6417a6c8d1c1ee909bbbae66793431b5e139
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 31 15:21:10 2015 -0700

    made 1d gsrb truly rb

Src/LinearSolvers/F_MG/cc_smoothers.f90

commit b1979641e3bf4d7a7c1401f88bb73171310b1935
Merge: 5e8cc7a28 51b026562
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jul 31 12:26:02 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 5e8cc7a28320186c7244a8b46b420aed590baa78
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jul 31 12:24:57 2015 -0700

    Update release tag ID

Tools/CMake/BoxLib_Version.cmake

commit 51b02656299912ff397abc6113d5129945f888a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 31 11:06:39 2015 -0700

    mfiter: fixed a special case in which there is no local boxes at all

Src/F_BaseLib/layout.f90

commit 4cdc323aaa455ffeb2dc47138c4b14c5bdc72c40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 31 13:17:12 2015 -0400

    sometimes if there is a crash before output, then our check on the
    number of levels fails and we get a wordy error message in the
    overview table.  Now we check if the result is an integer to
    prevent this

Tools/RegressionTesting/testnew.py

commit 26696ce0bd92af118484e3ed99dd603d24d019a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 31 13:01:09 2015 -0400

    fix the storing of the diffDir if it paradoxically is a file

Tools/RegressionTesting/testnew.py

commit 25eef79fa6c133d5eefb65733326b127f986a86b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 31 10:50:30 2015 -0400

    fix the --complete_report_from_crash functionality

Tools/RegressionTesting/testnew.py

commit 2f29d89ccbaeba92967b558b13b81f9d3933774b
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jul 30 13:13:22 2015 -0700

    If the domain at level i is not divisible by blocking_factor[i], a regrid could generate new fine grids outside the allowable domain.  Rather than enforcing the restriction on bf, we intersect the resulting grids with the domain and warn the user that the new grids do not satisfy the specified bf.

Src/C_AMRLib/Amr.cpp

commit 712152814163e579169a0839d14106facb6ed2a8
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jul 29 18:13:37 2015 -0700

    Increment index of blocking_factor array used to build bf_lev in grid_places so that grids at level i have blocking factor i when all is said and done

Src/C_AMRLib/Amr.cpp

commit 4824384033d70b474510fa67ba46374535ad8b9c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 29 14:31:54 2015 -0700

    touch the memory pool in mempool_init()

Src/C_BaseLib/MemPool.cpp

commit c7539972a3a61bed1664603fdcf22655d49dcd44
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 18:07:46 2015 -0700

    always pre-allocate some memory in memory pool when boxlib is initialized

Src/C_BaseLib/MemPool.H
Src/C_BaseLib/MemPool.cpp
Src/F_BaseLib/boxlib_f.f90

commit 70aebcb5054bb0ca2e4c08cb811cdfa74f9cf026
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Jul 28 16:21:31 2015 -0700

    MultiFab, Geometry: add #ifdefs so that sidecar functions won't compile without MPI
    
    The whole notion of sidecars and in-transit processes is ill-defined
    without MPI, so make the compiler skip them altogether if we're not
    using MPI.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit a45adf905e8f68eb173e4ea400413cd17cdab4cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 16:57:09 2015 -0700

    fixed 2D tilearray_build

Src/F_BaseLib/layout.f90

commit 816cced9cbafd5ed1fdf76edc116b7a7e4d1638e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 16:29:35 2015 -0700

    PGI: link to cpplib

Tools/F_mk/comps/Linux_pgi.mak

commit fc578d5d45ecaf0bfe2e5abd7448a01b94a105bc
Merge: 382b7ad75 f42c1c77e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 15:32:31 2015 -0700

    Merge branch 'mempool' of gamera.lbl.gov:/usr/local/gitroot/BoxLib into mempool

commit 382b7ad751b2af60f6760d715fc421cc31dd9b61
Merge: edde99b79 e804efc82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 15:32:07 2015 -0700

    Merge branch 'master' into mempool
    
    Conflicts:
            Src/F_BaseLib/multifab_f.f90

commit f42c1c77ec298b9f4a3c878e189b432a4a47043e
Merge: 25a3ca1e1 edde99b79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 15:29:57 2015 -0700

    Merge branch 'mempool' of gamera:/usr/local/gitroot/BoxLib into mempool

commit edde99b79fc6a012081d98f63da261ac528ec411
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 13:26:36 2015 -0700

    added CXX and CXXFLAGS to some make files

Tools/C_mk/Make.defs
Tools/F_mk/comps/Darwin_ibm.mak
Tools/F_mk/comps/Darwin_intel.mak
Tools/F_mk/comps/Linux_cray.mak
Tools/F_mk/comps/Linux_intel.mak
Tools/F_mk/comps/Linux_lahey.mak
Tools/F_mk/comps/Linux_nag.mak
Tools/F_mk/comps/Linux_pathscale.mak
Tools/F_mk/comps/Linux_pgi.mak
Tools/F_mk/comps/Linux_sunstudio.mak
Tools/F_mk/comps/g95.mak
Tools/F_mk/comps/xlf.mak

commit bee5e8a258a57a6340619ad4aca2d0af22e51d2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 11:31:27 2015 -0700

    cleanup Make

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/Linux_catamount.mak
Tools/F_mk/comps/Linux_xt4.mak
Tools/F_mk/comps/crayx1.mak
Tools/F_mk/comps/irix64.mak

commit 2bd2cda64dbbccbfc17b79ec3f86e8a622863818
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 11:03:23 2015 -0700

    removed some retired systems and added CXX to some systems

Tools/F_mk/GMakeMPI.mak

commit 25a3ca1e153901d0ba92205c2ed207c06b3ce337
Merge: 8ee18bbf7 e804efc82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 27 17:06:58 2015 -0700

    Merge branch 'master' into mempool
    
    Conflicts:
            Src/F_BaseLib/multifab_f.f90

commit 8ee18bbf7201e762a190953b7d66a4539b49cabc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 27 16:42:39 2015 -0700

    include C_BaseLib whenever F_BaseLib is included

Src/F_BaseLib/GPackage.mak
Tutorials/Tiling_Heat_F/GNUmakefile

commit e804efc820af5daa83e7fb970d0f3031ae8178b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 27 16:36:24 2015 -0700

    ability to handle restarting from and old checkpoint that does have the same number of states

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit b91e52e6640022b04eba3dd89f4d2f876a7e0bcc
Merge: 31b89d835 0f63e3608
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Jul 27 13:11:40 2015 -0700

    Merge branch 'sidecar'
    
    This series of commits expands Vince's original stubs for in-situ performance
    monitoring framework. It introduces the notion of "sidecars", which are a set
    of MPI processes in a second, non-overlapping MPI group. They do not perform
    the "main" grunt work of the application -- this is undertaken by the "Compute"
    MPI group -- but rather can perform auxiliary tasks such as in-situ
    post-processing of MultiFab data, dynamic optimization and regridding
    strategies, etc.
    
    One annoying feature of this implementation is that the number of sidecars must
    be specified at compile time, not run time. This is because of the complicated
    initialization procedures in BoxLib and ParallelDescriptor which prevent the
    use of a ParmParse before MPI initialization has completed. This should
    definitely be fixed in the future if the sidecars become a popular tool.

commit 0f63e3608ea96aef45c1529d427aa2d6de4a66e7
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jul 24 15:31:47 2015 -0700

    Tutorials: added example "Sidecar_EX1" to show how to send data to "sidecar" MPI group

Tutorials/Sidecar_EX1/GNUmakefile
Tutorials/Sidecar_EX1/GridMoveTest.cpp
Tutorials/Sidecar_EX1/Make.package
Tutorials/Sidecar_EX1/inputs_3d
Tutorials/Sidecar_EX1/run.sh

commit 708feb26be031e7d675c28b1f9aaafc589eea970
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jul 24 15:16:17 2015 -0700

    Geometry: add static function SendGeometryToSidecars()
    
    This clones a Geometry from the compute MPI group onto the "sidecar" MPI group.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 7cdf868c82e84f6e39f525de8e33370ee5552665
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jul 24 15:15:15 2015 -0700

    MultiFab: add static function SendMultiFabToSidecars()
    
    This clones a MultiFab from the compute MPI group onto the "sidecar" MPI group.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 93a366321f6bdac21163667b7c5727f664f8a4f4
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jul 24 15:39:25 2015 -0700

    ParallelDescriptor: add static function InCompGroup()
    
    This function is analogous to InSidecarGroup().

Src/C_BaseLib/ParallelDescriptor.H

commit f530c49466373c20d4d39cb98b61ac4471a25bd5
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Jul 21 13:45:12 2015 -0700

    ParallelDescriptor:: remove some roll-call print statements

Src/C_BaseLib/ParallelDescriptor.cpp

commit e2187c9c47fd3650aeb301d7ae47857ce76efc4d
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jul 24 15:29:55 2015 -0700

    ParallelDescriptor: Communicator(), MyProc(), and NProcs() return values in the "local" communicator
    
    A large number of funtions assume the existence of only a single, global
    communicator, even though they operate on local objects. This approach worked
    fine until we introduced the notion of distinct MPI groups for computation and
    in-transit analysis. These MPI functions frequently break when operating on the
    in-transit processes because they request the computation communicator, which
    is undefined on those processes.  Rather than introducing a million if-else's
    to all these functions, forcing them to explicitly return CommunicatorComp() or
    CommunicatorInTransit(), we just let Communicator() pick the correct
    communicator automatically.

Src/C_BaseLib/ParallelDescriptor.H

commit 5c3ff4fe589c5a21ba4fa4f5701a92eb6bf0156a
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jul 24 15:12:55 2015 -0700

    ParallelDescriptor:: rename "perfmon" -> "sidecar"

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 362bf9bdd2a43ddcfa3ca896bd7e55a03d6c598a
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Jul 21 13:37:10 2015 -0700

    BLProfiler: remove perfmon stubs

Src/C_BaseLib/BLProfiler.H
Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BoxLib.cpp

commit 31b89d83528e0cbe6878d174146c92a4ac277244
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jul 27 10:07:54 2015 -0400

    remove the old compareToolDir -- it is now part of BoxLib

Tools/RegressionTesting/Maestro-tests.ini

commit bf5aef306e5e9370f3533b0eaaa8d1fc1af7e72f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 25 21:59:57 2015 -0400

    add e-mail to the maestro-development group upon failure

Tools/RegressionTesting/Maestro-tests.ini

commit 3c6888bb4b550dd113591d7b577a73bffc7f4286
Merge: c7ba23a7d 9cacd2b87
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jul 24 12:59:08 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c7ba23a7ddd8ae2cf917aac82e374a58985a5c2e
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jul 24 12:54:39 2015 -0700

    created a fortran get_allnodaltilebox for nodal-in-all-dimensions boxes

Src/F_BaseLib/multifab_f.f90

commit 6922bbbb9b4967ea97e932e47efcc7dcc2f7ce07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 22 17:07:14 2015 -0700

    minor tweaks

Src/F_BaseLib/boxlib_f.f90
Src/F_BaseLib/multifab_f.f90
Tools/F_mk/comps/Linux_intel.mak

commit abe0a20dddfb7cd0a915661eae34d7a535ad3a68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 22 15:04:30 2015 -0700

    added CXXFLAGS for Intel in Fortran makefile

Tools/F_mk/comps/Linux_intel.mak

commit 5e629d517b209217c24869a0e7215618cd988f83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 22 14:59:05 2015 -0700

    each thread must destroy its own memory

Src/F_BaseLib/layout.f90

commit 0207cc9d70a7adbd74adeb545966f668a98535d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 22 14:06:25 2015 -0700

    new makefile for Fortran

Src/C_BaseLib/GPackage.mak

commit 3b47b226b7feb035535e31c50dd6fc5428f2b264
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 22 14:00:37 2015 -0700

    started a branch that can use memory pool in Fortran BoxLib codes

Src/C_BaseLib/BLassert.H
Src/C_BaseLib/MemPool.cpp
Src/C_BaseLib/mempool_f.f90
Src/F_BaseLib/boxlib_f.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90
Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak
Tools/F_mk/comps/gfortran.mak
Tutorials/Tiling_Heat_F/GNUmakefile

commit 9cacd2b872fa4a1090a3712677123a85d32361d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 21 23:30:54 2015 -0700

    Fortran mfiter: only let master do memory allocation and deallocation

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit 3cdc26f3fc6abf2f982d217f0efd2642f431a2a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 21 17:27:42 2015 -0700

    Fortran mfiter: save tilearray in layout

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit 28c9cf564a3ac570b93ed218e5f4894c9da2df8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 21 12:24:12 2015 -0700

    Fortran mfiter: fixed a bug in tilearray checking and return the head if a tilearray is found.

Src/F_BaseLib/layout.f90

commit 10a09b8580dfecb8e1d2aa86343ba85b702b95dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 21 09:50:56 2015 -0700

    rewrote Fortran mfiter; hopefully it's faster with multiple threads

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit 43c635035b8c1ff42db3a1192e7f43909bd586d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 20 20:53:32 2015 -0700

    identation

Src/C_BaseLib/FabArray.cpp

commit 33404a026ca7592ffbb04598391ac364b855f9f8
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jul 20 18:51:55 2015 -0700

    Move .H and .cpp listings in the CMakelists.txt in C_Baselib

Src/C_BaseLib/CMakeLists.txt

commit cf128bb98f02aca46ebfa4ae746667a1cf6b8c2a
Merge: 2536a2ac2 10b25a707
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jul 20 18:49:52 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 50205de555dc5bea99fe144dcb65a89643abc143
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 20 16:45:19 2015 -0700

    swap pair test.

Src/C_AMRLib/Amr.cpp

commit 10b25a7078f20f5649b6b52cf2ab5308cf2c3442
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jul 20 16:19:04 2015 -0700

    Included timing files and run script

Tutorials/Tiling_Heat_F/results/babbage_omp.run
Tutorials/Tiling_Heat_F/results/results.txt
Tutorials/Tiling_Heat_F/results/t1a.txt
Tutorials/Tiling_Heat_F/results/t1b.txt
Tutorials/Tiling_Heat_F/results/t2a.txt
Tutorials/Tiling_Heat_F/results/t2b.txt
Tutorials/Tiling_Heat_F/results/t3a.txt
Tutorials/Tiling_Heat_F/results/t3b.txt
Tutorials/Tiling_Heat_F/results/t4a.txt
Tutorials/Tiling_Heat_F/results/t4b.txt
Tutorials/Tiling_Heat_F/results/t5a.txt
Tutorials/Tiling_Heat_F/results/t5b.txt
Tutorials/Tiling_Heat_F/results/t6a.txt
Tutorials/Tiling_Heat_F/results/t6b.txt
Tutorials/Tiling_Heat_F/results/t7a.txt
Tutorials/Tiling_Heat_F/results/t7b.txt

commit 7001eeb557fdda3ee37bf384c83f4e10ccb268da
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jul 20 16:09:21 2015 -0700

    Changed configuration to match tests on Babbage, includes some results

Tutorials/Tiling_Heat_F/advance.f90
Tutorials/Tiling_Heat_F/inputs_3d
Tutorials/Tiling_Heat_F/results.txt

commit 95de324e255b809a94ae466a7d1da4aa8b290653
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jul 20 13:18:05 2015 -0700

    Added timer

Tutorials/Tiling_Heat_F/advance.f90

commit 0bf633f84bb93fb1ee671987ba49557019268a89
Merge: f3fc9318a 7761f0e4a
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 20 12:09:59 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7761f0e4a37b0d8c1f44766af257eb1548a402ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 20 10:54:53 2015 -0700

    fixed uninitialized values to quiet valgrind; added some comments

Src/F_BaseLib/layout.f90

commit e4b1a441d37f18add4b4dd0a88248a9e98b1016b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jul 20 10:51:00 2015 -0700

    end if -> endif

Tools/F_mk/GMakedefs.mak

commit 7aef0b5d8ccca54cfb091e0f37813d8d3c3d1327
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jul 20 10:48:39 2015 -0700

    if compiled with MIC=t, add .mic to executable

Tools/F_mk/GMakedefs.mak

commit f3fc9318a6d4fe98268742388a60c9eed3610aeb
Merge: 5f45ec05c 223afd83a
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 20 10:45:49 2015 -0700

    merge conflict.

commit 223afd83a2a0ed1fd5b4c260a3699e856ce46ed5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 20 10:26:21 2015 -0700

    fixed a new bug in FabSet: wrong source index

Src/C_BoundaryLib/FabSet.cpp

commit 8424a15cbd152cb5c4cf31d1cfbd44a8cafef523
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 20 06:56:16 2015 -0700

    fixed another new bug in parallel copy

Src/C_BaseLib/FabArray.H

commit 883c4d5171e20a6a5fbdfb2aad86861a7d80d9fc
Merge: 0194fdd4d bef075c62
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 20 06:16:52 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0194fdd4d6d7b56c5b558171686610d66826307a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 20 06:16:42 2015 -0700

    fixed a new bug in parallel copy: shouldn't set n_grow twice

Src/C_BaseLib/FabArray.H

commit bef075c62034958a04f4682e34c868ec24235fc2
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jul 19 17:48:36 2015 -0700

    Make: updated Babbage detection to work on any of the login nodes when selecting compiler flags in F_mk

Tools/F_mk/comps/Linux_intel.mak

commit cb8b11f15fda04fc7b0e4152789ca339ea9adc30
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Jun 29 14:06:51 2015 -0700

    Make: added Makefile variable "ITAC_TRACE" to define compiler flags and libs used with Intel Trace Analyzer and Collector

Tools/C_mk/Make.Linux

commit 9e38bee0c40b86cfcc2cf59cc2c646aa9d73d6e4
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Jun 29 13:51:10 2015 -0700

    Make: added "-xHost" flag to Intel compiler when compiling for Edison or the Xeon host on Babbage
    
    This flag generates the highest available instruction set on the native
    architecture. Without it, the compiler defaults to SSE2, while many newer
    instruction sets exist, including AVX, AVX2, SSE3, and SSE4.1/4.2.
    
    However, when compiling code for the MIC we can't use "-xHost" or any other
    instruction set request flag, hence all the logic around Babbage in this
    commit.

Tools/C_mk/Make.defs
Tools/F_mk/comps/Linux_intel.mak

commit cd32992bbf19839acc67ec1e2c7d5b4e23647ee7
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Jun 29 13:56:04 2015 -0700

    Make: added Makefile variable "MIC" for compiling native code for Intel MIC
    
    This adds the "-mmic" flag to the Intel compiler if the MIC variable is
    defined.

Tools/C_mk/Make.Linux
Tools/F_mk/comps/Linux_intel.mak

commit 36e8f785e1d54a22ba41bccf90d9610a5f05d93f
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Jun 9 12:20:25 2015 -0700

    Make: use MPI compiler wrappers on orga
    
    No need to specify include/library directories by hand. Let the wrappers
    do all the work.

Tools/C_mk/Make.mpi

commit 56cec70ec483f75a24d30b1edc099709eb5dc41f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 19 10:52:10 2015 -0700

    Option to call dimension agnostic Fortran subroutines in deriving.  Note that it is OK to mix the two types Fortran functions in the derive list.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp
Src/C_BaseLib/ArrayLim.H

commit 1193f2069cc2bdda71cf0974c3076226e436ee6e
Merge: 1c9af9c57 c66c00fc4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 19 06:55:19 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c66c00fc461b2cb020d2db310bc10b215a01a436
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Fri Jul 17 17:21:59 2015 -0700

    Swaps pointers between phi_old and phi_new instead of using actual multifab_copy to avoid allocating and de-allocating data.

Tutorials/Tiling_Heat_F/advance.f90

commit f8139c4e886804db5c22380a04f5625d32693813
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Fri Jul 17 16:59:06 2015 -0700

    Combined compute_flux and update_phi subroutines into advance_phi.

Tutorials/Tiling_Heat_F/advance.f90
Tutorials/Tiling_Heat_F/main.f90

commit 1c9af9c578cf1384def1e40a6a81a56a4991e3ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 17 15:37:55 2015 -0700

    Parallel copy can now include ghost cells for both source and
    destination.  Note that it will not handle periodic boundary properly
    if the desitnation box includes ghost cells because MultiFab does not
    even know about periodicity.

Src/C_BaseLib/FabArray.H
Src/C_BoundaryLib/FabSet.cpp

commit 0b4d7bb4c8c13558a21fa170726b7d5fc0da6386
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 17 14:50:11 2015 -0700

    comment

Src/C_BaseLib/MultiFab.H

commit 4364fe05ec8b0c517ddafc095a03132c980226f6
Merge: df2e4ff77 2071e53e1
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Fri Jul 17 13:08:16 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit df2e4ff776c5075cd1cdf5c73a3427c59245b4fe
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Fri Jul 17 13:07:30 2015 -0700

    Starting off Tiling_Heat_F as a copy of HeatEquation_EX1_F

Tutorials/Tiling_Heat_F/GNUmakefile
Tutorials/Tiling_Heat_F/GPackage.mak
Tutorials/Tiling_Heat_F/advance.f90
Tutorials/Tiling_Heat_F/init_phi.f90
Tutorials/Tiling_Heat_F/inputs_2d
Tutorials/Tiling_Heat_F/inputs_3d
Tutorials/Tiling_Heat_F/main.f90
Tutorials/Tiling_Heat_F/write_plotfile.f90

commit a4811dca751ebfefd5faa287f79c9477c2da990c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 16 21:37:42 2015 -0700

    added optional argument for number of ghost cells in parallel copy;
    this relieve the user's burden and avoids creating a temporary
    mulitfab.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 2071e53e18da05f994fccb09eeeb035d5d4844cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 16 20:49:59 2015 -0700

    added a new macro BL_TO_FORTRAN_N_3D provide by Max K. and moved ZFILL to ArrayLim.H

Src/C_BaseLib/ArrayLim.H
Src/C_BaseLib/BLFort.H

commit 15db178dd4572e5f9679494f647b07d5117f1d86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 16 15:34:44 2015 -0700

    fixed a new bug

Src/C_BaseLib/FabArray.cpp

commit e72c670eb8fc70801df2a6dc94961ef1e0f6bf8a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 16 15:11:04 2015 -0700

    FillPatchIterator now interally has a normal MulitFab with non-overlapping grids

Src/C_AMRLib/AmrLevel.cpp

commit 23076025dbca3c4fe1fd7f1cb5ad39db4b82ddc6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 16 14:52:29 2015 -0700

    allow MultiFab change n_grow without changing the data; this is useful for avoiding too local MultiFab to MultiFab copies in parallel copy, which only copies from valid to valid regions;

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit b8094d0e05c72d57db3fb5668e9b6848f2d5112a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 16 14:14:20 2015 -0700

    Fortran mfiter: added get_grownnodaltilebox

Src/F_BaseLib/multifab_f.f90

commit 5a8d872e57e12b2a4b6e503a826cba4e55acfd43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 16 13:33:43 2015 -0700

    don't think boxarray in FabArray needs to be mutable

Src/C_BaseLib/FabArray.H

commit 5f45ec05c9a68971aa6ecd59f8816bd697dc35f0
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 16 13:06:59 2015 -0700

    more random cluster tests.

Src/C_BaseLib/DistributionMapping.cpp

commit 470c103a0cd424422161820871ba73f3db486938
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 16 12:23:49 2015 -0700

    random cluster distribution test.

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit d57c8abcf7178f280900c331580bd1c900734b27
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 16 10:47:27 2015 -0700

    added a new macro ZFILL that in 1D and 2D take a real array like dx, make it three elements long, and fill the new elements with zero; it won't do anything in 3D

Src/C_BaseLib/BLFort.H

commit 5ace37d5d9f176c8417e319a484d8cc1eccd9c5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 15 20:47:12 2015 -0700

    MemPool: tidy

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/MemPool.H
Src/C_BaseLib/MemPool.cpp
Src/C_BaseLib/mempool_f.f90

commit cf89d0cc6591de2d235f7228ae14898be4f764d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 15 17:36:40 2015 -0700

    revert my accident commit

Tutorials/Tiling_Heat_C/advance_3d.f90
Tutorials/Tiling_Heat_C/init_phi_3d.f90

commit b2155f78ddbad46ecdb03f21aaa23256f3ad7737
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 15 17:21:27 2015 -0700

    modified some macros to pass 3d integer index arrays right-filled with zeros in cased of 1d or 2d

Src/C_BaseLib/ArrayLim.H
Src/C_BaseLib/BLFort.H

commit 93efab8f8b597bbe2d8a8067fe8154d532e602ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 15 16:07:46 2015 -0700

    Max's change that increases the optimization level of Cray compiler

Tools/C_mk/Make.Linux
Tutorials/Tiling_Heat_C/advance_3d.f90
Tutorials/Tiling_Heat_C/init_phi_3d.f90

commit a26bcb6ac760e4e6ae83830c2cecea986f132df6
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jul 15 13:57:07 2015 -0700

    Add kumonga to make system

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 13b54e1b53dff612bd4590a4d2c8c87c1ca3495b
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 14 15:03:13 2015 -0700

    staggered cluster test.

Src/C_BaseLib/DistributionMapping.cpp

commit 96e63113c795faec71f1ceb728caa9b64fad5123
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 14 10:20:33 2015 -0700

    initialize the timers

Tutorials/HeatEquation_EX1_F/main.f90

commit c17d858699c6135dea523326b585623cd020722e
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 14 09:44:29 2015 -0700

    add some timers

Tutorials/HeatEquation_EX1_F/advance.f90

commit d3f900316567ccc65438e062c5a0a1150c919e8a
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 13 16:56:22 2015 -0700

    more staggered grids.

Src/C_BaseLib/DistributionMapping.cpp

commit b50973ff688de92f4d03deb33546c78b5f8a6581
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 13 16:52:36 2015 -0700

    more staggered grids.

Src/C_BaseLib/DistributionMapping.cpp

commit 9d41bd7eadfec962d2749c8581ad8b5e526ebd8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 13 16:27:28 2015 -0700

    revert 'always use cray wrappers' because it causes problems for vtune

Tools/C_mk/Make.Linux

commit 5596501d7e3267a3376bb0e38922a2691846d36a
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 13 13:52:52 2015 -0700

    added stagger option for mlpfc.

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H

commit c442c6b4a051f5e5f946a910c143db9c355804a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 12 22:27:05 2015 -0700

    allow Intel compiler more memory and time

Tools/C_mk/Make.defs

commit a9ec1a9382dd53205f6b875aa112c3fe888a82f4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 12 22:23:26 2015 -0700

    always use cray wrappers

Tools/C_mk/Make.Linux

commit 388df1111bb96f8a59d0b2f6ae33cae361830d7c
Merge: 1c037ec09 0daf98b14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 12 22:22:09 2015 -0700

    Merge branch 'mempool'

commit 0daf98b14b2277b8b78e71f8ff5acb4aa1aa0150
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 12 20:33:15 2015 -0700

    implemented a thread friendly memory pool that can be used in both C++ and Fortran to increase the speed of allocating and deallocating arrays inside OMP.

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/CArena.H
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package
Src/C_BaseLib/MemPool.H
Src/C_BaseLib/MemPool.cpp
Src/C_BaseLib/mempool_f.f90

commit 1c037ec099ea278fad0f1c7dbdbe9d8b0a8b2997
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jul 9 08:57:42 2015 -0700

    works on any babbage login node now

Tools/F_mk/GMakeMPI.mak

commit 83b7805f116931bb41548055393bae674420c335
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 7 15:15:11 2015 -0700

    some cleanup.

Src/C_BaseLib/FabArray.H

commit 993cd56b9c1c0a7a72f541c0dc3c44ee7be3e541
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 7 13:46:00 2015 -0700

    more multilevel distribution maps for moveallfabs.  we now have full control.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H

commit 0a9c9404d29b265f5197f4780a8e261778875e13
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 7 12:50:02 2015 -0700

    starting a new branch for PGAS and split FillBoundary into two functions

Src/C_BaseLib/FabArray.H
Tutorials/PGAS_HEAT/GNUmakefile
Tutorials/PGAS_HEAT/Make.package
Tutorials/PGAS_HEAT/advance_3d.f90
Tutorials/PGAS_HEAT/init_phi_3d.f90
Tutorials/PGAS_HEAT/inputs_3d
Tutorials/PGAS_HEAT/main.cpp
Tutorials/PGAS_HEAT/writePlotFile.H
Tutorials/PGAS_HEAT/writePlotFile.cpp

commit 705e5e5f9af762379444b8855a35facb3ade7c49
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 30 12:56:15 2015 -0400

    remove debugging prints

Tools/RegressionTesting/testnew.py

commit 0e150b11fdbb74b9a8541a3e165ef6fc9bb4e943
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 30 12:55:27 2015 -0400

    catch AttributeError for the compilation failure too

Tools/RegressionTesting/testnew.py

commit 3cf40930565d2945445f0ecb5b6c66607149e75f
Merge: bc11c7f0d 0e91fb26f
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Tue Jun 23 15:21:52 2015 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit bc11c7f0d3b4faa11580789139c3b1b8dbea6fc5
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Tue Jun 23 15:21:21 2015 -0500

    Add OpenMP to sub-chandra postprocessing

Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/GNUmakefile
Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90

commit 0e91fb26fcb9989e055a1ce669f5934557d5c06a
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jun 22 13:30:10 2015 -0700

    Changed path

Tools/F_mk/GMakeMPI.mak

commit afee0b7188c7e21b4908c205be6d8a55cc95aa07
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 18 17:20:18 2015 -0700

    Add 3D UniformVelocity test.

Tools/RegressionTesting/BoxLib-tests.ini

commit 2f68afe8fa9e68a1ecbd6c304fec4d460ab953e3
Merge: 1d14256b9 85cf744c6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 18 17:19:23 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 1d14256b9524ff3260e735c6616a0f4125a92fdd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 18 17:18:52 2015 -0700

    1) Make the blobs less discontinuous so we don't deal with undershoot.
    2) Make 3d regression test.

Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_2d.f90
Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_3d.f90
Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt.3d

commit 85cf744c696639fb5770dff15304ad5307c5c7c8
Merge: d3384e7b0 7faaba1dd
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Thu Jun 18 14:31:16 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d3384e7b0ce3d5fecd0375c52a11129cec747abb
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Thu Jun 18 14:30:43 2015 -0700

    Turned off Intel compiler runtime warnings.

Tools/F_mk/comps/Linux_intel.mak

commit 7faaba1dd8f3b747e48d4ab0aafbb9f870e84fe0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jun 18 11:49:37 2015 -0400

    fix a bug I recently introduced that makes tests that were not run show
    up as failures in the suite overview webpage

Tools/RegressionTesting/testnew.py

commit ad645b062c6e99c559580c2ab31a284fe8d0ac3e
Merge: 4575c7bdd c7e07a89f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 16 14:06:06 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 4575c7bddfd3d565da1fac1dbd5bad3059f54471
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 16 14:05:14 2015 -0700

    Make the default velocities be completely diagonal.

Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_2d.f90
Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_3d.f90

commit 88fbc7422d7ed0681a8456539e6e14376016e164
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 16 14:04:21 2015 -0700

    Change plt file names for 2d vs 3d.

Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.3d

commit 9a94f3964d5e4822e4bb196e19b81f8a1e770c33
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 16 13:37:18 2015 -0700

    Fix bug -- wrong dimensioning of uin in consup.

Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90

commit 72872c0ed81f1eb87f360e1843f3f65ebec899c5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 16 13:37:00 2015 -0700

    Reformat warning to look more like 2d.

Tutorials/AMR_Advection_C/Source/Src_3d/ACT_3d.f90

commit f42524199757feaa5151c89d922cafa33f4d7b55
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 16 13:04:14 2015 -0700

    Remove print statement

Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90

commit 24e1972c4bc6fde3381051259866930a530f9886
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 16 12:56:58 2015 -0700

    Fix bug in calling transxy.

Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90

commit c7e07a89fb488d571d13c2e88193a5c5ae158b2a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 16 10:48:46 2015 -0700

    SMC miniapp: added collapse to loop-level omp

MiniApps/SMC/kernels.f90
Tools/C_mk/Make.defs

commit a65d192a633089466d68d2c992ff719c86ccd1a5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 16 09:55:09 2015 -0700

    Fixed misuse of j for k.

Tutorials/AMR_Advection_C/Source/Src_3d/React_3d.f90

commit 04d7ee1cde3433b93bb5d47bd8186248a1146890
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jun 15 17:10:58 2015 -0700

    Fixed various indexing errors.

Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90

commit 68a5a4fe0f9debc86af8d3ff3a5ec7783d95eeb9
Merge: 5dea14ee2 b0aee021f
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jun 15 13:17:36 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5dea14ee213af0701d9211790013aef0b8f124a8
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jun 15 11:53:30 2015 -0700

    added function to move fabs to a new distribution map for all fabarrays sharing the same distribution map.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Tutorials/MultiFabTests_C/GridMoveTest.cpp

commit 681f7db621b3d35e4cd26131e764b4a91d4f062a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 10 14:19:19 2015 -0700

    added id for distmaps.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit b0aee021fb1c5b8636c9cc4bfea101cc53204a5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 9 13:39:49 2015 -0700

    update the comments

Tutorials/Tiling_Heat_C/results/run-babbage.sh

commit 41c17cfaa199ee144ca269e768e87bb2bba34286
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 9 13:27:44 2015 -0700

    SMC: extra optimization flags for babbage

MiniApps/SMC/GNUmakefile

commit ff7b4f7b98b196b806deebe8025b0d0a1b3dc333
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 9 13:26:52 2015 -0700

    added babbage to make system in Fortran

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/comps/Linux_intel.mak

commit 66066ded4134afc61ca0070773ddc2193c976062
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 9 13:23:48 2015 -0700

    fixed a new 2D bug

Src/F_BaseLib/list_box.f90

commit 04b8d8ddf6cbdb26152cf52984c9d8c35a258efb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 9 13:07:01 2015 -0700

    SMC: added thte original loop-level omp for comparison

MiniApps/SMC/_parameters
MiniApps/SMC/advance.f90
MiniApps/SMC/inputs_SMC
MiniApps/SMC/kernels.f90

commit 874cec177b3b9c9ea41cd4ed3122125b1846320e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 8 20:59:02 2015 -0700

    tiling in fill_boundary

Src/F_BaseLib/layout.f90
Src/F_BaseLib/list_box.f90

commit bb45a1318b22a63dd9d6dd84554760a355a9e8c2
Merge: b223fa023 9c2d8b0f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 8 13:16:22 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit b223fa023557a42b9c7b5a433f03e1e99eea090e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 8 13:15:15 2015 -0400

    if we are using BOXLIB_USE_MPI_WRAPPERS=1, then explicitly add
    -lmpichf90 to the libraries, some machines seem to need this, and
    it doesn't seem to mess up the others.

Tools/C_mk/Make.mpi

commit 9c2d8b0f7d310b1ed6b3e954676f7d6fe157d30f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 16:33:39 2015 -0700

    Fortran mfiter: fix the fix

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit 110effc6cdb364001d2203c37929dc083dca6d5e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 16:25:24 2015 -0700

    Fortran mfiter: fixed a bug when grid cannot be split evenly into tiles

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit 3ff1f2ac04e16208229f50309b237b9bc040da95
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 14:36:58 2015 -0700

    Fortran mfiter: fixed nodal bug

Src/F_BaseLib/multifab_f.f90

commit 8baba9cce6219731fd36029c8ca781f06d38e912
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 13:57:24 2015 -0700

    Fortran mfiter: add a reset subroutine and rename get_tile to more_tile

MiniApps/SMC/advance.f90
MiniApps/SMC/init_data.f90
Src/F_BaseLib/multifab_f.f90

commit 2b3a9eb5bfce349acba5a2f207e83caf2917e8c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 10:36:08 2015 -0700

    added SMC as a mini app for playing with tiling

MiniApps/SMC/GNUmakefile
MiniApps/SMC/GPackage.mak
MiniApps/SMC/LiDryer.c
MiniApps/SMC/_parameters
MiniApps/SMC/advance.f90
MiniApps/SMC/chemistry_module.f90
MiniApps/SMC/derivative_stencil.f90
MiniApps/SMC/init_data.f90
MiniApps/SMC/initialize.f90
MiniApps/SMC/inputs_SMC
MiniApps/SMC/kernels.f90
MiniApps/SMC/main.f90
MiniApps/SMC/make_plotfile.f90
MiniApps/SMC/probin.template
MiniApps/SMC/smc.f90
MiniApps/SMC/smcdata.f90
MiniApps/SMC/time.f90
MiniApps/SMC/transport_properties.f90
MiniApps/SMC/variables.f90

commit d9784556406a03cac4666844acdee422a3050bff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 10:33:47 2015 -0700

    tiling in Fortran multifab copy

Src/F_BaseLib/multifab_f.f90

commit cfd100b2e3a63e54b8511d4ebe5c66203112ecd3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 10:11:19 2015 -0700

    Fortran mifter: fixed a bug and tiled setval

Src/F_BaseLib/multifab_f.f90

commit 57665917ca2b01816d899943fb5d2d13c7e495d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 09:33:13 2015 -0700

    Fortran mfiter: changed the default to match C++ version

Src/F_BaseLib/multifab_f.f90

commit 206be04df693231ea6ffcced6f136738dd911871
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 07:56:45 2015 -0700

    Fortran mfiter: added optional argument, tiling

Src/F_BaseLib/multifab_f.f90

commit c0b2ae1001e96cd7a167f1265448b30cefc1b622
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 07:38:30 2015 -0700

    Fortran mfiter: minor renaming

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit c6a51ea197a5fe6f1c579ed663acf97c290b3e89
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 6 13:50:00 2015 -0700

    Fortran mfiter: can change tile size

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit 429c04468d06f4f5c57e247aba95525f15cf7681
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 6 10:33:39 2015 -0700

    Fortran mfiter: added more functions

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit 77d5318304d589adf89ca55120074558d0eb1678
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 6 09:41:34 2015 -0700

    minor cleanup of mfiter

Src/F_BaseLib/multifab_f.f90

commit 3c596615b21b19f01fa0857f09c518cd0ffb3f72
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 5 23:24:01 2015 -0700

    started working on tiling in Fortran

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit 3669e78b7bf6ba4b0e48bf51b8a6f1b93c9dd86f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 3 20:15:53 2015 -0700

    rename FabArrayBase::fpb_boxarray_max_size to FabArrayBase::comm_tile_size (communication tile size)

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Tutorials/Tiling_Heat_C/inputs_3d

commit 942ed06140050cd8eaa26b5e61c102bffbce901f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 3 17:40:38 2015 -0700

    changed defaults

Src/C_BaseLib/FabArray.cpp
Tutorials/Tiling_Heat_C/inputs_3d

commit 3bb782118f56460d9bd57f773799da2c61124e6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 3 12:11:52 2015 -0700

    removed an unnecessary std::max

Src/C_BaseLib/BoxList.cpp

commit 38233d6f46efb30aa6724446fda1dbcc92f1bf2f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 3 11:28:14 2015 -0700

    It turns out maxSize is not suitable for chopping a nodal box into small chunks in the recent changes in FabArray because maxSize() returns overlapping nodal boxes.  So a new function is added to chop a box into a list of non-overlapping tile boxes.

Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit 8e121f227ba1fdfc1ec9fff9c174c44f2686485e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 2 17:31:09 2015 -0700

    no need to build boxarray if it's not used

Src/C_BaseLib/FabArray.cpp

commit 1a237057789bc03499cc48ecaef5d2aed2db8d49
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 2 20:16:42 2015 -0400

    fix a bug with --single_tests pointed out by Ann

Tools/RegressionTesting/testnew.py

commit b83a93df608b5d95450c6c5e02b1c1a1ab8f6a05
Merge: a06a53d3a 4fb9f9044
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Jun 2 16:13:45 2015 -0700

    Merge branch 'fpb_thread_friendly'
    
    These commits improve thread efficiency when updating periodic boundary
    conditions by splitting Boxes which intersect domain edges into
    BoxArrays of smaller Boxes. Each individual thread then copies data from
    each smaller Box to the corresponding region elsewhere on the domain,
    rather than a single thread copying the entire intersecting Box while
    all the other threads spin idly.
    
    Preliminary tests using 120 threads on Babbage at NERSC have indicated a
    ~20x speedup for the boundary value update step, compared to the same
    number of threads updating boundary values using the old method. On
    systems with less concurrency the performance gain from these changes
    will likely be smaller.

commit 4fb9f9044391af2c932f11adbfb89ac0d7d8198a
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed May 27 11:14:11 2015 -0700

    FabArrayBase: split Boxes into BoxArrays in TheFB() for thread friendliness

Src/C_BaseLib/FabArray.cpp

commit 3c5f2ec2f9685821f3b828da5a7c8a5119d5803d
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed May 27 11:13:22 2015 -0700

    FabArrayBase: split Boxes into BoxArrays in TheCPC() for thread friendliness

Src/C_BaseLib/FabArray.cpp

commit 4a31da5ad073b5b4e6bc78236e8e970bf75ca9e1
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed May 27 10:44:03 2015 -0700

    Tiling_Heat_C: added timers to FillPeriodicBoundary() to test threading performance improvement

Tutorials/Tiling_Heat_C/main.cpp

commit 7babc0e4061e7fbecc21be46f2ce09565d29f6e4
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue May 26 14:45:47 2015 -0700

    Geometry: changed box boundaries with periodic BCs to box arrays to improve performance with lots of threads

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Tutorials/Tiling_Heat_C/inputs_3d

commit a06a53d3a32e1a23d0d1d16668c099c5eb15bfcf
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 1 14:30:36 2015 -0700

    remove broken links in doc

Docs/GettingStarted/GettingStarted.tex

commit 806c0f535c41448281d164f82c4a112138c23739
Merge: d70e110b9 1c01a851c
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jun 1 14:03:29 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d70e110b9115614615821a86f26d153a2c7709e4
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jun 1 14:02:44 2015 -0700

    Fixed typos

Docs/GettingStarted/GettingStarted.tex

commit 1c01a851c2f056dd40a09486402eac817237e055
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 1 13:50:26 2015 -0700

    added macros for calling dimension agnostic Fortran code

Src/C_BaseLib/ArrayLim.H
Src/C_BaseLib/BLFort.H

commit 5ece0aecace987dc44acf5bd64b0a5b0825df23b
Merge: e0844ee91 b53e16d91
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jun 1 10:12:20 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e0844ee9161a8915f01d01a84a7b165482e00776
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jun 1 10:10:55 2015 -0700

    fixed a typo

Docs/GettingStarted/GettingStarted.tex

commit b53e16d9123ab3a18bf38eba8b80dda0baf2606b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 29 18:29:22 2015 -0700

    Further fixes for the 3d version of AMR_Advection_C.

Tutorials/AMR_Advection_C/Exec/Make.ADR
Tutorials/AMR_Advection_C/Source/Src_2d/Tagging_2d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/Derive_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90

commit 9ea83131067fbdc1564fa2b2347b7a815fed53ee
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri May 29 11:49:43 2015 -0700

    if plot_int <= 0, don't print any plotfiles

Tutorials/HeatEquation_EX1_F/main.f90
Tutorials/HeatEquation_EX2_F/main.f90
Tutorials/HeatEquation_EX3_F/main.f90
Tutorials/HeatEquation_EX4_F/main.f90
Tutorials/HeatEquation_EX5_F/main.f90

commit 2b2822b9a3e14cefe58747a80289657e833d7eae
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 28 18:28:43 2015 -0700

    movegrid tests, random copy from movedgrid mf.

Tutorials/MultiFabTests_C/GridMoveTest.cpp

commit 22221b3702fe1341f0ac66d11eb0bb3fb7471afd
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 28 14:10:11 2015 -0700

    added function to move fabs in a fabarray given a new processor map.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Tutorials/MultiFabTests_C/GNUmakefile
Tutorials/MultiFabTests_C/GridMoveTest.cpp

commit cbb561ddeb71c5adac48baaa2f96d5980e7c9d0d
Merge: ec83007f6 86a04a261
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun May 24 15:24:54 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ec83007f6230d8ea753584fd1bfbe8cdfd9f9bce
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun May 24 15:24:36 2015 -0700

    More changes for 3d plus cleaning up 2d.

Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_3d.f90
Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.3d
Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.3d
Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90

commit 58cda477006d557ce7305d8f3f501e2ca44773af
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun May 24 15:24:04 2015 -0700

    Fixing 3d source files ...

Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/EstDt_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/slope_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90

commit a2e3658dfe160ce8602ba7e76fbddb91ed64216d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 22 18:29:05 2015 -0700

    This version compiles in 3d (and fixes a small bug in the transverse stuff in 2d)

Tutorials/AMR_Advection_C/README
Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/Make.package
Tutorials/AMR_Advection_C/Source/Src_2d/trans_2d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/ACT_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/ACT_sums_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/Derive_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/EstDt_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/Make.package
Tutorials/AMR_Advection_C/Source/Src_3d/React_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/Tagging_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/bc_fill_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/ext_src_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/fill_diff_coeff_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/slope_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90
Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90

commit 86a04a261837641a57fecb333a08b845cd7b0f86
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri May 22 17:55:58 2015 -0700

    profiling: added Babbage run script for tiled version of heat solver

Tutorials/Tiling_Heat_C/results/run-babbage.sh

commit 20deeaa2ca49a8cb01ae54e4f22b54537b7ecb34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 22 16:49:37 2015 -0700

    added Intel 15 to make

Tools/F_mk/GMakerules.mak
Tools/F_mk/comps/Linux_intel.mak

commit ecc4865c9b3b1000e2e8877611e7a2482cb22bdb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 22 16:23:21 2015 -0700

    crayftn --> ftn, craycc --> cc

Tools/C_mk/Make.Linux

commit d2a7723fb8e5d49a6a4e6f07aa25c64bd7ef92aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 22 15:57:50 2015 -0700

    checked in job script and timing result

Tutorials/Tiling_Heat_C/results/results.org
Tutorials/Tiling_Heat_C/results/run-edison.sh

commit 957fbef4d043a2452306ea5d0b96c1cbfd4e4695
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 22 15:45:11 2015 -0700

    Revert "use allocatable arrays in the non-tiling version so that it does not cause stack overflow"
    because this made the non-tiling version much slower.
    
    This reverts commit 288e893057a10503a5c0ad46a01739cf4d985ef8.

Tutorials/Tiling_Heat_C/advance_3d.f90

commit 288e893057a10503a5c0ad46a01739cf4d985ef8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 22 12:32:33 2015 -0700

    use allocatable arrays in the non-tiling version so that it does not cause stack overflow

Tutorials/Tiling_Heat_C/advance_3d.f90

commit 379511ed09b59bcdcb11cfc9b1f2fb071c85d0ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 22 12:31:39 2015 -0700

    default USE_MPI to FALSE

Tutorials/Tiling_Heat_C/GNUmakefile

commit 6447e71eeab9df5fc646c86d252577ec50f38879
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu May 21 14:43:05 2015 -0700

    make: added support for Babbage, the Intel MIC testbed at NERSC
    
    This assumes you will be running natively on the MIC card, not on the Xeon
    host. NERSC recommends this approach since Cori will have a native MIC
    architecture with no co-processors.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 771776cf0aaf1bc0c783b38bd11c31a20882f6a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 21 14:14:18 2015 -0700

    change default compilers to Intel in makefile

Tutorials/Tiling_Heat_C/GNUmakefile

commit 37cf1209e6b41b86957fdf899ce8d06aaa1663ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 21 14:00:28 2015 -0700

    added nowait for the omp on loops version

Tutorials/Tiling_Heat_C/advance_3d.f90

commit e3226f09704255a2a98e504f3cac58ba1d9f9be4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 21 13:47:48 2015 -0700

    a new tutorial code for tiling

Tutorials/Tiling_Heat_C/GNUmakefile
Tutorials/Tiling_Heat_C/Make.package
Tutorials/Tiling_Heat_C/advance_3d.f90
Tutorials/Tiling_Heat_C/init_phi_3d.f90
Tutorials/Tiling_Heat_C/inputs_3d
Tutorials/Tiling_Heat_C/main.cpp
Tutorials/Tiling_Heat_C/writePlotFile.H
Tutorials/Tiling_Heat_C/writePlotFile.cpp

commit 7f3548be22b6bd94d410eecc36cb920a015b0b43
Merge: fe12ff02a 06bf62978
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 19 17:45:34 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit fe12ff02a30855c01dfe98b8f19a7bed8bbb6572
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 19 17:45:25 2015 -0700

    use MultiFab's norm function because it's threaded

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 06bf62978759ea93b656fa60fc99ecb5ff33beee
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 19 16:21:47 2015 -0700

    test performance of mkdir and rename.

Tests/MKDir/GNUmakefile
Tests/MKDir/MKDir.cpp

commit 64c27475843946cc09e535174a195d23085e99c7
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 19 16:00:01 2015 -0700

    test for random grid copies.

Tutorials/MultiFabTests_C/GNUmakefile
Tutorials/MultiFabTests_C/GridMoveTest.cpp
Tutorials/MultiFabTests_C/Make.package
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp

commit e2505fa979eeb293b15b039a0996fdfb6a0cc65a
Merge: f4f152790 1150498b8
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 19 15:58:56 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 1150498b8ded461b593cd2e673a062344d1450ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 19 10:57:15 2015 -0700

    added -lmpichf90 to bluewaters.

Tools/C_mk/Make.mpi

commit 58a6b255dc1a873ec448c9902d927f86abe37e7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 19 12:17:03 2015 -0400

    more cleaning

Tools/RegressionTesting/testnew.py

commit 88268d4e4b006c34ec5d27d88cb1b961584312ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 19 10:27:24 2015 -0400

    return the compilatoin string in the build_f method

Tools/RegressionTesting/testnew.py

commit d1d21c076d9e5019fe66aad2e90277055f61705c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 18 22:09:45 2015 -0400

    some pyflakes fixes

Tools/RegressionTesting/testnew.py

commit c33217f3cfb4218574b662417a61ed337afd8dd6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 18 22:05:50 2015 -0400

    remove the hack we used to encode the extra build directory in the build directory
    list by instead storing a tuple in the list.

Tools/RegressionTesting/testnew.py

commit 8c7f84bf70d93bb5ca15be6e41e2d906f2b0e130
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 18 21:09:15 2015 -0400

    rename classes to be more PEP-8-y

Tools/RegressionTesting/testnew.py

commit 30876874f1808117f0897630b17d016ead83b11b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 18 21:06:53 2015 -0400

    add build_f() and make_realclean() methods to the suiteObj class.

Tools/RegressionTesting/testnew.py

commit fd2909ce267c095aa163c8041bc639ee8cfbe64d
Merge: f4a5d26fe edafbda56
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon May 18 14:52:55 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f4a5d26fe702f875ecf2d4ed20bb2e17f9fef0c1
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon May 18 14:52:02 2015 -0700

    print out # of MPI processes and # of threads, even with there is only 1 MPI proc (still useful info for OpenMP on one node)

Src/F_BaseLib/boxlib_f.f90

commit edafbda56ca07ab3bd2a500ea8aa02b5bf01a9b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 18 13:22:16 2015 -0700

    Heat equation: fixed bug

Tutorials/HeatEquation_EX4_F/main.f90
Tutorials/HeatEquation_EX5_F/main.f90

commit 435262d80a977cf299d60c036a48688695b19df2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 18 13:06:00 2015 -0700

    fixed heat equation ex5

Tutorials/HeatEquation_EX5_F/main.f90

commit 90390fca7fb8024f7de015957de304af9862d457
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 18 12:55:46 2015 -0700

    quiet valgrind

Src/F_BaseLib/vector_i.f90

commit 05622bf0e25303f0f2966dc452fca42d6ff38f21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 18 12:54:56 2015 -0700

    comment

Tutorials/HeatEquation_EX4_F/main.f90

commit 9fc9f7bf697cfb9e99160889fb36f758d7087c3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 18 12:32:00 2015 -0700

    Fill ghost cells if tagging needs ghost cells

Tutorials/HeatEquation_EX4_F/main.f90

commit c441bde6246e18df0f61caae7f93c3aec35863e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 18 12:30:23 2015 -0700

    fixed number of component. removed duplicated multifab_fill_boundary and physbc calls

Src/F_BaseLib/regrid.f90

commit ec6e11039f12c0c355f2e63033d8084656e9bff9
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon May 18 10:17:28 2015 -0700

    the 'tagging_needs_ghost_cells' option now has a call to multifab_fill_ghost_cells.  fixes some problems where tagging is done with a gradient, but valgrind still complaining so no promises yet...

Src/F_BaseLib/regrid.f90

commit f4f152790bf204b62e44103a44d71a7f07b4150f
Merge: d7d2ada16 595449168
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 14 13:51:57 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2536a2ac21d598a0104c63813abab4c2b2cece86
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon May 11 17:48:01 2015 -0700

    Add f90 file pattern to VPATH for f90 files in C_BaseLib.  Probably should be a better way to do this...

Tools/C_util/AmrDeriveTecplot/GNUmakefile

commit 595449168c5c595e83e89e91127636d735e38e9f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 8 15:03:10 2015 -0400

    switch from getopt to argparse -- this is self-documenting and cleaner.
    Also fix the make_benchmark stuff -- the switch to shutil requires me
    to remove an existing benchmark before copying in the updated one.

Tools/RegressionTesting/testnew.py

commit 31511481b2977a0db94430c1a1f57f3ca2de9b3b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 8 10:44:54 2015 -0400

    some more simplifications

Tools/RegressionTesting/testnew.py

commit e016090b7b7256e6b33c024228471cde51283177
Merge: cbd37a0a6 17987ed45
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 8 08:44:31 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit cbd37a0a6940ed50eb3e35367c14f6e171dad152
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 8 08:44:09 2015 -0400

    fix num_threads -> numthreads for pure OMP

Tools/RegressionTesting/testnew.py

commit 17987ed454a053739319019b85a60d1759b0b9d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 7 20:03:30 2015 -0400

    fix the hydrostatic_adjust case

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 309ffb56690707c6e0db9714c90a28c6c881ef72
Merge: 089b96741 e10ddf2c8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 7 14:12:13 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 089b96741898724c414a283eb3bdb3ecfbc08bb4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 7 14:11:39 2015 -0400

    sometimes we might encounter a plotfile with boxes that begin at
    negative indices -- this handles that now.

Src/F_BaseLib/bl_stream.f90

commit e10ddf2c8c271e76a68f11233011c54ecf1e87f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 7 12:50:10 2015 -0400

    we were constructing the actual form of the command to run (w/ or w/o MPI/OMP)
    in 4 separate places.  Consolodate that into a function

Tools/RegressionTesting/testnew.py

commit d7d2ada16256688520a5d40db16b418d00d7fb83
Merge: d1e7d25e1 53328b8b8
Author: vince <vebeckner@lbl.gov>
Date:   Wed May 6 17:33:17 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 53328b8b8281e2d33f4dc009ca9ef49fbbc2bc28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 6 09:32:54 2015 -0400

    update the sub_chandra build location

Tools/RegressionTesting/Maestro-tests.ini

commit d92a3a3707d27099622da00058cbe486d2db6b67
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 6 09:18:35 2015 -0400

    our check on whether the compilation was successful was not correct

Tools/RegressionTesting/testnew.py

commit 26f0d0fc268530b6e16e2d03af9eff46dfd67000
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 5 19:21:23 2015 -0400

    more simplification of the run commands

Tools/RegressionTesting/testnew.py

commit c098a66ac9c1b7bf6a26d6345fa7d4d61dc7a88c
Merge: ce5db33bd 115000cbf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 5 17:19:13 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit ce5db33bd43f5d8c4ddd7ed03493d658744ba0fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 5 17:18:53 2015 -0400

    remove redundant code

Tools/RegressionTesting/testnew.py

commit 115000cbf9bd76fa983c61d63e2384d25355854f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 5 13:11:41 2015 -0700

    OMP'd GetVolume and GetFaceArea

Src/C_BaseLib/COORDSYS_1D.F
Src/C_BaseLib/COORDSYS_2D.F
Src/C_BaseLib/COORDSYS_3D.F
Src/C_BaseLib/COORDSYS_F.H
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/Geometry.cpp

commit 8f501bbba5336540744e2e92309bd75d0a2fec85
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 5 15:04:12 2015 -0400

    fix typo

Tools/RegressionTesting/testnew.py

commit 9b57b0bb8290539313a7664cd25564f39c716020
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 5 14:59:00 2015 -0400

    some more cleaning / modernization

Tools/RegressionTesting/testnew.py

commit cdb61a0ebb09f987dd0bd213c063b34bd22199e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 5 14:13:42 2015 -0400

    some more modernization with list comprehensions

Tools/RegressionTesting/testnew.py

commit bccc00a68fe6de181d422443068e5922af3376e2
Merge: d403ac2f3 471529dfb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 4 20:43:20 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d403ac2f3da76244fae2c94d681f42b08ae51b1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 4 20:43:02 2015 -0400

    more systemCall -> run() replacement

Tools/RegressionTesting/testnew.py

commit 471529dfb2d2f3e854ec0f7d671f6808ecd8010d
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon May 4 17:33:52 2015 -0700

    Remove underflow protection code in LINCCINTERP.  Was using a hardwired number, and overwrote crse data.  Bad enough, but then appears to be totally unnecessary anyway.  Let me know if this breaks someones code.

Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F

commit 2557e17f7d3f1364a83f3fc392d781959f369bcb
Merge: b72267227 215f3bb35
Author: vince <vebeckner@lbl.gov>
Date:   Mon May 4 14:58:04 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b7226722728908e721007962d9f63435d4c808d7
Author: vince <vebeckner@lbl.gov>
Date:   Mon May 4 14:57:57 2015 -0700

    ensure intermediate flushed database is complete.

Src/C_BaseLib/BLProfiler.H
Src/C_BaseLib/BLProfiler.cpp

commit 098a42e815b24a87570d98031e94eff1e4dd2dce
Author: vince <vebeckner@lbl.gov>
Date:   Mon May 4 11:34:56 2015 -0700

    nostart option for var.

Src/C_BaseLib/BLProfiler.H
Src/C_BaseLib/BLProfiler.cpp

commit 215f3bb351b65058d6aa4d2b42c043b58cb6c0f7
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon May 4 08:05:47 2015 -0700

    f90 mpi on atragon

Tools/F_mk/GMakeMPI.mak

commit c1a0cc9903f2b93014e50cb6aa3bf857c9bb07ef
Author: vince <vebeckner@lbl.gov>
Date:   Fri May 1 15:05:34 2015 -0700

    removed buf size restriction in Concatenate.

Src/C_BaseLib/Utility.cpp

commit db2adae4696ef513181bf7f6bb763dbf198d59e3
Merge: 084e0bae8 f11a0b44c
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Fri May 1 15:35:09 2015 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 084e0bae8208bda0fe79601b92944a6c6c1554ed
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Fri May 1 15:34:54 2015 -0500

    Enable OpenACC for Cray compiling, remove obsolete target flag

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/Linux_cray.mak

commit f11a0b44c61473add43f280dc6a0b70705b8fd59
Merge: aab98d928 e7beb6e61
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 30 15:40:05 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit aab98d928a8a960f17c7f1f3e3a1ce8cfcc85597
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 30 15:39:47 2015 -0700

    mpi on orga

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit d1e7d25e1a87aec8227e85f8d5add71cbdb7ab3a
Merge: 57db8fc04 e7beb6e61
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 30 15:30:54 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e7beb6e611d182a8a3a80b335d5ec03fce999072
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 30 15:01:13 2015 -0700

    another Bcast interface, additions for serial.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 57db8fc04339c9e2109e03de5e09168f6e4576a4
Merge: 3dba3eb25 fe79c41e3
Author: vince <vebeckner@lbl.gov>
Date:   Tue Apr 28 16:51:14 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit fe79c41e3bc14c5e966bacb2f01f02e3747ab367
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 28 14:42:35 2015 -0700

    define BL_ALIGN_BYTE and BL_SIMD_LEN

Tools/C_mk/Make.defs

commit 9e042cd328388d5ed324cfd430f0b922f09e612e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 28 12:58:29 2015 -0400

    some more cleaning -- run() can now optionally output to a file

Tools/RegressionTesting/testnew.py

commit e861c07f60b63a4020d523ef9356ba37f6bce6d0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Apr 26 20:48:07 2015 -0400

    we no longer need to store stderr separately, since run now
    pipes stderr into stdout

Tools/RegressionTesting/testnew.py

commit a10d37b94673eed1aecd120499189cc78f5557ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Apr 26 20:46:01 2015 -0400

    switch all the git stuff to the run() function instead of doing
    their own subprocess stuff.

Tools/RegressionTesting/testnew.py

commit a89a72a1276c629baa91bd50fa51a83478a6dc6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 26 11:17:45 2015 -0700

    add BL_ALIGN_? to make for array alignment

Tools/C_mk/Make.defs

commit f609f9b903bfbcc3503fa283ce054c2d7ce766d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 24 23:07:21 2015 -0700

    support F90 that will be preprocessed

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules
Tools/C_scripts/moddep.pl

commit 92eeb8ce8000db3441957fc927df9eae8ea0b2fa
Merge: 8b92bf520 d18fb9a05
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 22 17:21:18 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8b92bf52024f20e961ad9006ad1c4665401a3660
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 22 17:21:09 2015 -0700

    nesting fix.

Src/C_BaseLib/BLProfiler.cpp

commit d18fb9a0596a42e47c31c74bcc8b065f0710ccc9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 22 16:42:16 2015 -0700

    removed -target=linux for hopper

Tools/C_mk/Make.Linux

commit 16c06a4541d7997430ad0614105115e557569289
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 22 16:40:04 2015 -0700

    added -lmpichf90 for edison and hopper.  may need to do this for some other machines too, especially ones with cray mpich.

Tools/C_mk/Make.mpi

commit a8c27e19846b6c812a4ce6a7b871d018e380d6a0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 21 19:21:02 2015 -0400

    some more clean-ups

Tools/RegressionTesting/testnew.py

commit ed67104f24b91d3a0d69a9dcfe8317dc617b1667
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 21 15:23:46 2015 -0700

    Fixed a problem on Windows.  I do not have access to any Windows machines.  But I believe the new overloaded functions in parallel module would not compile on Windows because c_long is the same as normal Fortran integer and the overloaded functions inside interface must have different kind.  This also means the lastest BoxLib would not compile in the unlikely case that the compiler does not support long integer.

Src/F_BaseLib/parallel.f90

commit c91b0127c63838ed0a60c453f5139be23c868993
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 21 12:31:47 2015 -0700

    Let codes tell BoxLib the boundary functions are thread-safe.  By default, BoxLib assumes that EXT_DIR is not thread safe, whereas other types are.

Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp

commit c9d7d4ad2020c9ff0a20abf357156122a3a8442c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 21 13:37:08 2015 -0400

    more clean-ups -- eliminate some functions/logic in favor of list comprehensions

Tools/RegressionTesting/testnew.py

commit 8e6a0c52680a9f8c5aa8ebcc750bbec0f942aabf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 21 12:46:05 2015 -0400

    some more cleaning -- especially to the restart execution string

Tools/RegressionTesting/testnew.py

commit e86b6c8e3457fc4ac8dc2423c1b862f7de5cc17d
Merge: edff26f6f af317ca82
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 21 12:05:52 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib
    
    Conflicts:
            Tools/RegressionTesting/testnew.py

commit edff26f6f2c55895efac96bcf866e96c67d59163
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 21 12:03:00 2015 -0400

    more clean-up -- now the run commands are greatly simplified (since aside from
    the MPI and OMP stuff, the command is the same in all cases).
    
    Also fix the single suite run output page (columns were mixed)

Tools/RegressionTesting/testnew.py

commit af317ca82fbfec9c8bdd668acce866e260266127
Merge: d95f67bed 348fa66ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 20 21:51:32 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d95f67bed6acdb20975eb13d89e56eb73bf3adb9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 20 21:50:04 2015 -0700

    Inflow boundary in IAMR and LMC is too complicated to be made thread safe.  So an OMP critical region is added for EXT_DIR.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp

commit 348fa66ad1c5a46a78f379f664193d8aa7aae83f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Apr 20 20:20:37 2015 -0400

    remove some os.system() calls with shutil -- this is safer

Tools/RegressionTesting/testnew.py

commit 77543ff2d9f631723888f5db1011d35b54f1fd17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 20 16:55:28 2015 -0700

    changes OMP approach in FillPatchIterator

Src/C_AMRLib/AmrLevel.cpp

commit 5a0598f43ee3766001361365a6b06e421636b683
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 19 20:36:32 2015 -0700

    tidy

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c

commit 46f24a16691733507a9f07317bc714003028de75
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 19 17:28:48 2015 -0700

    change user function in MPI_Op_create from fortran function to subroutine because it has no return value

Src/F_BaseLib/parallel.f90

commit 7dcf39b773ecc0b7b085d1ec36052b8d906c0872
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 19 15:45:05 2015 -0700

    create MPI_SUM, MIN and MAX for c_long in Fortran

Src/F_BaseLib/parallel.f90

commit d6a2579c8e23529c0f332217e07f3ba67ab404d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Apr 19 18:25:38 2015 -0400

    call MPI_Type_create_f90_integer with 'r', not '5' -- fixes typo

Src/F_BaseLib/parallel.f90

commit 1530aaf7ff4b5ce9e85389898276d05134847e68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 19 14:28:17 2015 -0700

    use (C) long integer for offset and size in fabio so that i can handle large files

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/particles_f.f90
Src/F_BaseLib/plotfile.f90

commit 3a9a99e2aaadf0ee23ab5482e148f978eef59863
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 19 14:24:16 2015 -0700

    typo in comment

Src/F_BaseLib/bl_types.f90

commit e45b9fdbe6ded9f3074205b4aef356a010f65735
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 19 14:23:47 2015 -0700

    add MPI support for (C) long integer in Fortran

Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit 3dba3eb253a343cb12ca8b630415a05a6ec4e5d6
Merge: 2f49ffb5d a10baeab5
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 16 15:21:38 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit a10baeab50a849611081f9bb6127d83bfe1dcbfe
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 16 11:07:17 2015 -0700

    fix a print statement

Src/F_BaseLib/fab.f90

commit ab03951c126f2439022f0b638b9af300e3f2258d
Merge: 70ba120d7 7cb6274cc
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 15 14:42:58 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 70ba120d7a7b630a74f34ce2bf8134c88e5f89b9
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 15 14:42:48 2015 -0700

    more support for amrprof.

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 2f49ffb5dd52bc93532c9fc95f091da40df36472
Merge: 3f7291f49 7cb6274cc
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 15 10:36:00 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 7cb6274cc87771e8d7478ef092841fd6bf259f6f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Apr 15 13:14:09 2015 -0400

    if the last plotfile output was plotfile 0, then we give a warning and don't do the
    comparison.  Also output the name of the file we used to compare to in the test output
    table.  Finally, some clean-ups.

Tools/RegressionTesting/testnew.py

commit c40d4c0cd3f68263eeb5b7d197f5674bee4afef5
Merge: bac731a1f 555b76896
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 14 18:55:31 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 555b768969963710ffbd123b27f7b6f21f5ba830
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 14 18:54:52 2015 -0400

    switch fboxinfo over to run()

Tools/RegressionTesting/testnew.py

commit bac731a1fe4e5dbd51a00de2834ae5bc37c1458e
Merge: b5a9bff4d 3d3f2221e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 14 14:10:48 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit b5a9bff4d0116641e929abe120c15dfa0cbb16fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 14 14:10:38 2015 -0400

    some more run()

Tools/RegressionTesting/testnew.py

commit 3d3f2221e5eb21dec855ae58388bc2b3c6375595
Merge: 8173ca8ca f544ca56c
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 9 15:52:13 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f544ca56c82aa88c9e282741c66b1a5ca13c1150
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 8 11:45:56 2015 -0700

    clean up Intel's optimization reports

Tools/C_mk/Make.rules

commit 29c8e84164cacb36ccc78646311023bb655fa1e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 8 09:31:39 2015 -0700

    For Intel on Edison, add vectorization report

Tools/C_mk/Make.defs

commit 53101cc8b546a10f75664f88be30c83cbd3571ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 7 12:37:35 2015 -0700

    save stdout and strerr of make in make.out

Tools/RegressionTesting/testnew.py

commit 8173ca8cacf3bd5bbe8ac63452058e60ab65cb61
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 6 14:01:08 2015 -0700

    some perfmon cleanup.

Src/C_BaseLib/ParallelDescriptor.cpp

commit e683857ffb1f214d5da0b608d48e275305a55546
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 6 13:21:11 2015 -0700

    some cleanup for perfmon.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 178844985c1b743c02a0094753e0677480590ed0
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 6 13:20:35 2015 -0700

    fix for serial.

Src/C_BaseLib/ParallelDescriptor.H

commit b9b8b1b311f44ea1ddd05853852a1c39cf04ee85
Merge: 4980a2e01 fa615023f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Apr 6 10:25:27 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 4980a2e0168b405010c87ed44632fe846c98cf3d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Apr 6 10:25:06 2015 -0400

    update xrb_mixed location and aprox13 test to use MICROPHYSICS_DIR

Tools/RegressionTesting/Maestro-tests.ini

commit fa615023f0f9e3d0df61d9d3b04eac2d1f10c885
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Apr 6 10:20:29 2015 -0400

    take another git hash directory to accomodate MICROPHYSICS_DIR

Tools/F_scripts/makebuildinfo.py

commit 2414f8c37cb2c6ab42da878650e9b799beed2f4e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Apr 5 20:57:50 2015 -0400

    turns out that when we specified an alternate location in the .ini file for
    a microphysics routine, like:
    
    addToCompileString = NETWORK_TOP_DIR='$ASTRODEV_DIR/networks' NETWORK_DIR=aprox13
    
    it was not using the ASTRODEV_DIR that was set via
    
    extSrcDir = /home/zingale/gfortran-testing/AstroDev/
    extSrcCompString = ASTRODEV_DIR
    
    but instead was using whatever the value was through the system.  This
    is because we were using os.system() and bash to do the make.  Now we instead
    switch all of the build stuff from os.system() to subprocess -- this is a lot
    more flexible.  As a result, we now have access to stdout, stderr, and the
    return value

Tools/RegressionTesting/testnew.py

commit 2e5bb828ac799d07af82e1d87ea60a0a7a984a74
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 4 21:50:31 2015 -0700

    Allow check_int and check_per coexist in inputs files (submitted by Max Katz)

Src/C_AMRLib/Amr.cpp

commit ad11d6f89d10fdfb8e23f4f2306576ea031a2b2c
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Apr 2 14:45:12 2015 -0700

    Uptick tagged version number

Tools/CMake/BoxLib_Version.cmake

commit a97cc244f5d701eb6a7c93138fffb2ab291e79e3
Merge: bb239a93d 2806f6b60
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Apr 2 14:41:34 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2c565299d21e18ce994c9d602f19356be1f2fb2d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 1 18:22:11 2015 -0700

    support for multiple perfmonproc processes.

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit d0d428c90d753daa38043f867c7d3932c792fcc3
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 1 18:18:45 2015 -0700

    support for multiple perfmonproc processes.

Src/C_BaseLib/BLProfiler.cpp

commit 2806f6b60ca7c6f5b39634ce4fdb6027500963d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 1 17:14:58 2015 -0700

    Warn rather than Abort when both plot_int and plot_per are set

Src/C_AMRLib/Amr.cpp

commit 7d5b856958807f0cce0f7984646c42d876739552
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 1 17:11:03 2015 -0700

    fixed a couple of things so that we can compile with PRECISION=FLOAT

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit e87bd00807309b6ee428be13287eecfd50679331
Author: Regression Tester account <regtester@battra.lbl.gov>
Date:   Fri Mar 27 12:26:32 2015 -0700

    update make file for battra again

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit ecb7d270be4b91df93919ddf886beffc96b53877
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Thu Mar 26 11:05:25 2015 -0700

    updated makefile for battra

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit c0d485fa28da258eaccd488face342593214d4a0
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 25 11:48:43 2015 -0700

    added more profiling.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp

commit 9067de54d40cc29bd559cb38493fe8bf60a69b9c
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 25 11:47:52 2015 -0700

    checks for zero size arrays, percent for cov.

Src/C_BaseLib/BLProfiler.cpp

commit 79ae9d79cee62c9b404a30cbbdbccd4d0fb82aa0
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 19 12:49:12 2015 -0700

    added coefficient of variation.

Src/C_BaseLib/BLProfiler.cpp

commit 3f7291f493dc7eea75dbfd7f4f085f86cc19b201
Merge: ffcd18897 685bdfdcb
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 18 15:33:11 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 685bdfdcba169be3b1ea64d8fb42c306e9a9f2e1
Merge: f8b699ae1 41fe36541
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 18 15:31:19 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f8b699ae1f2f34c2e4435c0df9b2443f6df42481
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 18 15:30:56 2015 -0700

    showpoint to avoid 0 parse.

Src/C_BaseLib/BLProfiler.cpp

commit 41fe365414ca73770fe7272c84994779b6dc114b
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon Mar 16 14:39:05 2015 -0500

    Update rules for Blue Waters compiling

Tools/F_mk/GMakeMPI.mak

commit 9fc7d040e738e516b5e829c4fdd519f86c6585d5
Merge: d7c93f4a1 c4b21a7f0
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon Mar 16 13:04:53 2015 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 42d448e3b11c2def1e21fc534b5c0ec54074fa6f
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 12 17:43:27 2015 -0700

    makefile update.

Tests/IOBenchmark/GNUmakefile

commit c4b21a7f00b37627b638db122a012ef271e8ec42
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 17:20:20 2015 -0700

    better name for turning on c++11 support

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit e0d2e54956000d8d088b0aa00eba6790b8b869f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 17:16:35 2015 -0700

    make c flags immediate so that we can later add c++ only flags

Tools/C_mk/Make.defs

commit 27e5fc004071d964bbd18b7b969f115de10597f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 17:14:52 2015 -0700

    increased buffer size for backtracing

Src/C_BaseLib/BLBackTrace.cpp

commit 39f4752e70f4dff7b093842a995cd4e987ccaf44
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Mar 10 15:27:09 2015 -0400

    add a comment based on a question from a student

Tutorials/WaveEquation_F/advance.f90

commit bb239a93d100ae8b116f347939d01a535b8cbf8f
Merge: b40b7e086 6c4cec0da
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Mar 9 17:41:12 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d80767ebb62ca6c595f8186c33b04f6602a7aa67
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 6 17:35:41 2015 -0800

    extra send interface with comm.

Src/C_BaseLib/ParallelDescriptor.H

commit 6c4cec0da4d2bc5ccdc48af65f3bae4436eb9fb7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 5 22:13:30 2015 -0800

    use range based for in Lazy

Src/C_BaseLib/Lazy.cpp

commit f5e41ea6ef1cb724e2c1f1c6b76b0a14be88a04a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 5 14:18:56 2015 -0800

    added laziness in a number of places where messages are printed when verbosity is on;  added optional argument to a number of functions to allow for local reduction

Src/C_AMRLib/AuxBoundaryData.cpp
Src/C_AMRLib/Particles.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/iMultiFab.H
Src/C_BaseLib/iMultiFab.cpp

commit b40b7e086fed9bb64d83d8cacf4c4bea674a0a5b
Merge: 5dce185f6 2993fd2f8
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Mar 5 14:17:01 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2993fd2f8601d75b3f06de1317e5e9add4c221f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 5 13:55:28 2015 -0800

    fixed a typo that made the high water mark of FAB wrong

Src/C_BaseLib/BaseFab.H

commit 27a2cf1f359ef53c73c705c4cbbc30b2f9a39ccc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 21:24:50 2015 -0800

    added parameter amr.message_int to control how often to check messages touched by user

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 43277faec5a05c97ca830c6ec94990ed186ec607
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 17:30:20 2015 -0800

    optional argument for contains_nan and contains_inf to control reduction

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit a4d97fc7b38eeed7b16e9804c4d9ce98bb2f0b77
Merge: cbb5871d5 38364677e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 17:20:06 2015 -0800

    Merge branch 'lazy'

commit cbb5871d5d7351e266b4fc9602cc54ebe7f7141a
Merge: a062b389e d69a6e3e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 17:16:22 2015 -0800

    Merge branch 'lazy'

commit 38364677e3bc63529e56756282005971e521b530
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 13:58:54 2015 -0800

    fixed it for Intel

Src/C_BaseLib/Lazy.H

commit d69a6e3e680f52594490f36eeeaec4b58ef69ab4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 13:55:23 2015 -0800

    forgot to add new files

Src/C_AMRLib/Make.package
Src/C_BaseLib/Lazy.H
Src/C_BaseLib/Lazy.cpp
Src/C_BaseLib/Make.package

commit 8da3dfcafc4369ef82d89dce7d6573364f5681af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 13:42:40 2015 -0800

    implemented prototype lazy evaluation that can delay MPI bulk synchronization till it hits a necessary bulk synchronization

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Make.package
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Tools/C_mk/Make.defs

commit 5dce185f60d1e95d8f014a423d5c1f29eb88d111
Merge: 12aa2b080 a062b389e
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Mar 4 13:15:52 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d7c93f4a1409ce116409ed2c8fe8d9bc07328105
Merge: b5d48ea6a a062b389e
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Mar 4 10:53:34 2015 -0600

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit a062b389e1fe6ff229a0c20332c34ec7062a8e65
Merge: 70e236e7e 6028ca963
Author: vince <vebeckner@lbl.gov>
Date:   Tue Mar 3 12:46:16 2015 -0800

    commit merge.
    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 70e236e7e69434ef630168ef65e577f13a4448a5
Author: vince <vebeckner@lbl.gov>
Date:   Tue Mar 3 12:46:06 2015 -0800

    update the profiling doc.

Docs/Readme.profiling

commit 6028ca963b5f0cd15fe113401ddc8e21946a5b94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Mar 3 09:39:02 2015 -0500

    update some problem locations

Tools/RegressionTesting/Maestro-tests.ini

commit 12aa2b080e89d414ab3615e6065077aa7e025231
Merge: e4a52bc5a a827762bc
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Mar 2 16:43:13 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e4a52bc5a7c7ae64a473e6aa05bf13ffcac001b2
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Mar 2 16:42:53 2015 -0800

    For gfortran and g95, prefer  -ffixed-line-length-0  over -ffixed-line-length-132 to avoid padding of character strings to col 132 when the string is split across continued lines.

Tools/C_mk/Make.defs

commit a827762bcc00798b2315cf103dcec9743d12190d
Merge: 195cd03d9 55db75df7
Author: vince <vebeckner@lbl.gov>
Date:   Mon Mar 2 11:59:47 2015 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 55db75df71d2e286ec4a34a18dcd17355c2ab38b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Sat Feb 28 05:56:22 2015 -0800

    mpi on gamera

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit ffcd188979033b783e3675efce10d08ad6b9b41b
Merge: e464d797f 195cd03d9
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 27 15:33:46 2015 -0800

    rename dir test.
    Merge branch 'master' of naphta.lbl.gov:Development/BoxLib

commit 195cd03d9cd1b119098c88efb2f6686db7d8fe87
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 27 15:33:32 2015 -0800

    rename directory function.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 94e390213aabf926660219054556dd0c9b980f53
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Feb 27 12:53:41 2015 -0800

    Propagate change to use BLMap in linop stuff

Src/LinearSolvers/C_CellMG4/ABec2.cpp
Src/LinearSolvers/C_CellMG4/ABec4.cpp

commit 6feb196f94173f8648d89df379b1b1dd4a2a585e
Merge: 800a7be06 1fc9480e4
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Feb 27 12:49:51 2015 -0800

    Merge master

commit 1fc9480e47713447747b7f037090eb82dddb67d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 26 14:25:36 2015 -0800

    minor change to slient compiler warning

Src/C_AMRLib/Particles.H

commit 4eeb0d3d59175ba3b603f3c599495111fbaa0460
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Feb 25 16:13:53 2015 -0800

    mpi on battra

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit a76e7d73f9b4a36061d6adc1cc1537ea3bd92340
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 24 09:23:07 2015 -0500

    a little more cleaning

Tools/RegressionTesting/testnew.py

commit 006e9588ba75ba1bc1699a24ba6ea4630c293b4a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Feb 23 14:16:57 2015 -0500

    more clean-up, remove some redundant/unused modules are reported by
    pyflakes

Tools/RegressionTesting/testnew.py

commit 3077d4849a124b8cee9cb38985491be0ce6c9c48
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Feb 23 12:52:19 2015 -0500

    some more cleaning and PEP-8ing

Tools/RegressionTesting/testnew.py

commit fca030bfa67df3851140c58ad9c619679fa47092
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Feb 23 11:09:48 2015 -0500

    a little bit of clean-up -- use setattr to set a lot of the suite-wide
    parameters instead of needing a separate elif for each.  Still need to
    do this for the test stuff.
    
    Also add a purge_output option to delete all but the comparison plotfile
    from the output directory.
    
    Finally do a little PEP-8 cleaning.

Tools/RegressionTesting/testnew.py

commit 350097cf6200929664b967909aa2124bfb6b496b
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Feb 20 10:51:21 2015 -0800

    gimantis MPI for f90 boxlib

Tools/F_mk/GMakeMPI.mak

commit 31944457c5be8fe3b9bbde4066d627fcfd88b9a3
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 20 10:36:20 2015 -0800

    changes for gimantis.

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 5af5997551d8317b47affa47ade08b689f69f132
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 18 10:14:15 2015 -0500

    add some latex ignores

.gitignore

commit b5e39d9cb68972fe9f1feea80e4402ed56ce6a0d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 18 10:08:49 2015 -0500

    remove stray }

Tools/C_scripts/makebuildinfo_C.py

commit f0f89067ac86a37e4946b7e23e0c0814c2af775e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 18 10:06:20 2015 -0500

    update header with new functions

Tools/C_scripts/buildInfo.H

commit 0b572423fc982f9ad59af26c1db9127a7b5aaa01
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 18 09:58:19 2015 -0500

    add a build_git_name and build_git_dir for problems that are built in
    special places...

Tools/C_scripts/makebuildinfo_C.py

commit f3e2ce5a4e5f6597b879acbac1533d7b0916e857
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 17 18:50:23 2015 -0500

    if we set the extra directory (ASTRODEV_DIR for MAESTRO) and the directory
    doesn't actually exist, then handle this gracefully and still make
    a build_info.f90.

Tools/F_scripts/makebuildinfo.py

commit 536be1ec5c2717ab92f44b4aefde76d5b4ff88aa
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Feb 17 15:08:27 2015 -0800

    gigan MPI

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit c8a85f7b7b572d0a091f59e86af49ee3e336d1da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Feb 15 11:05:11 2015 -0500

    update to reflect new locations of test2 -> reacting_bubble and
    hydrostatic_adjust.  Also fix the analysis hooks for the Sod_stellar
    stuff by passing sourceDir as the argument now.  Finally, make sure
    that we run hydrostatic_adjust with the right network (we were doing
    it wrong all this time...)

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 498ef39e57f5578383378d25442fe4da696102b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 11 15:13:11 2015 -0500

    update to reflect fcompare.f90 now lives in BoxLib.

Docs/GNUmakefile
Docs/Regression/test_suite.tex

commit 0bff6352bbcc09c907cf79462b5b1510025c758f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 11 15:10:58 2015 -0500

    we no longer need to specify the compareToolDir, since it lives in BoxLib/ now

Tools/RegressionTesting/Castro-SBU-tests.ini
Tools/RegressionTesting/testnew.py

commit 72bc645f9533a15407473485af4d56714c4d5534
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 11 15:04:17 2015 -0500

    make BOXLIB_HOME relative

Tools/Postprocessing/F_Src/GNUmakefile

commit dbd9cad003ae51e7da490c32f24f40b76691bffc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 11 14:50:39 2015 -0500

    move these from AmrPostprocessing

Tools/Postprocessing/F_Src/CASTRO_radiation/GNUmakefile
Tools/Postprocessing/F_Src/CASTRO_radiation/fgaussianpulse.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/flgt_frnt1d.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/fradshock.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/fradsource.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/fradsphere.f90
Tools/Postprocessing/F_Src/CASTRO_radiation/frhdshocktube.f90
Tools/Postprocessing/F_Src/GNUmakefile
Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/GNUmakefile
Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra.f90
Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90
Tools/Postprocessing/F_Src/MAESTRO_tests/GNUmakefile
Tools/Postprocessing/F_Src/MAESTRO_tests/fgaussianpulse.f90
Tools/Postprocessing/F_Src/MAESTRO_tests/fmlcompare.f90
Tools/Postprocessing/F_Src/MAESTRO_tests/fmlconverge.f90
Tools/Postprocessing/F_Src/MAESTRO_tests/fnorm.f90
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/GNUmakefile
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/feint.f90
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo.f90
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo_driver.py
Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fwdconvect.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/GNUmakefile
Tools/Postprocessing/F_Src/MAESTRO_xrb/fad_excess.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/fbuoyancy.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/fconv_slopes.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/frates.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/fspec_total_mass.f90
Tools/Postprocessing/F_Src/MAESTRO_xrb/fspeciesmass.f90
Tools/Postprocessing/F_Src/Palette
Tools/Postprocessing/F_Src/faverage.f90
Tools/Postprocessing/F_Src/fboxinfo.f90
Tools/Postprocessing/F_Src/fcompare.f90
Tools/Postprocessing/F_Src/fextract.f90
Tools/Postprocessing/F_Src/fextrema.f90
Tools/Postprocessing/F_Src/ffdcompare.f90
Tools/Postprocessing/F_Src/fsnapshot2d.f90
Tools/Postprocessing/F_Src/fsnapshot3d.f90
Tools/Postprocessing/F_Src/ftime.f90
Tools/Postprocessing/F_Src/fvarnames.f90
Tools/Postprocessing/F_Src/old_flame/GNUmakefile
Tools/Postprocessing/F_Src/old_flame/fbubble_position.f90
Tools/Postprocessing/F_Src/old_flame/fbubble_position_3d.f90
Tools/Postprocessing/F_Src/old_flame/fcusp.f90
Tools/Postprocessing/F_Src/old_flame/fcylflame.f90
Tools/Postprocessing/F_Src/old_flame/fflamelength.f90
Tools/Postprocessing/F_Src/old_flame/finteg.f90
Tools/Postprocessing/F_Src/old_flame/fturbkin.f90
Tools/Postprocessing/F_Src/old_flame/fwidth.f90
Tools/Postprocessing/F_Src/python/README
Tools/Postprocessing/F_Src/python/column_depth.py
Tools/Postprocessing/F_Src/python/conv_slopes.py
Tools/Postprocessing/F_Src/python/dumpparthistory.py
Tools/Postprocessing/F_Src/python/eos_data.txt
Tools/Postprocessing/F_Src/python/helmeos.py
Tools/Postprocessing/F_Src/python/parseparticles.py
Tools/Postprocessing/F_Src/python/test_helmeos.py
Tools/Postprocessing/F_Src/python/test_parseparticles.py
Tools/Postprocessing/F_Src/python/timestamp_00.REMOVED.git-id
Tools/Postprocessing/F_Src/python/timestamp_02.REMOVED.git-id
Tools/Postprocessing/F_Src/tutorial/GNUmakefile
Tools/Postprocessing/F_Src/tutorial/fspeciesmass2d.f90
Tools/Postprocessing/F_Src/tutorial/fwrite2d.f90

commit 48f9f90d367aa63ff5e277546dbc6128232b9464
Merge: 8d5d28bc1 30e224f5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 11 14:49:31 2015 -0500

    Merge branch 'master' of /home/zingale/temp/AmrPostprocessing

commit 30e224f5b9923ce6b6b68ba6cf483f8e1434290e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 11 14:47:12 2015 -0500

    moving

F_Src/CASTRO_radiation/GNUmakefile
F_Src/CASTRO_radiation/fgaussianpulse.f90
F_Src/CASTRO_radiation/flgt_frnt1d.f90
F_Src/CASTRO_radiation/fradshock.f90
F_Src/CASTRO_radiation/fradsource.f90
F_Src/CASTRO_radiation/fradsphere.f90
F_Src/CASTRO_radiation/frhdshocktube.f90
F_Src/GNUmakefile
F_Src/MAESTRO_sub_chandra/GNUmakefile
F_Src/MAESTRO_sub_chandra/fsubchandra.f90
F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90
F_Src/MAESTRO_tests/GNUmakefile
F_Src/MAESTRO_tests/fgaussianpulse.f90
F_Src/MAESTRO_tests/fmlcompare.f90
F_Src/MAESTRO_tests/fmlconverge.f90
F_Src/MAESTRO_tests/fnorm.f90
F_Src/MAESTRO_wdconvect/GNUmakefile
F_Src/MAESTRO_wdconvect/feint.f90
F_Src/MAESTRO_wdconvect/fthermo.f90
F_Src/MAESTRO_wdconvect/fthermo_driver.py
F_Src/MAESTRO_wdconvect/fwdconvect.f90
F_Src/MAESTRO_xrb/GNUmakefile
F_Src/MAESTRO_xrb/fad_excess.f90
F_Src/MAESTRO_xrb/fbuoyancy.f90
F_Src/MAESTRO_xrb/fconv_slopes.f90
F_Src/MAESTRO_xrb/frates.f90
F_Src/MAESTRO_xrb/fspec_total_mass.f90
F_Src/MAESTRO_xrb/fspeciesmass.f90
F_Src/Palette
F_Src/faverage.f90
F_Src/fboxinfo.f90
F_Src/fcompare.f90
F_Src/fextract.f90
F_Src/fextrema.f90
F_Src/ffdcompare.f90
F_Src/fsnapshot2d.f90
F_Src/fsnapshot3d.f90
F_Src/ftime.f90
F_Src/fvarnames.f90
F_Src/old_flame/GNUmakefile
F_Src/old_flame/fbubble_position.f90
F_Src/old_flame/fbubble_position_3d.f90
F_Src/old_flame/fcusp.f90
F_Src/old_flame/fcylflame.f90
F_Src/old_flame/fflamelength.f90
F_Src/old_flame/finteg.f90
F_Src/old_flame/fturbkin.f90
F_Src/old_flame/fwidth.f90
F_Src/python/README
F_Src/python/column_depth.py
F_Src/python/conv_slopes.py
F_Src/python/dumpparthistory.py
F_Src/python/eos_data.txt
F_Src/python/helmeos.py
F_Src/python/parseparticles.py
F_Src/python/test_helmeos.py
F_Src/python/test_parseparticles.py
F_Src/python/timestamp_00.REMOVED.git-id
F_Src/python/timestamp_02.REMOVED.git-id
F_Src/tutorial/GNUmakefile
F_Src/tutorial/fspeciesmass2d.f90
F_Src/tutorial/fwrite2d.f90

commit 8d5d28bc16445f9c0cc2557b86310bf3ff9b5f7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 11 14:38:52 2015 -0500

    update to reflect mainline Sod_stellar

Tools/RegressionTesting/Castro-SBU-tests.ini

commit e464d797f5706141c35da2438a00ccda5491d7cf
Merge: 90116106a f97a0ae57
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 10 19:43:12 2015 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 90116106a5ce7a4756c04f1cace30f0767ed4e8d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 10 19:42:49 2015 -0500

    test.py is the old version -- should not be used anymore

Tools/RegressionTesting/test.py

commit f97a0ae5702c1abf4780071635aac9ad8dc5f306
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 10 14:08:48 2015 -0500

    update for helmeos stuff

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 7cb72cacc218098dffe2934febc93fd7b0e6cf7d
Merge: 90d6d44c6 dfbf164d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 10 14:01:23 2015 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 90d6d44c64e33df87921e244f835c5b994a4b7f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 10 14:01:01 2015 -0500

    update docs on test suite to reflect removal of helmeos stuff

Docs/Regression/test_suite.tex

commit dfbf164d47fa8da8b009a3f91df3901c9380f7d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 10 13:59:35 2015 -0500

    remove special treatment for helm_table.dat -- now we should specify
    it as a link?File parameter to a problem

Tools/RegressionTesting/Maestro-tests.ini
Tools/RegressionTesting/testnew.py

commit 9447670f1bbfa12c361bc5bd7e6d008be827582a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 10 13:21:54 2015 -0500

    move the regression test suite info from Maestro Docs to here,
    and update it.

Docs/Regression/test_suite.tex
Docs/Regression/testsuite.eps
Docs/UsersGuide.tex

commit e16258f9b6ab9e1fdb1733ee60c22981a156be79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 23:31:37 2015 -0800

    clean up BACKTRACE and update Reame

Docs/Readme.backtrace
Src/C_BaseLib/BLBackTrace.H
Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.cpp
Tools/C_mk/Make.defs

commit aa8d5b2a8c60a52180985fbe924ac992a40a079a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 14:20:46 2015 -0800

    fixed typo

Docs/Readme.backtrace

commit c1f6360a7b362b51532365da118199dc7d4cd4c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 13:59:12 2015 -0800

    updated Reame.backtrace

Docs/Readme.backtrace

commit 9a53025754ce5fc7ed3c0be06e480ae95763c9d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 13:48:55 2015 -0800

    updated Readme.backtrace

Docs/Readme.backtrace

commit e85c006c8a0e983c101f0359fac64ae327b69c39
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 13:24:22 2015 -0800

    better support of threads in BLBackTrace

Src/C_BaseLib/BLBackTrace.H
Src/C_BaseLib/BLBackTrace.cpp

commit 5652d3501ae54914cc4b23c7a1955806dce23f72
Merge: cc73dfc06 a8c89543b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 13:22:25 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit a8c89543b4d236ce008a5cc6020f4307196add22
Author: Anuj Chaudhri <chaudhri@lbl.gov>
Date:   Fri Feb 6 10:33:19 2015 -0800

    Rodan MPI

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit cc73dfc06439563a5ad2036b8c0b834fc201d4cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 10:32:19 2015 -0800

    moved -rdynamic flag to LDFLAGS

Tools/C_mk/Make.defs

commit 7b94bbf5550ca83bc3b4105c2bbba92975af6ff2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 09:48:51 2015 -0800

    fixed multithreading in BLBackTrace

Src/C_BaseLib/BLBackTrace.cpp

commit a3db40bfe542e53c4bd174b0d4deb52429f16e4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 5 21:09:14 2015 -0800

    Implemented backtrace capability in case of segfault.  See Docs/Readme.backtrace for details.

Docs/Readme.backtrace
Src/C_BaseLib/BLBackTrace.H
Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package
Tools/C_mk/Make.defs

commit 74311dc6e80d80be6b4bd2665eeda0aecbe584fd
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Feb 5 13:21:25 2015 -0800

    mothra MPI

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 2f88232f9cbc96f9192bde66f163dd9e7de9b42b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Feb 2 16:12:15 2015 -0500

    in debug mode, switch from a nan to an snan (signaling NaN).  This can
    be caught at runtime and help us find places we are using uninitialized
    variables.  This should be good for gfortran >= 4.5.

Tools/F_mk/comps/gfortran.mak

commit acc5289235a6946e55979cee1cac899c27463fca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 2 10:51:33 2015 -0800

    Added Amr::DataLogName to return the file names.
    
    Changed datalog from ofstream to fstream per Max's request.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit abbd4490e84689585b8b9d203cab53b6bad72261
Merge: 69e109c2e 34627e982
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 30 16:42:49 2015 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 69e109c2e70ed0b84963f7e489e254ad0e54d116
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 30 16:42:42 2015 -0800

    added a version of ParticleBase::NexID that does not contain omp critical

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 34627e982a0ea3afc5a0856071fd267c6818f1be
Merge: 6e901d7e6 6d73495b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jan 30 10:12:38 2015 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 6e901d7e63b92757f040c20eeb46c7bdbfc86f5d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jan 30 10:12:20 2015 -0500

    switch titan over to using whichlinux

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 6d73495b25a4d4655968eb0c3dd4d73bd6e954f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 29 17:06:00 2015 -0800

    removed some omp critical

Src/C_BaseLib/MultiFab.cpp

commit 2c778298f4550b4ac86399059a4c10dbc1461e73
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 29 15:38:38 2015 -0800

    defs for new os.

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 48910b75706c37723d104dc9dbc6a91b3e742f35
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 29 12:33:44 2015 -0800

    update atragon mpi library directories
    
    lijewski no longer exists

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 505ee88c7ab52e7a8fce05bf7759617966175330
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 29 10:56:38 2015 -0800

    update makefile per Andy's suggestion after os upgrade

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 81001b61e24e116545943622fbc722376e9c929d
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jan 28 15:49:16 2015 -0800

    Modify make config per Andy suggestion

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 8b02edb0da776c40cd9ee15ffbc76598ca4f659c
Merge: d72171122 75974a2f6
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed Jan 28 13:53:17 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d721711229211fa3771a5be90c2bdf1bb792fb73
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed Jan 28 13:52:43 2015 -0800

    PyBoxLib: Fix fboxlib build and fix memory error.

Src/Python/F90/Makefile
Src/Python/F90/src/fboxlib.f90

commit 75974a2f6797c488c4596c1fdfe7e7d4a83fc6e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 28 12:45:41 2015 -0800

    fixed assertion

Src/F_BaseLib/multifab_f.f90

commit ed4150f4c27942da93250eae89d164d029ab4ea8
Merge: 4451852a3 1a9df61e2
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed Jan 28 12:33:40 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 1a9df61e2f3b62e035e63d957c3d4d030fef411d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 27 22:13:31 2015 -0800

    fixed a bug in my last commit

Src/C_BaseLib/FabArray.cpp

commit d8d206559b4739e2201ef87a3f7886444ae8eb20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 27 15:00:03 2015 -0800

    minor cleanup

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Utility.cpp

commit 2c03e67829b7ad923916c6383a97b726ef70b2b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 26 10:35:41 2015 -0800

    set the type of nodaltilebox correctly to satisfy assertions

Src/C_BaseLib/FabArray.cpp

commit cd6b5802b5ac0f862b1cfc18166579dc668fe334
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 24 21:00:58 2015 -0800

    added an optional argument, chunksize, to MFIter that can be used to fine tune work sharing

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit f35c4b8feec4d1ce1b5a5816c37d28ddcc86ca68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 23 10:47:15 2015 -0800

    converted to tiling in two places

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 960b4695a64c05c65915ece619b29656117e3998
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 23 10:09:26 2015 -0800

    removed an extra endif

Tools/C_mk/Make.mpi

commit 78285d85c42c8ed087e5844024126c8238339057
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 23 10:04:43 2015 -0800

    take a shortcut in make_particle_dmap

Src/C_AMRLib/AmrLevel.cpp

commit 4a6f57b190addb0df22105ef0254dec912e9eb1d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 23 09:48:21 2015 -0800

    Make the manda options identical to the megalon options.

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 7fefe724ae57fe86a39ce7bea95acc751ccbfa75
Merge: 6ab3afa08 ec813843e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 21 13:54:09 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 6ab3afa08e6ded07966ca8b25a6a0baa610b0a6f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 21 13:52:31 2015 -0800

    fixed a bug in Particle and optimization for non-periodic case

Src/C_AMRLib/Particles.cpp

commit ec813843e5fdc51cacb7a659e62becb13c3fb571
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 20 17:43:50 2015 -0800

    point ebirah to correct MPI installation after upgrade to Ubuntu 14.04

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 7e6f568b44b174bf9189d2b686a142f69023b141
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 20 17:11:19 2015 -0800

    nodalbox -->> nodaltilebox

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp

commit 9e9f856918047c3007cbb28c2a7430b917af76ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 19 16:36:07 2015 -0800

    backtrace when BL_ASSERT fails

Src/C_BaseLib/BoxLib.cpp
Tools/C_mk/Make.defs

commit 635a125f9635936b974cab5e7ea8d61e4b4d4ca4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 18 11:57:07 2015 -0800

    merged RRKS into KnapSack

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 5ddedfd9a3fcfb1de7c9c4a7c0224d69efe41c15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 15 17:06:30 2015 -0800

    print put the number of particles too

Src/C_AMRLib/Particles.H

commit fa4238ad89f46458fe881ea504fc37842fdcb606
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 15 16:36:19 2015 -0800

    fixed a typo

Src/C_BaseLib/DistributionMapping.cpp

commit bac2a1c764f2c022358e33956517f42dde40b415
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 15 16:30:03 2015 -0800

    A new distribution mapping strategy called RRKS, which combines
    RoundRobin with KnapSack.  It's not as greedy as KnapSack.  It tries
    to keep the number of boxes balanced while considering box weights.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit ebef6242f9017c4e15a6f6a57e2d1c71515a815a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 15 13:41:41 2015 -0800

    fixed a bug in regression test script

Tools/RegressionTesting/testnew.py

commit 85deb13a02f207b6dcc3f3edcc6fbb07bb477a19
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 15 12:57:37 2015 -0800

    regression test: link file can be a directory

Tools/RegressionTesting/testnew.py

commit 71250f05d848cf468c56bcb883b16a24de57300a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 14 20:52:16 2015 -0800

    single quote to double

Src/C_AMRLib/Particles.H

commit 10178750df02a7bae02e9cc2779a860ddabbbecc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 14 20:50:10 2015 -0800

    new function that put distribution map in cache

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit e9c66745d45e71efd971f4032d9ea0d6de34f1a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 14 20:49:41 2015 -0800

    added extra \n

Src/C_AMRLib/Particles.H

commit 1fd56f32e03ecdf49f0ec688e566be840955e3e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 14 20:11:17 2015 -0800

    added new Amrlevel constructor and StateData::define that take distribution map

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit cf72682b38b5a6e6302836466fdfcf6697927971
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jan 14 22:18:15 2015 -0500

    when writing the auxFiles to the webpage, remove the root.  Also some
    neighboring pep-8 fixes

Tools/RegressionTesting/testnew.py

commit 8c81c46a5db005d1de2dfb88eeaff9a15c1666a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 14 09:59:55 2015 -0800

    fixed typo

Src/C_AMRLib/MLSDCAmrEncap.cpp

commit 1964b55af20a47f95721fa682d1c88d3c78e5489
Merge: 92355251b cc6aa0b41
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jan 13 15:01:07 2015 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit cc6aa0b414090684a1df071cb54d3b083c89df86
Merge: f995f51f0 7070f543c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 13 14:57:19 2015 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f995f51f0ff58fc71549c22c538eba6a8330a56c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 13 14:57:11 2015 -0800

    more openmp

Src/C_AMRLib/TagBox.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 7070f543ce0b7d5fc94bd9005c6f20897b8cddd6
Merge: ebca90c77 5d1f0e1ea
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 13 13:23:10 2015 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ebca90c77240c06f53540b9b57c1ecef2c6161dd
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 13 13:22:30 2015 -0800

    point to mpich on megalon... I can compile but get n instances of the program running

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 5d1f0e1eae8f2715efea2a550c5943388b30204c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 13 13:04:11 2015 -0800

    fixed typo

Src/C_BaseLib/iMultiFab.cpp

commit 278a203ab6688c51c2cccd20c6e6de2bc62316fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 13 13:01:40 2015 -0800

    added OMP to iMultiFab::min, max, and norm

Src/C_BaseLib/iMultiFab.cpp

commit 0d63263c4055b5c70f7a06625453c39f96a496de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 13 12:48:19 2015 -0800

    fixed new bugs

Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/iMultiFab.cpp

commit cb3c0a11d0b2a9d7d466e4caec54163bf75bc7f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 13 12:41:54 2015 -0800

    fixed a new bug

Src/C_BaseLib/MultiFab.cpp

commit 90b5127129e180776eaba6ddaeb4046d69b8d33a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 13 11:25:28 2015 -0800

    added OMP to MultiFab norm, min, and max....

Src/C_AMRLib/MLSDCAmrEncap.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/SPECIALIZE_1D.F
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F

commit 34d53e23441d40f48e92afa9020d7a21801f6252
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 12 15:28:01 2015 -0800

    removed an unstarted BL Profiler

Src/LinearSolvers/F_MG/ml_cc.f90

commit 92355251b8a85d5a2aa7b2c2da874933059a192d
Merge: 238cd9054 4c50a257c
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jan 12 14:50:09 2015 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 238cd90541bccfb8ee5d3f7a2e458228f0aaae43
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jan 12 14:49:48 2015 -0800

    test code.

Tests/C_BaseLib/TPROFILER.F
Tests/C_BaseLib/tProfiler.cpp

commit b822ef019ffacdf6a11bccce6b3d11a60f8b7b04
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jan 12 14:49:01 2015 -0800

    trace optimizations, flushing

Src/C_BaseLib/BLProfiler.H
Src/C_BaseLib/BLProfiler.cpp

commit 9d5e8cb53316cffcb84b10fe299fb1f43eaf4b1d
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jan 12 14:45:42 2015 -0800

    added FAB_NATIVE_32 format for faster conversions.

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FPC.H
Src/C_BaseLib/FPC.cpp
Src/C_BaseLib/FabConv.cpp

commit 4c50a257c55c102ecf0b8353e25a3943ade80ec3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 12 14:42:30 2015 -0800

    fixed an unmatched profiler

Src/LinearSolvers/F_MG/ml_cc.f90

commit bd1477e967ad0e448c7b54fea8de3815a61fd24d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 12 14:34:25 2015 -0800

    make BL Profilers in F90 codes work again for C++ codes

Src/F_BaseLib/BLProfiler_f90.f90
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/bl_prof_stubs.f90

commit e14f69871479063c5a2f48560c05f32db107cd6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 12 10:27:53 2015 -0800

    commented out BL_PROFILE in BoxArray::intersections

Src/C_BaseLib/BoxArray.cpp

commit 8080b99c0f8865ab253be35f357df6361cb0e140
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jan 10 12:33:56 2015 -0500

    latest version

Tools/RegressionTesting/Maestro-tests.ini

commit 3ef67f1765f5b979787ad20faf8fcf15414d125e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 9 20:16:54 2015 -0800

    For tiling version of derive, set xlo to the lower left corner of the tilebox

Src/C_AMRLib/AmrLevel.cpp

commit 41f38cebeebbaf1907fb13fa246c0072681ef845
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 9 16:55:45 2015 -0800

    in the new tiled derive, we should use the dst mf to initilize MFIter

Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/MultiFab.cpp

commit f97a42dfc6453885054744d1d0118da765544d3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 9 15:39:32 2015 -0800

    If CRSEGRNDOMP is defined, tile AmrLevel::derive.

Src/C_AMRLib/AmrLevel.cpp

commit 27c44a381eb00511f9e442fe187b405ff3235f85
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 9 15:28:55 2015 -0800

    fixed a bug in my last commit

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit d9dfb12dcf630ede881d527987a604f669935ed3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 9 15:06:19 2015 -0800

    use the new FillPatch function

Src/C_AMRLib/AmrLevel.cpp

commit 8027859381e1ff0e83d6f93b5ee9c44c20d6f30c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 9 13:34:42 2015 -0800

    Eliminated a few OMP critical directives by having threadprivate
    copies of variables like total_bytes_allocated_in_fabs.  The trick is
    we can delay the summation of the numbers till we need them.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/DistributionMapping.cpp

commit aa285634dfdd5c96fd74b8fdb7a7223585a69124
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 8 13:36:37 2015 -0800

    fixed new bug

Src/C_AMRLib/TagBox.cpp

commit 1b2abd179a07cfa883be4e171ef0b78db5f73614
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 8 13:09:34 2015 -0800

    added tiling functionality to TagBox

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 3c8183d0ffba16bbef47456ece64c01d9f53d414
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 6 12:22:04 2015 -0800

    fixed a bug I introduced two weeks ago

Src/C_AMRLib/Particles.cpp

commit 5eb4e754c23737d062d2ecea0c2fdd706fea2087
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 5 21:32:07 2015 -0800

    added an assertion

Src/C_AMRLib/AmrLevel.cpp

commit edde48f7196fdf54fd5ba71775cf52302f5fae81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 5 20:53:51 2015 -0800

    Added a static member function FillPatch to AmrLevel. This function
    takes the same argument as FillPatchIterator, but unlike
    FillPatchIterator, it fills the MultiFab.  For example
    
      FillPatch(amrlevel,S_new,0,cur_time,State_Type,0,NUM_STATE);
    
    will fill-patch the MultiFab S_new.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/MultiFab.cpp

commit ab4ff09e65ff5bd2055eb7677a526cbbe5c13209
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 3 07:58:32 2015 -0800

    MFIter: rename fluxbox nodalbox for consistence

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp

commit d249fc64c4c8f816881ab21a647105bfa3e96132
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 31 19:59:16 2014 -0800

    added a new member function to FillPatchIterator t return the filled temporary MultiFab; this is useful for tiling loops that used to use FillPatchIterator

Src/C_AMRLib/AmrLevel.H

commit 293377fe50a3548e2ff39845854f6de5b400c3ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 31 14:22:47 2014 -0800

    print out the smallest and biggest grid on each level after regrid if verbose > 0

Src/C_AMRLib/Amr.cpp

commit 6fba3555c2d20f145223c6ba71f3338df532d777
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 28 21:06:55 2014 -0800

    minor: use a more meaningful name

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit 86eb32ac95ca94875e6e62898c84b37b2115b3c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 28 20:36:45 2014 -0800

    fixed a new bug

Src/C_BoundaryLib/FabSet.cpp

commit c7f7db7c7b50f85483bcae9c487067e12a916373
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 28 16:00:29 2014 -0800

    added OMP to MGT_Solver

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 2ca268e6226f45a84cd8c73e7df6c52aff286a69
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 28 15:13:10 2014 -0800

    added tiling and OMP in serveral palces

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BoundaryLib/FabSet.cpp
Src/C_BoundaryLib/InterpBndryData.cpp

commit 52bfbf7875867d01c98e0e69646816cdfcc5da05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 24 15:35:06 2014 -0800

    fixed similar OMP issue in C++

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp
Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit 55341540cce4e2c919ff387cc63c00bb8a9012fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 24 10:37:22 2014 -0800

    Fixed an omp bug in F90 fill_boundary of nodal multifab with periodic boundary.  In this case, fill_boundary actually copyies from valid cells to valid cells.

Src/F_BaseLib/layout.f90

commit 03973aee21ae485bb716f86e5ab8504e33ccd700
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 23 14:12:42 2014 -0800

    removed an unintended nested OMP parallel region

Src/C_BaseLib/MultiFab.cpp

commit 6ad38a1ca9e9fa9201c4928133af10b423ee30d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 23 13:16:32 2014 -0800

    cleanup

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 6c850e723c5246e256702d35363109fa1507b8ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 23 11:25:22 2014 -0800

    implemented OMP in packing and unpacking for MPI

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit 948a0177276fb1ff85060422d15b2dd0392f7b28
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 22 20:06:25 2014 -0800

    minor shortcuts

Src/F_BaseLib/layout.f90

commit 45c1b8ea266d8572d4ac5349f03d5f67eab4c142
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 22 16:35:01 2014 -0800

    C++: work in progress: refactor OMP in packing and unpacking for MPI

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit 15915756edf746017d45d22eb19c91e8e8e659e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 22 15:50:33 2014 -0800

    fixed a new bug

Src/F_BaseLib/layout.f90

commit 60f0456b186eb9ccb76fe1ff1e46c931f6747efc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 22 15:09:03 2014 -0800

    F90: Added thread safety flags for multifab copy and fill_boundary, and
         fixed a 2-year old OMP bug in multifab copy.  Added OMP to
         sum_boundary.  This might break some regression tests.

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit ec2a379ac017310821c7e312fa75312d39d7c61e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 22 12:49:29 2014 -0800

    fixed OMP data races introduced today

Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit cce3104c9464f27c4ed549e82f78587695190a1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 22 11:16:41 2014 -0800

    removed random shuffle from FabArray because it is no longer used

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 4f2d1bda977382421244c2ca73009fdb508fcb65
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 22 11:14:00 2014 -0800

    OMP in SumBoundary

Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit d9dcfa7cacd10a7bb7b67279f979685b5b76ade6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 19 14:28:55 2014 -0800

    added a new distribution method, RRSFC, which do roundrobin on space filling curve.  This is good for job balance in the case where the amount of work is correlated with position, such as Sedona.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 0905363b5ecc371520647108ed81c7a272ad556b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 19 11:53:17 2014 -0800

    moved memory allocation out of OMP parallel region

Src/C_AMRLib/AmrLevel.cpp

commit 0265ec1a5f2615a5386a6a4c77b0ea97f68e70b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 18 16:05:12 2014 -0800

    minor optimization and clean up

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Utility.cpp

commit 0a8b947a83221f5cea51a14c400a97550a490e98
Merge: 9b5c4771f 0f37aea00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 18 11:23:53 2014 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 9b5c4771f4a9be550ed6faa84adb84c7447cc894
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 18 11:23:50 2014 -0800

    added timers

Src/C_BaseLib/FabArray.cpp

commit 0f37aea007dff4584123cec30ef680742549953c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 17 16:42:42 2014 -0800

    fixed a new bug in parallel copy

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit d75d71ad8a26bb0412f99040329ab932157deafd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 17 15:06:57 2014 -0800

    OMP parallel copy

Src/C_BaseLib/FabArray.H

commit 17a3a47c4d21d77e2557b116e5c48a65ebacd55c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 17 13:57:52 2014 -0800

    more OMP in FillPeriodicBoundary

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit b8a31db3cb10597a5a13c1420ea98bfef4f695dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 17 13:05:40 2014 -0800

    added OMP to FillPeriodicBoundary

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit c95df9000524695c24391fa844c9468283850d1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 17 12:48:54 2014 -0800

    option to turn off nested threading in MFIter

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 4e3d470d6516bc3c8323aa472e1055c9bb8cac5d
Merge: ab8037bb7 05e5a0b52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 17 10:38:41 2014 -0800

    Merge branch 'master' into commopt

commit ab8037bb7bcb737e69ea1dc6aaa01678d49ebe78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 17 10:37:53 2014 -0800

    more OMP in FillBoundary

Src/C_BaseLib/FabArray.H

commit 05e5a0b5216124cf0b934150174d8ce9a91fb1ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 16 21:19:12 2014 -0800

    fixes for gcc 4.8 and above

Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp

commit 3c95337cdd5ffd76e410b11fa693cf011231a3b7
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 16 17:20:10 2014 -0800

    typo.

Src/C_BaseLib/BLProfiler.cpp

commit 575e894c6daea765eb08bbb486c9d7dc69e707b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 16 14:24:59 2014 -0800

    OMP two loops in FillBoundary

Src/C_BaseLib/FabArray.H

commit ecd04b908a7a7482260c0b1b2978c8cb4c3c0a09
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 16 13:42:48 2014 -0800

    array size.

Src/C_BaseLib/BLProfiler.cpp

commit 13c622525d0bc8f87db12c88d732e1fd63ab21e0
Merge: 1bf21680c a9325afda
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 16 12:35:02 2014 -0800

    Merge branch 'master' into commopt

commit a9325afdabf5a78f4aa89811353921220e005463
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 16 12:27:36 2014 -0800

    removed the update argument and optimized Where()

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 6194d99ca5ad65c5ade409f54100e9da1828c9f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 16 10:10:12 2014 -0800

    Since particle can intersect with only one grid, we can set first_only=true in serveral calls to BoxArray::intersections

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 1bf21680cbdab5f62175fe1812170e7fe5923d2a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 16 09:51:37 2014 -0800

    minor

Src/C_BaseLib/FabArray.cpp

commit 8e34447dc2580547b4503fad5bc373533f93da8e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 12 14:13:00 2014 -0800

    removed using std::isinf for Cray compiler on Hopper

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 76a9e0f71b3c5df3b6234f0e3d802bbfd06baa44
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 12 14:12:08 2014 -0800

    removed tgmath.h and added std:: to sqrt for PGI on Hopper; tests show that it works for all compilers on Hopper and Edison, and my desktop with gcc 4.4.3

Src/C_BaseLib/BLProfiler.cpp

commit f54294d8fe7cda83b4f44147cf637bfb0c3f77d8
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 12 13:58:04 2014 -0800

    fix for sqrt, ioproc parens.

Src/C_BaseLib/BLProfiler.cpp

commit f6aceb6899c063e4a2ea6d82851011480dc522e1
Merge: e95303fa0 301757f03
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 12 11:56:31 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e95303fa00a6f8ccefec9adebec9578fc2d23116
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 12 11:56:16 2014 -0800

    changed double to Real in SumPeriodicBoundary so PRECISION=FLOAT will compile.

Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit 301757f0372228b069a8a530d54c4ef576513ac5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 11 17:25:07 2014 -0800

    reverted my last change because it created new problems

Tools/C_mk/Make.defs

commit 4a973a84200a0c8680c0c01c00259914078e80c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 11 16:30:39 2014 -0800

    added -std=c++0x to gcc as needed by the new BLProfiler

Tools/C_mk/Make.defs

commit 6867fc9015a6fb86cc75131a316e4e7c0a227062
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 11 11:04:02 2014 -0800

    another donev machine.

Tools/C_mk/Make.defs

commit 32cfd40caef422600efe24641c7dac2d28280e18
Author: vince <vebeckner@lbl.gov>
Date:   Wed Dec 10 15:35:21 2014 -0800

    renamed Profiler to BLProfiler (class and files).

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/Particles.H
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/BLProfiler.H
Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/iMultiFab.cpp
Src/C_BoundaryLib/FabSet.cpp
Src/C_TowerLib/Layout.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/tProfiler.cpp

commit 97bfed1c0b5026ccf30c04456fcde721d20e79e7
Merge: 1cdf3bcb9 5b87ef250
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 9 14:33:23 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1cdf3bcb974c47659ed7f208bc4c509fc5c64631
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 8 16:59:41 2014 -0800

    added more statistics.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 5b87ef2503faa677dfece61c3d3ca4af068b12bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 5 13:05:57 2014 -0800

    fixed 2 new errors

Src/C_AMRLib/Particles.cpp

commit ef7c6a70123659ca2e0c6863a7fb7c10c4ab71e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 5 13:03:18 2014 -0800

    fixed a new error

Src/C_AMRLib/Particles.H

commit 988c2b844d472987af7a2105e6146b7b27aef1dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 5 12:51:50 2014 -0800

    more const T -->> const T&

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Utility.cpp
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/WaveEquation_C/main.cpp

commit 1ff8db4980f313309e8ecb8f44a7eef7c8a2f566
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 5 12:27:09 2014 -0800

    more const T -->> const T&

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BoundaryLib/InterpBndryData.cpp
Src/C_BoundaryLib/MacBndry.cpp
Src/C_TowerLib/Layout.cpp
Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp
Tools/C_util/ViewMF/viewMFdiff.cpp
Tools/C_util/ViewMF/viewMFdiffHardWire.cpp
Tools/C_util/WritePlotFile.cpp
Tutorials/AMR_Advection_C/Source/ADR.cpp
Tutorials/AMR_Advection_C/Source/Diffusion.cpp
Tutorials/AMR_PETSc_C/Source/Darcy.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp

commit fa9c35776fe71c819328ad101df25ad963dbbf29
Merge: f27233702 83b90f00c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 4 21:55:58 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f272337029a0b94fcc7d1fbc169700bc5cf15617
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 4 21:06:07 2014 -0800

    minor optimization using a nice feature of C++: temporary variable created as the rhs of assignment to const T& lhs has the same lifetime as the lhs variable.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/AuxBoundaryData.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/iMultiFab.cpp
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/InterpBndryData.cpp
Src/C_TowerLib/Layout.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Tests/C_BaseLib/tBA.cpp

commit 83b90f00cd6c751fc544b7db144b1c79803cc156
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 4 06:13:04 2014 -0800

    added -lquadmath for gcc 4.9

Tools/C_mk/Make.Linux

commit 72efff827fe903f6f0499146a1bbdcc39ae941e5
Merge: e24f58bc6 e4a318184
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 21:15:44 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e24f58bc613c0cc74570c4147f127a7ddd390138
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 21:02:00 2014 -0800

    minor optimization

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/iMultiFab.cpp

commit e4a31818427bfed89e5715c111354e1fe3029a4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 16:58:22 2014 -0800

    OMP'd part of FabArray::copy

Src/C_BaseLib/FabArray.H

commit adc736adf00d8d423a5f416c9cfc113c77e60850
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 16:21:51 2014 -0800

    added a timer to BoxArray::intersections

Src/C_BaseLib/BoxArray.cpp

commit 1333ac2e7ba4e95250908424ce49d3b2f408d373
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 15:59:41 2014 -0800

    added a timer to FabArray::copy from a Fab

Src/C_BaseLib/FabArray.H

commit 2c6d3e5d46f62ab99d014b97c68353c6142a15ed
Merge: d23f402ca 83f33cd75
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 15:44:39 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d23f402cad00ca4dd46efb32c0b6fc7a566233be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 15:40:28 2014 -0800

    removed OMP from BaseFab saxpy so that we can do OMP on MultiFab

Src/C_AMRLib/MLSDCAmrEncap.cpp
Src/C_BaseLib/SPECIALIZE_3D.F

commit 7375dcb7a164742e4f93c7158c806cc05f7f6710
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 15:31:59 2014 -0800

    add tiling to FabSetIter and use it in FluxRegister::SumReg

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BoundaryLib/FabSet.H

commit 09fc9aed10427d7a09afc364f56a1b041147e4cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 15:25:13 2014 -0800

    cleanup

Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 3de88036bae7a864d2ca66912ef5266f96c9b277
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 15:05:31 2014 -0800

    tiled MultiFab::contains_inf and contains_nan

Src/C_BaseLib/MultiFab.cpp

commit 76c9647e218fcdd60937c6fc60be7b7465828f4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 14:49:27 2014 -0800

    tiled a number of MultiFab functions

Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/iMultiFab.cpp

commit 7561402089db70c6f0b3340a4cdc335fae9ae994
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 14:19:31 2014 -0800

    minor optimization by moving omp critical out of MFIter loop

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp

commit 83f33cd757b014bd39889ea6bd549812956a2fea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 12:31:25 2014 -0800

    minor

Src/C_BaseLib/BaseFab.H

commit c8b548ed04604cdaa659878f4727ec0e188db1e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 12:04:53 2014 -0800

    tiled setVal

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit d6b572ef2051c9c5be99e97135600a0b263c4d30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 11:51:15 2014 -0800

    Added MFIter::growntilebox that returns the tile box grown to include ghost cells; cleanup

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit af0f7127e02bfc0cbb7de66537059ed74c7c9a0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 1 17:01:38 2014 -0800

    Do not set initialized to false in CGSolver and MultiGrid::Finalize so that we don not
    have to query ParmParse again and again.

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit b2b16cb83e66286cc68918dd4dd877ff9e5341a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 1 16:56:17 2014 -0800

    Do not set initialized to false in LinOp::Finalize so that we don not
    have to query ParmParse again and again.

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 65544a61b0124310c40ca1972c7952342f53f860
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 1 15:57:42 2014 -0800

    more tiling in C_CellMG

Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/LP_1D.F
Src/LinearSolvers/C_CellMG/LP_2D.F
Src/LinearSolvers/C_CellMG/LP_3D.F
Src/LinearSolvers/C_CellMG/LP_F.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/MG_3D.F
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit cf3bc4c6ea1cbea3cf84b4a26558bae0a96353d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 1 15:16:36 2014 -0800

    fixed a new bug

Src/LinearSolvers/C_CellMG/ABec_2D.F

commit e57c7f7eb4d1f2b92d4a620362cc64b1c830da03
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 1 14:56:35 2014 -0800

    more tiling in C_CellMG

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/ABec_1D.F
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/ABec_F.H
Src/LinearSolvers/C_CellMG/LO_1D.F
Src/LinearSolvers/C_CellMG/LO_2D.F
Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 6cf35951da4e26df78fabb2f4e32dd37d2044bb5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 1 14:56:16 2014 -0800

    added fluxbox to MFIter

Src/C_BaseLib/FabArray.H

commit 0241f72b95eedda23865220b00677870c45b4eea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 28 14:39:54 2014 -0800

    BLMap: tidy

Src/C_BaseLib/BLMap.H

commit 2b1720ce9fac976c5410d216f36f9e55305fd72a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 28 14:15:53 2014 -0800

    added local_size() function to FabArray.H; added reserve() to BLMap.H; fine tune BLMap::operator[]

Src/C_BaseLib/BLMap.H
Src/C_BaseLib/FabArray.H
Src/C_BoundaryLib/FabSet.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 5e45246eda11b7f1b54eaa2192a76398eef4afe2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 27 23:30:56 2014 -0800

    comments

Src/C_BaseLib/BLMap.H

commit 10c6fcb0f2cf08bcacb486719d6998414dc0970c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 27 23:22:39 2014 -0800

    comments

Src/C_BaseLib/BLMap.H

commit 880c5364021c8ed03d4d250a0d59803d8d6270d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 27 23:16:53 2014 -0800

    added more comments

Src/C_BaseLib/BLMap.H

commit 76f61044ef3333336688d5dc727f2935c2db8fd5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 27 22:19:03 2014 -0800

    added BLMap, a lightweight and thread-safe (in reading) class with some features of std::map; use BLMap instead of std::map in LinOp

Src/C_BaseLib/BLMap.H
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit be98d7267ed905a2cfdcc43f0c0d20a85ce11a8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 26 20:47:49 2014 -0800

    use std::lower_bound in local index search

Src/C_BaseLib/FabArray.H

commit acdb6a691a3965a5c3673c6ece7176aa6149d88b
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Nov 26 08:57:45 2014 -0800

    plug a memory leak for the case when you try to use bottom_solver_type=4 but the grid layout isn't appropriate

Src/LinearSolvers/F_MG/mg.f90

commit 9e3dda83667c4b45de63d675306a217373e53627
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 26 07:00:00 2014 -0800

    tiled C_CellMG/GSRB

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/ABec_F.H

commit 4e9afa22993202bed86db68b316dc54c379fdb0f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 25 13:41:23 2014 -0800

    Add profiling to particle moveKick and moveKickDrift routines.

Src/C_AMRLib/Particles.H

commit dd5a57ddaa8397796b092b08da2fe023e72671eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 24 10:22:29 2014 -0800

    more mf[mfi.index()] --> mf[mfi]

Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp
Tests/LinearSolvers/ComparisonTest/compute_norm.cpp
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp
Tutorials/AMR_Advection_C/Source/ADR.cpp
Tutorials/AMR_Advection_C/Source/ADR_advance.cpp
Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp
Tutorials/MultiGrid_C/main.cpp

commit e3895129400adfe59f10ce2ba60e174c1b9fb5c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 24 09:43:46 2014 -0800

    more mf[mfi.index()] --> mf[mfi]

Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/InterpBndryData.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/Python/src/boxlib_wrap_1.cpp.REMOVED.git-id
Src/Python/src/boxlib_wrap_2.cpp.REMOVED.git-id
Src/Python/src/boxlib_wrap_3.cpp.REMOVED.git-id
Src/Python/swig/boxlib.i

commit 807786eaf76dd4c26d803b0c5bb6f0f99f608c1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 23 21:35:00 2014 -0800

    fixed tiling bug in MFIter when inside OMP parallel region

Src/C_BaseLib/FabArray.H

commit a936f17600d7d8e785ecf05690690f8683290d37
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 23 20:43:47 2014 -0800

    adde an omp atomic to fix a race condition

Src/C_BaseLib/BaseFab.H

commit adf02cdc413f26cb3591e222e73564fe8cdf3eda
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 23 14:52:54 2014 -0800

    clean up

Src/C_BaseLib/FabArray.H

commit 3651bdc5643988b16ab8ef449919123755027c83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 22 22:07:02 2014 -0800

    use binary search for local index

Src/C_BaseLib/FabArray.H

commit b3f3e1488accc54739807e5e7e308d1a7aad2bf0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 22 20:34:51 2014 -0800

    added a local index array that maps thread private index into local index of fab vectors

Src/C_BaseLib/FabArray.H

commit 84d695bca0c1aa946a0f0f9a877961cf6c59d477
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 21 22:27:21 2014 -0800

    defensive programming: changed the name of the variable storing FAB* from m_fabs to m_fabs_v. we recently changed the variable type from map to vector for thread safety.  So the meaning of operator[] has changed.  Changing the name can prevent that variable being used directly be other classes.  The last new bug I just fixed was due to direct use of the varible (i.e., not through member function) in TagBox ().

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/FabArray.H

commit be0fd779a8de6995a7df23a995cd470546afef0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 21 22:10:07 2014 -0800

    fixed another new bug

Src/C_AMRLib/TagBox.cpp

commit b43045203c7f8b21386eaf28e422482b8cb4160e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 21 21:01:51 2014 -0800

    fixed a new bug

Src/C_AMRLib/AmrLevel.H

commit 11da6250b4a504bef73844d8747684ffaf36404b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 21 19:17:21 2014 -0800

    fixed a bug in localindex of the new vector based FabArray

Src/C_BaseLib/FabArray.H

commit 512a8c5c1555d898d80c3f05b54e16c94475cc5e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 21 17:01:39 2014 -0800

    In many palce, use mfi instead of mfi.index() to access fab.  This is now the preferred way because it is more efficient.

MiniApps/MultiGrid_C/main.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/iMultiFab.H
Src/C_BaseLib/iMultiFab.cpp

commit abae665a00efc01d69f74a8d3e6fce616550ffa5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 21 15:59:51 2014 -0800

    In FabArray, use vector instead of map to store fab pointers.

Src/C_BaseLib/FabArray.H

commit a93f8ee5695b83fdca4d9b73a0f3b2f8756ef0ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 21 13:16:57 2014 -0800

    Revert "tiled GSRB in C_CellMG" because of thread safety.  The problem
    is C++ std::map::find is not thread safe.
    
    This reverts commit 7b452ac3e3eb9e1834fa8e8b4be8fce8ab7ded62.

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/ABec_F.H

commit f075d6a603172ebfd6b9536132616ca6a6af8d08
Merge: 7b452ac3e c5fc3205e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 21 11:29:32 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c5fc3205efedc9227ef8d7eaa33975df37fa95fd
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 21 11:19:23 2014 -0800

    removed some debugging output.

Src/C_BaseLib/DistributionMapping.cpp

commit 9b577a0b32e3fdfa950a96afbdfd4842eddb410a
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 21 11:11:48 2014 -0800

    removed unused vars.

Src/C_BaseLib/DistributionMapping.cpp

commit 7b452ac3e3eb9e1834fa8e8b4be8fce8ab7ded62
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 21 10:47:17 2014 -0800

    tiled GSRB in C_CellMG

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/ABec_F.H

commit f356e494665d45067c992cb6a4dfbbc034f60eb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 21 10:18:14 2014 -0800

    added some timers to C_CellMG

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 2768bd22a34164c214fcb551e26eb6d19602d683
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 20 20:45:00 2014 -0800

    added tilebox function to MFIter; added a parameter for controlling tile size via ParmParse; another MFIter constructor that used the default tile size.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Tutorials/Tiling_C/main.cpp

commit f4383963a99320815b2ca6c8f3690ad897d626e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 20 20:02:21 2014 -0800

    fixed un-deleted heap memory to quiet valgrind

MiniApps/MultiGrid_C/main.cpp
Tests/LinearSolvers/ComparisonTest/main.cpp
Tutorials/AMR_Trilinos_C/driver.cpp
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/MultiGrid_C/main.cpp
Tutorials/WaveEquation_C/main.cpp

commit 01943697212463e9f8bcf92cd88daa0f960b11d0
Merge: 05950d7b2 942074565
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 20 17:23:35 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 05950d7b2cfb0196e6ca02f58c54afd13663b868
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 20 17:23:25 2014 -0800

    binary format for individual proc prof data.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 942074565e6c31fd1cb2d2e7a91707e5c6c71bd0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 20 13:01:32 2014 -0800

    validbox in MFIter must have the correct indexing type

Src/C_BaseLib/FabArray.H

commit 800a7be06fee2b8afa49b1e977ee2c1273b55526
Merge: ef6771baf d6f0727ec
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Nov 20 10:39:49 2014 -0800

    Merge branch 'master' into 4thOrderMG

commit d6f0727ece932becc9903790d59be47a888a7c02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 20 10:38:42 2014 -0800

    added a tutorial code showing how tiling version of MFIter can be used.

Tutorials/Tiling_C/GNUmakefile
Tutorials/Tiling_C/Make.package
Tutorials/Tiling_C/main.cpp
Tutorials/Tiling_C/work.f90

commit ef6771baf402ad1f5a8b0cee34ed070f42eaf30a
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Nov 20 10:37:58 2014 -0800

    Initial commit of branch for 4th order mg

Src/C_BaseLib/BLFort.H
Src/C_BoundaryLib/BndryData.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_CellMG4/ABec2.H
Src/LinearSolvers/C_CellMG4/ABec2.cpp
Src/LinearSolvers/C_CellMG4/ABec2_2D.F
Src/LinearSolvers/C_CellMG4/ABec2_3D.F
Src/LinearSolvers/C_CellMG4/ABec2_F.H
Src/LinearSolvers/C_CellMG4/ABec4.H
Src/LinearSolvers/C_CellMG4/ABec4.cpp
Src/LinearSolvers/C_CellMG4/ABec4_2D.F
Src/LinearSolvers/C_CellMG4/ABec4_3D.F
Src/LinearSolvers/C_CellMG4/ABec4_F.H
Src/LinearSolvers/C_CellMG4/CMakeLists.txt
Src/LinearSolvers/C_CellMG4/Make.package
Src/LinearSolvers/C_CellMG4/OpenSource.txt
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Tools/C_mk/Make.mpi
Tutorials/MultiGrid_C/COEF_2D.F
Tutorials/MultiGrid_C/COEF_F.H
Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_C/inputs.3d
Tutorials/MultiGrid_C/main.cpp

commit e3aad315d19cf8361c0cd020fa0a1103db46d534
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 20 10:20:23 2014 -0800

    Implemented a tiling version of MFIter.  This should not affect the
    results of any codes unless a tiling version of MFIter is actually
    used.

Src/C_BaseLib/FabArray.H

commit ae9018b0141247ffc9a7387916053dcb5f401d2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 19 16:19:10 2014 -0800

    commented out a cout

Src/C_BaseLib/DistributionMapping.cpp

commit be3a3b06363d4f04312d216df9baf8c6b84e1367
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 19 14:54:58 2014 -0800

    moved readBoxArray from StateData to BoxArray, removed dependencies in DistributionMapping.

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/DistributionMapping.cpp
Tests/C_BaseLib/GNUmakefile

commit 5412143cd81176440cebb52dfadcb69bdb93e237
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 19 14:48:54 2014 -0800

    added to the docs.

Docs/Readme.profiling

commit cb61af8f51b7a3fa933a0bf893773204bd12b276
Merge: 98e661c43 e82350f56
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 19 13:30:48 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib
    
    Conflicts:
            Src/C_BaseLib/DistributionMapping.cpp

commit 98e661c4373ac5aeb264a25c646cdaab1d8fec92
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 19 13:19:46 2014 -0800

    Tutorials/HelloWorld_C: changed domain size

Tutorials/HelloWorld_C/main.cpp

commit 2ea6a56f9610834d7e7fc0d00ebc76d5f83ada1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 19 09:30:41 2014 -0800

    removed an unused variable

Src/C_BaseLib/threadbox.f90

commit e82350f5638d42fb0f2b827dececdbf9f54f3cb8
Merge: be8cb5dc4 c83298cc6
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 18 14:28:02 2014 -0800

    more merge cleanup.

commit be8cb5dc49e6bfa366f913f56b50b4d17c25fca4
Merge: 3a0dc1f2c dd4da37c2
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 18 14:12:31 2014 -0800

    merge resolution.

commit 9b6897a0257ba448c7e84619ef16c94dd60554f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 18 13:57:54 2014 -0800

    minor

Src/C_BaseLib/DistributionMapping.cpp

commit c83298cc633919448f3831d2f8d52a1a7a80c0f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 18 13:23:08 2014 -0800

    Removed the long long int stuff I recently committed and the long long
    int stuff in Particles I did a while ago.  But I added a warning about
    the size of long int, if it is too small.  I give up because: (1)
    there are many places that have to be changed if we really want to
    make sure BoxLib can handle really big runs on systems like Windows
    where long int is only 4-byte wide; (2) on most if not all Unix
    systems, long int is 8-byte wide.

Src/C_AMRLib/Particles.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ccse-mpi.H

commit 5a602e79816cb90b6ec55c113886f12dbb8813fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 18 11:16:29 2014 -0800

    minor cleanup: std::map::insert checks if the element to be inserted already existed, so we do not have to do it ourselves

Src/C_BaseLib/DistributionMapping.cpp

commit 3a0dc1f2c1fcbdd48255420233b5cb12e3332f85
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 18 10:25:25 2014 -0800

    some fortran profiling tests.

Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/TPROFILER.F
Tests/C_BaseLib/TPROFILER_F.H
Tests/C_BaseLib/tProfiler.cpp

commit 68f11eb7a13df2fe5d263e5dfa2de1eead8ee0ff
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 18 10:24:03 2014 -0800

    made regular profiling for ParallelDescriptor functions a special profiling option.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 90b22c61f2837a2cf66db311fe021f2be7e61a51
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 18 10:22:21 2014 -0800

    some cleanup before the merge.

Src/C_AMRLib/Amr.cpp

commit c46cdf96bb3d9072cda72a8fec452045f52569e8
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 18 10:21:44 2014 -0800

    added faster fortran interface for functions with a large number of calls.

Src/C_BaseLib/BLProfiler_F.f
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit dd4da37c2064776fed6460b44080d6ebc88d3505
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 18 06:26:45 2014 -0800

    fixed typo and made it compile again. added comment on long long int.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/DistributionMapping.cpp

commit 9febb8d587cb796657bc1f832edb12b975b40b7d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 17 16:43:13 2014 -0800

    Make stable sort in LeastUsedCPUs truly stable.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 15d47dc36a0c06f328a8bea93e807186fa00eed7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 17 16:33:39 2014 -0800

    Use long long int for storing the total bytes allocated.  The maximum
    value of long int is only slightly larger than 2e9, whereas a compute
    node of Edison has 64 GB memory.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/DistributionMapping.cpp

commit ed546a3fb9322a3996453fad2f57817d6fc0e45a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 17 15:17:51 2014 -0800

    comment

Src/C_BaseLib/DistributionMapping.H

commit 2954e0eca64dcbe9219573c8aa9100ce48734966
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 17 15:05:03 2014 -0800

    Added one more digit to a few constants to achieve machine accuracy.
    For example, (1.d0/6.d0 .eq. 0.1666666666666667d0) is false, whereas
                 (1.d0/6.d0 .eq. 0.16666666666666667d0) is true, if IEEE
    754 is used.

Src/C_BaseLib/CONSTANTS.H

commit 6c6be22973915863be5fef531e00dc11ba8fa428
Merge: 716d8e27b b12571515
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 17 12:07:35 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 716d8e27be9a80e063175415bdf1a3fe90fb8622
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 17 12:05:54 2014 -0800

    Fixed Box::isEmpty().  The old version would abort on an empty box in
    DEBUG mode because of an assertion.

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp

commit 22b2aa16a05773b5fe404e83dc92f0bc1cac0c3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 17 11:04:59 2014 -0800

    minor cleanup

Src/C_BaseLib/Box.H

commit 24e3d0b53fabdaafa048528e9eb174509e939162
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 14 13:26:02 2014 -0800

    added long long type for number of points in a BoxArray

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit e6df95f8e8bebcca2f4375b7a9465c35807d2ff7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 14 13:25:07 2014 -0800

    modified comment

Src/C_BaseLib/Pointers.H

commit f1e61ecb6cb97f9992eb75dd15211c8bd6d3a3ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 13 17:08:18 2014 -0800

    clean up USE_F90_SOLVERS

Tests/LinearSolvers/C_CellMG/GNUmakefile
Tools/RegressionTesting/IAMR-tests.ini
Tools/RegressionTesting/LMC-tests.ini

commit ad8c5100a156826d74e617bcda78c01292d6f3fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 13 16:29:13 2014 -0800

    removed an old obsolete file

Src/C_BaseLib/std/limits

commit 4209fbf4ab1bf553d311e051b522e860470bddc9
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Fri Nov 14 00:25:10 2014 +0300

    PyBoxLib: Tidy a lot and use relative imports.

Src/Python/F90/fboxlib/__init__.py
Src/Python/F90/fboxlib/boxarray.py
Src/Python/F90/fboxlib/fab.py
Src/Python/F90/fboxlib/fabutils.py
Src/Python/F90/fboxlib/layout.py
Src/Python/F90/fboxlib/multifab.py
Src/Python/F90/fboxlib/plotfile.py
Src/Python/F90/fboxlib/regrid.py
Src/Python/F90/fboxlib/utils.py
Src/Python/F90/tests/regrid.py

commit 48a0809280d010a63cc0419e6906a8e56d78e7c8
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Fri Nov 14 00:05:59 2014 +0300

    PyBoxLib: Update README files and add test script.

Src/Python/F90/README
Src/Python/F90/setup.py
Src/Python/F90/test.py
Src/Python/README

commit 067ecf979a2e954d14652696886243c0d8d1c26d
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Nov 13 23:56:02 2014 +0300

    PyBoxLib: Flesh out new wrapper, regridding works.

Src/Python/F90/fboxlib/__init__.py
Src/Python/F90/fboxlib/base.py
Src/Python/F90/fboxlib/fab.py
Src/Python/F90/fboxlib/layout.py
Src/Python/F90/fboxlib/multifab.py
Src/Python/F90/fboxlib/pybl.py
Src/Python/F90/fboxlib/regrid.py
Src/Python/F90/src/boxlib_numpy_c.c
Src/Python/F90/src/boxlib_numpy_f.f90
Src/Python/F90/src/fboxlib.f90
Src/Python/F90/src/fboxlib_c.c
Src/Python/F90/src/make_new_grids.f90
Src/Python/F90/src/tag_boxes.f90

commit 6166cbc4c27592bac8712c72a8440e743638dc94
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Nov 13 16:27:04 2014 +0300

    PyBoxLib: Begin new wrapper.

Src/Python/F90/Makefile
Src/Python/F90/fboxlib/__init__.py
Src/Python/F90/fboxlib/boxarray.py
Src/Python/F90/fboxlib/layout.py
Src/Python/F90/src/fboxlib.f90
Src/Python/F90/src/fboxlib_c.c

commit 3632ee5185d0eb232daf620cef54a5f0383df90f
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Nov 13 12:21:31 2014 +0300

    PyBoxLib: Add tagging callback throughout.

Src/Python/F90/fboxlib/regrid.py
Src/Python/F90/src/fboxlib.f90
Src/Python/F90/src/make_new_grids.f90
Src/Python/F90/src/regrid.f90
Src/Python/F90/src/tag_boxes.f90

commit 22607336e4a317554643c4f368dadf7afc5ee46a
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Nov 13 10:47:11 2014 +0300

    PyBoxLib: Mandatory boxes when creating a box array.

Src/Python/F90/fboxlib/boxarray.py
Src/Python/F90/fboxlib/pybl.py

commit 1479f6d446dc71920cd8491960e0721549c1c1cb
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Nov 13 10:46:43 2014 +0300

    PyBoxLib: Add preliminary regrid capabilities.

Src/Python/F90/fboxlib/__init__.py
Src/Python/F90/fboxlib/regrid.py
Src/Python/F90/src/fboxlib.f90

commit bbb501972895e5080448d8fbc4120cd9d131949a
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Nov 13 10:45:51 2014 +0300

    PyBoxLib: Try to be a bit more defensive in `base.py`.

Src/Python/F90/fboxlib/base.py

commit 5b504c66ee7ab9c738bc1964e91ad7d7a38dff2c
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Nov 13 10:02:01 2014 +0300

    regrid: Change an inout to an in, set nlevs_old properly.

Src/F_BaseLib/regrid.f90

commit 80ccfebb33f6be3a70889159c7e4e5d536ac8e0c
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 12 18:04:56 2014 -0800

    some profiling test codes.

Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/TPROFILER.F
Tests/C_BaseLib/TPROFILER_F.H
Tests/C_BaseLib/tProfiler.cpp

commit 6ef851f63f9601dcd8ec7e21da0844102c5d088b
Merge: 5f7586482 f32674690
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 12 16:11:33 2014 -0800

    Merge branch 'master' into commprof
    
    in ParallelDescriptor.cpp, readded the deleted BL_COMM_PROFILE
    calls before the calls to mpi functions, they are required.
    left the BL_PROFILE calls in the code but commented out.
    
    some after merge cleanup.
    
    Conflicts:
            Src/C_AMRLib/Amr.cpp
            Src/C_BaseLib/Make.package
            Src/C_BaseLib/ParallelDescriptor.cpp
            Src/C_BaseLib/Profiler.H
            Src/C_BaseLib/Profiler.cpp
            Src/F_BaseLib/bl_prof.f90

commit 5f75864824656f59b300d8555f6a0fe02ebf6fc4
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 12 15:24:07 2014 -0800

    cleanup before merge.

Tests/C_BaseLib/GNUmakefile
Tutorials/MultiFabTests_C/GNUmakefile
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp

commit f326746902c11ddc679e4550a4d4f2aeb9a9a912
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Nov 12 23:13:32 2014 +0300

    PyBoxLib: Fix installation of fboxlib.

Src/Python/F90/Makefile
Src/Python/F90/fboxlib/fab.py
Src/Python/F90/fboxlib/pybl.py
Src/Python/F90/setup.py

commit b4baf63c9d654bd88bf768d1007cfb18a94d9fdd
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Nov 12 17:25:43 2014 +0300

    PyBoxLib: Tidy.

Src/Python/GNUmakefile_F90.mak
Src/Python/fsrc/blobjects.f90
Src/Python/fsrc/blobjects.py
Src/Python/fsrc/boxlib_numpy_c.c
Src/Python/fsrc/boxlib_numpy_f.f90
Src/Python/fsrc/fboxlib.f90

commit 8aa1b7c40369fd2d61abeecad5c9ac95cef03f7d
Merge: 6190502b7 cc4785f2c
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Nov 12 17:21:10 2014 +0300

    Merge branch 'master' of gamera.lbl.gov:/home/CCSE/gitroot/BoxLib

commit 6190502b73f7e8f9805ced0a5eb2aa354d2ade41
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Nov 12 17:20:46 2014 +0300

    PyBoxLib: Restore Fortran version in Src/Python/F90.

Src/Python/F90/Makefile
Src/Python/F90/fboxlib/__init__.py
Src/Python/F90/fboxlib/base.py
Src/Python/F90/fboxlib/boxarray.py
Src/Python/F90/fboxlib/fab.py
Src/Python/F90/fboxlib/fabutils.py
Src/Python/F90/fboxlib/layout.py
Src/Python/F90/fboxlib/multifab.py
Src/Python/F90/fboxlib/plotfile.py
Src/Python/F90/fboxlib/pybl.py
Src/Python/F90/fboxlib/utils.py
Src/Python/F90/setup.py
Src/Python/F90/src/blobjects.f90
Src/Python/F90/src/blobjects.py
Src/Python/F90/src/boxlib_numpy_c.c
Src/Python/F90/src/boxlib_numpy_f.f90
Src/Python/F90/src/fboxlib.f90

commit cc4785f2c29e6d06fc2d19a98e780649578474fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 11 12:55:22 2014 -0800

    removed xHost from intel compiler options because the executable may run on different processors than the host processor where it is compiled

Tools/C_mk/Make.defs
Tools/F_mk/comps/Linux_intel.mak

commit d3e8dcf35fa1eccb6ee2646c2189d5a15c9b66af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 11 10:35:25 2014 -0800

    added a fortran module that can do domain decomposition for threads

Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package
Src/C_BaseLib/threadbox.f90

commit e081696a1f506998e2f2127054d7595d1de91211
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Nov 11 16:43:55 2014 +0300

    PyBoxLib: Bring back Fortran version of PyBoxLib.

Src/Python/GMakerules.mak
Src/Python/GNUmakefile_F90.mak
Src/Python/GPackage.mak
Src/Python/fsrc/blobjects.f90
Src/Python/fsrc/blobjects.py
Src/Python/fsrc/boxlib_numpy_c.c
Src/Python/fsrc/boxlib_numpy_f.f90
Src/Python/fsrc/fboxlib.f90

commit dec7bcb702e46c3201efb9c702a726cf72ad0ff7
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Nov 11 16:11:47 2014 +0300

    PyBoxLib: Another fix for libgfortran.

Src/Python/GNUmakefile_CXX.mak

commit b16328852b1dece9580e706d13a0c23df9d73cc3
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Nov 11 09:58:08 2014 +0300

    PyBoxLib: Better gfortran detection (from Aron Ahmedia).

Src/Python/GNUmakefile_CXX.mak

commit efc2229c2913dd525092b4bf544eaeb66afeeacc
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Nov 11 09:57:21 2014 +0300

    PyBoxLib: Revert back to distutils instead of setuptools.

Src/Python/setup.py

commit d62b7b8698d983ccb5542408c5314a72fec6167f
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Sun Nov 9 22:26:57 2014 +0300

    PyBoxLib: Fix BOXLIB_HOME for hashdist.

Src/Python/GNUmakefile_CXX.mak

commit 4451852a3552b063944acf000a86cb70d026bb2c
Author: Matthew Emmett <memmett@gmail.com>
Date:   Sun Nov 9 07:10:06 2014 -0800

    PyBoxLib: Tweak BOXLIB_HOME.

Src/Python/GNUmakefile_CXX.mak

commit b5681298a91e29f23b6e0459bfdbfeff74eefdec
Author: Matthew Emmett <memmett@gmail.com>
Date:   Sun Nov 9 05:15:30 2014 -0800

    PyBoxLib: Get 'python setup.py develop' working.

Src/Python/setup.py

commit 4f0a09e09e2cacb6d3234a5c1c0939593872edad
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 7 16:35:22 2014 -0800

    typo, removed old code.

Src/C_BaseLib/Profiler.cpp

commit f4c2e8c5509b25082a9cc79d4092c123b705f7a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 7 12:49:56 2014 -0800

    put the new mpi_waitall code inside 'if' so that it won't break assertion in BaseFab

Src/C_BaseLib/FabArray.H

commit 147b64e4be6cacc25f52f08fac6d5a9908affb30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 7 08:16:14 2014 -0800

    fixed OMP in Jacobi smoother

Src/LinearSolvers/C_CellMG/ABec_3D.F

commit 2db23654823f105eddb576995fae71f3fe1df48c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 6 16:59:18 2014 -0800

    C++: Use isend instead of send and replace waitsome with waitall.  This makes fill boundary noticeably faster just we have observed in F90 codes.  Note that MPI_Waitsome is always slower than MPI_Waitall because the former does a lot more testing, and unpacking the data is much cheaper than the overhead of waitsome.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 1acde6d06951c4befd2ca8a5a0686e47a1fd146f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 6 16:46:43 2014 -0800

    shut down compiler warning by removing some unnecessary const prefixes to functions return plain numbers

Src/C_BaseLib/Profiler.H

commit 3589f957d00211f264b8173535e9b3d7a66799e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 6 16:43:34 2014 -0800

    removed BL_PROFILE (not BL_COMM_PROFILE) from ParallelDescriptor because (1) there is already commprof; (2) this reduces clutter in the profiling report and gives a better idea about the cost of fill boundary and copy.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit f6c6fddfb9d51840d5e6c941125f0b79dd97eae6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 6 13:21:38 2014 -0800

    call applyBC before calling jacobi smoother (now mirrors GSRB)

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 0141cebb0749026ac21372b81315a52b78d2b9d9
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 6 13:20:27 2014 -0800

    properly implement jacobi smoothing in 2d and 3d

Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F

commit 6ad37e7a908f301357bc9914667d0fe4842bf899
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 5 20:39:14 2014 -0800

    F90: send -> isend.  We used to call irecv's followed by send's. Changing to isend makes multifab_copy and multifab_fill_boundary 20+% faster.

Src/F_BaseLib/multifab_f.f90

commit eb5d1a780e2a978f822299f0569ffff551840435
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 5 09:35:54 2014 -0800

    F90: removed "intent(in)" from parallel_bcast because (1) it currently
    causes seg fault on Edison when compiled with gfortran; (2) it is
    incorrect: only for root rank that argument has intent(in), whereas it
    should be intent(out) for other MPI ranks.

Src/F_BaseLib/parallel.f90

commit fa7626269a1dfa0ec2193648f8dee4730354dec8
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Nov 5 09:21:37 2014 -0800

    cims.nyu.edu

Tools/C_mk/Make.defs

commit 812acd140d830ede903f2cc651866d49bb764b2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 4 20:14:35 2014 -0800

    make Cray compiler on edison happy

Src/F_BaseLib/layout.f90

commit 852696a18b412c8d78055710885013cfd940952b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 4 11:32:08 2014 -0800

    wrap up ml layout strategy stuff

Src/F_BaseLib/ml_layout.f90

commit eb49fdc55aa78d5608314dbc17fd7cf705091730
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 3 16:38:37 2014 -0800

    more work on multi-level strategy 2

Src/F_BaseLib/ml_layout.f90

commit ec2c2e9d009c6c158489bdfb56851a1893698457
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon Nov 3 19:02:01 2014 -0500

    Further increase maximum pathname size, and get rid of magic numbers.

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/plotfile.f90
Src/F_BaseLib/ppm_util.f90
Src/F_BaseLib/ppm_util_c.c

commit 3472e1f923779615876b93a0d737a0665c21eb64
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 3 14:08:41 2014 -0800

    Donev updates

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit becc8e9c4be3cf60cf5f314105049c1161ffff3c
Merge: d302b3b9d 5c7d22417
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Nov 1 19:39:46 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 35715c3fd2335ce103123413f98fa181a89d8678
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 31 14:46:03 2014 -0700

    added comments

Src/F_BaseLib/create_umac_grown.f90

commit e3c13fdb6a0edcc4398ef44da2cdbb350ddc6927
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 31 14:30:26 2014 -0700

    fixed the fix

Src/F_BaseLib/create_umac_grown.f90

commit d9840f8060b20a4299afc4b8c018e82f50de4cf8
Merge: 042067fe7 35260a88f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 31 14:21:51 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 042067fe72c0368fc566b684e1be817538e507a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 31 14:21:46 2014 -0700

    fixed a new bug in create_umac_grown

Src/F_BaseLib/create_umac_grown.f90

commit 35260a88f166c9e8e1e41c9b917e94084dfb1b85
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 31 14:20:38 2014 -0700

    Add InitCosmo1ppcMultiLevel for IAG folks.

Src/C_AMRLib/Particles.H

commit 25e55d893e12ad4243b908b739ad9a5cbc9ef318
Merge: 004bd5c47 2609dcefe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 30 17:35:27 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 004bd5c471d273b97c9c7c1a081386873b306ad2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 30 17:05:03 2014 -0700

    removed one parallel copy from fill ghost cells

Src/F_BaseLib/create_umac_grown.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit f661d72b6803af2f8bbcc898c763e8168ad72cff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 30 16:35:19 2014 -0700

    added argument to create_umac_grown to tell whether we need to fill fine boundaries

Src/F_BaseLib/create_umac_grown.f90

commit c2334f4665a2f7cfbb98a29370737c5e595f20ab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 30 16:29:03 2014 -0700

    cleanup

Src/F_BaseLib/create_umac_grown.f90

commit e5bcb7c45be1401f2f721bdd93ff731fe87b3908
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 30 16:06:06 2014 -0700

    removed a parallel copy and fill_boundary from create_umac_grown

Src/F_BaseLib/create_umac_grown.f90
Src/F_BaseLib/layout.f90

commit 657b439bd84bf1da3c360628d3928d0b8cb7aa45
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 30 10:03:59 2014 -0700

    merge ghstassoc with fgassoc

Src/F_BaseLib/create_umac_grown.f90
Src/F_BaseLib/layout.f90

commit 0e59aa042a44cc24dad9eafa4ee359a24731ddb7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 30 09:55:42 2014 -0700

    simplify the boxarray in ghstassoc

Src/F_BaseLib/layout.f90

commit 1b2970a6a21e41c9d6edd8ca5eaea181f7297730
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 29 17:53:34 2014 -0700

    work in progress for ghstassoc, which is intended to replace fgassoc

Src/F_BaseLib/boxarray_f.f90
Src/F_BaseLib/create_umac_grown.f90
Src/F_BaseLib/layout.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90

commit 0a159b682f2e3f116db702b12cbadb2478f9ea16
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 29 13:53:54 2014 -0700

    put all output into one directory, bl_prof (or user specified name).
    write inclusive times option.
    trace flush threshold.
    directory creation cleanup.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 0ff5c471c44122a341ea13f6e3db5bcf052129fd
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 29 13:49:57 2014 -0700

    optional barrier in ccd.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit edcf4c51d6f653a049acb163f075eebfe1023b75
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 29 12:51:23 2014 -0700

    clean up directory creation.

Src/C_AMRLib/Amr.cpp

commit ea99ba554c46fd1eb91d571a09694c4132c10219
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 29 12:14:50 2014 -0700

    make ml layout strategy 1 more load balanced

Src/F_BaseLib/fab.f90
Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/ml_layout.f90
Src/F_BaseLib/sort_i.f90

commit 68d38d08e031c3f1f6660aea2a062ace89439a5f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 29 11:49:41 2014 -0700

    create clean directory function.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit b5d48ea6ad5111abef8de7dc1cbe10c687d95182
Merge: 6ca23d19c 2609dcefe
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Oct 29 10:56:57 2014 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2609dcefe467d1eefe5a34fad981aafa130448d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 28 20:34:29 2014 -0700

    removed some includes

Tutorials/HelloWorld_C/GNUmakefile

commit e4ab59d0346867db81453b10bb485683ba040f48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 28 17:34:10 2014 -0700

    Added a "hello world" type program for people to try tiling.

Tutorials/HelloWorld_C/GNUmakefile
Tutorials/HelloWorld_C/Make.package
Tutorials/HelloWorld_C/main.cpp
Tutorials/HelloWorld_C/work.f90

commit d302b3b9dc2cc1d045ca919b9a994b1208b256f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 28 20:21:51 2014 -0400

    add a trim()

fvarnames.f90

commit 5c7d224176b06eb1b46d6de83df514fc4ab8ba7f
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Tue Oct 28 17:10:52 2014 -0400

    Add comparison temp histograms using the EoS.

MAESTRO_sub_chandra/GNUmakefile
MAESTRO_sub_chandra/fsubchandra.f90
MAESTRO_sub_chandra/fsubchandra_mod.f90

commit 4d8d58e9cc520ece0736a35fcf86f8b1d4cc94c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 28 14:06:33 2014 -0700

    F90 ml layout strategy 1: use prefilled version of knapsack for
    unassigned boxes.

Src/F_BaseLib/ml_layout.f90

commit 2490dbf547a444e097195acbd5ddf3c560fc7f2f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 28 14:05:40 2014 -0700

    F90: new knapsack that can have processors prefilled with boxes

Src/F_BaseLib/knapsack.f90

commit 04ef81cfc8915bb56ac792edfd54b81a6aedea77
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 27 15:38:12 2014 -0700

    added call trace data flushing.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 79106b16218ef782ccafaed6f21b4a90ecc7d73c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 27 15:17:18 2014 -0700

    F90: fine tune ml layout strategy 2

Src/F_BaseLib/ml_layout.f90

commit 0f79fe02a18b8067f728830cb077199826f61e1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 27 14:59:56 2014 -0700

    F90: fine tune ml layout strategy 2

Src/F_BaseLib/ml_layout.f90

commit 100e9e66a6823fd5d371a01059a220d0207699c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 27 14:20:28 2014 -0700

    F90: implemented ml layout strategy 2

Src/F_BaseLib/ml_layout.f90

commit 1e873a181478c9f2d0c2d31d38e61658e99f5295
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 21:36:48 2014 -0700

    cleanup

Tutorials/HeatEquation_EX7_F/GNUmakefile

commit 23fdc8b4b82e083e4ae88da81ae78ce10b8852d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 21:29:15 2014 -0700

    update comments

Src/F_BaseLib/ml_layout.f90

commit 5dc6f66c4d44cc5dca4962ce46738243cf2476d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 21:27:56 2014 -0700

    F90: use the simple version for tutorial

Tutorials/HeatEquation_EX5_F/main.f90

commit 4cf6808de2162dad96b911dba4e747cddf2cb743
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 21:20:25 2014 -0700

    minor

Tutorials/AMR_Adv_Diff_F/main.f90

commit 81e7332be666dae1610ad5da0231ad3143a74da1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 21:19:28 2014 -0700

    fixed a bug in Tutorials/AMR_Adv_Diff_F

Tutorials/AMR_Adv_Diff_F/compute_flux.f90

commit 9b3014acbef3da122f826776f9acec0c4b8da6bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 19:38:01 2014 -0700

    F90: destroy unused layouts

Src/F_BaseLib/ml_layout.f90

commit 6d015082d8df1b834b2f426968230f333761ab63
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 15:15:18 2014 -0700

    F90: back to use lower corner of boxes in sfc for testing, and some other minor changes

MiniApps/AMR_Adv_Diff_F90/main.f90
Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/ml_layout.f90

commit 6aa0c987205848e719fa79be1303833504e31b3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 14:01:51 2014 -0700

    F90: implemented the ignore_fine_in_layout_mapping strategy in ml_layout.f90

Src/F_BaseLib/layout.f90
Src/F_BaseLib/ml_layout.f90

commit a7df7dc62a1a2e9102bc43f2d2084121319d4c18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 11:37:57 2014 -0700

    F90: moved ml layout optimization stuff into ml_layout module, and do it when building ml_layout

MiniApps/AMR_Adv_Diff_F90/main.f90
MiniApps/AMR_Adv_Diff_F90/write_plotfile.f90
Src/F_BaseLib/CMakeLists.txt
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/ml_layout.f90
Src/F_BaseLib/ml_optimization.f90
Src/F_BaseLib/ml_remap.f90
Src/F_BaseLib/regrid.f90
Tutorials/HeatEquation_EX5_F/main.f90

commit 95e959dfb9dc44400065e43f7085a970aff1b31a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 25 21:37:18 2014 -0700

    renaming: ml_layout_remap --> ml_remap; and flesh out more interfaces

Src/F_BaseLib/CMakeLists.txt
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/ml_layout_remap.f90
Src/F_BaseLib/ml_optimization.f90
Src/F_BaseLib/ml_remap.f90

commit 8b22442d14c2d5e846738bc1747500594b8fb8b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 25 20:36:13 2014 -0700

    F90: cleaned up layout by removing obsolete pn_children

Src/F_BaseLib/layout.f90
Src/F_BaseLib/ml_layout.f90

commit b256351283fb329eb85f5f43448965fe3e5dee1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 25 20:50:03 2014 -0400

    add a 1-d routine, in prep for the Maestro flame problem.  Also some styling syncing with that version

Src/F_BaseLib/multifab_physbc.f90

commit 3c33fa93410f0c42f03245df91bdf30bd94a8a94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 24 21:18:03 2014 -0700

    F90: flesh out ml layout remapping

Src/F_BaseLib/CMakeLists.txt
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/ml_layout_remap.f90
Src/F_BaseLib/ml_optimization.f90
Src/F_BaseLib/regrid.f90

commit 7061443c2396c3f415e2b95bf38d6d299d4630af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 24 17:17:36 2014 -0700

    F90: use center of boxes instead of lower corner in sfc

Src/F_BaseLib/knapsack.f90

commit 934530bcd9388daf4ed264de2bff2bd6d5bd10bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 24 16:35:31 2014 -0700

    F90: split sfc_i into two functions, and save sfc order in layout

Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/layout.f90

commit b2e823c45b9c4539849b9534de24d388f61dec03
Merge: ada8195be f83d67e3a
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Oct 22 17:40:11 2014 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing
    
    Conflicts:
            F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90

commit ada8195beb70d0cf0fed7ebffc84fb6ba1dd58dc
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Oct 22 17:38:02 2014 -0500

    Add ability to handle full star geometries to sub-Chandra
    analysis routine.

MAESTRO_sub_chandra/fsubchandra.f90
MAESTRO_sub_chandra/fsubchandra_mod.f90

commit f83d67e3a025012755c42df235fe6ae74a07b864
Merge: 04a1bde19 9d49ed7ea
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Oct 22 18:35:45 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 04a1bde19337fea4f5c940673d7f3cf520bd5fe8
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Oct 22 18:35:07 2014 -0400

    Add caclulation of temperature histogram data for the lengthscale
    of each level of refinement.

MAESTRO_sub_chandra/fsubchandra.f90
MAESTRO_sub_chandra/fsubchandra_mod.f90

commit 6ca23d19c4d28c385cdf55a13fa74f1995014e57
Merge: 74cae01e9 a710adc26
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Tue Oct 21 15:37:49 2014 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib
    
    Conflicts:
            Tools/F_mk/comps/Linux_intel.mak

commit 74cae01e93529fe385cd5c5067859a00a7a5f95f
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Tue Oct 21 15:34:15 2014 -0500

    Add version 15 of the Intel compiler to Linux_intel.mak.  This
    is the version on Blue Waters.

Tools/F_mk/comps/Linux_intel.mak

commit a710adc2677cc775866842fdc541a94909e2372f
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Oct 21 12:48:25 2014 -0700

    MLSDCAmr: Use AmrLevel constructors for MLSDCAmrLevel.

Src/C_AMRLib/MLSDCAmr.H

commit 7a7d585389b18315af009182e4abbd55e5e39e6d
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Oct 21 12:42:39 2014 -0700

    Add MLSDCAmr.

Src/C_AMRLib/MLSDCAmr.H
Src/C_AMRLib/MLSDCAmr.cpp
Src/C_AMRLib/MLSDCAmrEncap.cpp
Src/C_AMRLib/Make.package

commit 893a1ff11679a2f13c8110ed6edad761e5dee4c7
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 21 11:16:01 2014 -0700

    added file

Src/C_BaseLib/BLProfiler_F.f

commit b5304da1a09954588c75af84de0f73f65c4145f1
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 21 10:50:12 2014 -0700

    added proffort interface to master branch.

Src/C_BaseLib/Make.package
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp
Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/bl_prof_stubs.f90

commit d081130b301f101175f877a55fd983e36dfddd01
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 20 13:37:54 2014 -0700

    added step regions.

Src/C_AMRLib/Amr.cpp

commit 831e0ca4c5d29dc531a5dfd87c8c74e39b2e0bbc
Merge: 97a909929 e31c68669
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 20 10:16:50 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 97a909929b67b795acef20ca2a681e995e012478
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 20 10:12:57 2014 -0700

    When printing fab byte spread information, let's us MB as units for avoiding integer overflow and readablity

Src/F_BaseLib/fab.f90

commit e31c686698610167a7831207e1cc1484fda05cf7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Oct 19 15:50:39 2014 -0400

    add "tooltips" when you hover over a test's cell in the master table of all
    the runs.

Tools/RegressionTesting/testnew.py

commit 4b7c1180bac396265f384ee84bfa9af7e7e4b5e6
Merge: fe652a729 e3d58afc0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Oct 19 06:20:16 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit fe652a729500d7753310ade92b834a44636605ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Oct 19 06:19:48 2014 -0700

    remove support for Intel versions 8 and 9 -- these are about 10 years old and
    unlikely to work (or to be found anywhere)

Tools/F_mk/comps/Linux_intel.mak

commit e1f41c11d09995b284446c1cc7efdfd883ea7ec2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Oct 19 06:19:25 2014 -0700

    kraken no longer exists (RIP...)

Tools/F_mk/GMakeMPI.mak

commit e3d58afc017b17ed1618421e6a1d7ee7685e434f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 18 07:42:26 2014 -0700

    F90: tweaked the copyassoc_check to make it go much faster; now we can afford to increase the maximum count of the copyassoc allowed

Src/F_BaseLib/layout.f90

commit 1d449c1d702d97c7ad6e5948c5516efa5f539620
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 17 21:02:16 2014 -0700

    F90: added OMP to sfc

Src/F_BaseLib/sort_i.f90

commit 4938e68747bb592963ed55fb67e787a1de06cb1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 17 17:56:41 2014 -0700

    F90: added a timer to find out how much time is spent in copyassoc checking

Src/F_BaseLib/layout.f90

commit 309b02a119ee787d61bb55e59e0278ce945a1f73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 17 15:58:30 2014 -0700

    F90 profiler: print warning to the profiling result file instead of stdout

Src/F_BaseLib/bl_prof.f90

commit f1b58f09c33557bf6067a7c5511269ebd5b8e529
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 17 15:56:58 2014 -0700

    F90: added OMP to multifab copy

Src/F_BaseLib/multifab_f.f90

commit d3fe9d7fdfc12bbf275a12953cb363644cba3769
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 17 08:48:02 2014 -0700

    F90 profiler: print out profiling results for each individual processor even if the call trees are different

Src/F_BaseLib/bl_prof.f90

commit c7d7b2625c2ae4a777defd4f7061d7c59725765d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 16 17:53:56 2014 -0700

    F90 profiler: to help debug, print out more information when the call trees are not identical.

Src/F_BaseLib/bl_prof.f90

commit d18d35d6b35f4f84810f3c9e658fee855888104d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 16 17:23:20 2014 -0700

    F90 linear solver: fixed bl_prof_timer issue arisen from MPI communicator that does not include all ranks

Src/LinearSolvers/F_MG/itsol.f90

commit b6a89471f07d134f110f505d9d79bad08167c230
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 16 16:33:04 2014 -0700

    F90 ml_cc_solve: no need to build fine mask here becuase we have one already in ml_layout

Src/LinearSolvers/F_MG/ml_solve.f90

commit 174c466f4c5772ccc27fc60873fdcaddbecb7f8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 16 14:41:28 2014 -0700

    removed a few unsafe bl_prof_timers because they might be inside OMP parallel region

Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit 1ba4035f52f3519cb09a181e114b8c0710b85503
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 16 14:16:09 2014 -0700

    F90 linear solver: made the number of ghost cells of cell and edge coefficients consistent with alpha and beta passed in; there is no reason to always have one ghost cell

Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/ml_solve.f90

commit 6100020bfb854f1da904cf75d0c9d78ec0ce9eda
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 16 11:55:18 2014 -0700

    macros from the commprof branch.

Src/C_BaseLib/Profiler.H

commit ee53eba2f1b2f7e416d0a479c463fb8a33477587
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Oct 15 14:58:48 2014 -0500

    Increase the maximum filename and full pathname from 128 character
    to 256 for the Fortran codebase.

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/plotfile.f90
Src/F_BaseLib/ppm_util.f90
Src/F_BaseLib/ppm_util_c.c

commit 5937f521e8cdedae5d15d7bbf12adac460852c56
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 15 11:15:04 2014 -0700

    F90 linear solver: use the 8-byte integer versions of volume functions to find out if we cover the entire domain (if supported)

Src/LinearSolvers/F_MG/mg.f90

commit ac8bcef08e42c79e955056e74fe36d7f7318f757
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 15 11:13:01 2014 -0700

    F90: added a 8-byte integer version of box volume function, and used it in boxarray volume function

Src/F_BaseLib/box_f.f90
Src/F_BaseLib/boxarray_f.f90

commit f1f3555a6d6d58f9529c7f53b1abf5c89cc13e86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 15 11:11:37 2014 -0700

    F90: added query functions that return whether or not quad precision or 8-byte integer is supported

Src/F_BaseLib/bl_types.f90

commit 47287f33ad4c2554f9c8ef18d9a49c94949b30ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 14 20:33:14 2014 -0700

    clean up the new ml_layout_build_la

Src/F_BaseLib/ml_layout.f90

commit 958b2a45bb0efb2d9156f9887ca105f12925d9d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 14 17:41:23 2014 -0700

    new ml_layout_build that copies another layout

Src/F_BaseLib/ml_layout.f90

commit e172dad694404461ef6c885d65900fdba32772b3
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 14 16:11:51 2014 -0700

    better bounds checking for debug.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 1bb399d8a993ed54a19c84e004755670c4b84607
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 14 15:43:43 2014 -0700

    made the meaning of sfc_threshold in F90 consistent with C++

Src/F_BaseLib/layout.f90

commit e77cdb8c40e52ef75feb95539bf7ff82040fc509
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 14 15:30:55 2014 -0700

    F90: only allow sfc to not sort in the least_used_cpus function

Src/F_BaseLib/fab.f90
Src/F_BaseLib/layout.f90

commit 651d3340f57c15d900f59f381ec257c0841916e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 14 15:20:13 2014 -0700

    F90: removed an unused function that was recently added

Src/F_BaseLib/fab.f90

commit 340996c0e4a8e1d219791de09f1a9372fb7002ef
Merge: 3903414d3 fcbd126d2
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Oct 14 11:11:17 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3903414d3cdf65439c43f59c74c7033d5a55c48b
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Oct 14 11:09:46 2014 -0700

    Add GetParticles method to ParticleContainer.

Src/C_AMRLib/Particles.H

commit fcbd126d2ccd068662926ec002dbc05026f270bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 14 13:59:12 2014 -0400

    add a description provided by Weiqun`

Src/F_BaseLib/cluster_f.f90

commit 620361827b169d5115fc037739e088be7f201553
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 14 10:18:31 2014 -0700

    F90: check allocation status of imask

Src/F_BaseLib/cluster_f.f90

commit 4585b8731d0e243f0c61e70af6058a1cd1297b09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 13 17:15:30 2014 -0700

    fixed comments

Src/LinearSolvers/F_MG/ml_solve.f90

commit eaebbec608ca9b63152141019af0be09bedd7d4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 13 17:14:13 2014 -0700

    F90: updated OMP for non-blocking multifab_fill_boundary so that it
    can be used for nodal mfs.

Src/F_BaseLib/multifab_f.f90

commit 28408dd293673983a70e9ecfe4f66932139fbadd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 13 13:26:50 2014 -0700

    F90: speed up cluster a little bit

Src/F_BaseLib/cluster_f.f90
Src/F_BaseLib/fab.f90

commit be77cbc85e6d67b9075583de1ca5f7a9db3d37ee
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 13 12:21:44 2014 -0700

    added several regions.

Src/C_AMRLib/Amr.cpp

commit 0969346955358e3811e640e15a0af79bea8e8158
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 13 12:15:46 2014 -0700

    more regions and trace profiling, allow regions
    for commprof without traceprof.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 8dd9b8b49612b0ee08967384e03ed37a773b65b6
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 13 12:12:03 2014 -0700

    added TRACE_PROFILE and new prof suffix and defs.

Tools/C_mk/Make.defs

commit e76ca5fea08a25c6406bb672cb2a7f289e519bb3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 10 20:59:33 2014 -0700

    F90: use merge sort rather than heap sort in SFC for speed

Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/sort_i.f90

commit 2c099e34c4b6712ba8d6ae7dbf37494833d54981
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 10 17:06:04 2014 -0700

    some reorg, relative minmax calltimes.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 902ee7d318d247a09791f973c104d72d1c7485ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 10 16:02:27 2014 -0700

    fixed indentation

Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90

commit 3a098deb1f70cad80d58e8ecac295cabaf3a72c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 10 12:11:24 2014 -0700

    added timer to create_nodal_mask

Src/LinearSolvers/F_MG/nodal_mask.f90

commit 7046c241c07cb6f676a69ae3142f0f43f55a7a09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 10 11:22:20 2014 -0700

    removed a duplicated copy of create_nodal_mask

Src/LinearSolvers/F_MG/ml_solve.f90

commit 0791d9591f828063aeba0b952ccd1e5f180570d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 10 13:34:46 2014 -0400

    fix the summary table for when we make benchmarks

Tools/RegressionTesting/testnew.py

commit 603f48c42f71ca6df39d3e7409117d237b26ce88
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 10 12:19:55 2014 -0400

    add the wall time to the summary table

Tools/RegressionTesting/testnew.py

commit dcea25ffcea0965b7924627b7bcdf177b98bb797
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 9 18:10:21 2014 -0700

    F90: option to keep cpu order in providing the list of least used cpus

Src/F_BaseLib/fab.f90
Src/F_BaseLib/regrid.f90

commit f1ed215fc0f9d88772aa60b9c0b10feedc0e7595
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 9 16:46:38 2014 -0700

    added const.

Src/Extern/amrdata/AmrData.H

commit 2395dcba90abb0c6c502cb6058d0a361674699a9
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 9 16:36:37 2014 -0700

    added const.

Src/Extern/amrdata/AmrData.H

commit 8cb847a7c79cdab08deff48aac9507c01cc200f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 9 16:32:13 2014 -0700

    F90: incresed maximum # of copyassocs from 25 to 50

Src/F_BaseLib/layout.f90

commit 3b8afda46b5371c7f7d30005991c14f3c81a58e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 9 14:55:53 2014 -0700

    F90: rebuild fine layout too when not properly nested

Src/F_BaseLib/regrid.f90

commit e926d47a7bf668f86e0ace334f76f860483d4b38
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 9 14:42:02 2014 -0700

    F90: new strategy for which item to remove when the copyassoc list is full

Src/F_BaseLib/layout.f90

commit 39bc961bcd625349fd3cdcdbf9e316f304fd4f38
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 9 16:45:37 2014 -0400

    prettification

Tools/RegressionTesting/testnew.py

commit 0e9f83d09934626aa89316c54a08a8e74fa1cfb8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 8 22:28:57 2014 -0400

    make the test run summary more informative

Tools/RegressionTesting/testnew.py

commit d8bfca92cc3b3a8f3f445de4cf0d812a92c503e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 8 21:32:57 2014 -0400

    keep track of the number of levels by running fboxinfo on the output
    -- this is stored in the test object

Tools/RegressionTesting/testnew.py

commit 252cac246afea514935ce1e001564be6f5c02768
Merge: 2c7b1a202 74e22b36e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 8 20:38:31 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2c7b1a2024acc8a9fa9addbc81e3ce290ab3e343
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 8 20:38:14 2014 -0400

    latest version

Tools/RegressionTesting/Maestro-tests.ini

commit 9d49ed7ea5dada415d6e2969768b5b6694c5c856
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 8 20:25:22 2014 -0400

    fix compilation

fboxinfo.f90

commit b9844a45c96e73942c80b57326884e7c8762fbbe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 8 20:24:06 2014 -0400

    add a -l option that only prints the number of levels -- I'm going
    to use this in the test suite shortly...

fboxinfo.f90

commit 74e22b36e2957bb967fe2098f9065c12371b20bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 8 16:34:43 2014 -0700

    F90: ignore fine in layout mapping

Src/F_BaseLib/regrid.f90

commit 31415a1ef7d24d57804b223f1750ffa9969ce8a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 8 16:27:32 2014 -0700

    F90: We now have more control on the least used cpus function.  This can be used by regrid to ignore fine in layout mapping

Src/F_BaseLib/fab.f90
Src/F_BaseLib/layout.f90

commit 36b12d038748f203f2eb6d3d89b85011c94c088e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 8 13:32:03 2014 -0700

    tidy

Src/F_BaseLib/regrid.f90

commit e637ca5998105171134e36b2734d9b8dca7a6ba4
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 8 13:21:33 2014 -0700

    made profiler output functions generic.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 467b28c54243df740ff4be32ce6c7dd4ee7181f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 8 13:15:11 2014 -0700

    Do not fill ghost cells in regrid unless told so by tag_boxes
    module. Do not call fillpatch if the new grids are the same as the
    original ones because a simple multifab copy is sufficient in this
    case.

Src/F_BaseLib/regrid.f90
Src/F_BaseLib/tag_boxes.f90

commit 2ac6e9941608b5604c7602ecc5673d4d1f4241da
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 8 10:21:57 2014 -0700

    moved text call tree to postprocessing.

Src/C_BaseLib/Profiler.cpp

commit 038a10222481b0095f536495212b0f49e4d86df6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 8 09:49:58 2014 -0700

    fixed a bug in miniapp

MiniApps/AMR_Adv_Diff_F90/compute_flux.f90

commit 90155764a8a76125c012e3b773c38ce126996380
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 8 09:41:03 2014 -0700

    fixed a new bug in index slicing in ml_boxarray

Src/F_BaseLib/ml_boxarray.f90

commit f07dc7457e2daf0ec73ac3678ade280f5b034f66
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 7 16:05:12 2014 -0700

    moved html output to postprocessor.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit d75cc277b981275a57d354b48b3c1b233b21e42f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 7 14:20:16 2014 -0700

    added optional argument ref_ratio to cluster routine

Src/F_BaseLib/cluster_f.f90
Src/F_BaseLib/make_new_grids.f90

commit c86401a5a47756ac7ea50e8e5fb07b91bc45ab73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 7 14:04:11 2014 -0700

    added arm_ref_ratio to ml_boxarray_module to make regrid easier to get
    that information

MiniApps/AMR_Adv_Diff_F90/main.f90
Src/F_BaseLib/ml_boxarray.f90
Src/F_BaseLib/regrid.f90
Tutorials/AMR_Adv_Diff_F/main.f90
Tutorials/HeatEquation_EX3_F/main.f90
Tutorials/HeatEquation_EX4_F/main.f90

commit 7f176edab4c2254fa35508b87b5b037325ab5ea1
Merge: f4729fca5 0aed1d30b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 7 14:01:49 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit f4729fca5b4fb4f794256cf153ad51cdb26aaa4a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 7 14:01:02 2014 -0400

    have the list of active tests be what is defined in the .ini file -- this way we still
    see all the old active tests in the web report when we run with --redo_failed

Tools/RegressionTesting/testnew.py

commit 0aed1d30b914e62a8364f91718cbf9e12f6cc8b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 7 10:43:05 2014 -0700

    make regrid use ref ratio stored in the mla argument

Src/F_BaseLib/regrid.f90

commit 53c9396a32c39b270191c7acbe5374831205b16f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 7 10:02:38 2014 -0700

    Remove unused variables.

Src/F_BaseLib/ml_nd_restriction.f90
Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit 2f35ab8786be07e6d42e11e0f1b7f934ebd88617
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 7 10:42:30 2014 -0400

    add the --redo_failed option.  This will automatically find all the
    tests that failed when the suite was last run and only rerun those.

Tools/RegressionTesting/testnew.py

commit 40e3477e70332e468f2a54758dae703e3de70816
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 6 17:05:51 2014 -0700

    sync names function into output, organized some code.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit ef9ef08c8e16faa651692ce65b38476248492bfb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 6 15:42:15 2014 -0700

    moved the new regid subroutine that does not change the base level into F_BaseLib

MiniApps/AMR_Adv_Diff_F90/GPackage.mak
MiniApps/AMR_Adv_Diff_F90/main.f90
MiniApps/AMR_Adv_Diff_F90/regrid.f90
Src/F_BaseLib/CMakeLists.txt
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/regrid.f90
Tutorials/AMR_Adv_Diff_F/GPackage.mak
Tutorials/AMR_Adv_Diff_F/main.f90
Tutorials/AMR_Adv_Diff_F/regrid.f90
Tutorials/HeatEquation_EX4_F/GPackage.mak
Tutorials/HeatEquation_EX5_F/GPackage.mak
Tutorials/HeatEquation_EX5_F/regrid.f90

commit 1ff038a97b62e2fd32a2f78d2ee653b3d2ba8fca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 6 14:59:38 2014 -0700

    option to keep coarse layout when destroying multi-level layout

Src/F_BaseLib/ml_layout.f90

commit 73d60856a0aae989f4dc116b593c262cb27d80af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 6 14:57:19 2014 -0700

    added a new line in printf

Src/C_AMRLib/Amr.cpp

commit b5e86adad1e6fa27c73c88d7c0143b44dedc4688
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 6 14:10:51 2014 -0700

    fix for serial.

Src/C_BaseLib/Utility.cpp

commit d97a2ce359f16198217df4e74016bc06cfd0e58d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 6 13:39:22 2014 -0700

    Update to work with new restrictions files...

Tests/LinearSolvers/F_MG/cc_multi.f90
Tests/LinearSolvers/F_MG/nodal_multi.f90

commit fd311a48ba8024504deb60f8877362bdac10eb66
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 6 13:02:53 2014 -0700

    Initialize variable so we don't get compiler warning.

Src/F_BaseLib/box_f.f90

commit 1e8747412169bdd5b5523450339bb2b679334c21
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 6 12:59:20 2014 -0700

    Remove unused variable.

Src/F_BaseLib/fabio_c.c

commit 5d56b18105fb6cfebaffc375ce260cb4ba096808
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 6 12:47:40 2014 -0700

    Remove unused variable.

Src/F_BaseLib/layout.f90

commit 76e0148cefc7f31066528835683337cebebeeadd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 6 11:22:01 2014 -0700

    Add test on plot_int < 0 so we can turn off plotfiles by
    setting plot_int negative in the inputs file

MiniApps/AMR_Adv_Diff_F90/main.f90

commit 75db8a8b43e6d64ffc6c3c9ec28d1d19ee102bea
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 3 12:52:03 2014 -0700

    added function to sync sets of strings over procs.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 94cdb670f5f75d9a118534ae40d7d5035c0d9df8
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 2 11:10:40 2014 -0700

    mask for NoRegion region.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 1df7bcbab00a66056659d1af9cb46887c364490c
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 1 14:46:29 2014 -0700

    added time values and NoRegion to region prof.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 37061ed37e840ea9245432bbc232ce797ab43632
Author: vince <vebeckner@lbl.gov>
Date:   Mon Sep 29 16:07:18 2014 -0700

    streamlined binary callstats format.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 9f18b8e899f8fe63e21d82328da48df17b5e280e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 29 09:05:29 2014 -0700

    Replace HeatEquation_EX6_F by AMR_Adv_Diff_F in documentation -
    this now correctly reflects what is in the code itself.
    Please enter the commit message for your changes. Lines starting

Docs/F_AdvancedTopics/F_AdvancedTopics.tex

commit d5862ceb1f3d2059981fa22f26208df6467bb59c
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 25 16:12:30 2014 -0700

    binary format for trace data.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 27e89d06697ae9b059fd3625abaac2cd3e30e38b
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 24 17:47:02 2014 -0700

    Set default for tecplot tool to not require tecplot bin libraries

Tools/C_util/AmrDeriveTecplot/GNUmakefile

commit c89ed40571ff86ec5eec542823e8ead5eb3b6c1a
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 24 17:39:38 2014 -0700

    Add script to generate flattened pltfile format for Tecplot

Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp
Tools/C_util/AmrDeriveTecplot/GNUmakefile

commit e2040f95ff47dcf621d2358ed98c417bc6c6aaae
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed Sep 24 11:26:11 2014 -0700

    PyBoxLib: Add --disable-mpi build option.

Src/Python/README
Src/Python/setup.py

commit f41494b9f7bea8fcc9494cc3c0fd924148c2966f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 23 15:23:37 2014 -0700

    fixed a bug in index of stencil array

Src/LinearSolvers/F_MG/cc_ml_resid.f90

commit 362630e1c8f2b15323b24dc25ba49676bf95fe57
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Sep 23 13:14:37 2014 -0700

    PyBoxLib: Honor USE_MPI environment variable.

Src/Python/setup.py

commit 8409f066203c2e265f63fdcfc7212fcb0d07337c
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Sep 23 12:50:37 2014 -0700

    PyBoxLib: Add a more informative error message when mpicc can't be found.

Src/Python/setup.py

commit 2b34a94066120697c7bea02472dea04e2595969d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 22 16:51:52 2014 -0700

    cleanup

Src/F_BaseLib/ml_layout.f90

commit 72ced02cfce8d0ef560056fdf0d2563a9b96bd6c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 22 15:25:25 2014 -0700

    more cleanup

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 69d0d6bd64b64878f0a0a7c2d8014df89d528b1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 22 15:16:46 2014 -0700

    clean up

Src/F_BaseLib/multifab_f.f90

commit 57e5f79b9f5fd04c7b4ad007f68c0ced29580b6e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 22 14:49:39 2014 -0700

    removed pingpong.f90 from CMake

Src/F_BaseLib/CMakeLists.txt

commit d456083e44a168640f3307828f5dde8c89c7b88d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 22 14:08:51 2014 -0700

    F90 BoxLib: moved boxarray_intersection_bx into ml_boxarray and made it private because
                (1) it is only used by ml_boxarray;
                (2) the naive implementation works perfectly because bx intersects with every boxes in ba.

Src/F_BaseLib/layout.f90
Src/F_BaseLib/ml_boxarray.f90

commit 97a0c055757d18538eeeb57f9987fae80b640012
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 22 13:43:25 2014 -0700

    F90 BoxLib: reimplemented boxarray-box intersection routines using the hash

Src/F_BaseLib/layout.f90

commit a4960165f769e7625ee2225c2585c6887386bc26
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 22 11:17:34 2014 -0700

    removed subroutines that do naive boxarray-box intersectin from boxarray module to layout module so that they can be reimplemented.

Src/F_BaseLib/boxarray_f.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/ml_boxarray.f90

commit 0de8c31b99e817e19c288847f0779031f6c11269
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Sep 21 19:51:16 2014 -0400

    we were using the wrong variable in the indxmap for the bndryreg
    
    j = indxmap(j)  -->  j = indxmap(i)

Src/LinearSolvers/F_MG/cc_ml_resid.f90

commit f28bee18c3db8e6e81f8a1dff007fe1de10c6416
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 19 13:59:10 2014 -0700

    added nooutput option.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 3f5652791f439782ec599577dd4de353c4b79665
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 18 11:56:21 2014 -0700

    more region profiling.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 9da1a05b7596c3ff1b039b19dd15f98435cb257f
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Sep 16 14:36:12 2014 -0700

    Uptick version number

Tools/CMake/BoxLib_Version.cmake

commit 47547ded742b348d9b32145a5860528e0c60fc71
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 16 11:26:04 2014 -0700

    minor cleanup

Src/F_BaseLib/layout.f90

commit c6d36bd20581d6229ff46eb39b9d87d766202231
Author: Matthew Emmett <memmett@gmail.com>
Date:   Mon Sep 15 22:13:16 2014 -0700

    PyBoxLib: Fix inclusion of libgfortran and libquadmath.

Src/Python/GNUmakefile_CXX.mak

commit 7721947b4d7f89dc11d7c838ff712a0e4cb495a4
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Mon Sep 15 10:52:54 2014 -0700

    PyBoxLib: Add library path for quadmath.

Src/Python/GNUmakefile_CXX.mak

commit 0cef41d13567367c6d78719e35c78c047247417b
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Mon Sep 15 10:52:32 2014 -0700

    Make.defs: Increase template depth to support clang (LLVM).

Tools/C_mk/Make.defs

commit 7e3c0f1de5863575fd8a2db287212cf76842b559
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Fri Sep 12 16:13:08 2014 -0700

    PyBoxLib: Set MPI_HOME according to location of mpicc by default.

Src/Python/setup.py
Tools/C_mk/Make.mpi

commit 400c9806ea9e9505fb9aa963b3efd45c6a51d777
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Fri Sep 12 15:30:06 2014 -0700

    PyBoxLib: Simplify PYLIBS.

Src/Python/GNUmakefile_CXX.mak

commit cafef0788cccc2bea527ac22efd3c2f7a2cfd2bb
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Fri Sep 12 13:15:33 2014 -0700

    PyBoxLib: More trickery for Darwin.

Src/Python/GNUmakefile_CXX.mak
Src/Python/setup.py

commit b9967948f0a0a872b4790c923179da593d5450f4
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Fri Sep 12 13:15:10 2014 -0700

    Make.mpi: Don't change FC, F90 etc on Darwin.

Tools/C_mk/Make.mpi

commit bc09acde57335390279611ceeb8ddc994d338f91
Merge: 56ddf44bb a85b2a66d
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Fri Sep 12 12:15:48 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 56ddf44bb2e903ce09eec0c2ec42bc06d72fd5af
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Fri Sep 12 12:15:37 2014 -0700

    PyBoxLib: Move compiler defs to GNUmakefile and honor env CXX and CC.

Src/Python/GNUmakefile
Src/Python/GNUmakefile_CXX.mak

commit d78dfed39e58e2f6d931aebea58efb2ee5cd6c78
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Fri Sep 12 12:14:44 2014 -0700

    Make.defs: Set defaults after checking USE_GCC, honor env CXX and CC if USE_GCC is true.

Tools/C_mk/Make.defs

commit a85b2a66d7dc511f57cb25149fa6b5970c07599f
Merge: f0c82ad3c 4cddcc905
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Fri Sep 12 12:39:07 2014 -0600

    merge
    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f0c82ad3c819a1712f9b236a98959d3dcb64ec93
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Fri Sep 12 12:39:02 2014 -0600

    dont use libmpi_f77 on my Mac!

Tools/C_mk/Make.mpi

commit ff275283384f58e8b831669b277a9b6eefcd0442
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 12 14:34:15 2014 -0400

    change option name

fcompare.f90

commit 3a6cdf6e87e3f02c2cf783d5aaa8e96bcc3ea300
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 12 14:20:19 2014 -0400

    start of support for outputting a plotfile of diffs

fcompare.f90

commit 490739f030b90f2d7f6757d64614223a4ae6285b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 12 14:17:37 2014 -0400

    layout_build_ba now requires the pd argument

tutorial/fwrite2d.f90

commit 4cddcc90526076fdb4cdebaba213b80aa120de9b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 6 13:41:44 2014 -0700

    F90 BoxLib: use stable sort in building the list of least used cpus. There is no reason for not doing this, and this makes it consistent with C++ BoxLib.

Src/F_BaseLib/fab.f90

commit f42eaa67bc1f9d3bd3993f72ddeea660b36c32f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 5 22:09:13 2014 -0700

    minor update in F90 flux register

Src/F_BaseLib/bndry_reg.f90

commit f1d5f8891e89732418116ffb33430d2cbc6cbde6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 9 21:21:58 2014 -0700

    Only if there are no periodic boundaries, we can return immediately from multifab_copy when ng=0

Src/F_BaseLib/multifab_f.f90

commit fb5db3b03ad7b259bdd05afdebc043ad2aca6709
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 9 10:59:33 2014 -0700

    remove some outdated comments

Src/F_BaseLib/multifab_f.f90

commit c25366d52ff53b71ae573e8a0c4b50e2c2ade5e2
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Sep 9 08:59:53 2014 -0700

    multifab_fill_boundary and multifab_physbc return if ng==0

Src/F_BaseLib/multifab_f.f90
Src/F_BaseLib/multifab_physbc.f90

commit 5a1c4fa295fcde2f0e0f42cb2dcc497093f2f84e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 8 16:09:28 2014 -0700

    added one moer argument to ml_restrict_and_fill so that n components can share one type of boundaries

Src/F_BaseLib/ml_restrict_fill.f90

commit 265d0fa585a41b90878510bf7755920722a07537
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 8 14:00:53 2014 -0700

    should not include ml_restric_fill_module in FParalleMG.mk

Src/F_BaseLib/FParallelMG.mak

commit 8eac360e1c5287d630079bf11c5ae6e80c7340d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 8 13:44:17 2014 -0700

    update to the new flux register

MiniApps/AMR_Adv_Diff_F90/GPackage.mak
MiniApps/AMR_Adv_Diff_F90/advance.f90
MiniApps/AMR_Adv_Diff_F90/compute_flux.f90
MiniApps/AMR_Adv_Diff_F90/init_phi.f90
MiniApps/AMR_Adv_Diff_F90/main.f90
MiniApps/AMR_Adv_Diff_F90/reflux.f90
MiniApps/AMR_Adv_Diff_F90/regrid.f90
MiniApps/AMR_Adv_Diff_F90/update_phi.f90

commit 1e6886811f1dd2fa6a189dc8543a988d335de3d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 8 13:41:23 2014 -0700

    forgot to add in last commit

Src/F_BaseLib/ml_restrict_fill.f90

commit bfd4b589f3463a179f0691f898505f2b0fcd8ee2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 8 13:16:31 2014 -0700

    Added a new module for doing multi-level restriction and then fill all the boundaries because this needs to be done in so many places, and the new module saves half of fill_boundary calls for levels from 2 to nlevs-1.

Src/F_BaseLib/CMakeLists.txt
Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/GPackage.mak
Tutorials/AMR_Adv_Diff_F/init_phi.f90
Tutorials/AMR_Adv_Diff_F/regrid.f90
Tutorials/AMR_Adv_Diff_F/update_phi.f90
Tutorials/HeatEquation_EX3_F/advance.f90
Tutorials/HeatEquation_EX3_F/init_phi.f90
Tutorials/HeatEquation_EX4_F/advance.f90
Tutorials/HeatEquation_EX4_F/init_phi.f90
Tutorials/HeatEquation_EX4_F/regrid.f90
Tutorials/HeatEquation_EX5_F/advance.f90
Tutorials/HeatEquation_EX5_F/init_phi.f90
Tutorials/HeatEquation_EX5_F/regrid.f90

commit bf3d3a11e30f40584d349a04bcba5bb673979d02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 6 21:44:06 2014 -0700

    changed multifab_fill_ghost_cells to intentionally break (i.e., won't compile) codes that rely on the old behavior of ml_cc_restriction

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 9a608f43769aa5abeda45b33343b36498ea43bda
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 5 17:40:39 2014 -0700

    remove bl_error module from sort_i_module because bl_error_module uses
    sort_i_module

Src/F_BaseLib/sort_i.f90

commit f149db8023def5de71fec66f464bc9b3dec35f01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 5 17:32:34 2014 -0700

    added a stable merge sort method

Src/F_BaseLib/sort_i.f90

commit e0330fd6bf7ca3f3c46df469bfdf79844651e369
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 5 15:55:10 2014 -0700

    removed multifab_fill_boundary from ml_cc_restriction

Src/F_BaseLib/ml_cc_restriction.f90

commit 4d1323850145433910ac9788cda92da8d316a3e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 5 14:10:23 2014 -0700

    update due to new way of including mt19937ar.f90

Tutorials/MultiGrid_F/GNUmakefile
Tutorials/MultiGrid_F/mt19937ar.f90

commit 5728d31e809791a0d1b45c80f617c9f7430094a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 5 13:46:15 2014 -0700

    comments

Src/LinearSolvers/F_MG/cc_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 55abc796bca076bb73baadab8968adb641cbfa85
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 5 11:18:22 2014 -0700

    made prof dir names user settable.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 36d3ae4b28937f2eae1f21190adf89c467e6a213
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 5 08:36:59 2014 -0700

    added 'is up to date.' as an indication of successful compilation to regression test script

Tools/RegressionTesting/testnew.py

commit 77104f10bb8756df54066b33d5ea95d8bd258cf7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 5 08:26:54 2014 -0700

    updated Tutorial/AMR_Adv_Diff_F due to flux register

Tutorials/AMR_Adv_Diff_F/GPackage.mak
Tutorials/AMR_Adv_Diff_F/advance.f90
Tutorials/AMR_Adv_Diff_F/compute_flux.f90
Tutorials/AMR_Adv_Diff_F/main.f90
Tutorials/AMR_Adv_Diff_F/reflux.f90
Tutorials/AMR_Adv_Diff_F/regrid.f90
Tutorials/AMR_Adv_Diff_F/update_phi.f90

commit b6465507084ae0cf2e3e90639aeaecc04ecdd8b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 5 08:24:55 2014 -0700

    added flux register for subcycling to F90 BoxLib

Src/F_BaseLib/bndry_reg.f90

commit 66f6ebe3212d8a8f027db8ac279fc8e922595c45
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 5 08:22:25 2014 -0700

    F90 BoxLib: fixed a memory leak in multifab_fill_ghost_cells_t for subcycling

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 54bba805f8c185203f017f5d7c9b3a9727b4f860
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 4 17:53:46 2014 -0700

    added region profiling and parser support.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 5c2afed18377f0f92a986bdf4e26b3fca6baf5bb
Merge: c4f11a21b e7d1eff4b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 4 13:23:25 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c4f11a21b2d49e996d3ee71525182e40147d4a03
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 4 13:21:42 2014 -0700

    Have one test for implicit method and one for explicit method
    in the regression testing.

Tutorials/HeatEquation_EX5_F/inputs-rt-expl
Tutorials/HeatEquation_EX5_F/inputs-rt-impl

commit e7d1eff4b3df77333c3d977978fc025a14681689
Merge: 5cfc1a1c8 c35a30cdb
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Thu Sep 4 13:51:06 2014 -0600

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5cfc1a1c87573544240974ce588c96bcc39f6b92
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Thu Sep 4 13:50:48 2014 -0600

    updates for my machine

Tools/C_mk/Make.Darwin
Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit c35a30cdb18998e8143ddecf68ea3cd218d655fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 4 14:05:46 2014 -0400

    if RANDOM is defined, then add mt19937.f90 to the f90sources

Src/F_BaseLib/GPackage.mak

commit 9947a3924a14b701fad37f679290dd6c0c5bdadb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 3 20:40:00 2014 -0700

    commented on why OMP is removed in previous commit

Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit 20dde7730698d6592c8619ec65d662f1c4d041a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 3 17:55:48 2014 -0700

    removed another OMP PARALLEL DO becuase it is no longer safe in the new bndry_reg

Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit 8469ca6184460cd22e11f75e3491e54baeca39a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 3 17:54:34 2014 -0700

    intent(inout) --> intent(in)

Src/LinearSolvers/F_MG/cc_ml_resid.f90

commit b42b6d7269aeb996ccaf10ab00f7fae757f83c61
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 3 17:02:27 2014 -0700

    removed an OMP PARALLEL DO becuase it is no longer safe in the new bndry_reg

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 21291febd604b2616845dab3b4cfe49d512e11e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 3 14:45:01 2014 -0700

    F90 BoxLib bndry reg for cc linear solver: merged NDIM mulitfabs into one

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit 34ab9897cc704e6d705817b8063a6f0b5f5dbe54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 3 12:29:58 2014 -0700

    F90 BoxLib bndry reg for cc linear solver: merged the two faces into one so that it now contains NDIM multifabs instead of 2*NDIM multifabs.  This amortizes a lot of works such as building copy assoc.

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90

commit a2bfbb528e8d6f442374b551b1c6e6167d52e722
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 2 20:18:04 2014 -0700

    F90 BoxLib: use boxhash in the subroutine for removing overlaps in a boxarray

Src/F_BaseLib/boxarray_f.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/mt19937ar.f90

commit 48e3b8bed4925c22ba967fb8abef764f50e5f91c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 29 15:45:04 2014 -0700

    F90 BoxLib:
      (1) Added optional argument "all" to saxpy.
      (2) Added optional argument "ngsrc" to multifab copy. Parallel copy
          used to only copy from valid region to valid region, whereas now
          it copies from valid region + ngsrc ghost cells to valid
          region.  The caller is responsible for having good data in ghost
          cells of the source multifab if ngsrc is not zero.  Note that
          the destination is still valid region only for reasons I will
          not go into details.
      (4) fillpatch: If coarse multifab does not have ghost cells while
          fine grids touch physical domain, a temporary multifab with
          enough ghost cells will be built.  This relieves the burden from
          the caller.
      (3) Refactored fillpatch_t and multifab_fill_ghost_cells_t.

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_f.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit ecf7f30e1784c00022c7a3abc3e87183bf96f116
Merge: d01ac2858 90ba4be80
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 29 10:42:17 2014 -0700

    conflict fix.

commit d01ac285856ff424ddee302ee089237083c7ce75
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 29 10:36:52 2014 -0700

    added profiling.

Tutorials/MultiGrid_C/main.cpp

commit 02f149bd734ba3f1ac3d41abbf28f13cd539b6a6
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 29 10:35:44 2014 -0700

    more f90 profiling.

Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/bl_prof_stubs.f90
Src/F_BaseLib/layout.f90
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90
Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/compute_defect.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90

commit 90ba4be80dde46b35bd32294df9cbea45f59ea05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 28 20:30:13 2014 -0700

    updated fillpatch_t too

Src/F_BaseLib/fillpatch.f90

commit 358ec873133f713f453b58819876779e2c7bb108
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 28 20:03:27 2014 -0700

    added assertion and cycle when cbx is empty in fillpatch

Src/F_BaseLib/fillpatch.f90

commit e947b5e760aa2aa748a7040f528ef33290d2adc1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 28 20:01:47 2014 -0700

    fixed a bug; did not set stencil_width when stencilwith_in is present

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 78b198c1080594e7d492ee70ccbe0e74f86f7f5b
Merge: 6dde29d7c 898757b89
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 28 18:12:10 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 6dde29d7cccc971f12f37f88d9c6ce06c0d1d1b7
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 28 18:11:43 2014 -0700

    fixed array dim, k instead of 1.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 898757b89d4e47b220fb755ef32670fcd913b09f
Author: Chris Malone <cmalone@lanl.gov>
Date:   Thu Aug 28 14:12:05 2014 -0600

    this avoids an OSError if a repo doesnt exist

Tools/C_scripts/makebuildinfo_C.py

commit 13b8d23b2f1ce069f15d8dc885c6e1c1d1755029
Author: Chris Malone <cmalone@lanl.gov>
Date:   Thu Aug 28 10:55:43 2014 -0600

    remove vestigial loop

Src/C_AMRLib/Amr.cpp

commit 229c28e06cdd12a7740db638b0e5ac5295357799
Merge: 430c13f9b e89066db7
Author: Chris Malone <cmalone@lanl.gov>
Date:   Thu Aug 28 10:53:53 2014 -0600

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 430c13f9b661807c8a85cef245c3e868fb372b24
Author: Chris Malone <cmalone@lanl.gov>
Date:   Thu Aug 28 10:53:38 2014 -0600

    updates for LANL machines

Tools/C_mk/Make.mpi

commit e89066db739a720757ab49350658f69ff93aff04
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 28 06:27:56 2014 -0700

    Forgot to move define_bc_tower.f90 from the LinearSolvers/F_MG/FParallel.mak
    into the F_BaseLib/FParallel.mak

Src/F_BaseLib/FParallelMG.mak
Src/LinearSolvers/F_MG/FParallelMG.mak

commit e9cc859c37ef00893d3dc91ada139d6be87751cf
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 27 20:33:35 2014 -0700

    Remove LinearSolvers/F_MG from the GNUMakefile ... this was kinda
    the point!

Tutorials/AMR_Adv_Diff_F/GNUmakefile
Tutorials/HeatEquation_EX3_F/GNUmakefile
Tutorials/HeatEquation_EX4_F/GNUmakefile
Tutorials/HeatEquation_EX7_F/GNUmakefile

commit 4f9245ea7bb4fe9029736de8012003bf973dbff3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 27 20:29:53 2014 -0700

    This is replaced by README_F

Tutorials/README_HeatEquation_F

commit 2b09b4f7dc24576438296f2da980771e1414c550
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 27 20:29:11 2014 -0700

    Fix up the Tutorials...

Tutorials/AMR_Adv_Diff_F/advance.f90
Tutorials/AMR_Adv_Diff_F/compute_flux.f90
Tutorials/AMR_Adv_Diff_F/init_phi.f90
Tutorials/AMR_Adv_Diff_F/inputs_2d
Tutorials/AMR_Adv_Diff_F/inputs_3d
Tutorials/AMR_Adv_Diff_F/regrid.f90
Tutorials/AMR_Adv_Diff_F/update_phi.f90
Tutorials/HeatEquation_EX3_F/advance.f90
Tutorials/HeatEquation_EX3_F/init_phi.f90
Tutorials/HeatEquation_EX4_F/advance.f90
Tutorials/HeatEquation_EX4_F/init_phi.f90
Tutorials/HeatEquation_EX4_F/regrid.f90
Tutorials/HeatEquation_EX5_F/advance.f90
Tutorials/HeatEquation_EX5_F/init_phi.f90
Tutorials/HeatEquation_EX5_F/regrid.f90

commit e710eeae739b118b422ca4bf635dd8e428783de2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 27 18:56:55 2014 -0700

    More fixes due to the recent changes ... with this version VARDEN now builds.

Src/F_BaseLib/ml_nd_restriction.f90
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90

commit c5f731746f8e2c9cf0d03c867b1a30fc5e3cd640
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 27 18:43:30 2014 -0700

    Oops ... missed two changes ...

Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_divu.f90

commit 8f086d2b69b9ab117d25206fa06477e74f4ea97a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 27 18:36:49 2014 -0700

    Move a bunch of files from LinearSolvers/F_MG to F_BaseLib because they
    are needed for multilevel operations (mostly restriction), in particular
    in subcycling codes, and not just in the linear solvers.  We don't want
    to have to include everything in LinearSolvers/F_MG when we're not
    doing a linear solve.

MiniApps/AMR_Adv_Diff_F90/GNUmakefile
MiniApps/AMR_Adv_Diff_F90/advance.f90
MiniApps/AMR_Adv_Diff_F90/compute_flux.f90
MiniApps/AMR_Adv_Diff_F90/init_phi.f90
MiniApps/AMR_Adv_Diff_F90/inputs_2d
MiniApps/AMR_Adv_Diff_F90/inputs_3d
MiniApps/AMR_Adv_Diff_F90/regrid.f90
MiniApps/AMR_Adv_Diff_F90/update_phi.f90
Src/F_BaseLib/CMakeLists.txt
Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bc_functions.f90
Src/F_BaseLib/cc_restriction.f90
Src/F_BaseLib/edge_restriction.f90
Src/F_BaseLib/ml_cc_restriction.f90
Src/F_BaseLib/ml_nd_restriction.f90
Src/F_BaseLib/nodal_neumann_bcs.f90
Src/F_BaseLib/nodal_restriction.f90
Src/F_BaseLib/nodal_stencil_bc.f90
Src/LinearSolvers/F_MG/CMakeLists.txt
Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90

commit e419e44f868b941ced5e7d423268a590455161e3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 27 18:00:47 2014 -0700

    Dont have regression test in the miniap.

MiniApps/AMR_Adv_Diff_F90/inputs-rt

commit 20b1535bd1aa303c40695e0b64a01a8dc10c1fcd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 27 18:00:29 2014 -0700

    Fixed in 3d.

MiniApps/AMR_Adv_Diff_F90/compute_flux.f90
MiniApps/AMR_Adv_Diff_F90/init_phi.f90

commit 6ef4dc792a5e97b986f06bdb60dbcfb54b621c43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 27 16:42:26 2014 -0700

    F90 BoxLib: Assume grids are properly nested in fillpatch.  So we no longer need to do the expensive O(N^2) check of whether one box array contains another box array.

Src/F_BaseLib/fillpatch.f90

commit 56bc524e750104d7a5e41d52ce8d56b2fce50030
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 27 15:49:18 2014 -0700

    added timer to boxarray_boxarray_contains function

Src/F_BaseLib/boxarray_f.f90

commit 6e389fb2721f71ad65cdfa415c1c8e935b3c54a0
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 27 15:33:48 2014 -0700

    output cleanup.

Src/C_AMRLib/StateData.cpp

commit 21867f6cb180243db49b8a8ff841ebbb2a803b37
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 27 14:58:29 2014 -0700

    remove redudnant resizes.

Src/C_BaseLib/DistributionMapping.cpp

commit fecc1c7c9e7a865143d4592a94ba97cc113ae2da
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 27 14:33:33 2014 -0700

    redid defaults for pfc topology.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/DistributionMapping.cpp

commit 21dcde773ad4e803a7dca235a44d67d7faf54486
Merge: b90b06501 14736185e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 27 10:26:41 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit b90b065016a4a0b5efd56ae4c30df999b2b67642
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 27 10:26:34 2014 -0700

    destroy bl_prof_timer before returning

Src/F_BaseLib/boxarray_f.f90
Src/F_BaseLib/ml_boxarray.f90

commit 14736185eace9e8ad67f0de61c6d052c685a5044
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 26 16:41:51 2014 -0700

    Fix name of MultiFabTests to be consistent with others...

Tutorials/MultiFabTests_C/GNUmakefile
Tutorials/MultiFabTests_C/Make.package
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp

commit 886709e7404110e1a75bffcdc9cfe96c80d65b29
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 26 16:36:27 2014 -0700

    Fixed comment re particles leaving the domain.

Src/C_AMRLib/Particles.H

commit 7d8b1239000364ce5c01a27c98c27140a28d4f9e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 26 16:17:09 2014 -0700

    Remove unused variable "ns_in"

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 48ee37c5e585571289daade1bd2a9777fad33ac5
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 25 17:24:53 2014 -0700

    more diagnostics.

Src/C_BaseLib/DistributionMapping.cpp

commit c4aa9d91c1bf344d4b0a9a802d3f071029d9bd71
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 22 12:42:53 2014 -0700

    This directory was renamed AMR_Adv_Diff_F

Tutorials/HeatEquation_EX6_F/GNUmakefile
Tutorials/HeatEquation_EX6_F/GPackage.mak
Tutorials/HeatEquation_EX6_F/advance.f90
Tutorials/HeatEquation_EX6_F/compute_flux.f90
Tutorials/HeatEquation_EX6_F/init_phi.f90
Tutorials/HeatEquation_EX6_F/inputs-rt
Tutorials/HeatEquation_EX6_F/inputs_2d
Tutorials/HeatEquation_EX6_F/inputs_3d
Tutorials/HeatEquation_EX6_F/main.f90
Tutorials/HeatEquation_EX6_F/prob.f90
Tutorials/HeatEquation_EX6_F/reflux.f90
Tutorials/HeatEquation_EX6_F/regrid.f90
Tutorials/HeatEquation_EX6_F/tag_boxes.f90
Tutorials/HeatEquation_EX6_F/update_phi.f90
Tutorials/HeatEquation_EX6_F/write_plotfile.f90

commit 8f8686aab515614b48f7f3028beaa4ad9a97dbdf
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 22 12:42:28 2014 -0700

    Renamed some stuff, moved some stuff ...

Tutorials/AMR_Adv_Diff_F/GNUmakefile
Tutorials/AMR_Adv_Diff_F/GPackage.mak
Tutorials/AMR_Adv_Diff_F/advance.f90
Tutorials/AMR_Adv_Diff_F/compute_flux.f90
Tutorials/AMR_Adv_Diff_F/init_phi.f90
Tutorials/AMR_Adv_Diff_F/inputs-rt
Tutorials/AMR_Adv_Diff_F/inputs_2d
Tutorials/AMR_Adv_Diff_F/inputs_3d
Tutorials/AMR_Adv_Diff_F/main.f90
Tutorials/AMR_Adv_Diff_F/prob.f90
Tutorials/AMR_Adv_Diff_F/reflux.f90
Tutorials/AMR_Adv_Diff_F/regrid.f90
Tutorials/AMR_Adv_Diff_F/update_phi.f90
Tutorials/AMR_Adv_Diff_F/write_plotfile.f90
Tutorials/Exp_CNS_NoSpec_F/CNSEquations.tex
Tutorials/Exp_CNS_NoSpec_F/GNUmakefile
Tutorials/Exp_CNS_NoSpec_F/GPackage.mak
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.c
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.h
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/bench.c
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.h
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.x86.c
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/Make.package
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/timer_c.c
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/Make.package
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/README
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/advance.f90
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/main.f90
Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/README
Tutorials/Exp_CNS_NoSpec_F/README
Tutorials/Exp_CNS_NoSpec_F/advance.f90
Tutorials/Exp_CNS_NoSpec_F/init_data.f90
Tutorials/Exp_CNS_NoSpec_F/inputs.jbb
Tutorials/Exp_CNS_NoSpec_F/inputs_3d
Tutorials/Exp_CNS_NoSpec_F/main.f90
Tutorials/Exp_CNS_NoSpec_F/write_plotfile.f90
Tutorials/README_F

commit 9fb0089c3d72ce2334a13f902ceaa052a67273e0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 22 12:34:17 2014 -0700

    Add a MiniApps/AMR_Adv_Diff_F90 directory as a MiniApp to be used
    for profiling, and rename the Tutorials/HeatEquation_EX6_F directory
    to be Tutorials/AMR_Adv_Diff_F to reflect the fact that it is an
    AMR code with subcycling in time that handles advective and
    explicit diffusive fluxes.

MiniApps/AMR_Adv_Diff_F90/GNUmakefile
MiniApps/AMR_Adv_Diff_F90/GPackage.mak
MiniApps/AMR_Adv_Diff_F90/advance.f90
MiniApps/AMR_Adv_Diff_F90/compute_flux.f90
MiniApps/AMR_Adv_Diff_F90/init_phi.f90
MiniApps/AMR_Adv_Diff_F90/inputs-rt
MiniApps/AMR_Adv_Diff_F90/inputs_2d
MiniApps/AMR_Adv_Diff_F90/inputs_3d
MiniApps/AMR_Adv_Diff_F90/main.f90
MiniApps/AMR_Adv_Diff_F90/prob.f90
MiniApps/AMR_Adv_Diff_F90/reflux.f90
MiniApps/AMR_Adv_Diff_F90/regrid.f90
MiniApps/AMR_Adv_Diff_F90/update_phi.f90
MiniApps/AMR_Adv_Diff_F90/write_plotfile.f90
Tutorials/HeatEquation_EX6_F/advance.f90

commit f855924756e7026db348efe3c2000ddc300cf272
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 22 12:26:23 2014 -0700

    nstates.

Src/C_BaseLib/DistributionMapping.cpp

commit 5f10859663e00a840ae994b42666ab24d1758d5d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 22 12:25:52 2014 -0700

    These are updated to include advective fluxes and fixed previous
    bugs in the refluxing.

Tutorials/HeatEquation_EX6_F/GPackage.mak
Tutorials/HeatEquation_EX6_F/advance.f90
Tutorials/HeatEquation_EX6_F/compute_flux.f90
Tutorials/HeatEquation_EX6_F/main.f90
Tutorials/HeatEquation_EX6_F/prob.f90
Tutorials/HeatEquation_EX6_F/reflux.f90
Tutorials/HeatEquation_EX6_F/regrid.f90
Tutorials/HeatEquation_EX6_F/update_phi.f90

commit 3e0531457a231e65b22f001b99bddade0610e692
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 21 17:02:48 2014 -0700

    multilevel distribution map.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 8bfdecd0100e845f71fe5c3e3d446a384f9879cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 21 16:06:04 2014 -0700

    Here, "rt" actually stands for regression test.
    
    Revert "Remove inputs.rt -- it didn't really do the RT problem"
    
    This reverts commit 16200b37f9b4f9b974003b2777ec03b033d905d6.

Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt

commit 16200b37f9b4f9b974003b2777ec03b033d905d6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 21 15:02:36 2014 -0700

    Remove inputs.rt -- it didn't really do the RT problem

Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt

commit 1dc300b9fac6a9bfcfc768dd43f0cd0466f095ce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 19 17:24:41 2014 -0700

    removed parallel_reduce in sanity check in fillpatch

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_f.f90

commit a32c3141cfa99f2a5802672d82efe0018fe8c7c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 19 17:10:50 2014 -0700

    double precision --> dp_t for consistence

Src/F_BaseLib/bl_constants.f90
Src/F_BaseLib/create_umac_grown.f90
Src/F_BaseLib/cutcells.f90
Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/interp.f90
Src/F_BaseLib/multifab_physbc.f90
Src/F_BaseLib/particles_f.f90
Src/F_BaseLib/tag_boxes.f90
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_interface_stencil.f90
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/cc_restriction.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/coarsen_coeffs.f90
Src/LinearSolvers/F_MG/compute_defect.f90
Src/LinearSolvers/F_MG/edge_restriction.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/nodal_applyop.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_newu.f90
Src/LinearSolvers/F_MG/nodal_restriction.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_apply.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90
Src/LinearSolvers/F_MG/sparse_solve.f90

commit 2e7367572e7bb989098589c2542578a7fbc4d766
Merge: b32248c40 c7b63bbc6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 14 22:12:58 2014 -0700

    Merge branch 'master' into dev

commit b32248c4091d34041bff91ebc212f3c4b01670bf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 14 22:09:46 2014 -0700

    added operator+= to BndryRegister class

Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit c7b63bbc66ae6b24fe3d58c9acaa162facf50759
Merge: 0d414258c 8e6a22889
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Aug 14 12:34:08 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0d414258c97ddec677e1b977b2e4a15bf49129cc
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Aug 14 12:33:45 2014 -0700

    CIMS machines

Tools/C_mk/Make.defs

commit 8e6a2288957c8510f48a7bba4ae4576b52023f50
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 14 11:24:02 2014 -0700

    Fix the stupid typos from the last commit.

Src/C_AMRLib/Amr.cpp

commit 65d098b78b961a3b3f97de6912f0c602ebb9e5af
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 14 11:12:12 2014 -0700

    Allow the user to set regrid_int = -1 as a signal not to regrid
    (at all or at that level)

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H

commit 89db152b047b8e87b94ec722fb86944e970ba969
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 13 16:24:22 2014 -0700

    added function to read checkpoint headers.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit da2e03ce297db1c50a57187dec192ea8c64d55c2
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed Aug 13 15:29:51 2014 -0700

    PyBoxLib: Tidy up make files, pull in isinf and isnan from std on Darwin.

Src/C_BaseLib/FArrayBox.cpp
Src/Python/GNUmakefile_CXX.mak

commit e9312f5b880ae186a2e7325e881189467949093e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 13 12:49:11 2014 -0700

    Add the option to use relativistic weighting of the mass (i.e. multiply by gamma)
    if the relativistic flag is set, which currently is only allowed if
    the NEUTRINO_PARTICLES flag is defined.

Src/C_AMRLib/Particles.H

commit 3eea21ac061f46448a548eba081c13089515a26f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 12 13:56:34 2014 -0700

    Add a README so we can keep track of the different F90 HeatEquation*
    examples in BoxLib/Tutorials.

Tutorials/README_HeatEquation_F

commit 611ba4746d182ba0a7b6a4f9f0a2bda662bfa89d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 12 13:41:41 2014 -0700

    Update subcycling description.

Docs/F_AdvancedTopics/F_AdvancedTopics.tex

commit f257c735d50c3bdde7d84a9e8119e56790c26d69
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 12 09:45:47 2014 -0700

    Remove flags for ROSE compiler.

Tutorials/HeatEquation_EX1_F/GNUmakefile
Tutorials/HeatEquation_EX5_F/GNUmakefile

commit 1146ba3d3645b15aeb1332a4af6cd0eb8b3ff992
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 12 09:10:20 2014 -0700

    Set NDEBUG = t

Tutorials/HeatEquation_EX6_F/GNUmakefile

commit 5747eafcd5970fecdc959954ffc22a88e86da809
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 12 09:08:01 2014 -0700

    Get 3d working ...

Tutorials/HeatEquation_EX6_F/inputs_3d
Tutorials/HeatEquation_EX6_F/reflux.f90
Tutorials/HeatEquation_EX6_F/tag_boxes.f90

commit 03d32123a15640c021975c0044007661ecf58bf7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 12 09:02:44 2014 -0700

    set n_cell = 64 and max_levs = 3 in inputs file.

Tutorials/HeatEquation_EX6_F/inputs_2d

commit 3fbac6ba77f6bb475642d987f9ea6808279f8e3c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 12 09:01:36 2014 -0700

    Fix bndry_reg copy when n > 1.

Tutorials/HeatEquation_EX6_F/advance.f90

commit 5f540dd915f38f9e30702821b0f9aa257bc799e6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Aug 11 20:40:35 2014 -0700

    Modify the Tutorials/HeatEquation_EX6_F code for explicit subcycling
    so that it uses new bndry_reg functions and new modified fillpatch and
    multifab_fill_ghost_cell routines.   This works for max_levs = 2
    but not yet for max_levs = 3.

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90
Tutorials/HeatEquation_EX6_F/GNUmakefile
Tutorials/HeatEquation_EX6_F/GPackage.mak
Tutorials/HeatEquation_EX6_F/advance.f90
Tutorials/HeatEquation_EX6_F/cc_restriction.f90
Tutorials/HeatEquation_EX6_F/compute_flux.f90
Tutorials/HeatEquation_EX6_F/inputs_2d
Tutorials/HeatEquation_EX6_F/main.f90
Tutorials/HeatEquation_EX6_F/ml_restriction.f90
Tutorials/HeatEquation_EX6_F/reflux.f90
Tutorials/HeatEquation_EX6_F/regrid.f90
Tutorials/HeatEquation_EX6_F/subcycling.f90
Tutorials/HeatEquation_EX6_F/tag_boxes.f90
Tutorials/HeatEquation_EX6_F/update_phi.f90

commit aa076f5aeb4a958e5e7f40b61e8dd7ff1b939901
Author: Matthew Emmett <memmett@gmail.com>
Date:   Mon Aug 11 15:57:03 2014 -0700

    PyBoxLib: Add python libs to linking stage.

Src/Python/GNUmakefile_CXX.mak

commit 1c4da796cfb8e492c270fec297548da863d53c73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 12:25:53 2014 -0700

    reduce the number of parallel reduce in Linear Solver

Src/LinearSolvers/F_MG/ml_nd.f90

commit f0a7bd0d5ab6983f43bc692dfad70bca80a61900
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 12:16:48 2014 -0700

    fixed typo

Src/LinearSolvers/F_MG/itsol.f90

commit 66960bc198163617e8ca5eafa808dbd0bff700e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 12:13:31 2014 -0700

    removed more unsafe saxpy; clean up

Src/LinearSolvers/F_MG/itsol.f90

commit 28866df9e61db22fac3cea49c6ca0af0d4529fea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 11:58:01 2014 -0700

    Changed a potentially unsafe call to saxpy because Fortan arrays are not supposed to aliased.

Src/LinearSolvers/F_MG/compute_defect.f90

commit e10775c954d68e05ddaa0ec110e5799c80731451
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 11:45:38 2014 -0700

    reduced number of parallel reduce in multi-level nodal convergence check

Src/LinearSolvers/F_MG/ml_nd.f90

commit 108cdd95d07bdd8c20b10310402c364e3264414c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 11:19:05 2014 -0700

    fixed a new bug

Src/LinearSolvers/F_MG/cc_ml_resid.f90

commit 96b94eccc99081471ad2f1558033e939aef4a06b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 10:37:13 2014 -0700

    remove a multifab_fill_boundary in nodal solver

Src/LinearSolvers/F_MG/ml_nd.f90

commit c076f376ed0564178e8a8688b45313f184227fa1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 09:50:30 2014 -0700

    removing more multifab_fill_boundary's in Linear Solver

Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit 4df53eb9ca353aa2214f6f03189d7aee0e6975c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 09:18:52 2014 -0700

    cleanup

Src/LinearSolvers/F_MG/ml_cc.f90

commit 8adca6d9c7fa77bed222c26c18076d373cc3e5d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 09:07:43 2014 -0700

    removed more multifab_fill_boundary's in Linear Solver

Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/compute_defect.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 8d412a2f311738e218e4ef61860ba7c683c40eeb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 07:27:33 2014 -0700

    renaming for consistence; removed more multifab_fill_boundary's

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit 2e135d14c613664a0e0d1fc3ec7d05492a7b36bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 7 21:50:31 2014 -0700

    cleanup

Src/LinearSolvers/F_MG/ml_cc.f90

commit 8d55d8cbde81ab651a3ca5a5424d33f91cbdcbcc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 7 21:38:38 2014 -0700

    remove a number of redundant mf_fill_boundary calls

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit 3b50a4badea5357558102ea231b4e66c3eef12f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 7 18:03:22 2014 -0700

    reduce the number of parallel reduce in checking multi-level convergence

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit 4dda5d672c9626733cae2010b5ea445b1f5fece8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 7 14:58:17 2014 -0700

    Modify loops ... still some more to be done ...

Src/F_BaseLib/bndry_reg.f90

commit 4ca7b457b4a7ea66e159bb44fa9f22f14271e5ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 7 13:56:24 2014 -0700

    fixed a bug in new bndry_reg when fine box touches physical boundaries

Src/F_BaseLib/bndry_reg.f90

commit c863ba245bc618628160be7d5947c993fddec66d
Merge: 863672981 668e9f0a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 7 12:48:50 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 8636729815e03a35aa8a5d9c5d8126f7ecac64b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 7 12:48:03 2014 -0700

    Get around an Intel compiler bug by removing a name clash in the size interface so that maestro can compile with intel again.  Note that Fortran standard permits name clash for generic interfaces by requiring a compiler to merge interface blocks.

Src/F_BaseLib/particles_f.f90

commit 668e9f0a8b24968a7271c0cc85570fada1b4de7b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 7 11:41:42 2014 -0700

    Fix the section on the bndryreg

Docs/GettingStarted/GettingStarted.tex

commit 2d8c671b1fd9e0e776608099c725341c4d97c3fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 7 09:30:04 2014 -0700

    get around Intel compiler issue

Src/F_BaseLib/bndry_reg.f90

commit 8379ff5f7e6a26a1b0168e6f1802c97c31b17c15
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Aug 6 21:21:41 2014 -0400

    add the linear solver text I wrote for Maestro

Docs/F_AdvancedTopics/F_AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex
Docs/UsersGuide.tex

commit 2bc35796cffb36e8ec1137181fb8e0d6428c7f15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 6 14:18:34 2014 -0700

    Added a new option to bndry_reg_module: Some fabs in bndry reg are
    entirely covered by the fine grids.  The new option controls whether
    or not to keep these useless fabs.  The default is to keep them (even
    though this increases the amount of data for communication and the
    amount of work for filling these fabs) because removing these boxes
    from the layout requires some expensive box calculus.

Src/F_BaseLib/bndry_reg.f90

commit 49578d6d31427970e874e5e798cc0e0a7ec0a590
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 6 12:05:54 2014 -0700

    special parallel copy for multi-level bndry_reg

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit c1bfc445408fb38b18258ecfe86d083c7e8969b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 5 15:51:43 2014 -0700

    clean up

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90

commit 82aa3463eb0fecbc42e7986f7ced534c71c3ea57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 5 13:31:04 2014 -0700

    bndry_reg: reduce the number of parallel copy from 6 to 3

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/cc_interface_stencil.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90

commit aeb2b143b9e89810a523f03f8e1bb531ce204a9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 5 13:26:57 2014 -0700

    removed useless fabs (i.e., covered by fine grids) from bndry reg

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90

commit a9c553f195481816f17a3b15bd4f4c96a4c287fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 5 13:22:30 2014 -0700

    fixed a memory leak in the linear solver comparison test

Tests/LinearSolvers/ComparisonTest/main.cpp

commit 9acd7dba5dc35b7829779f9e59aa0aa20b1c6e84
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 1 08:34:48 2014 -0700

    Add this subcycling figure.

Docs/F_AdvancedTopics/subcycling_algorithm.eps

commit 4d0a88cc2aee4b13a5121ef238fc91239e1326df
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 31 18:34:03 2014 -0700

    Add commentary about how subcycling is done in the F90 Tutorials
    example in HeatEquation_EX6_F.

Docs/F_AdvancedTopics/F_AdvancedTopics.tex

commit cf53b834919a8a7db4d563f52e03d2a23842ada2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 31 18:33:25 2014 -0700

    Modify these advance routines to look more like the one in the
    subcycling example, just so what changes is clearer.

Tutorials/HeatEquation_EX3_F/advance.f90
Tutorials/HeatEquation_EX4_F/advance.f90
Tutorials/HeatEquation_EX5_F/advance.f90

commit ccd5d63fd8a596c33af92f613a014e2aa83962ae
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 31 18:32:25 2014 -0700

    Add a new Tutorials example which does subcycling in time for the
    explicit solution of the heat equation (an extension of
    HeatEquation_EX4_F).

Tutorials/HeatEquation_EX6_F/GNUmakefile
Tutorials/HeatEquation_EX6_F/GPackage.mak
Tutorials/HeatEquation_EX6_F/advance.f90
Tutorials/HeatEquation_EX6_F/cc_restriction.f90
Tutorials/HeatEquation_EX6_F/init_phi.f90
Tutorials/HeatEquation_EX6_F/inputs-rt
Tutorials/HeatEquation_EX6_F/inputs_2d
Tutorials/HeatEquation_EX6_F/inputs_3d
Tutorials/HeatEquation_EX6_F/main.f90
Tutorials/HeatEquation_EX6_F/ml_restriction.f90
Tutorials/HeatEquation_EX6_F/regrid.f90
Tutorials/HeatEquation_EX6_F/subcycling.f90
Tutorials/HeatEquation_EX6_F/write_plotfile.f90

commit 84f4419d706b247732887b2ec4e9df58b03d606f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 31 18:14:54 2014 -0700

    Modify the comment that subcycling is only in C++ since we have
    an F90 Tutorial example with subcycling.

Docs/Introduction/Introduction.tex

commit b67227211e3635616111dbeb945e6ded65693d3f
Merge: b1d8a242a ed2ec590b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 31 17:40:38 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ed2ec590b154168d891316e5aa72724f9f5af025
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 31 16:10:16 2014 -0700

    more code consolidation in multilevel cell-centered solver

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit 21d5f347ca3e76fab9e8c52aa866db9053dd7095
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 31 15:55:53 2014 -0700

    fixed a bug in bndry reg; minor cleanup

Src/F_BaseLib/bc.f90
Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit 3f4cbe4c2830ce6b81098014bc8b9c0824b20210
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 31 15:38:18 2014 -0700

    We have changed the way we use bndry_reg in the multilevel cell-centered
    solves to make them much more efficient.  Eliminated an extra parallel
    copy and consolidated code.

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit b1d8a242a9c62668dffcb8851d1f26b47c1c0ff8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 31 15:03:30 2014 -0700

    Fix spelling error in comment.

Src/LinearSolvers/F_MG/nodal_stencil_fill.f90

commit db6ea0862096f9440375d3eb57e73653f0e77bb2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jul 29 16:34:39 2014 -0700

    Get this test code to work for cell-centered solve at multiple levels.

Tests/LinearSolvers/F_MG/cc_multi.f90

commit a3be88a1a2fce4d512725aab74c66b3fd6ac53e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 25 15:32:52 2014 -0700

    added USE_ACC to the make system

Tools/C_mk/Make.Linux

commit d12203f27bab5880eefa247561ee1ccf3af80a46
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jul 25 12:01:58 2014 -0700

    Turns out the Cray compilers do not like the "isnan" function after all.

Src/C_BaseLib/FArrayBox.cpp

commit 0afb3fa96182c0b4c846ab9bc45873ae61ca8408
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jul 25 11:55:14 2014 -0700

    Restore this file to the previous version -- turns out this
    wasn't really the problem with the cray compiler.

Src/C_BaseLib/BLassert.H

commit d0c5be6d206f3ff5dbe6ab52b82bedb84a003792
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 24 22:34:31 2014 -0700

    For cray compilers, always run the opertion in BL_ASSERT to get around a possible Cray compiler bug.  Hopefully this will fix the crash of Castro compiled by cray.

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/BLassert.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/iMultiFab.cpp

commit 0af26b79ff3a187a5f13fe51cea3beceb62d1d4e
Merge: 90d9b43ad af8f7a4ed
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jul 24 17:53:58 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 90d9b43ad9385b5b62ac93b7cb39129e27ec9bfd
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jul 24 17:52:52 2014 -0700

    Make the DiffFab.cpp function usable in a specialized regression test framework

Tools/C_util/Convergence/DiffFab.cpp

commit af8f7a4edb772588220e9531af6e6cc4887829ad
Merge: c2baf150f 222751b81
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 24 18:26:05 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c2baf150ff9e404a111e4ad9dfb3dd6d5c34f3db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 24 18:24:23 2014 -0400

    sync this up to file movements

Tools/RegressionTesting/Maestro-tests.ini

commit 222751b818c0d2237aff9731443726731e1d6a06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 24 12:43:49 2014 -0700

    switch back to the old-style python formating in a print, since
    edison's default python (2.6.9) doesn't like the new style

Tools/C_scripts/makebuildinfo_C.py

commit 2690ab3dc9d70489d23e037afb29591db9d0069d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 23 22:55:09 2014 -0700

    removed #if defined's around isnan and isinf because they have been in the standard since C99 and C++11; all compilers on Edison and Hopper support them.

Src/C_BaseLib/FArrayBox.cpp
Src/F_BaseLib/fabio_c.c
Tools/C_mk/Make.Linux
Tools/F_mk/comps/Darwin_intel.mak

commit 9d74e0a1404d264834dc5897b186644de36aa2a6
Merge: ce24c80a5 b63add45e
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 22 16:19:19 2014 -0700

    Merge branch 'master' into commprof

commit b63add45e093bf7bcf8d8d73bd4ab2089eed1c3f
Merge: 9738b88d6 f0ad6d651
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 22 16:11:35 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9738b88d659119dfa2c88641842f6f0413f99153
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 22 16:11:17 2014 -0700

    comment out a broken timer until we figure out what's wrong

Src/F_BaseLib/list_box.f90

commit f0ad6d651ef34592145cb844faa0363312e9a0f7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jul 22 15:39:54 2014 -0700

    Change default to DEBUG = FALSE and add a pure-F90 inputs file.

Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_C/inputs.f90.3d

commit f2a66eeb7f1588aafa6384d447163ec65abcb3d6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 22 11:23:55 2014 -0700

    fixed a bpt_build error

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit a6d4709c574cdff87baa416144740b75581f574e
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 22 10:39:54 2014 -0700

    enable bl_prof timers with PROF=t (broken at the moment)

Tutorials/HeatEquation_EX5_F/main.f90

commit 334c4549cc08a283df589530b6fc136067002081
Merge: 5567bba5e 67b8c8470
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon Jul 21 18:42:28 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 5567bba5e502659977f99bc7d9755b7464575709
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon Jul 21 18:40:54 2014 -0400

    Change nesting enforcement so that the number of times it tries
    to fix nesting is relative to nlevs, not just the constant 3.

Src/F_BaseLib/make_new_grids.f90

commit 67b8c847089a208eb6a71751de8a689dd4b800b2
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Jul 21 14:50:04 2014 -0700

    renname f90 timers to avoid duplicate names

Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit ce24c80a54c109965de31845b2ff7c759d68741a
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 18 10:37:21 2014 -0700

    added text for fortran90 interface.

Docs/Readme.profiling

commit 2b06371e1044f3d0486f1a2b11901a07c1517fa3
Merge: c92e972e8 a4dc0aace
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 18 10:27:45 2014 -0700

    Merge branch 'master' into commprof

commit c92e972e8e65421eb2e7fe45cd0f08a3df2ae1c0
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 18 10:26:41 2014 -0700

    formatting.

Src/C_BaseLib/Profiler.cpp

commit 00bca4c7fa59565f69074817f410fc87af321285
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 17 16:55:16 2014 -0700

    more call stack tracing.
    inclusive and exclusive times in the html tree output.
    collapse html call tree at depth > 4 by default.
    added function name map to store ints in CallStats instead of strings.
    added report for inclusive function times, recursive times are subtracted.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit a4dc0aace2430234e07a6ab6fcb3d7a050429f64
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 16 19:57:55 2014 -0400

    some cleanups

Tools/F_scripts/makebuildinfo.py

commit e6142e8e9a5b15b0ad631d4b538f13630cfa99e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 16 19:57:28 2014 -0400

    argparse -> getopt -- argparse requires the latext python 2.7 which
    is not available everywhere.

Tools/C_scripts/makebuildinfo_C.py

commit dcae6d6ddf9315eefbdbf2a2c897d0407d4fa8a8
Merge: b1cba6ea0 929e73d4c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jul 15 11:23:03 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b1cba6ea0d6815484dc2efaf91429ced7232e2bc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jul 15 11:22:20 2014 -0700

    Fix the use of Amr::UseFixedCoarseGrids -- the call to constructAreaNotToTag
    was missing in the AmrLevel constructor.

Src/C_AMRLib/AmrLevel.cpp

commit 929e73d4c655fa9e0a737932712835747dbeccc5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 14 13:48:45 2014 -0700

    fixed makebuilinfo_C.py in case not all 3 git directories are set

Tools/C_scripts/makebuildinfo_C.py

commit 2f9e06f3c73482502fa07b1bbfee6c1cc35f6d77
Merge: ad89384b4 0d5116d4b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 14 11:02:24 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ad89384b479bb2d15da16d755244e5e81f72ca14
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 14 11:02:06 2014 -0700

    Add "Vater" 9-pt nodal stencil in 2d only.

Src/C_AMRLib/Particles.H
Src/LinearSolvers/C_to_F_MG/stencil_types.H
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/nodal_stencil_apply.f90
Src/LinearSolvers/F_MG/stencil_types.f90

commit 0d5116d4b77df19010ef072bd4ec7b7046d49c1e
Merge: 7b1888dac 9ecead84a
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Mon Jul 14 10:54:20 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 7b1888dacf65242687368cc6bbafc987fa319cb9
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Mon Jul 14 10:54:03 2014 -0700

    PyBoxLib: Use F90 for linking and include -lstdc++.

Src/Python/GNUmakefile_CXX.mak

commit 9ecead84a061ffabe8e316618908aa1c41c6a7d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 14 10:47:34 2014 -0700

    replaced -1e200 with -Huge()

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit c4f41857ed5645d8589c7cc86cf0ec7770deee6b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 12 19:24:14 2014 -0400

    add a new python routine to handle the buildInfo.cpp file -- this is
    far easier to extend and much more readable than the shell script
    version.  This mirrors the F90 one written for Maestro, and allows
    us to get the Castro buildInfo.cpp working again after the most
    recent commits broke it.

Tools/C_scripts/makebuildinfo_C.py

commit e689426115f63694d22411abcf86b3b046f8294e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 10 14:38:55 2014 -0700

    Add functionality (UseFixedCoarseGrids) to define fixed grids up to
    a certain level and use adaptive refinement at all finer levels.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 8e4b07739d9c9a808775302c4d668445bae27f90
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 10 14:01:23 2014 -0700

    Add additional functionality into the "buildInfo" capability --
    this came from Jan and Wolfram.

Tools/C_scripts/buildInfo.H
Tools/C_scripts/make_build_info_cpp

commit 61146c6ec1e179aae609aced4405c22be2ddb467
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jul 9 15:36:15 2014 -0700

    Allow a stencil_type_in into the nodal_applyop routine.

Src/LinearSolvers/F_MG/nodal_applyop.f90

commit d8b8ca38aa21a9022df695abdb9f80b8c7b859fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 8 11:29:21 2014 -0400

    kraken is no more.  Long live darter.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 2976f60b2a2c2f97d93e3723fe9e6222b8c170cb
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Jul 3 16:46:50 2014 -0700

    PyBoxLib: Add ReduceRealMax and Geometry.

Src/Python/boxlib/__init__.py
Src/Python/boxlib/bl1.py
Src/Python/boxlib/bl2.py
Src/Python/boxlib/bl3.py
Src/Python/src/boxlib_wrap_1.cpp.REMOVED.git-id
Src/Python/src/boxlib_wrap_2.cpp.REMOVED.git-id
Src/Python/src/boxlib_wrap_3.cpp.REMOVED.git-id
Src/Python/swig/boxlib.i

commit aba8762074b3a6e2c659809140232ccd6356a309
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Jul 3 16:46:04 2014 -0700

    PyBoxLib: Minor tweaks to Makefiles.  Update README.

Src/Python/GNUmakefile
Src/Python/GNUmakefile_CXX.mak
Src/Python/README

commit 595a5a72f72bbae43361a848a9988203e70fa645
Merge: df5c72466 a09eecfa5
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 1 16:44:06 2014 -0700

    Merge branch 'master' into commprof

commit df5c7246601b552a442301f2348c6b01693988a8
Merge: da9222a7d 49ac32483
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 1 16:42:14 2014 -0700

    Merge branch 'commprof' of gamera:/usr/local/gitroot/BoxLib into commprof

commit da9222a7d649dfd253d92df8960f0d9a465e152c
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 1 16:42:02 2014 -0700

    added inclusive and exclusive times to the call trace tree.

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit a09eecfa5aec7c18605ce351e1ce66ad842ee005
Merge: 7e77e449e 59ac03d2c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 30 17:37:30 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7e77e449ebb49782b70dd45ab337d342f28b5bcb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 30 17:37:02 2014 -0700

    Fix the add_rh_nodal stuff that is used in the initVortProj stuff in Projection.cpp

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 59ac03d2cfbe0856a4c8aa7f8f3926c36628f943
Merge: 23eade895 c98c9c04e
Author: Chris Malone <cmalone@lanl.gov>
Date:   Mon Jun 30 16:14:01 2014 -0600

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 23eade8951fd772c1229dd3ae55c9d90e005790b
Author: Chris Malone <cmalone@lanl.gov>
Date:   Mon Jun 30 16:13:54 2014 -0600

    some LANL machine stuff

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit c98c9c04e2f7615c4523f1e7c190a087947a14ca
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jun 30 15:11:51 2014 -0700

    Change interface to nodal_project solver to use PArrays

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 49ac3248305c3c1b554419148f51e046bd7e241e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 30 14:32:00 2014 -0700

    Sync this up with the master version.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 1105852be729b4d2c814ae9826f0d032be99cdf3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 30 14:30:34 2014 -0700

    Fix the print statements ... hopefully.

Src/LinearSolvers/F_MG/ml_cc.f90

commit b1c256797a20b3fcdfa0db2e8b5d7daab8ba3878
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 30 14:19:34 2014 -0700

    Trying to fix print statements (only print statements, not convergence tests)
    so it is clearer what is going on.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 46b787dd1d7fc6fe17e10439134bc41b41a09070
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 30 13:40:07 2014 -0700

    Correct spelling in comment.

Tutorials/HeatEquation_EX1_F/main.f90

commit d9a2bf7842bf94ac25e46144d411447cedb3580f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 30 12:50:00 2014 -0400

    change the definition of the relative norm.  Before we were doing
    ||(A-B)/A||, now we do ||A-B||/||A|| -- this is more correct.

fcompare.f90

commit 7c81fd86a11470760368d4466746085def199d49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 27 10:56:06 2014 -0700

    made an essentially identity transformation to accommodate Cray compiler

Src/LinearSolvers/F_MG/coarsen_coeffs.f90

commit 080530e942b32a0b9272ffe8d5533a323608cfb1
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 25 08:45:57 2014 -0700

    bugfix: in the nodal restriction, we assumed the mask multifabs had the same number of components as the thing you are restricting.  the mask should only have 1 component

Src/LinearSolvers/F_MG/ml_restriction.f90

commit a4f99bf68c3aab34c51c702b9eff6a6fca5744cd
Merge: 769228ca4 271f23d43
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 25 06:25:38 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 769228ca4da257bf3f9eed76b47c95c231be4aa7
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 25 06:25:08 2014 -0700

    get this compiling again,  won't affect results as fixed code wasn't being called by anything

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 271f23d43ee44fd9253e1c508afe32a8be48efb6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 25 06:22:02 2014 -0700

    modified the interface of the new ml restriction wrapper so that the code can compile

Src/LinearSolvers/F_MG/ml_restriction.f90

commit d8d49e7aed990575abd0a27c2e8fe71f34e25416
Merge: 22bc1151d 07808fda8
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 24 17:01:58 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 22bc1151d6fccb89192c18da21633a137045a441
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 24 17:00:42 2014 -0700

    added a simplified interface to do direct injection nodal restriction that only requires an ml_layout, bc_tower, and bc_comp passed in.  testing underway.

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 07808fda8144607e3cec558b7abf1b087dd7c1c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 23 14:15:09 2014 -0400

    remove a parallel_reduce by doing the rh norm_inf (bnorm) locally
    and then packing it into the parallel reduce already in this code.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 6338fc40bbba6b61045839d740d3bcb9ed8504e1
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 19 14:22:19 2014 -0700

    added more mpi types.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp
Src/C_BaseLib/VisMF.cpp
Src/C_TowerLib/Layout.cpp

commit 644f094cbda847bfc05edbc4260f384b881aa79f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jun 19 08:45:54 2014 -0700

    greatly simplified this cell-centered heat equation implicit example by hooking into the simple ml_cc_solve interface.  no more building mg_towers, coefficients, etc., in the advance routine.  comes up clean in my regression

Tutorials/HeatEquation_EX5_F/advance.f90

commit a451968fa19e9ada250685903aff4ece2dd9d963
Merge: 33183ff38 bbe1c9af2
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 18 14:19:27 2014 -0700

    merge fix.

commit 33183ff38a62a1e1e3262b6b636115bbfb558d79
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 18 14:13:39 2014 -0700

    bl loc.

MiniApps/FillBoundary/GNUmakefile

commit 479b5aa79df4813df480ab6389f1fbab7083b410
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 18 14:05:00 2014 -0700

    more pfc.

Src/C_BaseLib/DistributionMapping.cpp

commit da0e46e1a6d3966130801dbfdbada7fe173b304f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 18 14:01:15 2014 -0700

    added function tracing.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit ac671cfe6274c9a1e1c4f3f573e6633f797203e1
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jun 2 16:22:44 2014 -0700

    create default if no topological map is found.

Src/C_BaseLib/DistributionMapping.cpp

commit bbe1c9af2cc72f83426d840ec5d3505035fcf253
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 30 17:46:30 2014 -0700

    fixed a number of memory leaks

Src/C_AMRLib/Particles.H

commit c188580368cbec5b3065217c585d33ab50d8dfb6
Merge: 4aebcaba0 435eca6c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 30 16:59:14 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4aebcaba048f21d129ee71c4351342fab710441d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 30 16:59:11 2014 -0700

    Fixed invalid conversion from const MultiFab * to MultiFab * that is not tolerated by some compilers.

Src/C_AMRLib/Particles.H

commit 435eca6c9e86dccba4e76b9ac7d891cf1cee1bfc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 30 12:22:45 2014 -0700

    nodal_enforce.f90 --> nodal_enforce_dirichlet_rhs.f90

Src/LinearSolvers/F_MG/CMakeLists.txt

commit cc7e537a7828ceb82842e3e8c288887e7105060a
Merge: a40811067 350752c6b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 29 12:00:09 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a408110678667cb4fd537b599a0e817341b58d2c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 29 11:59:17 2014 -0700

    Add new variable in Amr -- which_level_being_advanced -- with an
    access function level_being_advanced() so that the AmrLevel routines
    can know if post_regrid is being called within the advance for a
    level (which_level_being_advanced) which is different from lbase.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 350752c6ba5ef9c0f34cb4909108c1548bb6dfc3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 28 16:36:22 2014 -0700

    Need to allocate mgt%bottom_mgt inside a later test so that if we
    are unsuccessful in get_bottom_box_size we don't allocate it at all.

Src/LinearSolvers/F_MG/mg.f90

commit f355cd832b48dabfbf32d3c18e75bff5d5101f27
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 28 16:31:00 2014 -0700

    Remove un-needed print statements.

Src/LinearSolvers/F_MG/nodal_interface_stencil.f90

commit 020fa77a701657d732c276f0e2e70f0932eec04f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 28 14:54:04 2014 -0700

    Version_One_Dot_Zero should default to reading *double* precision,
    not single.

Src/C_AMRLib/Particles.H

commit b1a92fdba898b8fe5132b6e99da965ec3adc1783
Author: vince <vebeckner@lbl.gov>
Date:   Wed May 28 11:39:48 2014 -0700

    reindex.

Src/C_BaseLib/DistributionMapping.cpp

commit 131e8de0822a0d44f7d8ac2cb7d7578cf3f0a824
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 23 15:41:59 2014 -0700

    moved the code for regridding single-level run on restart to a function so that it can be called by derivative of Amr

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 97a713512070520bbb201bed8c458a70b11f529b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 23 10:54:15 2014 -0700

    use omp_lib --> include 'omp_lib.h' to make Cray compiler work

Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/INTERP_3D.F

commit 57fa06190f307f2db4cce50d13160942dca154b0
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 22 13:38:19 2014 -0700

    removed cout.

Src/C_BaseLib/DistributionMapping.cpp

commit 4a7c38b4c3ed5bd8132560fe25256622abed889b
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 22 13:36:12 2014 -0700

    added prof and commprof flags.

Tests/C_BaseLib/GNUmakefile

commit 727bf5c487eab3bb48ff5bea673c4b11dec52565
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 22 13:33:10 2014 -0700

    added tests.

Tests/C_BaseLib/tFB.cpp

commit 8b3a341560efb1ac01481af482e7048c8ecfc6fc
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 22 13:02:08 2014 -0700

    added some profiling.

MiniApps/MultiGrid_C/main.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 363dec5b56b02abebdb9af51744f1b8d3f1982fc
Author: beckner2 <vebeckner@lbl.gov>
Date:   Wed May 21 10:08:37 2014 -0700

    changes for intel compiler on cab.

Tools/C_mk/Make.Linux

commit bc6a7ac3db79554a27261aecdebf0f5232490195
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 21 09:33:04 2014 -0700

    The 1d stencil didn't have enough space allocated.

Src/LinearSolvers/F_MG/mg.f90

commit 92b5d6338320a02af02d1b405d192e3158ed7bb9
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue May 20 16:49:12 2014 -0700

    Copy fsnapshot stuff here from AmrPostProcessing to simplify distribution to external collaborators

Tools/Py_util/GNUmakefile
Tools/Py_util/README
Tools/Py_util/fsnapshot.f90
Tools/Py_util/plotsinglevar.py

commit 0553c66c0a7ad159b554d3ecb329722292c20d49
Merge: 99a6d6380 6cb2cfe78
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue May 13 20:36:31 2014 -0700

    Resolve conflict in plotfile.f90

commit 99a6d6380778264ca795dbf7daa3ddc62df7b872
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue May 13 20:34:22 2014 -0700

    Add parameter to MultiGrid_C tutorial to avoid build f90 solvers

Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_C/main.cpp

commit 15951c0a0fe8ee5161284088d59214d50ccd81d4
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue May 13 20:33:32 2014 -0700

    Allow longer variable names in plotfiles

Src/F_BaseLib/plotfile.f90

commit 6cb2cfe780adad9483aeaf9c5978d074f2c6d7b5
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue May 13 14:57:06 2014 -0400

    more work on the analysis bits

Tools/RegressionTesting/Castro-SBU-tests.ini
Tools/RegressionTesting/testnew.py

commit 627ba324a1844dab64354a92eaea1ab63ac26b51
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue May 13 11:17:07 2014 -0400

    update to add analysys plots to more tests

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 699805b00aebd341a3df786fddea22c826195081
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue May 13 10:37:48 2014 -0400

    add the ability to do post-test analysis

Tools/RegressionTesting/Castro-SBU-tests.ini
Tools/RegressionTesting/testnew.py

commit d2f9a86738b018fb24f3aef4e282d5ac7634a6c8
Merge: 3ec2fafec 10086696b
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Tue May 13 09:16:09 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 3ec2fafecd39174d7dde5e4f5ded40067eacfcb5
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Tue May 13 09:15:51 2014 -0400

    add analysis

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 10086696b13a6c2accf546306502927f1996be47
Merge: ed38fcd58 af6972b70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 12 21:11:06 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit ed38fcd584f5baae7f59f6d872cf5f0afcd2f5ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 12 21:10:41 2014 -0700

    PGI compiler requires explicit casting of int for std::sqrt

Src/C_BaseLib/IArrayBox.cpp
Src/C_BaseLib/iMultiFab.cpp

commit af6972b7008a418938ef43194e934ee03d25672e
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon May 12 17:08:22 2014 -0700

    fix the # of stencil points for higher-order stencils

Src/LinearSolvers/F_MG/mg.f90

commit 63a291291bbe406f7c28a26cc9263bf2a0187afb
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Mon May 12 19:00:11 2014 -0400

    when not using --infile1 OR --infile2, we were not incrementing the farg
    counter.  When using atleast one of --infile1 or --infile2, we were ok.

fcompare.f90

commit 8d4a193fafd2a197084a1f844bad1dc78503b662
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Thu May 8 13:59:25 2014 -0400

    add a -d switch that has the suite only run tests of a given dimensionality

Tools/RegressionTesting/testnew.py

commit e427815a5ee38e7f9c3420c7b918c0cc69568a73
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 6 16:18:04 2014 -0700

    more pfc, diagnostics still in the code.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit cfcfa36352df74641422953c460636176c1bfc8a
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue May 6 19:01:32 2014 -0400

    the Castro tests we run at Stony Brook

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 4ac304b9716eb5eaf70e0cea6da31f289efa458c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 6 14:28:07 2014 -0700

    fixed a minor thing that some compiler complains about

Src/F_BaseLib/boxarray_f.f90

commit 5877a41596edecf57080ecf1b22a999e141a7df7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 6 13:34:19 2014 -0700

    Re-insert two lines which were accidentally removed.

Src/LinearSolvers/F_MG/ml_solve.f90

commit 17d111c3855af852e20df6e491a38462ad37d4c5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 6 13:34:01 2014 -0700

    Remove some unneeded dependencies.

Src/LinearSolvers/F_MG/nodal_enforce_dirichlet_rhs.f90

commit e204203d00a6be7ad81a54bcc9e0862efdbae48a
Merge: 53679a154 773ee0948
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue May 6 09:40:45 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 53679a154ccb222e0d5e907b41445c9e2206ad7b
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue May 6 09:40:12 2014 -0700

    generalize make.defs to handle aliased gfortran versions

Tools/C_mk/Make.defs

commit 773ee0948e395892236b8ec6ac37acbd114f12d0
Merge: 48f4b96d4 416771560
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon May 5 16:07:11 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 48f4b96d44666f3832e9426f54f5e11dde9febb0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon May 5 16:05:44 2014 -0700

    Modify enforce_outflow_on_divu_rhs to be enforce_dirichlet_rhs so that
    it sets the nodal rhs to zero anywhere the mask is dirichlet, not just
    at ouflow values.  This takes care of setting the nodal rhs
    to zero at fine nodes at the coarse-fine interface.  This routine is called
    inside of ml_nd_solve, so should not be called in codes which call ml_nd_solve.
    Moved the enforce... code out fo nodal_divu.f90 and
    into a new file: nodal_enforce_dirichlet_rhs.f90

Src/LinearSolvers/F_MG/CMakeLists.txt
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_enforce_dirichlet_rhs.f90

commit adf21957a4496c5d3dd22dcc496e46744947fca8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon May 5 16:05:31 2014 -0700

    Remove extra printing of tres in ml_cc.f90

Src/LinearSolvers/F_MG/ml_cc.f90

commit 416771560dde5592569a3de706bb8e432667dbde
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 5 14:39:55 2014 -0700

    added a new function that returns whether a BoxArray intersects with a Box

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 51049d7b97d8627e31aa678a286f03bdaaf04698
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Apr 30 12:21:12 2014 -0700

    Increase max name length to 50 (from 20) for plotvars...probably should code this more robustly someday

Src/F_BaseLib/plotfile.f90

commit 960b7b0531585baefa42481d7254e9f897c79287
Merge: be6543a4a e53999e85
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Apr 29 13:46:08 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit be6543a4a6fe172aa2e82eb04e1114255d057a09
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Apr 29 13:45:18 2014 -0700

    1) Compute tres0 based on res, not rh
    2) Use max_norm instead of bnorm in the first convergence test.

Src/LinearSolvers/F_MG/ml_cc.f90

commit e53999e858634fcdb9f274211829f39981b780a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Apr 26 20:27:34 2014 -0700

    updated make system for Edison

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/F_mk/GMakeMPI.mak
Tools/F_mk/comps/Linux_intel.mak

commit 00705295adfb9d0158b9f5e3ee096677ec19389c
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 22 16:14:33 2014 -0700

    update to new solver interface

Tests/LinearSolvers/F_MG/cc_multi.f90
Tests/LinearSolvers/F_MG/nodal_multi.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit b8bebd8496e37a5301b1a697411875256ac6795a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 22 14:34:57 2014 -0700

    added norm functions that can do multiple components so that MPI reduce calls can be aggregated

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 1bc9ff6009afaa476930688636124c235b9ba0ae
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Apr 18 12:29:22 2014 -0700

    In mg_tower_cycle, use the cycle type "cyc" that is passed in, rather
    than using mgt%cycle_type.  This allows us to use different cycle types
    for different iterations to test whether a combination of F- and V-cycles
    works better than pure F- or pure V-cycles.

Src/LinearSolvers/F_MG/mg.f90

commit 748222b03f037d84398dda782447756e0135127d
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Thu Apr 17 14:20:34 2014 -0400

    only print the intepolation warning message from the IOProcessor

Src/LinearSolvers/F_MG/ml_cc.f90

commit 43b16b8c2c961c096d6d4b3ea44b4314e6724e4f
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 3 16:46:55 2014 -0700

    reworked reduction tracking.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 7462dc41e66d680651e637d56d816881b12afb10
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 3 15:46:03 2014 -0700

    stencil_apply_nodal_xd works now matter how many ghost cells the "dd" multifab has, where dd is the nodal result "L(phi)".  Before it required 1 ghost cell, which doesn't make sense since it only returns dd on the valid region and the boundary nodes

Src/LinearSolvers/F_MG/compute_defect.f90
Src/LinearSolvers/F_MG/nodal_stencil_apply.f90

commit 438c087fb2e8dacf99a0d11b5048b63463892713
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 3 12:31:23 2014 -0700

    added error checking and reporting for the fortran interface.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit c1a80ecc8a9d0ac1bfba5fb74a91f9468ae96681
Merge: e9b6be546 5ad92e91c
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 28 12:20:06 2014 -0700

    Merge branch 'master' into commprof

commit e9b6be5467abc7fe6d3bab8e7cab065ba1f6c368
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 28 12:18:25 2014 -0700

    unconst

Src/C_BaseLib/Profiler.H

commit 5ad92e91c48626f90520aeaba3c31c7bd13f828c
Merge: 8cd3ee0e6 a96717834
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 28 12:14:58 2014 -0700

    streamretry tweaks.

commit 8cd3ee0e644adcb71b396e9218434ae885feda9b
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 28 12:10:31 2014 -0700

    streamretry tweaks.

Src/C_BaseLib/Utility.cpp

commit a967178346ea3a4ed260117e786da911de10a193
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 27 16:04:22 2014 -0700

    update make files for edison

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/comps/Linux_intel.mak

commit 0fcbb902dc70035cd2b0ebf85ec409a1ec606967
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 16:13:49 2014 -0700

    need to scale residual by -1 so nodal_applyop returns +del dot beta grad phi.  appears to be working now

Src/LinearSolvers/F_MG/nodal_applyop.f90

commit a90e5cbcdb821f734b26301ee8f9d0fcba62f8cf
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 15:48:51 2014 -0700

    cleaning out cc_applyop

Src/LinearSolvers/F_MG/cc_applyop.f90

commit 350ec5db82da61ead21f2c91ec5845e56a7e7463
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 15:48:46 2014 -0700

    add nodal_applyop.f90

Src/LinearSolvers/F_MG/GPackage.mak

commit 6220b7cbbffe722de45634bc6b633a323213bf6c
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 15:48:30 2014 -0700

    writing a nodal_applyop... wip

Src/LinearSolvers/F_MG/nodal_applyop.f90

commit ebfa59870e6980340c7c603f1e1191ed62ca9171
Merge: ad13e2134 ca6da43db
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 09:57:17 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ad13e2134b5a2fb1fc8e19bd904fddd100dcac81
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 09:57:03 2014 -0700

    make ml_cc_applyop public

Src/LinearSolvers/F_MG/cc_applyop.f90

commit ca6da43dbf3e1d595d9bf71f58eeee6186994451
Merge: efc9aaca5 0a629adbe
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Tue Mar 25 12:16:10 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit efc9aaca55f93d7935b69d3c548ed4c149e4272e
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Tue Mar 25 12:15:56 2014 -0400

    spelling

Src/F_BaseLib/bl_constants.f90

commit 678f0d390623a22edc97e0d889f95d9806bda380
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Tue Mar 25 12:15:08 2014 -0400

    add TWELVTH and SEVEN12TH

Src/F_BaseLib/bl_constants.f90

commit 0a629adbe4db28e3816942ad5ef4d5a306d71df4
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 08:36:52 2014 -0700

    remove a comment

Src/LinearSolvers/F_MG/ml_solve.f90

commit 27ce734dbc95beb831895682e9a3caf965e18743
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 08:04:17 2014 -0700

    update comments

Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/mg.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90

commit fe06ba663db57dae1b6df80c2733e71369ce55af
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 08:02:16 2014 -0700

    move mac_applyop into cc_applyop (delete mac_applyop.f90) and renname the function cc_applyop to be consistent with the rest of the mg naming convention.

Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/mac_applyop.f90

commit b29eaafa072e6e474e1fe98fd9eb9fd61fc486ce
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Mar 24 16:31:30 2014 -0700

    eliminate scale_residual subroutines and just use a mult_mult_s_c.  bonuts points is that 3d is now openmp'd

Src/LinearSolvers/F_MG/cc_applyop.f90

commit bcd4d065b486c62ea840389b029a2dfddf12e45e
Merge: 3085caade b4d57c5dd
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 20 15:44:35 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3085caadef5ea6b5d776a28cd99132eb4d6939c6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 20 15:44:14 2014 -0700

    nodal_divu now works regardless of the number of ghost cells u or rh have

Src/LinearSolvers/F_MG/nodal_divu.f90

commit b4d57c5dd9beae760eea2c70c8519274c4c7b418
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 20 13:13:48 2014 -0700

    norm_cor is no longer used.

Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit 1ae85820f4ab5e663aa29f8c187f802e89eff591
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Mar 19 22:24:06 2014 -0400

    add --complete_report_from_crash -- this allows you to generate
    the reports for a test suite run where the main test program
    crashed (or was disconnected from when run remotely).

Tools/RegressionTesting/testnew.py

commit 1e5991f1506b313f0b58d718bd5b9a27880f9dde
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Mar 17 17:51:30 2014 -0700

    fix error in max_level logic for ml_nd_solve_1 and ml_cc_solve_1

Src/LinearSolvers/F_MG/ml_solve.f90

commit 762411c90ebed6c33b74bfaae15ab03cf90071c3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Mar 17 16:19:27 2014 -0700

    moved the bottom solver (for type 4) logic test into ml_nd_solve_1 and ml_cc_solve_1

Src/LinearSolvers/F_MG/ml_solve.f90

commit 3dbd530f7ca603d7f00207a5529d205737a664fd
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Mar 17 16:02:41 2014 -0700

    more elaborate testing to determine mgt(n)%max_nlevel in both ml_cc_solve_1 and ml_nd_solve_1

Src/LinearSolvers/F_MG/ml_solve.f90

commit 117cd8f777464579102d6a850cec68c83092acb2
Merge: 5a8657fba 0a114070f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Mar 17 11:00:27 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5a8657fba2bdf90072b7795018293e673725b5c3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Mar 17 11:00:00 2014 -0700

    stencil_order is now an optional argument with a default value of 2 if not passed in

Src/LinearSolvers/F_MG/mac_applyop.f90

commit 0a114070fc08700ba106bf5ffa4dc6911e80591b
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Mar 17 10:56:54 2014 -0700

    Uptick tag version number

Tools/CMake/BoxLib_Version.cmake

commit f3024f2c96fc277c569023b68a5b9015cc37e876
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Mar 17 10:54:08 2014 -0700

    Explicitly cast the args in the pow function to quiet older compilers

Src/C_BaseLib/IArrayBox.cpp

commit fd256e44bb68699b368be11d60acfd504652a823
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Mar 14 15:32:55 2014 -0700

    mgt_nodal_solve() now takes in eps and abs_eps as arguments (as it used to earlier in the week) and copies these values into the mg_tower object

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit be75e0292149c453a308e31ce057e5a1e6af4f0d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 13 21:31:55 2014 -0700

    Modified BSD license stuff.

README.txt
license.txt

commit eed5bf54f479e29f80d5201e2c84dec4b65eb2a8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 13 21:30:25 2014 -0700

    These are the new versions for our official modified BSD release
    of BoxLib version  02-28-2014.

README.txt
license.txt

commit c81c8513ddad6fc2f59ceef1770e75173e3fb329
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 13 16:35:47 2014 -0700

    added the flexibility to pass in optional "S" and subtract this from the RHS for nodal solves

Src/LinearSolvers/F_MG/ml_solve.f90

commit 8a5db38c3e2d2c03b14d09cc0d51fbeed3b2b3a3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 13 16:01:20 2014 -0700

    cleanup only

Src/LinearSolvers/F_MG/ml_solve.f90

commit fc9f71ad6cff07a2aa80f3d8c58e6231f5706eef
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 13 15:56:13 2014 -0700

    use new add_divu_to_rhs feature, fix comments

Src/LinearSolvers/F_MG/ml_solve.f90

commit 7d10d2fda8bd329b49a628af38453cf337cece97
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 13 15:46:33 2014 -0700

    add optional logical argument to subtract_divu_from_rh to *add* rather than *subtract*

Src/LinearSolvers/F_MG/nodal_divu.f90

commit d8078bf91cc718768ad7dced9f10c6bc97e53351
Merge: 477ed7211 3f146ad73
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 13 15:20:12 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 477ed7211fb596d5f364dc10368d25a5165b72e1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 13 15:19:12 2014 -0700

    Make sure we use the tol and abs_tol that are passed in through the C++
    interface -- they come in through the call from C++ in "mgt_solve" then
    are used to define mgts%mgt_eps and mgts%mgt_abs_eps which are actually
    used by the solver.  Note that the C++ solvers always have to pass in
    the tolerance, they are not currently wired to use the default.

Src/LinearSolvers/F_MG/cc_mg_cpp.f90

commit 3f146ad732a05275e150dfc04cc8fe4f6fd6c9aa
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 13 14:28:40 2014 -0700

    plug memory leak.  also fix sign convention in rhs for nodal solve.  still wip.  varden works, need to check MAESTRO for nonzero S to see if the sign convention holds

Src/LinearSolvers/F_MG/ml_solve.f90

commit 6b6c79fd9b4115d0c9e7753676a563dfe2ad58b2
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 13 13:12:18 2014 -0700

    remove unnecessary optional arguments

Src/LinearSolvers/F_MG/ml_solve.f90

commit de2c45d387b79dc984204e5bf68109d82843faf6
Merge: 104e43214 a87d89357
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 13 13:02:59 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 104e432149e8d06bf04ca989c704a923f114fe58
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 13 13:02:33 2014 -0700

    need to pass in a boundary register to cc solver interface.  projections need the boundary flux of phi to update at CF interfaces

Src/LinearSolvers/F_MG/ml_solve.f90

commit a87d893575b381547c954ef9bfb63721beb79aaa
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Mar 13 11:45:50 2014 -0700

    PyBoxLib: Add setup.py.

Src/Python/GNUmakefile
Src/Python/GNUmakefile_CXX.mak
Src/Python/setup.py

commit 5343466a47339071e932f90c7ec5ad875d0cd056
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Mar 13 11:12:53 2014 -0700

    PyBoxLib: Update basic multifab test, tidy up a bit.

Src/Python/read.py
Src/Python/tests/test-multifab.py
Src/Python/write.py

commit 376211419d7e9f65a98b714eabd8c49e0ca05f0a
Merge: 5849550a1 74eb364c5
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Mar 13 11:09:41 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5849550a132882ca5d822f76452135cfb7a2d209
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Mar 13 11:09:28 2014 -0700

    PyBoxLib: Remove old Fortran wrappers, update C++ wrappers (very basic for now).

Src/Python/GMakerules.mak
Src/Python/GNUmakefile
Src/Python/GNUmakefile_CXX.mak
Src/Python/GNUmakefile_F.mak
Src/Python/GPackage.mak
Src/Python/README
Src/Python/boxlib/__init__.py
Src/Python/boxlib/bl1.py
Src/Python/boxlib/bl2.py
Src/Python/boxlib/bl3.py
Src/Python/boxlib/fbl/__init__.py
Src/Python/boxlib/fbl/base.py
Src/Python/boxlib/fbl/boxarray.py
Src/Python/boxlib/fbl/fab.py
Src/Python/boxlib/fbl/fabutils.py
Src/Python/boxlib/fbl/layout.py
Src/Python/boxlib/fbl/multifab.py
Src/Python/boxlib/fbl/plotfile.py
Src/Python/boxlib/fbl/pybl.py
Src/Python/boxlib/fbl/utils.py
Src/Python/contrib/chemSupport.H
Src/Python/contrib/chemSupport.cpp
Src/Python/contrib/support.H
Src/Python/contrib/support.cpp
Src/Python/fsrc/blobjects.f90
Src/Python/fsrc/blobjects.py
Src/Python/fsrc/boxlib_numpy_c.c
Src/Python/fsrc/boxlib_numpy_f.f90
Src/Python/fsrc/fboxlib.f90
Src/Python/src/boxlib_wrap_1.cpp.REMOVED.git-id
Src/Python/src/boxlib_wrap_2.cpp.REMOVED.git-id
Src/Python/src/boxlib_wrap_3.cpp.REMOVED.git-id
Src/Python/swig/boxlib.i

commit 74eb364c59db31f640b1c335180cca4eabb45614
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Mar 12 16:55:16 2014 -0700

    index bug fix in new cc solver

Src/LinearSolvers/F_MG/ml_solve.f90

commit 6c5e86d52ed7db8bf3c2fdd75cef66107ccac099
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Mar 12 15:49:12 2014 -0700

    new interface for ml_nd_solve complete.  now for testing

Src/LinearSolvers/F_MG/ml_solve.f90

commit 844b241d9d4b470e596b35b49b685511475c3068
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Mar 12 14:51:15 2014 -0700

    more progress on nodal solver interface.  still not sure if sign convention on rhs is correct

Src/LinearSolvers/F_MG/ml_solve.f90

commit d881574c1a2830f556048ad19064339cfffa0fba
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Mar 12 12:12:48 2014 -0700

    move enforce_outflow_on_divu_rhs to nodal_divu.f90 since each nodal projection code had its own local copy

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/nodal_divu.f90

commit 53d9a1bf92aa1f2d0bf5f13b8f425f605708f1c3
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Mar 12 10:46:03 2014 -0700

    fixed a bug in the new cc multigrid interface... passing in wrong bc comp to mg_tower_build.
    
    some work on the new nd multigrid interface... WIP

Src/LinearSolvers/F_MG/ml_solve.f90

commit 17c036ee3ffc4dae9b4120a87448744018abcb81
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Mar 12 10:32:51 2014 -0700

    ml_cc_solve_1 internally figures out of the problem is parabolic now and sets is_singular to false in the call to mg_tower_build.  for elliptic problems, no optional is_singular argument is passed in and mg_tower_build still checks the boundary conditions internally to see of the problem is singular

Src/LinearSolvers/F_MG/ml_solve.f90

commit f7641dd3abf55b2d798eeeafe405fa2924362bd7
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 11 13:38:24 2014 -0700

    clean up the interface to the cc solve, and add a new simple interface to call the cc f90 solver

Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mac_applyop.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 9589b356ad68006a27cbe4b547d5c3134bb13a79
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 11 11:22:19 2014 -0700

    cleanup only

Src/LinearSolvers/F_MG/mg.f90

commit 11ee3291f552f9cc101d9fc8f831bd9a4cb9b57a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 11 10:38:13 2014 -0700

    interface changes to keep up with f90 solvers

Src/LinearSolvers/F_MG/cc_mg_cpp.f90

commit 86cdf8c960af4b9c9595e6efc237c1123b275930
Merge: 51a18aaa6 17b093ec8
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 11 10:30:06 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 51a18aaa6e67751960a851982a6f11b92455437a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 11 10:27:11 2014 -0700

    don't pass in optional abs_eps and rel_eps arguments to ml_cc_solve and ml_nd_solve anymore and use the versions in the mg_tower object
    
    don't pass in ref_ratio anymore since it's available in the ml_layout

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90
Tutorials/HeatEquation_EX5_F/advance.f90

commit 17b093ec8febe0370bc0670d5cdcc8694c6e55f8
Merge: 78ab9eb96 8cad46286
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Mar 11 10:15:06 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 78ab9eb96cc1bbc7850a4de7491a49f8551d187f
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Mar 11 10:14:51 2014 -0700

    PyBoxLib: F90 version: Fold C routines into libpyfboxlib.

Src/Python/GMakerules.mak
Src/Python/GNUmakefile_F.mak
Src/Python/GPackage.mak
Src/Python/boxlib/fbl/fab.py
Src/Python/fsrc/boxlib_numpy_c.c

commit 12d90a963b416da47efa110d5a0c86eb715848c3
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 11:58:24 2014 -0800

    merge with master.

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit 9002dad422be09eb31f7a8687782a70df1e224be
Merge: b3c209cfb 8cad46286
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 11:51:32 2014 -0800

    Merge branch 'master' into commprof

commit 8cad46286a071739ae070f374031140d5746ba13
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 11:33:14 2014 -0800

    removed dumpi vars, they are now in Tools/C_mk.

MiniApps/FillBoundary/GNUmakefile

commit ff05b9aba11b1105a7d00713ebf17187ddb83745
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 11:31:55 2014 -0800

    added dumpi support to make system.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit c174932e63fe95df77318a8d185b1f0949b80bab
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 10:30:29 2014 -0800

    new ncube code.

MiniApps/MultiGrid_C/main.cpp

commit bcef866b78625a96fcb93ebedbd8d2431ab514aa
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 10:29:54 2014 -0800

    added ipm, dumpi, prof flags.  made more consistent with fillboundary.

MiniApps/MultiGrid_C/GNUmakefile

commit b3c209cfbbfc7d38f2bca879a2666ebe3f402895
Merge: 5c10f2b9b 9f14e3455
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 10:13:41 2014 -0800

    merge with master.

commit 9f14e34550fbafac4bed2e2afe221b4ce8390d0d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 09:07:04 2014 -0800

    iop around error output.

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit 466eed7a9e88d13766fc241413e959adc43575d0
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 09:05:47 2014 -0800

    we dont need the map since we are not going to reuse it.

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit 5c10f2b9b3ce6abaf6d54e6e9d5564293841e2a2
Merge: c864be4e7 e30e31f25
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 17:33:59 2014 -0800

    merged with master.

commit c864be4e7e2dae8c5859889331547339e3cd6b51
Merge: bf0a35879 f5f0cbe58
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 17:29:37 2014 -0800

    about to merge the latest versions.

commit e30e31f250f7f973d2183c1b9e86004b2b67d00f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 17:02:02 2014 -0800

    added vector initialization for older compilers.
    rewrote the N cubed check with a simple map lookup for small
    values.  exp(log...) breaks sometimes because of roundoff
    (nprocs = 1000 for example).  yes, it is always something.

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit 38d7b7a8db2774c5f98f6aa979fd293414cd5dd8
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 17:01:34 2014 -0800

    added new/old compiler flags and temporary dumpi support.

MiniApps/FillBoundary/GNUmakefile

commit e48a7d49b5d7f8020fa6fcd2a69f4caed9dcea0d
Merge: c3f29f15c e9d6dcb9e
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Mar 5 17:59:39 2014 -0500

    Merge in sub-Chandra analysis routines in branch 'fsub_dev'

commit e9d6dcb9e18fee233472cd9090aa7ef5829c3768
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Mar 5 17:56:15 2014 -0500

    Committing the latest version of the sub-Chandra analysis routines.

MAESTRO_sub_chandra/GNUmakefile
MAESTRO_sub_chandra/fsubchandra.f90
MAESTRO_sub_chandra/fsubchandra_mod.f90

commit f5f0cbe5877f15a41a0e544984247d922bc5ad02
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 12:24:26 2014 -0800

    added run time.

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit bf0a35879c7d218872592ac1ff2a5d2959e01972
Merge: d0c993252 afbb1e2da
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 11:44:16 2014 -0800

    made these similar to the master branch versions.

commit afbb1e2da6d15cf78185c64acfc6c861faed3ea4
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 11:27:13 2014 -0800

    added other run sizes.

MiniApps/FillBoundary/qsub.ipm.bat

commit efec85076e488c159334984332be4dc1c396dbdc
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 11:23:11 2014 -0800

    changed filename.

MiniApps/MultiGrid_C/README

commit af59c68e6e39fd7ec07ea2dead7b90a699bb1bed
Merge: 9b981521b 5f60ddd01
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Mar 5 10:37:43 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9b981521bdae666ac551633fe38338714e08b226
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Mar 5 10:37:35 2014 -0800

    PyBoxLib: Move Fortran based version to its own directory.  Begin importing C++ based version from Marc.

Src/Python/GMakerules.mak
Src/Python/GNUmakefile
Src/Python/GNUmakefile_CXX.mak
Src/Python/GNUmakefile_F.mak
Src/Python/GPackage.mak
Src/Python/boxlib/__init__.py
Src/Python/boxlib/fbl/__init__.py
Src/Python/boxlib/fbl/base.py
Src/Python/boxlib/fbl/boxarray.py
Src/Python/boxlib/fbl/fab.py
Src/Python/boxlib/fbl/fabutils.py
Src/Python/boxlib/fbl/layout.py
Src/Python/boxlib/fbl/multifab.py
Src/Python/boxlib/fbl/plotfile.py
Src/Python/boxlib/fbl/pybl.py
Src/Python/boxlib/fbl/utils.py
Src/Python/fsrc/blobjects.f90
Src/Python/fsrc/blobjects.py
Src/Python/fsrc/boxlib_numpy_c.c
Src/Python/fsrc/boxlib_numpy_f.f90
Src/Python/fsrc/fboxlib.f90
Src/Python/pyboxlib/__init__.py
Src/Python/pyboxlib/pybl.py
Src/Python/swig/boxlib.i
Src/Python/swig/numpy.i
Src/Python/tests/test-multifab.py

commit 5f60ddd012bb693b23dc75447413048975a81559
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 5 10:16:09 2014 -0800

    1) Modify MultiGrid.H / MultiGrid.cpp so we can set a new flag (do_fixed_number_of_iters)
    in the MultiGrid class -- can only be set using SetFixedIter -- if this is set to 1 then the
    MultiGrid class will do exactly maxiter iterations without checking for convergence.
    The default value is 0, so if this is not set to 1 then the code will behave as before.
    2) Modify the MiniApps/MultiGrid_C main.cpp so that it calls setFixedIter(1) to do just
    one iteration and stop without crashing.  We also no longer need inputs.3d

MiniApps/MultiGrid_C/inputs.3d
MiniApps/MultiGrid_C/main.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 5e21da8590f3c1bedb34bebeb15d321477a0a317
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 3 12:43:51 2014 -0800

    Create a multigrid MiniApp that doesn't require any inputs file.
    It creates a single 64^3 grid on each MPI process, and requires that
    the number of processes be a perfect cube so that the domain is
    N*N*N grids where N = cube root of NProcs.

MiniApps/MultiGrid_C/COEF_3D.F
MiniApps/MultiGrid_C/COEF_F.H
MiniApps/MultiGrid_C/GNUmakefile
MiniApps/MultiGrid_C/Make.package
MiniApps/MultiGrid_C/README
MiniApps/MultiGrid_C/RHS_3D.F
MiniApps/MultiGrid_C/RHS_F.H
MiniApps/MultiGrid_C/inputs.3d
MiniApps/MultiGrid_C/main.cpp
MiniApps/MultiGrid_C/qsub.ipm.bat

commit 1a702ffb43633be10a208ce6fc6c43969cc1b607
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 3 10:33:53 2014 -0800

    Add suggested numbers of processors.

MiniApps/FillBoundary/README

commit d0c9932523ca9707ab6d4427e0ab22796b9b582e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 3 10:32:11 2014 -0800

    Add suggested runs.

MiniApps/FillBoundary/README

commit 114650dd70c12aeb8849170bf2c9180ebf8bcf4a
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 28 14:29:49 2014 -0800

    added ipm support for hopper.

MiniApps/FillBoundary/GNUmakefile
MiniApps/FillBoundary/README
MiniApps/FillBoundary/qsub.ipm.bat

commit b8d154f56b59812272a2c1f4491ccd4bf83807cf
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 28 13:21:31 2014 -0800

    sanitized version for ipm/dumpi tracing.

MiniApps/FillBoundary/GNUmakefile
MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
MiniApps/FillBoundary/README

commit 294b9467de71dba19cb4c405a8e595d779c42521
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 28 12:23:57 2014 -0800

    files from commprof.

MiniApps/FillBoundary/GNUmakefile
MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
MiniApps/FillBoundary/README

commit 964e8b13fd9057dc317ef0c1ebe00eebce66dcac
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 21 00:12:33 2014 -0800

    test3d --> fbtest3d

MiniApps/FillBoundary/README

commit c212b268b3e93fdd58e7d127e37af209897ee78c
Author: vince <vebeckner@lbl.gov>
Date:   Thu Feb 20 18:03:51 2014 -0800

    squished into nested loops, added commprof tags.

MiniApps/FillBoundary/GNUmakefile
MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit c7043bbec4f6379d6d2f1c48e8c02e1f86af3281
Author: vince <vebeckner@lbl.gov>
Date:   Thu Feb 20 17:59:54 2014 -0800

    removed some diagnostic output.

Src/C_BaseLib/DistributionMapping.cpp

commit 14c5981beeb74e9f7383b0b7337b5b65b5dc20b8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 20 16:07:36 2014 -0800

    Fixed domain_hi.

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit e42f6e9f9a3309ebdb098d40d2d6ad38a424537e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 20 16:03:28 2014 -0800

    Fixed.

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit a38c90d1bfd52d5439efd60fe79bd469da42e811
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 20 15:50:30 2014 -0800

    Added info on how to build and run the code.

MiniApps/FillBoundary/README

commit d59a7f52515d95c04d4570dde57f7d5e25194d2e
Merge: 975ae4a11 09aff0e1f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 20 15:40:41 2014 -0800

    Merge branch 'commprof' of gamera:/usr/local/gitroot/BoxLib into commprof

commit 975ae4a11b3596adc6907e762a042dda1d7ab305
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 20 15:40:30 2014 -0800

    This code is a very simple code designed to profile communication patterns
    associated with the MultiFabFillBoundary operation, which exchanges ghost cells
    between the FABs in a single multifab.
    
    All this code does, for a certain set of parameters, is to
     * create a MultiFab which has "nGhost" ghost cells and "nComp" components
     * fill the data with the value 1.0 everywhere
     * exchange "nGhost" ghost cells of "nComp" components of the data in the FABs in this MultiFab
     * exchange either the faces only ("cross" = true) or all 26 nearest neighbor exchanges ("cross" = false")
    
    We have a separate call for each combination:
    
     * nComp = 1, 4, 20
     * nGhost = 1, 2, 3, 4
     * cross = true or false

MiniApps/FillBoundary/GNUmakefile
MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
MiniApps/FillBoundary/README

commit 09aff0e1f93668afd1245633d0d33404e5938604
Author: vince <vebeckner@lbl.gov>
Date:   Thu Feb 20 14:56:26 2014 -0800

    added information to header, rename bl_comm_prof dir if it exists.

Src/C_BaseLib/Profiler.cpp

commit ceb2f6742692de8453a82c30d2adf391eebc3670
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Thu Feb 20 17:48:32 2014 -0500

    allow for 2 extra build directories

Tools/RegressionTesting/testnew.py

commit c67e088d1a333948d42c0ecd47712667d16c5377
Merge: 8b080ad78 6451e7bc3
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 19 10:23:28 2014 -0800

    Merge branch 'master' into commprof

commit 6451e7bc31e41088198a01acda162af559ced768
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Feb 19 13:14:02 2014 -0500

    update of mostly comments + 1 parameter (time) in the wrong object

Tools/RegressionTesting/testnew.py

commit a7539a654804ea68f6233c5d3dfa22aec0f7a564
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Feb 19 11:59:42 2014 -0500

    take care of the rarely encountered situation of having no active tests
    defined, in which case, we do not want to print a row in the main webpage

Tools/RegressionTesting/testnew.py

commit 8b080ad784111057c62598f849c0bbc55da324b2
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 18 17:33:39 2014 -0800

    added enum num.

Src/C_BaseLib/Profiler.H

commit 5acb5f9e309162aca4b05f3a2ccc26fb1ec07fbb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Feb 13 13:56:00 2014 -0800

    I've been doing some experimentation regarding the order sends() in
    MPI Irecv/Send pairs.  This code randomly shuffles the order of the sends.
    The idea is better spread the MPI traffic across the network.  I'm
    checking the code in with the controlling variable defaulted to false.
    Got to gather more data to decide when/where it's really useful.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H

commit 2c951c1c1478bc3a268f834b71bc6e19e910dc5c
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Feb 12 15:59:32 2014 -0800

    Uptick version

Tools/CMake/BoxLib_Version.cmake

commit e6110f8e9284b692387c8a3a61b4827c125ee3e4
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Feb 12 15:58:13 2014 -0800

    Test mulitcomp

Tests/C_BaseLib/tMF.cpp

commit 320df5ee1cdaf968bd0a6914ca0b2ff4bf59c247
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 12 12:59:48 2014 -0800

    added timer for commstats flushing.

Src/C_BaseLib/Profiler.cpp

commit e0475f7c64e75d16db7424717633a046a2c55848
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 12 12:03:17 2014 -0800

    removed some nametag tracing.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit ecc779fd71a8c63750695aa6dea71f9c16955852
Merge: 63497f348 613599605
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 12 11:43:05 2014 -0800

    fix merge conflict.

commit 63497f3483dcfc2eab03a85b495a5e0ab0bbb607
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 12 11:28:57 2014 -0800

    added -DDEBUG flag

Tools/C_mk/Make.defs

commit e1fe5ac69c796f1066396982d7e5aa8b5efc0dfc
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 12 11:26:47 2014 -0800

    temporary diagnostics for new mappings.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.cpp

commit 2c450bcebc1e70b55e155f744cfcb4286544439f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 12 11:24:51 2014 -0800

    more work on proximity mapping, diagnostics are still in the code.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/Profiler.H

commit 613599605e5552ac7143795782bf24f4a67a5275
Author: cmalone <malone@ucolick.org>
Date:   Wed Feb 5 21:23:29 2014 -0800

    shouldn't need libg2c anymore, if using GCC4.x+

Tools/C_mk/Make.CYGWIN_NT

commit 48ede641c7198eb0462abfe8b3affe2463ec2282
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 5 14:16:21 2014 -0800

    regression test script: added diff to restart test

Tools/RegressionTesting/testnew.py

commit dc164ba7be6c4d470021ea7c5d4cb4ff1d30c7f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 5 11:11:04 2014 -0800

    get around an Intel compiler 14.0.1 bug

Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit d7d84e5789b53ced6411f863840466efe794467c
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 4 14:01:37 2014 -0800

    mpi lib fix for mothra.

Tools/C_mk/Make.mpi

commit 165d70d40f5edcc1276e0dfcaf26c994483e12f4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 3 09:03:07 2014 -0800

    Reverted out my latest mods; they were unnecessary given how we
    checkpoint.

Src/C_AMRLib/Particles.H

commit 88061881bd1aa6063a2f24d059b1cb4c6322150d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jan 31 10:06:42 2014 -0800

    Comment out some debugging output.
    The Intel compiler doesn't like one of my format statements.

Src/F_BaseLib/layout.f90

commit ac91571ce6d9b1db9602f04aa1da0dda901597f9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 30 14:13:34 2014 -0800

    Merged Vince's stream retry idea into Checkpoint().

Src/C_AMRLib/Particles.H

commit 247bf8893f0490711e5e362cb9bb7f8204f11e88
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 30 14:12:44 2014 -0800

    Added const std::string Unnamed to be used as default argument in
    ParallelDescriptor::Barrier() instead of creating a string on the fly.

Src/C_BaseLib/ParallelDescriptor.H

commit 9793a45fea52546971b1251916ce51efaf5d44cb
Merge: 382f14ad0 8defec763
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jan 29 10:02:23 2014 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 382f14ad0f7e658d6b82f33e38d5d60bad3332ef
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jan 29 10:02:09 2014 -0800

    Add Mattis machine to list of known machines

Src/C_BaseLib/ParmParse.cpp
Tools/C_mk/Make.Darwin
Tools/C_mk/Make.defs

commit 8defec7633af93039de1a3143983ba547af56194
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jan 27 14:14:19 2014 -0800

    More aggressize free()ing of memory in RedistributeMPI().

Src/C_AMRLib/Particles.H

commit d64de77f6fa118c38b03169f7ae9b087e7659a83
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jan 27 14:13:49 2014 -0800

    Increased fabarray.maxcomp to 25.

Src/C_BaseLib/FabArray.cpp

commit 571e50dd7743a4e90318b69071ac89760dbd1a98
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 24 16:12:23 2014 -0800

    removed output.

Src/C_AMRLib/Amr.cpp

commit 3c58105910aff179b7bfc49945221a5920427574
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Fri Jan 24 15:50:42 2014 -0500

    Modified fillpatch.f90 to safely handle empty boxes.  Problems were noticed
    when attempting to refine the sub-Chandra MAESTRO problem to 4 levels.

Src/F_BaseLib/fillpatch.f90

commit ca3c6cf22c829ba05321a779796130d21b4b0df7
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 24 11:52:44 2014 -0800

    comment.

Src/C_AMRLib/Amr.cpp

commit 4e347c6bf27f3b7f9e137d33d0674538f01e92bb
Merge: 786ed5a27 61d55284f
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 23 15:26:38 2014 -0800

    Merge branch 'master' into streamretry

commit 61d55284fafc9793244951b90fcc1db3d72eeca6
Merge: 0839880f7 efae9210c
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 23 15:26:18 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 786ed5a27da9759f909bd411bb1fdfacc264a34f
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 23 15:25:33 2014 -0800

    less verbosity.

Src/C_AMRLib/Amr.cpp

commit 39e1329c469e2a2eab11cb89552e658dcc35f3e1
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 23 14:30:29 2014 -0800

    changed temp file verbose output.

Src/C_AMRLib/Amr.cpp

commit 981b912a76b4f3e1b30321e7d1176bf78e316868
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 23 13:55:44 2014 -0800

    more stream information on retry.

Src/C_BaseLib/Utility.cpp

commit efae9210cf2a609caa703122fd2231d67e4dbe59
Merge: 696c31845 f9e1facca
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Jan 23 14:32:28 2014 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 696c31845faebabf122de8065d9c543347959c1f
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Jan 23 14:31:20 2014 -0500

    add some optional arguments to allow for potentially empty boxes.
    These changes should not affect any output, but will be used for
    a safer fillpatch to come...

Src/F_BaseLib/box_f.f90
Src/F_BaseLib/boxarray_f.f90
Src/F_BaseLib/multifab_f.f90

commit 6e5efc72983682ccd0ce9304210174b2e62b7767
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 22 15:36:26 2014 -0800

    checkpoint and plotfiles now have temporary names until
    they are complete.  then stream retry will rename them
    if there were stream errors.  if the checkpoint or plotfile
    names exist, those directories are renamed with a random
    suffix.  this includes the temporary file names.
    more output from stream errors.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit f9e1faccad9e6a9a0d8ad0d9038d893ad3165c76
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jan 22 11:22:28 2014 -0800

    Modest reduction in memory use for TagBoxArray::collate().
    This function collects all the tagged cells to the I/O processor,
    who then removes duplicates and broadcasts'm back, as part of the
    grid generation procedure.  The tagged cells are passed around as
    arrays of IntVects. Duplicates are removed by first sorting the
    vector of IntVects. On the 9000 core LMC run I'm currently nursing
    on edison, I've got roughly 13000 grids at level 2.  This leads to
    about 360000 tagged cells out of which about half turn out to be
    duplicates.  This is a pretty large array to be sorting.  Luckily
    the sort algorithm is NlogN.

Src/C_AMRLib/TagBox.cpp

commit 0839880f777d51edef85c98e3e73b7e8fd3de11d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 16 16:22:25 2014 -0800

    make temporary filenames for plotfiles and checkpoints,
    then rename them only if they are complete.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 914755561f18ee8831d963f4b4e985e10473ca2d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 16 14:10:50 2014 -0800

    delay reset of fab format.

Src/C_AMRLib/Amr.cpp

commit 0e5a543239d0e67bf3a33e37e345b2cc0b9d6a8b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 16 11:15:28 2014 -0800

    Define the pd in line 200 of fillpatch rather than using the not-yet-defined "cdomain".

Src/F_BaseLib/fillpatch.f90

commit e41f84fca7f18e63528b0090d40ddf0e3859f930
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 9 14:56:52 2014 -0800

    Some simplification.

Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/ParmParse.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 5a175be3101502223ab36572e401ad809181f1dd
Merge: a42a5afab ae21e5185
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 9 11:25:00 2014 -0800

    Merge branch 'master' into commprof

commit ae21e5185848ddb942cd6021d6eb4e74d1625a03
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jan 7 09:48:07 2014 -0800

    A little simplification.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit 2035bcddae7fe2cc06e59296c0c88fe3bda57ba4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jan 6 15:27:29 2014 -0800

    Now print out particle byte spread in Redistribute if m_verbose > 0
    instead of m_verbose > 1.

Src/C_AMRLib/Particles.H

commit 9d69f548db80dd6a451162a0e8b985eb75b8cd07
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jan 6 13:42:34 2014 -0800

    Some more cleanup to quite the compiler.

Src/C_BaseLib/FabArray.H
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit 0c9bf88da00a459c86a91531ccf5801d39379d45
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jan 6 12:34:00 2014 -0800

    Always use F90 solvers.

Tests/LinearSolvers/C_CellMG/MacOperator.cpp

commit 6b1eb18b93766487956742f23c7e73e931a8d05f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jan 6 12:13:53 2014 -0800

    Shut up compiler about "possible" uninitilized data.

Src/F_BaseLib/bc.f90

commit 2024c2f802317418ff022b738b11ede8d222fb98
Merge: c3a32c84d a9df0246d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 2 15:22:18 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c3a32c84d3a9fa6a083ab1cfa8212481081472d3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 2 15:22:02 2014 -0800

    add USE_WBAR option

Tools/C_mk/Make.defs

commit a9df0246d2419d83096fbf80d331124c51070cc0
Merge: 9e97f4777 26bd28d04
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Jan 2 17:03:26 2014 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 9e97f47779c185b9dc72f7cece090f13c8210f97
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Jan 2 17:02:19 2014 -0500

    Updated GMakeMPI.mak from jaguar to titan.

Tools/F_mk/GMakeMPI.mak

commit 26bd28d049c6ee1a4d2fd0aa86910339e233c3eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 2 10:52:02 2014 -0800

    fixed a bug in 1D fifth-order interpolation

Src/C_AMRLib/INTERP_1D.F
Src/C_AMRLib/Interpolater.cpp

commit a6aeedc1e9e73e243a649d4616b7698359f64c9d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 2 10:17:19 2014 -0800

    Removing the high water counters for boxarray.  They really uglified the code.
    Now that I "think" I've got the metadata heap issues resolved they're not
    really needed anyway.  We do use lots of boxarray; the more levels the merrier.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 4ba9c16e1cf5377f676d1467dc5d9a4b397bbf80
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 2 07:55:08 2014 -0800

    I think I finally figure out why I'm having memory issues on very large runs
    where I'm trying to squeeze as much FAB data onto a processor as possible.
    Basically it comes down to a quirk of how std::deque are implemented.  The
    really short, cryptic, problem with std::deque, when you have potentially tens,
    or hundreds of thousands of'm lying around, is that they can waste memory.
    They allocate memory in large "chunks", much of which can go to waste,
    depending on how many entries you end up pushing into the deque.
    Weiqun suggested I try "massif" which is a heap-profiling tool in valgrind.  It was
    playing around with massif that I noticed the "unused space" in the heap.  Switching
    to using std::vector in the data caches, I can use a trick (once I've build
    all the vectors for a given operation) to force the vector to use the minimal amount
    of memory needed to contain all the elements I've add to it.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 48e6c8d6d702421e54cc75a1589114eefbf6b814
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 30 15:57:03 2013 -0800

    We now flush the meta-data caches on every regrid, not just on a level
    0 regrid.  Most of the hard work is going on the finest level anyway.
    There's still something weird going on with my 21k runs on hopper which
    I can't duplicate on smaller runs.  Basically all the meta-data caches, as well
    as the high water marks for the number of BoxArrays are all nicely bounded, but
    the amount of bytes contained in BoxArrays is growing more or less monotonically.
    Not sure what's going on.  There are no memory leaks as far as valgrind is concerned.
    I'm starting to wonder if it's a feature of the newer g++ on hopper.

Src/C_AMRLib/Amr.cpp

commit be639c644027432608ee5997dba02ec124eaab8f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 27 16:06:50 2013 -0800

    Some more compressing of meta data.

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit 29f6cd355082f7e254afde5c504478a946c0c44e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Dec 21 08:35:20 2013 -0800

    More massaging of meta data statistics.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/BoxArray.cpp

commit cd3623d77d1593863d9049032627dfff3c95da79
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Dec 19 16:49:02 2013 -0800

    in the tensor solve, when looking at the inf_norm of the rhs or residual, look at all the components instead of just the first.

Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit 7aaa49b1af63e5270d7f6552adbd68f0400758d1
Merge: b9f636646 8a9a55123
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Dec 19 15:36:20 2013 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 8a9a55123472a9a58653fe7ae043d895c96e3128
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 19 14:08:01 2013 -0800

    Forgot to remove a debug statement.

Src/C_BaseLib/FabArray.cpp

commit a6a8671bcedd90746efe7cf526ce1502f6ec718f
Merge: 14eb3879f c7a21f31f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 19 14:03:34 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 14eb3879f19277fab2592173455083d2e5804244
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 19 14:02:02 2013 -0800

    Decreased the default sizes of the Fill_Boundary() and copy() caches to
    25.  This seems to get a majority of the reuse cases without leading to
    excessive metadata size.

Src/C_AMRLib/AuxBoundaryData.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit c7a21f31f4aa92a24492082a576bd436e06e1392
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 19 13:11:39 2013 -0800

    fixed comment

Src/C_BaseLib/FabArray.H

commit 55e484a35abc2fa27641f5831e4ebcbf67d8ae50
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 18 14:19:43 2013 -0800

    Some cleanup.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BoundaryLib/BndryData.cpp

commit 0a0b0845b0e181f7656e07b126ecc2e71cd87e6e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 18 11:20:55 2013 -0800

    Exclude the AuxBoundaryData parallel copy()s from being cached.

Src/C_AMRLib/AuxBoundaryData.cpp
Src/C_BaseLib/FabArray.cpp

commit e934e3b82d3c9db6ec2c8c4c7635eb03a81913c6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 18 10:35:41 2013 -0800

    Added ability to specify not to cache the data patterns for parallel copy.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit fdb518aa6d27c8c564ac9164f74ec019cf9b61c6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 18 09:03:51 2013 -0800

    Removed a redundant line.
    Reduced the default max size of the copy cache from 200 -> 100.
    Might have to go even smaller unless I can squeeze out more memory
    from the BoxArrays.  Or another route would be to not add the chemistry
    parallel copy()s to the cache.

Src/C_BaseLib/FabArray.cpp

commit 37870b6f3e13537e15a429142e8df68f347d854b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Dec 17 14:11:18 2013 -0800

    Removed BoxArray::reserve().  As best I can tell this is not used
    anywhere.  If someone is using it, you should be able to just delete the
    call to it and all should be well.  It's really just a hint to the
    underlying containing to "reserve" memory for future operations on
    the BoxArray.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 3823c4ff1ca3cfd13e14e2760e645308b9b4a91b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Dec 17 14:05:29 2013 -0800

    Some cleanup.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit fc37e7e5f84e970d4b8e7f448b40fa057dee011a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Dec 17 11:12:34 2013 -0800

    I'm now also keeping track of the total number of bytes stored in
    BoxArrays.  This turns out to be surprising difficult to do given
    the various ways BoxArrays can built and destroyed.  Hopefully I'm
    at least close to having in correct.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit b9f63664670d3b10e0901b5020ae07b71c74977a
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Dec 17 10:19:35 2013 -0800

    Double colon rule so we can extend if necessary

Tools/C_mk/Make.rules

commit 3dc63f6e64cebe358dcc6bd11582dd64e8f9e657
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 16 16:51:39 2013 -0800

    One more try to get the I/O I want.

Src/C_AMRLib/Amr.cpp

commit 666f88f11111620093fa54ff21a406c8b4b6f431
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 16 16:41:53 2013 -0800

    Cleaned up some verbose output.

Src/C_AMRLib/Amr.cpp

commit 6b796779c89086de14a0fa66d9644081a835319b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 16 15:34:45 2013 -0800

    Added counters for the high water mark of distinct BoxArrays and
    build hash tables.  It looks like I've been overestimating the amount
    of data in hash tables.  I missed a place in the code (hidden in the .H
    file not the .cpp file) where hash tables can go away.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit a42a5afabc468d764c5fc443b72badf28bcbbb76
Merge: 80f93b01c 5158d5741
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 16 15:12:44 2013 -0800

    Merge branch 'master' into commprof

commit 5158d57411912b76fee25001ae5d371d30e18321
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 16 13:58:19 2013 -0800

    Squeezed out some more memory from the hash tables.

Src/C_BaseLib/BoxArray.cpp

commit f09c2c015f2a26dec7e9353f539d72e7aad3f8e5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 16 12:28:08 2013 -0800

    Added code to print out the high-water mark of bytes held in BoxArray
    hash tables at the end of each coarse time step (similar to FAB bytes
    spread).  As best I can tell these hash tables are the only thing in the
    C++ code that grows as the total number of Boxes, not the total number of
    Boxes that a CPU owns.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 0886ef64524fea4d74e225e049661ee35f4e2731
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Dec 15 20:00:54 2013 -0800

    Add an option to moveKick in Particles.H that allows one to store
    the acceleration at the particle location in the data of the particle.
    This option is only exercised if the component passed in is relevant,
    aka > the components of the data used to store the velocity.

Src/C_AMRLib/Particles.H

commit 0094bb4772a147d968ec5a5a314699a4bc585c4b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 13 11:00:22 2013 -0800

    More BoxHash statistics.

Src/C_BaseLib/BoxArray.cpp

commit d10568f6f6cdb48f72df5d9aa95ecf3a8998bdf9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 13 10:40:59 2013 -0800

    Added a clear_hash_bin().  AddBox() calls intersections() ...

Src/C_AMRLib/FluxRegister.cpp

commit 0d275e200155e13cd66cde4ff2f1b610bb7ddf74
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 13 10:40:40 2013 -0800

    Added a clear_hash_bin().

Src/C_AMRLib/TagBox.cpp

commit c3f29f15c9ca9a3da46ca7395819fab463b86eac
Merge: 6b6173ad7 2301d2fe1
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Fri Dec 13 12:08:09 2013 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 6b6173ad7f6c8f89d55860f77755dc123df79d0f
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Fri Dec 13 12:07:45 2013 -0500

    don't require --infile1 --infile2

fcompare.f90

commit 99c5a38e4cdf8da4480e0218c82497dab25fce06
Merge: 54455d099 b0f52489b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 12 21:06:01 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 54455d099333385481f04cce1f1ef7d96c2e43a9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 12 21:05:31 2013 -0800

    Set default value of regrid_int = 1; you will now get a warning
    instead of an error if you don't set it in the inputs file.

Src/C_AMRLib/Amr.cpp

commit b0f52489bd4ecd9dba8c8e2a935558aeef575370
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 12 15:30:07 2013 -0800

    Some debugging stats for init_box_hash_bin().
    I'd like to turn this into a "map" but it Fortran ...

Src/F_BaseLib/layout.f90

commit 87fcf0a786506ff613978ef8056056c0cb093219
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 12 14:42:03 2013 -0800

    Remove left over print statement.

Src/C_AMRLib/Particles.H

commit 073e517498db8a364599af46401490b35595c0e9
Merge: 5ae0aa654 e61253f14
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 12 14:37:29 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5ae0aa65408f100c5e9adb9da9adf040762cc8e5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 12 14:31:09 2013 -0800

    Add the access function GetParticleCPU.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/Particles.H

commit e61253f1426d731075d2b56f61ca8ed34d596a20
Merge: aecad7327 9501c07f0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 12 13:39:00 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit aecad7327fc9cfcfdf8ca5c75075ce7448d443d7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 12 13:38:24 2013 -0800

    Added more debugging statistics to box hash bin code.

Src/C_BaseLib/BoxArray.cpp

commit 9501c07f0891dbb8686cdcec84125097e3e357e5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 12 13:37:09 2013 -0800

    Modify the "GetParticle.." routines to change how we access the
    particle data, and pass it through the Amr object to the outside.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/Particles.H

commit 24ed8b623b65f9183936949f7a4fdb6283ab8a5c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 11 12:23:51 2013 -0800

    On edison use -target=compute_node instead of -target=linux on compiles.

Tools/C_mk/Make.Linux

commit 0cb5cf9f2a952563cb513f0e00675381b353db8e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 11 10:55:03 2013 -0800

    Much more memory efficient implementation of the Box Hash stuff.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 4d19780fbaa4ee32409b556b5f488c2689428a1d
Merge: 945be8a4b 1b1022d08
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Dec 10 17:56:23 2013 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 945be8a4b387d2fcbfadcc6425616b367468920b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Dec 10 17:55:00 2013 -0800

    I'm adding back in the critical region that builds the hash bins.
    I seem to recall that the particle code needs this.  Something along
    the lines of particles using BoxArray::contains() in OMPd loops,
    where contains() calls the intersect code under the covers.

Src/C_BaseLib/BoxArray.cpp
Src/F_BaseLib/layout.f90

commit 1b1022d081e70f75b7eb60f9ed4d054394b495b7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 10 17:21:40 2013 -0800

    Removed commented line.

Src/C_AMRLib/Particles.H

commit 7f4dbd2ecd773919e7df8ffc1a772d30e224fd5b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 10 17:18:08 2013 -0800

    Add the virtual routine particle_redistribute so that we can call it from
    Amr::ParticleRedistribute.

Src/C_AMRLib/AmrLevel.H

commit 86711b56231a9f9263e2d8ef8c5eea153aaa66ed
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 10 17:14:46 2013 -0800

    1) Make the default ref_ratio be 2 for all directions and levels, instead
    of setting it to zero and having an error if not set in the inputs file.
    2) Clean up the geometry stuff: we now define an external geometry by
    setting the intersection points of grid lines with the boundary in each
    coordinate direction (both hi and lo).   This is a crude representation --
    just one location for the face in each cell where it intersects.
    3) Add Real coarseTimeStepDt which is the same as coarseTimeStep except
    it returns the dt that it used.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit eab5cd44d834e31f0d10212eb9b353334fa6136f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Dec 10 15:25:06 2013 -0800

    Be a little more aggressive clearing box_hash_bin.

Src/F_BaseLib/layout.f90

commit 8b3d74ccb0a3499fbafc63182d8a36478de1080d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Dec 10 12:53:32 2013 -0800

    Don't OMP loops containing layout_get_box_intersector calls.

Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit 0e2a5c4a257a146cd8ed8e0f07008c7aca26a9bf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Dec 10 12:53:04 2013 -0800

    Some cleanup.

Src/C_BaseLib/BoxArray.cpp

commit 854f9b632dc0ec1a1871a9a1529c42ec05d10ac6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Dec 10 12:24:34 2013 -0800

    Some simplification.
    Also removed the critical section around the innards of intersections().
    It's now no longer thread-safe.  Hope I've found all places where I
    was trying to do intersections in threads and remomved'm.

Src/C_BaseLib/BoxArray.cpp

commit 5a96be8830ce893841aa6652104484c452d042ac
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 21:51:31 2013 -0800

    Increased verbosity level at which some debug output appears.

Src/F_BaseLib/layout.f90

commit db809ba217350f29cf12ab62aca235bb3aa3863c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 21:27:05 2013 -0800

    Yet one more clear_hash_bin() call for the evening.

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit a3fc87a222a7c5d3fbe51ae08ef75112203a09f2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 21:24:14 2013 -0800

    Inserted more clear_hash_bin() calls.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit 46aa58e636678c640900ce51cddd2389dcf494e6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 21:15:12 2013 -0800

    Merged in some calls to BoxArray::clear_hash_bin().

Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/FabSet.cpp

commit aeecb9d0b30c3db7b15680044f95c5598b78b0ae
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 21:08:09 2013 -0800

    Clear out the hash bin in a BoxArray after using intersections() to
    put a cached object into the FillBoundary() and parallel copy() caches.

Src/C_BaseLib/FabArray.cpp

commit 6641c63dc865d3e0227c41667be4ddfc4fa7997c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 21:04:11 2013 -0800

    Merged in call to clear_hash_bin().

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 34c53faa1d30158202324572cad9e73697f02089
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 21:03:01 2013 -0800

    Added BoxArray::clear_hash_bin().

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 17cf353a3aff597b990250c4604d5c692f0bd49f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 21:02:39 2013 -0800

    Removed some debugging output.

Src/F_BaseLib/layout.f90

commit ae5f02d46ab013a2b7655d54a16fdb9c0dc2e0d2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 20:40:35 2013 -0800

    Compressed out some of the memory in the fast box intersection hash
    routine.  This routine (and the one in F90) are looking like the metadata
    memory hogs that I've been searching for. I think there's more that can be
    done to cut down memory use here.

Src/C_BaseLib/BoxArray.cpp

commit 3a8c25e72a0966e48956b2d9226558a68a2d3e31
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 15:08:34 2013 -0800

    Added clear_box_hash_bin().  There may be some strategic places where
    we can call this routine to cut down on memory usage.

Src/F_BaseLib/layout.f90

commit 8058550e7eac2d0aef64ac70490452126f991bb8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 14:37:31 2013 -0800

    Squeezed out some memory from the boxarray hash.

Src/F_BaseLib/layout.f90

commit 937f7dd31d9096c08e62530e95fad181eeaaa430
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 12:48:21 2013 -0800

    Added some code to calculate the maximum # of bytes in a boxassoc -- the
    structure that is used by layout for managing FillBoundary()s.

Src/F_BaseLib/layout.f90

commit 33c76f15356bc1af23bdaccc8e08a74f9a18acc9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 12:09:01 2013 -0800

    Pulled something from the stack and put it on the heap.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 70c17746bcd664ec0c276fd866ded1091ba45519
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 10:44:37 2013 -0800

    Some cleanup.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 60bcd5cea1aab117e68857b8b44bb69cbbed6a50
Merge: b0598e875 ae59f33d8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 10:22:22 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b0598e8758e9a52bacc3edd4984c3ba9beebb014
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 10:21:47 2013 -0800

    Don't build the mask() lmultifabs in the ml_layout.
    They appear to only be used by the cell-centered code.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 15125246349905723d05ebf2d7c4d9e5b0b34247
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 10:20:53 2013 -0800

    Only try to delete the mask() lmultifabs if they've actually been built.

Src/F_BaseLib/ml_layout.f90

commit ae59f33d8eaf2024366be1d0da3472016fc5c33d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Dec 7 12:12:18 2013 -0800

    Add sanity checks and comments in ParticleContainer::addOneParticle()

Src/C_AMRLib/Particles.H

commit 49043a8ff794b176dfa6845fc399100bf3140f22
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 6 14:14:47 2013 -0800

    Fix typo.

Src/C_BaseLib/FabArray.cpp

commit c4c328e5dda9ed6d9626d2d5d01d56b9cf2be509
Merge: 45923b1e7 f51c278f0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 6 13:54:51 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 45923b1e783926e2c6a5559262d354d03e24ca32
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 6 13:51:05 2013 -0800

    Parallel copy() is now set up to do fabarray.maxcomp components at once.
    That is to say, we agglomerate MPI messages as always, but we only do
    fabarray.maxcomp (instead of ncomp) at one time.  I'm occasionally
    getting killed by the Out-Of-Memory process of hopper.  I'm wondering
    if it's because the internal MPI buffers are getting too big.  So I want
    to do somewhat smaller MPI transfer.  Large transfer happen, in
    particular, when we're rearranging state data for chemistry solves,
    amongst other times.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit f51c278f0dd449c6380b5813d48ba70f37b44c14
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 4 14:01:25 2013 -0800

    Fix coefficients in tridiag.

Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit a45f1b2de98a205fea872fe2bd69b9f271194de3
Merge: 8dea6f284 6cd84b159
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 3 16:20:23 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8dea6f284219934d582b5903f12fa41a6aa31642
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 3 16:20:11 2013 -0800

    Add new files to Make.package

Src/C_BaseLib/Make.package

commit f4cd0a5c3ae833ef72e932cc83cb6463dd0e0940
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 3 16:19:29 2013 -0800

    Add iMultiFab.{H,cpp} and IArrayBox.{H,cpp} to the repo.

Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/IArrayBox.H
Src/C_BaseLib/IArrayBox.cpp
Src/C_BaseLib/iMultiFab.H
Src/C_BaseLib/iMultiFab.cpp

commit 6cd84b15942581f59c790b8a41ea28a53eb19c68
Merge: 464efc4bc f5ded3935
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 21:27:22 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 464efc4bca8669ffae14cb69df3018fcad5b979d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 21:27:15 2013 -0800

    use OMP ATOMIC instead of OMP CRITICAL in a few places

Src/C_AMRLib/Particles.cpp
Src/C_BaseLib/BaseFab.H
Src/F_BaseLib/bl_mem_stat.f90

commit f5ded39350c5173978c8c3cc54d8cfd4cd52fd1b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 2 13:44:47 2013 -0800

    DatasetClient.H no longer lives in this directory.

Src/C_AMRLib/CMakeLists.txt

commit daf3dfbf38d78b6d2b7475f3694128b9616d9dd5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 2 13:22:35 2013 -0800

    Add nodal_stencil_apply.f90 to CMakeLists.txt

Src/LinearSolvers/F_MG/CMakeLists.txt

commit b7497068128a17c9d99b03d37bc59c92278dedb4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 2 13:19:02 2013 -0800

    Add compute_defet.f90 to CMakeLists.txt

Src/LinearSolvers/F_MG/CMakeLists.txt

commit 24977ac52d148b2ff552974976d3132a50389bef
Merge: db7734e2f ee50cde90
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 2 13:01:23 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit db7734e2fd87bb2962a9f24ad90c752bf84988a1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 2 13:01:02 2013 -0800

    Update mg_tower_smoother.f90 --> nodal_mg_tower_smoother.f90 and cc_mg_tower_smoother.f90

Src/LinearSolvers/F_MG/CMakeLists.txt

commit ee50cde9044c0655d8007ad17bf063c2bb8ccf2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 11:27:16 2013 -0800

    Avoid using result, a Fortran keyword, as variable name although it is legal.

Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 134fd58f06f37ae4c7714b6811a2979132893818
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 10:40:09 2013 -0800

    fixed OMP bugs

Src/LinearSolvers/C_TensorMG/MCLO_3D.F

commit 72d2d83153979a3b0a498f6511d1588a73292b55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 10:06:46 2013 -0800

    fixed an OMP bug

Src/F_BaseLib/create_umac_grown.f90

commit 9a1bb1e7171afd9e7952b2eea42f98ba3706c949
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 09:46:33 2013 -0800

    removed unsafe OMP. The OMP do was on fine index, whereas the loop body wrote to an array on coarse grid.  Thus it was possible that two threads with different fine index might write to the same coarse index.

Src/C_AMRLib/INTERP_3D.F

commit 6f2757fdbce61e8089e82ba5f6d8949ee02fab5b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Nov 30 19:32:22 2013 -0800

    Set some defaults for mg.maxiter and mg.maxiter_b for F90 calls from C++.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 3ddddebc8292184cfa1dde80d3531377b7c7b2ab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 27 12:39:03 2013 -0800

    Removed OMP from TagBoxArray::mapPeriodic because it is unsafe. Note that the valid boxes in TagBoxArray are actually grown boxes.  So cells in a TagBox can have multiple sources during the merge with periodically shifted TagBoxes.

Src/C_AMRLib/TagBox.cpp

commit 15273708fa30982edea975e8e5058596df34c0cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 27 10:54:50 2013 -0800

    Removed OMP from reflux because it's not safe. Suppose there is a coarse cell next to the joint of the two fine boxes.  Then the reflux onto the corase cell comes from two fine boxes.  Thus it is unsafe to OMP over intersection boxes of the flux registers based on the fine grid and the coarse grid.

Src/C_AMRLib/FluxRegister.cpp

commit a8e6f4f676151ebac7024e821b24e83909039044
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 26 14:34:33 2013 -0800

    fixed a minor OMP problem

Src/C_BaseLib/BaseFab.H

commit 27bd3fcba68060e82ec6ab998809f15d22816848
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 25 20:11:39 2013 -0800

    fixed OMP bugs in my recent commit that will lead to race condition if the number of threads is large

Src/C_AMRLib/FLUXREG_3D.F

commit 6ff0478d4b6b07dd102f3407a11e54acb125241e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 25 20:00:51 2013 -0800

    Some OMP fixes.

Src/LinearSolvers/F_MG/ml_nd.f90

commit dbf5c7b51521767125d9afd4930abd98ddbcee70
Merge: c12be2ac9 4731d7142
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 25 19:34:35 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib
    
    Conflicts:
            Src/LinearSolvers/F_MG/ml_nd.f90

commit c12be2ac917e1ccb40116b6c3f5553f51e0f83f5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 25 19:33:00 2013 -0800

    Fix indices in nodal_stencil_norm.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 4731d7142973e7396985dc1b194a2a14b8cb58e0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 25 19:24:16 2013 -0800

    Some OMP bug fixes.

Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/nodal_stencil_apply.f90

commit 76c9d75e490b256ad53bc76b6098b592f91f1dd6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 25 17:42:41 2013 -0800

    1) remove unused variable in nodal_smoothers.
    2) fix nodal_stencil_norm.

Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit 4d632064aa7556d37b29aaa75841ce5ff4d29e4a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 25 16:58:06 2013 -0800

    We need to use a different function for the stencil norm for the nodal solver.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 34b1a5eb396ccc4758d8f3f3632548a70727ef4a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 25 16:46:11 2013 -0800

    Remove lp from OMP declaration where it isn't used

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 80f93b01ca69eda2040a3f409afb5689ebf2a76a
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 25 14:34:15 2013 -0800

    reset strategy fix.

Src/C_BaseLib/DistributionMapping.cpp

commit 23ad74d5cd219963e6e86d7b2a2b2f31c4165725
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 25 13:32:00 2013 -0800

    fixed a bug in nodal stencil

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 318dc85f0868960a852096f24e4fb6cfb3c69fa3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 25 10:16:27 2013 -0800

    Fixed new OMP bugs.  Also added "collapse".  If compilers have trouble
    with "collapse", we can take it out, and move "omp do" two loops down.

Src/C_AMRLib/FLUXREG_3D.F

commit afba92b0f6d67530abe98c5a6da8ff66929ff1e7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 25 08:53:00 2013 -0800

    Make the C-F MG translation code understand CABiCG solver.  Set it up
    so that it CG, BiCG and CABiCG get properly translated between C++ and
    Fortran.  While in the C++ code we set cg_solver as cg.cg_solver we
    allow cg.cg_solver and mg.cg_solver.  Default to CABiCG if nothing is set.
    If you want different bottom solvers in C++ and Fortran use
    mg.bottom_solver, set to the correct F90 value.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 48cb1ff9b69b6ec7bc2367e5347a7f57609d9f59
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 22 15:42:22 2013 -0800

    Fixed typo.

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 771ad0ca781794ac139fdef97eed673d8ad187bf
Merge: 3534844d6 1208cf040
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 22 15:35:42 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3534844d6e732cfbe3c008e5a15539b9966b9729
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 22 15:35:22 2013 -0800

    Fix the way we impose Neumann bc's on sg in nodal stencil fill.

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90

commit 1208cf0404abbcc3082e20057bde4eb5a67d2de7
Merge: 70514976e 286446875
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 22 12:40:04 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 70514976e9aff8bb8ffbf63422be9f59d8759c22
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 22 12:37:21 2013 -0800

    Added code so that we thread a couple of these routines if they're
    NOT called from within a parallel region.  In general, the most common
    place to call these routines from is within FillPatch, where they're
    called by threading over boxes in C++.

Src/C_AMRLib/INTERP_3D.F

commit 286446875950a0b91c551879cc21796a333ad8e5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 22 11:16:25 2013 -0800

    Only have diagonalize=true for nodal solve.

Src/LinearSolvers/F_MG/itsol.f90

commit 364ed421238af14b0ae505c6c3023e65cbb30c97
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 22 11:09:09 2013 -0800

    No longer pass ns into mg_tower_build.

Tutorials/HeatEquation_EX5_F/advance.f90

commit a2c8773e23c85823b89160aca5017170a3d52701
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 22 11:03:08 2013 -0800

    More changes to be compatibale with the new nodal stencil (and the fact
    that we no longer pass ns into mg_tower_build).

Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 7411f531a53c5c1dc46a382a726b03042a7cbb80
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 22 10:50:08 2013 -0800

    Turns out there's an easy way to figure out whethe or not we're currently
    in an OMP parallel region.  The FineAdd Fortran routines are now written
    to only thread if they're not in an OMP region.  When the MultiFab version
    of FineAdd() is used we thread in C++ over the boxes and hence don't
    thread within the Fortran.  When the FAB version of FineAdd() is called
    we thread the Fortran.  More of this to come ...

Src/C_AMRLib/FLUXREG_3D.F

commit 67e497c75796015a271cae2add3573fbe33e7761
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 22 10:43:41 2013 -0800

    ns --> mgt%ns

Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90

commit 001c73e24828f250114594b120c6e752a797d592
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 22 10:43:07 2013 -0800

    These are the new versions of the nodal solver which carries the cell-centered
    coefficient rather than filling the nodal-based stencil.

Src/LinearSolvers/F_MG/compute_defect.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/nodal_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_apply.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 20aa80c46b6c3db22acf052357639c44b55c800a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 22 10:16:35 2013 -0800

    Use mgt%ns, not ns.

Src/LinearSolvers/F_MG/mg.f90

commit b476c15405745e1fe6b3c9db02e93c8b0f1a1378
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 21 16:41:46 2013 -0800

    These are the nodal files that used the stencil-based as opposed to the
    new sg-based nodal stencil.

Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/compute_defect.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/itsol.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/ml_nd.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/ml_solve.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_interface_stencil.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_mg_cpp.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_mg_tower_smoother.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_smoothers.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil_apply.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil_fill.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_sync_resid.f90

commit 2ca4e87d5759eea0cc36f6109a387c3aee73b390
Merge: f13c4100f f451ddb07
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 21 16:40:12 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f13c4100fb1797663e105e779e2adab5fb2e4df9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 21 16:39:38 2013 -0800

    Create a new directory: BoxLib/Tests/LinearSolvers/F_MG_Old_Nodal_Stencil
    to hold the source code and test code for the stencil-based nodal solver.

Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/GNUmakefile
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/bc_interp.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_edge_coeffs.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_multi.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_rhs.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_2d_1lev
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_2d_2lev
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_3d_1lev
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_3d_2lev
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/init_cell_coeffs.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.2d.nodal.cross
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.2d.nodal.dense
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.3d.nodal.cross
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.3d.nodal.dense
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/main.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/makefile
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_multi.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_rhs.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/regression
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/t_smoother.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/t_stencil.f90
Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/wrapper.f90

commit eea8556a0e4b9bf1176d1beedfa959728ee10c70
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 21 16:38:06 2013 -0800

    No longer keep these scripts.

Tests/LinearSolvers/F_MG/test_dir
Tests/LinearSolvers/F_MG/test_script

commit 33107689e7fe654bf6ab6bd8393b1aa68d44f75f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 21 16:37:43 2013 -0800

    These are the new test routines for the new sg-based nodal solver.

Tests/LinearSolvers/F_MG/cc_multi.f90
Tests/LinearSolvers/F_MG/init_cell_coeffs.f90
Tests/LinearSolvers/F_MG/nodal_multi.f90
Tests/LinearSolvers/F_MG/nodal_rhs.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit b8219db9e952ba63b7e4b55c876392d5bfd0ddc6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 21 16:32:35 2013 -0800

    More cleanup -- no functional change.

Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/mac_applyop.f90

commit f451ddb0783d6b5631273cdc026ae8f4b8fcdc19
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 21 13:06:38 2013 -0800

    fixed makefile in F_MG for C++ codes

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 37d373f2a46d991073fbc8f515998633748762ec
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 21 12:30:12 2013 -0800

    These changes should not make any difference in the answers, they are
    just rearrangement and some renaming of subroutines.

Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/compute_defect.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_apply.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit be6420325dddf7a4caf565a11baeded10004c323
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 14:20:13 2013 -0800

    Update the testing routines with new inputs*nodal* files and
    new grids files.  Clean up the printouts as well.

Tests/LinearSolvers/F_MG/grids_2d_1lev
Tests/LinearSolvers/F_MG/grids_2d_2lev
Tests/LinearSolvers/F_MG/grids_3d_1lev
Tests/LinearSolvers/F_MG/grids_3d_2lev
Tests/LinearSolvers/F_MG/init_cell_coeffs.f90
Tests/LinearSolvers/F_MG/inputs.2d.nodal.cross
Tests/LinearSolvers/F_MG/inputs.2d.nodal.dense
Tests/LinearSolvers/F_MG/inputs.3d.nodal.cross
Tests/LinearSolvers/F_MG/inputs.3d.nodal.dense
Tests/LinearSolvers/F_MG/nodal_multi.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit c153ac9ace79f0f5e89f3e3a2204f6e469fd4329
Merge: 338ba0351 ab8cfa3bd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 12:37:05 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 338ba03513f88beb2b9e1cefddfc5ace108e1916
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 12:36:45 2013 -0800

    Clean up of nodal multigird and the testing program in Tests/LinearSolvers/F_MG.

Tests/LinearSolvers/F_MG/GNUmakefile
Tests/LinearSolvers/F_MG/cc_edge_coeffs.f90
Tests/LinearSolvers/F_MG/cc_multi.f90
Tests/LinearSolvers/F_MG/nodal_multi.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit 23813471edb80c674dc6af7a7fa4dbd1fef74350
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 12:36:08 2013 -0800

    The filest are listed in GNUmakefile instead.

Tests/LinearSolvers/F_MG/GPackage.mak

commit 803a729eaadb86df36645a8c6be4f23099ba4f31
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 12:33:32 2013 -0800

    Get rid of Jacobi options within smoothers.

Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit 1dfc4a42a2cb1d866a443b71cb466036ecdac43c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 12:33:12 2013 -0800

    Better formatting.

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 9c155a3910dfe8d9669d502abbc133dda99cbd4a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 12:32:37 2013 -0800

    Make sure rh has exactly one ghost cell.

Src/LinearSolvers/F_MG/ml_nd.f90

commit a9a546922ba28eded57cba98b9268f78667fbedc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 11:28:47 2013 -0800

    Get rid of Jacobi smoother.

Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit ab8cfa3bde5154d0e5bb6b6f6553322c1aafaaab
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Nov 19 12:03:37 2013 -0800

    Verbose flags should be integer.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 956acec5f3d84ac93d162b236a5686ff4b88bbab
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Nov 19 09:50:47 2013 -0800

    Added a verbose option, defaulted to false, to MGT_Solver.  This way we
    can set the default on a case by case basis, instead of just using the
    ParmParsed valued of mg.v.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 8c3e78c724b3176be0e25934328cd9c2f7fe5066
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 18 15:08:48 2013 -0800

    Example now shows how to reduce a map where the key is a structure.
    I use and IntVect since BoxLib knows how to sort IntVects.

Tests/C_BaseLib/tMF.cpp

commit a45ed369c9c37f831536454f57477e5e4cef8c09
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 18 14:13:54 2013 -0800

    A little cleanup.

Tests/C_BaseLib/tMF.cpp

commit ff06d0d671caa944bb0d8fc5db33328f37047020
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 18 14:10:38 2013 -0800

    This test is now a simple example of how to reduce a std::map<int,Real>
    across CPUs.

Tests/C_BaseLib/tMF.cpp

commit b1f7ed0caf83d88be872a42c8197f8ed716bedec
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 15 12:18:53 2013 -0800

    Add check on whether mf is nodal in build_nodal_dot_mask.

Src/F_BaseLib/multifab_f.f90

commit 825538d256944b942b864d89d3bac091668b062b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 13 15:42:37 2013 -0800

    added proximity order diagnostic.
    added simulation of hopper distributions for testing locally.
    pfc order looks correct.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 7af7e68ae4de13f3d7af8c05b6ee2d1fde6e26d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 13 11:19:41 2013 -0800

    sum_integrated_quantities does not need to be virtual

Tutorials/AMR_Advection_C/Source/ADR.H

commit 2301d2fe1c14e2d3d2542c667918cccdb3d88e8c
Author: Chris Malone <malone@ucolick.org>
Date:   Tue Nov 12 18:23:52 2013 -0800

    remove debug print statements

MAESTRO_xrb/fbuoyancy.f90

commit 777cbfaf5f66c756c05d7b547e52eee6bbc471b5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 12 16:18:17 2013 -0800

    We no longer use mgt%st

Src/LinearSolvers/F_MG/mg_tower.f90

commit 2d1ea50456d1699f34095c24feb1a0a761cd1c32
Author: Chris Malone <malone@ucolick.org>
Date:   Tue Nov 12 15:21:44 2013 -0800

    get this compiling again

MAESTRO_xrb/fbuoyancy.f90

commit 9809e560cd149f6a74446789c3bfcc9c66400172
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Nov 11 18:13:16 2013 -0800

    Redo solve_ function to look more like scalar solve, add access function to AmrData, uptick ccse lib version

Src/Extern/amrdata/AmrData.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp
Tools/CMake/BoxLib_Version.cmake

commit f7a4a80846c9b83845da8cd6de85ce8252ff379b
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 11 12:00:18 2013 -0800

    removed print.

Tests/IOBenchmark/IOTest.cpp

commit 706bfea493e83150f168dd1a8eea0de842008ae9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 11 11:53:16 2013 -0800

    removed DatasetClient.H and .cpp from a couple of makefiles because DatasetClient has been moved to ArrayView

Tools/C_util/Convergence/Make.package
Tools/C_util/Statistics/Make.package
Tools/C_util/ViewMF/Make.package

commit 0cc049ebad52c5f93fa0bc03b1264d89be48ca7c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 11 10:07:40 2013 -0800

    Fix to quiet PGI compiler.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit dbb2a1ddbbf09cfa705e6c642c1d7f1fb0fde9c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 5 16:45:35 2013 -0800

    update regression test files

Tools/RegressionTesting/BoxLib-tests.ini
Tools/RegressionTesting/Castro-tests.ini
Tools/RegressionTesting/LMC-tests.ini
Tools/RegressionTesting/Nyx-tests.ini
Tools/RegressionTesting/RNS-tests.ini
Tools/RegressionTesting/SMC-tests.ini
Tools/RegressionTesting/VARDEN-tests.ini

commit a803c9de2ac77526cd852e6f15b25e5115a929a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 5 16:23:50 2013 -0800

    removed middle data stuff; these were intended for SDC, but now SDC is done in a different way

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/SPECIALIZE_1D.F
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H

commit 19664675dd48a00cb0e0ac958c11f48fcff8a785
Merge: bd94fa89d 22f02da2f
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 4 12:09:31 2013 -0800

    Merge branch 'master' into commprof

commit 6b72b245761faf034ae249709594b61f2a48f89b
Author: Chris Malone <malone@ucolick.org>
Date:   Fri Nov 1 09:42:41 2013 -0700

    new routine to calculate the total mass on the grid for all species

MAESTRO_xrb/fspec_total_mass.f90

commit bd94fa89df0a6944a7b16f53733fa41a50fb1406
Merge: ba3a3524e 29128de49
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 31 11:23:55 2013 -0700

    Merge branch 'commprof' of gamera:/usr/local/gitroot/BoxLib into commprof

commit 22f02da2fe74a665fc7c29d11d3468af1a19be41
Merge: 78f8f87e7 71ecc2a85
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 29 16:30:21 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 78f8f87e78ed8056b7ed911edd6fe0301256de3a
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 29 16:30:00 2013 -0700

    fixed parallel bug for fabs and multifabs.

Src/Extern/amrdata/AmrData.cpp

commit f0e54bd4e413b2b0c4611f61ed0025b141df991f
Author: Chris Malone <malone@ucolick.org>
Date:   Mon Oct 28 17:02:11 2013 -0400

    actually add a usage statement

MAESTRO_xrb/frates.f90

commit 71ecc2a852651cb8ddea9d466f6e792cab2e0c0c
Merge: 029b6b67d 6643af2eb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 28 09:23:19 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6643af2eb356230f3f0ddcb7553486d4063d8580
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Oct 27 10:32:53 2013 -0700

    Examine NERSC_HOST as well as uname for the hostname.
    Currently edison doesn't appear in 'uname -a'.

Tools/C_mk/Make.defs

commit 029b6b67d3f7cb7ec30758bf3a5096ea63b2cbb6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 25 14:58:08 2013 -0700

    Added version of bCoefficients() that takes a FArrayBox and grid # instead
    of a MultiFab.  Also ZeroACoefficients(); it's equivalent to a call of
    aCoefficients() where the passed MultiFab was setVal()d to zero, without
    having to build the MultiFab.

Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_TensorMG/DivVis.H
Src/LinearSolvers/C_TensorMG/DivVis.cpp

commit ba3a3524ed066ac599442f8c9aab61fc95fe6be9
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 25 11:42:22 2013 -0700

    close file.

Src/C_BaseLib/VisMF.cpp

commit 956cc01b4db574823977fe8f99486bf44a0e5f1d
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 25 11:42:05 2013 -0700

    close file.

Src/C_BaseLib/DistributionMapping.cpp

commit 29128de49448912b20d8c91d25f8bc51322c2bad
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 24 15:28:35 2013 -0700

    hopper test.

Src/C_BaseLib/DistributionMapping.cpp

commit a2515efec704a241d39140980e7b2f1c2b4dd96a
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Oct 24 12:37:40 2013 -0700

    Add code to fill corner cells at phys corners...if0 it out, but leave it around for later use

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 07783e0be527d2d6a1ea7b28ed23b77a62652791
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 23 15:54:22 2013 -0700

    hopper test.

Src/C_BaseLib/DistributionMapping.cpp

commit fa09f5521c25e10557918b817ed669d806e88e80
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 23 15:14:29 2013 -0700

    procname.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 9bf88b2cc0d9a37cd0751e9fb2279dcf1396c3e8
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 23 14:51:30 2013 -0700

    no report for zero perfmon procs.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 5b0a555cd93cb3ac157205a2f42d7916adb4957b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 23 14:30:38 2013 -0700

    hopper fix.

Src/C_BaseLib/Profiler.cpp

commit e7b2f60f1a9e28dfdd512a90e64fa0afb3d1de95
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 23 14:19:58 2013 -0700

    more proximity mapping.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/Profiler.cpp

commit 18a24a56abfee0fc923610d04a0f9f3dd371864d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 21 09:58:46 2013 -0700

    No more DatasetClient.cpp in CMakeList...

Src/C_AMRLib/CMakeLists.txt

commit 370ea59a519cd4c2ca7bc78d5e82fff8f43b8fbe
Merge: abdf551b9 5c0b00718
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 18 15:16:25 2013 -0700

    Merge branch 'master' into commprof

commit 5c0b00718828a38aaf59190b76a3c298e403fc2f
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 18 15:12:47 2013 -0700

    added arrayview support.

Tools/C_mk/Make.defs

commit 8eb35d155df6e5e4bd72a4a27ad5d5bf9537d53f
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 18 15:10:50 2013 -0700

    added arrayview support.

Src/C_AMRLib/DatasetClient.H
Src/C_AMRLib/DatasetClient.cpp

commit abdf551b9b96a6c9e6f3e920c0fe0fcaefbec19f
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 15 14:22:50 2013 -0700

    more proximity mapping.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 49ff570e8fb97afc196985cc6e108ab56f0132e1
Merge: 75941244d 479a9faf4
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 11 15:12:08 2013 -0700

    Merge branch 'master' into commprof

commit 75941244da19951d74bb45f32522251ace3ba7b2
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 10 16:10:41 2013 -0700

    helper functions for proximity ranking.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 479a9faf4fda6c1d7ad6a0a490f6856a4044d1ca
Merge: 1b456f267 007af70f3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 9 13:28:05 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1b456f26795ec273a68f7c644dc5f914e66483f3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 9 11:02:23 2013 -0700

    Added version of contains_nan() and contains_inf() that take an IntVect
    that gets set to a relevant cell when the routines return true.

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp

commit 007af70f39e2d17b438c050e3039ce0cc28d77b3
Merge: 92fb28b7c 3aac624ec
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Oct 9 10:33:45 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 92fb28b7c81b844be0ca5b4b51238ede879dbd64
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Oct 9 10:33:34 2013 -0700

    AmrLevel: Add fineRatio.  StateData: Remove unused setMidData.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit 3aac624ec4259a70ee438130504630d5a4ecc82d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 8 21:48:18 2013 -0700

    Only print the warning (about not using linear interp if ref_ratio = 4
    instead of 2) once per solve rather than once per v-cycle.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 6ef670b353eefd989a99c2cf456c56637b61f7f5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 8 12:29:27 2013 -0700

    Remove the Tests/LinearSolvers/C_NodalMG directory since we
    no longer support the code that this tests.

Tests/LinearSolvers/C_NodalMG/files.2d
Tests/LinearSolvers/C_NodalMG/files.3d
Tests/LinearSolvers/C_NodalMG/gt_breaks_27pt
Tests/LinearSolvers/C_NodalMG/inputs
Tests/LinearSolvers/C_NodalMG/proj.cpp
Tests/LinearSolvers/C_NodalMG/test_grids/3d_4_level.grids
Tests/LinearSolvers/C_NodalMG/test_grids/gr.11
Tests/LinearSolvers/C_NodalMG/test_grids/gr.15
Tests/LinearSolvers/C_NodalMG/test_grids/gr.16
Tests/LinearSolvers/C_NodalMG/test_grids/gr.19
Tests/LinearSolvers/C_NodalMG/test_grids/gr.19l3
Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s2
Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s2.4
Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s4
Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s4.1
Tests/LinearSolvers/C_NodalMG/test_grids/gr.292.11
Tests/LinearSolvers/C_NodalMG/test_grids/gr.292.25
Tests/LinearSolvers/C_NodalMG/test_grids/gr.7
Tests/LinearSolvers/C_NodalMG/test_grids/gr.8
Tests/LinearSolvers/C_NodalMG/test_grids/gr.8a
Tests/LinearSolvers/C_NodalMG/test_grids/gr.ann.1
Tests/LinearSolvers/C_NodalMG/test_grids/gr.sstanley.1
Tests/LinearSolvers/C_NodalMG/test_grids/gr0
Tests/LinearSolvers/C_NodalMG/test_grids/gr0a
Tests/LinearSolvers/C_NodalMG/test_grids/gr0b
Tests/LinearSolvers/C_NodalMG/test_grids/gr1
Tests/LinearSolvers/C_NodalMG/test_grids/gr1mike.thin
Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick2
Tests/LinearSolvers/C_NodalMG/test_grids/gr2
Tests/LinearSolvers/C_NodalMG/test_grids/gr2.0
Tests/LinearSolvers/C_NodalMG/test_grids/gr2.1
Tests/LinearSolvers/C_NodalMG/test_grids/gr2.inf
Tests/LinearSolvers/C_NodalMG/test_grids/gr2a2
Tests/LinearSolvers/C_NodalMG/test_grids/gr2a4
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l0
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l1
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l2
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p1
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p2
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p3
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p4
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p5
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p6
Tests/LinearSolvers/C_NodalMG/test_grids/gr2b
Tests/LinearSolvers/C_NodalMG/test_grids/gr2c
Tests/LinearSolvers/C_NodalMG/test_grids/gr2cross
Tests/LinearSolvers/C_NodalMG/test_grids/gr2d
Tests/LinearSolvers/C_NodalMG/test_grids/gr2d2
Tests/LinearSolvers/C_NodalMG/test_grids/gr2d4
Tests/LinearSolvers/C_NodalMG/test_grids/gr2dave
Tests/LinearSolvers/C_NodalMG/test_grids/gr2e
Tests/LinearSolvers/C_NodalMG/test_grids/gr2f
Tests/LinearSolvers/C_NodalMG/test_grids/gr2g
Tests/LinearSolvers/C_NodalMG/test_grids/gr2h
Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike
Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike1
Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike2
Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike3
Tests/LinearSolvers/C_NodalMG/test_grids/gr2r1
Tests/LinearSolvers/C_NodalMG/test_grids/gr2r2
Tests/LinearSolvers/C_NodalMG/test_grids/gr2r3
Tests/LinearSolvers/C_NodalMG/test_grids/gr3.rz
Tests/LinearSolvers/C_NodalMG/test_grids/gr3a
Tests/LinearSolvers/C_NodalMG/test_grids/gr3ann
Tests/LinearSolvers/C_NodalMG/test_grids/gr3ann2
Tests/LinearSolvers/C_NodalMG/test_grids/gr3b
Tests/LinearSolvers/C_NodalMG/test_grids/gr3c
Tests/LinearSolvers/C_NodalMG/test_grids/gr3mike
Tests/LinearSolvers/C_NodalMG/test_grids/gr3mike.3
Tests/LinearSolvers/C_NodalMG/test_grids/gr3rick
Tests/LinearSolvers/C_NodalMG/test_grids/gr3rick2
Tests/LinearSolvers/C_NodalMG/test_grids/gr4
Tests/LinearSolvers/C_NodalMG/test_grids/gr4level
Tests/LinearSolvers/C_NodalMG/test_grids/gt.32
Tests/LinearSolvers/C_NodalMG/test_grids/gt.bill1
Tests/LinearSolvers/C_NodalMG/test_grids/gt.inputs.3d.spin.grids
Tests/LinearSolvers/C_NodalMG/test_grids/gt.jbb.1
Tests/LinearSolvers/C_NodalMG/test_grids/gt.sas
Tests/LinearSolvers/C_NodalMG/test_grids/gt.scott.1
Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_2.32
Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_2.64
Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_3
Tests/LinearSolvers/C_NodalMG/test_grids/gt0
Tests/LinearSolvers/C_NodalMG/test_grids/gt010
Tests/LinearSolvers/C_NodalMG/test_grids/gt012
Tests/LinearSolvers/C_NodalMG/test_grids/gt016
Tests/LinearSolvers/C_NodalMG/test_grids/gt05
Tests/LinearSolvers/C_NodalMG/test_grids/gt1
Tests/LinearSolvers/C_NodalMG/test_grids/gt12
Tests/LinearSolvers/C_NodalMG/test_grids/gt12.2
Tests/LinearSolvers/C_NodalMG/test_grids/gt12.3
Tests/LinearSolvers/C_NodalMG/test_grids/gt2
Tests/LinearSolvers/C_NodalMG/test_grids/gt2t1
Tests/LinearSolvers/C_NodalMG/test_grids/gt2t3
Tests/LinearSolvers/C_NodalMG/test_grids/gt2t4
Tests/LinearSolvers/C_NodalMG/test_grids/gt3
Tests/LinearSolvers/C_NodalMG/test_grids/gt3ann
Tests/LinearSolvers/C_NodalMG/test_grids/gt3ann2
Tests/LinearSolvers/C_NodalMG/test_grids/gt4
Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2
Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2.4.4
Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2a
Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4
Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4.2.4
Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4.4.2
Tests/LinearSolvers/C_NodalMG/test_grids/gt5
Tests/LinearSolvers/C_NodalMG/test_grids/gt5s2
Tests/LinearSolvers/C_NodalMG/test_grids/gt5s4
Tests/LinearSolvers/C_NodalMG/test_grids/gt6
Tests/LinearSolvers/C_NodalMG/test_grids/gt6s
Tests/LinearSolvers/C_NodalMG/test_grids/gt6s2
Tests/LinearSolvers/C_NodalMG/test_grids/gt6s4
Tests/LinearSolvers/C_NodalMG/test_grids/gt7a
Tests/LinearSolvers/C_NodalMG/test_grids/gt7aa
Tests/LinearSolvers/C_NodalMG/test_grids/gt8
Tests/LinearSolvers/C_NodalMG/test_grids/gt8a
Tests/LinearSolvers/C_NodalMG/test_grids/gt8b
Tests/LinearSolvers/C_NodalMG/test_grids/gt8c
Tests/LinearSolvers/C_NodalMG/test_grids/gt8ms2
Tests/LinearSolvers/C_NodalMG/test_grids/gtbig
Tests/LinearSolvers/C_NodalMG/test_grids/gtbig2
Tests/LinearSolvers/C_NodalMG/test_grids/gtbig3
Tests/LinearSolvers/C_NodalMG/test_grids/gtbig4
Tests/LinearSolvers/C_NodalMG/test_grids/gtbig5
Tests/LinearSolvers/C_NodalMG/test_grids/gtclearlarge
Tests/LinearSolvers/C_NodalMG/test_grids/gtclearsmall
Tests/LinearSolvers/C_NodalMG/test_grids/gtgrav2
Tests/LinearSolvers/C_NodalMG/test_grids/gtgrav4
Tests/LinearSolvers/C_NodalMG/test_grids/gtjbb
Tests/LinearSolvers/C_NodalMG/test_grids/gtjbb2
Tests/LinearSolvers/C_NodalMG/test_grids/gtpfail
Tests/LinearSolvers/C_NodalMG/test_grids/gtrick

commit aeef800a7bcd6838d589cf08566bca5f71b38678
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 8 12:28:47 2013 -0700

    Removing the Src/LinearSolvers/C_NodalMG directory since this
    code is no longer used by any of the applications.

Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/OpenSource.txt
Src/LinearSolvers/C_NodalMG/RegType.H
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real2d.2.f
Src/LinearSolvers/C_NodalMG/amr_real2d.f
Src/LinearSolvers/C_NodalMG/amr_real3d.2.f
Src/LinearSolvers/C_NodalMG/amr_real3d.f
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_avg2d.f
Src/LinearSolvers/C_NodalMG/hg_avg3d.f
Src/LinearSolvers/C_NodalMG/hg_cg.cpp
Src/LinearSolvers/C_NodalMG/hg_cg2d.f
Src/LinearSolvers/C_NodalMG/hg_cg3d.f
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.f
Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f
Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.f
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.f
Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f
Src/LinearSolvers/C_NodalMG/hg_proj2d.f
Src/LinearSolvers/C_NodalMG/hg_proj3d.f
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.H
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit d3cba7d875424223c059c4246fd4bbefb10c8dde
Merge: 014247c3a 724ae0ace
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Mon Oct 7 19:23:39 2013 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 014247c3a1646a3dcaef5a62e09754ec1e545e98
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Mon Oct 7 19:22:22 2013 -0400

    move the warning of dropping to piecewise constant prolongation
    if ir /= 2 up higher in the call stack so it is not output as
    much -- note: this does not affect MG.  No output differences should
    occur except for a lot fewer warnings.

Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit 724ae0ace551bb74aa2c3b43bffa602b33f60224
Merge: e29e7b769 c802343b5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 7 16:21:42 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e29e7b769423b64472d6a9b8d91f04e742a40045
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 7 16:20:47 2013 -0700

    Don't thread over calls to setPhysBoundaryValues().  It doesn't play
    well with the Inflow code.

Src/C_AMRLib/AmrLevel.cpp

commit c802343b5dcb9b122f39da1ce8ddc402dddcb4bb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 7 14:13:23 2013 -0700

    Put comments in the inputs.3d.nodal.dense and set ba_maxsize = 128
    so at first this will have only one grid.

Tests/LinearSolvers/F_MG/inputs.3d.nodal.dense

commit 5c3948c452e12571a4e58fe0276d397f37fbcfa2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 7 14:08:11 2013 -0700

    Create a new 3d nodal dense smoother -- subroutine nodal_smoother_3d_opt --
    that can be used to experiment with optimizations having to do with not
    storing the stencils.

Src/LinearSolvers/F_MG/mg_tower_smoother.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit 30e0a236d267f01256acc8d2a4649da403ad8727
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 7 13:28:06 2013 -0700

    Inputs for nodal dense stencil test.

Tests/LinearSolvers/F_MG/inputs.3d.nodal.dense

commit ac79074fa1fcd842cb13c3c6b474a1e196b7988d
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Oct 6 20:38:36 2013 -0400

    change the way the defaults are indicated -- now we do a logical and output "[*]" via
    a merge instead of printing the default value alongside the current value.  This is
    a lot easier to read.

Tools/F_scripts/write_probin.py

commit 447ba9f1ce3c1f9b7c8d928ccec8eff725eb2591
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 4 17:04:45 2013 -0700

    We can now restart from a plotfile if the appropriate data has been
    stored in the plotfile.  This works for both grid data and particles,
    but the application must be in charge of making sure it can find the
    data that it needs.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Particles.H

commit ac193cebce3c01e474daaae51fa415c9a5c52c8c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 3 14:53:18 2013 -0700

    Uses can now choose single -vs- double precision at compile time.
    The C preprocessor symbol BL_SINGLE_PRECISION_PARTICLES, when defined at
    compile time causes floating point particle data to be stored as floats
    instead of the default, which is doubles.

Src/C_AMRLib/Particles.H

commit 8ec807a24fcefcd78ea10500247936c59b909b20
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 3 14:27:59 2013 -0700

    I'm now appended "single" or "double" to the version string in checkpoint
    files for particles.  This allows me to know how they were written so that
    I can properly read them in.  It thus gives us the ability to decide at
    compile time whether to use single or double precision for storing
    floating point data in particles.  As of this commit all you have to do is
    edit Particles.H and change one typedef.  To come will be a way to do this
    when compiling.  The default floating-point precision as of this commit is
    back to double precision.

Src/C_AMRLib/Particles.H

commit b46a3dad7312bbf3ca64fbcde16c4cbb9dfe2711
Merge: cd670f134 c6972484f
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Wed Oct 2 20:41:06 2013 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit cd670f1345a386dcdc758a8142fdede3cb74614f
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Wed Oct 2 20:40:42 2013 -0400

    add default values in [] in the print routine

Tools/F_scripts/write_probin.py

commit c6972484f7a6ee228933276deeb08f99e20f94b4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 2 14:37:26 2013 -0700

    PeriodicShift() now returns bool indicating whether or not it shifted the
    particle.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 3cc2fe303c6dd031af290ed10f66b06c537c5030
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 2 14:07:31 2013 -0700

    When a particle is out of or on the boundary we now shift a fixed
    .125*CellSize() to try and get it back it.  Got some strange precision
    issues with mixed float and double arithmetic.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 74e4904f85045743297cd5c387b7b4ccaf012ea6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 2 12:52:44 2013 -0700

    Particles positions and data are now stored as floats instead of doubles.
    The code should be able to read old and new checkpoint files.
    Likewise it should be able to read binary double as well as binary float
    particle input files.

Src/C_AMRLib/Particles.H

commit 0cba9469c8d837babdbbd290f5230dbf99619399
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 2 12:51:16 2013 -0700

    Incremented version string for particles using float not double data.

Src/C_AMRLib/Particles.cpp

commit a5f6100fe7d0fb7ff56505d15c149e3956b1ea93
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 2 10:22:55 2013 -0700

    InitFromBinaryFile() can now automagically read either float or double data.

Src/C_AMRLib/Particles.H

commit c764f82846264e236c997a1ae02b79335430a54a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Oct 1 16:27:45 2013 -0700

    More work on double -> float conversion.

Src/C_AMRLib/Particles.H

commit f07d166aa9efc65247c5fd370e5c42b8bc3f44f6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Oct 1 16:18:27 2013 -0700

    Some work storing/using real data in particles as float instead of double.

Src/C_AMRLib/Particles.H

commit 32cc164b27b16be39d3bb3180c7f461fd17a6001
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 1 15:18:38 2013 -0700

    This change defines USE_PARTICLES instead of BL_USE_PARTICLES -- this
    is the flag that is seen in the rest of the code.

Tools/CMake/CCSEOptions.cmake

commit 59f6503c44f6d7441796fe0de6bac4e9c5be811c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 1 11:12:40 2013 -0700

    Add ParticleBoxArray option for AdvectWithUmac.

Src/C_AMRLib/Particles.H

commit 76fac8eff863dfd68a09dfe71ba10be71d5ad296
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 30 21:36:53 2013 -0700

    Must remember to make the particle DistributionMap on restart
    as well as on initialization -- put that section of code into a new
    routine,  make_particle_dmap,  which is called from init and from
    restart.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit d10713c754250d8f8ea7ad978b2a722cff0b228b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 30 16:54:56 2013 -0700

    Decided we don't need to worry about copy on ghost cells as long as
    we copy after the temporary mf has completed SumBoundary.

Src/C_AMRLib/Particles.H

commit c77d74c0bc7985d5a12387e81dfec9e6ae04a495
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 30 16:38:42 2013 -0700

    This version has the working multilevel AssignDensity which allows
    for particle_grids != grids.  Still not sure what to do about ghost
    cell copies though.

Src/C_AMRLib/Particles.H

commit 6df6e56c7329afd8062f4618aa7f584b4d96520c
Merge: 8e14b6cc2 586687569
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 30 12:44:53 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8e14b6cc2778b919427a96a3cb43b5393fcdccd7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 30 12:43:14 2013 -0700

    Inside addOneParticle, if a particle seems to be on the domain boundary
    we move it slightly inside.

Src/C_AMRLib/Particles.H

commit 586687569325d599cb008a3c1f1e1c2be2108878
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Mon Sep 30 09:57:36 2013 -0700

    Remove MLSDC from BoxLib (moved to RNS).

Src/C_AMRLib/MLSDCAmr.H
Src/C_AMRLib/MLSDCAmr.cpp
Src/C_AMRLib/MLSDCAmrEncap.cpp
Src/C_AMRLib/Make.package

commit b4fbbd08f50f50639644d3bc1016f15e2dd24ae6
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Mon Sep 30 09:54:45 2013 -0700

    Add setMidData.

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit 16e90f7768365682a2a1f13c2f152960a540ef0a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 30 08:59:27 2013 -0700

    Back out latest changes to get this to work again.

Src/C_AMRLib/Particles.H

commit 5bf99a3dbd122e58c8f5f0bfee1416a11fc81f74
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 30 08:50:39 2013 -0700

    Allow the particles to live on a different boxarray than the grid
    data lives -- this is particle_grids as opposed to grids.  The default
    for now is that the boxarrays are identical.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 17114cc2c1b0337803256bad8baaa8b45e9f5ad4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 27 13:22:47 2013 -0700

    optimization of the 5th-order interpolator

Src/C_AMRLib/INTERP_1D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F

commit 5bb660c3d5f6e52a687448f0ac50a8bdc0c1a278
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 27 11:07:09 2013 -0700

    5th-order interpolation in 3D

Src/C_AMRLib/INTERP_3D.F

commit 15c00d42c832de9d40374cecfd43223eb4a9dfb8
Merge: 539a89ce9 244bc86a0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 27 08:23:27 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 539a89ce96227093d98368d976090ce144baf25a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 27 08:22:29 2013 -0700

    Modify the test at the end of moveKickDrift so that particles at level 0
    flying along at cfl > 1 can leave a grid and not have their velocities
    and positions correctly updated, but still not get lost entirely.

Src/C_AMRLib/Particles.H

commit 244bc86a03625969fde27730872b1ba1908b92a2
Merge: 6661744a4 393583d8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 26 22:17:42 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6661744a4fbd6d55eb653678c3c24ba8dd024acd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 26 22:12:29 2013 -0700

    added 5th-order interpolation based on quartic polynomial dimension by dimension;  so far 1D and 2D are implemented;

Src/C_AMRLib/INTERP_1D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp

commit 393583d8f549e9f130527e03fb30688e4b8e4341
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 26 15:54:03 2013 -0700

    Little more tweaking of output in InitFromBinaryMetaFile()

Src/C_AMRLib/Particles.H

commit 7ae21fa76ceb71fd726cc0651f1b94bd2a7f1f1c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 26 15:41:53 2013 -0700

    Added some verbosity.

Src/C_AMRLib/Particles.H

commit f2f8b536a3fde6079f9df8e06cb613e84e949174
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 26 15:38:42 2013 -0700

    Added InitFromBinaryMetaFile().

Src/C_AMRLib/Particles.H

commit 18b17f750aa4ea68c5f933bcd75f9169b4341878
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 26 12:52:02 2013 -0700

    Restore DistributionMapping.{H,cpp} to be the same as before the
    previous commit -- we don't need that extra define after all.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit ec4f9d656b5dce42fc7aa8f03bb0bb9a80b09520
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 26 11:16:14 2013 -0700

    proximity mapping tests.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.cpp
Tools/C_mk/Make.Linux

commit 3d887e647f456471b287436ecbadc497a72656f0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 26 10:07:47 2013 -0700

    Remove left-over print statement when particles left the domain
    before being periodically shifted back in.

Src/C_AMRLib/Particles.cpp

commit 163228ee5fe388df0556af3db58229dbf18bced2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 26 09:17:24 2013 -0700

    Add a new version of DistributionMapping::define which takes an
    already-made pmap as an argument.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit f80372f3a0a23f5e8dacadc542190e66b8810f65
Merge: 6804de4fc 21410eb94
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 24 12:44:58 2013 -0700

    Merge branch 'master' into commprof

commit 21410eb944523da5067a73183a3b253ccc88db87
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue Sep 24 10:07:54 2013 -0400

    update Maestro tests

Tools/RegressionTesting/Maestro-tests.ini

commit ffecfd932b198cac595bf154d07e920f60279722
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Fri Sep 20 13:50:00 2013 -0400

    fix globalAddToExecString

Tools/RegressionTesting/testnew.py

commit d0785d1d4d10ff7b2287d2011c70e35d72aa3b48
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 20 09:29:40 2013 -0700

    Remove GETPLANE.

Src/F_BaseLib/fabio_c.c

commit b530dfae3a7c8602d86df14f02b0f62718d77b04
Merge: 12bea5320 9046677e1
Author: jbb <jbbell@lbl.gov>
Date:   Thu Sep 19 20:06:27 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 12bea5320767975c64846187f57975eb71bf1272
Author: jbb <jbbell@lbl.gov>
Date:   Thu Sep 19 20:05:46 2013 -0700

    fixed bug in check of uniform mesh

Src/LinearSolvers/F_MG/mg.f90

commit 9046677e16948a78535e83168700cf2b3f07d09f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 19 17:12:46 2013 -0700

    made the regression testing script write out correct html page in the
    case variables names contain special characters "<" and ">".

Tools/RegressionTesting/testnew.py

commit 1c7ebd8804f1f3912b3a1fcd588845f542ad034f
Merge: 79deeb35a b4d9c0c53
Author: jbb <jbbell@lbl.gov>
Date:   Thu Sep 19 10:47:34 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b4d9c0c53d961a9184a6b43257c57a5b45211dfd
Merge: f7d3e1cef 4854c02d4
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 18 17:30:09 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit f7d3e1cef8bac451914be36494219570cb4b5fd2
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 18 17:30:00 2013 -0700

    Fix up declaration/define strings with D_DECLs, fix CMakeLists.txt to properly remove Particle stuff is BL_USE_PARTICLES is set to 0

Src/C_AMRLib/CMakeLists.txt
Src/C_AMRLib/Particles.H

commit 4854c02d467951365a7d2bf3599c8c6577242db4
Merge: e29c9eaec 000e0fac9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 18 15:58:36 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e29c9eaec00b556bfb93231639cb1b448ab9c711
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 18 15:57:35 2013 -0700

    Fixed up the case when the domain is not periodic and particles live
    in the cell next to the domain boundary.  Before this wasn't allowed; now
    if we set the flag "allow_particles_near_boundary" to true then the
    particles can live in those cells, but the part of their contribution
    to AssignDensity that falls outside the domain will be ignored.

Src/C_AMRLib/Particles.H

commit 000e0fac95241cceb7e6b7da0dc0294491beb907
Merge: 99926f67c 6069e79b9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 18 15:20:30 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 99926f67cca9001c9bfcde4f279cb8c0ec504dc4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 18 15:18:10 2013 -0700

    Some work on FORT_GETPLANE().  This is needed to implement INFLOW
    on the F90 side of the house.  It's a translation of
    IAMR/Source/INFLOW/inflow.cpp.  It's not done yet as there's an issue
    with "long" int values.  We don't currently use such things, but the
    offsets into turbulence files in 3D get bigger than can be held in a
    standard Fortran integer.

Src/F_BaseLib/fabio_c.c

commit 6069e79b9a3ef1a7e0abe46a8a27d8553a55fc58
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 18 12:49:45 2013 -0700

    up the tagged version num

Tools/CMake/BoxLib_Version.cmake

commit 99faad02f872880bf99928502433f2b37097aca8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 18 12:46:52 2013 -0700

    Changed mpi module name to fboxlib_mpi so not to conflict with
    system-supplied names.

Src/F_BaseLib/parallel.f90
Src/F_BaseLib/pingpong.f90

commit 42ba19b714c7d9684ae2e782a686c0abf9ba390a
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Sep 16 16:58:13 2013 -0700

    Redo CMake stuff to more properly use command-line options to the cmake command for setting/overriding defaults

CMakeLists.txt
Tools/CMake/CCSEOptions.cmake
Tutorials/MultiGrid_C/CMakeLists.txt

commit 971e67c3192f6249a7b10b7295021f56fffc4b60
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 16 09:29:39 2013 -0700

    Made AmrLevel::addOneParticle not pure so that classes derived from
    AmrLevel can be instantiated without implementing addOneParticle.

Src/C_AMRLib/AmrLevel.H

commit 59ca02bdafc0f2314d8c9d87ae66d1e624cd5815
Merge: df4e3075c fa60838f8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 13 11:43:29 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit df4e3075c0e7545ab037a9bf9ca816be861fc3f8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 13 11:42:43 2013 -0700

    Modify Amr and Particle classes to allow Amr to be defined from an
    outside class and not to read from inputs file.  Also allow particles
    to be copied in one by one.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit fa60838f809f20f7015c6835eae3b1e1863ce49a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 13 10:04:14 2013 -0700

    Added constructors to FabArray and MultiFab that take a DistributionMap.
    This way folks don't have to do the usual two-step process of
    creating a MultiFab and then calling define() if they want to specify
    their own DistributionMap.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 3ed20f94aa677b8de47e3432d1ef0a69bd41b72d
Merge: 912dc6043 7f63035e2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 12 16:00:13 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 912dc60434e76884b0a879dd91b47c428911cdf8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 12 15:59:54 2013 -0700

    Make the minimum physical box size 1.e-8 instead of 1.e-6.

Src/C_BaseLib/RealBox.cpp

commit 6804de4fcf02664e7cde12ed3452b064292582e5
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 12 15:44:17 2013 -0700

    procnums and names.

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 7f63035e210582dc5ad6ebc086a27ac4087e331c
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 12 12:29:08 2013 -0700

    Add usage comment, remove debugging note

CMakeLists.txt
Tools/CMake/InstallManager.cmake
Tutorials/MultiGrid_C/CMakeLists.txt

commit 685922dc94d363e966060ada160d501112d1eb02
Merge: 53099d016 9d40f4f61
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 12 12:16:53 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 53099d0169e9065af09e99a7f030dba02405e6c8
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 12 12:16:43 2013 -0700

    never-ending mods to cmake files...

CMakeLists.txt
Src/CMakeLists.txt
Src/F_BaseLib/CMakeLists.txt
Src/LinearSolvers/F_MG/CMakeLists.txt
Tools/CMake/CCSEOptions.cmake
Tools/CMake/FindCCSE.cmake
Tools/CMake/InstallManager.cmake
Tutorials/MultiGrid_C/CMakeLists.txt

commit 9d40f4f6127abaa3639172b6b1fc008283995497
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 12 11:32:47 2013 -0700

    Allow us to initialize an AMR object with RealBox and coord already
    set so we don't have to parmparse those in Geometry.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 3e0fedeabce3e0657a4b97732ab752e8643cd3f1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 12 10:02:25 2013 -0700

    Add domain vs lev0_grids check in defBaseLevel.

Src/C_AMRLib/Amr.cpp

commit 722ca85420f7ab5057ff7cdeb7bf024d4705ccaf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 12 08:38:33 2013 -0700

    Consolidated the two versions of initialInit() and defBaseLevel() into
    single routines.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 92c8956cc619d1602a867f027fcea8cb2d7b9f67
Merge: 094ba4536 3b9d54b21
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 11 17:19:32 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 094ba4536c44dd775b3d6f44d729f7094cb0d049
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 11 17:18:45 2013 -0700

    Add versions of init, initialInit and defBaseLevel that take both
    a BoxArray and a pmap.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 3b9d54b21fb3be0d2a8caa92e260829d03ee8c74
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 11 16:48:49 2013 -0700

    Update version file

Tools/CMake/BoxLib_Version.cmake

commit d084ab5733b7761d4b91aa57280d7679a0735f18
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 11 16:42:55 2013 -0700

    ick...more hacking on cmake

CMakeLists.txt
Tools/CMake/BoxLib_Version.cmake
Tools/CMake/InstallManager.cmake

commit cd6569d33774b6c31544ceb804938746b7e95242
Merge: b05593c08 7de30444d
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 11 15:52:21 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit b05593c08b7f9c81d311c8da9a6b97805010a5fb
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 11 15:52:13 2013 -0700

    Final twiddling of CMake files for now (I hope)

CMakeLists.txt
Tools/CMake/BoxLib_Version.cmake
Tools/CMake/CCSEOptions.cmake
Tools/CMake/InstallManager.cmake
Tools/C_scripts/gen_release_tarball

commit 7de30444dcf652e1ae199c867abb5ec9c97b0127
Merge: 11437bdc4 779f0784d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 11 15:18:35 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 11437bdc4b9c7a866c1a9c42ecb22a56d2c948ad
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 11 15:17:23 2013 -0700

    Added ability to pre-load the distribution mapping cache by simply
    building a DistributionMapping with a pmap and asking for it to
    be added to the cache.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 779f0784df4ea975a5000acd1ab831a8414305e0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 11 14:16:02 2013 -0700

    Make the first lines of DM/Header in a plotfile be the same as the first
    lines of DM/Header in a checkpoint file.

Src/C_AMRLib/Particles.H

commit de5e5f03aa14fe55768a7eb46bd2a500d6b18c99
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 11 13:07:29 2013 -0700

    Clean up Solver.cpp and add contact info for Tulin.

Tutorials/AMR_Trilinos_C/README
Tutorials/AMR_Trilinos_C/Solver.cpp

commit 78e363325dfa75a7c9dbca1b5a1944845df98da1
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 11 10:31:46 2013 -0700

    More tweaks to CMake files

Src/F_BaseLib/CMakeLists.txt
Src/LinearSolvers/F_MG/CMakeLists.txt
Tools/CMake/CCSEOptions.cmake

commit 0acb7e688d872c0a14e5aae92539156ddadccea6
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 11 10:16:38 2013 -0700

    Add a couple tests to the CCSEOptions to be sure stuff is defined

Tools/CMake/CCSEOptions.cmake

commit eda0e9008ede8320960cbcc89435c0121c355938
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 11 09:45:30 2013 -0700

    Small mods working with Andreas

Src/C_AMRLib/Particles.H
Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/FabSet.H

commit b68eaef35be3fd26f28ce8ff1f2d0bd11578b3e5
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 11 01:18:03 2013 -0700

    CMake install the mod files

Src/CMakeLists.txt

commit 7ad9bdc6d0e47daf332682d5024ab8f0d2d82e54
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 11 00:41:49 2013 -0700

    Start to collect BL_DEFINEs throughout, and set some defaults

CMakeLists.txt
Tools/CMake/CCSEOptions.cmake

commit b2d4666d54ea6b8e18ed5e49cd36173ee3142d24
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Sep 10 23:56:02 2013 -0700

    Add buildInfo.H to install

CMakeLists.txt

commit 169b7d29eeff62e30a5d7529bf58040562199673
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Sep 10 18:47:50 2013 -0700

    Add Particles.cpp and Particles.H to CMakeLists

Src/C_AMRLib/CMakeLists.txt

commit 17e469a78c3b5891ab08e565b330485137ca98f6
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Sep 10 18:12:24 2013 -0700

    Consolidate all the CMake-built C++ libs into one using the OBJECT library feature post 2.8.8

CMakeLists.txt
Src/CMakeLists.txt
Src/C_AMRLib/CMakeLists.txt
Src/C_BaseLib/CMakeLists.txt
Src/C_BoundaryLib/CMakeLists.txt
Src/LinearSolvers/C_CellMG/CMakeLists.txt
Src/LinearSolvers/C_TensorMG/CMakeLists.txt
Src/LinearSolvers/C_to_F_MG/CMakeLists.txt
Src/LinearSolvers/F_MG/CMakeLists.txt

commit c2acf0b9f51d940b35901163babfaa4330a9aadb
Merge: e4c6ecb43 2aefba4c0
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Sep 10 15:31:01 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2aefba4c0b120e98b7d08000eb03c3b474b7dec9
Merge: b6bbaecf4 8c0c8dcf0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 10 14:57:12 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit b6bbaecf4fd6d3209d76a53aa4ce1c4dd721c57b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 10 14:56:26 2013 -0700

    Some cleanup using latest gnu compiler on edison.

Src/F_BaseLib/boxarray_f.f90
Src/F_BaseLib/cluster_f.f90

commit e4c6ecb43aaededd1b7afbeb679181de36668aba
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Sep 10 14:26:45 2013 -0700

    Working cmake a bit...in progress

CMakeLists.txt
Src/CMakeLists.txt
Src/LinearSolvers/C_TensorMG/CMakeLists.txt
Tools/CMake/CCSEOptions.cmake

commit 8c0c8dcf062b7d15baa8c34b59ee81b0233d391b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 10 13:23:33 2013 -0700

    Add comment about RHS and SOLN and visualizing these.

Tutorials/AMR_Trilinos_C/README

commit bd8c6d2d0dbc9c36db55caa808d2dd9f71c7082c
Merge: ddaf6d709 9c35e04c8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 10 13:21:11 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ddaf6d70991b2faeba3be20737eaf448f1fb8cf2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 10 13:20:48 2013 -0700

    Tutorial example of how to call a Trilinos solver (Epetra) from a
    BoxLib C++ code.

Tutorials/AMR_Trilinos_C/GNUmakefile
Tutorials/AMR_Trilinos_C/Make.package
Tutorials/AMR_Trilinos_C/README
Tutorials/AMR_Trilinos_C/Solver.H
Tutorials/AMR_Trilinos_C/Solver.cpp
Tutorials/AMR_Trilinos_C/SolverBoundary.cpp
Tutorials/AMR_Trilinos_C/driver.cpp
Tutorials/AMR_Trilinos_C/inputs
Tutorials/AMR_Trilinos_C/writePlotFile.H
Tutorials/AMR_Trilinos_C/writePlotFile.cpp

commit 9c35e04c849400cf08c77f9729511087988cc260
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 10 12:23:01 2013 -0700

    merged 2 MPI_Bcast into 1

Src/C_AMRLib/Amr.cpp

commit 0acfc7802d48f8c23b7740bfa9f353579f09e8fc
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Sep 6 20:12:37 2013 -0700

    Small changes...one for portability to CGSolver.cpp (works on the machines
    I tested...let me know if it fails on yours), and few virtuals added to
    MCLinOp.H to ease extensions to other cases, and a slight redef of a
    CMake oddity...anyone love CMake as much as I do?

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Tools/CMake/PreprocessBoxLibFortran.cmake

commit f0d0efd1d4febb92f08a718701791fb0733b6a42
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Sep 6 19:04:55 2013 -0700

    Revert "Small changes...one for portability to CGSolver.cpp (works on the machines I tested...let me know if it fails on yours), and few virtuals added to MCLinOp.H to ease extensions to other cases, and a slight redef of a CMake oddity...anyone love CMake as much as I do?"
    
    This reverts commit fd5ca5be470f61cc3ee8696734886ee72d4423aa.

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Tools/CMake/PreprocessBoxLibFortran.cmake

commit fd5ca5be470f61cc3ee8696734886ee72d4423aa
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Sep 6 18:12:08 2013 -0700

    Small changes...one for portability to CGSolver.cpp (works on the machines I tested...let me know if it fails on yours), and few virtuals added to MCLinOp.H to ease extensions to other cases, and a slight redef of a CMake oddity...anyone love CMake as much as I do?

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Tools/CMake/PreprocessBoxLibFortran.cmake

commit 7346d93bbd394e91b68845e7993a28286b853e14
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Fri Sep 6 13:01:41 2013 -0400

    find the / detection

fextract.f90

commit 145ac8ffa1451e426c7028a99d557450e843e8dc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 4 15:15:02 2013 -0700

    Reduced the amount of data transferred via MPI in the Reflux() routines to
    the bare minimum.  Previously Cy noticed that we "ship" more data than
    needed.  We were sending a full FluxRegister boundary data set whenever
    some coarse FAB needed any of its data. This was due to the difficulty of
    figuring out intersections of cell-centered entities with face-centered
    ones.  I've checked it with HyperCLaw and LMC.  We'll see if
    the regression tests turn up anything.

Src/C_AMRLib/FluxRegister.cpp

commit b13670cdebeba00d2e166bad651493936e17fbba
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 3 14:04:07 2013 -0700

    added interface callable from f90.

Src/C_BaseLib/BLProfiler_F.f
Src/C_BaseLib/Make.package
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 3919d17f0f5a327d154082492651aab65daecf39
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 30 12:26:30 2013 -0700

    Add interface to estTimeStep in Particles.H that doesn't take "a"

Src/C_AMRLib/Particles.H

commit 6baa30aae5f62f6a2f2965ee2f83013d65d92da1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 30 08:23:29 2013 -0700

    Minor bug fix.  Wasn't properly indicating "good" failure of CABiCGStab
    back to the MG solver when we want to do additional smooths.  I noticed
    this when a case I was running was doing additional bottom smooths in
    the BiCG case but was not in the CABiCG case.  Curiously, in that case,
    both the CiCG and the CABiCG MG solves converged in the same number of
    iterations. The additional smooths done when the BiCG didn't solve the
    bottom problem to the requested precision, didn't do much of anything,
    except waste time.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 611715b869b3d890a752a5702ab726b3e9ecf1c2
Merge: 87d070e0c 90d485a37
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Aug 29 00:45:08 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 87d070e0c297486d5cb2abf91bbb9297e6688b47
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Aug 28 20:02:16 2013 -0700

    more minor mucking with cmake

Src/LinearSolvers/C_TensorMG/CMakeLists.txt

commit ddda8fdfb6a431ebd0ec658b4f91b05de52d8ed7
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Aug 28 19:45:37 2013 -0700

    minor mucking with cmake

Src/CMakeLists.txt
Src/LinearSolvers/C_TensorMG/CMakeLists.txt

commit 90d485a37b4cfa428453507d52ed65871bdb098d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 28 13:31:33 2013 -0700

    Now use trilinear interp instead of piecewise constant.

Src/LinearSolvers/C_CellMG/MG_3D.F

commit 6967154f5b363a672fd4ded4750aa4cabb076c23
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 28 11:58:52 2013 -0700

    Now use bilinear interp instead of piecewise constant.

Src/LinearSolvers/C_CellMG/MG_2D.F

commit 4c31c5ad8916bcc9498ddad172966f0ee3678532
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Aug 26 20:58:48 2013 -0700

    Moved function into MCLO_3D.F

Src/LinearSolvers/C_TensorMG/DV_3D4.F

commit b47cf54cbae2190c6969877393f8434c20a5d5ef
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Aug 26 20:42:55 2013 -0700

    Small changes to tensor solver code to enable generalization to similar, but different, systems

Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLO_2D.F
Src/LinearSolvers/C_TensorMG/MCLO_3D.F
Src/LinearSolvers/C_TensorMG/MCLO_F.H
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp
Src/LinearSolvers/C_TensorMG/Make.package

commit f1e40111713d5416c35bfcd960893fe463ae7f1f
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 26 16:17:27 2013 -0700

    additions so compiles work with mpi/prof/commprof on/off.

Src/C_BaseLib/Profiler.cpp
Src/C_BaseLib/ccse-mpi.H

commit d034bc900a705d9da38c81b5d83ec209dda59813
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sat Aug 24 14:21:21 2013 -0400

    if a job_info file exists, store its contents (commented out) at the
    end of the slice file -- this gives us context

fextract.f90

commit fe330e16b9ccb5bd6e9e415a0f05db8e7b21df1e
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sat Aug 24 13:56:44 2013 -0400

    depreciate the "-p" option and allow a plotfile to be specified at the
    end of the commandline -- this is more in line with the other routines

fextract.f90

commit ad2dd6ad271f27e15f9459bdc789bf19414fe582
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 23 12:34:57 2013 -0700

    added amr init information.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 37d1de0f9268f7fa9ddfba5e49e6b3237638ea7c
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 22 16:00:00 2013 -0700

    version support, global header file, procnames.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 98eae4aa343800220f6c7708a67e649c4ca0023f
Merge: 01ff1a202 91b2704e2
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 22 12:41:25 2013 -0700

    Merge branch 'master' into commprof

commit 91b2704e2b6a4bedc8dfc7b56505d586157c0846
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Aug 20 14:59:28 2013 -0700

    Make regrid virtual, add InitAmr routine to avoid repetition.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 01ff1a20231d06db693f7e4bbccdb1d7cb1475c8
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 16 15:51:16 2013 -0700

    more in-situ, on/off, noprof, prof, commprof.

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit bdae32d5a003f7070916a93d8e30aa91b20af331
Author: Jonathan Wang <jmwang214@atragon.lbl.gov>
Date:   Fri Aug 16 10:38:43 2013 -0700

    Changed REaDME

Tutorials/MultiGrid_F/README

commit d46257269787ebdf253b8658d2acbefe38cb7d4a
Author: Jonathan Wang <jmwang214@atragon.lbl.gov>
Date:   Fri Aug 16 10:37:50 2013 -0700

    Added 3d inputs files

Tutorials/MultiGrid_F/inputs_fmg_lin_3d
Tutorials/MultiGrid_F/inputs_fmg_pc_3d
Tutorials/MultiGrid_F/inputs_v_lin_3d
Tutorials/MultiGrid_F/inputs_v_pc_3d

commit da1e5c2817ae9881f5fdd78e9f34b9ef0504256c
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 15 14:55:11 2013 -0700

    more in-situ support.

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp
Src/C_BaseLib/ccse-mpi.H

commit f4e7deb456ea7ac259827c41b34a858b91288303
Merge: d7bbc61dc 31f91ddac
Author: Jonathan Wang <jmwang214@atragon.lbl.gov>
Date:   Thu Aug 15 13:16:58 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d7bbc61dc199d75719ed335a82b5ba96db935005
Author: Jonathan Wang <jmwang214@atragon.lbl.gov>
Date:   Thu Aug 15 13:16:05 2013 -0700

    Remove executables; added parallel_IOProcessor to fmg_cycle.f90

Tutorials/MultiGrid_F/fmg_cycle.f90
Tutorials/MultiGrid_F/main.Linux.gfortran.exe.REMOVED.git-id
Tutorials/MultiGrid_F/main.Linux.gfortran.mpi.exe.REMOVED.git-id

commit 31f91ddac88ec3df444c72faf71f94ebc6053c0e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 15 11:13:34 2013 -0700

    Only print memory stats if we set memory_verbose = .true.

Tutorials/MultiGrid_F/main.f90

commit 378dbf43194a6a70b27cb3aa8dd80730f6928b04
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 15 11:08:41 2013 -0700

    1) Don't want to have executables in the repo.
    2) Don't need GPackage.mak since the files are listed in the GNUmakefile.

Tutorials/MultiGrid_F/GNUmakefile
Tutorials/MultiGrid_F/GPackage.mak
Tutorials/MultiGrid_F/main.Linux.gfortran.exe.REMOVED.git-id
Tutorials/MultiGrid_F/main.Linux.gfortran.mpi.exe.REMOVED.git-id

commit aae84d6b788db5ea4ceb3f79010f13b1d8644f6a
Merge: 5f7660940 71a9d0321
Author: Jonathan Wang <jmwang214@atragon.lbl.gov>
Date:   Thu Aug 15 11:03:39 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5f76609409d47849671f34744e8426caf41b12b3
Author: Ann Almgren <jmwang214@atragon.lbl.gov>
Date:   Thu Aug 15 11:01:32 2013 -0700

    New Tutorial for fortran 90, multigrid, Jonathan

Tutorials/MultiGrid_F/GNUmakefile
Tutorials/MultiGrid_F/GPackage.mak
Tutorials/MultiGrid_F/README
Tutorials/MultiGrid_F/constants.f90
Tutorials/MultiGrid_F/cycle_tower.f90
Tutorials/MultiGrid_F/fmg_cycle.f90
Tutorials/MultiGrid_F/init_coeffs.f90
Tutorials/MultiGrid_F/init_rhs.f90
Tutorials/MultiGrid_F/inputs_fmg_lin_2d
Tutorials/MultiGrid_F/inputs_fmg_pc_2d
Tutorials/MultiGrid_F/inputs_v_lin_2d
Tutorials/MultiGrid_F/inputs_v_pc_2d
Tutorials/MultiGrid_F/main.Linux.gfortran.exe.REMOVED.git-id
Tutorials/MultiGrid_F/main.Linux.gfortran.mpi.exe.REMOVED.git-id
Tutorials/MultiGrid_F/main.f90
Tutorials/MultiGrid_F/mt19937ar.f90
Tutorials/MultiGrid_F/solve.f90
Tutorials/MultiGrid_F/traverse.f90
Tutorials/MultiGrid_F/v_cycle.f90

commit 71a9d0321e1d9a8c86c006980f9645e22a25abae
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 14 09:52:40 2013 -0700

    and an mpilib....

Tools/F_mk/GMakeMPI.mak

commit ba17a1e94e9ebc72eb05a31316d44df30e52e131
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 14 09:48:54 2013 -0700

    and for fortran.

Tools/F_mk/GMakeMPI.mak

commit 4bc1ce87f6120ff57bb1424314a25ae726f56998
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 14 09:45:00 2013 -0700

    fix for gigan.

Tools/C_mk/Make.mpi

commit e9098e07a1cc2be447849e10cfb581f2c6721910
Merge: 68a80a8e3 395bf788c
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 8 15:06:42 2013 -0700

    Merge branch 'master' into commprof

commit 68a80a8e31674984c35fb713415c07741adbf805
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 8 12:48:40 2013 -0700

    working version of in-situ mpi process for dynamic optimization.
    the process doesn't do much yet, just rides along.
    not yet tested with the finalize function stack not empty.

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 395bf788cab9e5da6d3c9e9b42a8e7677c9c2a85
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 7 10:41:02 2013 -0700

    Removed the qaxpy() stuff.  It didn't appear to work properly.
    Not a big deal anyway.  The dots() and sums() are the important stuff.
    Now to see if it makes any difference on real problems in parallel.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit fa135ceeb24e5fbe2f1bf16bb318132e84857119
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 6 14:33:05 2013 -0700

    In qsotxy() do the parallel reduction in quad precision by sending all the
    partial sums to the IO processor and having it do the sum in quad
    precision and then broadcast it back to the other processors.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 49350f1697459d2135f38d901d8cac8106d59fcb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 6 13:57:33 2013 -0700

    Some code rearrangement to get XBLAS & non-XBLAS code to coexist.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit a11ce8acec5e90e08b3c72d82e61a783e632b964
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 6 13:42:48 2013 -0700

    Added qdotxy().

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 3ff7b93a56b893fb428406d264048605d893e691
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 6 12:31:13 2013 -0700

    Some work on adding a version of CABiCGStab that uses the quad
    precision routines from XBLAS.  It's disabled at the moment so it
    shouldn't affect anyone.  My plan is to see if a more accurate bottom
    solver can solve some problems with fewer iterations.  It may also be the
    case that with a more accurate bottom solver we can up the max "S" in the
    CABiCGStab from 4 -> 8 or somesuch.

Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit ad85ec68b8a8b3f490024195883d0c6972d9ac9a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 5 15:02:10 2013 -0700

    Some code rearrangement to make some multi-level testing I'm doing easier.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 9e76c8827fe196b542db290247c9377fc0d97d47
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 5 14:59:49 2013 -0700

    Checked in some code that builds cfine in the cfine -> fine multilevel
    prolongation routines with one grow cell so that the interpolation
    doesn't have to do piecewise-constant interp on the grid boundaries.
    It's disable for now until I do more testing.  Also added similar
    code for the nodal multi-level prolongate.

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit c30ce2fefc2bbd6e1dedde50c07b2f7d590de2b3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 5 12:46:50 2013 -0700

    Make lininerp the default for cell-centered interpolators.

Src/LinearSolvers/F_MG/mg_tower.f90

commit d1b147f53a23ac80cf004d1889046c23e0857f0e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 5 11:41:15 2013 -0700

    Just a little code rearrangement.

Src/LinearSolvers/F_MG/mg.f90

commit 9a666662bcc41fc199a626133867001f653c6f42
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 5 11:22:06 2013 -0700

    Changed how I impose BCs for #D CC interpolators.

Src/LinearSolvers/F_MG/mg.f90

commit 90f9944b6079be910633a3b89adbbe50813444fd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 5 09:50:38 2013 -0700

    Changed how I impose 2D BCs for CC interpolators.

Src/LinearSolvers/F_MG/mg.f90

commit 2f1f68c99cffad6fa17f0dca88e293f4e69c2b1c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 1 15:22:05 2013 -0700

    Some code rearrangement.
    Put the lininterp pys BC stuff into their own routines.

Src/LinearSolvers/F_MG/mg.f90

commit 02c6c3c214c23559a5c2a9832cf57f05cd080f2c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 1 14:08:32 2013 -0700

    Some work on edges & corners for 3D lininterp.

Src/LinearSolvers/F_MG/mg.f90

commit 48ad430e1ecdec46744f56de51893ecbf278e49e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 1 10:26:51 2013 -0700

    Work on getting corners right for 2D interp.
    Still got to do corners & edges for 3D.
    I'm checking this stuff in with the lininterp defaulting to FALSE.
    I want to get it pushed to the repo before I get too ahead of myself.
    Soon we'll want to default to lininterp but I'm not yet ready.

Src/LinearSolvers/F_MG/mg.f90

commit 5b4e5d6c3a62cb4a91ca28d169005e5363f14198
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 1 09:20:42 2013 -0700

    Can now set linear or piecewise constant on command line or inputs file.

Tests/LinearSolvers/F_MG/wrapper.f90

commit 3578598173ee359f1dd60fd434dca0efb7e13e70
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 1 08:59:51 2013 -0700

    mg tower now takes a "ptype" and we can set it on the command line or inputs file.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 96a8943fb685464794bd90b69d7646add26adb3e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 1 08:06:49 2013 -0700

    Added phys BCs to mg tower. Need'm to get BCs for lininterp.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower.f90

commit d7775fd47da02d8faebb56dd3d2baf1b340ad908
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 31 13:30:25 2013 -0700

    Added use_lininterp to mg_tower, defaulting to false.
    In mg_tower_build, if not passed as an argument, set it to true for 3D.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 55cdbe597962731acba6cbbb73203da7602ef413
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 31 13:29:46 2013 -0700

    Removed a reference to ml_cc_prolongation which isn't called from here.

Src/LinearSolvers/F_MG/cc_applyop.f90

commit 75b67cd77fa153ed5d7f81f3285cff84f872100a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 31 10:35:50 2013 -0700

    Consolidated where all the various parameters for prolongaton are set.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 522b2b05cfdbbc5ee454ec5f2e5c830842f29ecf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 30 17:04:31 2013 -0700

    Fixed a calling sequence bug I recently introduced.
    Made the calling sequences for PC on linterp look like the stuff in mg.f90.

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 873ff05c3527ee0b28cd967e967c239c3b69a61b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 30 16:56:16 2013 -0700

    A little cleanup.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit d20ff565f837cf0927160776205ee72b1e81fbd4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 30 16:09:51 2013 -0700

    Some code rearrangement in mg_tower_prolongation.
    We should think about making linear interp the default for cell-centered.

Src/LinearSolvers/F_MG/mg.f90

commit fa822fbbfc58e9636431db262840651a7376ca6e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 30 15:55:21 2013 -0700

    Changed the cell-centered lininterp routines to use ghost cells or not
    depending on how they're called.  If the coarse fab has one grow cell it
    will use it, otherwise it'll use PC interp on the face cells and linear
    interp on the interior.
    Moved the setting of cc_ptype and nodal_cubic into mg_tower_prolongation.
    My testing showed that lininterp is a benefit, but only if you do it in
    both the F and V-cycles.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit d3ba32081b9d79f7081a5929c5a4b68c6357852e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 30 14:55:45 2013 -0700

    Bug fix.

Src/LinearSolvers/F_MG/mg.f90

commit cfa44d21f4cbdc43b31f1790032e49756ffb99cd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 30 13:45:54 2013 -0700

    Added some commented out debugging code.

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit ff7364983078205204c03ad916dc5c3dd7ca67c9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 30 13:36:14 2013 -0700

    Tricubic interpolation also doesn't assume it has ghost cells.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit e60c74b4ca2e43b53635f399d1744e99316b8345
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 30 13:30:06 2013 -0700

    The bicubic will now call linear interp if it doesn't have enough grow
    cells, and then call itself on the interior.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 80b3646501882adcdb5fe8d363b2c3b8fb03162a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 30 11:12:13 2013 -0700

    Separated out the [bi,tri] cubic nodal prolongation stuff into own
    functions.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 6a995cc0a47f6275b5c62e2791943c56b3b61ffd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 29 15:34:38 2013 -0700

    Added some debugging code.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 49a62af5794bfeee3783b0899fe18212534a8820
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 29 15:33:44 2013 -0700

    mg.cycle_type is now ParmParse'd so we can pass it to F90 MG.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 8edf03a4957382de62c0aa3f51e4a1422dc6a755
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 29 15:33:12 2013 -0700

    Print out cycle_type when outputting settngs.

Src/LinearSolvers/F_MG/mg.f90

commit 14150e1e08fe0c3a520dc74d564cfcf182f2cc5f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 29 12:29:39 2013 -0700

    Some cleanup.

Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit cb76b6ebea9c5613041e7d722d3861c55a8bbcc4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 26 17:38:49 2013 -0700

    I "think" the tricubic interpolators are working.
    Still got more testing to do though.
    Checking'm in so I don't lose'm over the weekend.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90

commit f99bdb81a9c2f095a6c88a9d3c3d1ac2d8d050f7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 26 17:14:26 2013 -0700

    bicubic wasn't quite right on high nodes.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 6df575963b75af3a6fb0452e9f897f51286f15e9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 26 16:56:51 2013 -0700

    More work on tricubic.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 7941eeee7db12f3030a70e8db48d670cbe943cf6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 26 16:10:30 2013 -0700

    More prep work for tricubic.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit a07ae518d486d6d2186a4135db7b619b07e780b6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 26 15:31:46 2013 -0700

    Some preparation for trying to implement tricubic nodal prolongators.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90

commit ef46d899f58901927519aa7f321d66565ad32a5e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 26 15:25:39 2013 -0700

    Removed some divides.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit ff0f38e7adfcfed7a743e1c52759337bde9f2d6f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 26 14:44:56 2013 -0700

    Merged back in specialized unrolled PC interpolators for ir=2.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit d0969812e442f507373f5dc0be59d1a92e09bc7a
Merge: 4c9b082ad 1ecae5aa9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 26 14:22:54 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4c9b082adbb4572d89a5223f36f669a66831e6de
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 26 14:15:27 2013 -0700

    The multi-level solves now have the ability to call either the piecewise
    constant or linear prolongators, just like in the multigrid code proper.

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit c1209ce40c52c7888668075cd43de26e4f879d20
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 26 14:01:46 2013 -0700

    Made the multigrid and multi-level solves both call the same piecewise
    constant cell-centered prolongators.  Used the interface of the
    multi-level solves and integrated those into the multigrid ones.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 1ecae5aa9f3879416f436964a23b27b2ad3b9de0
Author: vince <vince@gimantis.lbl.gov>
Date:   Fri Jul 26 10:32:03 2013 -0700

    fix for intel on gimantis.

Tools/C_mk/Make.defs

commit 09d9bc46de58ae6575d1fa76fe6194f5451d72b2
Merge: 862fbe01f 4f0e3edcf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 25 15:28:11 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 862fbe01f7c0fa0fc29628faa512158cb3d7cff7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 25 15:25:56 2013 -0700

    Checked in specialized nodal_prolongation_2d().  This mirrors the 3D one
    in that it minimized the number of arithmetic operations.  It was my
    starting point for developing the bicubic.  Might as well use it when
    ir=2.  It'll be faster, but both it and the 3D version may produce
    slightly different numbers due to floating point roundoff compared to
    the more general versions.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 8e55aae4003e55033d3dd158ebd1f7583aa6f81c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 25 15:11:47 2013 -0700

    Specialized version of nodal_prolongation_3d that assumes ir=2.  It
    minimizes the number of arithmetic operations and doesn't need a
    temporary allocatable array.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 29171c2ed000fcf3a21598a46d248bafdc8511b2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 25 14:45:40 2013 -0700

    Got bicubic working again (but checked in disabled).

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 86925e0188bff401d5a8bfc3772d8d6e0029e422
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 25 12:30:19 2013 -0700

    We now use the nodal prolongators in mg_prolongate.
    Got to do the same for cell-centered.

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 15da49f0de12ecb04f2749917de3d1ab73b4d177
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 25 11:18:25 2013 -0700

    Rewrote interfaces to nodal prolongation routines.  I want to call
    the routines in mg_prolongation in ml_prolongation. No need to
    have duplicated routines lying around.  I like to see if bicubic
    has any effect in 2D multi-level solves too.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 4f0e3edcf1d5b3da9610d72480efa29ca12bb554
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Jul 25 10:40:16 2013 -0700

    MLSDC: Add multi-level SDC files (work in progress).

Src/C_AMRLib/MLSDCAmr.H
Src/C_AMRLib/MLSDCAmr.cpp
Src/C_AMRLib/MLSDCAmrEncap.cpp
Src/C_AMRLib/Make.package
Tutorials/.gitignore
Tutorials/AMR_Advection_C/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_Advection_C/Source/main.cpp

commit ae7906899c364713dd365cab6a9acb96a01e6190
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 24 17:08:40 2013 -0700

    Had a bug in how cc() was dimensioned in nodal progate 3D.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90

commit e89d0bf8ddadcc3da9ce53012e19ad76043b93d4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 24 16:47:26 2013 -0700

    Implemented classic #D full-weighting restriction.

Src/LinearSolvers/F_MG/nodal_restriction.f90

commit cd810d276767c93340e3027f03da7092bbdc1e12
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 24 16:47:04 2013 -0700

    Removed those HACK multiplies after restrictions.

Src/LinearSolvers/F_MG/mg.f90

commit 1e0c733a72ea292c81b2c717594df3517629d5ef
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 24 15:29:43 2013 -0700

    Implemented full weighting 2D nodal restrictor.  The previous restrictor
    took FABs of constant one and restricted them to constant four.  That's
    why mg.f90 had that weird multiplicative factor in it.  The previous
    restrictor didn't weight the fine cells quite right either.

Src/LinearSolvers/F_MG/nodal_restriction.f90

commit 6abfb421409b7fd742ae2887ff24cbbaf7bfa4b3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 24 13:37:50 2013 -0700

    Finished mucking with bicubic for now.  Doesn't look like a win generally :-(

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 376097d2985679a6b9e2f13df10a3944b9f4b8b0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 24 11:07:16 2013 -0700

    Added an assertion that we have enought ghost cells.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 3da73826a3e44c2f8b132398789254e541d7e893
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 24 10:49:30 2013 -0700

    Some cleanup.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90

commit e0db65c889e1378071935667b333ba648daa739a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 24 09:01:14 2013 -0700

    Checked in so we don't use the 2D bicubic nodal prolongation stuff.

Src/LinearSolvers/F_MG/mg.f90

commit f39d1dccff2e2ee310e10305eb17ba5c76afe4d8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 24 08:30:42 2013 -0700

    More work on bicubic.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90

commit d847ae283cf05cbadf8bd40cfdec7aa96ffae146
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 23 16:56:12 2013 -0700

    More work on bicubic.  Still not sure I like how BC_DIR are done.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 950d86536798c0b4cfc0d074798ebbaa9dfeacb4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 23 16:27:59 2013 -0700

    Some work getting bicubic prolongation to work for 2D nodal.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90

commit f2a97605a646b4398e8b4d2ca37a13a69d02af65
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 23 15:07:54 2013 -0700

    added support for wrapped sequence numbers for partial queries and io bracketing.

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit faab0d9926d91e14f5367fe964060e766649b66c
Merge: 8b5ea0d7f 85624973a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 23 10:05:46 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 85624973a6f8a664469c342ccbca7f60e29e3efa
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 22 12:37:15 2013 -0700

    Add new file cc_edge_coeffs.f90

Tests/LinearSolvers/F_MG/GNUmakefile

commit a7cf3d1927274a294cd256ba8c78bf9e4f8c0ed1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 22 11:48:38 2013 -0700

    We now have coeffs_type = 0: constant coefficients ( = 1)
                coeffs_type = 1: variable coefficients in [1,11]
                coeffs_type = 2: variable coefficients in [1,101]

Tests/LinearSolvers/F_MG/cc_edge_coeffs.f90

commit 6eb1e729825ac029b5eebb3a97549b2b35c82294
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Mon Jul 22 14:19:57 2013 -0400

    squash some compiler warnings: lwb(), upb(), and get_dx() all return
    arrays of the actual dimensionality rather than MAX_SPACEDIM.  This
    was picked up by the debug flags, but there is no real memory issue here.

fextract.f90

commit e28596c8a118ee1e26be4368094dc0473101a6b2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 22 10:36:54 2013 -0700

    Change the default value of nub from 10 to 0.  This is the number of
    smooths that are automatically done after a CG or BiCG bottom solve has
    reduced the residual by the requested orders of magnitude.  In theory
    we shouldn't need to do any relaxations here, but one can always set it
    in the inputs file to 10 or higher if needed.

Src/LinearSolvers/F_MG/mg_tower.f90

commit 04db2a8f993daaa718ca15cf3ae7408ecbdd61a5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Jul 21 07:09:22 2013 -0700

    If you set coeffs_type = 1 now you get variable coefficients for the
    solve  -- currently they vary by about  1:100.

Tests/LinearSolvers/F_MG/cc_edge_coeffs.f90
Tests/LinearSolvers/F_MG/cc_multi.f90
Tests/LinearSolvers/F_MG/test_script
Tests/LinearSolvers/F_MG/wrapper.f90

commit 8b5ea0d7f6ca897f698ded6348a1b538ee8da1f9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Jul 20 21:35:21 2013 -0700

    Added specialized versions of pc interp & restrict operators in 2D & 3D for ir==2.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 995db26d3b643865eb086d9488a72685a319b4a6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Jul 20 21:34:08 2013 -0700

    Added specialized versions of pc interp operators in 2D & 3D for ir==2.

Src/LinearSolvers/F_MG/cc_restriction.f90

commit 6b9dce38403ede60d7a6533c0813326517931f83
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 19 17:07:08 2013 -0700

    Removed the need for a fill_boundary on prolongation.
    The linear interpolators do PC interp on faces & linear on interior.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 4439960d5d98047262ccf1fbbb0b65b09ad048f2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 19 14:52:44 2013 -0700

    Little more cleanup.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 77dc95ed85f950d094f84bd153f5e37e456e8cae
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 19 13:45:05 2013 -0700

    Some cleanup of new linear prolongation operators.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 5e84f4d881577186f7b10442554288bd553fc4e0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 19 12:04:18 2013 -0700

    Removed unnecessary fill_bounary() in special bottom solver.

Src/LinearSolvers/F_MG/mg.f90

commit e0d2d50cd6745ef0bfb89aa758bb49159f20f4b4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 19 11:14:05 2013 -0700

    Removed some unnecessary neumann stuff from 1D nodal restriction.

Src/LinearSolvers/F_MG/nodal_restriction.f90

commit 4a51703c92eda9905f9f95c3dc45657a3e1bd648
Merge: 25c31dfab dfba1990f
Author: Ann Almgren <jmwang214@atragon.lbl.gov>
Date:   Fri Jul 19 10:45:51 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 25c31dfabd851cf63c5afb6c3521790c87d8f1fd
Author: jmwang214 <jmwang214@atragon.lbl.gov>
Date:   Fri Jul 19 10:44:28 2013 -0700

    Add random nmber RHS for Tests/LinearSolvers/F_MG.

Tests/LinearSolvers/F_MG/cc_rhs.f90

commit dfba1990f604c67ded1bb5fe8f549edf8b47bbfe
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 19 10:28:53 2013 -0700

    Added optional argument "eps" to mg_tower_bottom_solver().
    I want to test the effect of bottom solver tolerances on the F cycle.

Src/LinearSolvers/F_MG/mg.f90

commit 16158b3fc199cc657f4db7bc1257d9ff4539ed77
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 19 10:21:44 2013 -0700

    Some cleanup.  Removed unnecessary mg_defect() calls from fmg_cycle.
    Removed bl_timer routines from mg_tower.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower.f90

commit ea2547ec0fbf07070706ad81b5809f154cd5967b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 18 15:59:39 2013 -0700

    Add inputs for the new problem with Dirichlet bc's

Tests/LinearSolvers/F_MG/inputs.2d.fcycle.dir
Tests/LinearSolvers/F_MG/inputs.2d.vcycle.dir
Tests/LinearSolvers/F_MG/inputs.3d.fcycle.dir
Tests/LinearSolvers/F_MG/inputs.3d.vcycle.dir

commit bec4e3096f592ba85e3483542800083a44080a49
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 18 15:58:34 2013 -0700

    Add test problem where we start with exact phi, compute the Laplacian,
    then use that as the RHS.  This works with Dirichlet bc's.

Tests/LinearSolvers/F_MG/cc_rhs.f90
Tests/LinearSolvers/F_MG/test_dir

commit 16cc6dc1703d9ebeff01efb3c40a2fe4291383ef
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 18 15:56:48 2013 -0700

    Add options for linear interpolation in 2d and 3d.  Currently the linear only
    works for ref_ratio = 2.  Default is still to use piecewise constant so this
    shouldn't change anything.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 6d5b98107bd406fbd6d8f2c086c1151070ae7b4c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 18 14:06:25 2013 -0700

    Fix up this code so it is easier to run different test problems, with
    different rhs or using F- vs V-cycle

Tests/LinearSolvers/F_MG/cc_multi.f90
Tests/LinearSolvers/F_MG/cc_rhs.f90
Tests/LinearSolvers/F_MG/inputs
Tests/LinearSolvers/F_MG/inputs.2d.fcycle
Tests/LinearSolvers/F_MG/inputs.2d.vcycle
Tests/LinearSolvers/F_MG/inputs.3d.fcycle
Tests/LinearSolvers/F_MG/inputs.3d.vcycle
Tests/LinearSolvers/F_MG/test_script
Tests/LinearSolvers/F_MG/wrapper.f90

commit 3b08cc4bd1258cd9642b8e2683fb74b616f5edfa
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 18 13:10:32 2013 -0700

    Separate out the rhs routines from nodal_multi.f90 and cc_multi.f90

Tests/LinearSolvers/F_MG/GNUmakefile
Tests/LinearSolvers/F_MG/cc_multi.f90
Tests/LinearSolvers/F_MG/cc_rhs.f90
Tests/LinearSolvers/F_MG/nodal_multi.f90
Tests/LinearSolvers/F_MG/nodal_rhs.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit 5950edb119c3f3f7e80eeb3158a0de2e65ff8b51
Merge: 1aeb6c00c 553372ea8
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Wed Jul 17 08:59:10 2013 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 1aeb6c00c1794663717e04aa7c401820b4d0e291
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Wed Jul 17 08:54:11 2013 -0400

    add FIVE3RD

Src/F_BaseLib/bl_constants.f90

commit 553372ea81d1fd85e6fd60b56ee04d2d2d0ec158
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 16 15:08:15 2013 -0700

    Nodal FMG cycle now seems to be working.
    At least it takes no more cycles than does V-cycle.

Src/LinearSolvers/F_MG/mg.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit 8406279233f0226b42e2f03235854adf27e38228
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 16 10:06:28 2013 -0700

    omega is no longer part of mg_tower

Tutorials/HeatEquation_EX5_F/advance.f90

commit b3f9b1151ee5d268de1272d868c2dc761fa6f29f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 15 15:32:49 2013 -0700

    Add timer stuff to f_cycle.

Src/LinearSolvers/F_MG/mg.f90

commit af9fb0a8e460347dc2dc52bee0e66c3030bb6e5a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 15 15:30:57 2013 -0700

    Remove unused nodal_flag in fmg_cycle.

Src/LinearSolvers/F_MG/mg.f90

commit 4668443b165517bcd500b10cff4bd2171499abcb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 15 14:54:23 2013 -0700

    Removed the GS_LEX smoother stuff.  Never used.  Just use GSRB.

Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/mg_tower_smoother.f90

commit 7afdd9d31a7d74fdac89c940048112a964662fe2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 15 14:37:43 2013 -0700

    Omega is no longer a part of the mg_tower.
    Nor is omega passed to the smoother routines.
    The smoother routines now use their own omega.
    Also removed the unused lgs_* smoother routines added by Chuck long ago.

Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/mg_tower_smoother.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit 11335bd16ce17a5ae85719e5000d63d6b2f99e7e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 15 13:43:20 2013 -0700

    Only set mgt%face_type if nodal.

Src/LinearSolvers/F_MG/mg.f90

commit 9d8f16f60a65210d3d5804b119fb66fa6b6e4933
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 15 13:22:28 2013 -0700

    Skewed stuff.

Src/LinearSolvers/F_MG/mg_tower_smoother.f90

commit 3ef8e6cf4f2be5221c2dd64daae532ced2694b3c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 15 13:21:43 2013 -0700

    Only build mgt%skewed and mgt%skewed_not_set if cell-centered.

Src/LinearSolvers/F_MG/mg.f90

commit e133afa37d06c4c30d622d278f727a14c2f42fc9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 15 12:11:56 2013 -0700

    Do error check for cycle_type.

Src/LinearSolvers/F_MG/mg.f90

commit d844836f97b46b40c93eb2ad8a958471d8ca7c8e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 15 12:11:37 2013 -0700

    Added --cycle_type.

Tests/LinearSolvers/F_MG/wrapper.f90

commit 6a91c1e7330981d85f9d07d13d92f7165cada24e
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 15 11:41:51 2013 -0700

    spacing.

Src/C_BaseLib/Profiler.cpp

commit 29cef88b1555cdd48b4a22973359c1a513904fa6
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 15 10:46:01 2013 -0700

    optimized nametags.

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 2e89dd7603df0af7d214a5dc9de378679f486a61
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 11 07:42:26 2013 -0700

    updated some tests due to the removal of gamma from mg_tower_build interface

Tests/LinearSolvers/F_MG/wrapper.f90
Tutorials/HeatEquation_EX5_F/advance.f90

commit cf8ee73e5f3fbd0cbdbf210cf2f949abca2f3074
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Jul 10 13:36:43 2013 -0700

    comments for mg_max_levels function

Src/LinearSolvers/F_MG/mg.f90

commit 6c1e221000dc930298ab8e951ddd36005ba1d9af
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jul 10 12:43:33 2013 -0700

    Add default value of 1.33 for omega for 1d nodal only.

Src/LinearSolvers/F_MG/mg.f90

commit 39ea8ff10067a3922aa83144132c2db37d08a6b5
Author: jmwang214 <jmwang214@atragon.lbl.gov>
Date:   Wed Jul 10 12:41:21 2013 -0700

    1) Fix the F-MG cycle -- it can be used by setting cycle_type..
    2) remove gamma and omega from the inputs of mg_tower_build

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit f301b64e2e36e773d79a94e58cc747df54a914e8
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 10 11:49:38 2013 -0700

    more profiling, timer time.

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit b98dd34a8637e9c8ab462bf7ff7e56dc17fa8b7e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jul 10 11:19:07 2013 -0700

    Remove gamma and omega as inputs from the mg_tower_build call.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit aa2117997b708ff500fd8022bfc89883e03c5f2f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jul 10 11:18:27 2013 -0700

    Remove gamma and omega from the calling sequence when calling from C++.

Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 8ec0ba34da7d0af6558d481d0df1c0f55998b263
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 8 15:52:40 2013 -0700

    Declare mgt%visited.

Src/LinearSolvers/F_MG/mg_tower.f90

commit c7e2338491380253d7f53c7e82eea4b296d542eb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 8 15:52:27 2013 -0700

    Try to fix the logic for the F-cycle.

Src/LinearSolvers/F_MG/mg.f90

commit 0f42bcae4c817f6c8281d92cda9cc5cfbce39451
Merge: 006f51d58 ed5334763
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 8 13:34:06 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ed53347632d752367ed5120a47f9ef27c5902e72
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 8 10:13:21 2013 -0700

    More work speeding up nodal_restriction; hadn't done all cases.

Src/LinearSolvers/F_MG/nodal_restriction.f90

commit 353d818955d750a8e396e7c974d6300bd2c33b66
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 8 09:33:49 2013 -0700

    Rearranged the nodal_restriction code to be faster & more memory
    efficient.

Src/LinearSolvers/F_MG/nodal_restriction.f90

commit 006f51d58d4217fee746a3bd586450651cff90e3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jul 6 10:01:34 2013 -0700

    We were printing the wrong final number of iterations.

Src/LinearSolvers/F_MG/ml_cc.f90

commit e5bbcc8a0f7a2470ff580ffea087efdbf99fbb11
Merge: 147ee88b5 7a337048a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Jul 6 09:27:49 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7a337048a66dcdaf54a5cca09d842ca6e14ceae9
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Jul 5 09:19:20 2013 -0400

    remove duplicate tests (if any) when using the --tests "..." argument.
    Otherwise we crash

Tools/RegressionTesting/testnew.py

commit 147ee88b5e2557aa1187eea59f9ccace275d5787
Merge: c59454aab 1be5d09bf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 2 14:54:21 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1be5d09bff9ef9a9c7a6a732ae23fa7bd30099e0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jul 2 13:45:57 2013 -0700

    Add WritePlotFile in Particles.H

Src/C_AMRLib/Particles.H

commit c59454aab6b93f3e73e0b3172275789518fbdc70
Merge: 2093cf3a4 e519b89e7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 2 11:05:40 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e519b89e70f5ddfc8f3581aaecef7a54bb12007e
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 2 10:59:43 2013 -0700

    don't prevent nodal solves from reducing to a global 2x2 bottom solve.  certain bc's means this becomes a problem with 1 unknown which we've seen can stall multigrid

Src/LinearSolvers/F_MG/mg.f90

commit 2093cf3a479dce8cc62109b031cf9022a32a4d9b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 1 15:21:55 2013 -0700

    Moved the memory stats stuff till after we've flushed the copyassoc cache.
    Checked it in commented out.

Tests/LinearSolvers/F_MG/main.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit 35d949d2645a2b4dfdd984173000c2b8551aec3c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 1 13:05:37 2013 -0700

    Reverting right back out the four-color dense 2D GS smoother.  Sometimes
    better smoothers aren't necessarily a win; especially when they're so much
    more communication intensive.

Src/LinearSolvers/F_MG/mg_tower_smoother.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit 403a7e55ecf3b57a0c7c48d84a1fd7b5a304e1fb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 1 13:02:15 2013 -0700

    I've implemented  four-color GS scheme for the dense nodal 2D stencil.
    I'm checking it in here to document it.  I'm going to immediately revert
    out these files to their previous contents.  Turns out doing four
    FillBoundary()s per smooth is a serious lose in 2D.  On my test case my
    nodal solves were about 20% slower on 64 cores on hopper, and about 50%
    slower on 512 cores.  This despite the four-color scheme being a "better"
    smoother, sometimes leading to fewer V-cycles in the MG.

Src/LinearSolvers/F_MG/mg_tower_smoother.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit b04b99b31bbe350fec3748e277e4bb49341fa6d4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 1 12:41:48 2013 -0700

    Made the bottom solve timer work for bottom_solver=4.

Src/LinearSolvers/F_MG/mg.f90

commit 65957dae4dbe7e9a9b0008bb2a6e749a9f0f0bc1
Merge: 1edd6bc6e e737a9cd7
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Jul 1 10:36:23 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1edd6bc6e4c33eb146c7140ab9549326f9a84cfb
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Jul 1 10:35:57 2013 -0700

    fixed some mg level calculation weirdness that prevented cc fancy bottom solver from converging

Src/LinearSolvers/F_MG/mg.f90

commit e737a9cd723528b3edc75f078bdc0020e6c5b85d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 1 08:30:55 2013 -0700

    get around a PGI compiler bug

Src/F_BaseLib/multifab_f.f90

commit e74ff2acd38d73f3ca8ad3fb11c8f4608c6333e7
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Jul 1 08:16:52 2013 -0700

    fixed logic to handle the case when you try to invoke the fancy bottom solver and you have between 1 and (2**dm)-1 grids... in this case you can't use it so revert to bottom_solver_type=1

Src/LinearSolvers/F_MG/mg.f90

commit 603149054b97a896a9272103a3246740f690a729
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Jun 28 16:01:22 2013 -0700

    change default value of max_bottom_nlevel to 3 so fancy bottom solver coarsens two levels (i.e., reducing # grids by factor of 8)

Src/LinearSolvers/F_MG/mg_tower.f90

commit 8d7029f7ff732e987937d722c8c1b79da9ef7e40
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Jun 28 15:59:36 2013 -0700

    eliminated some fancy bottom solver logic that was
    
    a) preventing the fancy bottom solver from ever being used if there are exactly 8 grids in the original bottom solve
    
    b)  always forcing the max number of new levels to be 3.  this should be controlled by max_bottom_nlevel, which will be default 3

Src/LinearSolvers/F_MG/mg.f90

commit e538c479f4f4e7e2d797f55996351ee006e12fc0
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Jun 28 15:07:11 2013 -0700

    when calling_tower_build, you can pass in an optional argument "fancy_bottom_type_in" that controls the bottom solver for bottom_solver type 4.  This is useful if you would rather do smooths than the default BiCGStab

Src/LinearSolvers/F_MG/mg.f90

commit 1619a2162dd955a32ca379ad5b2e8ce18d73f785
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 26 11:12:26 2013 -0700

    Rearranged lin_cc_interp_3d to do fewer allocate()s and be more cache
    efficient.

Src/F_BaseLib/interp.f90

commit cdc3ae04c80f104913c97bd0552cfac440cc932f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 26 11:08:28 2013 -0700

    Removed some trim() calls on string comparisons.

Tutorials/AMR_Advection_C/Source/network.f90

commit 331e03d24cf35842fa4d94c5477077bd8ffe9db3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 26 08:11:33 2013 -0700

    Got another 20% out of fourth_order_interp_2d().

Src/F_BaseLib/interp.f90

commit 8132e4cddbfc09d436105186db54149aa077e2f1
Merge: cb7dc7c63 129e41478
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 25 15:38:10 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 129e4147873a04e33bfb7fd36e5fac8fd7314ae0
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jun 25 14:52:15 2013 -0700

    added nametags.

Src/C_BoundaryLib/FabSet.cpp

commit 46f9b03be5414476ba1bd8741822bfef3d7d7e20
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jun 25 14:51:20 2013 -0700

    added nametags.

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit 5bbda07491084de7ac93b5c60510c6ad4b23095a
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jun 25 14:48:15 2013 -0700

    added nametags.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp

commit 58e31d8c93a60969a698f7851258e3935bf062d3
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jun 25 14:41:41 2013 -0700

    added to docs for comm profiling.

Docs/Readme.profiling

commit cb7dc7c632d1c5be1a6a55d12b4992d81dbca8f8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 25 10:40:52 2013 -0700

    Build and use a local copy of the transpose of A2 in the fourth
    order interpolator.

Src/F_BaseLib/interp.f90

commit feb179c601aed2283e3c3f02c860665acfc63961
Merge: c0751132a 95572b8f3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 24 16:21:27 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c0751132a0d5843bacbb7871f60909d8892c2703
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 24 16:17:38 2013 -0700

    Made fourth_order_interp_2d() more cache efficient by declaring the tmp
    variable c(:,:,:,:) such that the first dimension holds the values at each
    cell, not the last dimension. It could be made more efficient if A2 in
    fourth_order_interp_coef_module were defined as A2(15,0:3) instead of the
    other way around. But that could only be done all routines using it were
    changed as well.

Src/F_BaseLib/interp.f90

commit 95572b8f38725f63d63f462496c71465fbbc2ddd
Author: cmalone <malone@ucolick.org>
Date:   Mon Jun 24 18:06:45 2013 -0500

    cray compiler requires IO unit on flush

Src/F_BaseLib/parallel.f90

commit 7220636412b95efbabe18f3027e3f94227af1462
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 24 15:55:15 2013 -0700

    kind=8 -> kind=dp_t

Src/F_BaseLib/fourth_order_interp_coeffs.f90

commit ca332897acbbc6ff1c0a65bab3fa58dc5ad0ef75
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Mon Jun 24 16:34:00 2013 -0400

    fix the _1d stuff -- the ss(0) was defined incorrectly (all ss's should
    sum to 0)

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit ff1d1e88cc4a959f2737daea1e271f7b44626140
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 24 09:53:32 2013 -0700

    No ghost cells are needed; having no ghost cells can also eliminate a lot of Valgrind warnings

Tutorials/AMR_Advection_C/Source/ADR_setup.cpp

commit e5a4f3b73689a251a5e22931e4cf27a871420ccf
Merge: 6b5a0ec16 b66983729
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 23 21:45:48 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6b5a0ec16694db6d12ec33200b82292660922092
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 23 15:17:48 2013 -0700

    fixed a minor memory issue

Tutorials/AMR_Advection_C/Source/ADR_setup.cpp

commit b669837294274d86b118ae4d6b452a6cade563f9
Merge: b1b6204ae 83736f590
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Jun 23 07:57:50 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b1b6204ae1066ba4ad1ad0fd8248a9a8137c09fb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Jun 23 07:57:30 2013 -0700

    Mod to parallel_create_communicator().

Src/F_BaseLib/parallel.f90

commit 83736f590f998e513330b4183e0d3caff9c9a76d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jun 21 15:56:23 2013 -0700

    Update the Tutorials/AMR_Advection_C/Exec/UniformVelocity test problem.

Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_2d.f90
Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt
Tutorials/AMR_Advection_C/Exec/UniformVelocity/probdata.f90
Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.2d
Tutorials/AMR_Advection_C/Source/ADR_setup.cpp

commit e06519fc697f6e20d994a2b2d56bd9d6a4249d59
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 21 14:20:36 2013 -0700

    Added back in Ann's tweak to get_bottom_box_size().

Src/LinearSolvers/F_MG/mg.f90

commit 5f5ceddb868a9b289f0811a0a7e7165a8b90575e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 21 14:18:54 2013 -0700

    Can't use bl_error_module; just print & abort by hand.

Src/F_BaseLib/parallel.f90

commit c452e410448f2b06026a576c5a395145cb1a13dc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 19 15:26:06 2013 -0700

    Some cleanup.

Src/LinearSolvers/F_MG/mg.f90

commit 81fa3d9d9cfe520d37c62c90c7c810076023eeff
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 19 15:25:38 2013 -0700

    Added signatures for functions I recently added to parallel.f90.

Src/F_BaseLib/parallel_stubs.f90

commit ef1c126bb38b907d9e28b3d89edde7dfc9f770b2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 19 14:56:50 2013 -0700

    Added parallel_null_communicator().
    Added optional comm argument to parallel_ioprocessor().

Src/F_BaseLib/parallel.f90
Src/LinearSolvers/F_MG/itsol.f90

commit 56cc55cba61f1cb57ba288fa611ff08651762185
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 19 14:37:46 2013 -0700

    Used parallel_communicator() instead of MPI_COMM_WORLD.

Src/LinearSolvers/F_MG/mg.f90

commit d719549ebe1a3bc10f522d6c74b4cf1fe865d155
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Jun 19 14:33:06 2013 -0700

    BaseFab: Tidy SAXPY signature, fix SAXPY domain bug.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp

commit 297838f8ad9a1bd6410261a6fa814257a9b299be
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 19 14:30:28 2013 -0700

    Added parallel_create_communicator() and parallel_free_communicator().

Src/F_BaseLib/parallel.f90
Src/LinearSolvers/F_MG/mg.f90

commit 5ed901c14a609e70c872aad5545fb47bc376a04f
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Jun 19 14:18:02 2013 -0700

    BaseFab: Add SAXPY.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/SPECIALIZE_1D.F
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H

commit c1f7a09ae5a48b1c52ee330b28eab7f5448b2c2b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 19 13:57:28 2013 -0700

    Some initial work getting bottom_solver=4 to use its own communicator.

Src/LinearSolvers/F_MG/mg.f90

commit b7a15c7a50e1087494793915192aefa214147362
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 19 13:55:12 2013 -0700

    First cut at making BICGStab and CABiCGStab work with a given MPI
    communicator instead of the default one: MPI_COMM_WORLD.

Src/LinearSolvers/F_MG/itsol.f90

commit 8f45746d891c28cc30d0d92e718507027427e877
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 19 13:52:35 2013 -0700

    Changed the default of max_bottom_nlevels from 10 -> 4.
    Added an MPI communicator data member that will be set in the mg_tower
    that does the bottom solve for the bottom_solve=4 case.  The idea
    is that we pick a communicator that includes only those MPI procs
    involved in the bottom solve and pass it to routines that do global
    reductions to make those reductions go faster.

Src/LinearSolvers/F_MG/mg_tower.f90

commit 7d5a2c317429048ef5b2c8c9136d3273be837479
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 19 13:51:34 2013 -0700

    multifab_dot() and multifab_norm_inf() now take optional MPI communicators.

Src/F_BaseLib/multifab_f.f90

commit 83293019744ebb9da18470239003795674867b88
Merge: fbe99e5bb 850b16801
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Jun 19 12:17:43 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit fbe99e5bb36f97eddabcb857aa9d8f24b45eb7db
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Jun 19 12:17:35 2013 -0700

    Amr.H: Mark timeStep as virtual, sync parameter names with Amr.cpp.

Src/C_AMRLib/Amr.H

commit 850b16801b01ad699dd081706a9408a393587328
Author: Chris Malone <malone@ucolick.org>
Date:   Wed Jun 19 11:52:50 2013 -0700

    updates for hyades.ucsc.edu

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit 0ebbbd284e46abcb824b1695dc3fd44dbe57ce7a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 19 08:00:34 2013 -0700

    3d nodal dense test case on 256^3 base grid with 64^3 grids for Legion
    folks.

Tests/LinearSolvers/F_MG/inputs.simple.3d

commit 63adb8585a1a54c8c03908594bdbe053ab6037e2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 19 08:00:02 2013 -0700

    Set up for non-MPI non-OpenMP for Legion folks.

Tests/LinearSolvers/F_MG/GNUmakefile

commit 2e2f196538c3ce0fa36f2eae5cbd23c30ca82d0b
Merge: d7480296e 4bbd22d11
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 18 14:17:50 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d7480296e462381bf80309acafc62d3d35a65e8c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 18 14:17:26 2013 -0700

    Remove unneded "use" statements.

Tests/LinearSolvers/F_MG/main.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit e91bdf0255b993942a1354b3e977f7fd119ddee9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 18 14:06:44 2013 -0700

    Updated which modules are included.

Tutorials/WaveEquation_F/main.f90

commit 4bbd22d1144011f20933b591d90433b46505e3ba
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 17 16:26:03 2013 -0700

    Some mods to get it to compile again.

Tests/LinearSolvers/C_CellMG/main.cpp

commit 5e05ab50da21b4ba9aee04b8e5b3462ec867db43
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 17 16:24:32 2013 -0700

    Thread sxay() over FABs in the MultiFab.  The FABs themselves are too
    small to make threading over their Fortran boxes cost effective.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit ffd8c4b967c513cadecdec0f7a3a677d027f6580
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 17 16:08:38 2013 -0700

    Removed the multiply by alpha in axpy() since it's always one.
    Likewise optimized gemv() knowing alpha==1.0 and beta==0.0.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 681c2d4a549c75f5e31270be6fa526970ae581c8
Merge: 2e343961e d4465b78b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 17 14:40:54 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2e343961ed9d17d16e2f1cd67052982a1afe2788
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 17 14:40:26 2013 -0700

    Removed grow cells on MultiFabs in BiCGStab that weren't needed.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 1ad7c53e51fe5059adafd424434406610945909a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 17 14:22:51 2013 -0700

    Beefed up error checking in CABiCGStab.
    Also removed ghost cells from MultiFabs where not needed.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 6b6ecabbc778a65025015977c6af0aa5b3c5644c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 17 14:11:17 2013 -0700

    FApply() didn't correctly use src_comp, dst_comp and num_comp.

Src/LinearSolvers/C_CellMG/Laplacian.cpp

commit d4465b78b3af378410e2da61e9e48d86d6f1702d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 17 11:50:14 2013 -0700

    Fix some comments only.

Src/LinearSolvers/F_MG/cc_stencil_apply.f90

commit ef53d634cec9f40e251094ae008b96730c72bbe5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 14 18:48:08 2013 -0700

    Little more OMP tweaking of my previous mod.

Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/itsol.f90

commit 406a64270fda32ef7b615f27aaeed463793dd0e8
Merge: c922a5637 4132beb88
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 14 15:19:32 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c922a563785d4893e2f4d1af32ea348c8dc40c3c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 14 15:17:57 2013 -0700

    Make itsol_defect() aware when it's being called from the bottom solver.

Src/LinearSolvers/F_MG/itsol.f90

commit dfa068f3c1036b9bd2f895d7dfcc852ac0c8b4ea
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 14 15:11:28 2013 -0700

    We now pass a flag to itsol_stencil_apply() indicating whether or not
    we're doing a bottom solve.  It passes that flag to the relevant 3d apply
    routine, which then threads its loops if it's NOT in a bottom solve.
    This threads better for fewer boxes than threading over the calls to
    the apply op itself.

Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 29bc9ed5fa6ee96da23b5512e776fd98e24d3765
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 14 14:18:55 2013 -0700

    Changed the name of a constant.

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 3806e12bcd569d79a43f6d66219bf6c18d27c75b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 14 11:58:44 2013 -0700

    Attempted to make some of the minion stencils more memory efficient
    by doing as much work as possible on them in one pass instead of
    multiple passes. Also, OMP over the bit twiddling in mask.

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 05594729a22b3dce60a1b4f155243a7d16312a8e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 14 10:52:40 2013 -0700

    Some OMP tweaking.

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 4132beb88232b6d81850bbfffa282d4d8c684101
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 13 21:33:10 2013 -0700

    fixed a bug in my new code; now fillpatch seems to be working in cases that don't need interpolation in time (which is the case for multi-level SDC)

Src/C_AMRLib/StateData.cpp

commit ae39dafa13d0b2103ce99db7667a759b6eb535c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 13 17:56:30 2013 -0700

    added multi-level SDC nodes

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/BaseFab.cpp

commit c4e35a45c13bc5e415957e20d70e925005df6404
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 13 17:16:22 2013 -0700

    Added some barriers.

Tests/C_BaseLib/tFB.cpp

commit 965b5600eefeb67d02d69d2e2dc122673649e812
Merge: 224b9f55e 4af1dd8ca
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 13 12:58:22 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 224b9f55e1bb1da9e37b548071d639c3d0c1f9d5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 13 12:51:53 2013 -0700

    New FillBoundary() test I want to run.

Tests/C_BaseLib/tFB.cpp

commit 4af1dd8ca891ce7e9d839b2ee68094b104dba179
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 13 10:11:31 2013 -0700

    added some functions for getting, allocating and removing middle data in AmrLevel

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit e71ad749db2a7bd14c0da1554994205a70b0f40e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 12 17:52:46 2013 -0700

    added quadratic interpolation in BaseFab, but the Fortran code is not implemented yet

Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/SPECIALIZE_1D.F
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H

commit 5568ef7e7921b312d98c7e38bcf53b7d70f04ae8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 12 12:44:47 2013 -0700

    rename linInterp Interp because it will no longer only do linear interpolation

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 8c6cd115e071255d5f4f3d51b68edfba607e7c57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 12 11:21:19 2013 -0700

    pass MultiFabId and time of middle SDC nodes into time interpolator

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit aa404ca98561633fa8d7c7352ae8e902b3113354
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 12 16:07:10 2013 -0700

    quick fix for omp prof, need to track individual thread times, scoping issue.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit f7150e91aaacfe4b6bc49fb8f027dd562cbfb8fb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 12 14:35:07 2013 -0700

    PR in itsol_CABiCGStab doesn't need any ghost cells.

Src/LinearSolvers/F_MG/itsol.f90

commit b6e011c881e8ef29d77a765ff57f04ea52392ada
Merge: baa8cb13d f0a3abfae
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 12 14:08:37 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit baa8cb13d16723a71d30f87b1ebd05d6c9539724
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 12 14:08:15 2013 -0700

    Mods due to formal argument changes.

Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit c2ae04f8f7add7a4e625e0cb8c5b3d1e880be031
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 12 13:46:04 2013 -0700

    Destroy a boxarray.

Tests/LinearSolvers/F_MG/wrapper.f90

commit dd4b40150f68841602f454a8bf6b69d421f6f95c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 12 12:54:13 2013 -0700

    Removed a bunch of unused variables and formal arguments.
    Really trying to get the code to compile clean in debug mode.

Src/F_BaseLib/multifab_f.f90
Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg_tower_smoother.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Tests/LinearSolvers/F_MG/cc_multi.f90
Tests/LinearSolvers/F_MG/nodal_multi.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit 1c21e3c7940efa62406fc551eb746e5e6f1a2eba
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 12 11:01:27 2013 -0700

    Fix bug in s_simple_1d_nodal().

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit b00526a9dd7ec5af56e80fefe9be129f753a4dd8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 12 10:54:30 2013 -0700

    Fixed bug in stencil_set_bc_nodal().
    Added set_faces_edges_corners_2d().

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 74e0ecbdef14b1cdd97236418f50b7cc8254190a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 12 10:30:08 2013 -0700

    Some OMP tweaking.

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90

commit f0a3abfaecd5cc7c2bab6a33320c9bef52f9ecce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 11 21:41:58 2013 -0700

    pass SDC node times into StateData

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit fbafe0c5268eeb4e6c2ca7458660371b42f9ae8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 11 17:45:46 2013 -0700

    added SDC nodes information to Amr

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit d6533e1430cdd964280d40e0b54978483e80ca68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 11 15:28:56 2013 -0700

    added mid_data to StateData class for the storge of SDC middle nodes

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/PArray.H

commit 9350fb7040ffe371b57b1d71c76bf030418dd274
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 10 10:37:41 2013 -0700

    A little memory cleanup.

Src/C_AMRLib/StateData.cpp

commit 30f00044614dcb731264100bd7a75847c4dc9391
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 10 10:29:06 2013 -0700

    Fixed OMP bug.

Src/C_AMRLib/AmrLevel.cpp

commit 7571772210af9a063b51e9d640a3c7442460f55a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Jun 9 19:29:07 2013 -0700

    Added version of linInterp() in which the two src boxes & the dest box are all the same.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/MultiFab.cpp

commit fabe75e25750d40aa8cc78a682aee7e8de91462f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Jun 9 18:56:18 2013 -0700

    Added specialized version of BaseFab::sum() for Reals.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/SPECIALIZE_1D.F
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H

commit 272cdb01701269ff36b4920f31400aa183ad5868
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Jun 9 17:38:28 2013 -0700

    Added some profilers.

Src/C_AMRLib/AmrLevel.cpp
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.cpp

commit c4cabc4d70e0c420caded84a24df06f03b45df23
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 6 13:46:24 2013 -0700

    Reverting out the eight-color nodal dense smoother.
    With the number of fill_boundary()s required it's a lose.

Src/LinearSolvers/F_MG/mg_tower_smoother.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit a755746070af26c8923eeb2b221d38686b58756c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 6 13:13:21 2013 -0700

    Removed the OMP from multifab_dot_cc().
    Do the calculaton as a sum of partial sums.

Src/F_BaseLib/multifab_f.f90

commit 63284f8b7110a405d8b0f12ccc37a3a1561160dd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 6 13:13:02 2013 -0700

    Named the critical section.

Src/C_BaseLib/BaseFab.H

commit cf728d42d5de1ef0adee26e2207e4ec01876da0d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 6 12:56:20 2013 -0700

    Had to add a critical region around the code in BaseFab::define() in which
    we maintain global track of the amount of data allocated in FABs.
    Multiple threads can hit this code at the same time.

Src/C_BaseLib/BaseFab.H

commit e4a460da5a074319594442c30e75f7f44dfcc48f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 6 07:30:35 2013 -0700

    Fixed OMP bug.

Src/F_BaseLib/multifab_f.f90

commit d05f0e9db2d374827dde544ccf56b9f3d06fe8ae
Merge: 3292f936c 9aa35369e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 14:14:55 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3292f936c24a6a796e83c3eb7e4fb43a53a0b97a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 14:08:50 2013 -0700

    OMP over operations on boxes in boxarray.

Src/F_BaseLib/boxarray_f.f90

commit 9f08aca704fdd5053fb9a26b82e3dda3ae041997
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 13:51:20 2013 -0700

    OMP over the various loops in BoxArray that operate on all the boxes.
    This appears to be a win a modest # of boxes.  Should be a big win
    with very large box counts.

Src/C_BaseLib/BoxArray.cpp

commit 9aa35369e7cbe56c43057d2190c7d5d163a144ed
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jun 5 12:06:29 2013 -0700

    Need different template depth if USE_IN_SITU is true.

Tools/C_mk/Make.defs

commit c971eda7c658726f224df5b2d5f1b49f497c30e1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 11:00:09 2013 -0700

    Explicitly write out the sum() operation in multifab_dot_cc().

Src/F_BaseLib/multifab_f.f90

commit 87d76c9c70fd9193cefe16946d11e63dc1dea8b8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 10:26:27 2013 -0700

    A little cleanup.

Src/C_AMRLib/AmrLevel.cpp

commit d77a259d5058233ea8720bac4af6bbf5cc347950
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 10:05:19 2013 -0700

    OMP over number of boxes when building proper grid for FabSets.

Src/C_BoundaryLib/BndryRegister.cpp

commit e7fa42bce9a26e20f47be06871168904105262d4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 09:21:53 2013 -0700

    OMP over faces when interpolating bndry data.

Src/C_BoundaryLib/InterpBndryData.cpp

commit 6d7ab2f0defc6b2cece6479a4fe3f043eafe0e26
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 09:21:15 2013 -0700

    Promote MultiFab::IndexMap() to be a public member.

Src/C_BoundaryLib/FabSet.H

commit f8937b3463e53ed98bf608038d82a42e922849e1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 08:37:03 2013 -0700

    OMP over the tagboxes in a tagboxarray.

Src/C_AMRLib/TagBox.cpp

commit 1cad8026b610ef7a533cd289d6d6366ace79e849
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 08:36:15 2013 -0700

    OMP over the various faces in fluxregisters not in the individual
    Fortran routines themselves.

Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/FluxRegister.cpp

commit fe5acbf00dafd836939a5df85b07cb7567053e03
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 08:35:11 2013 -0700

    OMP fillpatch.  We want to be able to OMP over all the small boxes.
    Especially for the interpolations.  This means we don't OMP in the
    interpolator routines themselves.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/INTERP_3D.F

commit ffc8d3ab182dc53fb27f5ad9eb5557ef62aa169b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 4 19:30:32 2013 -0700

    Fixed OMP bug.

Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit d4af672f8b05c23de1d64ebf1d8df12ab37cd8e5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 4 17:09:46 2013 -0700

    Fixed OMP bug.

Src/F_BaseLib/multifab_f.f90

commit f80c0c85b421ba58e179a640d352906a666ff7d4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 3 17:45:29 2013 -0700

    The stencil apply functions are only called by the bottom solver.
    The boxes are too small to profitably OMP.  Instead OMP over FABs.

Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 48be938ac8bb41b95fd4031dd40d6a59cd01e3ec
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 3 17:18:47 2013 -0700

    Use cpy_d() instead of generic pointer copy assignment.

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/create_umac_grown.f90
Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit b3120a5e9002abe83b6a9d842ec2a9a51d8a5158
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 3 16:33:52 2013 -0700

    Some OMPing.

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit c1e74e55c8d3b9d7d86c5e6cd6bf4e6d1ac38440
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 3 14:59:39 2013 -0700

    Now print out solve time and accumulated time in the bottom solver.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 36bb633db039df48a6aac5301a6366f389f4d773
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 3 10:59:04 2013 -0700

    Some cleanup.

Src/F_BaseLib/multifab_f.f90

commit 1e55ddb531b1071147cd23322f907ac220b838c1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 3 10:36:07 2013 -0700

    Added multifab_norm_l2_doit().

Src/F_BaseLib/multifab_f.f90

commit c9f030559ffe33b9ae89ac6229bb4dad13329223
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 3 10:24:40 2013 -0700

    Thead over FABs in multifab_dot().  They're almost always called with tiny
    boxes that can't be threaded over individually.

Src/F_BaseLib/multifab_f.f90

commit f4a1a2e11dcebe304fb631ad56d24806e2f69b8c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 3 09:18:09 2013 -0700

    Tweaking the OMP IF constaints on some loops.

Src/F_BaseLib/multifab_f.f90

commit 76132aed7cd1fd0e93d44bd092118790faae44f1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 29 16:17:37 2013 -0700

    Can now call gs_lex_dense_smoothers in mg_tower_smoother.

Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/mg_tower_smoother.f90

commit a2613a6cd80ddaf0634ecf1941bc0438333fbf66
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 29 16:00:43 2013 -0700

    Some cleanup.  Also, make sure mg_tower_smoother calls the fourth order
    smoothers the proper number of times.  Only the 2-D HO cross stencil does
    red-black; the others do a full sweep.

Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/mg_tower_smoother.f90

commit af798e7726cf6947e49b18798f887c4a99c6041b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 29 15:14:15 2013 -0700

    Only use the 8-color dense nodal smoother if OMP=t and don't have enough FABs.

Src/LinearSolvers/F_MG/mg_tower_smoother.f90

commit dd91b45e2ba6c07e9ee6455ad88b26e846efa63f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 29 15:13:31 2013 -0700

    Can now use the F90 omp_module from the C++/Fortran side of things.

Src/F_BaseLib/FParallelMG.mak

commit 6bd4e0602e0d70a3c4e862195982aee78f18b833
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 29 13:51:03 2013 -0700

    Added an 8-color GS nodal dense smoother for 3D that's OMP'd.
    It's only called when the number of FABs in the multifab is fewer
    than the maximum number of threads available. Otherwise we thread
    over the FABs in the multifab when calling the nodal dense smoothers.

Src/LinearSolvers/F_MG/mg_tower_smoother.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit 9a42bcd0b03dbfee237f95c641658476b7297980
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 29 12:26:36 2013 -0700

    I'm partially backing out some of my recent OMP changes.
    I want to use the old threading model over FAB boxes, and
    the new way of threading over multifabs only when the FAB box
    can't be threaded.

Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/mg_tower_smoother.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90

commit 0593d8b5f0ea755f41b8c0c536f65850821b9856
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 28 21:21:32 2013 -0700

    Fixed an assertion bug in initializing random number generator.

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 2bfcd50ab3adce68bc409a43240ecb95d2989b1d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 28 18:24:22 2013 -0700

    Back to old way of doing some OMP.  Nesting has too much overhead.

Src/F_BaseLib/multifab_f.f90

commit d0bc11c3e86d2a266f353cfeb46834cb864f5ca8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 28 16:50:47 2013 -0700

    Had a tmp array in BuildGramMatrix() dimmensioned too small.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 7aaac044187a802a0b96846300a86c0bebf610c5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 28 16:23:17 2013 -0700

    More uses of only_small_boxes().

Src/F_BaseLib/multifab_f.f90

commit 739dd1eeb9489ae06c16ee5a31c4d08c36840eb7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 28 15:40:12 2013 -0700

    disable nested OMP parallel regions by default

Src/F_BaseLib/boxlib_f.f90

commit aee52bc703dca26cc3cabdfb9cb40eef44e4ec8e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 28 15:22:12 2013 -0700

    Added only_small_boxes() which returns whether or not a multifab
    only has "small" boxes.  We use it to decide whether or not to
    OMP some loops.

Src/F_BaseLib/multifab_f.f90

commit 9b96165cca37586b4a8f647af14fa3c6334578d7
Merge: 7f3356929 fab13473f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 28 14:21:36 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7f3356929b184c2da25742fdf38801580f546bc4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 28 14:18:35 2013 -0700

    In mf_fb_fancy_*, turn off some unsafe OMP parallel regions for nodal
    multifabs.  In principle, the unsafe scenario could also happen for
    cell-centered multifabs that have overlapped valid cells.

Src/F_BaseLib/multifab_f.f90

commit fab13473f19041a3ba72c635f978fd47bd8c399e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 28 13:55:52 2013 -0700

    Only reduce the upper triangle of the Gram matrix.
    After reduction fill in the rest via symmetry.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 13859d215a3cbf5c92853c1712fb9eb17fbc7658
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 28 13:06:23 2013 -0700

    Only reduce the upper triangular part of the Gram matrix in the CABiCGStab
    instead of the whole matrix.  Use symmetry to fill it in after the
    allreduce().

Src/LinearSolvers/F_MG/itsol.f90

commit 2bfd7365f10d239af0f5cabb7c940713e1c1ec41
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 28 11:25:04 2013 -0700

    Some OMPing.

Src/LinearSolvers/F_MG/ml_solve.f90

commit ceed66499769a741a9853bb552d95834590700fb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 28 10:22:34 2013 -0700

    Remove boxarray_boxarray_diff() and its synonym boxarray_complementIn().
    Force people to use layout_boxarray_diff().

Src/F_BaseLib/boxarray_f.f90

commit 8b3347f5d6570bdb66d902c5e20808e4aa33e666
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 28 10:22:16 2013 -0700

    Use layout_boxarray_diff() instead of boxarray_boxarray_diff().

Src/F_BaseLib/make_new_grids.f90

commit c938d060a945607363bfaae49fb2cdb22a4d13e2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 28 09:11:48 2013 -0700

    OMP over call to ml_interface_[123]_crse() that include calls to
    layout_get_box_intersector(). Not sure what I tweak exactly to make
    this work but I'm going with it.

Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit 9b002d3c92d26ad5f038ca6a501f965b476912a8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 28 09:11:13 2013 -0700

    Further refinement of critical region placement for layout_get_box_intersector().

Src/F_BaseLib/layout.f90

commit 103884c33d528173d2486b92959f04477b0bdbf2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 27 18:40:25 2013 -0700

    Refined the critical area in layout_boxarray_diff().  I'd really like
    to understand why I can't call layout_get_box_intersector() directly
    in an OMP loop.

Src/F_BaseLib/layout.f90

commit ab16587a4f3fdee823249e2a68c6110320bb077b
Merge: b60bd36a2 0ee9eb1a3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 27 17:52:53 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b60bd36a258302346e4763633bfeb17679be60ac
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 27 17:52:13 2013 -0700

    Removed some OMP loops in the multifab_sync routines.

Src/F_BaseLib/multifab_f.f90

commit 0ee9eb1a3e9ddab2faaa790026ee07b5c79794ec
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 27 16:56:41 2013 -0700

    Fixed bug I recently introduced.

Src/F_BaseLib/multifab_f.f90

commit 14e6d30a23f1f5c992f7484c44b95267434fe387
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 27 13:40:40 2013 -0700

    Moved critical section to inside of layout_boxarray_diff() instead of
    around it.  I still don't understand why layout_get_box_intersector()
    isn't thread-safe.

Src/F_BaseLib/layout.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90

commit a2edf6c3cb62bb37cb74a4998d3019896fc392f2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 27 11:11:18 2013 -0700

    Made some internal layout routines much more efficient for large boxarrays.

Src/F_BaseLib/layout.f90

commit 0ceee12536c7d2b9f1154d1949d5d6c390267c77
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 27 10:34:01 2013 -0700

    Added layout_boxarray_diff().  This is a much more efficient version of
    boxarray_boxarray_diff().  Use this in place of the latter, which I'll be
    removing soon.

Src/F_BaseLib/layout.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90

commit 8eccbdb32ad09dd76729df699c6ea2eaf82e1c27
Merge: f09a25794 957d48a62
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun May 26 18:26:17 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 957d48a6244f0ca42d89f05df26e0c19a6b86eb2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun May 26 18:06:07 2013 -0700

    Fix typo.

Src/LinearSolvers/F_MG/itsol.f90

commit f09a2579485f329273714a1f0ed27a761cb81008
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun May 26 10:39:01 2013 -0700

    Moved most of the OMP for MG over the FAB in a multifab.  This turns out
    to be a big win.  We do a lot more calls of the smooth() and apply() on
    very small boxes.  And as problems get bigger this will only increase.
    It doesn't help the extreme case (much) where you only have one grid per
    MPI process, but for multilevel problems where you almost certainly have
    multiple grids per MPI process it's a clear win.

Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/edge_restriction.f90
Src/LinearSolvers/F_MG/mg_tower_smoother.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90

commit 3eaa6724124c4d4c587290146aa70c875e1e6de1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun May 26 10:22:54 2013 -0700

    Fixed typo.

Src/F_BaseLib/multifab_physbc.f90

commit 7b69628394474045c9f7b0d0583c930da0281d07
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat May 25 22:09:53 2013 -0700

    Some more OMPing.  I'm lifting OMP loops out of simple routines and
    writing loops around nfabs() or nboxes() instead in cases where the amount
    of work to do in the original OMP loops is small.

Src/LinearSolvers/F_MG/cc_interface_stencil.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/nodal_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_mask.f90

commit 50933c9e21a82808e78d3a8ab0a14d686476693d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat May 25 20:19:39 2013 -0700

    More OMP polishing.

Src/F_BaseLib/multifab_f.f90
Src/LinearSolvers/F_MG/itsol.f90

commit cd1ac4699d34169866260bfc724a1bf6e31af884
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat May 25 20:18:59 2013 -0700

    Make the memory statistics stuff thread safe using critical regions.

Src/F_BaseLib/bl_mem_stat.f90

commit a55b857e3c1497de08f590d3fbf25e22315a1d7a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat May 25 19:09:20 2013 -0700

    Don't OMP the interp routines.  Instead OMP over all the typically small
    grids in routines like fillpatch, make_umac_grown and fill_ghost_cells.

Src/F_BaseLib/create_umac_grown.f90
Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/interp.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90
Src/F_BaseLib/multifab_physbc.f90

commit dddb059e8f619649ede8c7b59e82ac4a0904ccb8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat May 25 11:29:05 2013 -0700

    Don't thread dot() or saxpy(); they're mostly used on really small boxes.

Src/F_BaseLib/multifab_f.f90

commit b5f7f9270751d943346d2eb0fedbe4ec20364de0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat May 25 10:23:45 2013 -0700

    Tweak to CABiCGStab.  Needed to fill both components of "ph" with "uu" at start.

Src/LinearSolvers/F_MG/itsol.f90

commit e7015baec104ec762ac455c9c378a2c53262d42b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 24 15:06:57 2013 -0700

    Removed some OMP loops that were effectively nested.

Src/LinearSolvers/F_MG/itsol.f90

commit 1dc821139326d539ee61e48a87ce9124c300284f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 24 14:46:25 2013 -0700

    OMPing across FABs instead of within FABs on MG routines that often use
    small boxes.

Src/LinearSolvers/F_MG/cc_restriction.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/coarsen_coeffs.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/nodal_restriction.f90

commit f051c8d570c434a77e340f1fdd34e9a3597ffe08
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 24 14:45:20 2013 -0700

    OMP'd a loop.

Src/LinearSolvers/F_MG/mg_tower_smoother.f90

commit 5a7bb4a22b2acff96d69727e6b54fa2de14ddbba
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 24 14:33:34 2013 -0700

    Added an IF directive to an OMP loop.

Src/LinearSolvers/F_MG/cc_stencil_apply.f90

commit fd476bc9e1a701c1fd1dc6eac0d11121e664136c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 24 14:04:50 2013 -0700

    For things used in the bottom solver I'm now OMPing over FABs not within
    the very small FABs.

Src/LinearSolvers/F_MG/itsol.f90

commit fa273ae45560affce1098e077f9d15d48b0257cd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 24 14:03:27 2013 -0700

    Did some more OMPing in things like the copy()s in FillBoundary() and such
    places.  Also, for things like saxpy() that are primarily used in the
    bottom solver, I'm OMPing over the FABs in the MultiFab, not across the
    FAB, which could be very small.

Src/F_BaseLib/multifab_f.f90

commit d0f13c679e502b4d1051c4db573a7cbb1e72a9de
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 24 09:14:52 2013 -0700

    Added a critical section around the call to init_box_hash_bin().

Src/F_BaseLib/layout.f90

commit 415fc462245427d81c39858d8197120b71127712
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 17:03:28 2013 -0700

    OMP's part of BuildGramMatrix().

Src/LinearSolvers/F_MG/itsol.f90

commit 0a529046c43bd807ae82177ed7428245d61a20ab
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 16:19:14 2013 -0700

    Call itsol_apply_stencil() on pp & rr together in the CA algorithm.
    Cuts out half the fill_boundary() calls.

Src/LinearSolvers/F_MG/itsol.f90

commit 116ad24495325c69a7dcddebbf98c72d84c866ce
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 15:44:46 2013 -0700

    Some OMP loop polishing.

Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 65d4dd0ab4b1f6a93073c70452f97be8fdfca000
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 15:15:39 2013 -0700

    Put some small arrays on the stack instead of the heap.
    Polished up some of the OMP loops.

Src/LinearSolvers/F_MG/cc_smoothers.f90

commit 51a7d8b9c27dbaa7c69ea10eb88d3871b5655353
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 14:24:43 2013 -0700

    Removed some unnecessary setval()s.

Src/LinearSolvers/F_MG/itsol.f90

commit ab4ff4202538713305acb34ba1f7aa74809d2890
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 14:05:53 2013 -0700

    More cleanup.

Src/LinearSolvers/F_MG/itsol.f90

commit 50d342aa1e81201c36593659988453d3aa1ff30a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 13:28:10 2013 -0700

    Some cleanup.

Src/LinearSolvers/F_MG/itsol.f90

commit d79268b2f9d984bc740ba43d1af170ce40c66117
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 13:01:11 2013 -0700

    Added is_an_inf() and is_a_nan() routines for checking single double values.

Src/F_BaseLib/fab.f90
Src/LinearSolvers/F_MG/itsol.f90

commit 558b1e9d780c919d99764e7b7b741e1c447eca4a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 12:51:38 2013 -0700

    Made BuildGramMatrix() a contain'd routine.

Src/LinearSolvers/F_MG/itsol.f90

commit b66969e46133573e41882386bbd27c5f0d4395ae
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 12:21:37 2013 -0700

    Integrated in isinf() stuff.

Src/LinearSolvers/F_MG/itsol.f90

commit a46f509259096b66400ec384828bb8f3a0df0451
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 12:09:32 2013 -0700

    Added val_is_nan() and val_is_inf() routines.

Src/F_BaseLib/fabio_c.c

commit b0519ceeaa9cd6006bef959bd932b90349c669e9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 10:54:29 2013 -0700

    Elided some multiplies via strategic use of parentheses.

Src/LinearSolvers/F_MG/nodal_restriction.f90

commit e0e21c182c7b5dfcea422e9ee6206492ea7e3378
Merge: bf8310278 4982ee7de
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 16:13:09 2013 -0700

    Merge branch 'CA'

commit 4982ee7de76efa624fe329606918cfceabcaa1d3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 16:08:17 2013 -0700

    Fixed bug I recently introduced.

Src/F_BaseLib/multifab_f.f90

commit e31da1fab01be2a02f5be93b1a3840266e681707
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 16:02:53 2013 -0700

    More cleanup of unused formal subroutine parameters.

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90

commit bf8310278e26a5319ec924d04c53071aa45e75bd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 21 15:42:21 2013 -0700

    Fixed the cc wrapper and removed the memory print statements.

Tests/LinearSolvers/F_MG/cc_multi.f90
Tests/LinearSolvers/F_MG/nodal_multi.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit cb4ff4b2affe1b8bfd0e6e51e221927b8b260f8c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 15:30:37 2013 -0700

    Cleaned up some unused formal subroutine arguments.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit dab91a7cf951486c21bdfeebee73e4f5b8e7c8e8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 15:21:09 2013 -0700

    Removed the unused "uu" argument to itsol_converged().

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90

commit f7dba8978fe382f4679b5f8fb2483a08e32e81ef
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 15:16:13 2013 -0700

    Some more cleanup.

Src/LinearSolvers/F_MG/itsol.f90

commit 189860aa227467a258b7b5f72fd4ee4253fcb239
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 15:01:05 2013 -0700

    Seems to work; at least for a simple nodal solve.

Src/LinearSolvers/F_MG/itsol.f90

commit 0034acec085a13e3ad118016e73f0d23e072ea17
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 14:46:24 2013 -0700

    Still working on CABiCGStab.

Src/LinearSolvers/F_MG/itsol.f90

commit 744b602aa312c748e1961279b6129d87dc656fff
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 13:56:33 2013 -0700

    Yet more progress on CABiCGStab.

Src/LinearSolvers/F_MG/itsol.f90

commit 0c49cfeb6313b7d2007383794dfc6763a8638e1e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 13:01:36 2013 -0700

    Added a optional args nodal_mask and local to multifab_dot_cc.  Now
    multifab_dot_c() and multifab_dot() both call that routine.

Src/F_BaseLib/multifab_f.f90
Src/LinearSolvers/F_MG/itsol.f90

commit 98088be68b1678264f1c3cb1ec5125358be021d9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 11:21:39 2013 -0700

    Some work on building Gram matrix.

Src/LinearSolvers/F_MG/itsol.f90

commit 7b741b03a9d9f67ffd6b35f917ca193bec609dde
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 10:19:25 2013 -0700

    Got "PR" filled. No way to know whether it's right or not yet.

Src/LinearSolvers/F_MG/itsol.f90

commit 432433d65a3235f32cf58e42abff85ea2ffebee1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 09:27:14 2013 -0700

    Elided some more reductions.

Src/LinearSolvers/F_MG/itsol.f90

commit 10a082decd6fd58b85aa9c2a0cdb07669d79a0cf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 08:58:14 2013 -0700

    Some cleanup on the way ...

Src/LinearSolvers/F_MG/itsol.f90

commit f3fb9d8269858dd27d532658228f90f27d9beb3b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 20 13:34:33 2013 -0700

    Some cleanup of DGEMV().

Src/LinearSolvers/F_MG/itsol.f90

commit d2eecbdb801945d7b2f73d1d228c9548f4a35020
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 20 13:28:48 2013 -0700

    Merged in slightly simlified version of the BLAS DGEMV() matrix-vector multiply routine.

Src/LinearSolvers/F_MG/itsol.f90

commit ff3571c6512ee121ba7e8f2c82f67b594a330bce
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 20 11:28:19 2013 -0700

    Added SetMonomialBasis().

Src/LinearSolvers/F_MG/itsol.f90

commit b594672c0d91f22e39871049ec3ebd68a6e2530b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 20 11:06:35 2013 -0700

    Still plugging away at CA algorithm.

Src/LinearSolvers/F_MG/itsol.f90

commit 47cf7f234dc452cfbd3956b8b84d9c2b7d2bc0fb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 20 10:50:14 2013 -0700

    Yet more work on CA bottom solver.

Src/LinearSolvers/F_MG/itsol.f90

commit 8e0acc7d076a19e0d850d1999c75cf53ad58f6c9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 20 09:48:29 2013 -0700

    Just getting started with CA BiCGStab algorithm.

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit aff94e0367cdee4d4fdf896c4f62c6eb004e5f54
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 17 16:19:12 2013 -0700

    Added BL_PROFILE() calls around MPI_Alltoall and MPI_Alltoallv in
    CollectData().

Src/C_BaseLib/FabArray.H

commit 45be522aeb1d82f3e21766a39706cf28780b7d84
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 17 10:34:19 2013 -0700

    Used an OMP region instead of sequence of parallel do loops.

Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90

commit 3ab12cab946f3e0d6df32b2e05f79e0d9a7fbbfc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 17 10:22:50 2013 -0700

    Removed some divisions.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit f126c77f7e052a52e7efb51167006cc93d318ebf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 17 09:59:39 2013 -0700

    Some OMPing and code simplification.

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit f2d59f01ed42b574d5236734cb39d12ff85e3468
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 16 22:12:49 2013 -0700

    More OMPing.

Src/LinearSolvers/F_MG/nodal_interface_stencil.f90

commit 88eda120b51b19da6d05cec6f699ceb793a5c738
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 16 21:09:31 2013 -0700

    Some OMPing.

Src/LinearSolvers/F_MG/nodal_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90

commit 081e2f273f0049e756543272c9af25887bfee00e
Merge: 2d6785e76 a90167a62
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 16 20:19:56 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a90167a62f76f7f568ad83e836513f49ebb8940f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 16 19:15:57 2013 -0700

    This is a cleaned up version that appears to work, for the nodal dense
    stencil in 2d anyway (using inputs.simple)

Tests/LinearSolvers/F_MG/GNUmakefile
Tests/LinearSolvers/F_MG/cc_single.f90
Tests/LinearSolvers/F_MG/inputs.simple
Tests/LinearSolvers/F_MG/main.f90
Tests/LinearSolvers/F_MG/nodal_multi.f90
Tests/LinearSolvers/F_MG/nodal_single.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit 2d6785e76234d850a19b85955e387497cdb79574
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 16 15:44:51 2013 -0700

    Regularized some constants in the code.

Src/LinearSolvers/F_MG/nodal_interface_stencil.f90

commit 6b603fde54703ad38c5882d09b29c2dae846b413
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 16 14:30:31 2013 -0700

    Removed some divides.

Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_newu.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 282f1b267bbf99b53a6c58bb3896cf1b3ae245b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 16 12:25:40 2013 -0700

    added functions to reset random number seed

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 01121c8ac4c4c90a99b7fc33e20c4a2fb06255cc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 15 14:11:31 2013 -0700

    Some code cleanup.

Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit d3493605bff62e346e25643ee82b38d70b9f4a18
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 15 13:34:33 2013 -0700

    Now can print out solve time for tensor solve.

Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit 1f04c3098c011e28a57c7de71cdc40d7220a3d26
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 15 13:34:21 2013 -0700

    Tweak to output.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit c68cc3c711f24a9f75c6fe4464f94b62f24d0926
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed May 15 09:50:28 2013 -0700

    Add zmq_suffix and hdf_suffix.

Tools/F_mk/GMakedefs.mak

commit 46c4cab4ff7f33c12244435ce468a6c602e0946d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 14 14:14:10 2013 -0700

    PGI does not like to have threadprivate as the last line in a class definition

Src/C_BaseLib/Utility.H

commit 75cc3f48c5986f5f11804c92e2be573236d18a9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 14 12:09:57 2013 -0700

    made changes because PGI is picky about where threadprivate directive is put.

Src/C_BaseLib/Utility.H

commit 22b9e1e1a9c680d0723dbfd8f6eb88e35d9a8129
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 13 17:53:10 2013 -0700

    added functions to return the size of the random number generator state

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 56364e863f848c0448064512ca4ea79f35e8369f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 13 12:28:50 2013 -0700

    Unpacked some "array" assignments so I could OMP the loops.

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 082e05b561ca9f53bcb7203b40a70c389ac7d1a7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 13 12:27:20 2013 -0700

    Removed unused variable.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 000b4e454960b6f6161f58cab9a292bc248c1c81
Merge: 967f2f329 d0fc0f62e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 13 11:26:36 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d0fc0f62e2708bf1d028bf5b8f9e0912b7485fe4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 13 11:12:58 2013 -0700

    minor changes to the initialization of random number seeds

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/Utility.cpp

commit 967f2f329eec4d0272a0017c49868d3c9e82b26b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 13 10:58:48 2013 -0700

    More MPI_Allreduce() elimination/reduction.

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 63971e4b334f6d10b66212694f67f17cdd1779ad
Merge: 29df26d59 d1fa3ab08
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 13 10:58:29 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d1fa3ab0838beb4e459fe6cf44910fe4cb4f96b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 13 10:55:09 2013 -0700

    made random number generator thread safe

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 29df26d597d0bf12edef02d49455ab12eaad6499
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 13 10:11:02 2013 -0700

    Little more OMPing.

Src/LinearSolvers/F_MG/cc_stencil.f90

commit affac169ecf00ce5d01649d40a4b0c2b63e7b4e6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 13 10:02:10 2013 -0700

    For stencil_norm and max_of_stencil_sum we thread on fab boxes
    not within fab boxes.

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 0501a99d7c790f1f0a7479235f6c09b410533b2a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 20:35:59 2013 -0700

    Simiplification.

Src/F_BaseLib/fab.f90

commit 380fa6291f9d7554ad3a0c0a232ecd8191aadb40
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 20:35:26 2013 -0700

    Fixed a bug I introduced earlier.

Src/LinearSolvers/F_MG/cc_stencil.f90

commit d476ec557fbc326cebe5db2eb6b1a0159846b950
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 20:10:03 2013 -0700

    OMP'd max_of_stencil_sum().

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 7d805b06a4617a9b51d4769b5d038cfe8a0f480c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 19:49:09 2013 -0700

    Threaded BuildGramMatrix() except for the reduction.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 91390572b51d0de91d0a72ecc65cba8959a2c381
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 15:30:24 2013 -0700

    Tad bit of refinement.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_norm.f90

commit ddad0537023c264e921db784f021529397fc58d3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 14:19:44 2013 -0700

    Elided more reductions.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 5726458df6f87089297c191f34990fa47c5d1511
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 14:19:17 2013 -0700

    Added optional "local" flag to max_of_stencil_sum().

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 9a106d613dc0b22b6f2c63dad070cb82c50af237
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 13:39:29 2013 -0700

    Yet more parallel reduction elision.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 65f57a7a32e253436740541255b64c0e20ee4582
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 13:31:14 2013 -0700

    Some parallel reduction elimination.

Src/LinearSolvers/F_MG/mg.f90

commit 8d70c47a39a70746bb3da284da9349d6f1986e8d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 13:30:11 2013 -0700

    Added optional "local" flag to ml_norm_inf().

Src/LinearSolvers/F_MG/ml_norm.f90

commit 3a84d385e331ba9c2d181140e37566c54f57d662
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 10:47:57 2013 -0700

    More debugging & performance analysis output.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 585e1f3b938fb9c6107441865ce43d76ac148395
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 9 22:40:59 2013 -0700

    Elided some global reductions.

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit fa27ae34a772e459f5dcde95c20d52a5be27572c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 9 21:50:46 2013 -0700

    Now can print out the multigrid time and accummulated bottom solver times.

Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 683d7656cb817b63af59a4d4e20d6ee53ccf8833
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 9 17:21:51 2013 -0700

    Removed multifab "sh" from BiCGStab; reuse "ph" instead.

Src/LinearSolvers/F_MG/itsol.f90

commit 152df4fc1186e8039f29f737ac69088529dc813f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 9 14:50:03 2013 -0700

    Some cleanup and code simplification.

Src/LinearSolvers/F_MG/itsol.f90

commit c0e4a8ee21694b75c2d4a9b3b6d889b12c662b64
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 9 14:20:43 2013 -0700

    Elided a few more reductions.

Src/LinearSolvers/F_MG/itsol.f90

commit 9ae2a658a3701902c5efc8f8b74b6f695ef02bb6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 17:31:38 2013 -0700

    added reducelonglongsum to non-MPi build

Src/C_BaseLib/ParallelDescriptor.cpp

commit deb55b69b26a3c21e14ee27cd5d32059cff185bb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 17:22:51 2013 -0700

    added -lmpich back

Tools/C_mk/Make.mpi

commit 972f4cc5bc4fbb76c8819565f73331d68eb90949
Merge: 4369b5b01 a4d54e6c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 16:24:22 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4369b5b0122ddd2dc02f45cf50df0c88906ad1f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 16:21:05 2013 -0700

    Added long long to Mpi_typemap.
    
    Use long long for total number of particles in some functions.  Some
    were not updated because it would require more significant changes.

Src/C_AMRLib/Particles.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ccse-mpi.H

commit a4d54e6c46c8f09f0841cce4114542965252654d
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed May 8 19:20:25 2013 -0400

    force double precision plotfiles + other changes

Tools/RegressionTesting/Maestro-tests.ini

commit 9bbb335719e1486f9ed67e5483ebccdd42fbae4d
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed May 8 19:19:57 2013 -0400

    ok -- for real now...

Tools/RegressionTesting/testnew.py

commit ead14f52c53ec177f4609267e49ee714623bdb4b
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed May 8 19:03:57 2013 -0400

    self -> suite in the enw parameter

Tools/RegressionTesting/testnew.py

commit d11fbbcbdef25583dabb895573062fbe066c8ee1
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed May 8 18:56:36 2013 -0400

    add globalAddToExecString argument to allow a runtime option to be
    appended to all jobs.  For Maestro, e.g., this is useful for
    forcing all plotfiles to be double precision via:
    
    globalAddToExecString = "--single_prec_plotfiles F"
    
    also fix a bug in the recent git updates that didn't work with the
    external build directories.

Tools/RegressionTesting/testnew.py

commit 3568310fe0f8c03ac73a465393938984137bff8d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 8 14:57:09 2013 -0700

    Increased SSS_MAX from 4 -> 6.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 0e08aa885ca39150a9f6e0257ca3a9a56d85127b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 8 13:51:32 2013 -0700

    Added some more verbose output.

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 45b6e025945915d083e1baf8a51333a67e38e179
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 8 11:19:29 2013 -0700

    Added option variable_SSS which implies we "telegraph" the outer
    CABiCGStab loop from 1 -> SSS_MAX.  This is on by default.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit bfce34457565d76321f3c51d2d348b3b823282a6
Merge: 55c0e55e8 ac1b3a666
Author: vince <vebeckner@lbl.gov>
Date:   Wed May 8 10:01:24 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ac1b3a666c086b3818de02d55458747fd0cf240a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 7 15:31:42 2013 -0700

    Some cleanup and improved comments.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 86ac79cda1698b5fe2e2d4d5ead32fab1aa3aabb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 7 14:58:34 2013 -0700

    Changed some of my verbose output.
    No longer try and calculate the norm_inf(r).
    Just go with the L2_resid as calculated by the algorithm.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 854dc7022069fdf61f1db0c380f2fb468a36b33d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 7 14:37:49 2013 -0700

    Merged in Sam's latest changes.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 55c0e55e84ca0fda2a07284f4eed760ec5043f21
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 7 14:35:42 2013 -0700

    prof def.

Tools/C_mk/Make.defs

commit e95bea145a9d7854375ba3d767701e09109b79c6
Merge: cf424f41d d2852871a
Author: vince <vebeckner@lbl.gov>
Date:   Mon May 6 12:25:06 2013 -0700

    Merge branch 'master' into commprof

commit 2a8c6bce89e00d09efb79c952257f115d8561ea5
Merge: f98256641 a29472d8d
Author: Chris Malone <malone@ucolick.org>
Date:   Mon May 6 11:43:36 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit f982566413d1b24ba90c61f5a0742ce3bd622e59
Author: Chris Malone <malone@ucolick.org>
Date:   Mon May 6 11:41:14 2013 -0700

    simple program that calls the make_rates routine for a network, and
    builds a plotfile of the local rates based on the thermodynamic state
    
    this assumes the network is structured similar to that done in AstroDev/networks/rprox

MAESTRO_xrb/GNUmakefile
MAESTRO_xrb/frates.f90

commit cf424f41df7cc0a5b90492debabf2fc55dcb4581
Merge: be86c1c86 68e4f73de
Author: vince <vebeckner@lbl.gov>
Date:   Mon May 6 11:28:04 2013 -0700

    Merge branch 'master' into commprof

commit d2852871af7aecd88d8f504a3dbb591c1cae49a0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 6 11:25:38 2013 -0700

    Still more include "file" -> include <file>
    Thought I had all of'm earlier.

Src/LinearSolvers/C_CellMG/CG_1D.F
Src/LinearSolvers/C_CellMG/CG_2D.F
Src/LinearSolvers/C_CellMG/CG_3D.F

commit be86c1c8686d09c383817db97d56e0961ef67144
Author: vince <vebeckner@lbl.gov>
Date:   Mon May 6 11:24:07 2013 -0700

    profiling doc.

Docs/Readme.profiling

commit 6d4c5dd163c4a60ccf6229c45cdf396a97d15277
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 6 10:40:46 2013 -0700

    A little code rearrangment.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 68e4f73ded6ed4f777c069814d030dfbba1e9746
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 6 10:07:34 2013 -0700

    The "S" in the CABiCGStab is now an input variable.
    It's currently limited to be in the range: [1,4].

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit b7d4bafcccf525cfce05d0aff8c2fadab76059fd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 3 16:05:17 2013 -0700

    Cut the number of apply() calls in CABiCG by two by doing each of the
    powers of p and r together in a single call instead of one call for each
    of the powers of p and r separately. Mostly this cuts down on
    FillBoundary() calls and should be a win in parallel.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit a0b8266219cde444f7fb8d9cdd2d7cf95ee56901
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 3 16:03:46 2013 -0700

    Removed a number of num_comp==1 assertions.  I wanted to be able to call
    apply() with more than one component.  Appears to work.

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit efeaf0671913329354714201d781dda83a092977
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 3 14:17:53 2013 -0700

    Changed some ifndef clauses to the more natural ifdef.

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit bcb36eb3df770f3d8a9d70dd46bf01374f7d1dc6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 3 13:58:58 2013 -0700

    Some more work on convergence criteria for CABiCG.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 2d4630b331ac3426e1df07771d47e1e5b502aa2c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 3 09:56:17 2013 -0700

    Be a little more careful about convergence tests.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit feda545f762b5f95d730ebb40d0266ba25956ba8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 3 09:05:18 2013 -0700

    Removed some unneeded code.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit ebb69b5c6d6594d50f974a14a4b0460b5d01d710
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 2 19:57:04 2013 -0700

    Some refinrements and bug fixes.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit a38faca3c9020a1803203d10a92347ae91525090
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 2 16:06:04 2013 -0700

    A little code rearrangement.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit a52da0ecd005f09dfeba4e86830b3e6dd557956a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 2 15:39:28 2013 -0700

    Some work on making CABiCGStab output like BiCGStab output.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit d5dc20de4928011bd0a9030455e05aedc1be2101
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 2 14:19:33 2013 -0700

    fix for serial.

Src/C_BaseLib/Profiler.cpp

commit 22ab0d2edbfd4f3b9988e772ec4fbf2266a551d0
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 2 14:09:20 2013 -0700

    added mf test code.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit f4c41047ad8d6b77c56cda2ef4c9b901b15b4d21
Merge: 2f5baa126 1631f8df5
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 2 14:08:17 2013 -0700

    merge issue.

commit ea2602cccb8a26594aec0e2ea590d0a913cb2b3a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 2 14:06:15 2013 -0700

    Added some profiler calls.  Seems to work in parallel.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 2297a7a2583949b82dabb48093de94917158dd94
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 2 12:49:54 2013 -0700

    Looks to be more-or-less working!

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 7c03932be11cc40600b5174d1b155b240d50dc8d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 17:20:46 2013 -0700

    Getting closer ...

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 979c34ea079a9da14e1c6ff05ef061d4b6067b97
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 16:40:44 2013 -0700

    Getting close to having something testable.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 9788e6d4bc7b6acd1e6f9178f7b38b9aac8ca053
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 16:12:05 2013 -0700

    Don't think I had BuildGramMatrix quite right.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit b537a44e3f2f95a28c58939b359c8c0ed25eece9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 15:39:59 2013 -0700

    Added BuildGramMatrix() code.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 69802194d69acaa4022f4e888f07bcd040129450
Merge: 3c8400801 8525cefd5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 14:51:55 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3c84008012765703453826cc600122f72796a4e3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 14:51:41 2013 -0700

    More work ...

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 84e6ed32e1fbddec6a7af1450aeffd0c505ac467
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 14:42:24 2013 -0700

    A little more progress.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 8406d0bf3529a3dc266f4baf40033e1c3c1c6a59
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 13:52:41 2013 -0700

    More work on CA BiCGStab.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 8525cefd53e37b161a48de4a975ef3fed810b96f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 1 13:37:16 2013 -0700

    added ReduceLongLongSum so that we can safely sum up big integers

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 674a50f2a4f67e5eccbac890acc6136a1ac331f5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 1 13:07:51 2013 -0700

    Changes for Blue Waters Cray compiler.

Tools/C_mk/Make.Linux

commit 00f35e832c7bc0fa8a226be9e5a6859e0db92936
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 12:58:24 2013 -0700

    Some work on CA BiCGStab.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 2010de83d487184f470cd5c80155558886f77c4d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 12:24:53 2013 -0700

    A little cleanup.

Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit b1b0de8e2f75c14eef18e34b98d837a4a54824dc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 11:13:21 2013 -0700

    Some setup to try & implement a communication avoiding BiCGStab solver.

Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 9380a35c3116f7eadf28faf69d359d5e019ca456
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 11:12:48 2013 -0700

    Removed stuff for setting default CG solver.
    It's now only in one place: in the CG code itself.

Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit afa293fcaa781aa0313c69c465bfa1964eb8d245
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 30 14:40:46 2013 -0700

    Added optional argument verbose to ParticleBase::Reset so that we can
    turn off a print statement.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 7a6c5573acc3f504e6874210748cc855055733e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 30 14:19:03 2013 -0700

    Added latex file describing equations solved by Exp_CNS_NoSpec.

Tutorials/Exp_CNS_NoSpec/CNSEquations.tex

commit 1631f8df5816625e223e34adb9c7e00e6230db3c
Author: beckner2 <vebeckner@lbl.gov>
Date:   Fri Apr 26 13:42:11 2013 -0700

    new machines.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 2f5baa1269d51e3dfc9bfa2e78e832744d5aaeec
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 24 16:05:07 2013 -0700

    fixed ivLevel, ivLoc.

Src/Extern/amrdata/AmrData.cpp

commit aa937d5f640f707b6da5fdbcc8e4e179294c0a32
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 24 13:02:03 2013 -0700

    Added more functions for random numbers.
    
    In addition to the old Real BoxLib::Random() that returns a number
    belonging to [0,1],
    
    Real BoxLib::Random1() returns a real number that belongs to [0,1);
    Real BoxLib::Random2() returns a real number that belongs to [0,1);
    unsigned long BoxLib::Random_int(unsigned long n) returns an integer belonging to [0,n).

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 22a273535577c9f6989071031a7b11c7dd6bc852
Merge: 1c2b8ba58 f9ed13314
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 19 16:31:55 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1c2b8ba582abd5ee4a45662b12abcc1d62870572
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 19 16:24:05 2013 -0700

    Removed an unnecessary setVal().

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 5cc42a554764bc0cb08bf5f2f3b7d5bddc3de096
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 18 15:03:02 2013 -0700

    before/after call changes.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.cpp

commit f9ed133141970d6307b9e19e7c9b9e1827dde1de
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Apr 17 15:49:08 2013 -0700

    Add parallel_set_comm.

Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit f1508ce08bde62993d0a22ad954f058a64d40aaa
Author: vince <vince@garnet02.erdc.hpc.mil>
Date:   Wed Apr 17 14:21:37 2013 -0500

    garnet.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit cd446ccd68e322fc454994018025351d9e372178
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 16 11:02:31 2013 -0700

    Using subprocess for git-checkout to avoid warning being sent to
    stderr of shell.

Tools/RegressionTesting/testnew.py

commit f475723f000ffa59ea8076bf172299fbb33fcebb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 15 10:18:29 2013 -0700

    OMP'd some more loops.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 46f70385c6ca272b68fbb9c3e96ef64c76986f34
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 15 10:07:15 2013 -0700

    OMP some more loops.

Src/LinearSolvers/F_MG/cc_stencil_apply.f90

commit cd16624f2d84bb156d959d00938741f46b405585
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 15 09:48:37 2013 -0700

    Some rearrangement to enhance vectorization.

Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit b2d4ad552a90d70271b0935b64790bf139f92092
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 12 15:39:34 2013 -0700

    Added some "IF" clauses to OMP loops so that we ignore threading
    when the Z dimension is too small to yield useful work.

Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab_f.f90
Src/LinearSolvers/F_MG/itsol.f90

commit a7355407c639ab45555c6d702c8bbd8057193aba
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 5 13:33:09 2013 -0700

    beforecall.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit e905bb0c385b4e107d7d4ce5758997ebe09c393b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 4 15:13:35 2013 -0700

    Yet more replacements of divisions by multiplications.

Src/LinearSolvers/C_TensorMG/DV_3D1.F
Src/LinearSolvers/C_TensorMG/DV_3D4.F

commit d4f97207a4df35a9eaad4b21d391ddb0ef6211cc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 4 14:49:21 2013 -0700

    Replaced more divisions with multiplies.

Src/LinearSolvers/C_TensorMG/DV_3D3.F

commit 3b0bc2926e2f70756e82d740019364922630e2f4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 4 13:20:27 2013 -0700

    Elide another reduction in the "singular" portion of BiCGStab.

Src/LinearSolvers/F_MG/itsol.f90

commit 0bce69fd1e977ae24168490566c541684847d7a4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 4 11:25:16 2013 -0700

    Elided another reduction in BiCGStab by combining the reductions for
    two dot-products into the same call.

Src/LinearSolvers/F_MG/itsol.f90

commit c350825d8c62e18d91aef59952767348a39ae071
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 4 11:23:44 2013 -0700

    Added optional "local" argument to multifab_dot() to calculate only
    the "local" value of the dot_product.

Src/F_BaseLib/multifab_f.f90

commit 008b7618973e15e0bcafd9de6e42b4b425413383
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 4 10:51:21 2013 -0700

    Elide some reductions in BiCGStab.

Src/LinearSolvers/F_MG/itsol.f90

commit 14f1e672df6320eea860b338faea30d98988a1db
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 4 10:51:00 2013 -0700

    stencil_norm() now takes an optional "local" flag.

Src/F_BaseLib/multifab_f.f90
Src/LinearSolvers/F_MG/cc_stencil.f90

commit e6c0469433b77b1a05940ce7337dbde748d6aa2d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 4 10:05:43 2013 -0700

    Added optional argument "local" to norm_inf() so we can calculate the
    local value of the norm without doing the parallel reduce.

Src/F_BaseLib/multifab_f.f90

commit 4616685846173995e45e8f4117fe0805279aeba7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 3 16:16:50 2013 -0700

    Elided another reduction in BiCGstab by calculating the local values of
    two norms() and then reducing them together.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 735105b9b533d8319f38c450aca343290daf3723
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 3 15:28:27 2013 -0700

    More eliding of divides.

Src/LinearSolvers/C_TensorMG/DV_3D1.F
Src/LinearSolvers/C_TensorMG/DV_3D2.F

commit d920c3b85c029fea9cfe6c8fd43e771007db4eae
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 3 15:00:39 2013 -0700

    Replaced most divides by multiplies in apply().

Src/LinearSolvers/C_TensorMG/DV_3D1.F

commit ac33c28c5665ad3c37336ef5d8de6fb2e25b2b46
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 3 13:30:26 2013 -0700

    nfiles for headers.  smaller header files.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Profiler.cpp

commit 44daec6c9f47d3caf4cdfa2c37ff2c3e7558dd90
Merge: bab312e30 d9baef115
Author: Chris Malone <malone@ucolick.org>
Date:   Tue Apr 2 15:08:27 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit bab312e308b18b047056b0beeb2e3033cd91c450
Author: Chris Malone <malone@ucolick.org>
Date:   Tue Apr 2 15:07:41 2013 -0700

    UCSC pleiades --> hyades changes

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit d9baef115645e1626128a5c223ccf34832f74651
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 2 13:46:04 2013 -0700

    Yet more cleanup of unused variables.

Src/F_BaseLib/parallel_stubs.f90
Src/LinearSolvers/C_TensorMG/DV_3D2.F
Src/LinearSolvers/C_TensorMG/DV_3D3.F
Src/LinearSolvers/C_TensorMG/DV_3D4.F

commit bc330180d5ee531641ce6716efe63a68f6bf16cd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 2 12:11:26 2013 -0700

    Cleaned out some unused variables.

Src/LinearSolvers/C_TensorMG/DV_2D.F

commit 59128b2e6ced09433758bf7962958cc5829c5ee9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 2 12:10:47 2013 -0700

    Added -Wno-maybe-unitialized flag to [f,F]DEBF.

Tools/C_mk/Make.defs

commit c1a80caf85f3f4a1bcf7d7b54891495004db895a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 2 09:10:22 2013 -0700

    Now gcc, g++ & gnu are equivalent when used as COMP.

Tools/C_mk/Make.defs

commit 5558da5748520ef743cc892c42db9a7b6169b7c1
Author: beckner2 <vebeckner@lbl.gov>
Date:   Mon Apr 1 16:40:33 2013 -0700

    fixed nfiles init.

Src/C_BaseLib/VisMF.cpp

commit d01971f54d6dc38d034608be941a0f6465801e2f
Author: beckner2 <vebeckner@lbl.gov>
Date:   Mon Apr 1 16:39:12 2013 -0700

    fixed init nfiles.

Src/C_AMRLib/Amr.cpp

commit 79deeb35afc617853928787601e8c167bfe9a197
Merge: 98d822a4e 36d111f2e
Author: jbb <jbbell@lbl.gov>
Date:   Mon Apr 1 15:07:19 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 98d822a4e2f996e1acfe882b3f6798d833b031c3
Author: jbb <jbbell@lbl.gov>
Date:   Mon Apr 1 15:06:56 2013 -0700

    fixed mpi path on mothra

Tools/F_mk/GMakeMPI.mak

commit c7c986a9c6704f25a6e3d63c6fc3714c30873e13
Merge: 7b60415aa bea384748
Author: beckner2 <vebeckner@lbl.gov>
Date:   Mon Apr 1 14:55:23 2013 -0700

    hera.

commit bea3847480c3284d9f5ea5c7948ad23afd6e63b8
Merge: fde2c3f61 36d111f2e
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 1 14:48:55 2013 -0700

    Merge branch 'master' into commprof

commit fde2c3f61fdf2bf2490d687c8b969f2a089171ce
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 1 14:47:45 2013 -0700

    tweak for waitsome.

Src/C_BaseLib/Profiler.cpp

commit 36d111f2e2d499fb4e5c86aaad533c7dc840816d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 1 14:08:39 2013 -0700

    A little cleanup.

Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/LP_3D.F

commit fe306cf69eba3be4d1660a696460fd2938b4d555
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 1 13:42:54 2013 -0700

    Elided one of the global reduction operations in the BiCGStab by doing
    the "local" part of two dot products and then calling one global reduction
    on the "pair" of values.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 7b60415aa1a88fb4cc9ffdfcb3d2faabdf15647b
Author: Vincent Eric Beckner <beckner2@hera840.llnl.gov>
Date:   Mon Apr 1 11:51:53 2013 -0700

    hera.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 1a563d14da6f8644638397fa9e34d47a4fda98bf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 1 11:11:31 2013 -0700

    Removed OpenMP stuff.  Not enough work in bottom solver to be worth it.

Src/LinearSolvers/C_CellMG/CG_3D.F

commit ccd7082165d17e5452b05dd2eefe4b92d6cc19cb
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 29 17:20:45 2013 -0700

    more support for send recv and nametags.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 8c92d23f96eb500c4074a3d42b7a517c45680623
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Mar 29 09:20:22 2013 -0700

    Changed many of the divides to multiplies for a modest speedup.

Src/LinearSolvers/C_TensorMG/DV_3D3.F

commit ad4ac342e975b83d1fb70203b2f3b233d7c0e24b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 20 16:18:04 2013 -0700

    improved flushing.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 8791cb85c8a26c2d7ab1f7cb213ec560ad59160e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Mar 20 15:59:49 2013 -0700

    Don't need -ftree-vectorize for gnu.  It's implied with -O3.

Tools/C_mk/Make.defs

commit 37eeb30dc74d19688efa5d72c15dbc13b43ef686
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 20 10:42:56 2013 -0700

    added more profiling.

Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/StateData.cpp

commit 6665c67d5d0868813df9eb0bacdbeb57b020e46a
Merge: 4ef6bf774 c88f2cd49
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Mar 18 14:18:23 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c88f2cd49459208e27100e9835808f52d10a1972
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 18 14:17:22 2013 -0700

    added -std=c99 to CFLAGS for gcc and icc ib F_mk

Tools/F_mk/comps/Linux_intel.mak
Tools/F_mk/comps/gfortran.mak

commit 4ef6bf77493dab05f3e79bf5dd51c324669b05d1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Mar 18 14:16:29 2013 -0700

    Turned on -std=c99 for both gnu & intel C compilers.  This allows the
    "restrict" keyword in C files; we want to add this in select places in
    our chemistry mechanism files as it leads to better optimization.
    Also, only for gnu, added the -ftree-vectorize option to the C optimization
    flags.

Tools/C_mk/Make.defs

commit bc3f5f901deb7409c0e7ea909d150bc2c31302b7
Author: vince <vebeckner@lbl.gov>
Date:   Mon Mar 18 12:50:41 2013 -0700

    more flushing.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 76b74d0293793d2388a4503417ea05603dc9ad0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 15 17:30:51 2013 -0700

    added vectorization to gcc in F_mk; if nothing breaks, we can add that
    to C++ part too.

Tools/F_mk/comps/gfortran.mak

commit d874380851c3f0109c4d2f0a58e1f1ba5e8efa37
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Mar 15 14:37:39 2013 -0700

    Changed the default optimization flags for Intel12 and Intel13 from
    "-O3 -ip -mp1" to "-O2 -ip -fp-model source -xHost".  This can be a
    big win for some codes.  On a MAESTRO test (wdconvect) my run went
    from 153 seconds -> 96 seconds with this change on edison.nersc.gov.

Tools/F_mk/comps/Linux_intel.mak

commit dd712ece83e9dc5b525f6221d99b81b811dbd356
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Mar 15 14:32:55 2013 -0700

    For Intel changed -fp-model precise -> -fp-model source
    Also added -xHost to optimization flags.

Tools/C_mk/Make.defs

commit 9cfd84c1f7379ee7ef90fca40d3fb3c97f0683b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 15 13:35:53 2013 -0700

    ifdef STDC99, add c99 support option to gcc and intel.  Note that pgi
    and cray now support c99 by default.

Tools/F_mk/comps/Linux_intel.mak
Tools/F_mk/comps/gfortran.mak

commit dcb4972adff853edacd09679eb2a6eac9d28ece3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 14 13:38:47 2013 -0700

    A little cleanup.

Tools/C_mk/Make.defs

commit 80bdc38e2c4f584ac7abf9a742e63c712516e922
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 14 12:56:37 2013 -0700

    Make sure C flags are same as C++ flags for gnu.

Tools/C_mk/Make.defs

commit 0bb9c429f4a21572d0cfe52746f3501c0a7bbb2b
Author: vince <vebeckner@lbl.gov>
Date:   Tue Mar 12 16:19:57 2013 -0700

    verified flushing, allow profiling without comm, named more barriers, cached times to header.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.cpp
Tools/C_mk/Make.defs

commit b990d85c9adf2d3723690882eec1e008afc8563e
Author: vince <vebeckner@lbl.gov>
Date:   Mon Mar 11 16:21:37 2013 -0700

    made call orders consistent.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit f3e6570c7ee4b5810d70941ac63a6c6ce8ce72cb
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 8 13:22:21 2013 -0800

    merged interfaces, added calls.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit a29472d8dfd7906fb74f85fdc2d00eab8e11f00a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 4 13:00:08 2013 -0800

    Option to dump a plotfile for errors in finite-difference fcompare

ffdcompare.f90

commit 4eb59f5a1dee502d0d1b836e6bb1f1234ce5159c
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 1 14:51:53 2013 -0800

    added tracking of reduction wait times.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 5381c7f30e54a84a334385f88a4763b951c9dbad
Merge: 566a141c9 52974d185
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Feb 28 13:31:30 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 566a141c963bd835c7f9737693069eff301b37ea
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Feb 28 13:31:24 2013 -0800

    Add profiling to multifab_saxpy_3.

Src/F_BaseLib/multifab_f.f90

commit 18779b057e7dbfc3cd0b5a0aafa713460cdebee9
Author: vince <vebeckner@lbl.gov>
Date:   Thu Feb 28 12:01:51 2013 -0800

    barrier changes.

Src/C_BaseLib/Profiler.cpp

commit 62a83c3b9d8ccb91ab34d2960df240852ea7cd7c
Author: vince <vebeckner@lbl.gov>
Date:   Thu Feb 28 11:24:38 2013 -0800

    more tags, reduced function parameters.

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 52974d185c6279a21d2dd61b1d9edf687250059d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Feb 28 10:22:01 2013 -0800

    cleanup of max_mg_nlevels.  also fixed the single-grid case, which was not allowing for a 2x2 bottom solve due to some messed up logic that was protecting us in the (unused to my knowledge) minwidth=1 case

Src/LinearSolvers/F_MG/mg.f90

commit 8bbe7e30f32f7941d7f35991b728b3b42705b366
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 26 09:08:23 2013 -0800

    Added "-fp-model precise" to the optimization options for both the C++
    and Fortran flags for Intel.  This fixes an optimization bug in the DME_jet
    problem on edison.  Weirdly, the default for Intel is to allow extensive
    floating point rearrangement during optimization.  The above option disables
    enough of that such that the problem appears to run correctly.

Tools/C_mk/Make.defs

commit b4d423c88a9768d239421439928725c24b577ec2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 26 07:21:39 2013 -0800

    A workaround to the tellp() bug we found on edison.nersc.gov.
    Hopefully it doesn't break anything else :-)

Src/C_BaseLib/VisMF.cpp

commit 51c883df928cd7216b777b5841b96ddb792e9532
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 25 13:37:14 2013 -0800

    fcompare for finite-difference results

ffdcompare.f90

commit 731b22279d0fb0f917a307f72d23854135161894
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Feb 23 17:19:02 2013 -0800

    Add GetParticleData access routine.

Src/C_AMRLib/Particles.H

commit 9deb2847018ed1e32df0576020644fd5a0ae9fcc
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Fri Feb 22 19:18:58 2013 -0500

    add -h fp0 to all the Cray optimized flags.  Experimentation on Titan
    has shown that this prevents strange compilation errors resulting
    in crashes in BoxLib.  This forces the compiler not to do any crazy
    optmizations that violate the floating point standard.

Tools/C_mk/Make.Linux

commit 3de72abfa656b5bfb23e5924ddd643443b25684f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Feb 21 16:49:10 2013 -0800

    A little cleanup.

Tools/C_mk/Make.defs

commit 09d454ea62292669fbddb59547ed947fd88a250b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Feb 21 14:58:35 2013 -0800

    Merged in GhostParticleID and VirtualParticleID and cleaned up
    CreateVirtualParticles() and CreateGhostParticles() a bit.

Src/C_AMRLib/Particles.H

commit 1c068b937e94ac3c94bb9026810586ffa3d4cc42
Merge: a9f35c7c6 75a5406c9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 20 12:54:05 2013 -0800

    Merge branch 'redistribute'

commit a9f35c7c6e7d09dfd37dc6ddf3036a2818cb8d92
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 20 08:38:53 2013 -0800

    Removed IF() qualifiers on OMP PARALLEL DO loops.  I recently found
    an example on edison where the presence of one of these qualifiers
    caused a compile to take 100x longer than when it's not present.
    I just don't think the compiler can be doing anything good/useful
    in that time.

Src/LinearSolvers/F_MG/cc_restriction.f90
Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/edge_restriction.f90
Src/LinearSolvers/F_MG/nodal_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_restriction.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90

commit d51e8c22051ee32646ca429b1bf8cc5ae3b627d2
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 19 17:36:57 2013 -0800

    added user filtering and name tags to separate parts of the code for easier communication analysis.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 4c75c8659529cf2c4394eea31d394d520d7f2a01
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 19 15:11:23 2013 -0800

    Got this stuff to compile again; it's been a while.
    Not sure whether it works or not.  Some of the stuff with the
    new way to specify stencils may require some modification.

Tests/LinearSolvers/F_MG/cc_multi.f90
Tests/LinearSolvers/F_MG/cc_single.f90
Tests/LinearSolvers/F_MG/nodal_multi.f90
Tests/LinearSolvers/F_MG/nodal_single.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit 6c33a16bafa01391f4e87a60d9edde4f09dc3fb0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 19 15:10:31 2013 -0800

    Added edison stuff to mirror hopper.

Tools/F_mk/GMakeMPI.mak

commit 052d256725fdd7a826d8788c4dbae8f7cc3a6e51
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 19 14:59:47 2013 -0800

    implemented flushing of the commstats.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit bc0e193844cef5aabe510bb79b76c2a178d70fb3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 19 13:58:14 2013 -0800

    Remove some COLLAPSE() stuff I recently added.  The Intel compiler
    on edison generates bad code.

Src/C_BaseLib/SPECIALIZE_3D.F

commit 7fe3ef6fde23bb2cc94e7a3b5715817dd1b0c74f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 19 12:35:13 2013 -0800

    Revert out all the recent OMP COLLAPSE stuff.  The lastest Intel
    compiler on edison (13.0.1) produces bad code.  Hopefully I can find
    a simple example that illustrates the bug to pass on to Intel.

Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab_f.f90

commit dfa81aac6c16efef3d3eacd63da1cd92619deea3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 19 09:08:15 2013 -0800

    Add -openmp flag for Intel C compiler when USE_OMP=TRUE.

Tools/C_mk/Make.defs

commit caef7a901564d19019494c8b805337250e8306e4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 19 09:04:41 2013 -0800

    Wrapped omp pragmas with ifdef _OPEN to shut up warnings when OpenMP is not enabled.

Src/F_BaseLib/fabio_c.c

commit bb57c9b81cc3b50112025696e30c9304664a326f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 19 08:18:11 2013 -0800

    Duplicated hopper stuff for edison.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 75a5406c9e2e453ad7e58677de0c28fea786c45c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Feb 16 21:19:27 2013 -0800

    Fixed bug in commit for case where boundaries aren't all periodic.

Src/C_AMRLib/Particles.H

commit 4178ef03779bc3946b49bb431b352d2acf2f1783
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Feb 16 19:08:13 2013 -0800

    Some cleanup.

Src/C_AMRLib/Particles.H

commit 2fbe6f14ee98b62c75f75dcd1854e0e0d2b7c25b
Author: vince <vebeckner@lbl.gov>
Date:   Thu Feb 14 15:25:14 2013 -0800

    named barriers, local message filtering, all/none filtering.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp
Src/C_BaseLib/VisMF.cpp

commit 51a920c36e22a5468c7270f0f569906a45b2f2f2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Feb 14 11:22:43 2013 -0800

    A little cleanup.

Src/C_AMRLib/Particles.H

commit c6d7f78568c39c7cc25370dd763f9c791a331c6b
Merge: e0268fede 766c05a90
Author: Chris Malone <malone@ucolick.org>
Date:   Thu Feb 14 13:44:55 2013 -0500

    Merge branch 'master' of https://ccse.lbl.gov/pub/Downloads/BoxLib

commit e0268fede151c9333cae64e1c397e4659f678f09
Author: Chris Malone <malone@ucolick.org>
Date:   Thu Feb 14 13:44:28 2013 -0500

    some cleanup and get this working with cce/8.1.3

Tools/C_mk/Make.mpi

commit 766c05a9008d6315d6f45eb20fd80ec325befb88
Merge: 2184e5753 4099ee3c6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 16:02:13 2013 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2184e5753d927ec4210c89314ad810a1a673c15e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 16:01:55 2013 -0800

    Made the destructor for ErrorRec virtual.

Src/C_AMRLib/ErrorList.H

commit 61d1bbe0b7e07d3ff6b9e4b8214d9ed6ca6b9168
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 15:53:24 2013 -0800

    Little more work on AssignDensityDoit().  Still needs testing.

Src/C_AMRLib/Particles.H

commit 3462886374a83200f2de381abfab22054da729f8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 15:14:08 2013 -0800

    More work on AssignDensityDoit().

Src/C_AMRLib/Particles.H

commit 4099ee3c6d16dc8709073da7d5fe7495c39abd18
Author: Chris Malone <malone@ucolick.org>
Date:   Wed Feb 13 17:33:08 2013 -0500

    generalize the fix for PGAS error for Cray versions >= 8.1.2

Tools/C_mk/Make.mpi

commit a1c576431d77856a43d5c51944d769c21ea9640b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 14:32:47 2013 -0800

    Some work on AssignDensityDoit() to use send/recv pairs instead of Alltoallv().

Src/C_AMRLib/Particles.H

commit 2b9bb0dfa4f3170151c51b8c940e922e92ab104e
Merge: 138819038 9c0a79140
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 13:07:35 2013 -0800

    Merge branch 'redistribute'

commit 9c0a79140c0a4749f4ace67d95c69d5891af6542
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 13:04:15 2013 -0800

    Merged RedistributeMPI() into AddParticlesAtLevel().

Src/C_AMRLib/Particles.H

commit 138819038ac8957e990591de3f6f6244977951e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 13 12:47:58 2013 -0800

    got around Cray compiler bug

Src/F_BaseLib/multifab_f.f90

commit bc29013aff6cd118760e197afeb44c1681de15d2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 12:25:52 2013 -0800

    Merged in RedistributeMPI().

Src/C_AMRLib/Particles.H

commit 07dc4c92ec454e69eec44b17eff9fb4fee3d15d8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 10:45:49 2013 -0800

    Finished Redistribute().  Now uses Send/IRecv instead of Alltoallv().
    AddParticlesAtLevel() needs to be redone as well.

Src/C_AMRLib/Particles.H

commit 83e71c3421988fbbfb34276300597b3db5148309
Merge: bf75c369d 9a5758554
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 12 16:52:13 2013 -0800

    Merge branch 'master' into commprof

commit bf75c369d40e2a165fd40444cb105a195d1774b2
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 12 16:51:10 2013 -0800

    some changes to the output format.

Src/C_BaseLib/Profiler.cpp

commit 4972f2a8b45a5521ffc9d7977672008e66618e91
Merge: d744b9519 a80712e76
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 12 11:03:52 2013 -0800

    Merge branch 'master' into commprof

commit d744b95195dd156e08ebc3686fd4492c8fde3286
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 12 11:03:35 2013 -0800

    more support for the output parser.

Src/C_BaseLib/Profiler.cpp

commit baf877ad6e7ff4d590663965c5a2c142b5f01343
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 11 21:14:25 2013 -0800

    Looking good.  Redistribute() now uses Send/IRecv pairs instead of
    Alltoallv.

Src/C_AMRLib/Particles.H

commit aa49f8c36763f910a0ec21b183e65bb27debda6b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 11 20:50:33 2013 -0800

    Closer still.  Appears to work.  A little more refining to go.

Src/C_AMRLib/Particles.H

commit a0f0285e2ae53aaa3b037f3ba23467f1951fc8f7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 11 19:55:41 2013 -0800

    More work on Redistribute().  Getting close.

Src/C_AMRLib/Particles.H

commit 30e1f57b67df23321213f8f9c95dde472d066945
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 11 19:24:06 2013 -0800

    Yet more work on Redistribute().

Src/C_AMRLib/Particles.H

commit c191aac43a4bb8b9a6506c9f6e7046a132757742
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 11 18:59:35 2013 -0800

    More work on Redistribute().

Src/C_AMRLib/Particles.H

commit bde99fbf1bda15798cdfc741903095c2c651d340
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 11 18:21:59 2013 -0800

    Some work on Redistribute().

Src/C_AMRLib/Particles.H

commit 70d3222cf3d3585e5df7ea77beb4fee683a76e70
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 8 14:58:46 2013 -0800

    binary nfile output with header.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 9a57585542e9d0eb887bdaf790d6191aa44db318
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 8 14:56:25 2013 -0800

    Reverting out previous mod.

Src/C_AMRLib/FLUXREG_3D.F

commit 489e912400499bd9712b4028f5d813683e1a40ec
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 8 14:03:51 2013 -0800

    Some OMP tweaking.

Src/C_AMRLib/FLUXREG_3D.F

commit 46d08c353342b570378b590b640786935cd9dd37
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 8 13:45:58 2013 -0800

    Some OMP tweaking.

Src/C_BaseLib/SPECIALIZE_3D.F

commit 808b7576faf5b9c6de0dadbd87e739f8e80b1b99
Merge: d3cc0d47b cfe1e71c7
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Feb 8 10:31:24 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d3cc0d47bf47451caa1278e3f194cd9625fe7fdb
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Feb 8 10:31:06 2013 -0800

    more bc types for stokes_preconditioner code

Src/F_BaseLib/bc.f90

commit cfe1e71c7920651526915388b56f447b3dd69f52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 7 21:59:07 2013 -0800

    It appears that Intel compiler has a bug in debug mode. It got some internal compiler errors with some new OpenMP stuff.  So some changes were made to get around that.

Src/F_BaseLib/multifab_f.f90

commit b6d4cbf66bab53778381dd2f4c9d44b42fd325bf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 7 17:12:34 2013 -0800

    added OMP to reshape_d_? in data packing/unpacking for MPI

Src/F_BaseLib/multifab_f.f90

commit b86d54cdd8d3f34c2dd8c0970080a7c3f3c24a7b
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Feb 7 10:46:33 2013 -0800

    Python: Minor tweaks.

Src/Python/pyboxlib/fab.py
Src/Python/src/fboxlib.f90

commit 0365100bc54b9cd861af0fcdaf93460a370bb71a
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Feb 7 10:45:19 2013 -0800

    Remove volume from finite-difference convergence tool.

Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp

commit fc961e42ed7d301581fb9181515102be4d2631c9
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Feb 7 11:41:20 2013 -0500

    More faverage edits/fixes to the RMS calculations

faverage.f90

commit ddcc2c52b6d51300c3edff26834c0a5cfa847eb0
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 6 17:22:53 2013 -0800

    added more message tagging support.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 2eccebf90229f5b2fcfa7868152c5222c720536c
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 6 16:19:02 2013 -0800

    implemented nfiles for bl_prof output from all procs.

Src/C_BaseLib/Profiler.cpp

commit 4117e35b2076300d26c0db1f18573656279d7ff3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 16:14:52 2013 -0800

    added OMP to setval in F_BaseLib

Src/F_BaseLib/fab.f90

commit bc4853f44d629cc457fa697cb98bf7a24da116fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 16:14:00 2013 -0800

    added OMP to sum_d in F_BaseLib

Src/F_BaseLib/multifab_f.f90

commit 95704452d929b4c924a4278e313687b81321cf41
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 6 15:30:50 2013 -0800

    added more counters.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 9add098c56d691e49207692819090ece3f34c3e7
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Feb 6 17:38:56 2013 -0500

    Fixed AmrPostprocessing/F_Src/faverage.f90 so that it properly weighs
    data from coarse cells.

faverage.f90

commit ba22852db7d2bdfa340396ccf34f5d77251aaf05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 14:23:54 2013 -0800

    OMP multifab copy in F_BaseLib

Src/F_BaseLib/multifab_f.f90

commit 62bc03e72db963a742655752ab1a02619f9e43d9
Merge: 0f141093b 0826b85cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 13:08:26 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0f141093b5f624cad89064203d21f8b64283f483
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 13:07:25 2013 -0800

    Collapsed some OMP DO's.

Src/F_BaseLib/multifab_f.f90

commit 0826b85cbed41614dd58b663e87e26c40f2b9299
Author: cmalone <malone@ucolick.org>
Date:   Wed Feb 6 12:00:30 2013 -0600

    updates for BW

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 4db455c576be9e1977339d859c2bc8751e87c534
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 5 16:32:46 2013 -0800

    more handling profiled names that are not on the ioproc.

Src/C_BaseLib/Profiler.cpp

commit 92cca5ae86d3febe8dbbbbd58d78494237bea528
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 5 15:58:15 2013 -0800

    handle profiled names that are not on the ioproc.

Src/C_BaseLib/Profiler.cpp

commit 57bd6f117fbc00c053adaea7c5bfae01eb90851d
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 4 15:05:19 2013 -0800

    synced profiled names list across procs.

Src/C_BaseLib/Profiler.cpp

commit da755fe74e8317503539df577d7147903384c4c7
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 1 14:11:32 2013 -0800

    nfiles for commstats, cleaner init.

Docs/Readme.profiling
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit f392d2cb8c015b3006ab0884348c04d461c5977b
Merge: d74183b13 66f8d7cd1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 1 13:51:28 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d74183b13aa7bfae8e26d263a4bb8d884b4601d4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 1 13:51:16 2013 -0800

    Add more functions to ParticleContainerBase.

Src/C_AMRLib/Particles.H

commit 66f8d7cd1efc85d46c95ab952f71b38f389ec940
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Fri Feb 1 15:02:11 2013 -0500

    one more clean-up -- there were two separate blocks for the GNU
    compilers, one invoked if we did COMP=gcc and the other for COMP=g++
    -- they both did the same thing.  Now we define a variable USE_GCC
    if we come in with either of these COMPs, and have a single block
    for the GNU compilers.

Tools/C_mk/Make.defs

commit 082302ee47cf1e2170125d77f5cf1ecf7dd8a45e
Merge: 03eedb10c a6eea6ddd
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Thu Jan 31 18:50:36 2013 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 03eedb10ceece8b2850c3def6287bb5c797cd279
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Thu Jan 31 18:48:37 2013 -0500

    remove atlas and yana -- they've been retired
    
    also remove the special stuff for sn.astro here -- it can use the MPI
    wrappers.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 2ec510a7a3c19316493b3dd6021bea93fb7ea748
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 31 15:47:20 2013 -0800

    implemented message filtering.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit a6eea6ddd673d53ccc23029600b959c949c0e8cb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 31 15:37:34 2013 -0800

    Add new functions to the ParticleContainerBase.

Src/C_AMRLib/Particles.H

commit dce29a5ac70f94e7c62ff0f8d1db4497c6e0581b
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Thu Jan 31 14:18:53 2013 -0500

    remove support for the Cray Y-MP, J90, and C90

Tools/C_mk/Make.CRAY
Tools/C_mk/Make.defs

commit 0b6a49edb0686a2a7f04d0e21fd4725da08e7187
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Thu Jan 31 13:58:51 2013 -0500

    some cleaning.  Remove old machines and architectures.  Cray X-1,
    IRIX, OSF1 (a DEC O/S), SUPERUX (NEC SX6), and the T3E.  Also Make.frank
    seems to have been orphaned.
    
    Finally, also remove the Franklin machine, since that no longer exists

Tools/C_mk/Make.CRAYX1
Tools/C_mk/Make.IRIX64
Tools/C_mk/Make.Linux
Tools/C_mk/Make.OSF1
Tools/C_mk/Make.SUPERUX
Tools/C_mk/Make.T3E
Tools/C_mk/Make.defs
Tools/C_mk/Make.frank
Tools/C_mk/Make.mpi

commit 7cd59e1dae472d05333425cca6781554c749255e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 31 10:13:11 2013 -0800

    Tweaks to InitFromBinary().

Src/C_AMRLib/Particles.H

commit b58385f27eaf6a7c22e66fca537c872e0389181f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 31 09:54:30 2013 -0800

    Added non-template abstract base class ParticleContainerBase from which
    the templatized ParticleContainer class now publicly inherits.  This is so
    we can maintain a list (or vector) of pointers to ParticleContaiers as
    ParticleContainerBases.  Any functions we wish to call using those
    pointers need to be declared as pure virtual functions in the base class,
    exactly matching the signature in the ParticleContainer class itself.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit e276c3ddc2dfa3fe116f55fe6b2dd8ed30b09838
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 30 17:19:50 2013 -0800

    barrier tagging, named comm types.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 8535168382cfbd454b4d34b61ebe413b9d2e8901
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 30 13:43:39 2013 -0800

    Correction to new impose_refine_grid_layout call (must pass in lbase
    as new_finest)

Src/C_AMRLib/Amr.cpp

commit d6cf73142b82ec9f6b00c3221725dfbad7a6b3d9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 30 13:42:22 2013 -0800

    Impose refine_grid_layout at level 0 earlier in the grid_places routine
    so that it is still imposed even if we return with fixed_grids.

Src/C_AMRLib/Amr.cpp

commit edc453753571e00bc475d2380c74198636c8912f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jan 29 16:47:45 2013 -0800

    An attempt to better distribute the NReader processes in
    IntFromBinaryFile() by building a set of NReaders processes from the
    full range [0,NProcs) using a random number generator. The idea is to
    minimize the number of reader processes per Node, so that each reader can
    use more of the available memory on the Node.

Src/C_AMRLib/Particles.H

commit a0a0d20165ca686a5c18eb6116d0e33d5c409567
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jan 29 15:48:06 2013 -0800

    more communications profiling.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit a80712e76c2821e0cfeb9820edb385054dd2de99
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 29 15:03:37 2013 -0800

    If we can't use mg.bottom_solver = 4 then just set it to one instead
    of aborting with an error.

Src/LinearSolvers/F_MG/mg.f90

commit 571b3193aac8750b598eddd336a9724a26c16017
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 29 10:29:42 2013 -0800

    Fix comment about Nprocs > ngrids.

Src/C_AMRLib/Amr.cpp

commit e569788d3a8a511f2143371ad6c57c8e539b16aa
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 29 10:21:49 2013 -0800

    We now impose the refine_grid_layout criterion (breaking up grids
    into smaller chunks if nprocs > ngrids) in a call from defBaseLevel
    as well as in a call from regrid so we fix the grids at level 0 at
    the initial time (unlike before) and if max_level = 0 (unlike before).

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 92a320fdda62a6dda9154ae7461e7a3bd7b62131
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jan 28 11:31:09 2013 -0800

    start of comm profiling.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 844566b5f89002f56fc1519a77402c537015822b
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 25 14:20:34 2013 -0800

    eliminated warnings.

Tests/RoseTests/CPP/NullTransTest/PROB_3D.F

commit e74e4f8fe46373c179e07807d09e636ec92030bf
Merge: e1a8550f0 0ea7403d0
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jan 25 14:15:49 2013 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 0ea7403d0fb6dd638ee0adf0b8bbb0b3b9865aae
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 25 14:13:49 2013 -0800

    added code to gracefully exit on user stop request, so the profiling will still print.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit e1a8550f05625ede943d838912ee388b681b2c88
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jan 25 13:42:21 2013 -0800

    Fixed other remnants of multi-component operator data

Src/C_BoundaryLib/InterpBndryData.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 252cb95afe4040542f3e27858197d6d6f899217a
Merge: e79624957 760742952
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 24 09:50:16 2013 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e79624957b678d52df3c5f6485a975c833f19933
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 24 09:49:53 2013 -0800

    Bad default value for bndry_comp

Src/LinearSolvers/C_CellMG/LinOp.H

commit 76074295241683314fb063222478c0268cc0d41c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 09:46:11 2013 -0800

    Fixed Tools/F_mk/comps/Linux_intel.mak

Tools/F_mk/comps/Linux_intel.mak

commit 82638b52edb67b6c4f760b22db4b2c5f5f2fbbf7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 09:21:11 2013 -0800

    Update makefile for Intel 13

Tools/F_mk/comps/Linux_intel.mak

commit e9ebb1d9178f586892c9f148e6f3ff18a51acf2b
Merge: e30ac42b9 2fcbad44d
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jan 23 18:37:46 2013 -0800

    Merge commit 'd573eaa'

commit 2fcbad44df8db7597517e54bb6ae60194c22f33e
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jan 23 18:36:29 2013 -0800

    Modify interface to a number of linear solver support structures to generalize access/usage

Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit e30ac42b96688169140ddffa66a2444f12638666
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 23 11:01:39 2013 -0800

    More OMP to the nonblocking multifab_fill_boundary

Src/F_BaseLib/multifab_f.f90

commit 00883ce89cd151f421929e0e7501cffe268f5838
Author: Chris Malone <malone@ucolick.org>
Date:   Wed Jan 23 12:54:14 2013 -0500

    fix how we capture version number for Cray; this is a hack

Tools/C_mk/Make.mpi

commit 73b4a949d1aaca18aa7b3576ca8483fd9c11ff55
Author: Christopher Malone <cmalone@titan-ext5.ccs.ornl.gov>
Date:   Wed Jan 23 12:40:15 2013 -0500

    titan updates

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit 09ff8675f9da9e217a7c8da3f82432516a544ce4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 22 13:41:01 2013 -0800

    OpenMP part of nonblocking fill_boundary

Src/F_BaseLib/multifab_f.f90

commit d716954356863a76b035e9a5e335cd107dae6b95
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 22 13:13:13 2013 -0800

    OpenMP FAB_CONTAINS_NAN and INF

Src/F_BaseLib/fabio_c.c

commit f4a3135d0c9e5a3162e24645b4b56335c5226f5f
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 20 18:53:04 2013 -0500

    remove python_plotfile

python_plotfile/vis.in

commit 2c0da77fac31d76e5552cac6e739b51d165448d6
Merge: 33bbe98e0 e0dd78252
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 20 18:52:39 2013 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 33bbe98e0021218408001f80e012d836ebf6b7b3
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 20 18:52:09 2013 -0500

    moved python_plotfile

python_plotfile/GNUmakefile
python_plotfile/contourcompare.py
python_plotfile/fsnapshot.f90
python_plotfile/plot1dflame.py
python_plotfile/plotparticles.py
python_plotfile/plotsinglevar.py
python_plotfile/plotsinglevar_parts.py
python_plotfile/runtimevis.py

commit e0dd782521138019546ccc2ce6df42c517db76c1
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 20 16:10:02 2013 -0500

    fix a comment

python_plotfile/plotsinglevar.py

commit 6cff139de9d11ff38d7e40b65be3a047aee2de85
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 20 16:08:55 2013 -0500

    greatly simplify the GNUmakefile -- we only really need the BoxLib F_Src

python_plotfile/GNUmakefile

commit d865661320552a45b4ddd26c238ac10b2b1c093a
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 20 13:32:16 2013 -0500

    sample runtimevis.py inputs file

python_plotfile/vis.in

commit a06844cbc0f830dfb8eaf7251759b3f605742b39
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 20 13:31:44 2013 -0500

    add tight_layout -- this really makes things look better.  Also fix
    the problem if the plt file ends in /

python_plotfile/runtimevis.py

commit 620c542ed9c1c9a2a05b52139ebaf789a3baa365
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 16 13:31:59 2013 -0800

    Remove XGRAPH stuff for BoxLib version of this.

Tutorials/AMR_Advection_C/Source/main.cpp

commit aebe3add3e7948700e69f4a571104f28658ec987
Author: Regression Tester account <regtester@battra.(none)>
Date:   Wed Jan 16 09:58:58 2013 -0800

    Regression Testing script: added capability of switching to non-master branches

Tools/RegressionTesting/testnew.py

commit a65a93f79a9e51e36b54ee3acd80a8015d4edeb5
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jan 15 16:05:14 2013 -0800

    changed flags for fortran.

Tests/RoseTests/CPP/NullTransTest/GNUmakefile

commit b6ac683b89a8ce6160007bc029a6603b2afbd1ef
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jan 14 15:21:46 2013 -0800

    added some simple rose translation tests.  see weiqun for the f90 parts.

Tests/RoseTests/CPP/NullTransTest/GNUmakefile
Tests/RoseTests/CPP/NullTransTest/PROB_3D.F
Tests/RoseTests/CPP/NullTransTest/PROB_F.H
Tests/RoseTests/CPP/NullTransTest/README
Tests/RoseTests/CPP/NullTransTest/RoseNullTest.cpp
Tests/RoseTests/F90/Readme
Tests/RoseTests/F90/test1/GNUmakefile
Tests/RoseTests/F90/test1/main.f90
Tests/RoseTests/F90/test2/GNUmakefile
Tests/RoseTests/F90/test2/main.f90
Tests/RoseTests/F90/test3/GNUmakefile
Tests/RoseTests/F90/test3/bc.f90
Tests/RoseTests/F90/test4/GNUmakefile
Tests/RoseTests/F90/test4/main.f90
Tests/RoseTests/F90/test5/GNUmakefile
Tests/RoseTests/F90/test5/main.f90
Tests/RoseTests/F90/test6/GNUmakefile
Tests/RoseTests/F90/test6/main.f90
Tests/RoseTests/F90/test6/omp.f90
Tests/RoseTests/F90/test7/GNUmakefile
Tests/RoseTests/F90/test7/main.f90
Tests/RoseTests/F90/test7/probin.f90
Tests/RoseTests/F90/test7/runtime.f90
Tests/RoseTests/F90/test8/GNUmakefile
Tests/RoseTests/F90/test8/init_data.f90
Tests/RoseTests/F90/test8/main.f90

commit 8a548f8b1c6a4f7486d4af6bb95c98993e9d1316
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jan 14 10:00:33 2013 -0800

    Compile fillfab.f into tFillFab.

Tests/C_BaseLib/GNUmakefile

commit e91336235e135e80e5fab3c9c410bb3459bff1cf
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Sun Jan 13 21:16:34 2013 -0500

    add time

python_plotfile/runtimevis.py

commit 4b14eac704902614284f3b3fbcdc3d3d814838d9
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Sun Jan 13 20:44:15 2013 -0500

    looking prettier now

python_plotfile/runtimevis.py

commit ab6f981fbf73df69f57850172d8e717c102448b8
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Sun Jan 13 20:29:57 2013 -0500

    basic functionality working

python_plotfile/runtimevis.py

commit 493d7b0bdec21c703c9c303d0d955268124f7cbb
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Sun Jan 13 18:21:10 2013 -0500

    more progress

python_plotfile/runtimevis.py

commit f3762790be4353659a0786196fe786658aad2bf9
Merge: 554da93a6 b979a3d74
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 13 18:09:28 2013 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 554da93a6449e61df63fafc38bdfd652286f3f30
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 13 18:00:08 2013 -0500

    start of a runtime vis script

python_plotfile/runtimevis.py

commit 6072455b4e7121dc815cecbec81f1cee0ee9936e
Merge: 056caf570 85f2b65a5
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 10 16:52:27 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 056caf5702b1b918cdf382b3103102553478ff98
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 10 16:51:06 2013 -0800

    introducing HOM_DIR bc type.  certain problems need to distinguish between EXT_DIR (e.g., for inflow) and HOM_DIR (e.g., for velocity at a wall)

Src/F_BaseLib/bc.f90

commit 85f2b65a55886bc992c50c81750caafbf3285b06
Merge: 5f246de87 092128efd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 9 15:21:54 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5f246de877722cc0465f5458fbf4b3b346bdd3ae
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 9 15:21:39 2013 -0800

    local_only --> only_local so declarations match.

Src/C_AMRLib/Particles.H

commit 092128efdc14a70ab0c947a3c50486f6480a635d
Merge: 7ca3c6e49 4741de849
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 9 14:49:16 2013 -0800

    Merge branch 'streamretry'

commit 4741de8491a9cce849441861758ffbdc31d109cc
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jan 8 16:15:19 2013 -0800

    stream retry for checkpoint and plotfiles.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 7ca3c6e4966a60e39ce6ce84ed5da2d178c3ae53
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jan 8 09:23:45 2013 -0800

    Check in with tMF enabled not tFillFab.

Tests/C_BaseLib/GNUmakefile

commit 542470e133c78bcaf05a29d18ac4d38c02bc23bd
Merge: e3a64d6c7 e3fab0d33
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jan 8 09:05:16 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e3a64d6c74b51b563e85f7d41aaa87977c8ef0a7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jan 8 09:04:49 2013 -0800

    Added FillFab stuff to add values from a file into a fab.
    Only works for 2D at the moment.

Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/fillfab.f
Tests/C_BaseLib/tFillFab.cpp

commit e3fab0d33eefcd3c796ac93b6f822e8936d00f9b
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Jan 7 06:50:39 2013 -0800

    bugfix; referencing wrong optional argument

Src/LinearSolvers/F_MG/mg.f90

commit 90734ced36e6fdedae9a6adeafebdc84bdfba0fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 4 16:54:09 2013 -0800

    Added -rose:openmp

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/gfortran.mak

commit 0ddf2f7ea201091b1c6d5a5b84a2a0f14fd476e7
Merge: 622139901 a459a6c9e
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Jan 4 15:38:32 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 622139901102d0fc2fc687f526b99acae49458e6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Jan 4 15:37:33 2013 -0800

    added the option for the code to *not* abort if you have reached the maximum number of v-cycles, as controlled by abort_on_max_iter in mg_tower.f90.
    
    Fixed a bug in the ml_cc solver where on the *last* v-cycle, the solver didn't actually do any smooths

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit a459a6c9e4b71503c547fd950b6c510c75954c23
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 3 16:40:08 2013 -0800

    Made make for ROSE again.

Tools/F_mk/GMakedefs.mak

commit a2e1a037a06af842c056193ba8eb2163815268c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 3 16:26:45 2013 -0800

    Fixed a bug in the make system introduced by me today.  The perl
    scripts require a space after "-I".

Tools/F_mk/GMakedefs.mak

commit 74b021f6cac585005db8be163a0c83a1b0dc34c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 3 16:13:28 2013 -0800

    Minor changes to make the code more readable and ROSE happy, because
    ROSE cannot handle d%d.

Src/F_BaseLib/cutcells.f90
Src/F_BaseLib/vector_i.f90

commit 25f4668f016d53c7faf06a23d8ac38a395524813
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 3 12:11:44 2013 -0800

    Fixed OMP bug.

Src/F_BaseLib/create_umac_grown.f90

commit c43ad437d67a91aa08d03ce604338b772bf0c388
Merge: 9225faa1f e6efe3dcf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 3 10:45:58 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9225faa1ff930416149a07e9ec1905c7191e08d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 3 10:44:51 2013 -0800

    Rose support for F_mk

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/gfortran.mak
Tools/F_mk/comps/rose.mak
Tutorials/HeatEquation_EX1_F/GNUmakefile
Tutorials/HeatEquation_EX5_F/GNUmakefile

commit e6efe3dcfa3ed9aabedd2e3433c01b8d9848fd68
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 3 08:42:36 2013 -0800

    interface changes to simplify mac_applyop

Src/LinearSolvers/F_MG/mac_applyop.f90

commit eb84a5045d5ea24055fc3b66958504fc779e84dd
Merge: a067b5fc1 f118e4256
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 3 08:26:29 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a067b5fc19147d889c45aee6c63488196a2ae5bb
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 3 08:24:53 2013 -0800

    move mac_applyop from VARDEN and MAESTRO into BoxLib/Src/LinearSolvers/F_MG... more applications will be needing this

Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/mac_applyop.f90

commit f118e425653a9af7313afed70641973f6b955e93
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Jan 2 19:05:39 2013 -0500

    explain Real in C++ and dp_t in F90

Docs/GettingStarted/GettingStarted.tex

commit a8f07c4897d9b23b364c305ce65b91bf89dec252
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 2 14:31:48 2013 -0800

    Get around an Intel compiler bug that makes unnecessary copy when
    a_pointer(a_type%a_integer:) is passed to the first argument of
    parallel_isend and parallel_irecv.

Src/F_BaseLib/multifab_f.f90

commit b992f8202c6203b3322cf3426ab07348c0e4d818
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 20 21:31:28 2012 -0800

    Use -h noomp rather than -h thread0 to disable OMP for craycc

Tools/F_mk/comps/Linux_cray.mak

commit c0a1a3822d679e6f46e518c0183fa3870d056534
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 20 17:34:04 2012 -0800

    Explicitly disable OMP for Cray C compiler when OMP is not defined.

Tools/F_mk/comps/Linux_cray.mak

commit f42381a2b7916efc91b38f48187cd89503901123
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 20 17:25:10 2012 -0800

    CFLAGS must also have -openmp when OMP is defined, otherwise SMC will fail when built with OMP using Intel.

Tools/F_mk/comps/Linux_intel.mak

commit 286a7607343ea723a0d3e4a873c870bbf73e3208
Merge: 959c92bd5 7db6b2c15
Author: vince <vebeckner@lbl.gov>
Date:   Wed Dec 19 16:12:26 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 959c92bd5fa639a6e4984f0e51c5402aa84555af
Author: vince <vebeckner@lbl.gov>
Date:   Wed Dec 19 16:12:12 2012 -0800

    added rose support for mk.

Tools/C_mk/Make.defs
Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/rose.mak

commit b979a3d7440617c6648d071cfa7aec86386b5137
Author: Michael Zingale <zingale@hopper10.(none)>
Date:   Wed Dec 19 09:26:59 2012 -0800

    use tight_layout() if it exists.  Also reduce the number of tick labels
    for very narrow domains

python_plotfile/plotsinglevar.py

commit 7db6b2c153760915c0298dea868436accb1fe52a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 18 08:14:12 2012 -0800

    Modify how we deal with initial_grids_file and regrid_grids_file -- we now read in
    the boxarrays soon after we parmparse the names of the files, and store these as
    static BoxArrays.  Then later when they are needed in grid_places() we have them
    stored and do not read them in again.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit a3c14989e94ad24dbcad01fec586676bf1e9452e
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Dec 17 13:02:57 2012 -0800

    a note about space/time-dependent boundary conditions in multifab_physbc

Docs/F_AdvancedTopics/F_AdvancedTopics.tex
Docs/Introduction/Introduction.tex

commit b4ae593c3e64a018cfd9348da02010d339db570e
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Dec 17 12:31:00 2012 -0800

    added optional arguments: time, dx(:), prob_lo(:), prob_hi(:) for space/time-dependent boundary conditions

Src/F_BaseLib/multifab_physbc.f90

commit 6cf9bad98784b2c11794e14e312228062bf6fec0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Dec 14 15:33:10 2012 -0800

    Add the option to set
    
    amr.initial_grid_file =
    
    as well as
    
    amr.regrid_file =
    
    This is similar to the regrid_file option, except that:
    
    1) it is only used to set the initial grids file; there is no file specified
    for later regrids.
    2) the max_grid_size criterion is not enforced on the initial grids generated
    this way, rather it is imposed after the grids are read.  The point is to allow
    us to initially read in grids specified by an external routine which did not
    know about max_grid_size.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit cfb8dfe9c8f319f955128d715ddee8ef62d3f1cf
Merge: 84589d673 d3d670015
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 13 17:23:37 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 84589d673b0bd38583e2babf7d3dd2a429be258f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 13 17:21:31 2012 -0800

    Fixed some minor probelms such as 0_dp_t should read 0.0_dp_t otherwise Cray compiler might be unhappy.

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/knapsack.f90

commit d3d670015f267148291c783b4745980b1d2bc0b8
Merge: a02be70f4 2ed05a07c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 13 11:00:06 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a02be70f40e2f864dce0895bdd3487180a129374
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 13 10:58:08 2012 -0800

    Added ParticleBase::MaxParticlesPerRead() for use in InitFromBinaryFile().
    It's the number of particles that each reader should try to read before
    everyone does a Redistribute().  Currently it's defaulted to 100000.
    It's ParmParse-able as particles.nparts_per_read.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 2ed05a07cb5f7e17da64f7aa867cf4f35f9792e4
Merge: 77cbb2a6c 4c2503a99
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Dec 12 19:51:21 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 77cbb2a6c9435477aa658ec8d0337efb8d235f96
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Dec 12 19:50:36 2012 -0500

    add a new printing clause that can be used to write a pretty printing
    method for the runtime parameters

Tools/F_scripts/write_probin.py

commit 4c2503a99663cde2faba78b35d8ee8297c447697
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 12 16:16:06 2012 -0800

    More work on InitFromBinaryFile().

Src/C_AMRLib/Particles.H

commit c2d70c646ac8dc2f851dea86e811f0709c7984d9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 12 15:57:52 2012 -0800

    A little more tweaking on InitFromBinaryFile().

Src/C_AMRLib/Particles.H

commit bcb80ee518a8975e68601fbf7523cd5088e6b071
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 12 15:52:27 2012 -0800

    More work on InitFromBinaryFile().

Src/C_AMRLib/Particles.H

commit c2c320eec8b04364f36491584400d5c946191eb0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 12 14:44:01 2012 -0800

    Some work making InitFromBinaryFile() faster in parallel with large
    numbers of particles.

Src/C_AMRLib/Particles.H

commit 8326ad3b4e4dba5bd6ca440c3068882c8a14ebd1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 11 11:32:02 2012 -0800

    Added writePlotNow routine to Amr.cpp and to AmrLevel.  In Amr
    this routine now contains the various tests on whether to write a
    plotfile at this timestep. In AmrLevel it allows the application
    at level 0 to tell Amr to write a plotfile now.  There should be
    no changes in the default behavior.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 65bff3680c2b0f6c651d8f76ce550712a9ec2ef9
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Dec 10 14:26:05 2012 -0800

    Virtualize a couple of functions to allow easier extensions into derived classes.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/ErrorList.H

commit 961947240f9b33a3411b3eefd8dd1ad26b34e19c
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 7 16:19:52 2012 -0800

    writeavg pct fix.

Src/C_BaseLib/Profiler.cpp

commit d403b60f6279434ac37d94bef158d452ef8fb1b5
Merge: c867f627d 05e4606c1
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 7 15:07:00 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c867f627dedca677a24b786e0076aead7a4f0121
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 7 15:06:28 2012 -0800

    fixed writeavg percent.

Src/C_BaseLib/Profiler.cpp

commit 05e4606c1f14c43d132aaabba1284189e4ff89f0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 7 14:53:38 2012 -0800

    some profiling tweaks

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/ParallelDescriptor.cpp

commit c62e5c678b3be0fa8b47a9f6f5862e56e2ae3853
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 7 13:19:38 2012 -0800

    Added profilers to SFC & KNAPSACK.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 20645ded8f015e44c3a5502af6b254f68fdc3658
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 7 12:41:29 2012 -0800

    added some Profilers

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BoundaryLib/FabSet.cpp

commit a5296f8e3b9056a06e02ecd0e50434b886fb42c3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 6 15:11:28 2012 -0800

    Comment out the "-warn all" stuff for Intel Fortran compiler.  The EGLib
    stuff is just to old & crufty to pass this test.

Tools/C_mk/Make.defs

commit e3aad1c4d7c9b1a852539232263de8b027242d4f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 6 10:40:04 2012 -0800

    Add more compile time checking when using Intel fortran compiler.

Tools/C_mk/Make.defs

commit c8403e62f6595852333b3c6655186a5a15732272
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 5 11:45:06 2012 -0800

    Made the nonblocking multifab_fill_boundary safer in case it is not used properly.

Src/F_BaseLib/multifab_f.f90

commit 1b1cab8354d1555caf43b204a2fac5a91d9e5fe7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 4 16:02:43 2012 -0800

    Switch the order of isend and irecv in the nonblocking
    multifab_fill_boundary.  In principle, posting irecvs before isends is
    the right thing to do.

Src/F_BaseLib/multifab_f.f90

commit 651ff06c16b25de2e590ebcc6499b14c3fd6c278
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 4 10:12:21 2012 -0800

    Fix typo

Tools/Release/release.py

commit 4e5d76c8f0ae23754fb0fc58feea7199828a4489
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 3 12:07:31 2012 -0800

    added stream retry for some output.

Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 317bef6bef5dcc3e76b12f5e255e37ae451e2625
Merge: 5b39c0d96 1d0cfaea4
Author: Matthew Emmett <memmett@gmail.com>
Date:   Sat Dec 1 08:47:21 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 5b39c0d96e5e7e9b05425725d51c15780d0f06ac
Author: Matthew Emmett <memmett@gmail.com>
Date:   Sat Dec 1 08:47:09 2012 -0500

    Add DiffSameDomainRefinedFD utility.
    
    Does the same as DiffSameDomainRefined, but for finite difference
    schemes.

Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp

commit 1d0cfaea4d2729c84398060651fd95b36ada4eff
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 27 17:36:11 2012 -0800

    update to the i/o benchmark.

Tests/IOBenchmark/IOTestDriver.cpp

commit 0effe73143dd34320aee12e332d6fdc6ab50c4ab
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 27 17:31:54 2012 -0800

    tweaked the profiling output.

Src/C_BaseLib/Profiler.cpp

commit 04c8054abf9b7e0aa134fb4b5f65fee4c2b5df95
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 14:48:12 2012 -0800

    Special treatment for the case of no MPI jobs in the nonblocking multifab
    fill boundary.

Src/F_BaseLib/multifab_f.f90

commit 9c0f7bf2ff194729ee28a8da6e126b74cea61a7f
Merge: 709e5f823 a0b2f1d39
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 12:20:42 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 709e5f8233314b6e0a5eda637caa159ac56bd4de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 12:17:56 2012 -0800

    Changed the default sfc_threshold from 4 to 0 for F_BaseLib.  This is
    a win for many tests.  Also, F_BaseLib is now consistent with
    C_BaseLib.

Src/F_BaseLib/layout.f90

commit a0b2f1d39fe0b55bd434201b7c7074654f6a1640
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Nov 27 10:54:47 2012 -0800

    Changed the default for sfc_threshold from 4 to 0. This way, even if we have fewer grids
    than cores we'll get the Space Filling Curve distribution.  Tests on hopper indicate this
    is a win.

Src/C_BaseLib/DistributionMapping.cpp

commit 5fe9a115f54f2c80cbc7055386673fc981a48bbd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 26 17:06:32 2012 -0800

    Fix a bug in parallel_test_one.  I don't think anyone ever used this function.

Src/F_BaseLib/parallel.f90

commit 0a3ae51666a8031d18a5f80afa164bffec2f52ea
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Nov 25 10:01:03 2012 -0800

    Cleaned up version.

Src/C_AMRLib/Particles.H

commit d3f0b736df362ef15978c75ff59c8b0e037b39cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 21 10:41:19 2012 -0800

    Fix a bug in my last commit.

Src/F_BaseLib/multifab_f.f90

commit d7555c1b90994c0686a7f3b3952f0f7a9a1fb684
Merge: 2811edbd0 daf2cb95f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 21 10:32:12 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2811edbd088e2dd3f3cbaa25a045e09111d688fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 21 10:29:51 2012 -0800

    Add multifab_fill_boundary_waitrecv that will return when messages are
    received regardless the status of sending messages.

Src/F_BaseLib/multifab_f.f90

commit daf2cb95f381845c236c26475bfa32a05709285a
Merge: 47e81b0be 7f8b03a7e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 20 17:27:51 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 47e81b0be60066173920af86798179e8bf08eebe
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 20 17:27:37 2012 -0800

    Add new access functions in Particles.H

Src/C_AMRLib/Particles.H

commit 7f8b03a7ee5a9c1a21d4cf8e674ec631d7987fc7
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 20 15:43:59 2012 -0800

    moved readme to docs.

Docs/Readme.profiling

commit a02eb25e4fed2cfb3132feb841a8719ec1886746
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 20 15:35:43 2012 -0800

    rewrote the c++ boxlib profiler.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp
Src/C_BaseLib/Readme.profiling

commit 5d69def97432f227bde8b372a84b47716b2330e9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 16 15:16:45 2012 -0800

    Add GetParticleVelocities routine.

Src/C_AMRLib/Particles.H

commit 64c404cae3c30a2b39d055268644a643e82a551a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 13 14:29:50 2012 -0800

    If bottom_solver type is not defined by the calling routine, then
    set default to BiCGStab (type 1) rather than type 3 which no longer exists.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit dd6d5f2a44706ed06ff5103190bbd698c05761ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 13 13:35:35 2012 -0800

    For nonblocking multifab_fill_boundary_nowait, MPI tag is passed in as argument.

Src/F_BaseLib/multifab_f.f90

commit e1e9ef6e606fe3d563024e34a95a6623ea5a0d34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 13 08:14:19 2012 -0800

    Option to initialize MPI with thread support

Src/F_BaseLib/boxlib_f.f90
Src/F_BaseLib/multifab_f.f90
Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit c4680d99d6e0b4686f1181b818569acaffa1c88e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 12 17:24:11 2012 -0800

    real "add mpi_test to the nonblocking multifab_fill_boundary"

Src/F_BaseLib/multifab_f.f90

commit 236f68cc5357d9cd0d4696880e3ca7e9674d80bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 12 17:21:52 2012 -0800

    Revert "add mpi_test to the nonblocking multifab_fill_boundary"
    because I accidently committed some files.
    
    This reverts commit c26377021d3906bafbcfef68a42cb66f6d5c2cbc.

Src/F_BaseLib/multifab_f.f90
Tests/LinearSolvers/ComparisonTest/main.cpp
Tools/C_mk/Make.Linux
Tools/F_mk/GMakeMPI.mak
Tools/F_mk/comps/Linux_cray.mak
Tools/F_mk/comps/Linux_pgi.mak
Tutorials/Exp_CNS_NoSpec/GNUmakefile

commit c26377021d3906bafbcfef68a42cb66f6d5c2cbc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 12 16:24:07 2012 -0800

    add mpi_test to the nonblocking multifab_fill_boundary

Src/F_BaseLib/multifab_f.f90
Tests/LinearSolvers/ComparisonTest/main.cpp
Tools/C_mk/Make.Linux
Tools/F_mk/GMakeMPI.mak
Tools/F_mk/comps/Linux_cray.mak
Tools/F_mk/comps/Linux_pgi.mak
Tutorials/Exp_CNS_NoSpec/GNUmakefile

commit 0f3b0e9dd6508916a31e9d35a214eb66046c5a88
Merge: f0e1468a7 9b748a687
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 8 17:25:26 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f0e1468a7d1bf8bf5c8efebe5995df147aadac15
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 8 17:25:15 2012 -0800

    added random initialization, mb2, and more compact boxarray.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/IOBenchmark/README

commit 9b748a6877016c06d048602f887af38fa1293872
Merge: 88ac51588 b5208013c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 8 17:12:06 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 88ac51588040b769d355eda7b17484098fdeefb7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 8 17:11:31 2012 -0800

    Revert my previous change because it does not make any difference in performance

Src/F_BaseLib/multifab_f.f90

commit b5208013c7542e11edcbfca6a84c965ae6b417f0
Merge: ad0bda7be 788d8cb75
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Nov 8 17:55:56 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit ad0bda7bebd06a5c37741a3026446cbe79df991a
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Nov 8 17:55:05 2012 -0500

    when indexing a multifab with the particles grid, we need to use
    local_index when getting the dataptr()

Src/F_BaseLib/particles_f.f90

commit 788d8cb7535685855a32cab0a83c9263f325abf3
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 8 14:24:34 2012 -0800

    added some profiling.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Profiler.H

commit b3291378a9d7af14a50292965780e2423f5147c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 8 14:11:31 2012 -0800

    nonblocking fill boundary: do mpi_test

Src/F_BaseLib/multifab_f.f90

commit 99aeb2b7a0b924021f5e68cb5701204805c798cf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Nov 7 13:11:37 2012 -0800

    Explicitly disallow copy assignment operator for ParmParse.

Src/C_BaseLib/ParmParse.H

commit 34bf15893f8a6e1b7aa85ce806466be280a4f28a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 11:29:12 2012 -0800

    Fix call to isend to make Cray happy

Src/F_BaseLib/multifab_f.f90

commit e1ef33546e4fae4e7fdf549bad2b18b722999b02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 10:54:48 2012 -0800

    fine tune nonblocking fill_boundary

Src/F_BaseLib/multifab_f.f90

commit d1f89a610be59548c992f917bde126bcd388bbd6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 6 16:59:01 2012 -0800

    Add nonblocking multifab_fill_boundary

Src/F_BaseLib/multifab_f.f90

commit 8394f1f97d7840e9711a70261ecdfd2e319650f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 5 13:41:09 2012 -0800

    CC linear solver:  The convergence test and the way to compute
    residues have changed.
    
    In the old way, at the beginning of ml_cc, a new RHS was computed
    using the initial guess, and then what the solver really solved was
    the redefined problem: Lap(\delta \phi) = RHS_new, where RHS_new =
    RHS_0 - Lap(\phi_0).  After the solver converged on the new problem,
    the full solution is updated as \phi += \delta \phi.
    
    In the new way, the convergence test uses the original RHS and the
    latest full solution.

Src/LinearSolvers/F_MG/ml_cc.f90

commit d982f6cecce31e1144c6a56b195e9502132849f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 22:41:23 2012 -0700

    minor improvement of the new fill_boundary

Src/F_BaseLib/layout.f90

commit 924d115f89e2fb5d057c671498c7625143d9eb3f
Merge: be7877559 f9ede3298
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 22:31:01 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit be7877559cb0cb6c90b29874005be896db64302c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 22:30:52 2012 -0700

    force cross to be true when idim .ne. 0 in the new multifab_fill_boundary

Src/F_BaseLib/multifab_f.f90

commit f9ede329880643442e6368087a568de053f02d63
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 2 22:08:06 2012 -0700

    added author list so we can officially be referenced

Docs/UsersGuide.tex

commit 87a953feedf014c6f09fffad020d4d61a820f93b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 17:54:41 2012 -0700

    multifab_fill_boundary can now fill boundaries in only one direction

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit 3fb1de2a02424d2fe46c8269cb01f89b8b1c968f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 16:48:46 2012 -0700

    Add optional argument dim to multifab_fillboundary; not doing anything yet

Src/F_BaseLib/multifab_f.f90

commit 0d0c0d5a0f74e871eb583406812a3f8eb94e7f44
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Nov 2 14:47:53 2012 -0400

    enforce string length limits by truncation

Tools/F_scripts/makebuildinfo.py

commit 1c7b23b1a47c0a4c54fb60ac165786b108aa47e9
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Oct 31 13:44:09 2012 -0700

    Add several minor features to speed converge

Src/C_TowerLib/MFTower.cpp
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file
Tutorials/AMR_PETSc_C/Source/Darcy.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES.H
Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp

commit 873b9372634aa0247508dc878a516d296429bffd
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Oct 31 10:27:33 2012 -0700

    Chase down a few memory leak issues, and add a 3-level example file

Src/C_TowerLib/Layout.H
Src/C_TowerLib/Layout.cpp
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_3lev.dat
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_PETSc_C/Source/Darcy.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES.H
Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp
Tutorials/AMR_PETSc_C/Source/MLBoundary.H
Tutorials/AMR_PETSc_C/Source/MLBoundary.cpp

commit 42614975d330834389ac6db954bbee4f142f3d73
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Oct 30 18:04:48 2012 -0700

    Add a README file

Tutorials/AMR_PETSc_C/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_PETSc_C/README

commit 17af2caa9b721fa0321492b57552e16728b69355
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Oct 29 19:31:04 2012 -0700

    slightly better PETSc run parameters

Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file

commit b5bfff1ea3cf5e5bbb5aa0d735dc8ca17df7dc04
Merge: 54ec788f9 b121df32d
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Oct 29 19:02:24 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 54ec788f9c353188413f1bf8f05d04264e80cd5c
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Oct 29 19:02:03 2012 -0700

    Fix up PETSc tutorial to work multilevel with a fixed-grid file

Src/C_AMRLib/Amr.H
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_2lev.dat
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file
Tutorials/AMR_PETSc_C/Source/Darcy.H
Tutorials/AMR_PETSc_C/Source/Darcy.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES_2D.F
Tutorials/AMR_PETSc_C/Source/MLBoundary.H
Tutorials/AMR_PETSc_C/Source/MLBoundary.cpp

commit b121df32d47515aacc93198b28222014054a8418
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 26 09:21:48 2012 -0700

    Remove OMP stuff from GetParticleLocationsAndMass since the "cnt" stuff
    won't work right with omp there.  This should only be used for low numbers
    of particles anyway.

Src/C_AMRLib/Particles.H

commit 304e67389f1e6107086440ce9966c9489471cbbb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 26 06:38:35 2012 -0700

    Only call MPI_Gather if BL_MPI is defined.

Src/C_AMRLib/Particles.H

commit 05616bafdd3a5843254d646b32fcee20a0038ead
Merge: f635b19dd 6ddd1f884
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 25 15:23:30 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f635b19dd7a8fd6eeba152567fd33f8a3b4d7299
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 25 15:23:13 2012 -0700

    Make the GetParticleLocationsAndMass new routine work in parallel.

Src/C_AMRLib/Particles.H

commit 6ddd1f8846b2115657fc92cd9949beafab312bba
Merge: 220d22244 50867f315
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Oct 25 13:58:44 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 220d222446f661a0e6b31c5d66b46179b208ab84
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Oct 25 13:58:20 2012 -0700

    Rearrange the boundary conditions code, and fix a bug in periodic

Src/C_TowerLib/Layout.cpp
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file
Tutorials/AMR_PETSc_C/Source/Darcy.H
Tutorials/AMR_PETSc_C/Source/Darcy.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES.H
Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp
Tutorials/AMR_PETSc_C/Source/MLBoundary.H
Tutorials/AMR_PETSc_C/Source/MLBoundary.cpp
Tutorials/AMR_PETSc_C/Source/Make.package

commit 50867f315e741322ec875789a54487e9669e8dde
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Thu Oct 25 12:48:28 2012 -0400

    fix the quotes when compile lines wrap to 2 strings

Tools/F_scripts/makebuildinfo.py

commit fffc5f319ae82405464801e8bb76dc3bf2bcea6a
Merge: 13d77c1d6 267de8e57
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Oct 24 19:54:05 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 13d77c1d64f4eee0402e04daabd33909be2fa10f
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Oct 24 19:53:44 2012 -0400

    add ability to specify min/max for second plot

python_plotfile/plotsinglevar.py

commit 70ab68fe0f7e9ea97bb8a13aca1543b6f7a64524
Merge: 6dd8847c5 8a9e08e6a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 24 15:39:08 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6dd8847c55fc0070f76ca1dca6e1aa216681a38a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 24 15:35:47 2012 -0700

    1) Added TotalNumberOfParticles to return total number of particles.
    2) Add GetParticleLocationsAndMass to return this data to an outside routine.
    3) Fix abs --> std::abs in estTimeStep so that we use the real, not integer, version of abs.

Src/C_AMRLib/Particles.H

commit 8a9e08e6a8ce51a60a96adc9fcde29646e5d8ebf
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Wed Oct 24 16:36:43 2012 -0400

    build_hash -> build_git_hash

Tools/F_scripts/makebuildinfo.py

commit a260612b80529d0ca4baca24739d6c2c081cfd33
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Wed Oct 24 16:31:45 2012 -0400

    python version of make_build_info -- the shell version was getting
    hard to maintain.  This one adds yet another git hash if it detects
    that we are compiling in a directory that is not part of the source tree,
    i.e. MAESTRO_Exec/ instead of MAESTRO/Exec/

Tools/F_scripts/makebuildinfo.py

commit 25a7cc05c3eda114403d49b6c2c18be3b7075e96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 22 17:09:19 2012 -0700

    print more information

Tools/RegressionTesting/reg_test_blame.py

commit d98aaae50713f9abf8a9a58864cc460d74f04a7c
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Oct 22 10:22:17 2012 -0700

    Minor tweaks to solver interface

Tutorials/AMR_PETSc_C/Source/Darcy.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES.H
Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp

commit d66dd8b8b3427b7a7077d9667943f6179e0fd813
Merge: f4cad54bf 19c294817
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Oct 19 14:13:10 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 19c294817273c4e0549b336f89af7b0b740a7d01
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Oct 19 10:57:00 2012 -0700

    Fix up PETSc tutorial problem to run to completion.  Still lots to cleanup though.

Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Prob_2d.f90
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_PETSc_C/Source/Darcy.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp

commit e842bbbffacaf874e2068c7e2d45f15981ead559
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Oct 18 17:45:54 2012 -0700

    Insert first cut of PETSc interface and MFTower/Layout structures needed to support it, along with a tutorial app to work out the kinks.  Note that the demo tutorial (Tutorials/AMR_PETSc_C) does not yet work and is still taking shape.  It does represent a considerable departure from the traditional BoxLib apps, in that it implements a fully-implicit time-discretization using Newton iterations (using the PETSc SNES and KSP solvers).  The tutorial app builds, but currently fails.  Not only is it being debugged, it is still be designed, adn it is being used to evaluate the MFTower implementation as well - many of the old-styles associated with the BoxLib C++/Fortran linkage are being cleaned out in this example, partly because the form of the solver used seems to dictate a more general approach to things like multi-level advance routines, as well as boundary conditions, etc.  Finally, note that I have put the MFTower/Layout classes in their own area (parallel to C_AMRLib for example) to keep my updates/reorgs from impacting the base BoxLib libraries - the plan will be to merge these structures into the C_BaseLib area when they become sufficiently stable.  Similarly, the tutorial will be documented properly when it reaches stability.  If you have any questions about this part of the CCSE codes, contact MSDay@lbl.gov

Src/C_TowerLib/Layout.H
Src/C_TowerLib/Layout.cpp
Src/C_TowerLib/MFTower.H
Src/C_TowerLib/MFTower.cpp
Src/C_TowerLib/MFTower_2D.F
Src/C_TowerLib/MFTower_3D.F
Src/C_TowerLib/MFTower_F.H
Src/C_TowerLib/Make.package
Tutorials/AMR_PETSc_C/Exec/Make.PETSc
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/.gdbinit
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Make.package
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Prob_2d.f90
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probdata.f90
Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probin.2d
Tutorials/AMR_PETSc_C/Source/Darcy.H
Tutorials/AMR_PETSc_C/Source/Darcy.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES.H
Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp
Tutorials/AMR_PETSc_C/Source/DarcySNES_2D.F
Tutorials/AMR_PETSc_C/Source/DarcySNES_F.H
Tutorials/AMR_PETSc_C/Source/Darcy_2D.f90
Tutorials/AMR_PETSc_C/Source/Darcy_F.H
Tutorials/AMR_PETSc_C/Source/Make.package
Tutorials/AMR_PETSc_C/Source/extern_probin.template
Tutorials/AMR_PETSc_C/Source/interpolate.f90
Tutorials/AMR_PETSc_C/Source/main.cpp

commit 267de8e578fddb6f9ab9c08b91e282c38a94d3e3
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Oct 17 17:58:58 2012 -0400

    get this compiling again

tutorial/GNUmakefile

commit f4cad54bfe0395ce749c8cd1de18aa6f75ebaa0c
Merge: cdf5481ba bf3871343
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Oct 15 13:49:59 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit bf387134385084c5cfee61c741d0f430fe64861f
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sun Oct 14 17:46:21 2012 -0400

    some formatting, add builddir if useExtraBuildDir is 1

Tools/RegressionTesting/testnew.py

commit 0d08c695863c45fc3eaf45ebd042e1994f799d04
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sat Oct 13 17:13:10 2012 -0400

    update to reflect changing directory structure and presence of
    MAESTRO_Exec

Tools/RegressionTesting/Maestro-tests.ini

commit e09b5332f274ac2caddeba071eb2ca75585c6076
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sat Oct 13 10:49:12 2012 -0400

    add extraBuildDir -- this can be selected on a problem-by-problem
    basis to enable compiling the problem in an alternate source tree
    (and git repo) from the SourceDir

Tools/RegressionTesting/testnew.py

commit 27bfdab84a43bd2c3aaa315da219321bc4244058
Merge: 18b27a285 c64a1fe95
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 11 14:53:41 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 18b27a2859d7506e1f651d9e378440bf3be63cb7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 11 14:48:47 2012 -0700

    Commented out some debug print statements that are not thread safe.

Src/C_AMRLib/INTERP_3D.F

commit c64a1fe95c865d7047dad5f95ac8646b7b900f86
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Oct 11 14:11:23 2012 -0700

    comment out the C++ stuff until we have something more substantial to say

Docs/UsersGuide.tex

commit e36aa6059c1d88f4548c4b2c32532ac8f2b7933e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 10 15:48:04 2012 -0700

    Fix long-standing bug in GSRB found as race-condition by helgrind.

Src/LinearSolvers/C_TensorMG/DV_3D3.F

commit 0715bbdf4a4cdf089b33eae496eb4905dce5d796
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 10 15:47:42 2012 -0700

    Tweak to OpenMP to quiet helgrind.

Src/C_BaseLib/SPECIALIZE_3D.F

commit eeea78047ad5bfc43b4e031897f5a2547bd679b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 10 11:22:31 2012 -0700

    Quit and print error message if COMP is not set properly.

Tools/F_mk/GMakedefs.mak

commit 5f37cf2f80e3ad5c296b01e56abcfabd83eaaa3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 10 11:21:20 2012 -0700

    Fix typos.  errorrr -> error

Tools/F_mk/comps/Darwin_intel.mak
Tools/F_mk/comps/Linux_intel.mak

commit 16d41e1680a3a7e3114d5c6fdabefaae25da069f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 13:50:05 2012 -0700

    Add a script for cleaning up old regression testing runs.

Tools/RegressionTesting/reg_test_gc.py

commit b3fbde45effb0c4c0f6981abb1b3271634eb260d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 12:38:30 2012 -0700

    Fix a bug in make_build_info2

Tools/F_scripts/make_build_info2

commit 23ad4cd938bef5e35a94b6388d8bcb4ffe801f5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 11:12:04 2012 -0700

    Add make_build_info2.  It is similar to make_build_info with an extra
    feature of allowing things like chemistry model being passed into the
    job info module.

Tools/F_scripts/make_build_info2

commit 662a9b2206bb6385f8faef76b11efbee4f21927d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 11:11:27 2012 -0700

    clean up reg_test_blame.py

Tools/RegressionTesting/reg_test_blame.py

commit 8efd3424ea3f56c33eb75f7b5a3726bb3ff6e020
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Oct 8 12:07:58 2012 -0700

    Add pp option for vismf verbosity

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 079ef6df190602c9f0d0cacca84f9ae0b1d02da1
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Oct 5 13:08:05 2012 -0400

    automatically take the abs() of the data if you are logging and any
    of it is < 0

python_plotfile/plotsinglevar.py

commit bfde31a6a70430727b795a4b406593eadd09b832
Merge: 9e6648ed8 0a97cdb05
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Oct 5 12:35:29 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 9e6648ed8b7c7bcd95424a82de65740183727e48
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Oct 5 12:34:58 2012 -0400

    fix limits for 3-d slices -- there should be a global limit used for
    all 3 slices

python_plotfile/plotsinglevar.py

commit f68b7499fe54fcdbd77a5ee06b05008fd5bdb90e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 21:38:42 2012 -0700

    Releasing tool: Fix the taget repo.

Tools/Release/release.py

commit 2bc854e443fa2f8457dd2c463a2919442ad7ffae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 17:43:05 2012 -0700

    Public releasing tool.

Tools/Release/ppCleanup.py
Tools/Release/release.py

commit ff0c18bd709d9bb50be29ff67fbe16bc96108f68
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 3 13:05:33 2012 -0700

    Fix MultiFab::norm0 so it now works correctly when the MF is all zero.

Src/C_BaseLib/MultiFab.cpp

commit b9d063d6b1c1842592be8cd35c2647a21fe948d6
Merge: 496d46906 6b1dbc3ef
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 3 12:31:34 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 496d469069fbffeb24c624ad4cf6345cd34990af
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 3 12:31:25 2012 -0700

    Get this compiling again.

Tests/F_BaseLib/t_main.f90

commit 6b1dbc3ef1a408ba18423ec9a145d035b28cf2a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 11:55:11 2012 -0700

    Regression testing script: add reportActiveTestsOnly option

Tools/RegressionTesting/BoxLib-tests.ini
Tools/RegressionTesting/Castro-tests.ini
Tools/RegressionTesting/IAMR-tests.ini
Tools/RegressionTesting/LMC-tests.ini
Tools/RegressionTesting/Nyx-tests.ini
Tools/RegressionTesting/testnew.py

commit 44ddd4a10d177c7f8ca05e46fe75e3aeaeafe2f2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 1 12:23:05 2012 -0700

    Fixed typos.

Src/F_BaseLib/multifab_f.f90

commit 0a97cdb05300fd15958f3716c799dc67f120a04b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 1 10:35:04 2012 -0700

    fcompare: Fix 2D case

fcompare.f90

commit 1f8bcf95d411e1acfd1795a8ee3edcb11014a41b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 1 09:42:23 2012 -0700

    Added contains_inf() and contains_nan() for multifabs to match calls for fab
    routines.

Src/F_BaseLib/multifab_f.f90

commit 69a4d4cdfd1ebd5e61f624504a79f4926c94ed33
Merge: b7ace7cd5 4ea093187
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 30 21:25:22 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/AmrPostprocessing

commit 4ea093187ac1f779475734319209951ac7836ac8
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sat Sep 29 12:53:49 2012 -0400

    not supported

fIDLdump.f90
fIDLdump3d.f90

commit d62704353e0e19881196f11e1fa674d8ae2776d7
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sat Sep 29 11:34:40 2012 -0400

    add NaN detection

fcompare.f90

commit 200fcf9aef3ce21fe1f3e3e8a42e41ae35b0faea
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 28 15:49:48 2012 -0700

    Substituted a select case statement for a long if/elseif string.

Src/LinearSolvers/C_TensorMG/DV_3D3.F

commit e3c7e4efee32f41e9ce5729810f6222724797df3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Sep 27 14:48:15 2012 -0700

    only providing OMP support for 3D in the base infrastructure now

Docs/GettingStarted/GettingStarted.tex
Docs/UsersGuide.tex
Tutorials/HeatEquation_EX1_C/advance_2d.f90
Tutorials/HeatEquation_EX1_F/advance.f90
Tutorials/HeatEquation_EX1_F/init_phi.f90
Tutorials/HeatEquation_EX2_F/advance.f90
Tutorials/HeatEquation_EX2_F/init_phi.f90
Tutorials/HeatEquation_EX3_F/advance.f90
Tutorials/HeatEquation_EX3_F/init_phi.f90
Tutorials/HeatEquation_EX4_F/advance.f90
Tutorials/HeatEquation_EX4_F/init_phi.f90
Tutorials/HeatEquation_EX5_F/advance.f90
Tutorials/HeatEquation_EX5_F/init_phi.f90

commit 49d88e1dad9c30f6bfc80733d45ab1a5757f2e72
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Sep 27 10:43:11 2012 -0700

    Fix regrid so that we delete the old multifabs before we delete the layouts on which they are based.

Tutorials/HeatEquation_EX5_F/regrid.f90

commit 7e2ceb0bbb45bc98be60fbe346b01d1da0e3c640
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 27 08:36:25 2012 -0700

    Move CASTRO_hydro routines into Castro/Diagnostics/Sedov.

CASTRO_hydro/GNUmakefile
CASTRO_hydro/fsedov1d.f90
CASTRO_hydro/fsedov2d_cart.f90
CASTRO_hydro/fsedov2d_cyl_in_cartcoords.f90
CASTRO_hydro/fsedov2d_cyl_in_cylcoords.f90
CASTRO_hydro/fsedov2d_sph_in_cylcoords.f90
CASTRO_hydro/fsedov3d_cyl.f90
CASTRO_hydro/fsedov3d_sph.f90

commit 65998a5d96d0bfe15683cac2d3abfad73e4ec40a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 26 13:35:34 2012 -0700

    Add protections against divide by 0, and clean up 1d/2d/3d a little.

fcompare.f90

commit 9026e709276e5f0c125a8bb5a0d1d680aca9948b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 24 12:16:34 2012 -0700

    Updated Nyx regression testing.

Tools/RegressionTesting/Nyx-tests.ini

commit c38897bc8b80955a9457204c8dca8eeab6082e7d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 24 12:15:36 2012 -0700

    Fix regrid so that we delete the old multifabs before we delete the
    layouts on which they are based.

Tutorials/HeatEquation_EX4_F/regrid.f90

commit 981b2dc056f82e9bb065d46b7da2c51139b7f76a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 24 12:10:52 2012 -0700

    When we take only 1/8 of the particles in WriteCoarsenedAsciiFile we
    want the mass in the domain to be unchanged (more or less) so we
    multiply each remaining particle's mass by 8.

Src/C_AMRLib/Particles.H

commit bd5af5fd29bdee43acd8feb5198bcdef536c5f67
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 24 11:27:26 2012 -0700

    Moved these files into Castro/Diagnostics.

CASTRO_gravity/GNUmakefile
CASTRO_gravity/fdustcollapse1d.f90
CASTRO_gravity/fdustcollapse2d.f90
CASTRO_gravity/fdustcollapse3d.f90

commit 0cc899e3768ed7a02170accaaaf91091183974c3
Author: Matthew Emmett <memmett@gmail.com>
Date:   Mon Sep 24 12:41:59 2012 -0400

    PyBoxLib: Simplify utils.

Src/Python/pyboxlib/utils.py

commit 786e78271c3787f38f0465b7777a1adc47628246
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 24 08:33:01 2012 -0700

    Need to include PArray.H -- now compiles again.

Src/LinearSolvers/C_NodalMG/amr_multi.H

commit 15427b9cef270f57fd9dbc98d89ff9df4135799f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 21 17:56:14 2012 -0700

    Replace CoarsenAndPrint by WriteCoarsenedAsciiFile which writes nparticles
    then only the particles from even cells into a new ascii file.

Src/C_AMRLib/Particles.H

commit 0f18ae598baafd80f7b155fab892c4ef27a43dac
Merge: 1625c4478 74be6e07d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 21 17:41:41 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1625c44784f419caf7b549b02aba645ec2622f0c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 21 17:41:05 2012 -0700

    Add a routine which writes out particles from every other cell --
    this is useful when creating coarser versions of existing particle
    files.

Src/C_AMRLib/Particles.H

commit 74be6e07d68d6ef8cd3a0ce9c9b72809827e714a
Merge: fcba448e3 d921c0ee4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 21 16:35:41 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d921c0ee421951167d3c0ec771c24b14383dc8d0
Merge: 938039071 21c8aa7dc
Author: cmalone <malone@ucolick.org>
Date:   Fri Sep 21 16:32:36 2012 -0700

    Merge branch 'master' of https://ccse.lbl.gov/pub/Downloads/BoxLib

commit 9380390718df4f16e26a4eeb3fa747e4df30f686
Author: cmalone <malone@ucolick.org>
Date:   Fri Sep 21 16:32:22 2012 -0700

    hanlde ifndef blocks properly

Tools/ppCleanup/ppCleanup.py

commit fcba448e3ca372577107547aed6da6712ff27efb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 21 16:31:30 2012 -0700

    a new ppCleanup python script for cleaning up IFDEF regions

Tools/Release/cleanWords.txt
Tools/Release/ppCleanup.py
Tools/ppCleanup/ppCleanup.py

commit 21c8aa7dc326e3d42bd5dd302e4aec11a364509c
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 21 18:00:33 2012 -0400

    Cleaned up some warning messages from g++.

Src/C_AMRLib/ErrorList.H
Src/C_BaseLib/FabArray.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/F_MG/itsol.f90

commit ca23fe981876c9ddefde2c70cbd6b46d0691bd77
Author: cmalone <malone@ucolick.org>
Date:   Fri Sep 21 11:48:21 2012 -0700

    I *think* this is working for the pathological nested cases

Tools/ppCleanup/ppCleanup.py

commit 5931433badc48498f373a5b9b2f3f7b9b21872e7
Author: cmalone <malone@ucolick.org>
Date:   Fri Sep 21 11:17:16 2012 -0700

    fix character eating with -o option

Tools/ppCleanup/ppCleanup.py

commit 36f1546b0f7e22c01f6cb235f8d3407563b05a7f
Author: Chris Malone <malone@ucolick.org>
Date:   Thu Sep 20 19:49:44 2012 -0700

    no longer need to have version 2.7.X

Tools/ppCleanup/README

commit e66a765c947ff4d488a38d5f94b428e610fb4101
Author: Chris Malone <malone@ucolick.org>
Date:   Thu Sep 20 19:44:27 2012 -0700

    workaround for versions less than 2.7 arg parsing

Tools/ppCleanup/ppCleanup.py

commit 5f5ea57cd87eb914f912c53698a90355fa699028
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 20 15:02:18 2012 -0700

    These are the ifdef sections we want to eliminate for the first
    public release of CASTRO.

Tools/ppCleanup/cleanWords.txt

commit 3e9c8ff3b09e22617c664d83edacde6a16e77d7a
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 19 13:45:42 2012 -0700

    Fix up CMake files

Src/F_BaseLib/CMakeLists.txt
Src/LinearSolvers/C_to_F_MG/CMakeLists.txt
Src/LinearSolvers/F_MG/CMakeLists.txt

commit b42acf5fcbd2668fca46a808cf2ca87a8768d6f4
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Tue Sep 18 18:12:08 2012 -0400

    forgot to commit this originally

Src/F_BaseLib/bl_prof_backtrace.f90

commit 6f887163f53dcaf045c97217f431756fd0d271c6
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Sep 18 13:03:58 2012 -0400

    bl_error cannot include the bl_prof stuff needed for a stacktrace,
    because when we run with PROF=t, we get circular dependencies.
    
    Now create a separate bl_error just for the backtracing stuff.

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_error.f90
Src/F_BaseLib/bl_error_backtrace.f90

commit a48cf41f4d3ed704ce5814a78d646ab5df70517b
Author: Matthew Emmett <memmett@gmail.com>
Date:   Mon Sep 17 20:58:15 2012 -0400

    PyBoxLib: Various updates to run utilities and fabric utilities.

Src/Python/pyboxlib/__init__.py
Src/Python/pyboxlib/fabutils.py
Src/Python/pyboxlib/plotfile.py
Src/Python/pyboxlib/utils.py

commit b7ace7cd5fe71a2222da9c67869fb01b716dd8bb
Merge: a144d1f28 a94ea2736
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 17 13:50:34 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/AmrPostprocessing

commit ae7ba37ef461b1db042643611863fa959afea64f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 17 13:49:06 2012 -0700

    Include <ParmParse.H>

Tutorials/AMR_Advection_C/Source/ADR.cpp

commit f07230fd82b77d7ec3f1a603b9a519f4505b2c7d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 17 13:39:33 2012 -0700

    Fix GNUmakefile in AMR_Advection_C Tutorial.

Tutorials/AMR_Advection_C/Exec/UniformVelocity/GNUmakefile

commit bb6450eb3c5eb722fbd54a2be201491b69f21f53
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 17 09:58:57 2012 -0700

    Modify 1d and 3d versions of diagonalization as well as 3d.

Src/LinearSolvers/F_MG/itsol.f90

commit 948716153d99d4afc509ca8641c3738717a5a16d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 17 09:57:21 2012 -0700

    Protect against divide by zero in diagonalization.

Src/LinearSolvers/F_MG/itsol.f90

commit a400f59e1bb8830b25be1b926631628dba30f05f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 18:03:57 2012 -0700

    Fix C_Src part of regression testing script

Tools/RegressionTesting/testnew.py

commit 871fc241787672377715443ac484d2ebd3b32565
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 14 16:31:16 2012 -0700

    instrumented the unoptimized hypterm.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90

commit 975a50ad69ca1e269e2b45376f8cb231ede3a229
Merge: 9fa4f4590 04faea34e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 14 09:37:05 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 04faea34e228f5cb7be2ad79d0d2718bd1d13e5d
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Sep 14 11:06:35 2012 -0400

    latest Maestro tests

Tools/RegressionTesting/Maestro-tests.ini

commit ca33abf1fbde952da7af4d24f5aa33696941a2f8
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Sep 14 10:54:20 2012 -0400

    add support for debug tests

Tools/RegressionTesting/testnew.py

commit 9fa4f45902516d33126bd87a87b61bc997dd8d97
Merge: 2ce4e17ba eef78283e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 13 20:44:51 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2ce4e17bacac69fb15f7cfc820a6e89102b06478
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 13 20:44:31 2012 -0700

    Specialized copyToMem() and copyFromMem() for Real.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/SPECIALIZE_1D.F
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H

commit feddf5e12083b9c9b066ef6bcfc5136492edefcb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 13 19:48:01 2012 -0700

    Merged in copyFromMem().

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 8a11e48ffd5f7e94a730851865fea74d7d546f04
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 13 19:47:25 2012 -0700

    Added copyFromMem() to complement copyToMem().

Src/C_BaseLib/BaseFab.H

commit 40fba1d7b6794ed8db200d7a24ba3408e83358c6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 13 19:13:16 2012 -0700

    Merged in new copyToMem() calls in place of doing a copy to a temporary
    fab and then a memcpy().

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit 5e29327afe832c6c2eaa8398f7f01427889606de
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 13 19:12:07 2012 -0700

    Renamed MemCopy() -> copyToMem() and made it a member function not a
    static member function.

Src/C_BaseLib/BaseFab.H

commit 6e83bf0f16b06d9bcbafdbbae799a54b55986b3d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 13 17:31:53 2012 -0700

    Added static BaseFab<T>::MemCopy().  Specialized version of copy() that
    goes from a FAB to a raw T* memory location.

Src/C_BaseLib/BaseFab.H

commit eef78283ea9aa467f5df3c7d45ec162b2f82734c
Merge: 150537920 fd828b1e3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Sep 13 15:00:16 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 150537920391432bdbbf9b43f8cf700a6a4b56d8
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Sep 13 14:59:32 2012 -0700

    changed the_bc_tower class to use local indices for boundary conditions instead of global indices.  Changed the rest of the source code to refer to the local indices.

Src/F_BaseLib/define_bc_tower.f90
Src/F_BaseLib/multifab_physbc.f90
Src/F_BaseLib/multifab_physbc_edgevel.f90

commit fd828b1e30d28b9f93285b488f75bfea93ddb12d
Author: Matthew Emmett <memmett@gmail.com>
Date:   Thu Sep 13 16:41:09 2012 -0400

    PyBoxLib: Remove (empty) utils.

Src/Python/pyboxlib/fabutils.py

commit 3b1db25f07d20d083660dab52354a5547af6a179
Author: Matthew Emmett <memmett@gmail.com>
Date:   Thu Sep 13 16:40:22 2012 -0400

    PyBoxLib: Print warning if libpycboxlib.so can't be loaded.

Src/Python/pyboxlib/fab.py
Src/Python/pyboxlib/pybl.py

commit 3fc1074826d443547885d031cbc966a62faedc59
Author: Matthew Emmett <memmett@gmail.com>
Date:   Thu Sep 13 16:35:39 2012 -0400

    PyBoxLib: Try again...

Src/Python/pyboxlib/pybl.py

commit 7b232aa72ed33c7bb8b0ca90c716864d275df3cf
Author: Matthew Emmett <memmett@gmail.com>
Date:   Thu Sep 13 16:33:50 2012 -0400

    PyBoxLib: Print warning of libpyboxlib.so can't be loaded.

Src/Python/pyboxlib/pybl.py

commit 346f882eee0fccf8de31b322748c671055b78bc7
Author: Matthew Emmett <memmett@gmail.com>
Date:   Thu Sep 13 13:57:54 2012 -0400

    PyBoxLib: Add fabutils.py.

Src/Python/pyboxlib/fabutils.py

commit 12b2dd736fd20a3355901fab038167ca6828d89d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Sep 13 10:27:03 2012 -0700

    bugfix: during regrid, after building the level 1 layout, you need to call bc_tower_level_build on level 1 so that the bc arrays are consistent with a possibly new layout

Tutorials/HeatEquation_EX4_F/regrid.f90
Tutorials/HeatEquation_EX5_F/regrid.f90

commit 34e7c60bd42b72c41e776a73a97df4b3fee37d54
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 13 10:16:34 2012 -0700

    updates for new boxlib changes.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/main.f90

commit ec61940b62f5553fe04d3b04a7e64162481a1cd4
Author: Matthew Emmett <memmett@gmail.com>
Date:   Thu Sep 13 11:22:54 2012 -0400

    PyBoxLib: Finish plotfile support and add "compare" routines.

Src/Python/pyboxlib/__init__.py
Src/Python/pyboxlib/fab.py
Src/Python/pyboxlib/multifab.py
Src/Python/pyboxlib/plotfile.py
Src/Python/src/boxlib_numpy_c.c
Src/Python/src/boxlib_numpy_f.f90
Src/Python/src/fboxlib.f90

commit e340783674accbf4e7c37d9f63ece98007d8efe2
Merge: ebaa6061e 0406d4261
Author: Matthew Emmett <memmett@gmail.com>
Date:   Thu Sep 13 11:23:15 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 0406d4261d04ed09cb904d374c124c30acd9058a
Merge: 35c74ffe5 e259e4f9e
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 12 14:23:13 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 35c74ffe50f1f3f4f24b697730b09eb0dc25e4b0
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 12 14:22:39 2012 -0700

    fix multilevel bug.  after ml_restricted_build, la_array is not consistent with mla%la.  Therefore we must redefine/build the_bc_tower stuff

Tutorials/HeatEquation_EX4_F/main.f90
Tutorials/HeatEquation_EX5_F/main.f90

commit e259e4f9e20d540d7331ac30cee1bd03405ccaec
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 12 13:14:19 2012 -0700

    Fix templatization issues in FillBoundary calls and add inline funcs in Amr

Src/C_AMRLib/Amr.H
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 15605c7d0203b996d6f438f523f51b22ff2384b7
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 12 11:55:07 2012 -0700

    Try again to fix cmake

Src/F_BaseLib/CMakeLists.txt

commit e85cb9e525d3bda3e1dcfdbfdad43d6e135c275a
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 12 11:42:36 2012 -0700

    Fixup CMakeLists.txt files in fort folders

Src/F_BaseLib/CMakeLists.txt
Src/LinearSolvers/F_MG/CMakeLists.txt

commit 7cdee3ef2723ac89b9b63f6c3a45d22f6c1a01a7
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 12 11:19:20 2012 -0700

    update CMakeLists file in F_Baselib

Src/F_BaseLib/CMakeLists.txt

commit 6bcf94b1d73b430e64c3dc818ac05f56d20375ca
Merge: 9d22582c9 4adea6416
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 12 10:48:42 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 9d22582c9229396352c261d6604aef6c9dbf1902
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 12 10:48:14 2012 -0700

    Remove check/plot writes in Amr destructor, move last writes to main

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 4adea64168bf775263daa9dac23726c06c5658d6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 12 10:29:57 2012 -0700

    more cleanup in preparation for EXASCALE

Src/F_BaseLib/define_bc_tower.f90

commit 27defe976dddeea5ac979a74fc6712ee026074c3
Merge: 48f18a47d af7dbd5da
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 12 10:07:37 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit af7dbd5da8180eb8294c59a9b03c3354b1558ba6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 12 09:35:20 2012 -0700

    some cleanup of define_bc_tower allocation/deallocation.  ngrids is also no longer part of the_bc_level.  prep work for upcoming switch to use local indices for bc stuff

Src/F_BaseLib/define_bc_tower.f90

commit 48f18a47d26ebe3328cf902d7be3f712888a47ff
Merge: 0f43f1356 bc0c5e46d
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 12 08:35:55 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit bc0c5e46d3e76233a5574713b2f332b003db46a1
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 12 08:01:29 2012 -0700

    bugfix... changed
    
           do i = 1, nboxes(fine%la)
              call push_back(pbl, box_nodalize(get_box(fine,i),fine%nodal))
           end do
    
    to
    
           do i = 1, nboxes(fine%la)
              call push_back(pbl, box_nodalize(get_box(fine%la,i),fine%nodal))
           end do

Src/F_BaseLib/fillpatch.f90

commit 2651849894c684c6023cf2c937dcbe7db0a9f1eb
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Wed Sep 12 09:47:11 2012 -0400

    add the backtrace stuff if we call bl_error.  For this to work,
    we need to set BACKTRACE := t in the GNUmakefile.

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_error.f90
Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/bl_prof_stubs.f90

commit 8463f1626f639e239630e26af81602e9cbde8b5f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Sep 11 14:48:06 2012 -0700

    local/global indexing bugfix

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 294a143efc336e72ed87ee2559b9db52b94848d6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 11 12:39:30 2012 -0700

    A little cleanup.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit ebaa6061e1ee4a9c42868b134e3f1911fd67afd9
Merge: c01714669 62d0ea971
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Sep 11 15:30:53 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c017146691782318d3bc89013589cea67321f433
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Sep 11 15:30:39 2012 -0400

    MODDEP: Ignore iso_c_binding module.

Tools/F_scripts/moddep.pl

commit 62d0ea971dfde79fc10e21c15b42527c29c949c4
Merge: aa742b54d 2c4744e8e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 11 12:09:37 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit aa742b54dc460903177e24de5643eaa972d933aa
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 11 12:07:42 2012 -0700

    Forgot to pass the multifab nodal flags to a couple box_nodalize() calls.
    For some weird reason the nodal flag argument to box_nodalize() is
    optional :-(

Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit 2c4744e8e6ffd635fda9809e1515c57f604524cd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 11 11:00:51 2012 -0700

    Add README file for new Tutorial example.

Tutorials/AMR_Advection_C/README

commit f2fa3e5d8c6252e35e97604b1428d21e01d963df
Merge: d7a8b15ff d5b6a72f4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 11 10:57:55 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d7a8b15ff4e8b4240846aa86f73844aa446f6cf5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 11 10:57:03 2012 -0700

    Add new example to BoxLib/Tutorials -- this is a multilevel ADR problem in
    the C++ framework.  About as simple as you can make an AmrLevel-type application.

Tutorials/AMR_Advection_C/Exec/Make.ADR
Tutorials/AMR_Advection_C/Exec/UniformVelocity/GNUmakefile
Tutorials/AMR_Advection_C/Exec/UniformVelocity/Make.package
Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_2d.f90
Tutorials/AMR_Advection_C/Exec/UniformVelocity/amrvis.defaults
Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.2d
Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt
Tutorials/AMR_Advection_C/Exec/UniformVelocity/probdata.f90
Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.2d
Tutorials/AMR_Advection_C/Source/ADR.H
Tutorials/AMR_Advection_C/Source/ADR.cpp
Tutorials/AMR_Advection_C/Source/ADRBld.cpp
Tutorials/AMR_Advection_C/Source/ADR_F.H
Tutorials/AMR_Advection_C/Source/ADR_advance.cpp
Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp
Tutorials/AMR_Advection_C/Source/ADR_error.cpp
Tutorials/AMR_Advection_C/Source/ADR_nd.f90
Tutorials/AMR_Advection_C/Source/ADR_react.cpp
Tutorials/AMR_Advection_C/Source/ADR_setup.cpp
Tutorials/AMR_Advection_C/Source/Derive_F.H
Tutorials/AMR_Advection_C/Source/Diffusion.H
Tutorials/AMR_Advection_C/Source/Diffusion.cpp
Tutorials/AMR_Advection_C/Source/Make.package
Tutorials/AMR_Advection_C/Source/Src_2d/ACT_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/ACT_sums_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/Derive_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/EstDt_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/MGutils_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/Make.package
Tutorials/AMR_Advection_C/Source/Src_2d/React_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/Tagging_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/bc_fill_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/ext_src_2d.f90
Tutorials/AMR_Advection_C/Source/Src_2d/fill_diff_coeff_2d.f90
Tutorials/AMR_Advection_C/Source/burner.f90
Tutorials/AMR_Advection_C/Source/extern_probin.template
Tutorials/AMR_Advection_C/Source/interpolate.f90
Tutorials/AMR_Advection_C/Source/main.cpp
Tutorials/AMR_Advection_C/Source/meth_params.f90
Tutorials/AMR_Advection_C/Source/network.f90
Tutorials/AMR_Advection_C/Source/prob_params.f90
Tutorials/AMR_Advection_C/Source/sum_integrated_quantities.cpp

commit d5b6a72f48540644aca9d104dc028d0b42c37ae0
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Sep 11 09:59:44 2012 -0700

    fix the boundary conditions so we refer to the global index.  seems to run fine now in parallel

Src/F_BaseLib/multifab_physbc.f90
Src/F_BaseLib/multifab_physbc_edgevel.f90
Tutorials/HeatEquation_EX4_F/init_phi.f90
Tutorials/HeatEquation_EX5_F/init_phi.f90

commit 24cc32c154870c8202dfd8f6c4d54533e0827ef6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 10 18:00:57 2012 -0700

    Moved some of the new multifab code into layout.

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90

commit a52600368050df6b5a62262ff13717ac77ff620c
Merge: 09c296588 92518cb25
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 10 17:54:42 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 92518cb258c4a94d3f15fa5480080d7319a8b51f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 10 17:06:16 2012 -0700

    fix lall option of multifab_volume

Src/F_BaseLib/multifab_f.f90

commit 09c2965885bf355ba271fa0d557fd11954a04573
Merge: c0ddd8999 731f5da6f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 10 16:16:05 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 731f5da6f1eaca2c129d6ec7ef7e96c24d99759a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 10 15:25:16 2012 -0700

    Fixed a very old bug that was exposed by the recent changes.

Src/F_BaseLib/bndry_reg.f90

commit 551fa4c86104fb1f6ccf37f01111b4d28fe1773e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 10 14:59:58 2012 -0700

    Update MG CC solver for the latest nfabs changes.

Src/LinearSolvers/F_MG/cc_mg_cpp.f90

commit c0ddd899961f2b224ec8c1a54b3eca2b507d218d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 10 14:53:13 2012 -0700

    Now using the same gfortran options as they use in the F90 side of the
    code.

Tools/C_mk/Make.defs

commit e6f12a8f650985005b6a75ecef58db3658c87358
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 10 14:49:21 2012 -0700

    update all fortran tutorials and documentation to update latest way to loop over grids

Docs/F_AdvancedTopics/F_AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex
Tutorials/Chemotaxis_F/advance.f90
Tutorials/Chemotaxis_F/chemotaxis.f90
Tutorials/Exp_CNS_NoSpec/advance.f90
Tutorials/Exp_CNS_NoSpec/init_data.f90
Tutorials/HeatEquation_EX1_F/advance.f90
Tutorials/HeatEquation_EX1_F/init_phi.f90
Tutorials/HeatEquation_EX2_F/advance.f90
Tutorials/HeatEquation_EX2_F/init_phi.f90
Tutorials/HeatEquation_EX3_F/advance.f90
Tutorials/HeatEquation_EX3_F/init_phi.f90
Tutorials/HeatEquation_EX4_F/advance.f90
Tutorials/HeatEquation_EX4_F/init_phi.f90
Tutorials/HeatEquation_EX5_F/advance.f90
Tutorials/HeatEquation_EX5_F/init_phi.f90
Tutorials/WaveEquation_F/advance.f90
Tutorials/WaveEquation_F/init_data.f90

commit e53b1ae8e73c0d3e8b0fb951903d0b1142de8041
Merge: 1e243e2ff 9ebd1c555
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 10 14:42:21 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1e243e2ff2c9de107964c96fd4dffa14aa381ffe
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 10 14:41:36 2012 -0700

    fixed buggy paralle logic in ml_interface_c

Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit 9ebd1c5552e8ffa3052c6addea22831e95c43ff2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 10 13:26:29 2012 -0700

    Shut up a couple warnings about unused variables.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp

commit 1d32b3ffc1e167e8be56c7065198402518c70851
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 10 13:16:12 2012 -0700

    nboxes => nfabs

Src/F_BaseLib/multifab_physbc.f90
Src/F_BaseLib/tag_boxes.f90

commit eead96b0f6a32b47eba35996484d65a1053b297e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 10 12:59:12 2012 -0700

    MAESTRO appears to work with new multifab stuff.

Src/F_BaseLib/cluster_f.f90
Src/F_BaseLib/create_umac_grown.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90
Src/F_BaseLib/multifab_physbc_edgevel.f90
Src/LinearSolvers/F_MG/cc_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_solve.f90

commit 8b68fb35649012232e85bc991104e13a7a28d097
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Sep 9 11:38:30 2012 -0700

    Use binary search in local_index().

Src/F_BaseLib/multifab_f.f90

commit e133615341a8e1b6aefe1440073a2d4a2d3ee745
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Sep 9 09:46:44 2012 -0700

    Merged in [ilz]multifab_global_index().

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/multifab_f.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit af773773e0ff7278490ffea2d40db68a341d3dc5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Sep 8 17:09:04 2012 -0700

    mf%nboxes ==> mf%nfabs
    [ilz]multifab_nboxes() => [ilz]multifab_nfabs()

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/multifab_f.f90
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_interface_stencil.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/coarsen_coeffs.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower_smoother.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_mask.f90
Src/LinearSolvers/F_MG/nodal_newu.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit b1a7830c828558d42d0b284c5da0c9afe5e37c03
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Sep 8 10:51:41 2012 -0700

    %nboxes -> nboxes() in a few places.

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/nodal_newu.f90

commit 1989d2b4086a1ab20e7b469954bdb9bd27d81fcd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Sep 8 10:40:22 2012 -0700

    More local_index() stuf.

Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/nodal_divu.f90

commit df3a0dcd8cae8640b54d0cabc0b8fc4bfc642207
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Sep 8 10:10:52 2012 -0700

    Space for face_type & skewed is allocated & defined only for FABs we own.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90

commit bf61c2049c96f4ac0b83abc40270f1ea835c0cdf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Sep 8 09:42:48 2012 -0700

    Merged in local_index().

Src/LinearSolvers/F_MG/nodal_interface_stencil.f90

commit ace4119fc279d5fa27204f1515fb1077d7fe18a3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Sep 8 08:24:45 2012 -0700

    Had to nodalize mask before growing it to get effective pbox.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit fd4c280901bd150ad594dc617fba80097b8c7ae0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 7 20:40:52 2012 -0700

    Closer to working code.  mgt%face_type(:,:,:) and mgt%skewed(:) must be
    indexed by global indices not local ones.

Src/F_BaseLib/ml_multifab.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 8900fde0e9735579e598b5f70df821ba503493c2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 7 16:35:26 2012 -0700

    Tweak to local_index().

Src/F_BaseLib/multifab_f.f90

commit e61124bc1ecea777e1fa63e683239eb71077c60a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 7 16:23:03 2012 -0700

    Merged in local_index() calls.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 175e50ee12cdd66b9b7134860f94c343483e6749
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 7 16:04:31 2012 -0700

    Got things to compile & run in serial. Almost surely there's parallel
    issues to be found.

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/ml_multifab.f90
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_interface_stencil.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/coarsen_coeffs.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/mg_tower_smoother.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_mask.f90
Src/LinearSolvers/F_MG/nodal_newu.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 18f66e595dc26a68dbd65f47034d9b1e58f40bcf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 7 13:02:09 2012 -0700

    get_[ip]*box() work on local indices.

Src/F_BaseLib/multifab_f.f90

commit 194fc5da1988beea9067298fe34a8bc20cbaf8b6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 7 10:41:33 2012 -0700

    Merged in local_index().

Src/F_BaseLib/multifab_f.f90

commit 4baa51710862cb407a06e663f2ebfaaa8834429e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 7 10:07:26 2012 -0700

    Added local_index().  Still need to merge into all the right places.

Src/F_BaseLib/multifab_f.f90

commit d1300884c8b8276f9e6ff08574cbeb960fca47dc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 7 09:27:54 2012 -0700

    Removed "most" remote() calls.  Got a couple that are more tricky to do.

Src/F_BaseLib/multifab_f.f90

commit a3b3dc3b6facfe53c63f32887de833c35a1583c4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 7 09:07:10 2012 -0700

    fbs(:) is now sized to be just the local fabs.
    idx(:) are the global boxarray indices for the local fabs.
    Removed remote() and local() functions.

Src/F_BaseLib/multifab_f.f90

commit 280aa5acbc8385b5cef4c3936db0b65c96e8ecce
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 6 15:23:23 2012 -0700

    Removed the Do_AllToAllV code.  This is unlikely to be useful as we
    move to exascale.  I left the multifab_set_alltoallv() function since
    I "think" that may be callable by some input parsing code -- it does
    nothing now.

Src/F_BaseLib/multifab_f.f90

commit a9d9e4db45f12450732f5efd195eb2a0f379014f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 6 12:52:27 2012 -0700

    Reverted out an ill-advised numcomp -> ncomp substitution.

Src/C_AMRLib/FluxRegister.cpp

commit 5302bf795b94eb435990a1ee0f4a36b1fd96bf86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 5 20:45:44 2012 -0700

    Fix a minor bug in make system I just introduced.

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 3343bf21e1733dd8d76aaac02e5044f07480a5e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 5 14:52:35 2012 -0700

    The make system can handle dependence of "include" lines in f90 files now.

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules
Tools/C_scripts/moddep.pl
Tools/F_mk/GMakerules.mak
Tools/F_scripts/moddep.pl

commit a1bdeceb40b3f12377aa05a2a25961e322c1f503
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 5 14:31:26 2012 -0700

    Made the CrseInit() that takes FABs a bit more memory efficient.

Src/C_AMRLib/FluxRegister.cpp

commit 3ababc4fe91cdbde7dcb7f01ce4ac2987ee7c124
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 5 09:02:51 2012 -0700

    Pulled some computation out of an inner loop.

Src/C_AMRLib/FluxRegister.cpp

commit cac9e4134241314716527c25b14919a818558944
Merge: 8665bbbcf e8d8cddf0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 4 15:01:01 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8665bbbcfcce714934d71368460a39ba54817f56
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 4 15:00:48 2012 -0700

    Simplified mapPeriodic() a bit.

Src/C_AMRLib/TagBox.cpp

commit e8d8cddf0c256b743818d4dfbb0d9870f8b1ff8b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 4 14:11:48 2012 -0700

    Fix test on ref_ratio -- we were just doing the wrong test on whether
    all the components were the same ... (was previously testing across
    levels, just meant to test across 1:dm)

Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit d9a50c8a531611e8b0c8f670ff2bc0b9773601b2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 4 12:25:19 2012 -0700

    Replaced the specialized CrseInit() parallel implementation with one that
    uses parallel copy()s. I'd like to do the same for the parallel
    implementation of Reflux() but that's more complicated ...

Src/C_AMRLib/FluxRegister.cpp

commit d8c967d0cfd70ede90262a51de867f9a823b51cc
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date:   Sat Sep 1 14:47:53 2012 -0400

    Yet more early exits from nested loops.  This about finishes (hopefully)
    my rewrite of our MPI communication and caching infrastructure.  We
    should be ready for exascale.  Metadata has been minimized & should not be
    an issue.  The new code is also significantly faster than the new, with
    the difference increasing as the number of MPI processors increases.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit 23db1acc901207629aa734b9cf695566c3a320f7
Merge: 0f88845c5 bec05050d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 31 13:39:43 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit bec05050d939a403a5117e88287f4ec13be94517
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 31 13:37:55 2012 -0700

    more make and output tweaks.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90

commit 0f88845c51dba752ccb1c3b209ae93c2925c2070
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 31 12:28:15 2012 -0700

    More short-circuiting out of loops.

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit c165dfd4dd9e3afd3f1a05427599c154560e0c83
Merge: 8c2c9a795 0d6949495
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 31 10:56:28 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8c2c9a7950f95febf4177d3f789af2e02ef5601e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 31 10:53:45 2012 -0700

    Have Finalize() flush cache.

Src/C_BaseLib/DistributionMapping.cpp

commit 0d69494953238ea2f373d97436e469f325fe0236
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 30 17:34:09 2012 -0700

    set up the makefiles to allow local setting of optimization flags.
    there is something wrong with the f90 flux minmax output for rho.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile

commit 45046d20a22b1c3aaf30aecd0101142fb76903ea
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 30 15:44:20 2012 -0700

    Refinement of the count of bytes held by the caches.  I was overcounting.

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit 04383c384aaf4b8893b427714b82e58adfa58f40
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 30 15:22:09 2012 -0700

    Some speedups.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit e323638ac689b34eb637e995e085e5b6a8ffe93f
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 30 13:23:58 2012 -0700

    added openmp flag for c.

Tools/C_mk/Make.defs

commit b8943740e35fb97964e2991605ea3ab0b98e347a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 29 16:13:28 2012 -0700

    undid some changes from hopper.

Tools/C_mk/Make.defs

commit 97035a229992903265f8a4cbf55d7cb7cd593a1e
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 29 16:07:07 2012 -0700

    set omp flag for regular c.

Tools/C_mk/Make.defs

commit ac7eef4e9066cf2604d9915d9bd729bfbf3f0088
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 29 15:54:22 2012 -0700

    omp fix.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F

commit 6afb27459948ddd1e2fd57134dbd5ac3b7ca595a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 29 15:24:03 2012 -0700

    made the output more consistent between cases.
    cleaned up some code.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.c
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/main.f90

commit 7245a35688b070e045a486751fbce0fa7499ed1d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 29 12:59:21 2012 -0700

    reused files.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.F
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.H
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/bench.c
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.h
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.x86.c
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer_c.c

commit 0e8432cffbedc705ad11d315cec5c36e87797189
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 29 11:06:36 2012 -0700

    Some cleanup.

Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H

commit 85bad3b9159086d648a65250b1279d72c463124f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 29 10:36:03 2012 -0700

    For now always print out the DistributionMapping cache stats; i.e. ignore
    whether or not verbose is set.  I want to get a good handle on the total
    amount of metadata being used.

Src/C_BaseLib/DistributionMapping.cpp

commit eae90f2b59655b3d37a8cb1da695af5ab741c589
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 29 10:28:29 2012 -0700

    Little code cleanup.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryRegister.H

commit c01f75d096ccbd8dc59e0dc8b6a5dee294744b23
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 29 10:13:03 2012 -0700

    Simpler (but equally good) key calculation for copy cache.

Src/C_BaseLib/FabArray.cpp

commit b05487efa7fb80461172bb42deac39858b7f125f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 29 10:10:31 2012 -0700

    Moving short inlines directly into class declaration.  This seems to
    make the code a little easier to read and cut down total amount of code.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AuxBoundaryData.H
Src/C_AMRLib/BCRec.H
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/StateData.H

commit dcffdef7bafbd99ffdd5a77d6a071381e429775e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 29 08:52:08 2012 -0700

    Wrapped some long lines.

Src/C_BaseLib/Array.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/Pointers.H

commit 6763e6d11e5673ff41a20ad8ee13b81a7ec7ec2d
Merge: d423475a5 2b028d606
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 28 16:49:25 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d423475a53cbedcd82881dc92677701a3eef3b5a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 28 16:46:21 2012 -0700

    Some simplification.

Src/C_BaseLib/Array.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/RealBox.H
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/UseCount.H

commit 2b028d60638e39a73fac7975ca16520d65ca804b
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 28 13:16:41 2012 -0700

    some cleanup.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/bench.c
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.h
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.x86.c
Tutorials/Exp_CNS_NoSpec/HyptermKernels/README

commit 6f6eee43fe6e96fa1aaa5c8f37058ebbdea0d733
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 28 13:05:13 2012 -0700

    they should all be working now.
    stil need to sync timings and consolidate duplicate files.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.F
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.H
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/Make.package
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.h
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.x86.c
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/main.f90

commit 6838e79f981c9b512597225ce2851a47a9375a6a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 28 11:17:54 2012 -0700

    A little cleanup of some output I had left in.
    I'd Key used in the copy cache is better than previously, but
    SyncRegister::FineAdd() can generate a number of distinct calls to
    plusFrom() that all yield the same Key :-(.

Src/C_BaseLib/FabArray.cpp

commit afc71d45b80603fe51516e3f4adf378c146178f7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 28 11:03:57 2012 -0700

    Came up with better Key into the multimap for the caches in an attempt
    to minimize the search time.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 96bd04bd24089eaa357c9ff99467c18febeac56a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 27 17:16:21 2012 -0700

    Shortcut out of a nested loop a little earlier than before.

Src/C_BaseLib/Geometry.cpp

commit fb8bddb6474343f988cc79d767ac014fcdf2ebac
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 27 16:56:02 2012 -0700

    Increase max size of FillPeriodicBoundary() cache.

Src/C_BaseLib/Geometry.cpp

commit ea2f3f76dc03dccc517aa878b0b4499262ad123f
Merge: 5b2a8391c b76b4c5c2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 27 16:44:14 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5b2a8391c0c03ccadf6ae281f5bcf2bebc93329e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 27 16:43:41 2012 -0700

    Implemented SunBoundary() using intersection & communcation info
    from the FillBoudary() cache.

Src/C_BaseLib/MultiFab.cpp

commit b76b4c5c2c808bd561b870e9e319fed786a75f95
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 27 16:15:04 2012 -0700

    added u and q initialization, fixed loop and pencil ranges.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.c
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.h
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c

commit 5c7dcdb84042922a3df9b88362e87fedf865baca
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 27 15:29:24 2012 -0700

    Some code consolidation.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit ad1c4ab357e5b1c62ce4bc521e3af77c38e6d569
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 27 15:07:24 2012 -0700

    Increased the size of the caches to 100 entries.
    Refined the count of number of bytes contained by the caches.

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit d2dcccba023e98e9141cd0485d8ac4fc1fcab21b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 27 14:18:01 2012 -0700

    New implementationof copyFrom()/plusFrom() that uses FabArray::copy().
    This means that it'll be able to use the copy cache & all that entails.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/FabArray.H
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit bca2d41fe46f3a5bfa1855701cbe99ca4ea4f6c2
Merge: 663e36aec 31af8dfae
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 27 12:18:06 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 31af8dfae9f67b28db0894252a16af9850094166
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 27 10:59:42 2012 -0700

    Fix a bug in getRecentFileName in regression testing python script

Tools/RegressionTesting/testnew.py

commit 663e36aeca2d812e9a1d890c6d44d22a5d00ce98
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 26 13:52:48 2012 -0700

    Call FabSet::Cache() on regrid of level 0.

Src/C_AMRLib/Amr.cpp

commit f22cb9829d0be64c06395da77374d6bd4c5b275e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 26 13:51:40 2012 -0700

    Added a cache for the grid intersection & communication info for
    copyFrom() and plusFrom().

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit ac37878b28f20190ad6e42150ca1e30f6a676943
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 26 12:47:31 2012 -0700

    Generalized the copy cache stuff so I can maintain separate copy
    caches for different purposes.  I want to have a copy cache for
    FabSet::copyFrom() and FabSet::plusFrom().

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 46c35981395d99a8820bb21c4527e66c650252c4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 26 09:55:55 2012 -0700

    Simplified Reflux().

Src/C_AMRLib/FluxRegister.cpp

commit cf770382a9b5b3ede1b4ef6caa873814dc582484
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 26 09:21:48 2012 -0700

    Simplified CrseInit().  Removed CrseInitDoit().

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit f6c359eaf033fab1599eb9c578761e55569195df
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Aug 25 19:43:54 2012 -0700

    Attempt to get a little communication/computation overlap.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 1187ddad5dddcfb554e4258fd90510ac6b16160b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Aug 25 19:11:41 2012 -0700

    Yet more code consolidation.

Src/C_BaseLib/FabArray.H

commit a623cc6f3a69de17de0e72bfcd5778484c34034e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Aug 25 15:06:31 2012 -0700

    Found my bug.  Back to the hand-optimized version of Reflux().

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 19f371bb5268727fa1cd56e68321ef0b8eea8ec6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 22:42:14 2012 -0700

    I'm reverting back to a slightly older version.  Something's weird.
    Running a single timestep multiple times on 256 cores on hopper, the FAB
    byte spread varies from run to run.  Unfortunately it should be the same
    for identical runs.

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit d1ab1d65d3570ab509f48205917a91487b7ebcab
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 22:14:40 2012 -0700

    Didn't have some logic quite right.

Src/C_BoundaryLib/BndryData.cpp

commit 39691ce6485c0382d1df298bf5ccb4f4de4c9ac6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 19:08:29 2012 -0700

    Uses iterators when running over pshifts.

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/Geometry.cpp

commit 5a91e5f65c12b157b118e7a6b3cd0b8d1a9b3755
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 18:20:49 2012 -0700

    Elide a periodicShift() call.  We call it twice in the same routine on the
    same Box.  Just reuse the pshifts result from the first call.

Src/C_BoundaryLib/BndryData.cpp

commit e6bfff18547e3f0362d0d2b8d5fbbd8de545282b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 16:53:39 2012 -0700

    Removed some #if 0 code.

Src/C_BaseLib/FabArray.cpp

commit ebf427193d14da2dff43d97532d2abd43c1b4738
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 16:46:45 2012 -0700

    Minor performance mod to periodicShift().

Src/C_BaseLib/Geometry.cpp

commit a066f85ee2b6dc60af6c372fe79e6260f01a0212
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 16:11:12 2012 -0700

    Changed some static member functions of FabArrayBase to member template
    functions and was able to consolidate more of the recent communication
    code I wrote.

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/FabSet.cpp

commit b47e005c519a81d44499d529ff13988d55d31b8d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 14:09:50 2012 -0700

    A little more refinement.

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/FabSet.cpp

commit c5cc93e5e8545ebebcbe1e68719e90d9a6b1f8bc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 13:30:35 2012 -0700

    A little more refinement.

Src/C_AMRLib/FluxRegister.cpp

commit 8c1f7c6d7583f1e28effcd20fabd0211b5a04a2a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 13:13:09 2012 -0700

    Handcoded optimized parallel Reflux routine.

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit c2901a659f0b7ecfb2095e339890912e817ac5e4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 23 17:35:59 2012 -0700

    Further simplification.

Src/C_AMRLib/FluxRegister.cpp

commit da4623e60be0eb7eeb30f93a9b0871fedac28428
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 23 15:58:04 2012 -0700

    Some more cleanup of Reflux().  I added another argument to
    FORT_FRREFLUX() -- an IntVect shift.  It's (0,0,0) if it's being called
    when the two boxes concerned overlap, but it's how much the dest fab must
    be shifted when being updated due to periodic shifts.

Src/C_AMRLib/FLUXREG_1D.F
Src/C_AMRLib/FLUXREG_2D.F
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/FLUXREG_F.H
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 44250bb178303274a28eeaede71ad595d0af55fc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 23 13:21:04 2012 -0700

    Very modest simplification of Reflux().

Src/C_AMRLib/FluxRegister.cpp

commit 44b9aaff981ebefb78ecb5748d5fe468614cc982
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 22 15:47:34 2012 -0700

    More typedef regularization.

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit 716827337c477a9aef15f439cf85b63007a3444d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 22 15:35:51 2012 -0700

    Regularized some typedefs.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 5657538a5e16e6a5b553f0f248065fa04596c8db
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 22 15:19:15 2012 -0700

    Some simplification.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 0c955f5f0372a26755c963aae5e32d71f9f11975
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 22 12:49:59 2012 -0700

    our cpp calling sam's c hypterm.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.F
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.H
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/Make.package
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/hyptermbench.c
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.h
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.x86.c
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer_c.c

commit 5e88ef995df840298645a23df0865ee3d25543b7
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 22 12:37:42 2012 -0700

    sam's c_c version.  need to check the answers.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/timer.h
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/timer.x86.c

commit e4854af457a4a86bc5b39ecb3fefa21bfc100206
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 22 12:27:28 2012 -0700

    Inlined some stuff that seems to matter at high CPU counts.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 842e8e35e8121b0addf582f3131eac73be4722b1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 22 11:11:31 2012 -0700

    OMP'd couple routines over ncomp.  At least for LMC ncomp is sometimes
    NSPECIES or BL_SPACEDIM so OMP "might" give us a nudge.

Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/FluxRegister.cpp

commit bcded6f7907a2f309a91a4ae7a9ff0d252088238
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 22 10:54:38 2012 -0700

    Made the constant volume Reflux() call the more general one.  Was able
    to get rid of a lot of code.  I'd like to simplify the more general
    Reflux() routine enough that I can provide a hand-optimized parallel
    version.

Src/C_AMRLib/FLUXREG_1D.F
Src/C_AMRLib/FLUXREG_2D.F
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/FLUXREG_F.H
Src/C_AMRLib/FluxRegister.cpp

commit 3caf944bed102cba11e58a770b62db2c9a58433b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 22 09:44:26 2012 -0700

    Removed PIRec and PIRMVector stuff -- no longer used.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit a8b17a43bc35029d150c51cb2537517875067071
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 22 09:37:16 2012 -0700

    Handcoded optimized parallel routine for SumPeriodicBoundary().

Src/C_BaseLib/Geometry.cpp

commit 6c7aba8980486e419fe889678f8e5fbb957afb1a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 22 08:28:49 2012 -0700

    Fixed compilation bug when !BL_USE_MPI.

Src/C_BaseLib/FabArray.cpp

commit 765ab7378b8a724faa877a326bdbd5e51b2ea022
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 21 20:13:59 2012 -0700

    Yet more code cleanup & consolidation of new parallel routines.

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 7bad31b4f6f84a247adc67891bc1a3ca8c067e9a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 21 19:30:31 2012 -0700

    Removed SIRec structure -- no longer used.

Src/C_BaseLib/FabArray.H

commit 4dfdc99956c48d763b332f7bef2af1ce28d5d3fc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 21 19:27:24 2012 -0700

    More code consolidation.

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/FabSet.cpp

commit fce07e7dbf0e85eb6f5d14eff0e59b79e5d7df55
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 21 17:45:26 2012 -0700

    Some code consolidation.

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 1a615c75ec352eaf45fefc390d6c77e674833a72
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 21 16:38:05 2012 -0700

    Handcoded parallel routine for SumBoundary().

Src/C_BaseLib/MultiFab.cpp

commit d745bff987c70c7f812bf6bf765aa6b9cf2e1624
Merge: fa47894d3 f2608c9c6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 21 16:37:45 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f2608c9c67ca62e25e64407e14f51a927cbb4e7d
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 21 16:05:29 2012 -0700

    the cpp_F version.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/Make.package
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/timer_c.c

commit 6cfe6f37adcfe46b771b6dac3c066715857e7b4d
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 21 15:53:41 2012 -0700

    the f90_f90 version.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/README
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/main.f90

commit fa47894d38ae6d7b0c49ccf6c894bc854f43ffc1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 21 15:02:17 2012 -0700

    Removed a data structure no longer used by CollectData().

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 2b0f795b17eeae9b9df9d940c63e9ff22471af99
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 21 13:41:17 2012 -0700

    Fix order of tests on bottom solver type when setting up mg_tower because
    in some cases the bottom solver type is set to 4 but we override that and
    set it to 1.  We need to make sure we make the nodal_mask after that change.

Src/LinearSolvers/F_MG/mg.f90

commit b6647ae740e37adf7882ecd8e324c87dcb9a5b90
Merge: 051ef928d 2135af5c8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 21 10:48:26 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 051ef928d61bb223dc79f02f141f19c684520621
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 21 09:22:08 2012 -0700

    Consolidated two CrseInit() functions into single CrseInitDoit()
    that they both call.

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit b5bf478ee8a1faee147dcffe934f5b042813e7b4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 20 21:59:18 2012 -0700

    Handcoded parallel routine for copyFrom(). Added an assertion that wasn't
    in the old code: I now check that ngrow <= src.nGrow().  I found one place
    in MacProj.cpp where it was calling copyFrom() on a src MultiFab and
    asking to fill more ghost cells than the MultiFab had.  I could have
    silently done the right thing in my code, but it just didn't seem right to
    allow people to ask for filling with more ghost cells than the MultiFab
    contains.  Hopefully MacProj.cpp is the only code that did that :-)

Src/C_BoundaryLib/FabSet.cpp

commit 2135af5c88c729763624f4d9ae3e1e1452b9db5c
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Aug 20 19:59:32 2012 -0700

    add support for USE_LMC_SDC.  Will compile in #ifdef LMC_SDC items

Tools/C_mk/Make.defs

commit 10e139c62c28af518954c9a26867bf6d5c60ff10
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 20 19:26:12 2012 -0700

    Some cleanup.  Two Reflux() functions still call CollectData(). I'll
    eventually get to them but they're a tad more complicated than the
    CrseInit()s.  I'll work my way up to'm.

Src/C_AMRLib/FluxRegister.cpp

commit 95163b082d55e0216f227a90904ca113040d01b8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 20 17:19:39 2012 -0700

    Handcoded special parallel routine for other CrseInit() -- the one
    that takes an area MultiFab.

Src/C_AMRLib/FluxRegister.cpp

commit 077f3b628e6357aabb719cba5ac28b7e6d0edcf7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 20 15:55:07 2012 -0700

    Handcoded parallel routine for FluxRegister::CrseInit().  This
    avoids the MPI_alltoall and MPI_alltoallv routines in CollectData().

Src/C_AMRLib/FluxRegister.cpp

commit 62802abf084ad649619c34e0c3bf61feadf3b8b4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 20 13:26:08 2012 -0700

    Deleted some no-longer-used static variables.
    Increased the maximum size of the caches.  We could "probably"
    go without limiting their size in any way, as they're cleared
    every level zero regrid.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 75d8bf8f72ca6bd2c71f50260d4f17b4f2e9a247
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 20 13:08:27 2012 -0700

    Final Final.

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit ea162ad6fe7239ce01c08bbd48ce039d510c3906
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 20 11:20:52 2012 -0700

    The caching stuff is looking good in tests on hopper & jaguar.  Hopefully
    this'll be the last update to this stuff for a while.  We're now running
    with bigger caches and each MPI process maintains the bare minimum amount
    of data it needs to do its job.  It's time to rewrite a few more of the
    routines that call CollectData() that can be rewritten to avoid
    MPI_alltoall and MPI_alltoallv calls.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 9b40dab41fa3030d243affe34bd37352df8c6b6f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 19 12:17:27 2012 -0700

    Fix bug in FlushCache() code.

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit 15b5817f8be6375b8636532b019ae1c75a743188
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 19 11:53:45 2012 -0700

    Fixed a bug I just introduced and did some cleanup.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit f5cfff6a1dc9f54a045370dc63bdfb1d7cfac4d5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 19 11:08:11 2012 -0700

    Don't insert FB objects into FillBoundary() cache if that particular MPI
    process doesn't have any work to do on it.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 9eade3566ba824c9bd320bc28e1df97a4b96ecd2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 19 10:40:54 2012 -0700

    Don't insert CPCs into the copy cache if that MPI proc has no work to do
    in the copy().

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 2d23fc744c7a4aa7def872997c1f498a223bb02a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 19 10:01:43 2012 -0700

    Don't add an entry to the FPB cache if that paarticular MPI procroc has no
    work to do.  This is a little tricky  ...

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 6a92b3d3dc68f5f21f4130ffdff6a6c34f5e92dc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 19 09:02:47 2012 -0700

    Print out the max amount of space used by the caches when they're being
    flushed.  This happens on regrid of level 0 and on program exit.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 60415b22109aa5acc61d0cbfdb8bd8d7258a8758
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 19 07:40:03 2012 -0700

    Increase the default size of caches.  I'm doing some experiements to
    see how big I can let these get.  For the FillPeriodicBoundary and
    FillBoundary ones we may be able to let these be unlimited in size,
    and then clear'm at a level 0 regrid.  For copy() not so much, at least
    for LMC, where we're doing a lot a rather unique copy()s for
    redistributing chemistry.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 1e06be05a0e8b3d9ee23794b71ca7e65c2ddab3c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Aug 18 18:40:11 2012 -0700

    Inlined FabComTag constructor.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit c5e8f266bbecadec6aa9df152cc1c5879c03a356
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Aug 18 18:24:43 2012 -0700

    Remove all the do_alltoallv stuff.  Never used.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit b751a89be663712f67c1959f0583cd3edd7ac75f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Aug 18 18:06:04 2012 -0700

    Minimized memory allocation & object construction in the cache stuff.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit e2f70000068212b5fdc0ccf1245a25006b235b5f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Aug 18 17:16:32 2012 -0700

    Inlined a couple heavily used member functions.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit b5b8fdd56b71d1df48cf10896b99e2dfe8d09a3c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Aug 18 10:54:58 2012 -0700

    Rewrote FillPeriodicBoundary() so it no longer calls CollectData().  This
    eliminates an MPI_Alltoall() and MPI_Alltoalv() call on initial build.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 2694e849df03640780ed8cec1d934bf0e8031388
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Aug 18 09:13:33 2012 -0700

    Untemplatized TheFPB().

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 5c7bb152c51e95da9bcfea9dae281196546b4cc7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 17 16:26:05 2012 -0700

    A little more error checking of input cache sizes.

Src/C_BaseLib/FabArray.cpp

commit ba43d34a796b1f7b39bdb8bf11d8380408356c91
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 17 16:23:13 2012 -0700

    Rewrote FillBoundary() to not use CollectData().  Should be faster since
    it avoids a MPI_alltoall() and MPI_alltoallv() on initial construction.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 4191b8f22d8f1bbffd30c3979d347baa2af26442
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 17 14:34:28 2012 -0700

    Moved some copy() code that doesn't depend on the templace type out of the
    .H file into the .cpp file.  Simplified code a bit.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit c69660c1b19941ae147c1577bb39be348941288d
Merge: eb8c2d0af e55252c53
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 17 13:56:51 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit eb8c2d0af30d87fde3b305d398afe82ac4df7fc9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 17 13:55:19 2012 -0700

    Moved the do_alltoallv stuff in copy() into its own function.
    I'm thinking of removing the do_alltoallv stuff entirely.  It's hard
    for me to imagine as we run on larger & larger machines & communication
    patterns get sparser that MPI_Alltoallv can beat MPI_Irecv/MPI_Send
    pairs.

Src/C_BaseLib/FabArray.H

commit b770f5bd47b1e22565c5611e39b3bf3db76db054
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 17 13:33:00 2012 -0700

    Moved the portion of CollectData() that uses do_alltoallv into its
    own helper function.

Src/C_BaseLib/FabArray.H

commit e55252c53e76b0bac666c1f78e76e2e28efb6b5e
Merge: 0332420ca 7aec5ef27
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 17 13:22:53 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 0332420cae3af3dcad8e07bcd2d5a142c413a507
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 17 13:22:23 2012 -0700

    gnu.

Tutorials/Exp_CNS_NoSpec/GNUmakefile

commit 7aec5ef278ac9a2460555e34cd88f4611aa97060
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 17 13:37:32 2012 -0400

    Use SameRefs() in copy  & fillboundary() cache code.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit d24047ab8c04734be8b8b0414b74d556c279a7da
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 17 13:35:26 2012 -0400

    Added static functon SameRefs() to test if the underlying reference
    counted pointers are the same.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit ade2714f21ffedd20abe79a5b88188931020245e
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 17 13:32:08 2012 -0400

    Inline operator==() in reference counted pointer class for testing if underlying pointers are the same.

Src/C_BaseLib/Pointers.H

commit dfbe31fc635f8e57e562fb01aa89e2000054c62c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 16 19:48:35 2012 -0700

    Built a map of iterators into FabComTagContainer to avoid a modest
    N^2 loop when receiving FAB data in CollectData().

Src/C_BaseLib/FabArray.H

commit ba73e896d1e5bd72c30f4f94e56f2287bb49df03
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 16 19:18:26 2012 -0700

    More performance tweaking in CollectData().
    Got one more thing I wnat to try before pushing this stuff.

Src/C_BaseLib/FabArray.H

commit ed900fb80387527348c521abb725b7cea4a8e9d0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 16 18:03:10 2012 -0700

    More tweaks to CollectData().

Src/C_BaseLib/FabArray.H

commit 16c71389229504dba58d900f1ef191469fef794b
Merge: c3a6c4716 9775f5f32
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 16 14:47:02 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c3a6c4716ab5a064ad147484fabf35ff0a07a27a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 16 14:46:49 2012 -0700

    Squished out more memory from CollectData().

Src/C_BaseLib/FabArray.H

commit 3ae6b1ace430ad47fb0c8175e53e9aba564e5681
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 16 13:03:21 2012 -0700

    Removed unused variable.

Src/C_BaseLib/FabArray.cpp

commit 9775f5f32bfa7b484d7f82ef7ac20b27cc8e6801
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 16 11:50:53 2012 -0700

    Add extra assertions and comments to make sure we understand the deletion
    of ghost particles at the end of moveKickDrift in Particles.H

Src/C_AMRLib/Particles.H

commit b11fc3984e846c2f470f64edbc217cdda179bf8c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 16 10:44:45 2012 -0700

    Changed how caches are passed to CollectData() to cut down on memory
    allocations.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit ecc35050513d896914a8132004087b846f6b39d9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 16 10:04:00 2012 -0700

    Changed the send count cache used by FillBoundary & FillPeriodicBoundary()
    from an Array<int> to std::map<int,int>.  This'll keep the size of the
    cache entries from growing as the number of cores grows. Hence we can
    increase the size of the cache a bit w/o much problem.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit bf277d92910413d04955c915bce038e518175ed5
Merge: 6ee84d5ec 110bf78ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 14 16:23:58 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 110bf78ef9165c447bf5e556980cc8773b08d2c1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 14 16:02:43 2012 -0700

    Added an optional third argument to KnapSackProcessorMap().  It's
    a pointer to a double into which the efficiecy will be placed if
    it's not NULL.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 6ee84d5ec665720ec9e346996a2f9e45219d4fd1
Merge: 018c29e28 bbc9cffe5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 14 10:37:31 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 018c29e282efcf307b3ff89ec97c0287b5ea4c16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 14 10:37:18 2012 -0700

    Fix a comment

Tools/RegressionTesting/testnew.py

commit bbc9cffe55afb28bd00e096de0b981504c168783
Merge: ac01b7ec7 a008f1027
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 14 09:35:59 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ac01b7ec7c46cb865cf2d67114dd7f9342f51758
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 14 09:11:08 2012 -0700

    Set verbose to false.

Src/C_AMRLib/AuxBoundaryData.cpp

commit a008f1027c25dfa429d2be5e262d508a8e778e09
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Aug 14 11:57:56 2012 -0400

    Add 'build' and 'destroy' interfaces to BC tower.

Src/F_BaseLib/define_bc_tower.f90

commit dbdf4a0696113835e08348201fe19d0336376206
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 13 22:18:33 2012 -0700

    Fix a bug in regression testing script for the case when extSrcGitHash is used

Tools/RegressionTesting/testnew.py

commit abbad860eea943db21b674e2515ad6911d2c403b
Author: Matthew Emmett <memmett@gmail.com>
Date:   Mon Aug 13 19:03:14 2012 -0400

    PyBoxLib: Begin adding plotfile support.

Src/Python/pyboxlib/base.py
Src/Python/pyboxlib/fab.py
Src/Python/pyboxlib/multifab.py
Src/Python/pyboxlib/plotfile.py
Src/Python/src/blobjects.f90
Src/Python/src/blobjects.py
Src/Python/src/fboxlib.f90
Src/Python/tests/test-multifab.py

commit 6f6f256efd85cd3ddf81b7b11aad834cc9c0cb0e
Author: Matthew Emmett <memmett@gmail.com>
Date:   Mon Aug 13 19:09:11 2012 -0400

    HeatEqaution: Tweak regrid.

Tutorials/HeatEquation_EX4_F/regrid.f90
Tutorials/HeatEquation_EX5_F/regrid.f90

commit a94ea27364cfce5850cd5bad778598a60ad1cf63
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Aug 8 21:10:40 2012 -0400

    some minor fixes (deallocates, comments)

python_plotfile/fsnapshot.f90

commit 0ee73c673eb746f877b7833c6dff8913e345b95b
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed Aug 8 19:35:28 2012 -0400

    CHEMOTAXIS: Tidy, use first-order stencils.

Tutorials/Chemotaxis_F/README
Tutorials/Chemotaxis_F/advance.f90
Tutorials/Chemotaxis_F/chemotaxis.f90
Tutorials/Chemotaxis_F/chemotaxis.py
Tutorials/Chemotaxis_F/chemotaxis.tex
Tutorials/Chemotaxis_F/codegen/README
Tutorials/Chemotaxis_F/codegen/__init__.py
Tutorials/Chemotaxis_F/codegen/compile.py
Tutorials/Chemotaxis_F/codegen/polyquad.py
Tutorials/Chemotaxis_F/codegen/symbolic.py
Tutorials/Chemotaxis_F/dtypes.f90
Tutorials/Chemotaxis_F/inputs.mwe
Tutorials/Chemotaxis_F/kernels.f90
Tutorials/Chemotaxis_F/kernels.py
Tutorials/Chemotaxis_F/kernels.tmpl.f90

commit c40565b9a98b3d07dfad4c1fe498b6550af9db43
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Aug 8 16:14:05 2012 -0400

    add new routine to make a plot of several variables from a flame_1d
    plotfile

python_plotfile/plot1dflame.py

commit 3264938566768737a17c3eb74d39364100f5e6b1
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Aug 8 14:37:34 2012 -0400

    add methods to get at the variable names

python_plotfile/fsnapshot.f90

commit 7f7b316e19f2914c01e0884b8029b3c6c9fcefa2
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Aug 8 12:48:08 2012 -0400

    add support for 1d data, for flame plotting

python_plotfile/fsnapshot.f90

commit ee711ba36a7859e663cb50675ff03f3a00aa7a0c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 7 20:28:35 2012 -0700

    Added extra constructor that takes a pointer to BndryData.
    We want to be able to reuse BndryData types in linear solves.

Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit f3ac2bdbf03d40e534fc9fb4fd2f3f08c39c095f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 7 18:53:03 2012 -0700

    A little cleanup of the BndryData hierarchy.

Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp
Src/C_BoundaryLib/MacBndry.H
Src/C_BoundaryLib/MacBndry.cpp

commit 1974d30aa18aab83ca4cd099f35d12e91abd6327
Merge: 7fb673949 fb97ef858
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 7 18:50:39 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit fb97ef8580070405c0b67045c2eb8d58d706fc4d
Merge: c1f369bfb b35a4773d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 7 17:28:04 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c1f369bfb3e1793f5f70337ef389a5e5f4c24b4b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 7 17:27:53 2012 -0700

    Increase the precision of numbers written to Header

Src/F_BaseLib/fabio.f90

commit 7fb673949b15adceccbf8f6a688803c0f8a2a730
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 7 10:31:53 2012 -0700

    Attempt to allow so reuse of BndryData objects.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp

commit b35a4773dd72731686153619b675819af4dc6e73
Merge: 0b21947c6 135cb6358
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Aug 7 10:13:10 2012 -0400

    Merge branch 'chemotaxis'

commit 135cb635815e08130a62356c41d1ed9b5ba39848
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Aug 7 10:11:46 2012 -0400

    CHEMOTAXIS: Add codegen, tweak some parameters.

Tutorials/Chemotaxis_F/GPackage.mak
Tutorials/Chemotaxis_F/advance.f90
Tutorials/Chemotaxis_F/chemotaxis.f90
Tutorials/Chemotaxis_F/codegen/README
Tutorials/Chemotaxis_F/codegen/__init__.py
Tutorials/Chemotaxis_F/codegen/compile.py
Tutorials/Chemotaxis_F/codegen/polyquad.py
Tutorials/Chemotaxis_F/codegen/symbolic.py
Tutorials/Chemotaxis_F/dtypes.f90
Tutorials/Chemotaxis_F/inputs.mwe
Tutorials/Chemotaxis_F/kernels.f90
Tutorials/Chemotaxis_F/kernels.py
Tutorials/Chemotaxis_F/kernels.tmpl.f90

commit 0b21947c6387d3443ede8a2d5eaecacb46cf2cae
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Aug 7 10:12:21 2012 -0400

    PyBoxLib: Bug fix.

Src/Python/pyboxlib/fab.py

commit 6b666b227420c8733e8b9bb9942c8d1734a8dfc4
Author: cmalone <malone@ucolick.org>
Date:   Mon Aug 6 14:06:29 2012 -0700

    ppCleanup is a C PreProcessor macro cleanup script that removes
    unwanted code associated with specified macros.  This is useful for
    stripping out bits of code before releasing it to the masses.
    Currently this requires python 2.7.X to run; let me know if this is a
    problem...

Tools/ppCleanup/README
Tools/ppCleanup/cleanWords.txt
Tools/ppCleanup/ppCleanup.py

commit 61e93d8ec279b59b3f22ddbb4502f0e7c2c9c7d3
Merge: 8a1560001 87c538892
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 4 20:52:32 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 87c5388925b28b8c33a1f930b2017e8c9404db36
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Aug 4 13:56:24 2012 -0700

    Changed define() so that we can reuse BndryData and derived types.  This way in LMC
    (and other codes) where we diffuse a raft of species, we can reuse these objects instead
    of building a new one for each component we diffuse.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp

commit 8a1560001c61a9c645d8be5eaede731f49f89524
Merge: f02a39ca5 1c690de70
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 3 10:49:19 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1c690de7035138be10ade0f182c14fffe538cceb
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Aug 3 10:41:58 2012 -0700

    revert

Src/F_BaseLib/define_bc_tower.f90

commit 526298a88956076011b93a908cc7bd5d33d58b57
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Aug 3 10:41:15 2012 -0700

    revert

Src/F_BaseLib/fabio.f90

commit f02a39ca518a03da35fcf10781c8d6ab562acdd8
Merge: 89b461758 4f146bfd9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 2 21:16:10 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 89b4617584a32e2a398dc010cefe8199e8b1a634
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 2 18:18:20 2012 -0700

    Update stencil_types.H according to stencil_types.f90.

Src/LinearSolvers/C_to_F_MG/stencil_types.H

commit ba700fdd2cc0f4abc8a4a02122ec7d76db9f44a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 2 18:13:55 2012 -0700

    Due to a bug in either etags or Emacs (on my Ubuntu 10.04?), absolute
    path has to be used in tagging.

Tools/F_mk/GMakerules.mak

commit 4f146bfd9d94788d57bfee9a8488fbf1454412a4
Merge: a1af24886 1867561d1
Author: Sandra May <smay@lbl.gov>
Date:   Thu Aug 2 16:51:12 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a1af248865060d5c27ba51e9e6bbe71b53f2a7a6
Author: Sandra May <smay@lbl.gov>
Date:   Thu Aug 2 16:48:50 2012 -0700

    typos

Docs/F_AdvancedTopics/F_AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex
Docs/Introduction/Introduction.tex

commit 1867561d19dda0f1a57d2d6d98abf2fdb85587ee
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Aug 2 16:37:51 2012 -0700

    test commit

Tutorials/HeatEquation_EX5_F/main.f90

commit a45761f0f4c200d513ae34998a7e2574780dd353
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 2 14:03:10 2012 -0700

    Fix a bug.  "if (stencil_type .eq. 1)" is no longer good.

Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 98fdb2daa9565a951f42db33d6a30326cf7bf47a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 1 21:19:08 2012 -0700

    Fixed the assignment of the "nodal" data member in [ilz]multifab_build()
    in the presence of an optional argument.  Interestingly, it was correct
    for multifab_build().

Src/F_BaseLib/multifab_f.f90

commit 0249714dad0c781ae31924f1d87e1cb0c568378a
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Aug 1 19:57:57 2012 -0400

    add a diffOpts attribute to tests -- this is the flags we want to
    invoke diff with when comparing plain text files (through diffDir).
    This is useful for instance to ignore comment lines in the output

Tools/RegressionTesting/testnew.py

commit 393c1e561c4b28a676d6a1dbc03b69d54a1ccb27
Merge: 8aecacdb7 c320b4137
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 1 14:45:31 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8aecacdb75941503ad804cdbbd6f7f18f80535e0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 1 14:45:07 2012 -0700

    Didn't have src_comp & dst_comp quite right in new compFlux().

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp

commit c320b4137356dfb2e9025a3da0797c5a4085a9bf
Merge: 9da9a14a3 076caf03f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 1 14:36:08 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9da9a14a395c550b794ea8bb21d2d70be238d23d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 1 14:35:48 2012 -0700

    More transition from size(ss) to using stencil_type.

Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower_smoother.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/stencil_types.f90

commit 076caf03f7a71c448b259c8319a0a7a3a79f00e2
Merge: 0ad9be847 c4f956598
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 1 13:38:10 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0ad9be84716ed13bd280aa98a24d7b4dc4c236d9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 1 13:34:16 2012 -0700

    More general compFlux().

Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp

commit ef86d1002f6199dc9f086c0108561297c781cec0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 1 13:33:55 2012 -0700

    Fixed typo in my previous fix.

Src/C_BoundaryLib/BndryData.cpp

commit 588a501a41d79895cea90b464586cbe3a7db1f95
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 1 12:51:54 2012 -0700

    Added scomp, dcomp & ncomp to compFlux() with obvious defaults.

Src/LinearSolvers/C_CellMG/LinOp.H

commit 59448172921f5b7d50433b6348deda934ace7216
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 1 12:49:57 2012 -0700

    ngrd -> grd in a couple find() functions.

Src/C_BoundaryLib/BndryData.cpp

commit c4f956598607497e57fcc7053886e752779af2ee
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Aug 1 14:47:59 2012 -0400

    add the execution time for each test on the test's web page

Tools/RegressionTesting/testnew.py

commit ab6bd1ae8655183d4ae8e3421cdaa82831ce3ef1
Merge: 9510c17cb a44bec09e
Author: Sandra May <smay@lbl.gov>
Date:   Wed Aug 1 11:13:14 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a44bec09eef1ff597bec18bc0b287a34896cf924
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Aug 1 11:12:07 2012 -0700

    added an lmultifab_build_edge subroutine

Src/F_BaseLib/multifab_f.f90

commit 1d5487133b9873b39217316c6b9c4d4af442fb1e
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Aug 1 12:55:37 2012 -0400

    add a --tests option to allow one to specify multiple individual
    tests to run, instead of just a single test via --single_test.
    Note, tests must be together in a single string with ""

Tools/RegressionTesting/testnew.py

commit 2659498080db20648cd687f61c00c8e1b589e502
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 31 19:32:02 2012 -0700

    Had argument order switch.

Src/C_BaseLib/MultiFab.cpp

commit 89d8fdeb1d5dd083906e12ab24132ccfba888750
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 31 18:40:15 2012 -0700

    Enable cross=true for FillBoundary() in LinOp::applyBC().
    My test indicate it isn't needed.
    We'll see what the regression tests say ...

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit ddb91c8c6ea2120e0d1de0a4a279ddf78edb8a87
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 31 17:33:03 2012 -0700

    Work on adding the "cross" idea to the C++ FillBoundary from FORTRAN.
    Then will have to add the add the calls to use it when appropriate.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit b54b0dbdf98f37c0c9f055858aa735f8b57606ae
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Jul 31 16:34:49 2012 -0400

    Chemotaxis: Implement SDC time-stepping.

Tutorials/Chemotaxis_F/advance.f90
Tutorials/Chemotaxis_F/chemotaxis.f90
Tutorials/Chemotaxis_F/inputs.mwe
Tutorials/Chemotaxis_F/main.f90

commit 9510c17cbfdd48945c55dd39945e874cf95970ee
Merge: 048e70adf 10ace5fa4
Author: Sandra May <smay@lbl.gov>
Date:   Tue Jul 31 12:32:30 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 10ace5fa49cc0e36449355ddd6da3ddb2480f0e4
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Jul 31 15:16:09 2012 -0400

    Chemotaxis: Minimal model working.

Tutorials/Chemotaxis_F/GNUmakefile
Tutorials/Chemotaxis_F/GPackage.mak
Tutorials/Chemotaxis_F/advance.f90
Tutorials/Chemotaxis_F/chemotaxis.f90
Tutorials/Chemotaxis_F/dtypes.f90
Tutorials/Chemotaxis_F/inputs.mwe
Tutorials/Chemotaxis_F/kernels.f90
Tutorials/Chemotaxis_F/main.f90

commit 7789eaa7dce86817fa31cb76e21d21012c07d894
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Jul 24 10:27:17 2012 -0400

    CHEMOTAXIS: WIP.

Tutorials/Chemotaxis_F/chemotaxis.py

commit 00a1184d4d52cbd1b1241f0e4fd1d48bba633aee
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Jul 24 09:59:00 2012 -0400

    CHEMOTAXIS: WIP.

Tutorials/Chemotaxis_F/GPackage.mak
Tutorials/Chemotaxis_F/advance.f90
Tutorials/Chemotaxis_F/chemotaxis.f90
Tutorials/Chemotaxis_F/chemotaxis.py
Tutorials/Chemotaxis_F/chemotaxis.tex
Tutorials/Chemotaxis_F/dtypes.f90
Tutorials/Chemotaxis_F/inputs.mwe
Tutorials/Chemotaxis_F/main.f90
Tutorials/Chemotaxis_F/sdcquad.f90

commit ffff709e03e916bd98750219ba5612acc1688b73
Author: Matthew Emmett <memmett@gmail.com>
Date:   Fri Jul 20 21:02:21 2012 -0400

    CHEMOTAXIS: Create skeleton chemotaxis example.

Tutorials/Chemotaxis_F/GNUmakefile
Tutorials/Chemotaxis_F/GPackage.mak
Tutorials/Chemotaxis_F/chemotaxis.f90
Tutorials/Chemotaxis_F/inputs.mwe
Tutorials/Chemotaxis_F/main.f90
Tutorials/Chemotaxis_F/write_plotfile.f90

commit e851724b8a3907d9a921272215df5b3cba285c20
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Jul 31 15:24:33 2012 -0400

    PyBoxLib: Update make structure, fix indexing with multiple components.

Src/Python/GMakerules.mak
Src/Python/GNUmakefile
Src/Python/GPackage.mak
Src/Python/pyboxlib/fab.py
Src/Python/pyboxlib/pybl.py

commit d753a35052bb32ddb2a0feda96321cd54fe821aa
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jul 31 11:11:19 2012 -0700

    Add definitions of FLOW, IRRFLOW, etc,

Src/F_BaseLib/cutcells.f90

commit e45399e4ebfe2582a5036145c7925d919da80553
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 30 16:27:57 2012 -0700

    Make these tests work with current MGT_Solver.

Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tutorials/MultiGrid_C/main.cpp

commit 09d40221c732766595f709c3dcbf0c0a6d6ec681
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 30 16:02:48 2012 -0700

    Delete one of the MGT_Solver constructor.
    
    Make stencil_type a non-optional argument of the MGT_Solver
    constructor, so that it will not compile without stencil_type.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit e53f151825e9815f36834806e837742ac0238bdb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 30 16:02:31 2012 -0700

    Add #ifndef _STENCIL_TYPES_H_ in stencil_types.H, and some comments

Src/LinearSolvers/C_to_F_MG/stencil_types.H
Src/LinearSolvers/F_MG/stencil_types.f90

commit 048e70adfc61d44641549f2b9a645e5ddd21f820
Merge: 0928570c9 feebc5b40
Author: Sandra May <smay@lbl.gov>
Date:   Mon Jul 30 10:11:04 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit feebc5b403936ffc45edb7ccaea78fe70f890aae
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Sun Jul 29 22:00:16 2012 -0700

    get this compiling and running again with latest interfaces changes to mg_tower_build

Tutorials/HeatEquation_EX5_F/advance.f90

commit 472d4487fa295db2cca7c6b579833a7006cb2180
Merge: 408298a50 a5450a02f
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sat Jul 28 21:12:32 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 408298a5023c414b8960ba06984d0205fd9566a9
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sat Jul 28 21:11:38 2012 -0400

    add a check on whether a restart test produced any output before
    going forward to the restart run.  Otherwise, abort the test
    and move onto the next.  This fixes a crash.

Tools/RegressionTesting/testnew.py

commit a5450a02f2143ce258d689f7e8430c99caa2aa34
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jul 28 17:48:25 2012 -0700

    Fix stupid logic mistake in defining mgt%lcross given mgt%stencil_type.
    Also fix more uses of lcross in ml_cc.f90

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit 6136ceb72f1c0318fd865a8041fa07d2036f42d3
Merge: c49274312 1f350be1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 28 07:28:39 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c492743125ffe4233ef8245efc5ab3e0b8ad0bf1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 27 22:29:30 2012 -0700

    Simplify the make_build_info script and add more comments

Tools/C_scripts/make_build_info_cpp

commit 1f350be1a19635fcaaef94fe5e7c472a2fde6a70
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jul 27 21:59:46 2012 -0700

    Start to use stencil_type rather than ncomp of the stencil to know
    which stencil we're actually using.

Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 08c07daf45bd3050e79901b13616c7b7582c5419
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jul 27 21:43:28 2012 -0700

    We now define a stencil_type and lcross as part of the mg_tower.   We will use
    stencil_type rather than testing on ncomp of the stencil to decide which stencil
    we're actually using.

Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/mg_tower_smoother.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 54b82b28c27ed21a3d6ce842b5ee502634db77d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 27 17:04:22 2012 -0700

    minor update of usage string

Tools/RegressionTesting/testnew.py

commit fa275bbda0fa29f6ef1e8df4e52ddd1cfcac9419
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 27 16:31:08 2012 -0700

    Add git hash to job_info file in plotfiles

Tools/C_scripts/buildInfo.H
Tools/C_scripts/make_build_info_cpp

commit 0c375332c4ed8a3ed35b01af678fcf0e895aa3c1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jul 27 14:31:32 2012 -0700

    Add stencil_types.f90

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/stencil_types.f90

commit 9334c387520501debefc559b4567682d486be3ca
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jul 27 14:29:05 2012 -0700

    We now pass the stencil_type explicitly through from the calling
    routine to the F90 multigrid -- this requires a change in the calling
    sequence from each application.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/C_to_F_MG/Make.package
Src/LinearSolvers/C_to_F_MG/stencil_types.H

commit 7563c83dddf14d140aac91151a2a7af8743a0e74
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 27 11:48:16 2012 -0700

    added debug checks for varnames.

Src/Extern/amrdata/AmrData.cpp

commit 440322bb4e3e8315572ac0ab600de0e1a9abae9a
Merge: d4fd568d6 76ef58d1e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 27 08:42:49 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d4fd568d67151bccdc89eb7a456f607539192d4d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 27 08:42:29 2012 -0700

    Some simplification.

Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit 76ef58d1ea9a448aeea9127b3773d6bb4da71e9f
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Jul 26 22:38:47 2012 -0400

    really fix it now...

Tools/F_scripts/make_build_info

commit 4cedbff6b4fbee5db42b2adfba7b304907678036
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Jul 26 22:37:49 2012 -0400

    fix compilation

Tools/F_scripts/make_build_info

commit a9e9e65e00c1223ed3787a58cf7068950cc8f293
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Jul 26 22:31:17 2012 -0400

    add git hashes for boxlib, source (e.g. Maestro). and extra (e.g. AstroDev)

Tools/F_scripts/make_build_info

commit ec9e708036df7e360012093d21cbe924a24200af
Author: Regression Tester account <regtester@battra.(none)>
Date:   Thu Jul 26 16:35:50 2012 -0700

    Add restart tests

Tools/RegressionTesting/IAMR-tests.ini
Tools/RegressionTesting/LMC-tests.ini
Tools/RegressionTesting/Nyx-tests.ini

commit ac5c879feb0c1d3ba38b4ffbaa283216d7cfd743
Author: Regression Tester account <regtester@battra.(none)>
Date:   Thu Jul 26 14:39:58 2012 -0700

    Add some regression restart tests

Tools/RegressionTesting/Castro-tests.ini
Tools/RegressionTesting/Nyx-tests.ini
Tools/RegressionTesting/radiation-tests.ini
Tools/RegressionTesting/testnew.py

commit 42f716e170299bdf82dd4e2690eea21cb6a034e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 26 13:09:21 2012 -0700

    The precision of Checkpoint Header is changed to 17 from 15.
    
    According to IEEE 754, if a double precision number is saved in clear
    text and is then convected back to double precision number, the clear
    text number must have at least 17 significant decimal for the new
    number to exactly match the original.

Src/C_AMRLib/Amr.cpp

commit fe4d6b5b1dce798d8c656859ac2b9600979e59c4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 24 13:56:09 2012 -0700

    More cleanup & simplification.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BoundaryLib/FabSet.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 7ee801e6c994442954c9053f81cbd84fb861f08f
Author: Regression Tester account <regtester@battra.(none)>
Date:   Tue Jul 24 12:11:15 2012 -0700

    inputs files for regression tests

Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir
Tests/LinearSolvers/ComparisonTest/inputs-rt-Neu
Tutorials/HeatEquation_EX5_F/inputs-rt

commit 608ce6980766b6d26dfc81985c436165d0d01321
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 24 12:03:39 2012 -0700

    Update README for regression testing scripts.
    
    helmeosDir is no longer required for a test suite that does not have
    any tests using helmeos.

Tools/RegressionTesting/BoxLib-tests.ini
Tools/RegressionTesting/Castro-tests.ini
Tools/RegressionTesting/IAMR-tests.ini
Tools/RegressionTesting/LMC-tests.ini
Tools/RegressionTesting/Nyx-tests.ini
Tools/RegressionTesting/README
Tools/RegressionTesting/radiation-tests.ini
Tools/RegressionTesting/test-Ubuntu.py
Tools/RegressionTesting/testnew.py

commit 17d23f1a299114e80672ee4c0eacbcfb52f8be4e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jul 24 10:29:02 2012 -0700

    These have a more general interface to s_dense_2d_nodal.

Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90

commit 7deb6bebce809b2b644d8104f9a5cb1bea638f3e
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jul 24 12:32:18 2012 -0400

    revamp the NEEDS_EOS_NETWORK stuff -- now it will work with stuff
    in AstroDev/ and also pull in the proper dependencies

GNUmakefile

commit 59acb76441c75fc0f8e1f6263a730f50445db0dd
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Jul 24 10:28:12 2012 -0400

    PyBoxLib: Add is_periodic argument to layout creation routines.

Src/Python/pyboxlib/layout.py
Src/Python/pyboxlib/pybl.py
Src/Python/src/fboxlib.f90

commit f37ce477372080bb6f138b7c43bde805460a1f77
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Jul 24 10:00:55 2012 -0400

    PyBoxLib: Added bxrange to fab and switched to global indexing.

Src/Python/pyboxlib/fab.py

commit dce757058418762cd7d183730e8def320aeec9e4
Merge: 71df56a47 32dfbe9a0
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Jul 23 21:35:27 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 71df56a47a374fc5104a8d8ed2d4f0ca62b3cfc7
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Jul 23 21:35:01 2012 -0400

    fix a comment in the mg_tower options

Tutorials/HeatEquation_EX5_F/advance.f90

commit 32dfbe9a0756dc64434d51ec34c05dde7516c5a9
Merge: e3c90a2f4 0dffc7858
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 23 18:23:03 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0dffc7858780777041eeb36c485352362849c3af
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 20 16:33:15 2012 -0700

    Using the new BoxArray::const_iterator.

Src/C_BoundaryLib/FabSet.cpp

commit b87d5058bff6d728608230d5618b40a5468f2ba2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 20 16:32:18 2012 -0700

    Using the new BoxArray::const_iterator.

Src/C_BaseLib/DistributionMapping.cpp

commit 7b86fa175ba2ddf2569dd572bdb375cdc42d7a4f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 20 15:56:27 2012 -0700

    Added const_iterators to BoxArray.  They can now be used like a const
    STL container.  We don't allow non-const iterators because BoxArrays are
    reference counted and we don't want folks to modify them without using
    the regular BoxArray interface.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit e3c90a2f4bd5dc1529163dd55ec7e1dcaabda9c6
Merge: 0964322ed 2b199421a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 20 14:51:01 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2b199421a4010e926c62bf781b42029f3d3049d6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 20 14:45:51 2012 -0700

    Used iterators more extensively.

Src/C_AMRLib/AmrLevel.cpp

commit 0964322edd13c989b26bd6cd0b234afcb332a12d
Merge: 9805b0577 effbad3ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 19 07:05:01 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9805b05770ae5422f3ea8dbc8298c30bf14ccc8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 19 07:04:54 2012 -0700

    Add baragon to F_mk

Tools/F_mk/GMakeMPI.mak

commit effbad3ed2ae0964034f8481e789febdc3bcf463
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Jul 18 23:54:59 2012 -0400

    add aux1 and aux2 to hold additional build information

Tools/C_scripts/buildInfo.H
Tools/C_scripts/make_build_info_cpp

commit ec59b73498f8ba9a2e1d683021498fe9991550d6
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Jul 18 23:34:19 2012 -0400

    add COMP and FCOMP

Tools/C_scripts/buildInfo.H
Tools/C_scripts/make_build_info_cpp

commit b975364b94ac585716bd5c5f38a71d2855c6f7d2
Merge: e62cbd39b b541a461f
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Jul 18 19:41:17 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e62cbd39bf397df1e05fb41be792868d7161897e
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Jul 18 19:39:47 2012 -0400

    add support for build information for job_info files for C++ codes

Tools/C_scripts/buildInfo.H
Tools/C_scripts/make_build_info_cpp

commit b541a461f0befef8424bb99f99ba81488bdd74d9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 18 16:13:53 2012 -0700

    Just a minor tweak.

Src/C_BaseLib/FabArray.H

commit 0fce2ee6c2dcebccfaf48e659d15244dfd37cca1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 18 15:04:54 2012 -0700

    Be more sophisticated when inserting elements into std::map<>s in
    those cases when we "know" the index is increasing, say when the index
    corresponds to the index into a BoxArray.

Src/C_AMRLib/AmrLevel.cpp
Src/C_BoundaryLib/BndryData.cpp

commit 7333f3da52d31a32775374fc7031fb6710cd6a48
Merge: 589b2528f 641f32a0e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 18 12:14:10 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 589b2528f3eb9915bd6f1b640b8c4adc393ba90d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 18 12:12:14 2012 -0700

    Fixed bug I introduced yesterday.  I was using the std::vector::back()
    function to refer to the last element in a vector.  That's fine as it goes
    but the reference returned can be invalidated if the vector is resize()d
    with the addition of new elements.
    Also shorted the names of some data members of FillPatchIteratorHelper.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit cdf5481ba2a73528cdceae38ef72747824f66de0
Merge: 2e3ed22b6 641f32a0e
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jul 18 12:02:43 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2e3ed22b6ebef1bde1871b21df1ff463b204add1
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jul 18 12:02:33 2012 -0700

    need quadmath on Marcs laptop

Tools/C_mk/Make.Darwin

commit 641f32a0ec95efa254aa88b66acb99844ea776f6
Author: Michael Zingale <zingale@jaguarpf-login2.ccs.ornl.gov>
Date:   Wed Jul 18 09:27:48 2012 -0400

    writes had an extra ',' in them -- Cray doesn't like this.  Get
    this compiling again.

Src/F_BaseLib/cutcells.f90

commit 0f43f1356872a4cbe7f6dca9ff7a9ba7dc2b002d
Merge: e061dc5e1 cb0de77f3
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jul 17 22:57:27 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit cb0de77f36d71c5205ec23868f56ff088ca2f1d1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 17 14:21:50 2012 -0700

    Added defineDoit() to consolidate two define() functions.

Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit 5dd8e159a23b9cf0cd3f105922c134f041c8c7a8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 17 14:21:07 2012 -0700

    Simplifed class declaration a bit.  Since we really only wrap an integer
    let the compiler generate copy constructor & assignment operator.

Src/C_BoundaryLib/BoundCond.H

commit e3c1166bc9010f779c8e0c6de0561393041b4559
Merge: d6db06214 4abd3e522
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 17 13:26:24 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d6db06214d597b8d719d9a2867ff4130e92e917b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 17 13:26:08 2012 -0700

    Squeezed out a little more memory.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit e061dc5e147c9527d7a0318ba0ff1021bd7553ea
Merge: e2927da3b 4abd3e522
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jul 17 11:24:24 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e2927da3b36a98d5375482558d7140804627516b
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jul 17 11:23:39 2012 -0700

    add TagBox include file

Tools/C_util/ViewMF/viewMF.cpp

commit 1ec96f93c0d7d68866b8e2c6be9076fe83a04a0e
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jul 17 11:23:07 2012 -0700

    Add special rules for hedorah

Tools/F_mk/GMakeMPI.mak

commit 4abd3e52284cca92adc6fe7b505ab526cf682779
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 17 10:52:22 2012 -0700

    Fixed a bug due to underestimating the complexity of git history.

Tools/RegressionTesting/reg_test_blame.py

commit 047d5cbec8e63832f4078bdf331125796324aaa2
Merge: 96e53fb94 94a2fd279
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 17 08:34:41 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 96e53fb946cf438edaebd54249bb6f06a5d18841
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 17 08:34:21 2012 -0700

    alpha and beta going into cc solve do not need ghost cells

Tutorials/HeatEquation_EX5_F/advance.f90

commit 94a2fd279135ef6b250e9353d12f14e5d7426ca1
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Mon Jul 16 16:43:44 2012 -0400

    get this working with the latest version of the test suite -- in particular, the
    extSrc replacing AstroDev stuff

Tools/RegressionTesting/Maestro-tests.ini

commit c538288b718fef40c59e2af527d235e753f71d83
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 16 10:36:47 2012 -0700

    Provide a specialization of invert() for Real.
    The implementation is an OpenMP'd Fortran function.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/SPECIALIZE_1D.F
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H

commit f83f80a181b7e28917e2dda3446c3d3000d7c8bf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 13 16:52:37 2012 -0700

    Pass MultiFabIDs by value not const reference. They're just integers.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 50322def0aa532c9e9795bde2686886801c2a4b8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 13 16:51:42 2012 -0700

    Inline the default constructor.
    Contrary to the previous documentation it does nothing.

Src/C_AMRLib/BCRec.H
Src/C_AMRLib/BCRec.cpp

commit 79492d67e04c724fd427738d6f9b284d37df858a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 13 16:51:05 2012 -0700

    Inline the FluxRegister::Rec constructors.

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 677cca87a3a4d900185160d03f028b8c488a68ee
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 13 16:05:48 2012 -0700

    Got rid of the "len" member data in RealBox.
    Had to throw out the length() member function.
    Calculate the len(dir) on the fly.
    Also had to throw out the length() member function in Geometry.
    This latter doesn't appear to have been used anywhere I could find.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/RealBox.H
Src/C_BaseLib/RealBox.cpp

commit 15827247ec7bd688faef2d7e866f27a09ec9ba53
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 13 15:50:00 2012 -0700

    Pass Orientations and IndexTypes by value not const reference.
    They're just fancy integers.

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit a6311943e99069c168a2fc2088bca07093c16c5b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 13 13:56:39 2012 -0700

    Minor cleanup.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 5fbcd2ff0fe37a3248c0fac0d4f173e9b20e383d
Merge: b24215abd 0d5dc2540
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 13 13:26:44 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b24215abde15dc836ee49ef1af8f8a3ce862d4dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 13 13:25:11 2012 -0700

    minor updated

Tools/RegressionTesting/testnew.py

commit 0d5dc25405b457c04ce4e5e798508adfc6b74c23
Merge: afa695a23 62564cf96
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 13 13:01:08 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit afa695a23b5da8d43e7a5874deaebf6a46ecafd8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 13 13:00:00 2012 -0700

    In BndryData changed the following member data:
    
        PArray<Mask> masks[2*BL_SPACEDIM];
    to
        std::map<int,MaskTuple> masks;
    
    Also, changed the following member function:
    
        const PArray<Mask>& bndryMasks (const Orientation& face) const;
    to
        const MaskTuple& bndryMasks (int igrid) const;
    
    using to the following typedef:
    
        typedef Tuple<Mask*,2*BL_SPACEDIM> MaskTuple;
    
    In MCLinOp.H, changed the following member data:
    
        Array< Array< Array< Mask*> > > maskvals;
    to
        Array< std::map<int,MaskTuple> > maskvals;

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/InterpBndryData.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 62564cf968d3151ff3981509208e8ecc58a63a5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 13 12:59:05 2012 -0700

    another bug

Tools/RegressionTesting/testnew.py

commit 70e7ff4451459b3f35b34547254a2277370cc0d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 13 12:43:22 2012 -0700

    fix bug

Tools/RegressionTesting/testnew.py

commit 1729079a3167a4b1ffd9f1e7c03ba5fd21685f7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 13 12:21:42 2012 -0700

    testnew.py now takes --no_update=value, where the case-insensitive
    "value" can "all" or "none" or a list of names separated by ",", such
    as "Castro,AstroDev".
    
    reg_test_blame.py now supports an extra git source other than the main
    source code and BoxLib.

Tools/RegressionTesting/reg_test_blame.py
Tools/RegressionTesting/testnew.py

commit 18b66a7ec9a05a998ace9f60baceaec2ad4b64f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 12 16:33:38 2012 -0700

    Fix outputFile.
    
    Add a new script called reg_test_blame.py that will find out which
    commit of either the main source code or BoxLib to blame.

Tools/RegressionTesting/reg_test_blame.py
Tools/RegressionTesting/testnew.py

commit 0928570c926ac809be55c8efbf27ad1074d87a9d
Author: Sandra May <smay@lbl.gov>
Date:   Thu Jul 12 15:38:08 2012 -0700

    changes to enable inflow and outflow b.c.

Src/F_BaseLib/define_bc_tower.f90

commit 77b95da20064f35cf3c13d1a167a5f255d758236
Merge: 1a731bfb9 58d1996a2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 14:29:58 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1a731bfb999d1ac9ba748f0f160b082d91f9a4f4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 14:27:57 2012 -0700

    Prototype of BndryData::bndryConds() changed from
    
      const Array<BoundCond>& bndryConds (const Orientation& face, int igrid) const;
    
    to
    
      const Array< Array<BoundCond> >& bndryConds (int igrid) const;
    
    The "new" outer dimension is over Orientation.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 2d4c37bfb9dc24750af6dc51743a03acded258e9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 14:08:15 2012 -0700

    Changed the prototype of BndryData::bndryLocs() from
    
    Real bndryLocs (Orientation face, int igrid) const;
    
    to
    
    const RealTuple& bndryLocs (int igrid) const;
    
    where RealTuple is defined:
    
    typedef Tuple<Real,2*BL_SPACEDIM> RealTuple;

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit caf98a6bd57fe939b2205fae5d553ef57951489b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 13:45:18 2012 -0700

    bcond is now a single map instead of an array of'm.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/MacBndry.cpp

commit 58d1996a276e608220d1427bfd13445eb39404a6
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 12 12:43:00 2012 -0700

    changed default.  this is not used anymore.

Src/C_BaseLib/VisMF.H

commit 54c8541cee166b3e2151e4ae128e5971b386b9e0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 12:37:41 2012 -0700

    Used std::map<int,RealTuple> for bcloc instead of
    Array<std::map<int,Real>> to cut down on memory overhead.  If we write the
    inner loops on Orientation this also puts data used per grid together.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/MacBndry.cpp

commit b1b6bb509d2c24323b8a3ac466acaa74715c8b37
Merge: 373f29185 3a9c9cae6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 11:00:07 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 373f29185750b5d6c97e673a41715b0cc8e71438
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 10:59:01 2012 -0700

    To further cut memory overhead, maskvals & lmaskvals use a
    Tuple<Mask*,2*BL_SPACEDIM> instead of Array<Mask*> for each grid they own.

Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit da4aa23458939d4de9ad63878907d050d59966ba
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 10:38:48 2012 -0700

    Squeezed out more memory by using std::map<>s for maskvals and lmaskvals.

Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit b745ad3eb1c5f88e60fdd594266bc2d4766159ed
Author: Sandra May <smay@lbl.gov>
Date:   Thu Jul 12 09:59:22 2012 -0700

    added integer parameter to define FLOW, SOLID, IRRFLOW

Src/F_BaseLib/cutcells.f90

commit 6ee2c12757e889f9e8ef0ccad5faef14e84e7d6f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 09:22:27 2012 -0700

    Replaced some uses of std::vector<bool> with Array<int>.  The former is
    great if you're trying to save storage, but it does bit twiddling which is
    more expensive than just accessing an integer.

Src/C_AMRLib/StateDescriptor.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_TensorMG/DivVis.H

commit 3a9c9cae6a9786aaa6bd6f0329b16772535bb8a1
Author: Matthew Emmett <memmett@gmail.com>
Date:   Thu Jul 12 11:35:10 2012 -0400

    PyBoxLib: Add read/write.  Tidy Makefiles.

Src/Python/.gitignore
Src/Python/GMakerules.mak
Src/Python/GNUmakefile
Src/Python/GPackage.mak
Src/Python/Makefile
Src/Python/README
Src/Python/pyboxlib/fab.py
Src/Python/pyboxlib/layout.py
Src/Python/pyboxlib/multifab.py
Src/Python/pyboxlib/pybl.py
Src/Python/read.py
Src/Python/src/boxlib_numpy_c.c
Src/Python/src/boxlib_numpy_f.f90
Src/Python/src/fboxlib.f90
Src/Python/write.py

commit b0cac50fd9ec3895c2afaf9ea2549e7b5eb81fdf
Merge: 9a5f30a6b 28a75ccd0
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed Jul 11 21:33:46 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 9a5f30a6b01f978bae601ed7f02531255d807807
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed Jul 11 21:33:27 2012 -0400

    PyBoxLib: Use boxlib_initialize instead of parallel_initialize.

Src/Python/src/fboxlib.f90

commit 28a75ccd0c83f5d1f75c00a578f2376c4eea933f
Merge: 24fa0cf1b 2f34a0611
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jul 11 18:18:55 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2f34a061166e3d356af448ccafc65be4ee4ba9ba
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 11 16:46:21 2012 -0700

    In BndryData, change the following member data:
    
        Array<Real> bcloc[2*BL_SPACEDIM];
    to
        std::map<int,Real> bcloc[2*BL_SPACEDIM];
    
    Changed the following member function:
    
        const Array<Real>& BndryData::bndryLocs (const Orientation& _face) const
    to
        const Array<Real>& BndryData::bndryLocs (const Orientation& _face, int igrid) const

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/MacBndry.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit d6a2b29609301581300f8a46c4519b143138c32b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 11 15:56:42 2012 -0700

    In BndryData, change the following member data:
    
        Array< Array<BoundCond> > bcond[2*BL_SPACEDIM];
    to
        std::map< Array<BoundCond> > bcond[2*BL_SPACEDIM];
    
    Changed the following member function:
    
        const Array< Array<BoundCond> >& bndryConds (const Orientation& face) const;
    to
        const Array<BoundCond>& bndryConds (const Orientation& face, int igrid) const;

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/MacBndry.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 24fa0cf1b1ef21e81737313f8774c731c40c8b5a
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jul 11 14:57:07 2012 -0700

    Fixed PList pop.

Src/C_BaseLib/PList.H

commit 50d45cf218eecde231a1ec01c8ed5f084683bd82
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 11 14:16:22 2012 -0700

    Got rid of the following data member in StateData.cpp:
    
      Array< Array<BCRec> > bc;
    
    Got rid of the member function:
    
      Array<BCRec>& StateData::getBCs();
    
    Changed the member function StateData::getBC() from
    
      const BCRec& getBC (int comp, int i) const;
    to
      const BCRec getBC (int comp, int i) const;
    
    This latter changes means that instead of writing:
    
      const int* b_rec = state[State_Type].getBC(strt_comp+n,gridno).vect();
    
    you'll have to write:
    
      BCRec bcr = state[State_Type].getBC(strt_comp+n,gridno);
      const int* b_rec = bcr.vect();
    
    I "think" I've made all necessary changes to stuff I have access to in
    the GIT repository.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/BCRec.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit da94587ab956068fae97076c33d0cd04e4fb990e
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jul 11 13:28:17 2012 -0700

    Added PList class for memory-managed lists of pointers.

Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package
Src/C_BaseLib/PList.H

commit 28628134a2ab20a5d4f2b7c2ae76ac55ba59bd68
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 11 12:25:13 2012 -0700

    Squeezed out some memory when running in parallel by using std::map<>s
    instead of Array<>s based on the length of the BoxArray.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 44134951f00854ffba7d407365b39d27773b39b5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 11 09:13:34 2012 -0700

    A little simplification.

Src/C_AMRLib/AmrLevel.cpp

commit e4959279c88e68633d631c10473b08722ad6dcee
Author: Sandra May <smay@lbl.gov>
Date:   Tue Jul 10 18:28:23 2012 -0700

    changed 2 things to be able to use the CartGrid option of amrvis

Src/F_BaseLib/fabio.f90

commit 2ab261c27eacaf26c1fe01c400d0c8c59e9a1f0d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 10 16:25:15 2012 -0700

    Cached a little more stuff for multifab copy().

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 68fa6b4a12e995be72ad003ab57ea7d2e45e4f4a
Author: Sandra May <smay@lbl.gov>
Date:   Tue Jul 10 13:06:54 2012 -0700

    added 2d option

Src/F_BaseLib/cutcells.f90

commit 5ccff3043226f4f7ed827507ee422acbb332fbbf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 9 20:11:26 2012 -0700

    Removed unused variable.

Src/C_BaseLib/FabArray.H

commit 87e5f5532ec24794252d9953adf67d5c8730607e
Merge: d08613c94 2dbe9053f
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 9 23:07:24 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d08613c94c51897d6a4d798b38794f37d3183219
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 9 23:06:46 2012 -0400

    A little more overlap of computation & communication.

Src/C_BaseLib/FabArray.H

commit 2dbe9053f66a85afe436500a5e7f6849981378bd
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 9 16:37:43 2012 -0700

    changed comp to gfortran

Tutorials/Exp_CNS_NoSpec/GNUmakefile

commit 16b57f02002a6f26bb2c9d1fc8a1333880fa7ec9
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jul 9 12:17:54 2012 -0700

    Removed debug messages

Src/C_AMRLib/Particles.H

commit 1f00c0b9078bb70f3f03e8612a6bf780c2dead11
Merge: a3ba992af 45514f14b
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jul 9 11:10:00 2012 -0700

    Merge branch 'master' into hybrid_sub

commit a3ba992afdd02adf13fe49a299836c2c630f1425
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jul 9 11:09:11 2012 -0700

    Added finest_level option to AssignDensity

Src/C_AMRLib/Particles.H

commit 45514f14b1118e9594e175108e55ec8544a91e9d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Jul 9 10:02:47 2012 -0700

    a call to FillPeriodicBoundary with do_corner=true now fills all corners, including those at periodic boundaries.  previously the corners were only filled if they were behind physical boundaries

Src/C_BaseLib/Geometry.H

commit 32a0267ff42a56170cace19c153ab10d454aad42
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 6 20:25:38 2012 -0700

    Sped up Checkpoint() by eliding work when no particles at a level.

Src/C_AMRLib/Particles.H

commit 62e6f30e59a42145872900b47451e994d8fe392a
Author: smay <smay@atragon.lbl.gov>
Date:   Fri Jul 6 10:26:37 2012 -0700

    added many arguments to the cutcell module, modified the build and print command

Src/F_BaseLib/cutcells.f90

commit 868ea9ca4a6c7a744fda8c0ca88a738b722a5bd3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 6 09:41:14 2012 -0700

    Turn off some uninformative Cray C++ compiler warning messages.

Tools/C_mk/Make.Linux

commit 3d2b1314c762dc177b56376e61e34aa5ec57ee36
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 6 09:21:02 2012 -0700

    Going with the NERSC-recommended Cray optimization flags: no explicit flags.

Tools/C_mk/Make.Linux

commit d85e82ad86e12c1ea6009f0ca44a864e5cc4e197
Author: cmalone <malone@ucolick.org>
Date:   Thu Jul 5 12:41:52 2012 -0700

    file not used in docs

Docs/Preface/preface.tex

commit efddf49666b45e24907c8f2e08a445cbe6a1aaad
Merge: 3348ba0b6 f821fcfe9
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Thu Jul 5 16:20:41 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 3348ba0b680e87341db0053fce8171ed75c6eef7
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Thu Jul 5 16:20:01 2012 -0400

    if we are doing a diffDir and making benchmarks, print a note about
    the diff file that was archived

Tools/RegressionTesting/testnew.py

commit f821fcfe95e58c891604bd97ede6da31b867d2c2
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 3 16:15:04 2012 -0700

    added enum back.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 88a3dbaaadad1e6d0287aa5ad1ed66638d2d0631
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 3 15:53:08 2012 -0700

    Sped up Timestamp a bit as well as added a ASSERT().

Src/C_AMRLib/Particles.H

commit 331d70899fba1acf23208da0aaae50eab7720cf2
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 3 15:40:43 2012 -0700

    added mf read benchmark.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit bbceb25c8088f3844428c40f44710268f0274fd6
Merge: 3f008b642 fb3d7f306
Author: vince <vince@gigan.lbl.gov>
Date:   Tue Jul 3 14:09:11 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3f008b642f113e529ea5495f706646804c38169b
Author: vince <vince@gigan.lbl.gov>
Date:   Tue Jul 3 14:08:44 2012 -0700

    changed VisMF::How and updated io benchmark.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit fb3d7f30604d91c17a7189f4c9ea14c20535ea97
Merge: 3cce76c18 19a30dd34
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 3 13:59:03 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3cce76c184a23776c9acf0e43e55ee65b71421ef
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 3 13:58:28 2012 -0700

    Added some more stuff to cutcells.

Src/F_BaseLib/cutcells.f90

commit 19a30dd342c62ace49af1f7eb29b61fe6b55f667
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue Jul 3 16:17:23 2012 -0400

    sync Maestro-tests.ini up with the latest directory structure + script.
    
    Merge in Weiqun's diffdir changes

Tools/RegressionTesting/Maestro-tests.ini
Tools/RegressionTesting/testnew.py

commit a510c67f5a206122a79a345b9bb4ad0bd0c259b7
Merge: 906d2a5c4 95d012814
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue Jul 3 15:16:24 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 95d01281443c432140c6216a04f8248d2927e416
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 3 09:52:44 2012 -0700

    Added ParticleContainer<N>::NumberOfParticlesAtLevel().

Src/C_AMRLib/Particles.H

commit 7940aa9fb640364a176265914718d1fc5c9a4545
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 3 09:52:20 2012 -0700

    Change the default value for verbosity from true to false.

Src/C_BaseLib/DistributionMapping.cpp

commit 611100c97630cd4fcf4a21c97d6bd8235ec80e3c
Merge: 5c94ddc5f 372fc2ca7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 2 12:53:42 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5c94ddc5f8c72acb27c9168cbd385ee8f4b85101
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 2 12:51:27 2012 -0700

    Some better memory management.
    Now KNAPSACK time also includes time spent in LeastUsedCPUs() which does
    an MPI_Allgather().  SFC time already included that time.
    I'd been wondering why SFC time was so much greated that KNAPSACK time
    when running large parallel jobs.  They should now be more comparable.

Src/C_BaseLib/DistributionMapping.cpp

commit 33848e8a2fee9e8779a48658fef52c5cc8e797b4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 2 10:52:18 2012 -0700

    Added a couple more typedefs to facilitate possible future tweaks.
    Removed some debugging code I left in.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 372fc2ca7150435e204a7fd65af20f1b151ab81e
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jul 2 10:45:41 2012 -0700

    Added setDtLevel for specific level.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 85b3f9ca1db9a402c6debdf8934220ad5c280244
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 2 09:59:07 2012 -0700

    Check that at most one of do_alltoall & do_async_send can be true.

Src/C_BaseLib/FabArray.H

commit 1e41472c683f0ba1ace9f9d524fa000ef34476f1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jun 30 09:08:39 2012 -0700

    Fix the bottom_solver = 4 option, hopefully for real this time!

Src/LinearSolvers/F_MG/mg.f90

commit 906d2a5c40385cc0b31519260f85cb93925c7941
Merge: e562ac7ea b13415c11
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Jun 29 20:20:24 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e562ac7eaac0720f08f4e7d22984f8f1f16f6db4
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Jun 29 20:20:00 2012 -0400

    start merging in some of Weiqun's changes

Tools/RegressionTesting/testnew.py

commit b13415c11f0dbd1613561508e68b53a311e415da
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 29 14:37:01 2012 -0700

    addition for ipm gnu

Tools/C_mk/Make.Linux

commit 2275750facb3904a2783d0cfcd44ad379dbbb9e2
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 29 14:20:02 2012 -0700

    instrumented the code with bl_prof.

Src/F_BaseLib/bl_prof.f90
Tutorials/Exp_CNS_NoSpec/advance.f90
Tutorials/Exp_CNS_NoSpec/main.f90

commit 257e58eadce324720b309db658163712d9b872dd
Merge: 99f241cca 4817c7a22
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 29 13:57:27 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 4817c7a2260e9803c533d3bb12facf4328be9829
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 13:26:06 2012 -0700

    Fixed something I just broke; forgot to test non-MPI.

Src/C_BaseLib/ParallelDescriptor.cpp

commit c6472d2a517617673bbbab0358836606ee799024
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 13:25:40 2012 -0700

    Defined MPI_DATATYPE_NULL for non-MPI builds.

Src/C_BaseLib/ccse-mpi.H

commit bce6f8721ea7abe0c437beac79730ee62e83c34c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 13:08:42 2012 -0700

    Moved "struct RF" from an unnamed namespace in the .cpp file into the
    class definition of FluxRegister.  Also renamed it to "Rec".  This way
    we can reuse this struct in other code.

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 3098356851ce630fdd2a9e7ad3ed0e67601206a2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 12:51:21 2012 -0700

    Fixed typo.

Src/C_BoundaryLib/FabSet.cpp

commit 4f1e9eb1521eb7d5d1677ad4db8a625848b060d3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 12:37:01 2012 -0700

    Removed some redundant code.

Src/C_BoundaryLib/FabSet.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 8dd6ad5b0981f62c25a3bcb7f2b3edd6a7d68f54
Merge: 005d55975 e45f5cb0c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 11:26:46 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 005d55975db65c07b8f2b7c11dddf08f3b81ca50
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 11:26:35 2012 -0700

    Removed some redundant code.

Src/C_BaseLib/BoxArray.cpp

commit e45f5cb0c8e4ff3e849349d904839859f335a4a1
Merge: a5e45e08b 11dd21187
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 29 11:19:38 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a5e45e08be28efd3e863782756c84c336c102899
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 29 11:18:28 2012 -0700

    Fix to initial timestep fix. It now pays attention to regridding -and- checks input flags

Src/C_AMRLib/Amr.cpp

commit 11dd2118721b6bf5794b1f8b4aaf4e4c42d61977
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 10:20:49 2012 -0700

    Added skeleton for cut cells stuff.

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/cutcells.f90

commit 0800b32a1f8c4e8e3f496078f32c39293680b80b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 10:17:08 2012 -0700

    Removed the isects.reserve() calls.  They're now embedded in the BoxArray
    intersections() calls.

Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 0145f3d54ac9a1bcf03cf5c2be5385159668bf2c
Merge: 397b601d0 37216f4ce
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 09:59:09 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 37216f4ce163dfba81f5c1d4c7bef24a186533d6
Merge: 8c07a3ea7 bee5cacae
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 29 09:56:19 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8c07a3ea771b8cb71191b130e014fa0d422be87a
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 29 09:54:46 2012 -0700

    Fixed bug where Level 0 initData could be called multiple times.

Src/C_AMRLib/Amr.cpp

commit 397b601d0081689f2c8527e11368cbcfbb7b92fa
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 09:40:47 2012 -0700

    A final bit of polishing.

Src/C_BaseLib/FabArray.H

commit d19c44581df24021c67fbc12ffa52faaec06981d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 09:14:45 2012 -0700

    Inlined & simplified some stuff.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit bee5cacae28aa50fafb849335792064136d4ed5c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 28 17:37:28 2012 -0700

    Inlined a few things.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 02a1ca287e7bb970bedc814489dc5c59f28dd081
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 28 17:08:43 2012 -0700

    Use std::deque<> for fabComTagList and fabCopyDescList instead of
    std::vector<>.

Src/C_BaseLib/FabArray.H

commit f9d45e422ed633f806377de1350df96ea325d698
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 28 15:47:26 2012 -0700

    Squished out some more memory.  Also added some new typedefs.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 09c5eecdcc0c523d7cc251e080ce835bc06024d4
Merge: 017989dd9 8a8ab5ee1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 28 15:45:07 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 017989dd937bd8ccef18d4d0e2f5f89b59c44259
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 28 15:24:03 2012 -0700

    Squished out a little more memory.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 8a8ab5ee148bb1900523c47176444264e504db80
Merge: 9283e75f6 e7742482a
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Thu Jun 28 15:18:54 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9283e75f6420a07c32a0c0ea8de57263c8b8a5bd
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Thu Jun 28 11:17:55 2012 -0700

    Subcycling bugfixes and a change to initial dt computation.
    This change may slightly change the size of the first timestep
    and break regression tests.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Particles.H

commit e7742482ae4032088b3d1c3b3e7b15444d4ac44e
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Thu Jun 28 15:48:55 2012 -0400

    all repos are now git.  Make the changelogs work for all the git
    and finish the AstroDev inputs

Tools/RegressionTesting/testnew.py

commit f4e8f625afd98d1ac63878aaf429af6f2aa89b85
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 15:17:20 2012 -0700

    Optimal Subcycling added.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit f1d0d9b85e371114dfb969bce5f6e7ab3258a8b2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 27 13:59:23 2012 -0700

    A little more cleanup.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/MultiFab.cpp

commit e731e53fa7c9d0cb0c0fb0054c5597a856c0446d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 27 12:45:11 2012 -0700

    Minor efficiency improvements.

Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp

commit c92de450af90489d49cfd2b1740416af9a4fe9eb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 27 12:26:46 2012 -0700

    Some memory efficiency improvements.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 8e202b0907ca929f2288659e355f2fc5c70e9b45
Merge: d01315c17 841d86e5c
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 12:26:06 2012 -0700

    Merge branch 'master' into opt_sub

commit 841d86e5c803cb7799e913c71aa24d787013aff6
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 11:28:53 2012 -0700

    One more ADDI fix.

Src/C_AMRLib/Particles.H

commit e481fe2c23511735ae8ee7c884deddc077ea2d1c
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 11:19:01 2012 -0700

    Level indexing fix for AssignDensityDoIt

Src/C_AMRLib/Particles.H

commit d981c716e0e49ea8f5aadd8c36ac477534839546
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 10:35:41 2012 -0700

    One more small virtual numbering change.

Src/C_AMRLib/Particles.H

commit 123dbd6ab42030ad909526fc6a25811b43ae1dc0
Merge: 1d48be39d a609992ec
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 10:30:56 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1d48be39dd4a5072db751484f32749f9e55fe211
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 10:30:02 2012 -0700

    Fix to AddParticlesAtLevel and virtual/ghost particle numbering.

Src/C_AMRLib/Particles.H

commit d01315c17ff37733f40262f346e90b1206c1bcc4
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 10:29:24 2012 -0700

    Work on optimal subcycling

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit a609992eca400d0c0c8c1493d7893ce450798cce
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 26 17:35:57 2012 -0700

    Minor simplification to collate().

Src/C_AMRLib/TagBox.cpp

commit b8d3ef752753cbb2451e4b7cadc1e460f3ce6f21
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 26 17:11:06 2012 -0700

    Some cleanup of minIndex() and maxIndex().

Src/C_BaseLib/MultiFab.cpp

commit 1c69d52df91600273c560f02cec9c8d8f746b6f5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 26 16:34:47 2012 -0700

    Cut down on number of heap allocations.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 53018677062b4ae7d5d29f125dabe8485b0c3efb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 26 14:42:50 2012 -0700

    Improved the memory efficiency of copy() and CollectData().
    Trying to miniminze the number of NProc size arrays needed.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 53105d4311974ed8cd3674e8b009daebec0e27d3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 26 14:14:32 2012 -0700

    Replaced as many uses of std::list<> with std::deque<> as possible for
    efficiency reasons.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/VisMF.cpp

commit 1627a19717ec9f1cc514c8351a9b7e8a7c8cbaa8
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue Jun 26 13:07:31 2012 -0400

    better way to do the labels

python_plotfile/contourcompare.py

commit 339b17ea5be87542ee170c078b8ba27cd656fad6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 22 14:12:56 2012 -0700

    We now have the capability to switch between using synchronous MPI sends
    and asynchronous MPI sends in CollectData() and copy(), controlled by
    ParmParse'd variables.  The default is to use synchronous sends as we've
    been using for years.  I had a vague hope that the asynchronous sends
    might be faster on hopper, but that doesn't appear to be the case.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit d5df165440d1f790e64f473aef90651735fd0eba
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 22 09:07:26 2012 -0700

    Cleaned up some warnings.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit b89b72deef3f6765e30ce5a31174ce9aa67e8231
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 21 17:00:42 2012 -0700

    add @echo SUCCESS for regression testing

Tutorials/HeatEquation_EX5_F/GNUmakefile

commit cfe97295371ca3f8e5116c686ed6fd348e93d74f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 21 15:27:25 2012 -0700

    Fix makefile for this tutorial

Tutorials/MultiGrid_C/GNUmakefile

commit cd83f7c1b607d963cbba2327ee8bd6be6d1b50cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 21 15:16:11 2012 -0700

    Add @echo SUCCESS so that regression testing would know whether or not
    the compilation is successful.

Tests/LinearSolvers/ComparisonTest/GNUmakefile
Tutorials/MultiGrid_C/GNUmakefile

commit 49f3f88a3648f180ff0f5c92e6fc431a82fe9c74
Merge: c93fb0515 cd12415df
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Jun 21 13:28:27 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit c93fb051597f313f340b274e035fff60305a5a2e
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Jun 21 13:27:58 2012 -0400

    new analysis routines for sub_Chandra

MAESTRO_sub_chandra/GNUmakefile
MAESTRO_sub_chandra/fsubchandra.f90

commit e3e80424bb045518c5c30040f312174226327e68
Author: Vince Beckner <vebeckner@lbl.gov>
Date:   Wed Jun 20 16:46:19 2012 -0700

    fix for battra.

Tools/C_mk/Make.mpi

commit 487fa6d6c73876bb31422d236d228312f0a4193a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 20 15:13:10 2012 -0700

    fixed error in makefile documentation

Docs/GettingStarted/GettingStarted.tex

commit d318519c0e7b111b05e0e357c33ace02e4d92a4d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 20 14:41:52 2012 -0700

    note about makefiles

Docs/GettingStarted/GettingStarted.tex

commit d93f86db6ebe40a84d4824e118aedeb40a7285e1
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 20 10:49:21 2012 -0700

    Added method for computing optimal subcycling.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit a45f8d984c63a6c918f2a1c24a347f23ef29a2fd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jun 20 09:35:59 2012 -0700

    Fix logic for whether we can use bottom_solver = 4 in the F90 mg --
    it should only be used when the grids completely fill their bounding box.

Src/LinearSolvers/F_MG/mg.f90

commit 8efc98b729d48b2c8e281bf1dd8751c6bc328637
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 19 17:33:24 2012 -0700

    Somehow the bottom_solver = 4 option can create more rather than
    fewer grids at the bottom level.  If this happens, ignore the
    new grids and use bottom_solver = 1 instead.

Src/LinearSolvers/F_MG/mg.f90

commit baa6426c132a22207c8c47d402ca82029cdc83c7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 19 16:23:49 2012 -0700

    Force a full regrid if we change n_cycle on restart (this is a prelude to
    optimal subcycling)

Src/C_AMRLib/Amr.cpp

commit 24905a0e20e293a2e8bf47564a406d2cf111f503
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 19 14:35:07 2012 -0700

    Merged in new BoxArray::intersections().

Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/FabSet.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit e3b3c18e3e8ff52e03571c9c61ed6ce95e5cf0c3
Merge: 0edb5813d cc96b7696
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 19 14:30:52 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0edb5813dd0f9ff578129ff22da94adfca6eb753
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 19 14:13:13 2012 -0700

    Added new version of intersections() that takes the std::vector<...> as an
    argument, instead of returning it.  For codes that use intersections() a
    lot (like Particle codes) this'll make things run faster.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit cc96b7696bf49bd92b3384e2efbb7b1b196fdae5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 19 13:28:59 2012 -0700

    Fix typo: "ghost" --> "ghosts"

Src/C_AMRLib/Particles.H

commit a503482941253cafcc6098c14a1aab8233743b21
Merge: 4259202de e88a49e69
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 19 13:26:27 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 4259202de49259ead068278d7c1e0526436ce508
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 19 13:25:47 2012 -0700

    Fix the logic when regrid_on_restart is true -- we should only do
    special case when max_level == 0, not when finest_level == 0.  Also
    replace "and" by "&&" in two places.

Src/C_AMRLib/Amr.cpp

commit e88a49e69d84b38fb1d530f9852ebf3f08ebed20
Merge: 3f77f5111 2c98c9488
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jun 19 15:55:43 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2c98c948871f371bc35a929b1de22d71d39402d1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 19 12:48:17 2012 -0700

    Pass PBoxes by reference in a few routines where they were being passed by
    copy.  Fixed some bugs in AddParticlesAtLevel().

Src/C_AMRLib/Particles.H

commit 3f77f511111a6f04c0e22d21fab00860b87c631b
Merge: baf683c18 821c51768
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jun 19 15:37:59 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit baf683c186f21ddb22cdfb5e523960be6ead6d8f
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jun 19 15:37:32 2012 -0400

    specify defaults on the declaration line

Tools/F_scripts/write_probin.py

commit 821c51768b5486d1023aaefc9e938cf70a132a40
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Tue Jun 19 12:13:16 2012 -0700

    Optimized ghost/virt creation and assignment and removed a stray print.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Particles.H

commit fab1f9eb3a97b7943d51cdc7fcb479d7a50b4c88
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 19 10:36:44 2012 -0700

    Simplified RemoveParticlesNotAtFinestLevel() & RemoveParticlesAtLevel()
    among other minor tweaks.

Src/C_AMRLib/Particles.H

commit cd12415df4fc64c029df1d2e25176ee17371a75a
Merge: 293eb66c1 6d9a5558e
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jun 19 13:09:16 2012 -0400

    tweaking of the makefile

commit 293eb66c1c4b4467fc087fda7dff26b7cbbe38f4
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jun 19 13:04:27 2012 -0400

    get this compiling again

GNUmakefile

commit 7b983114b54e8b92cca32f0d0178d0bfc45352b3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 19 09:27:37 2012 -0700

    Try to be a little more const correct.
    In FineCellsToUpdateFromCrse() use resize(0) instead of clear() to
    cut down on memory allocation.

Src/C_AMRLib/Particles.cpp

commit df4bbb550c0b9718f9f62045faf11974ccfa3048
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 18 15:20:01 2012 -0700

    Call CIC_Cells_Fracs_Basic() from CIC_Cells_Fracs() when dx_geom == dx_part.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 356ada175bb4fcf9519646ca622b14b1545011e0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 18 14:42:47 2012 -0700

    Un-inlined ParticleBase::CIC_Cells_Fracs(). Other minor cleanup.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 5a9bd264c68abf0619be2931814222486a18c08f
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jun 18 10:17:26 2012 -0700

    More cleanup

Src/C_AMRLib/Particles.H

commit 49eda20f13cc42ed837dd8e64e3783a6c480470b
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jun 18 10:16:21 2012 -0700

    Pre-push cleanup

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Particles.H

commit 5cd6ad2a1b109e43472b1e30f990571a12596aa9
Merge: e90391e76 8d0832877
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jun 18 09:40:35 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8d08328777ed2c18ead0ad6ef3e0e14c3ce20503
Author: Chris Malone <malone@ucolick.org>
Date:   Fri Jun 15 19:51:48 2012 -0700

    add libquadmath for all gfortran's in Darwin

Tools/C_mk/Make.Darwin

commit 00acc1625e31ede1f37d2ca085e53ba0d94484d4
Author: Chris Malone <malone@ucolick.org>
Date:   Fri Jun 15 19:19:51 2012 -0700

    add the optional do_finalize_MPI input to parallel_finalize calling sequence to sync up with parallel.f90

Src/F_BaseLib/parallel_stubs.f90

commit e90391e763def85956d52c2cf1b848422a25b446
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 15 17:59:58 2012 -0700

    Minor refactoring and debugs to variableSetup

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit e8cb9279124418f82cb839f63c3573e9e4660ec6
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 15 16:56:15 2012 -0700

    Minor additions to subcycling parse logic.

Src/C_AMRLib/Amr.cpp

commit 0c85cc97cbb2bc826fb322aadef83cc064de00b8
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 15 16:20:23 2012 -0700

    Big Commit.
    Added new subcycling controls/logic. Documentation to follow.
    Fixed a sneaky bug in nosubcycling AssignDensity.
    Added Particle Aggregation for virtual particles.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit fe33277b1cbc0a0c50a28ddedb6b2baed6624d90
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jun 15 15:56:06 2012 -0700

    The MPI_Comm_Free call seems to cause a core dump...so for now, we will live with a small mem leak

Src/F_BaseLib/parallel.f90

commit b724bfff6c7f0f9b2d387e172ab1ab9d00953885
Merge: 0afdbf3e1 59fc94004
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jun 15 14:26:50 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 0afdbf3e1348bcb9549447d25556ab1cb30a19bc
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jun 15 14:26:38 2012 -0700

    Add omega to f_mg args, clean up some loose memory, virtualize more of Amr, etc...

Src/C_AMRLib/Amr.H
Src/C_BaseLib/Utility.cpp
Src/F_BaseLib/parallel.f90
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 59fc94004ee42152d651b4564a728018f497bb06
Merge: 382eaf9d4 7d923f2c7
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Fri Jun 15 15:57:08 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 382eaf9d4cc4b17c9710042b5239b6b65e9ec121
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Fri Jun 15 15:56:30 2012 -0400

    remove references to Atlas and Franklin -- those machines no longer
    exist

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/comps/Darwin_intel.mak
Tools/F_mk/comps/Linux_intel.mak
Tools/F_mk/comps/Linux_pathscale.mak

commit 7d923f2c70703e2470818111058f3825a119ffe5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 15 10:01:35 2012 -0700

    Explicitely state that operators <, <=, > and >= are NOT strict weak
    orderings usable by STL sorting algorithms.

Src/C_BaseLib/IntVect.H

commit 6ba57f8f5658eccf5c472bcfefa22f7e07df21a7
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Jun 13 18:01:14 2012 -0400

    if we are storing velocities along with the particle info, we need to
    increase the number of fields in the format statement

Src/F_BaseLib/particles_f.f90

commit de8c957945550cf40763f2fca4658f480efc5ed8
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Tue Jun 12 15:17:28 2012 -0700

    Fixed fix to nosub, removed sum debug in subcycling AssignDensity.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Particles.H

commit 99f241ccab9c11e6988b4fc9f4d5832076ce44fc
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jun 12 12:53:13 2012 -0700

    added IPM suffix.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tutorials/Exp_CNS_NoSpec/GNUmakefile

commit 18385fc339043b4e7323cbf4bae6084fa47f0d7d
Merge: e2391576f 57b98e234
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue Jun 12 13:14:55 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e2391576ff8f3b9d709a10425b6d41ed88e0c522
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue Jun 12 13:08:34 2012 -0400

    remove bender-specific stuff.  With update to F17, we can use
    BOXLIB_USE_MPI_WRAPPERS

Tools/F_mk/GMakeMPI.mak

commit 8fce1fd20a9bd9d4ccbf6cbf7618b42565f5fe13
Merge: 8d5217cfd 57b98e234
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jun 11 09:30:05 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 57b98e234444c43ac4f9450daefaf82184c046be
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jun 9 17:35:34 2012 -0700

    Enforce that MGTSolver always sends a status flag to mgt_solve; note that
    ml_cc still has to take on if present(status) because the F90 codes may
    call ml_cc directly.  But mgt_solve is only called from MGTSolver so
    we can safely modify that interface.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit d0ad1081a647c295a9d66cb3c0eb95d75dffa166
Merge: c3d17f3ce b7e55de61
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jun 9 15:09:40 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c3d17f3ce853d6930638edde794a2263bb48fb48
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jun 9 15:09:09 2012 -0700

    Now the mgt_solve version does *not* take a status flag and mgt_solve_stat does.

Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 8b245b591daecf71d4aeb2016bbf0eac40043189
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jun 9 15:07:47 2012 -0700

    Need to differentiate between the ones that take a status flag and
    the ones that don't.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 8d5217cfd2366cb277a6d7f3c849a066f67d9c6b
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 8 16:38:32 2012 -0700

    DERP fix.

Src/C_AMRLib/Amr.cpp

commit 0e96ce047dd309fc1aee8e799ccfc3c9c76354d0
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 8 15:35:16 2012 -0700

    Fixed nosub setting in Amr.cpp, particle tweaks.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Particles.H

commit bf335c15e4fe916d6b937d9d62ea37ff134a6e9d
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 8 14:33:04 2012 -0700

    Fixes to subcycling assign density.

Src/C_AMRLib/Particles.H

commit b7e55de616083f37c2937843b3a7e9fa1ec82f40
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Fri Jun 8 10:23:54 2012 -0400

    remove references to nan -- we can use BOXLIB_USE_MPI_WRAPPERS now

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit fa36c37db90ba540d7e28861ea6bae2d724c52a5
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Thu Jun 7 16:23:19 2012 -0700

    Minor fix to periodic ghost cell densities.

Src/C_AMRLib/Particles.H

commit e7bacf1f0198d908c38e20295d8daa545266a62d
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Thu Jun 7 11:04:36 2012 -0700

    Debug to nonsybcycling redistribute.

Src/C_AMRLib/Particles.H

commit 395b1e7704f799ada8d2cc80e3e862b632ddbfa7
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Thu Jun 7 10:44:24 2012 -0700

    Modifications for working DM particle subcycling.
     - Ghosts, Virtuals
     - CIC for particles with arbitrary radii (at the CIC level, not the assign density level)

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 6d9a5558e8742fa9af0e74bee5ae39dbdeb695c1
Author: Christopher Malone <malone@ucolick.org>
Date:   Thu Jun 7 11:28:44 2012 -0400

    get this working with updated make system

GNUmakefile

commit ae05305c64f09e58a6731f20fc02824ffe8831f4
Merge: 8626cc4ab 860efc01f
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jun 6 13:20:52 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 8626cc4abb73eafdeab5e6d772e3641059db68d1
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jun 6 13:20:44 2012 -0700

    Fix uniinitialized status flag, and pull omega through the options

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit 860efc01f2a19a8f784555af822a36901aac14b1
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 6 13:08:58 2012 -0700

    init for max and div optimizations.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 06229c90b767152e8b4baecfd8ad17ad9e68581d
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Tue Jun 5 13:01:05 2012 -0700

    One more merge fix.

Src/C_AMRLib/Particles.H

commit 5a06978bcdd57e81c81872e051b9309d9ff77819
Merge: 3d53bf94e cb1cb9b45
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Tue Jun 5 12:56:41 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib
    
    Conflicts:
            Src/C_AMRLib/Particles.H
            Src/C_AMRLib/Particles.cpp
            Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit cb1cb9b45293fcffefee1e6db2e97c3c9b7eec8d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 5 11:47:30 2012 -0700

    Modify NReaders and NRedist in Particles.H in order to be able to read
    large particle files when N_processor >= 4K

Src/C_AMRLib/Particles.H

commit 6eb6014702570642b558174e13cf3b9b8666c2bd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 5 10:39:28 2012 -0700

    Added finest_level argument to Where() and PeriodicWhere() that defaults
    to -1.  The -1 implies to use m_amr->finestLevel().
    Changed Redistribute() and AssignDensity() to the effective finest level,
    not to blindly use m_amr->finestLevel().

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 92532dd5f2e881f71a0f95707f0328a36dc02821
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 5 08:13:42 2012 -0700

    give multifab_build_edge and multifab_build_nodal the optional "stencil" argument

Src/F_BaseLib/multifab_f.f90

commit 0e8a8587dd6db43372fc33101ff143a161e9016c
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 5 07:53:29 2012 -0700

    added subroutine multifab_build_nodal

Src/F_BaseLib/multifab_f.f90

commit a1e902e82e9940572e905ff71221c79274c0a2b8
Merge: a9038645e 7e20188a6
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Jun 4 20:17:25 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 3d53bf94ece34d492b7a0c265c141963bec41486
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jun 4 17:17:03 2012 -0700

    Working Ghost particles, debugs.

Src/C_AMRLib/Particles.H

commit a9038645e7836db646463f12ac82c6ba708ad2af
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Jun 4 20:16:14 2012 -0400

    remove constants and random as packages needed for the build

GNUmakefile

commit c7a1b0cc2d322ddd13152a5a53c4d6fc55f64ead
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Jun 4 15:27:04 2012 -0400

    add more flexibility to detecting the appropriate gfortran library.
    First look for libgfortran.a (as we were doing).  If gfortran
    just returns the name w/o a path, then it did not find it.  In
    that case, look for libgfortran.so.  Some linux boxes don't have
    the static libraries installed by default.

Tools/C_mk/Make.defs

commit 4e361e933e4e961013637a1e0685e1e0c25f7f80
Author: cmalone <malone@ucolick.org>
Date:   Mon Jun 4 11:12:10 2012 -0700

    removed extra -J definition; already handled in Make.defs for gfortran

Tools/C_mk/Make.Darwin

commit f1f446529747c8929402ddc9ad9097e5883550d0
Author: cmalone <malone@ucolick.org>
Date:   Mon Jun 4 10:11:59 2012 -0700

    swap and elifdef for an
    
    else
       ifdef
    
    as Macs don't like former syntax

Tools/C_mk/Make.mpi

commit 3d4befc7cdbe902275dd7903eb7bb112ab54c5fa
Merge: d2a50439b dc71f6060
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Jun 4 12:30:03 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d2a50439b69ebe0811a56f3babbfe0a51d5e9cbb
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Jun 4 10:28:11 2012 -0400

    make the list of modules an array so we can print them one per line.

Tools/F_scripts/make_build_info

commit dc71f6060107e8d13ab9ba60dabdff21b02f92fd
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sun Jun 3 20:56:49 2012 -0400

    add support for AstroDev

Tools/RegressionTesting/Maestro-tests.ini
Tools/RegressionTesting/testnew.py

commit 4ca67a0b1c3b9bfeb0d57f7e6f383c2285f49ab2
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 1 16:24:52 2012 -0700

    Modified Nyx move/density routines, added creation routines
    to support subcycling and virtual particles.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit cd0cf60dc35389d3e2539484072069f3e01baf1e
Merge: eee9a54d4 dc788ecf1
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 1 14:29:40 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit eee9a54d4220853efa6bab438e75422b906f0f0b
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 1 14:29:19 2012 -0700

    changes for battra and naphta.

Tools/F_mk/GMakeMPI.mak

commit a144d1f28c24041462feacc0f95c5c2615a26ddf
Merge: aded7cab5 7e20188a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 1 13:04:34 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/AmrPostprocessing

commit aded7cab50e6ef1416700b05955b2e1ff08a91dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 1 13:04:11 2012 -0700

    chmod a+x plotsinglevar.py

python_plotfile/plotsinglevar.py

commit dc788ecf188d47fcea0be6b11679e0820dbd32bb
Merge: 5372c2b16 700a16a7c
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu May 31 21:45:19 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 5372c2b16bc495fe508b1d6d17a651d273edae93
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu May 31 21:44:41 2012 -0400

    for a generic Linux machine, is BOXLIB_USE_MPI_WRAPPERS is set, then
    we compile with mpic++ and mpif90

Tools/C_mk/Make.mpi

commit f4feb176c6525332c050990b559dde3c378587c8
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Thu May 31 12:47:16 2012 -0700

    Started work on Nyx subcycling, change to assign density, bugfix to MGT_Solver

Src/C_AMRLib/Particles.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 700a16a7cbaad7551c719f67a62fc9967856120a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 31 10:43:24 2012 -0700

    For some reason, BL_ASSERT using (a == b == c) dies a horrible death,
    but BL_ASSERT (a == b) is fine.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit f5ea75d37fd05e58df9e63fe39d296d53b0f38c9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 31 09:54:56 2012 -0700

    No longer need cvs scripts.

Tools/F_scripts/cvs2cl.pl

commit 7183836c63238d70787b967e3ebcad9b5f9562d9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 31 09:54:13 2012 -0700

    Remove Tools/F_scripts/idlbl directory completely -- we don't want to support IDL stuff.

Tools/F_scripts/idlbl/README
Tools/F_scripts/idlbl/batch.pro
Tools/F_scripts/idlbl/color.pro
Tools/F_scripts/idlbl/color_index.pro
Tools/F_scripts/idlbl/colorbar2.pro
Tools/F_scripts/idlbl/dump_surface.pro
Tools/F_scripts/idlbl/flamelength.pro
Tools/F_scripts/idlbl/flash_colors.tbl
Tools/F_scripts/idlbl/get_idlbl_path.pro
Tools/F_scripts/idlbl/nolabel.pro
Tools/F_scripts/idlbl/partvelvec.pro
Tools/F_scripts/idlbl/plotflash.pro
Tools/F_scripts/idlbl/plotraw.pro
Tools/F_scripts/idlbl/rawread.pro
Tools/F_scripts/idlbl/rawread3d.pro
Tools/F_scripts/idlbl/scale_color.pro
Tools/F_scripts/idlbl/start_linux.pro
Tools/F_scripts/idlbl/tvimage.pro
Tools/F_scripts/idlbl/vcolorbar.pro
Tools/F_scripts/idlbl/xaverage.pro

commit 91979f901e48ecee7109faec985d0676585a7a84
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 31 09:53:13 2012 -0700

    Move Tools/C_util/regtests to Tools/RegressionTesting

Tools/RegressionTesting/Castro-tests.ini
Tools/RegressionTesting/Maestro-tests.ini
Tools/RegressionTesting/README
Tools/RegressionTesting/gen_compile_test.sh
Tools/RegressionTesting/radiation-tests.ini
Tools/RegressionTesting/test-Ubuntu.py
Tools/RegressionTesting/test.py
Tools/RegressionTesting/testnew.py

commit 24c55539d182f715b82255d54a2c74efd98dcf9e
Merge: 28b508671 19a030126
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Tue May 29 10:46:54 2012 -0700

    Merge branch 'subcycling'

commit 19a030126448b8cea051f09baf014a645ffbb077
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Tue May 29 10:43:52 2012 -0700

    Minor fix to Where

Src/C_AMRLib/Particles.cpp

commit 4584324c9b2136c1ed9efbede0e2b77ba5d64e46
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Tue May 29 09:55:15 2012 -0700

    Removed redundant method declarations, changed to default param.

Src/C_AMRLib/Particles.H

commit 28b50867151a744d2c2591e195990e434a32f549
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 24 13:02:16 2012 -0700

    Changes for Aleks.

Tools/F_mk/GMakeMPI.mak

commit f736038b400f822ee57aa4b75d3d95f4a7e394c5
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed May 23 21:16:36 2012 -0700

    builds correctly now after Ethan's re-org to add C_AdvancedTopics

Docs/GNUmakefile

commit 483a2d429945bf6c3fe0a6c3d77f055444a0a7c5
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed May 23 15:07:58 2012 -0700

    Added support for particles leaving the domain across a non-periodic
    boundary (they are invalidated and removed at the coarse timestep).

Src/C_AMRLib/Particles.H

commit 1010c3a7da4f792dabdfe7b565593b46c4168201
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed May 23 15:05:00 2012 -0700

    Important bugfix to 2d hoextraptocc (seldom used)

Src/C_AMRLib/FILCC_2D.F

commit d91e0014b0f7be34f7cc6f0cace5972d566e03c8
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Tue May 22 14:30:34 2012 -0700

    Debug fixes to particle subcycling

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit c4a3856d2ec2c266c7233a2eb44ab202bd4efcca
Merge: 09e8489f8 33894bd58
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 22 13:20:35 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 09e8489f8a2cfe7c6cf294032216aa52efab07c5
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 22 13:19:20 2012 -0700

    changed default PLOTPER test.

Src/C_AMRLib/Amr.cpp

commit 33894bd58e2b8d9fdb5c1fe1515ca587a99119b3
Merge: 3843d29b5 c92321544
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 22 11:08:16 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3843d29b54a015b59c91230ae5c6be6dd60737b9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 22 11:07:49 2012 -0700

    1) Formatting in mg.f90
    2) We no longer allow the dense stencil in 2D since the multilevel divergence operator is known to be wrong.

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/F_MG/mg.f90

commit c92321544510b012ae628a038bb64995657af492
Merge: 1190e8adc 52e8219ef
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue May 22 10:25:14 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1190e8adcb4967673631e757b7d7328cf6edd331
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue May 22 10:25:02 2012 -0700

    fixed a comment

Tutorials/HeatEquation_EX5_F/advance.f90

commit 52e8219ef4475b933139f4dc852702314afcf6f2
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue May 22 09:59:24 2012 -0400

    add OpenMP support for fParallel jobs

Tools/C_util/regtests/Maestro-tests.ini
Tools/C_util/regtests/testnew.py

commit 4347b47a968bfa1c14d1ffeb713429be13b20075
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon May 21 17:02:28 2012 -0700

    Seemingly working particle subcycling; more tests needed.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 1ea94681a8f3005dbeffed9303240f46784323df
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon May 21 16:37:03 2012 -0700

    Some small (hopefully ineffectual) changes to minimize redundant code

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 6842dcbbc15be94090df7569255064d0ba724458
Merge: 9c567a897 88afdb7c5
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon May 21 12:03:21 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 88afdb7c5eb7b0635ddf7376d12b86dad3423811
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Mon May 21 11:27:56 2012 -0400

    remove explicit inf section

Tools/F_mk/GMakeMPI.mak

commit 18957b6f115ab57205353c84ad2b45cb95eed770
Merge: 80d806ae7 22fb3ecc0
Author: Michael Zingale <zingale@sn.astro.sunysb.edu>
Date:   Mon May 21 11:20:27 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 22fb3ecc0efc0476dbc30d2e9e62a6c1a6fe5418
Author: Michael Zingale <zingale@xrb.astro.sunysb.edu>
Date:   Mon May 21 11:19:08 2012 -0400

    remove xrb specific section

Tools/F_mk/GMakeMPI.mak

commit 80d806ae76e49167539c0c5e6de0fa4c3335cc6a
Author: Michael Zingale <zingale@sn.astro.sunysb.edu>
Date:   Mon May 21 11:06:42 2012 -0400

    remove sn specific make -- use the generic BOXLIB_USE_MPI_WRAPPERS now

Tools/F_mk/GMakeMPI.mak

commit fd0afaadff22146c865e9bf804af2c61c031bbab
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Mon May 21 10:56:37 2012 -0400

    MAESTRO -> BOXLIB :)

Tools/F_mk/GMakeMPI.mak

commit 12c41a764b82d33f8431fa8b88cf70ed7dd10060
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Mon May 21 10:55:19 2012 -0400

    remove the nan-specific entry.  Add a generic Linux MPI that is
    more general than the old one -- now look for the environment
    MAESTRO_USE_MPI_WRAPPERS

Tools/F_mk/GMakeMPI.mak

commit 296cf9b78db925302b3d14a5b8027124302bb3d1
Merge: 84d8481b7 9a7e15047
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Mon May 21 10:33:25 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 84d8481b7abcd047e0d547d94d69fbbbf77505f7
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Mon May 21 10:33:04 2012 -0400

    some pretty printing stuff

Tools/F_mk/GMakedefs.mak

commit 9c567a8972179477e98df6d4f26923ca223efc14
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri May 18 14:31:02 2012 -0700

    More doc additions.

Docs/C_AdvancedTopics/C_AdvancedTopics.tex

commit 99ff76f41c3ee9c12efc175b564421568741cdc7
Merge: 557f3e7cd 9a7e15047
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
Date:   Thu May 17 15:38:12 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9a7e15047bc14f42ef7ebbf2c2efcdd31cffbb5a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu May 17 13:47:58 2012 -0700

    linear solver note

Docs/AdvancedTopics/AdvancedTopics.tex

commit 557f3e7cd30acb05c9b1e9c9b056b0b47bb708b0
Merge: 7d0c13778 56f6938c6
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
Date:   Thu May 17 13:46:26 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7d0c137785536ac46c9ac469521fc043192438f0
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
Date:   Thu May 17 13:45:57 2012 -0700

    Added Assertions to check vcomp validity.

Src/C_AMRLib/Particles.H

commit 98d10cd3a567c0bcf43beb156905809b30fdf4a9
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
Date:   Thu May 17 13:42:51 2012 -0700

    Added empty Users Guide section for "State Data"

Docs/C_AdvancedTopics/C_AdvancedTopics.tex

commit 88e2909e29df8fb3f51a34f093f2b4388fabe204
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
Date:   Wed May 16 16:45:36 2012 -0700

    Typo correction to main page, additions to particle documentation.

Docs/C_AdvancedTopics/C_AdvancedTopics.tex
Docs/UsersGuide.tex

commit 34ac08edbde155f4c6a006ce329db49e29cb6266
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
Date:   Wed May 16 16:13:29 2012 -0700

    Added a UsersGuide Stub chapter for Advanced Topics with C++
    that will cover particles.

Docs/C_AdvancedTopics/C_AdvancedTopics.tex
Docs/F_AdvancedTopics/F_AdvancedTopics.tex
Docs/F_AdvancedTopics/bc_example1.eps
Docs/F_AdvancedTopics/bc_example1.fig
Docs/F_AdvancedTopics/bc_example2.eps
Docs/F_AdvancedTopics/bc_example2.fig
Docs/F_AdvancedTopics/bc_example3.eps
Docs/F_AdvancedTopics/bc_example3.fig
Docs/F_AdvancedTopics/hopper_omp.run
Docs/GettingStarted/GettingStarted.tex
Docs/Introduction/Introduction.tex
Docs/UsersGuide.tex

commit 26ee365a0e75fe54f4787d1b6f475185138bd33c
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
Date:   Wed May 16 14:19:35 2012 -0700

    Added vcomp parameter to allow offset velocity storage in mdata.
    Minor documentation additions.

Src/C_AMRLib/Particles.H

commit 7e482f4b5b9f9a562d76df7435b11b28779f5840
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
Date:   Wed May 16 11:21:40 2012 -0700

    Added Periodic particle motion to AdvectWithUMAC. Minor Documentation additions.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 56f6938c6b8ba7bff5b3c58d0f506a83f2d72ea5
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed May 16 09:19:45 2012 -0700

    Rearrange so that solver fails give slightly more info

Src/LinearSolvers/F_MG/ml_cc.f90

commit f5124bd91aab713c95e49b2b7352c2b210ccc92d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat May 12 19:14:49 2012 -0700

    InitFromBinaryFile() appears to be working.
    Note that I didn't carry over the "Nrep" argument
    from InitFromAsciiFile().  If that's really needed it should
    just be a simple cut & paste.

Src/C_AMRLib/Particles.H

commit 2707402ea9c357882e4a9d2e212eb50964068234
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat May 12 17:23:15 2012 -0700

    A first cut at InitFromBinaryFile().

Src/C_AMRLib/Particles.H

commit ade7da1d666d87c3faea4a156943fb2a4f9409c0
Merge: c2934e505 6ed6ef97f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 10 13:30:26 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c2934e505e33669604c07a3662ab7ce9226c6f36
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 10 13:29:31 2012 -0700

    Shift the cell as well as the grid of a fine particle talking to a coarse
    grid across a periodic boundary.

Src/C_AMRLib/Particles.cpp

commit 6ed6ef97f9e6a52bf31efcbea307b7b21025cda4
Merge: af57493c1 77debfccd
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date:   Thu May 10 12:40:39 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit af57493c1cfebc25fda6dc2e5f49d55ec1161b8b
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date:   Thu May 10 12:39:02 2012 -0400

    Don't set more than the compiler when setting FC or fC.
    Any flags will be lost on machines like jaguar or hopper where
    the machine overrides FC and fC with ftn.  Put generic compiler
    flags into FFLAGS and fFLAGS.  This fixes the problem with .mod files
    not getting into the proper directory.

Tools/C_mk/Make.defs

commit ebda2e9d02053f13670474bcb61a15b139f1d068
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date:   Thu May 10 12:37:57 2012 -0400

    Removed some stuff that g++ doesn't like when run in strict mode.

Src/C_BaseLib/winstd.H

commit 77debfccd605b31cd12d396194506c5dd6c23c28
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed May 9 19:26:23 2012 -0700

    Not sure what happened, but the last version ended up broken....put it back

Src/LinearSolvers/F_MG/cc_mg_cpp.f90

commit 63b1e076cbbcb6ce90b071bd3940765573ce7fc9
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed May 9 19:14:35 2012 -0700

    Remove since it requires that I remember to manually update it

BoxLib_Version.txt

commit 22dd3c2ce8aef1f606777451285fad43ed430bfd
Merge: e72aeada4 61d414fba
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed May 9 19:10:54 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e72aeada4fd336d3a02bb3134836ba41f0365ac8
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed May 9 19:10:45 2012 -0700

    Forgot to pass the growth flag down into the levels.  flag was uninitialized without these lines....

Src/LinearSolvers/F_MG/cc_mg_cpp.f90

commit 61d414fba2affe50d4c8988dec3d696edb7e67c9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 8 13:13:11 2012 -0700

    Merged in protected_divide() to AssignDensity().

Src/C_AMRLib/Particles.H

commit 2f522ada671530363dab3e401a74be5018e9c987
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 8 13:11:33 2012 -0700

    Added protected_divide().  This is similar to divide() except it
    only does the division if the denominator is "true" or non-zero.
    In does nothing in the case where the denominator is not "true"
    or non-zero.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/SPECIALIZE_1D.F
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H

commit cd26936e78257c3ccabd33b2a353e3bd9b696a2a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 8 10:35:05 2012 -0700

    Fix the placement of velocities onto the grid in AssignDensityAndVels -- we need
    to sum up momenta then divide by total mass in the cell rather than summing up
    velocities

Src/C_AMRLib/Particles.H

commit 0b391ee96a34d50d6f62d1f6ef41563c60ea250c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 8 08:59:14 2012 -0700

    Also constrain mult() in single-level AssignDensity() as previous commit.

Src/C_AMRLib/Particles.H

commit 6418f07b31721eb4eb29fc7812fdbf07d85c2797
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 8 08:52:31 2012 -0700

    In AssignDensityAndVels in Particles.H,  we divide the mass by volume to get
    density, but don't divide the velocities by volume.

Src/C_AMRLib/Particles.H

commit 5b6b0981928fb44b1c44995a2940af6085c2f78c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 7 15:10:02 2012 -0700

    Inlined some ParticleBase routines.  Now go about 10% faster
    on my SantaBarbara test case on my machine with g++/gfortran.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit a62d2ca81df57dda4b5e77cadba8bd99270e548c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 7 10:31:08 2012 -0700

    Some more BL_ASSERT()s.

Src/C_AMRLib/Particles.H

commit 1b8bf767bd5663c1018882248248174e563f9f28
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun May 6 08:10:35 2012 -0700

    Got AssignDensity() working in parallel for > 1 components.
    Had to move it from ParticleBase to ParticleContainer.
    Now use ncomp components of m_data instead of m_pos.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit d5c10d4bc407b3c3a28ebc6cb492b4f9eb003397
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat May 5 08:38:06 2012 -0700

    Add the option in Particles.H to initialize the gas velocities as well as
    density from the particle file.

Src/C_AMRLib/Particles.H

commit 1d0b7f4ed49ae52b0aaabcb34502054a83abdc3e
Merge: 7b4f3f5d7 06e862baf
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 4 17:42:22 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7b4f3f5d7ba147e7e63276973ea4911e01372da6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 4 17:41:50 2012 -0700

    One more place to add max_L0_growth so that it is passed through from
    inputs file to ml_cc.f90

Src/LinearSolvers/F_MG/cc_mg_cpp.f90

commit 06e862bafe283f2a156a938023b21f36faab1809
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri May 4 17:20:09 2012 -0700

    manual update of version textfile

BoxLib_Version.txt

commit 2a50c46010c64fb02f7d412cd568364be288042a
Merge: 08cf50817 ca8220a40
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 4 16:50:11 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 08cf508178f57dc4b4c5ceed761f5125409ae474
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 4 16:49:11 2012 -0700

    Modify the mg stuff so that the max_L0_growth defaults to -1 and isn't used,
    but should be able to be set from the C++ inputs file.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit ca8220a40ec6e039ee3bd6cfcafeec4a4f0a4fd1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 4 14:53:11 2012 -0700

    Changed some large 2-D stack allocated arrays to be allocatable.
    Some OpenMP.

Src/F_BaseLib/create_umac_grown.f90

commit 4b7d1ae1937edf8a41e870177d35ae9e082ab18c
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri May 4 13:26:57 2012 -0700

    addition solved case

Src/LinearSolvers/F_MG/ml_cc.f90

commit ed9fcf27cb49cdae1967c0ad3b97104f899e96b1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 4 10:23:38 2012 -0700

    I've checked in an OpenMP'd Jacobi solver for the dense stencil into
    nodal_smoother_3d().  It's in the "else" part of a "if (.true.) then else
    endif" chunk of code so that the usual Gauss-Seidel solver is still used
    at the moment.  We'd like to give folks the option of using either Jacobi
    or Gauss-Seidel, with the code defaulting to Jacobi if OMP=t.  Got to
    think about how to do that.

Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit 266cf05a1c8136a4bf3f696d035266e00976cb91
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu May 3 13:45:03 2012 -0700

    some VisIt documentation

Docs/GettingStarted/GettingStarted.tex
Docs/GettingStarted/VisIt_2D.eps
Docs/GettingStarted/VisIt_3D.eps

commit f9351fa710fbf0865f334cc088814c0bfc3cc128
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu May 3 13:10:29 2012 -0700

    fix variable name

Tutorials/HeatEquation_EX1_C/writePlotFile.cpp

commit edbbd94e6e6e816be729a6bf8442f61c4141f30d
Merge: e6ce6f548 562de9149
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu May 3 12:32:55 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e6ce6f5489e08ad08bb4e1d86768f313d8cd671c
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu May 3 12:32:45 2012 -0700

    Begin process of adding status flag to fortran solvers so that they kick out if things are going south (rather than core-dumping after they have cratered).

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/ml_cc.f90
Tools/CMake/CCSEOptions.cmake

commit 562de914976ca593e22d7a8a1c4822abda7b0185
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 3 10:12:51 2012 -0700

    Add Sanchez-Pomraning boundary for radiation

Src/C_BoundaryLib/LO_BCTYPES.H

commit 7e20188a670d8be0d2667c31433042433126d49f
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed May 2 12:06:24 2012 -0400

    add the ability to zoom in by specify xmax, ymax, or zmax

python_plotfile/plotsinglevar.py

commit 1dba1f3d192289f3546dfee40ca5e3381f025f65
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 2 08:42:43 2012 -0700

    Didn't have my shortcut out of FillPeriodicBoundary() quite right for the
    case when the MultiFab is not cell-centered.  Curiously I did write it
    correctly for the SumPeriodicBoundary() routines.  Early Onset
    Alzheimer's?

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 2ab75e0ce5e1ac10c80cb9830d436e5001c12c0c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 1 13:32:50 2012 -0700

    Came up with a another way to shortcut SumPeriodic & FillPeriodic Boundary.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit ae44e053c2a80eb1eb97c594e89d6048c4c2226e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 1 11:20:12 2012 -0700

    Consolidated the innards of the two SumPeriodicBoundary() routines into
    one routine.

Src/C_BaseLib/Geometry.cpp

commit a3367e01cd152cca0b8412335bbddeca7c38d78d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 1 11:19:22 2012 -0700

    A little cleanup.

Src/C_BaseLib/FabArray.cpp

commit cfc4a3e94bc213e5bdc07f866e0172e98eedc6fa
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 1 10:37:52 2012 -0700

    Shortcut out of TagBoxArray::mapPeriodic() if there's no parallel work.

Src/C_AMRLib/TagBox.cpp

commit 4814e3bf4392599437834f3b2abb4746f31ac8d7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 1 10:02:32 2012 -0700

    Shortcut out of FillPeriodicBoundary() and SumPeriodicBoundary()
    if there's no work to do.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 658aacb01976a6d1833a1dde796fa0d26b6232ab
Merge: 33cc30e39 c69ccd566
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 30 17:07:12 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 33cc30e39b1e6b4d93eab0f4bb5a787d198b386a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 30 17:06:55 2012 -0700

    Some simplification & cleanup after merging in new sum_boundary() stuff.

Src/F_BaseLib/multifab_f.f90

commit a3e2b637256a80fd6ed403955c99667b6a8bbc87
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 30 17:06:21 2012 -0700

    New sumassoc stuff appears to be working.

Src/F_BaseLib/layout.f90

commit c69ccd566d907ad45ae8ab50563aee616a30cc72
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Apr 30 16:32:45 2012 -0700

    Dang, wrong text, wrong place....might be better now.

Tools/CMake/CCSEOptions.cmake

commit 5a8660fbf8290aa326f515c06d05c9b70ccfdd96
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 30 13:35:53 2012 -0700

    Cleaned up some unused variable warnings.

Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/nodal_divu.f90

commit b45ddf2a6e2565dc73d31d0759143323373cd88c
Merge: e2e7940e2 f1cadcf60
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 30 13:23:06 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f1cadcf606a00218be2fc5f5e4b8c5645028f6ed
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Apr 30 13:20:25 2012 -0700

    Fixup CMake files to deal with DEBUG=TRUE/FALSE via standard CMake variables

BoxLib_Version.txt
Tools/CMake/CCSEOptions.cmake

commit e2e7940e2e6d27d6685eb964d20508464f40f01c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 30 13:19:52 2012 -0700

    Merged new boxassoc_build() call that also can build optimized
    sumassoc structures into [l]multifab_sum_boundary().

Src/F_BaseLib/multifab_f.f90

commit 35d93808257f7f14a77f590bc4c640d22823b31f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 30 13:17:47 2012 -0700

    Added sumassoc_build_innards().  This routine does all the calculations
    needed to minimize the number of MPI communication needed for a
    sum_boundary() call.  It's called from boxassoc_build() when passed the
    appropriate flag. I haven't (yet) made a cache of these.

Src/F_BaseLib/layout.f90

commit e3226a4eadeeafb861ff30c9ab203e6a52907b39
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 30 12:07:07 2012 -0700

    Split out the box intersection stuff in boxassoc_build() into
    boxassoc_build_innards() in anticipation of adding an option to
    boxassoc_build() to build the appropriate optimized MPI structure for
    sum_boundary().

Src/F_BaseLib/layout.f90

commit 24613584704add65e4c6b56fb099bdf5d3166f5f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 27 16:18:34 2012 -0700

    cover fig

Docs/Introduction/varden1.eps.REMOVED.git-id
Docs/Introduction/varden2.eps.REMOVED.git-id
Docs/Introduction/varden3.eps.REMOVED.git-id
Docs/Introduction/varden4.eps.REMOVED.git-id
Docs/UsersGuide.tex

commit 714888d5f2dec4f0f844e1eb77731e9ea0e7d71f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 27 15:04:51 2012 -0700

    Added lml_internal_sync_fancy to match mf_internal_sync_fancy.
    Not sure anyone currently used this, but ...

Src/F_BaseLib/multifab_f.f90

commit a67d32cb59384022d64cb9b5711b2d64d2ea2dc5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 27 14:36:17 2012 -0700

    Merged sum_d and logical_or into the sum_boudnary() routines.
    Made some internal routines private.

Src/F_BaseLib/multifab_f.f90

commit 1193e457d384fa84e3da78d8a9bcc89d3c597fe2
Merge: df9fb35da 3d9015f3d
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Apr 27 09:53:40 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 3d9015f3d15b55278c1c1946ab34a88b2fb34c02
Merge: e7108b7f4 c0e9eaa48
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 26 17:11:50 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e7108b7f4812a77788f124b0e9a2a39ef01094ed
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 26 16:59:24 2012 -0700

    some User's Guide updates

Docs/Introduction/Introduction.tex
Docs/UsersGuide.tex

commit c0e9eaa48be02edfb02d30dd73008ca7b8dce909
Merge: 37856ddd3 a8f367102
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 26 15:53:09 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 37856ddd32b085181b33314a69545c50d576a709
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 26 15:52:36 2012 -0700

    Consolidated all the info for calculating CIC stuff into minimum number of
    required routines.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 70c16ebe6219bb84be38fde92827fb258d2680bf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 26 14:18:33 2012 -0700

    Some cleanup.

Src/C_AMRLib/Particles.H

commit b1cd50e703d77db569374ee0a22ca53081e4f70b
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 26 14:15:21 2012 -0700

    comments

Tutorials/HeatEquation_EX5_F/advance.f90

commit a8f367102aceeca41a2471fb3ab6196f6f695bd3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 26 13:40:35 2012 -0700

    remove print statement

Src/F_BaseLib/cluster_f.f90

commit a864f460260f560ea0c5fd6fb4f480aa1944bebf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 26 13:21:03 2012 -0700

    Use sum_boundary() and fill_boundary() to enforce a logical .or. on
    overlapping ghost & valid cells.

Src/F_BaseLib/cluster_f.f90

commit 95a3a95385c57f41ace7671b4abf87dc28820832
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 26 08:06:32 2012 -0700

    Added lmultifab_sum_boundary().  It does a logical "or" of all ghost
    cells that overlay valid cells with those valid cells.  Should be useful
    in error tagging.

Src/F_BaseLib/multifab_f.f90

commit 7b3cb2e10196880cd3003c96268e389c7877e283
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 26 07:55:32 2012 -0700

    Mods to get to compile again.

Tests/F_BaseLib/t_cls.f90
Tests/F_BaseLib/t_main.f90

commit 011a73848e98f3dd3e46978c3e57eb69f81e6633
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 26 06:02:31 2012 -0700

    put WaveEquation examples back until I make a multivariable tutorial based on HeatEquation with all the bells and whistlesZ

Tutorials/WaveEquation_C/GNUmakefile
Tutorials/WaveEquation_C/Make.package
Tutorials/WaveEquation_C/advance_2d.f90
Tutorials/WaveEquation_C/advance_3d.f90
Tutorials/WaveEquation_C/init_data_2d.f90
Tutorials/WaveEquation_C/init_data_3d.f90
Tutorials/WaveEquation_C/inputs_2d
Tutorials/WaveEquation_C/inputs_3d
Tutorials/WaveEquation_C/main.cpp
Tutorials/WaveEquation_C/writePlotFile.H
Tutorials/WaveEquation_C/writePlotFile.cpp
Tutorials/WaveEquation_F/GNUmakefile
Tutorials/WaveEquation_F/GPackage.mak
Tutorials/WaveEquation_F/advance.f90
Tutorials/WaveEquation_F/init_data.f90
Tutorials/WaveEquation_F/inputs_2d
Tutorials/WaveEquation_F/inputs_3d
Tutorials/WaveEquation_F/main.f90
Tutorials/WaveEquation_F/write_plotfile.f90

commit b78bf8e84bbe376e93be3d6ae56e5d439821fd75
Merge: f6953a4ec a911c31ef
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 25 15:44:06 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f6953a4ec1de58ebb27dc7f6a90f143135f5f1a7
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 25 15:42:56 2012 -0700

    temporary band-aid to get proper nesting to work properly.  You will lose information about buffered tagged cells that should have been passed to the valid regions of neighboring grids.  fix for that coming tomorrow.

Src/F_BaseLib/cluster_f.f90

commit a911c31ef75219c0d691273a25a71945e68636d2
Merge: 9796c0a84 d94f83a11
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 25 13:51:27 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9796c0a84068b86d28dc66449cb2c90ea70888af
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 25 13:50:01 2012 -0700

    Inlined Box::operator&=(Box), Box::operator&(Box) and
    Box::intersects(Box).  This greatly speeds up some BoxArray operations.

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp

commit d94f83a110018f24ffe540d9b10f71e08863c6a8
Merge: 15e6cc618 71d767dcf
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 25 13:43:51 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 71d767dcffe8b00bdbce6e1bf53687685b1a8f9a
Merge: e0c6ce933 950e03054
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 25 13:38:51 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e0c6ce933f5cc7c6c60274d022924f1aa45e4aed
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 25 13:38:38 2012 -0700

    Inlined some Box stuff.

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp

commit 950e03054fe76d305e3ef1193c4752e1942ac520
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 25 11:59:25 2012 -0700

    added comments clarifying creating a distmap with an array<int>.

Src/C_BaseLib/DistributionMapping.H
Tutorials/MultiFabTests/MultiFabReadWrite.cpp

commit 3fbd7f0a429906ebe5077495772deb107fa0f397
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 25 11:56:25 2012 -0700

    Final fix to FineToCrse() and hence AssignDensity().
    Problem was yet one more place where coarsening & refining don't
    quite work right when indices go negative.  This looks to be the
    last bug in this code :-)

Src/C_AMRLib/Particles.cpp

commit 15e6cc618d9b2304a832b73a1bc62a15efba647e
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 25 11:06:09 2012 -0700

    min_eff to 0.7

Tutorials/HeatEquation_EX4_F/inputs_3d
Tutorials/HeatEquation_EX5_F/inputs_3d

commit 83eb0e866fae0087555b2313a2af357877f71d93
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 25 10:54:46 2012 -0700

    update docs

Docs/AdvancedTopics/AdvancedTopics.tex

commit 10b49ded0e906d91979b39d8edd71d839f7277f8
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 25 10:27:15 2012 -0700

    shake out some bugs in implicit example

Tutorials/HeatEquation_EX5_F/advance.f90
Tutorials/HeatEquation_EX5_F/inputs_2d
Tutorials/HeatEquation_EX5_F/inputs_3d

commit 501db84e6ee295c8ed2755331c305be3b3d45092
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 25 09:43:27 2012 -0700

    linear solver progres

Tutorials/HeatEquation_EX5_F/advance.f90

commit df9fb35dab8497985c7e038e299a57bef967e948
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Apr 25 09:21:29 2012 -0700

    Add some robustness stuff in AmrData::FlushGrids, handling the case when it is called before any data is actually read

Src/Extern/amrdata/AmrData.cpp

commit eb6c9031e994c357fbe7faee2e0ec0ccaf6a6493
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 25 09:20:23 2012 -0700

    include ml_solve.f90 in F_MG/GPackage.mak

Src/LinearSolvers/F_MG/GPackage.mak

commit 012d3e6f3eccc6d1636fb3acae254ecf9e982a5a
Author: Michael Zingale <zingale@jaguarpf-login5.ccs.ornl.gov>
Date:   Wed Apr 25 10:20:15 2012 -0400

    add compiler version

Tools/F_mk/comps/Linux_cray.mak

commit b5fc2eb2a73ea94d820ba246d18a8a8fca4d942d
Merge: 9e1e6ab3b c0b4292c3
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Apr 25 10:13:09 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 9e1e6ab3bda9f099e86428cfff3f6318390b3536
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Apr 25 10:12:54 2012 -0400

    add support for compiler version # in output

Tools/F_scripts/make_build_info

commit e5d9222672dee201424745d1b7f04367315190c4
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Apr 25 10:12:30 2012 -0400

    add support for compiler version # in output

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/gfortran.mak

commit c0b4292c3a2c7f1f7cdd2b99aefdbdde1cf32864
Merge: 445781fb5 4bae23b75
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 24 16:58:58 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 445781fb5bd8068335a80db88989af442376f3f8
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 24 16:58:39 2012 -0700

    implicit example, just starting

Tutorials/HeatEquation_EX5_F/GNUmakefile
Tutorials/HeatEquation_EX5_F/GPackage.mak
Tutorials/HeatEquation_EX5_F/advance.f90
Tutorials/HeatEquation_EX5_F/init_phi.f90
Tutorials/HeatEquation_EX5_F/inputs_2d
Tutorials/HeatEquation_EX5_F/inputs_3d
Tutorials/HeatEquation_EX5_F/main.f90
Tutorials/HeatEquation_EX5_F/regrid.f90
Tutorials/HeatEquation_EX5_F/write_plotfile.f90

commit 4bae23b75f98a641ee3bec5a053de0820a2b60bc
Merge: c761f25d7 b2f84b6af
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 24 16:55:30 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b2f84b6af31f5ed60be4fdec94f9babcf33fd266
Merge: 5342efbee 608f1717f
Author: vince <vebeckner@lbl.gov>
Date:   Tue Apr 24 16:08:52 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5342efbeebe098fa9ed370be7a6a8da19f29ccc7
Author: vince <vebeckner@lbl.gov>
Date:   Tue Apr 24 16:08:29 2012 -0700

    fix for FlushGrids.

Src/Extern/amrdata/AmrData.cpp

commit c761f25d791e5bd6259bf21d1a9468a920f0aaac
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 24 15:33:36 2012 -0700

    Make sure the most common case can be accessed quickly.

Src/C_AMRLib/Particles.H

commit 86ec6465d01bc9e43eb8af7c6057d140c2d009d7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 24 15:01:27 2012 -0700

    Yet more cleanup.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 9f61cf3d6ad66a9203438b1b0fee5a11d926a924
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 24 14:41:50 2012 -0700

    remove local tag_boxes.f90

Tutorials/HeatEquation_EX4_F/tag_boxes.f90

commit 26dc4062e6a8c1c610feb39d412bd117dfa12816
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 24 14:41:10 2012 -0700

    modify initial condition so we can use the F_BaseLib version of tag_boxes.f90

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex
Src/F_BaseLib/tag_boxes.f90
Tutorials/HeatEquation_EX1_C/init_phi_2d.f90
Tutorials/HeatEquation_EX1_C/init_phi_3d.f90
Tutorials/HeatEquation_EX1_F/init_phi.f90
Tutorials/HeatEquation_EX2_F/init_phi.f90
Tutorials/HeatEquation_EX3_F/init_phi.f90
Tutorials/HeatEquation_EX4_F/init_phi.f90

commit 64d94b9b9b1509709649aaa78f77204d681879fb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 24 13:14:35 2012 -0700

    Some cleanup.

Src/C_AMRLib/Particles.H

commit 608f1717f55942e45ec1844835ca35620810a477
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 24 09:38:40 2012 -0700

    An attempt to minimize excessive memory allocation/deallocation in
    AssignDensity.  I'm allocating arrays in outer routines & passing'm into
    inner routines.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit b022e533994c64a2e30845629ebeab77d55c1ead
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 24 09:15:44 2012 -0700

    When shifting periodically into the fine level, I was using the coarsened
    version of the fine shift.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit aafeef073d82b13abd749135a0e840263aeb454b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 23 20:48:04 2012 -0700

    Call the single level version of AssignDensity from the multi-level
    version if there's only one level.  It's likely much faster.

Src/C_AMRLib/Particles.H

commit fbefac88376417722cf1225c4d7885f1dbf2b951
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 23 15:29:46 2012 -0700

    I'm going to push this stuff.
    I'm getting really close to having the various period special cases
    finished.
    I don't want to lose what I've got to date.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit f492708fc4b9be4fd1f7b98233b703dd7a03597e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 23 14:55:43 2012 -0700

    Dealt with the special case where the fine grids totally covers the coarse.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 3770a5621271f9fb06c53ea18ac441c75bb82350
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 23 13:41:24 2012 -0700

    More work on C-F periodic overlap.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 49a0da3ee63d10679574b47a280d5c0c489f2fb8
Merge: 03b9ce680 e8bb70380
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 23 08:51:32 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e8bb70380afeae1ccb360d23af8d0146ac4786fa
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 23 08:50:15 2012 -0700

    Simplify Make.mpi a tad to help someone's old version of make.

Tools/C_mk/Make.mpi

commit 03b9ce68097c5f73bea5f6af61e2efa351f13ecd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Apr 22 19:37:09 2012 -0700

    Some changes I want to save; still not soup yet!

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit efc253283db70d480efce299387701e614d74608
Merge: a1ace350c bb8566fd4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Apr 22 16:45:08 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a1ace350c3dfe765c6d62e5192b7f89b58d813a3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 20 16:26:32 2012 -0700

    More progress on Fine->Crse periodic.
    The case when level 1 is fully refined works.
    Other cases not so much.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit bb8566fd42cf92265a0d683382fa1c4c8802cc78
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 20 14:04:34 2012 -0700

    update to point to new HeatEquation tutorials in Fortran and C++

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex
Docs/GettingStarted/hopper.run
Docs/UsersGuide.tex

commit d5c8ac9a8f8f0ee156ed1129a1a603d1a9b6711f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 20 14:03:56 2012 -0700

    WaveEquation tutorials are now replaced by HeatEquation

Tutorials/WaveEquation_C/GNUmakefile
Tutorials/WaveEquation_C/Make.package
Tutorials/WaveEquation_C/advance_2d.f90
Tutorials/WaveEquation_C/advance_3d.f90
Tutorials/WaveEquation_C/init_data_2d.f90
Tutorials/WaveEquation_C/init_data_3d.f90
Tutorials/WaveEquation_C/inputs_2d
Tutorials/WaveEquation_C/inputs_3d
Tutorials/WaveEquation_C/main.cpp
Tutorials/WaveEquation_C/writePlotFile.H
Tutorials/WaveEquation_C/writePlotFile.cpp
Tutorials/WaveEquation_F/GNUmakefile
Tutorials/WaveEquation_F/GPackage.mak
Tutorials/WaveEquation_F/advance.f90
Tutorials/WaveEquation_F/init_data.f90
Tutorials/WaveEquation_F/inputs_2d
Tutorials/WaveEquation_F/inputs_3d
Tutorials/WaveEquation_F/main.f90
Tutorials/WaveEquation_F/write_plotfile.f90

commit 7234f939976537172dfe2aab8875dab4d26c6d56
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 20 13:58:02 2012 -0700

    More work on periodic in AssignDensity().

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 7454321eb3fd4364ccebb95b5d14393e24ba9fbd
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 20 13:35:54 2012 -0700

    added geom.FillPeriodicBoundary.  Now gives exactly same answer in 2D and 3D as fortran tutorial

Tutorials/HeatEquation_EX1_C/main.cpp

commit 14a1967e6b38417344582e40a9f12e12f45f0e68
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 20 13:24:39 2012 -0700

    index bug

Tutorials/HeatEquation_EX1_C/advance_2d.f90
Tutorials/HeatEquation_EX1_C/advance_3d.f90

commit ee16e1cfeeb28f1b0d26618d3ec23d85c7e27d82
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 20 12:45:52 2012 -0700

    C version compiles and runs, but doesn't give correct answer yet

Tutorials/HeatEquation_EX1_C/GNUmakefile
Tutorials/HeatEquation_EX1_C/Make.package
Tutorials/HeatEquation_EX1_C/advance_2d.f90
Tutorials/HeatEquation_EX1_C/advance_3d.f90
Tutorials/HeatEquation_EX1_C/init_phi_2d.f90
Tutorials/HeatEquation_EX1_C/init_phi_3d.f90
Tutorials/HeatEquation_EX1_C/inputs_2d
Tutorials/HeatEquation_EX1_C/inputs_3d
Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX1_C/writePlotFile.H
Tutorials/HeatEquation_EX1_C/writePlotFile.cpp

commit 0a8df097fc0122aa48c286f7b440711ded0471f3
Merge: 09ab8ee9d 6d700f95a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 19 20:51:31 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 09ab8ee9d5f68bb2f4819e1d3af12016b459632a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 19 20:51:02 2012 -0700

    note about new example

Docs/AdvancedTopics/AdvancedTopics.tex

commit 6d700f95a0e8d003ec7b0573b88be17523f9b335
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Apr 19 15:22:25 2012 -0700

    Set ng = nghost(uu) rather that using mgt%ng in calls to smoothers.

Src/LinearSolvers/F_MG/mg_tower_smoother.f90

commit 1dd52c89385d44074166d7bb00c26a96c3b44e11
Merge: 3b0279e41 677103d04
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 19 13:29:23 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3b0279e41bb6b3822698735149db2d7c845cb68b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 19 13:24:16 2012 -0700

    Contains Ann's latest changes to finetocrse.
    This is possibly as best as we can do.
    Also moved the SumBoundary() and SumPeriodicBoundary() into own
    loop after ParticleBase::AssignDensityDoit(mf,data) call.

Src/C_AMRLib/Particles.H

commit 677103d04b9396b64f0945036b39bec17d181468
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 19 13:12:46 2012 -0700

    turn off OMP and MPI by default

Tutorials/HeatEquation_EX1_F/GNUmakefile
Tutorials/HeatEquation_EX2_F/GNUmakefile
Tutorials/HeatEquation_EX3_F/GNUmakefile
Tutorials/HeatEquation_EX4_F/GNUmakefile

commit 38b503b650fd8b7f3c27b6f398e71402a5530961
Merge: b94d7b8fc 9f9742792
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 19 12:37:45 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit b94d7b8fcec472b7f59f7b5c4cdceb255a797e56
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 19 12:37:11 2012 -0700

    adaptive gridding works

Tutorials/HeatEquation_EX3_F/advance.f90
Tutorials/HeatEquation_EX3_F/init_phi.f90
Tutorials/HeatEquation_EX4_F/advance.f90
Tutorials/HeatEquation_EX4_F/init_phi.f90
Tutorials/HeatEquation_EX4_F/inputs_2d
Tutorials/HeatEquation_EX4_F/inputs_3d
Tutorials/HeatEquation_EX4_F/main.f90
Tutorials/HeatEquation_EX4_F/regrid.f90

commit c8685984dbe249e2adabf81e6141ea71adfb4d49
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 19 11:31:30 2012 -0700

    regridding seems to work - still needs cleanup.
    other various multilevel cleanups

Tutorials/HeatEquation_EX3_F/advance.f90
Tutorials/HeatEquation_EX3_F/init_phi.f90
Tutorials/HeatEquation_EX4_F/GPackage.mak
Tutorials/HeatEquation_EX4_F/advance.f90
Tutorials/HeatEquation_EX4_F/init_phi.f90
Tutorials/HeatEquation_EX4_F/main.f90
Tutorials/HeatEquation_EX4_F/tag_boxes.f90

commit 9f97427925e1c0629886241b7f427a8b3f8196cd
Merge: bcf9d2eb9 030fa6e89
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 19 10:41:00 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit bcf9d2eb9f3213a19ecfbbe9d8e7701b9eada7e6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 19 10:40:19 2012 -0700

    More refinement to finetocrse.
    May be the best we can do for now.
    Still have to deal with fine grid on periodic boundary ...

Src/C_AMRLib/Particles.H

commit 030fa6e8970406a104281fb56ec79bf46db71bd0
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 19 10:12:37 2012 -0700

    clean up some parallelization and memory issues

Tutorials/HeatEquation_EX1_F/main.f90
Tutorials/HeatEquation_EX2_F/main.f90
Tutorials/HeatEquation_EX3_F/main.f90
Tutorials/HeatEquation_EX4_F/main.f90
Tutorials/WaveEquation_F/main.f90

commit d1113131ea28e11ad49fcedf15ad01a440d1c7c7
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 18 16:50:08 2012 -0700

    more AMR progress, updating older examples

Tutorials/HeatEquation_EX1_F/main.f90
Tutorials/HeatEquation_EX2_F/main.f90
Tutorials/HeatEquation_EX3_F/main.f90
Tutorials/HeatEquation_EX4_F/inputs_2d
Tutorials/HeatEquation_EX4_F/inputs_3d
Tutorials/HeatEquation_EX4_F/main.f90
Tutorials/HeatEquation_EX4_F/tag_boxes.f90

commit c99b20ab34555c7feef4e85db4c2d162ddefb3fe
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 18 16:12:55 2012 -0700

    using the 'max_levs' convention that the AMR example will inherit

Tutorials/HeatEquation_EX3_F/inputs_2d
Tutorials/HeatEquation_EX3_F/inputs_3d
Tutorials/HeatEquation_EX3_F/main.f90

commit ab1353abb01f2e083620f8d9231e88ce9cff705e
Merge: 423064b72 56e0bb908
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 18 15:29:43 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 423064b72553d5b5a6c95c424f66c123ce3a90b8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 18 15:29:02 2012 -0700

    New improved version of how particles assign their density at coarse-fine interfaces.
    This one works better at faces but still is "off" at edges and corners.   It does not
    currently work for multiple fine grids.

Src/C_AMRLib/Particles.H

commit 56e0bb90843553304af2b213ba3941d3f1489fa5
Merge: 2373e62c2 9569f7e35
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 18 15:17:54 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2373e62c2c47f6ad440c6e2d32f427b41de16921
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 18 15:16:03 2012 -0700

    Integrated FineToCrsePeriodic() into FineToCrse().
    FineToCrse() now considers fine cells that are outside the fine domain
    and only considers them a FineToCrse boundary if that fine cell won't be
    periodically shifted into a valid fine region.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit bf3c4bc94e232d4f2fa798ba38bfcdda00728383
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 18 13:56:45 2012 -0700

    A little cleanup.

Src/C_AMRLib/Particles.cpp

commit f32fec308d4d872eb4b2793e3b9630715fb9cf3f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 18 13:33:56 2012 -0700

    Added FineToCrsePeriodic(). Need to integrated into AssignDensity().

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 9569f7e3533bfad2515d73c543810a84a4616c34
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 18 13:24:02 2012 -0700

    minwidth is now the minimum length on a side for any newly created fine regions.  before minwidth was applied to the blocking_factor-coarsed tagboxes logical multifab, so the min length on a side was minwidth*blocking_factor

Src/F_BaseLib/cluster_f.f90

commit adaa696011e1a3a19a1298163b15c2c6027c0623
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 18 11:02:16 2012 -0700

    saving progress - lots of AMR work

Tutorials/HeatEquation_EX4_F/init_phi.f90
Tutorials/HeatEquation_EX4_F/inputs_2d
Tutorials/HeatEquation_EX4_F/inputs_3d
Tutorials/HeatEquation_EX4_F/main.f90
Tutorials/HeatEquation_EX4_F/tag_boxes.f90

commit b925b34ddde194d1bea9bf4329e39708cb3718fa
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 18 09:19:25 2012 -0700

    AMR example

Tutorials/HeatEquation_EX4_F/GNUmakefile
Tutorials/HeatEquation_EX4_F/GPackage.mak
Tutorials/HeatEquation_EX4_F/advance.f90
Tutorials/HeatEquation_EX4_F/init_phi.f90
Tutorials/HeatEquation_EX4_F/inputs_2d
Tutorials/HeatEquation_EX4_F/inputs_3d
Tutorials/HeatEquation_EX4_F/main.f90
Tutorials/HeatEquation_EX4_F/tag_boxes.f90
Tutorials/HeatEquation_EX4_F/write_plotfile.f90

commit 51a13bf6c4347b48f7db00ae227d4c0841033bb2
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 18 09:17:57 2012 -0700

    tidying up

Tutorials/HeatEquation_EX3_F/main.f90

commit 2747e8f95a043705b620bf22eb57cf17b6ec383c
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 18 09:01:08 2012 -0700

    clean up tag_boxes, add comments

Src/F_BaseLib/tag_boxes.f90

commit a93bb9d55337ab33717ba882d284b0e80aa0c747
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 18 08:51:25 2012 -0700

    comment

Src/F_BaseLib/tag_boxes.f90

commit 3b66642d76a7360ffb1873bbdffeb24f5c40d086
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 18 07:10:39 2012 -0700

    comments in ml_layout.f90

Src/F_BaseLib/ml_layout.f90

commit 157a1e79b1792f6e74aaf60b1bf629064ced7b08
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 17 20:01:09 2012 -0700

    some cleanup of tutorials

Tutorials/HeatEquation_EX1_F/advance.f90
Tutorials/HeatEquation_EX1_F/init_phi.f90
Tutorials/HeatEquation_EX1_F/main.f90
Tutorials/HeatEquation_EX2_F/advance.f90
Tutorials/HeatEquation_EX2_F/init_phi.f90
Tutorials/HeatEquation_EX2_F/main.f90
Tutorials/HeatEquation_EX3_F/main.f90
Tutorials/WaveEquation_F/advance.f90
Tutorials/WaveEquation_F/init_data.f90
Tutorials/WaveEquation_F/main.f90
Tutorials/WaveEquation_F/write_plotfile.f90

commit a67ff7e58281650aac2082e1e8d45a0c9d98b816
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 17 13:48:26 2012 -0700

    More work on parallelization of AssignDensity().
    Seems to work but could use more testing.
    Still have to do the special Fine->Crse periodic case.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 4512bcf75f7066cca01bed1d181a728f704292c9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 17 13:16:32 2012 -0700

    Some work making new AssignDensity() work in parallel.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit d405ad7a3b5bd3c2e64eae4b6eaf11bfa9403788
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 16 13:03:45 2012 -0700

    Some cleanup.  Removed all OpenMP references in multi-level
    AssignDensity().  Just doens't seem worth it to try & OpenMP.

Src/C_AMRLib/Particles.H

commit aede0f2fbb7524826cd64c3126e3d61d3ed663c5
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Sun Apr 15 20:40:33 2012 -0700

    tweak the tutorial example by moving initial Gaussian profile slighly off-center (greatly helps with examining the effects of non-periodic boundary conditions)

Docs/AdvancedTopics/AdvancedTopics.tex
Tutorials/HeatEquation_EX1_F/init_phi.f90
Tutorials/HeatEquation_EX2_F/init_phi.f90
Tutorials/HeatEquation_EX3_F/init_phi.f90
Tutorials/HeatEquation_EX3_F/main.f90

commit 2b941e5cf757293b2ea0d68832a486441b5d6087
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 13 13:56:36 2012 -0700

    Factored some stuff in ParticleBase routines.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit f2c29cf257aa1450d5e425a1a4a4a8b85c89a88e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 13 13:12:27 2012 -0700

    Simplified FineToCrse().
    Removed "some" ref_ratio==2 assumptions.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit f2e1d4de4d4365b9773c8586f4013987c3e7b097
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 13 12:41:52 2012 -0700

    Damn! I've had this correct for some time. I forgot that
    I changed the offset in init.cpp from .5 -> .49 for some previous
    debugging.  You can't have uniform distribution if the particles
    aren't uniformly distributed.

Src/C_AMRLib/Particles.H

commit 831e77462f142e611051665d5ccdeb720c72ebd6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 13 10:07:05 2012 -0700

    Didn't have my CrseFine fractions -> Fine correct.

Src/C_AMRLib/Particles.H

commit f7ce7f99b64f91119b34f076f72685bd27e1fe74
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 13 09:16:08 2012 -0700

    Some more debugging tests.

Src/C_AMRLib/Particles.H

commit de6f8c51627cc7efefff59951bd43709bcaa09d3
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Thu Apr 12 20:21:16 2012 -0400

    add support for 3 plotfiles

python_plotfile/contourcompare.py

commit b577f1cafc0364f42eb6ebac6436cd9e1c237d33
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 11 16:12:04 2012 -0700

    I "think" I've come up with a way to calculate the fine cells and their
    respective fractions in the case when moving some mass from a coarse cell
    to a fine cell.  I'm still don't appear to be getting constant density.
    More to do ...

Src/C_AMRLib/Particles.H

commit fe1fff7ab56c4e2521461983edf358df588dd84b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 11 08:30:22 2012 -0700

    I'm going to commit and push the new AssignDensity().
    It isn't correct but it's close.
    The fine->crse stuff is OK (with the possible exception when coarse & fine
    overlap at a periodic boundary).
    It also doesn't work in parallel if you try with more than one level.
    I'll get it working in parallel after it's totally done.
    The sticking point is when we're at a coarse level and have some mass that
    wants to be placed on the fine level: how to calculate the cell indices &
    fractions for the fine level?

Src/C_AMRLib/Particles.H

commit 64ab809f1f933c287a9c8bfd77d770abb2fdc685
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 10 16:02:46 2012 -0700

    Crse->Fine is looking better.  Still not quite right.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit ccec48a6e7020f0db1b8ac1903156e6b1e1d0ee5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 10 14:10:35 2012 -0700

    I'm feeling pretty good about the Fine->Crse code.
    It's still serial but that can be fixed.
    The Crse->Fine still needs work.

Src/C_AMRLib/Particles.H

commit 807c3ecef1e224299d7b4d6041dde9e16db9ca08
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 10 10:13:09 2012 -0700

    The Fine->Crse stuff "might" be working in serial.
    Little hard to tell till the Crse->Fine is also working
    the the RH array in TestAdiabatic comes out looking uniform.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit f82bc644944dbe59b742be5a686f27cfa910b1c3
Merge: e79845aaa 5aa58215b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 9 17:33:56 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e79845aaa7e051b33e4f2fc6044fefa86f0493a5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 9 11:15:15 2012 -0700

    A little cleanup.  Still more to do on AssignDensity().

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 5aa58215b931bfdf34716e3e8d3ccfb2b8365eef
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Apr 9 11:09:59 2012 -0700

    a few more additions

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex
Docs/UsersGuide.tex

commit 4a363fb27a0dce43f3afd44d0dfbf9b73b7f6d2a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 9 10:50:23 2012 -0700

    CrseToFine() and FineToCrse() now use AssignDensityCoeffs().
    which is now a bool[].

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 5325b53d78d83642707a288f36233144a121e4eb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 9 09:32:25 2012 -0700

    Removed AssignDensityDoit().
    Implemented the single level & multi-level AssignDensity() separately.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 564ae4b627a8d741c5e21f27b50e96ec923c7a6a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Apr 8 10:28:30 2012 -0700

    Added some more comments to direct my future work on Crse->Fine.

Src/C_AMRLib/Particles.H

commit ebb4b4675e78099e111c352d38129cf1f69d2fb4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Apr 8 10:21:28 2012 -0700

    Some work on Crse->Fine issue in AssignDensity.  More to do.
    I've disable threading in AssignDeisntyDoit() for now.
    Once it's working I'll make sure threading works.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 12c3169541570c7430b6b20e1147d2d7d8ab9645
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Apr 7 19:05:23 2012 -0700

    Integrated in AssignDensityCoeffs().
    The Fine->Crse stuff looks good.  Crse->Fine to go.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit e4e67c6e5e99b146106c8dc2145e540b3e4f19a7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Apr 7 10:18:37 2012 -0700

    Some work on AssignDensity() Fine-Crse issue.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 1c3d58788abb5d1cc0d4e29c2a94831528216872
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Apr 7 08:29:22 2012 -0700

    Final (hopefully) tweak to FineToCrse().

Src/C_AMRLib/Particles.cpp

commit 0daba532258f31f7ce9056d1e6c6109034584dc0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Apr 7 08:26:55 2012 -0700

    Refined FineToAdd().

Src/C_AMRLib/Particles.cpp

commit ee6b14de0dbd69d10fb6bb2b7cad51bb73bd8be3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 21:21:28 2012 -0700

    more User's Guide and Tutorial progress.  In pretty good shape now.

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex
Docs/Introduction/Introduction.tex
Docs/Preface/Preface.tex
Tutorials/HeatEquation_EX1_F/advance.f90
Tutorials/HeatEquation_EX2_F/advance.f90
Tutorials/HeatEquation_EX3_F/advance.f90

commit 6c38a98176f704873310d14e1b7679c6c1bc9f1f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 16:55:29 2012 -0700

    tutorial

Docs/AdvancedTopics/AdvancedTopics.tex

commit 5c933173a2d9422b060893f9781bb3ab5003bbba
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 16:39:14 2012 -0700

    fix comments, get the multilevel example working by hooking into the F_MG restriction calls

Tutorials/HeatEquation_EX2_F/advance.f90
Tutorials/HeatEquation_EX2_F/init_phi.f90
Tutorials/HeatEquation_EX3_F/GNUmakefile
Tutorials/HeatEquation_EX3_F/advance.f90
Tutorials/HeatEquation_EX3_F/init_phi.f90
Tutorials/HeatEquation_EX3_F/inputs_2d
Tutorials/HeatEquation_EX3_F/inputs_3d
Tutorials/HeatEquation_EX3_F/main.f90

commit db271ecbab07654cefe9c64366e935967aeda919
Merge: c47493349 31f0af443
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 6 15:52:59 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c47493349f33d68311c68a4ded7a95a67885f4b3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 6 15:50:44 2012 -0700

    Added ParticleBase::FineToCoarse(). Needed by AssignDensityDoit().

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 31f0af443154403362fb3b949554b7806eea93b1
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 15:50:29 2012 -0700

    forgot to add init_phi.f90

Tutorials/HeatEquation_EX3_F/init_phi.f90

commit 06eb0f2580756910787cd40d7cf8f61be4d94a7e
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 15:50:06 2012 -0700

    this is as far as I can go before I move the restriction stuff into F_BaseLib

Tutorials/HeatEquation_EX3_F/advance.f90

commit 5ddf5155a64c20d8ae93c6b2050c2d13c69287af
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 15:39:15 2012 -0700

    first cut at multilevel extension of HeatEquation_EX2.  This one uses ml_layouts and ml_boxarrays instead of just arrays of layouts and boxarrays

Tutorials/HeatEquation_EX3_F/GNUmakefile
Tutorials/HeatEquation_EX3_F/GPackage.mak
Tutorials/HeatEquation_EX3_F/README
Tutorials/HeatEquation_EX3_F/advance.f90
Tutorials/HeatEquation_EX3_F/init_data.f90
Tutorials/HeatEquation_EX3_F/initialize.f90
Tutorials/HeatEquation_EX3_F/inputs_2d
Tutorials/HeatEquation_EX3_F/inputs_3d
Tutorials/HeatEquation_EX3_F/main.f90
Tutorials/HeatEquation_EX3_F/make_fluxes.f90
Tutorials/HeatEquation_EX3_F/write_plotfile.f90

commit f5ac0c0af21e5d04cd41e9e02c5e1e369a19c95c
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 15:00:13 2012 -0700

    destory the_bc_tower

Tutorials/HeatEquation_EX2_F/main.f90

commit eed1ac4425038faf3037e566a575dad6bc6c16ed
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 14:20:31 2012 -0700

    more Tutorial updates

Docs/AdvancedTopics/AdvancedTopics.tex

commit 258a3410790e2f670e4bf4638255395830ed9ae3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 13:38:07 2012 -0700

    bugfix; the ncomp feature wasn't implemented in multifab_physbc.f90

Src/F_BaseLib/multifab_physbc.f90

commit 1d591e378a7fe6e0429a1e1aad26e46894f91667
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 13:32:59 2012 -0700

    pass in hi to physbc_2d/3d instead of computing it with fortran size() tricks within

Src/F_BaseLib/multifab_physbc.f90

commit 8bd1c9aa46e59175ae50ed9895061aaff29c14f1
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 10:09:34 2012 -0700

    updated test problem description

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex

commit 571b77670c84f57edae7b39a89aa8cfdcf356b30
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 09:37:09 2012 -0700

    3d version of boundary conditions.

Tutorials/HeatEquation_EX1_F/advance.f90
Tutorials/HeatEquation_EX2_F/advance.f90

commit b197bd0339798acba279bbbe00a4a67e6613dcb1
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 22:22:44 2012 -0700

    bug in 2d bc's

Tutorials/HeatEquation_EX2_F/advance.f90

commit 00c8dd76c1210a3029d831c75164e5f0b6ebd03b
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 22:06:38 2012 -0700

    spruced up the first two heat equation examples.  the boundary condition example is finished, with options for a 'source' dirichlet wall, outflow (phi_n=0) and periodic

Src/F_BaseLib/define_bc_tower.f90
Src/F_BaseLib/multifab_physbc.f90
Tutorials/HeatEquation_EX1_F/init_phi.f90
Tutorials/HeatEquation_EX1_F/main.f90
Tutorials/HeatEquation_EX2_F/advance.f90
Tutorials/HeatEquation_EX2_F/init_phi.f90
Tutorials/HeatEquation_EX2_F/main.f90

commit 562d5155cb577d6c78cc44f801218b6d7f83f02f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 19:22:33 2012 -0700

    more bc example progress

Src/F_BaseLib/define_bc_tower.f90
Tutorials/HeatEquation_EX2_F/inputs_2d
Tutorials/HeatEquation_EX2_F/inputs_3d
Tutorials/HeatEquation_EX2_F/main.f90

commit 208fc1bc8aaa325e54bf9b0a5261af02bfd79135
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 18:13:41 2012 -0700

    some documentation updates

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex

commit 3b68a969007a93e47630408fb76cbc5d5b989cba
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 18:12:47 2012 -0700

    start the HeatEquation_EX2_F boundary condition example by copying the EX1 example.

Tutorials/HeatEquation_EX2_F/GNUmakefile
Tutorials/HeatEquation_EX2_F/GPackage.mak
Tutorials/HeatEquation_EX2_F/advance.f90
Tutorials/HeatEquation_EX2_F/init_phi.f90
Tutorials/HeatEquation_EX2_F/inputs_2d
Tutorials/HeatEquation_EX2_F/inputs_3d
Tutorials/HeatEquation_EX2_F/main.f90
Tutorials/HeatEquation_EX2_F/write_plotfile.f90

commit 093046f19000eddfc0e896592c68c405c7edb865
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 18:11:50 2012 -0700

    renname example

Tutorials/HeatEquation_EX3_F/GNUmakefile
Tutorials/HeatEquation_EX3_F/GPackage.mak
Tutorials/HeatEquation_EX3_F/README
Tutorials/HeatEquation_EX3_F/advance.f90
Tutorials/HeatEquation_EX3_F/init_data.f90
Tutorials/HeatEquation_EX3_F/initialize.f90
Tutorials/HeatEquation_EX3_F/inputs_2d
Tutorials/HeatEquation_EX3_F/inputs_3d
Tutorials/HeatEquation_EX3_F/main.f90
Tutorials/HeatEquation_EX3_F/make_fluxes.f90
Tutorials/HeatEquation_EX3_F/write_plotfile.f90

commit 7f34f8aaca449e3ba7ba76ae9175c79b55f5c8f6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 17:07:42 2012 -0700

    first attempt at a generic boundary condition type

Src/F_BaseLib/define_bc_tower.f90
Src/F_BaseLib/multifab_physbc.f90

commit 485309f0ea1487c3cb0cb41545674b84be7dfff4
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 17:07:13 2012 -0700

    don't need to include files already in F_BaseLib/GPackage.mak

Tutorials/HeatEquation_F/GPackage.mak

commit 0f1917ceed3f2596c5ef2bdfc1689109addbdb78
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 15:00:56 2012 -0700

    HeatEquation_F will use F_BaseLib boundary condition stuff

Tutorials/HeatEquation_F/define_bc_tower.f90
Tutorials/HeatEquation_F/multifab_physbc.f90

commit 5a2614b56bb85644246973fc0cfcce9aa0217f0c
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 15:00:17 2012 -0700

    f90sources += create_umac_grown.f90
    f90sources += define_bc_tower.f90
    f90sources += fillpatch.f90
    f90sources += multifab_fill_ghost_cells.f90
    f90sources += multifab_physbc_edgevel.f90
    f90sources += multifab_physbc.f90

Src/F_BaseLib/GPackage.mak

commit a02e95cf7f7a3ffbfe9d632fadab896fccb53fe6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 14:59:07 2012 -0700

    add define_bc_tower and multifab_physbc to F_BaseLib.  Still need to clean these up to be the 'simplest' case for use in HeatEquation tutorials.
    
    Now, the F_BaseLib/GPackage.make contains
    
    f90sources += create_umac_grown.f90
    f90sources += define_bc_tower.f90
    f90sources += fillpatch.f90
    f90sources += multifab_fill_ghost_cells.f90
    f90sources += multifab_physbc_edgevel.f90
    f90sources += multifab_physbc.f90
    
    so local codes won't have to

Src/F_BaseLib/define_bc_tower.f90
Src/F_BaseLib/multifab_physbc.f90

commit d1b68f81c3d4ed3671e96fc83a5ffaace0ea6cb2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 5 14:13:31 2012 -0700

    Little cleanup.

Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp
Tutorials/HeatEquation_F/main.f90

commit d404721615f29e83cbcd12e4a1ee7e84e1227455
Merge: 52cc86f2b bbdcd3121
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Apr 5 13:45:22 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 52cc86f2bc3772732b8bfeae1803110cbd398574
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Apr 5 13:45:13 2012 -0700

    Fix call to layout_build_ba.

Src/LinearSolvers/F_MG/ml_solve.f90

commit bbdcd3121fa21ba847e6eb92dd744421c3cf0367
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 13:36:13 2012 -0700

    completely eliminate the string "setbc" from all files and filenames in the fBoxLib source and HeatEquation tutorial

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90
Src/F_BaseLib/multifab_physbc_edgevel.f90
Tutorials/HeatEquation_F/GPackage.mak
Tutorials/HeatEquation_F/multifab_physbc.f90
Tutorials/HeatEquation_F/setbc.f90

commit a3fc8ca05ad5f9ff72513e7fe4f12a79920b9829
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 15:38:47 2012 -0700

    latest

Docs/AdvancedTopics/AdvancedTopics.tex

commit c779afa50c7e8a57fc19954f1bd54a2d49a26488
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 15:38:23 2012 -0700

    forgot to commit this

Docs/AdvancedTopics/hopper_omp.run

commit dc1c8d646e7eeb47d7f958ccdb7c4556e9bb3485
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 13:52:15 2012 -0700

    finished section on OMP and accompanying example code

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex
Docs/GettingStarted/hopper.run
Docs/Introduction/Introduction.tex
Docs/UsersGuide.tex

commit 584fa2ce051c6c6f56a4fba1f7287c96abe16999
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 13:28:08 2012 -0700

    code comments

Tutorials/HeatEquation_EX1_F/advance.f90

commit 849ead71bd97802b5ad14bbb9182a82ccf1359b7
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 13:26:57 2012 -0700

    comments

Tutorials/HeatEquation_EX1_F/advance.f90
Tutorials/HeatEquation_EX1_F/main.f90

commit a1fde75049dcfc729e4b6bec07df582a293755f1
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 12:47:24 2012 -0700

    more progress on User's Guide

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex

commit fc4b02eee2b3fb58bfe55bd15be5df78791be392
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 12:46:54 2012 -0700

    some cleanup of WaveEquation_F

Tutorials/WaveEquation_F/advance.f90
Tutorials/WaveEquation_F/init_data.f90

commit 6a580d3d8ab0aa42aa0c322195d19fa9ae2ad0b5
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 12:45:13 2012 -0700

    simple OMP-enabled heat equation example

Tutorials/HeatEquation_EX1_F/GNUmakefile
Tutorials/HeatEquation_EX1_F/GPackage.mak
Tutorials/HeatEquation_EX1_F/advance.f90
Tutorials/HeatEquation_EX1_F/init_phi.f90
Tutorials/HeatEquation_EX1_F/inputs_2d
Tutorials/HeatEquation_EX1_F/inputs_3d
Tutorials/HeatEquation_EX1_F/main.f90
Tutorials/HeatEquation_EX1_F/write_plotfile.f90

commit ce868bc0ff4f692dc6103a19279b19916e6aad56
Merge: e5a32dc2a cb07ca5f2
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 10:55:44 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e5a32dc2a0f8d67304a1ad4d0667fad2ef68bbec
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 10:55:19 2012 -0700

    rewriting advanced topics chapter

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/UsersGuide.tex

commit f3f535bc8ce22980df04ffcce58f3f801dcbecb6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 10:31:17 2012 -0700

    update to the new layout_build_ba interface

Tutorials/WaveEquation_F/main.f90

commit cb07ca5f2dddcd916bbde0e13601b710dbcce5bf
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 10:28:39 2012 -0700

    Fix the call to layout_build_ba.

Tutorials/Exp_CNS_NoSpec/main.f90

commit 22a641c508e58092afe336ef552d21c314873e71
Merge: aab4a4265 968af7334
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 10:26:03 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit aab4a4265d98c48e6da96fbc5e19c393f790d2be
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 10:25:34 2012 -0700

    Add boxarray_bbox(ba) to the layout build calls where needed since
    the problem domain argument is no longer optional.

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/cluster_f.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_f.f90
Src/LinearSolvers/F_MG/cc_interface_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90

commit 968af7334bdeb61bdbc0188dcebececffa26aa6a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 4 10:12:31 2012 -0700

    Destroy the_bc_tower and call layout_flush_copyassoc_cache() to keep
    valgrind happy.

Tutorials/HeatEquation_F/main.f90

commit 234aff90a7a859cb6e4c9231e5e8c7853611f310
Merge: fc4559dea ce5f59650
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 4 10:12:16 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ce5f596502b3beb41b27894fedd060f7bf16e23e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 10:09:06 2012 -0700

    The problem domain argument (pd) is no longer optional in the call to layout_build_ba
    in layout.f90

Src/F_BaseLib/layout.f90

commit fc4559deabfc2087b5e7a9d927ba7e672fa41f00
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 4 09:59:35 2012 -0700

    OMP'd.

Tutorials/HeatEquation_F/advance.f90
Tutorials/HeatEquation_F/init_data.f90
Tutorials/HeatEquation_F/make_fluxes.f90

commit bb7671044b3da03fc259ed0d624667a9f7cbd8cd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 09:15:48 2012 -0700

    Add 3d inputs file.

Tutorials/HeatEquation_F/inputs_3d

commit 9e31c43313715aa078884d452689fac12f288264
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 09:15:24 2012 -0700

    Get 3d version working.

Tutorials/HeatEquation_F/GNUmakefile
Tutorials/HeatEquation_F/init_data.f90
Tutorials/HeatEquation_F/make_fluxes.f90

commit f64374acac27226787aa7e064418212c30c0f6de
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 08:02:14 2012 -0700

    Don't let nlevs > 3 for now just because we haven't defined grids at the higher levels.

Tutorials/HeatEquation_F/main.f90

commit 98a6ccca5184ded7a4f3637a983aa100880efe3c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 08:01:15 2012 -0700

    Added README.

Tutorials/HeatEquation_F/README

commit 4575480fa0e8f974c42f11de7222cf35f9793dc8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 07:57:50 2012 -0700

    More cleanup...

Tutorials/HeatEquation_F/define_bc_tower.f90
Tutorials/HeatEquation_F/main.f90

commit 3cca78aab416373b51cc935efb9544912f4ea2ab
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 07:55:23 2012 -0700

    Add more comments.

Tutorials/HeatEquation_F/main.f90

commit 417f3d7c25513ed5206df2fd2c8264aa106bbc19
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 07:45:49 2012 -0700

    This is a multilevel explicit solver for the heat equation using forward Euler.
    The boxes are currently hardwired in the main.f90 routine.

Tutorials/HeatEquation_F/GNUmakefile
Tutorials/HeatEquation_F/GPackage.mak
Tutorials/HeatEquation_F/advance.f90
Tutorials/HeatEquation_F/define_bc_tower.f90
Tutorials/HeatEquation_F/init_data.f90
Tutorials/HeatEquation_F/initialize.f90
Tutorials/HeatEquation_F/inputs_2d
Tutorials/HeatEquation_F/main.f90
Tutorials/HeatEquation_F/make_fluxes.f90
Tutorials/HeatEquation_F/multifab_physbc.f90
Tutorials/HeatEquation_F/setbc.f90
Tutorials/HeatEquation_F/write_plotfile.f90

commit 402ebd7f92adffbc52aec2d8855944151b8128de
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Apr 3 12:41:31 2012 -0700

    What the heck...declare v1.0.0

BoxLib_Version.txt

commit 113e2345baf3c866c0fcb6799fc62547fc9cda38
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 29 15:51:34 2012 -0700

    Changed := -> : in a couple places.

Tools/C_mk/Make.defs

commit daa0c6fc8d929a8f679b3cacfc0451c7d47af540
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Mar 29 13:55:28 2012 -0700

    Generalize refinement and derive functionality to allow user to build at runtime

BoxLib_Version.txt
Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/ErrorList.cpp

commit e4cfd5ac0836e190cba712ef2d12a19efd4c7c1e
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Mar 29 13:24:48 2012 -0700

    Modify where data pulled in simpleg stencils to avoid creating inconsistent edge data

Src/LinearSolvers/F_MG/cc_stencil.f90

commit d8ad93fbb73f1ecc3459afff1266ad010fe69bd9
Merge: 914f6f45c 2553af5cf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 29 07:17:21 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 914f6f45c448e078d5a1bf915e26c871f86133b9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 29 07:16:48 2012 -0700

    Fix from Manuel Cotelo.

Src/C_BaseLib/FabArray.H

commit 2553af5cf15c25d67595d87ed1716910945731ef
Merge: 231c3334e 1db0382cf
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 28 10:38:03 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 231c3334ea69aafb29dc175128b013899ae93b38
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 28 10:37:43 2012 -0700

    added FillBoundary.

Tutorials/MultiFabTests/MultiFabReadWrite.cpp

commit 1db0382cfaf8d2ee8f164199fd111d49297161af
Merge: 1810b0a16 e4f87bf00
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Mar 28 10:33:21 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1810b0a168fe4fa2ef4de3432df906c661f5f85a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Mar 28 10:32:41 2012 -0700

    Mods requested by Donev.

Tools/C_mk/Make.defs
Tools/F_mk/GMakeMPI.mak
Tools/F_mk/comps/gfortran.mak

commit e4f87bf00458dd4051451571198ebd59cf5ab64d
Author: vince <vebeckner@lbl.gov>
Date:   Tue Mar 27 17:55:18 2012 -0700

    example to do multifab functions.

Tutorials/MultiFabTests/GNUmakefile
Tutorials/MultiFabTests/Make.package
Tutorials/MultiFabTests/MultiFabReadWrite.cpp

commit 244c544f592610dac2871d911424f722cfbffee9
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 22 12:35:26 2012 -0700

    mothra no longer overrides GNUmakefile to force Intel compilers

Tools/F_mk/GMakeMPI.mak

commit 672fec9496ff8f71ebd65925ec1df369edf48135
Author: Matthew Emmett <memmett@unc.edu>
Date:   Thu Mar 22 14:04:10 2012 -0400

    PyBoxLib: Tweak imports, add multifab.get_info method.

Src/Python/pyboxlib/__init__.py
Src/Python/pyboxlib/base.py
Src/Python/pyboxlib/multifab.py

commit aa03a399e863f279c36ebf053fe1662acbf4fab3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 16 12:32:24 2012 -0700

    Fix bug where RelaxType was called instead of RAPType in the Hypre stuff.

Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp

commit bd4400c5a83843e574a5c3432257f7d8d5253349
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Mar 15 18:22:29 2012 -0700

    Shoops....forgot the box transform for the derive source data.

Src/C_AMRLib/AmrLevel.cpp

commit d146b8b27bda387fd25afcda9b4151046507fa63
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Mar 15 17:56:37 2012 -0700

    Fix the derive function that does not use a Fortran function, specifically for the case that the source data needs to be larger than the derived data.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp

commit bc352b4529ef566f38703b63ef768a678642100d
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Mar 15 19:02:32 2012 -0400

    add functions to convert between the integer bc names to strings
    and vice-versa

Src/F_BaseLib/bc.f90

commit cf045fe724d85b14cd782f9059079983d45d9c12
Merge: 50c58a493 f5dbbd078
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 15 14:13:05 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 50c58a49317ebf3af13732e219139c05aacd388e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 15 14:12:24 2012 -0700

    When splitting grids we split on Z then Y then X.
    Then tends to be more efficient cache-wise than X -> Y-> Z.

Src/C_AMRLib/Amr.cpp

commit f5dbbd0782b0777503c2497e3e92e7b19f0f3bc1
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Mar 15 13:19:32 2012 -0700

    Make particle replication stuff dimension independent

Src/C_AMRLib/Particles.H

commit 49f9128d7e650c575b4b630c23d9abee620ed201
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Mar 15 13:17:58 2012 -0700

    Add define for particles used in some app codes

Src/C_AMRLib/Make.package

commit 9bf9a46693f57051fb199d6de728a49cbdaa133b
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Mar 14 13:52:30 2012 -0400

    switch etags to ctags -e for TAGS to allow for options that
    support Fortran interfaces.  Works great in emacs now.

Tools/F_mk/GMakerules.mak

commit ee85c651ff22a06e2018b7b2a2672dcb8265651a
Merge: f18d8d42b 1e1c5058e
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Mar 14 13:37:52 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit f18d8d42bbc5102fd2305450c7921ad609ba3e3b
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Mar 14 13:37:22 2012 -0400

    add support for Fortran interface blocks to the tags target

Tools/F_mk/GMakerules.mak

commit 25d3fb903cdca4aa1224d3e6840b263c7df30fdc
Author: Ryan Orvedahl <orvedahl@bender.astro.sunysb.edu>
Date:   Wed Mar 14 11:29:42 2012 -0400

    Ryan's routines for plotting particle data on top of plotfile
    variables.  The driver, plotparticles.py, makes a bunch of plots
    and movies.

python_plotfile/plotparticles.py
python_plotfile/plotsinglevar_parts.py

commit 1e1c5058ee1f42554a6f70f895c3fdf17c39e77e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Mar 13 14:06:27 2012 -0700

    Wrapped some output in mgt%verbose > 0.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 71010464d91021dd970cdcfefa4adf754f1a0245
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Mar 13 12:44:01 2012 -0700

    Removed -mp and added -ip for Intel.

Tools/C_mk/Make.defs

commit 5850e132d0b3ca86ae5a302a0044dca0a2c5c3f1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Mar 13 12:43:34 2012 -0700

    Commented out some really old Intel Version 5 stuff.

Src/C_BaseLib/winstd.H

commit f66324129a05cea069c0241fd2604965d51e3ff6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Mar 12 13:19:47 2012 -0700

    Revert out some of my previous changes.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.H

commit 761868adb4e12af370b1d97b4f4e0f19dc09a493
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Mar 9 10:24:23 2012 -0800

    remove some antiquated comments and redundant BL_ASSERT statement

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 1ce175892a0217529048d063e8eba08f11abeb74
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Mar 7 12:56:34 2012 -0800

    Use _OPENMP instead of BL_USE_OMP for wrapping #pragma omp lines.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxLib.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit cc461eedab71b4301d9b132827aff30233dcaea2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Mar 7 12:55:33 2012 -0800

    Fixed to not need/use LinOp::bndryData(BndryData&).

Tests/LinearSolvers/C_CellMG/main.cpp

commit 93c6dd4c7ec97deb98d9dfb0277eb5c6c75a7398
Author: Matthew Emmett <memmett@unc.edu>
Date:   Wed Mar 7 13:27:41 2012 -0500

    PyBoxLib: Use ctypes.

Src/Python/GMakerules.mak
Src/Python/GPackage.mak
Src/Python/Makefile
Src/Python/README
Src/Python/mkpyfboxlib
Src/Python/pyboxlib/__init__.py
Src/Python/pyboxlib/base.py
Src/Python/pyboxlib/boxarray.py
Src/Python/pyboxlib/fab.py
Src/Python/pyboxlib/layout.py
Src/Python/pyboxlib/multifab.py
Src/Python/pyboxlib/pybl.py
Src/Python/src/blobjects.f90
Src/Python/src/blobjects.py
Src/Python/src/boxlib_numpy.c
Src/Python/src/boxlib_numpy.f90
Src/Python/src/fboxlib.f90
Src/Python/test.py

commit 028c142d4b6a11bff1d8aa2b4bb184daa4669dd7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 2 13:58:08 2012 -0800

    Add subroutine simple_2d_const to fill 2d stencils when the coefficients beta
    are constant (already existed in 3d)

Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90

commit d8448582742fa28651721dbdc9977eb938228242
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Mar 2 13:38:57 2012 -0800

    1) Fix the computation of fluxes on high edges when using a higher-order
    cell-centered stencil (change to cc_stencil_apply.f90)
    2) Fix the computation of ghost cells between AMR levels when at an
    interior corner -- we need to first average the fine solution onto the
    coarse grid before using the coarse cells to interpolate, because the
    coarse cells under the fine grid can be used in constructing the
    slope in the coarse cell not under the fine grid.

Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit 2ffa11eda56cd52d463a29d7f41942678dc58226
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 1 14:22:07 2012 -0800

    Add REAME for the multigrid tutorial.

Tutorials/MultiGrid_C/README

commit 3a8c8a561fa91fdf62afb6d6402022ae6db6f70e
Merge: 46b6efc88 83d9ccd6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 29 16:38:30 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 83d9ccd6a4ccf2045b176c00fcb3230bb8dd72bb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 29 12:58:24 2012 -0800

    Commented out a couple warning messages.

Src/C_BaseLib/FArrayBox.cpp

commit 2a0ae8b2494bbb238f53e6bcfe6cd5819f138853
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Feb 29 11:17:16 2012 -0500

    get this compiling again

python_plotfile/GNUmakefile

commit 86799afeb8f4c9007d30c5d6d32092c644c5957c
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Mon Feb 27 19:20:00 2012 -0500

    add projection, eos, and incompressible tests.  Also update to the
    new data_processing location

Tools/C_util/regtests/Maestro-tests.ini

commit a7f53f34f3b3d2160ace117b8d15e46fecf50e74
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Mon Feb 27 19:06:31 2012 -0500

    more sensible (optional) fParallel location to get this to compile
    if you have a MAESTRO checkout at the same level as AmrPostprocessing

GNUmakefile

commit 78554fce22b0e9a8441ac55ba0e6f59041066190
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 24 13:10:20 2012 -0800

    Fix the quadratic terms in subroutine FORT_CQINTERP in INTERP_2D.F.  They were missing
    the 1/2 in front of phi_xx * dx^2 term.

Src/C_AMRLib/INTERP_2D.F

commit 8e2153069231b0ad5cd5ed152605228d241b2d70
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Feb 23 15:07:11 2012 -0800

    BOXLIB_HOME default should be ../../.. not ../..

Tutorials/MultiGrid_C/GNUmakefile

commit 8281538311c41fe6b9dac74ff891bd0678c38e1d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Feb 23 15:04:54 2012 -0800

    Make the BndryData member a const reference instead of a concrete data
    member.  This means that the BndryData object passed to the constructor
    had better not be destroyed before we use it.  The "right" way to do this
    would be to pass a reference-counted pointer to a BndryData.  I'll put
    that on my list ...

Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.H

commit 011daf8e344a6398bce506b6b3efe5a978cbcdbb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Feb 23 15:02:59 2012 -0800

    Disallow some copy constructors and assignment operators.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp

commit 5d75cb3ed633854d1b03f82848a0ca8bde73a630
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Feb 23 13:45:58 2012 -0800

    Make copy constructor & assignment operator private.

Src/C_BoundaryLib/FabSet.H

commit fef565de395cf6dbaee9653e5f098821e01604f4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Feb 23 13:29:38 2012 -0800

    Use PArrayNoManage instead of PArrayManage to cut down on copy()ing.

Tutorials/MultiGrid_C/main.cpp

commit aeccb241ceaee211d8a3f7975dc607e28d3d41aa
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue Feb 21 21:29:19 2012 -0500

    add the ability to add a string to the compilation command -- useful
    for forcing the code to use alternate microphysics.

Tools/C_util/regtests/testnew.py

commit 46b6efc886be881bb5fcf2e4fcca98e6b4240c05
Merge: 54d1b37dd 439f2bde4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 21 15:40:31 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 439f2bde4642e8efeaca0c771c2513c9381b843c
Author: John Bell <jbbell@lbl.gov>
Date:   Sat Feb 18 16:16:28 2012 -0800

    added note about how to build

Tutorials/Exp_CNS_NoSpec/README

commit a286a3544f6860b4a7a83f212edb70b9a6626c80
Author: John Bell <jbbell@lbl.gov>
Date:   Sat Feb 18 16:14:25 2012 -0800

    added a README to the compact app

Tutorials/Exp_CNS_NoSpec/README

commit 44a90d052d479b5bc0791de7fa0b6e670a2570b2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 17 16:25:10 2012 -0800

    Convert fParallel/data_processing to AmrPostprocessing/F_Src.

CASTRO_gravity/GNUmakefile
CASTRO_gravity/fdustcollapse1d.f90
CASTRO_gravity/fdustcollapse2d.f90
CASTRO_gravity/fdustcollapse3d.f90
CASTRO_hydro/GNUmakefile
CASTRO_hydro/fsedov1d.f90
CASTRO_hydro/fsedov2d_cart.f90
CASTRO_hydro/fsedov2d_cyl_in_cartcoords.f90
CASTRO_hydro/fsedov2d_cyl_in_cylcoords.f90
CASTRO_hydro/fsedov2d_sph_in_cylcoords.f90
CASTRO_hydro/fsedov3d_cyl.f90
CASTRO_hydro/fsedov3d_sph.f90
CASTRO_radiation/GNUmakefile
CASTRO_radiation/fgaussianpulse.f90
CASTRO_radiation/flgt_frnt1d.f90
CASTRO_radiation/fradshock.f90
CASTRO_radiation/fradsource.f90
CASTRO_radiation/fradsphere.f90
CASTRO_radiation/frhdshocktube.f90
GNUmakefile
MAESTRO_tests/GNUmakefile
MAESTRO_tests/fgaussianpulse.f90
MAESTRO_tests/fmlcompare.f90
MAESTRO_tests/fmlconverge.f90
MAESTRO_tests/fnorm.f90
MAESTRO_wdconvect/GNUmakefile
MAESTRO_wdconvect/feint.f90
MAESTRO_wdconvect/fthermo.f90
MAESTRO_wdconvect/fthermo_driver.py
MAESTRO_wdconvect/fwdconvect.f90
MAESTRO_xrb/GNUmakefile
MAESTRO_xrb/fad_excess.f90
MAESTRO_xrb/fbuoyancy.f90
MAESTRO_xrb/fconv_slopes.f90
MAESTRO_xrb/fspeciesmass.f90
Palette
fIDLdump.f90
fIDLdump3d.f90
faverage.f90
fboxinfo.f90
fcompare.f90
fextract.f90
fextrema.f90
fsnapshot2d.f90
fsnapshot3d.f90
ftime.f90
fvarnames.f90
old_flame/GNUmakefile
old_flame/fbubble_position.f90
old_flame/fbubble_position_3d.f90
old_flame/fcusp.f90
old_flame/fcylflame.f90
old_flame/fflamelength.f90
old_flame/finteg.f90
old_flame/fturbkin.f90
old_flame/fwidth.f90
python/README
python/column_depth.py
python/conv_slopes.py
python/dumpparthistory.py
python/eos_data.txt
python/helmeos.py
python/parseparticles.py
python/test_helmeos.py
python/test_parseparticles.py
python/timestamp_00.REMOVED.git-id
python/timestamp_02.REMOVED.git-id
python_plotfile/GNUmakefile
python_plotfile/contourcompare.py
python_plotfile/fsnapshot.f90
python_plotfile/plotsinglevar.py
tutorial/GNUmakefile
tutorial/fspeciesmass2d.f90
tutorial/fwrite2d.f90

commit 891b9d855b4f2921f3afda0fc32805ccea299977
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 17 14:56:04 2012 -0800

    Add new MultiFab norm0 function which takes a BoxArray.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 20936ac991c4944cf4501967b8f74f5ae09ee21a
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Feb 17 16:45:11 2012 -0500

    make individual tests links off the main results page

Tools/C_util/regtests/testnew.py

commit 8eb0e27af6be8fb83a86044ba8facbb40c3faf0b
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Feb 15 16:11:27 2012 -0800

    Remove -fast-math on GNU stuff due to vode finickyness

Tools/C_mk/Make.defs

commit 27b2501411fcbab30700143481e5cabf96925a9b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 15 14:28:38 2012 -0800

    Removed flags turning off exceptions for GNU.
    Either way it doesn't make much difference in run times.
    Added -ffast-math to the GNU optimization flags.
    This can make a sizeable difference in run times.
    This "can" break codes though.  In particular, we don't have it on
    in the F_mk stuff as it breaks MAESTRO somehow.

Tools/C_mk/Make.defs

commit 54d1b37dda958d18a1d06b44c3a0a6c18cfe056d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 15 14:11:00 2012 -0800

    Fix 3D inflow boundary for F90 nodal solver.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit bd6d4550a8ee8e82e47420f2bcea8a3812c83ea5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 15 14:01:46 2012 -0800

    Use -O2 instead of -O3 with gfortran.  The latter can sometimes be slower.

Tools/C_mk/Make.defs

commit 1f88d7568d96f73f081f1161c5cf9b2171c8f90e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 15 12:47:27 2012 -0800

    Don't output any plotfiles if plot_int <= 0.

Tutorials/Exp_CNS_NoSpec/main.f90

commit 5dc37e889b3e255bf461d556c98dd5fb68dd3a0b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 15 10:37:46 2012 -0800

    Make calculation of courno in ctoprim() optional.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 6da56df15584c29bc9a3668616cb67962c77da1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 14 16:01:50 2012 -0800

    Fix bugs for 2D inflow boundary.  3D still needs to be fixed.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit cc578d03ddecf28f594da4d8ad9cbc9fc7ceb18d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 15:53:05 2012 -0800

    Fixed typo.

Tutorials/Exp_CNS_NoSpec/write_plotfile.f90

commit 0b65cf3afa6e0d7b8415c5a4c9028c8e25d31ac6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 15:52:12 2012 -0800

    Made write_plotfile() more generic.

Tutorials/Exp_CNS_NoSpec/main.f90
Tutorials/Exp_CNS_NoSpec/write_plotfile.f90

commit 043143705ecf16b7480c4651e2cdb985eb8c9205
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 15:35:59 2012 -0800

    Moved final output statement before boxlib_finalize().

Tutorials/Exp_CNS_NoSpec/main.f90

commit d1a4846494b9bc8d286714892905fd5bc0e5c236
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 14:26:42 2012 -0800

    Some code rearrangement.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit bce89d965d34ff22074b37740af8d522e4ed3ef2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 13:44:12 2012 -0800

    New inputs file.

Tutorials/Exp_CNS_NoSpec/inputs.jbb

commit da5a874b06c1a0b87481ac6d7a0f904307b5f557
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 13:43:54 2012 -0800

    More like what JBB wanted.

Tutorials/Exp_CNS_NoSpec/init_data.f90
Tutorials/Exp_CNS_NoSpec/inputs_3d

commit a423817f00686214b6491406d760a3923271eb0d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 13:26:18 2012 -0800

    Replaced some divides with multiplies.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 20c0b584d55854572956cc8ecb3e84159c64c979
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 13:03:45 2012 -0800

    Some memory and performance improvements.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 6b49dc83fe140adb61f217e1216fb6fd2b5715dd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 12:34:50 2012 -0800

    Some cleanup.

Tutorials/Exp_CNS_NoSpec/advance.f90
Tutorials/Exp_CNS_NoSpec/init_data.f90

commit a382242b2862d72fd079020c097a7e002b34c9dd
Merge: 2444664aa 6ccd79989
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 11:12:14 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2444664aab53e7b2aa0452aa53b157f1a0fa24a7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 11:12:04 2012 -0800

    OMP init_data

Tutorials/Exp_CNS_NoSpec/init_data.f90

commit 6ccd79989133470578a0bedb21af6ad35e7a94cb
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue Feb 14 13:49:29 2012 -0500

    new main page format -- makes it easier to view many tests

Tools/C_util/regtests/testnew.py

commit a8f150f9f3a9852d48f0d474972d526351439cd4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 10:48:54 2012 -0800

    Some OMP tweaking.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 2d3e59d0e1047dace9743d3b2aa3cd75bf8b8e17
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 10:23:10 2012 -0800

    OMP'd diffterm().

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 6089cc7622f01d38dc0f48281f9d6cb0719a24a8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 10:01:44 2012 -0800

    OMP'd hypterm().

Tutorials/Exp_CNS_NoSpec/advance.f90

commit c9b8fb01a568e9e06d3684d7c6984f335c08ef73
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 21:23:05 2012 -0800

    Some renaming and added newer namelist stuff to example inputs file.

Tutorials/Exp_CNS_NoSpec/inputs_3d
Tutorials/Exp_CNS_NoSpec/main.f90

commit a13ef3ec3d291361304297f4f1cab4ac46603b8b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 20:58:08 2012 -0800

    Now write out when outputing a plotfile.
    Add more things to the namelist so they can be set in an input file.
    Some more cleanup.

Tutorials/Exp_CNS_NoSpec/advance.f90
Tutorials/Exp_CNS_NoSpec/main.f90
Tutorials/Exp_CNS_NoSpec/write_plotfile.f90

commit 696b2c7de74b5cb6e4be44ddd091aa28ba917e0a
Merge: 543c12467 d40620b11
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 20:28:22 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 543c12467f4c4dba05932cad3bf827d387d448bc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 20:27:52 2012 -0800

    Fixed bug; now appears to be working.
    Did some cleanup as well.

Tutorials/Exp_CNS_NoSpec/advance.f90
Tutorials/Exp_CNS_NoSpec/init_data.f90
Tutorials/Exp_CNS_NoSpec/inputs_3d
Tutorials/Exp_CNS_NoSpec/main.f90

commit 630493c829a6b6b29dadbe3a71bc1d1f5efa0ab6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 17:49:49 2012 -0800

    Fixed bug in difflux().
    Now calculate dt based on CFL/courno.

Tutorials/Exp_CNS_NoSpec/advance.f90
Tutorials/Exp_CNS_NoSpec/init_data.f90
Tutorials/Exp_CNS_NoSpec/main.f90

commit d40620b113a2c2abb5f71b970319799158a82f69
Merge: a09b0aeb6 71ecefda5
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Feb 13 20:39:01 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit a09b0aeb6ea8a47171401eaf47a2c6147b2abda3
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Feb 13 20:38:40 2012 -0500

    add compareFile parameter to tests to allow us to explicitly specify
    the file to be used in the comparison
    
    make sure that the buildDir is infact valid
    
    if all are compileTests, then don't worry about if the benchmark
    directory exists

Tools/C_util/regtests/testnew.py

commit 71ecefda5efba025de5be5777d588247a4f1a97b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 16:53:50 2012 -0800

    Getting closer to working code.

Tutorials/Exp_CNS_NoSpec/init_data.f90
Tutorials/Exp_CNS_NoSpec/main.f90
Tutorials/Exp_CNS_NoSpec/write_plotfile.f90

commit 045c4c197e3e8142bb30919833c48cbe58896f97
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 16:29:09 2012 -0800

    Added a couple more named constants.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 088c2810ba3402d383b46c7e0d536a41ea17e401
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 16:18:56 2012 -0800

    Now calling diffterm().
    Using dummy values for ETA and ALAM.
    Still got to init data correctly as well.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 2b107f23005d1f5e7b579ec285f4de346076f10f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 15:48:12 2012 -0800

    Some work getting diffterm().

Tutorials/Exp_CNS_NoSpec/advance.f90

commit c008a32063db8ef89004fe6dd2965de093feb185
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 15:20:48 2012 -0800

    Actually call ctoprim() & hypterm().

Tutorials/Exp_CNS_NoSpec/advance.f90

commit cf14e49b4ac6653cebe4d1f9f5050c758ef9d7c4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 14:47:28 2012 -0800

    Brought in ctoprim() and hypterm().

Tutorials/Exp_CNS_NoSpec/advance.f90
Tutorials/Exp_CNS_NoSpec/init_data.f90
Tutorials/Exp_CNS_NoSpec/main.f90
Tutorials/Exp_CNS_NoSpec/write_plotfile.f90

commit a248aa18a770980a150cc02491ea6152f1680df3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 12:11:40 2012 -0800

    Removed various flags used to turn off C++ exceptions.
    The various compilers on jaguarpf really want exceptions enabled.
    Shouldn't really effect performance.

Tools/C_mk/Make.Linux

commit 3b1ec9fe16dec95f4121c2141956292182b51021
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Feb 10 20:45:11 2012 -0800

    Virtualize a couple functions to support more generic control of plotfile and checkpoint output

BoxLib_Version.txt
Src/C_AMRLib/Amr.H
Tools/C_scripts/gen_release_tarball

commit 26f0f72eb9e8fc885f4fa0fd1e2e12a40dd93c1d
Merge: 3d51f048d 7a4a6867d
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Feb 10 20:44:45 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 7a4a6867d63ef6258d320b4a2153b6897b47868a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 10 16:02:04 2012 -0800

    Some cleanup.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit abdbeddd62cd55ad47784a501e2f6df88e729fcb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 10 16:01:49 2012 -0800

    Plug a couple memory leaks.

Tutorials/Exp_CNS_NoSpec/main.f90
Tutorials/WaveEquation_F/main.f90

commit 6ce0c23d7cdd17ecf7a7f88b551473b2b37a11d8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 10 15:26:35 2012 -0800

    Some work on RK3 algorithm.

Tutorials/Exp_CNS_NoSpec/advance.f90
Tutorials/Exp_CNS_NoSpec/main.f90

commit fa0215b730e735333cb82017e2b61a229ea39c2f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 10 14:12:38 2012 -0800

    A little more cleanup.  Still just WaveEquation.

Tutorials/Exp_CNS_NoSpec/advance.f90
Tutorials/Exp_CNS_NoSpec/init_data.f90

commit 62c79d63654a10f06591e66a4eb6a538dc996335
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 10 14:06:26 2012 -0800

    A little cleanup.

Tutorials/Exp_CNS_NoSpec/inputs_2d
Tutorials/Exp_CNS_NoSpec/inputs_3d
Tutorials/Exp_CNS_NoSpec/main.f90

commit dd839d6adaa81d39a809fe311ce09dac030f65b7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 10 13:38:49 2012 -0800

    Just copied files from WaveEquation_F.

Tutorials/Exp_CNS_NoSpec/GNUmakefile
Tutorials/Exp_CNS_NoSpec/GPackage.mak
Tutorials/Exp_CNS_NoSpec/advance.f90
Tutorials/Exp_CNS_NoSpec/init_data.f90
Tutorials/Exp_CNS_NoSpec/inputs_2d
Tutorials/Exp_CNS_NoSpec/inputs_3d
Tutorials/Exp_CNS_NoSpec/main.f90
Tutorials/Exp_CNS_NoSpec/write_plotfile.f90

commit f0d87b4b692ac1cbe97b448b8b9a3bd9a120f219
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 10 09:03:54 2012 -0800

    Some patches from Chris for Macs.

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 4531f6e08cd51b0681e891b7ab3b365b53ce90c1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 10 08:26:27 2012 -0800

    Put Mike's fixes in for gcc/g++.

Tools/C_mk/Make.defs

commit 573f5bd5e08b0b1d9a300ee91f2676c3ab7597d7
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Thu Feb 9 16:31:03 2012 -0500

    add a sort to the test problem

Tools/C_util/regtests/testnew.py

commit df39ebc07be178479ec7da207ca1080b6b861e90
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 9 12:58:19 2012 -0800

    The alpha term was incorrectly included in s_minion_cross_fill_2d and s_minion_cross_fill_3d

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 1a7b77957efd1ee4c7f5767a4a06c77bf560a7b9
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Feb 8 20:02:30 2012 -0500

    fix some typos

Tools/F_scripts/write_probin.py

commit c275e7e0515eb79b23595186214cf569aa4d0cd3
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Feb 8 20:00:43 2012 -0500

    make the problem names more unique.  Eliminate docs

Tools/C_util/regtests/gen_compile_test.sh

commit 5af08d4d17797825a858b0012e102cfd3d9f7327
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 8 09:14:26 2012 -0800

    A little more generalization in support of Aleks.

Tools/C_mk/Make.defs

commit a6e5bf356db06c4c7b330853e74f85c2a3176e0c
Merge: c3ae40bf9 547359a14
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Tue Feb 7 19:33:55 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c3ae40bf9a4037115c6d672313c5194a63e732f2
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Tue Feb 7 19:33:11 2012 -0500

    add a tool to automatically generate the compile test parameters for
    all problems with a GNUmakefile

Tools/C_util/regtests/gen_compile_test.sh

commit 547359a149520539d50dc8afb14adf9033c9b17d
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Tue Feb 7 19:17:17 2012 -0500

    add support for compile-only suites (no other parameters other than
    build directory are needed)
    
    fix the webTopDir checks (now makes sure there is a "/"
    
    minor output tweaks
    
    don't print cvs/git info on webpage if we ran with --no_update

Tools/C_util/regtests/testnew.py

commit e40d39953668c8f29750876d0dab1d61467c33f9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 7 13:07:24 2012 -0800

    Some mods to enable Aleks to use "gfortran46" instead of gfortran.

Tools/C_mk/Make.defs
Tools/F_mk/GMakedefs.mak

commit d45c5acc0a38408fab94c80edfd79bc80c94cc26
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 7 13:06:23 2012 -0800

    Use -O1 instead of -O when debugging.
    It compiles faster and gives better debug info inside gdb.

Tools/F_mk/comps/gfortran.mak

commit d544493b7d1aebaab5e2ab9cc34e7d1580a68c1e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 7 10:05:24 2012 -0800

    BOXLIB_HOME macro wasn't quite right.

Tests/LinearSolvers/ComparisonTest/GNUmakefile

commit f99af059784002311fde1e5d318ae82260540291
Merge: 9281a575b 64bee3d37
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 6 14:10:14 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9281a575baa662e6772f2fab744d9d669b89ff0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 6 14:09:21 2012 -0800

    OpenMP the sync residue subroutines.

Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 64bee3d379a8ef546bd147e5573efd67c07dccc2
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Mon Feb 6 14:09:53 2012 -0500

    add RT, update build directories to reflect new directory structure

Tools/C_util/regtests/Maestro-tests.ini

commit 102a70764c55bfce90b276dbb987c9bbd3655797
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Mon Feb 6 14:09:35 2012 -0500

    if we fail to compile during a normal test, show the make output

Tools/C_util/regtests/testnew.py

commit 8b5b4869b86a1a551a001fa638963870618ad6fe
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Feb 5 16:38:27 2012 -0800

    Define lo_inflow(:) and hi_inflow(:) instead of lo_inflow(3) and hi_inflow(3)
    in nodal_divu.f90/subroutine divu.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit ef22f6063771c22c26f7586c8801dc2a10bb75f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 2 17:59:22 2012 -0800

    Support the case when fine grids touch inflow boundaries.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit dc87d9c4472e4b0ce55f44ee63ad23f6e266a0cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 2 15:42:52 2012 -0800

    Call bl_error if nonuniform grids are used in the F90 nodal solver.

Src/LinearSolvers/F_MG/mg.f90

commit 424bb6c5d67e95ec4b9ede645b18156b36ac7189
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 2 13:41:17 2012 -0800

    Pass velocity in ghost cells into the F90 nodal solver in order to
    support inflow boundary.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit c71123bb376b949bb0bd56a901122619a4855c0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 1 17:00:03 2012 -0800

    put subtract_divu_from_rh back

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 3aa4a44dbb49afa46247dcc26b1e64accdb59098
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 1 14:09:03 2012 -0800

    Fix a bug in computing the new u in 3D nodal projection.  The bug was
    due to confusing rho and sigma (which is 1/rho).

Src/LinearSolvers/F_MG/nodal_newu.f90

commit 1dad7f7162d8e0de304498d62df0297d6e75a334
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 1 13:31:59 2012 -0800

    Fix a bug in 3D nodal projection with the dense stencil.  MG towers were
    used before they were built.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 51ff44fadce0339c75df0470eed5c559450ef8f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 1 12:50:39 2012 -0800

    Fix a bug in 3D nodal projection

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/nodal_divu.f90

commit a23edb764e04c5a7871e0d7cf07a247c36bdbdd5
Merge: e0a50f35c 3145a47ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 31 17:27:36 2012 -0800

    Merge branch 'dev'

commit 3145a47ed9d739691804fa3f767602671959f195
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 31 16:11:21 2012 -0800

    3D support for have_divu

Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit e0a50f35cd47a286be1b4e6d9be834000f879b77
Merge: 0cfb40e34 549c15363
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jan 31 19:01:04 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 0cfb40e34cdfdfcbd0509083fa9ef250c7fd89e3
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jan 31 19:00:17 2012 -0500

    remove -J and -I for nan -- the default Make.defs handles this now, and gfortran
    doesn't like it specified twice.

Tools/C_mk/Make.Linux

commit 549c15363858c97139f71f2da208b8455b5160c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 30 14:01:17 2012 -0800

    Fix bugs for the cases when both fine and coarse levels touch physical boundaries.

Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 3ecbd58fe31419ade98c400850a061c4ea82dbae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 27 16:18:57 2012 -0800

    Fix a bug. 2D version of mgt_set_vold was used in 3D.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 1bf2bb10a0c2a9877e3d7dd7572a003f8a15de60
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 27 13:21:32 2012 -0800

    Delete "call flush()" that was checked in accidentally.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 13bf0f77edbc8bb50c10d9be825c15baaf4b627d
Merge: 1ef07bdff 9642b15d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 27 13:15:47 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9642b15d99d25cd0eff7b4b285bdfd0950c6e02b
Merge: 04a35fe6d 002ce0d7f
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 27 13:12:27 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 04a35fe6de09752e76f8b0a89a2ed2960a3c253a
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 27 13:12:09 2012 -0800

    set version string for fabs and multifabs.

Src/Extern/amrdata/AmrData.cpp

commit 1ef07bdffc42fe23a5835e71e8b63694905a5128
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 27 13:11:19 2012 -0800

    Fix a bug in computing source at the interface due to passed rhs.
    
    Make bnorm = max(bnorm, tres0), otherwide we may have trouble if tres0
    is too big.

Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 002ce0d7f2aca6c86cdaf0a1067d5c634d9168ab
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jan 27 12:52:10 2012 -0800

    Added the ability to flush fortran output (unit=6).
    This can be used to help sync up C++ and Fortran output when debugging.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 7b2b3cfaad35ea373166dbbc6185e7f8a9975d53
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 26 13:49:50 2012 -0800

    Add some comments

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 45dc997da4dc466cbaedbfb5150ce72502263d4a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 26 13:43:26 2012 -0800

    clean up

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 8ac9b0018ae57bcc6e8567646a167a95b2e2fbcb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 25 17:51:13 2012 -0800

    support have_divu

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 3d51f048d2dff9cf0aee76f165dfc4f5e8900c4a
Merge: 9c1a93bbb 67d9dc7c7
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jan 25 16:38:01 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 9c1a93bbbb138c715d3db9b2b584440735a7b6d9
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jan 25 16:35:24 2012 -0800

    Remove CMake hack suggested by one of the Amanzi folks

CMakeLists.txt

commit 67d9dc7c77f19f90f57ef37312d087c72b7b86dd
Merge: 647a910dd a1b94f35e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 20 13:24:31 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 647a910dd7aebde3b8fee59b4312abaa0bb33671
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 20 13:23:38 2012 -0800

    Fix a parallel bug

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit a1b94f35edd59d41030435f0d36e107b3e09e4d0
Merge: beefe3db1 6eb27e917
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Jan 20 12:08:12 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit beefe3db1de22c97460d2bcca86c689817730293
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Jan 20 12:07:28 2012 -0500

    on bender, override the default compilers by mpif90 and mpicxx to
    be the versions that are in the current path.

Tools/F_mk/GMakeMPI.mak

commit 6eb27e91727e2aaa129c210bb5a51db40f126825
Merge: 4c9dfd40c 83076388c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 19 17:17:14 2012 -0800

    Merge branch 'dev'

commit 83076388cf880d435a37a2dcba22e7f9dbc2bd36
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 19 17:10:50 2012 -0800

    3D implemented for nodal sync residue.

Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 4c9dfd40c927af81b1e6a3d60fd2e75f9f2ab939
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 19 17:00:14 2012 -0800

    rle update pubtest 4

Tests/IOBenchmark/README

commit f10d5b42793783423e909015e9f3b7ad4c488ad2
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 19 16:46:28 2012 -0800

    rle update pubtest 3

Tests/IOBenchmark/README

commit 0fe7449d45e5fd768d50f138344e33a35915c13b
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 19 16:43:18 2012 -0800

    rle update pubtest 2

Tests/IOBenchmark/README

commit 71ad807b68035a4357dd5c32fdf444c51ab03437
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 19 16:38:05 2012 -0800

    rle update pubtest

Tests/IOBenchmark/README

commit 6e31a391a7af478946547057f78fce12e046cb29
Merge: 85360cee8 1f4cd361a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 18 15:49:48 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 85360cee8ceb790c42f2ddde726842511713d284
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 18 15:49:28 2012 -0800

    rme update 3

Tests/IOBenchmark/README

commit 1f4cd361a7b4ac5ca0e0fb60767020d186af48fe
Merge: 32e65e812 c428c2aa2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 18 15:34:42 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 32e65e812f2f7f78774bc460cdf0641764d04813
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 18 15:33:55 2012 -0800

    Fix a few memory leaks.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit c428c2aa2a40c588c14a6fbab0b5c8b2e79fe2ef
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 18 11:19:14 2012 -0800

    rme update 2

Tests/IOBenchmark/README

commit a101b1817ef1bc8eb0e661936a95baa6c098adff
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 18 11:08:17 2012 -0800

    rme update

Tests/IOBenchmark/README

commit f361fff44e719d6262f7146b716e0995b5db7dce
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Tue Jan 17 15:56:48 2012 -0500

    update inf for new F16 install

Tools/F_mk/GMakeMPI.mak

commit 07ae0bad2d7883618bf602c3e4c15f4f1e985530
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 13 15:51:52 2012 -0800

    Allow stencil type be passed to MGT_Solver.  MGT_Solver still reads
    mg.stencil_type.  But the optional _stencil_type argument in the
    MGT_Solver constructor, if provided, will have higher priority.  The
    reason for the modification is to make sure the MG solver and the
    nodal projection class in IAMR are consistent.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 4ee48fca13b59ea25e371061f0f869daecb2cbf7
Merge: 7b965b4ac da8422a6f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 13 14:26:40 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7b965b4ac4559bbf33460ca66f9de633a8200fc3
Merge: c65f06351 5cb61cff1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 13 14:26:23 2012 -0800

    Merge branch 'dev'

commit 5cb61cff151b921361e2656b890851a5905fc607
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 13 14:23:16 2012 -0800

    change the size of zero_rh from (nlevs) to (2:nlevs) because rh(1) was
    never used.

Src/LinearSolvers/F_MG/ml_nd.f90

commit da8422a6f6c89555611b96300da21ce175fc7d9c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jan 13 08:25:43 2012 -0800

    Some cleanup.

Tools/C_mk/Make.defs

commit 5ad761c7076a770079bcf9e5dbdec97b6fe79354
Merge: 766de365b aa6f683b2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 12 21:03:39 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit aa6f683b2d49b65b6e790326ec89db11fe34a0d8
Merge: e2015b91a 78fcd0be1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 12 20:27:37 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 766de365b48f0d9159800820618bf30a83a904d7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 12 20:24:27 2012 -0800

    Minor tweak to get .mod files in the right place on hopper.

Tools/C_mk/Make.defs

commit 78fcd0be1ad9d822bdb9aa7d153b72ed30393561
Merge: 12fec316e c65f06351
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 12 17:18:45 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 12fec316ec3feedfed4e0625262307317662020a
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 12 17:18:29 2012 -0800

    more 2D

Tutorials/MultiGrid_C/COEF_F.H
Tutorials/MultiGrid_C/main.cpp

commit 8064cbb629db4fc9a02874f20ffc82199fb2e00b
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 12 17:17:18 2012 -0800

    switch mpi on hedorah

Tools/C_mk/Make.mpi

commit da553035ba9de29ed1716cba30f9ed0a3eda8e27
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 12 17:15:11 2012 -0800

    Allow 2D in solver tutorial

Tutorials/MultiGrid_C/COEF_2D.F
Tutorials/MultiGrid_C/RHS_2D.F

commit e2015b91adaec57d38f9d772a78978599a33d5a1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 12 16:48:12 2012 -0800

    Fix to GNU FC stuff to get .mod files written to the appropriate place on
    hopper. The problem was that the "-J" flag was being set on the FC and fC
    lines, which are overwritten on Cray computers with ftn. Solution was to
    move all those flags set together with the compiler into [fF]FLAGS.

Tools/C_mk/Make.defs

commit c65f0635170d2ccdaa79e0e889f17023b3b18eee
Merge: e7148bb2f 2055d9cd2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 11 16:58:12 2012 -0800

    Merge branch 'dev'

commit 2055d9cd2efd465f1390c76d24cfcae82f83702b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 11 16:54:59 2012 -0800

    Change the way of getting sync resid from the MG solver for safety.

Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit e7148bb2fbf1bbd58d0fae19f34cba078d0034a5
Merge: 43a07818b f06e3eaaf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 11 15:35:28 2012 -0800

    Merge branch 'dev'

commit f06e3eaaf29ed3660e73bcaccb071b56d99bc6db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 11 15:32:01 2012 -0800

    Fix a bug.  The ghost cells of sync_resid should be set to zero.

Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 43a07818bffd0b34331f28385a7cd2bb57a050cb
Merge: 8fd653aa2 0c9c990f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 11 11:00:41 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8fd653aa2478818b19080976740bc12b1391484e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 11 10:52:53 2012 -0800

    Remove the hack in nodal smoother that try to match the C++ nodal
    solver.  The 2D hack had a bug.  Moreover, the old way is also
    problematic because the color (i.e., red or black) depends upon the
    layout of grids.

Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit 0c9c990f904d7fae8a02a3cd7affa50bda7d768a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 10 17:41:17 2012 -0800

    boundary condition figures

Docs/AdvancedTopics/bc_example1.eps
Docs/AdvancedTopics/bc_example1.fig
Docs/AdvancedTopics/bc_example2.eps
Docs/AdvancedTopics/bc_example2.fig
Docs/AdvancedTopics/bc_example3.eps
Docs/AdvancedTopics/bc_example3.fig

commit cde14fc3f6746b3325c44c3abea22337a259a664
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 10 17:40:37 2012 -0800

    starting a daunting documentation

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex

commit 15d4aad1b6fc7ff3d0583c3042c8bd8376a3ab62
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 10 16:35:45 2012 -0800

    moving this

Docs/GettingStarted/hopper.run

commit 0706f6a50deb519a2207fa4464f870f7c4b1e6b8
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 10 16:35:33 2012 -0800

    moving this

Docs/AdvancedTopics/hopper.run

commit 9da7729692bd300e7fb2346cbbb36a4bae23c2db
Merge: ac9795142 9e45d9488
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 12:50:28 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ac9795142089aed3eb623ad47276a92938938fc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 12:48:54 2012 -0800

    cleanup

Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 9e45d9488a5c250ad4cc381e02c95ac2d73b1b9d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Jan 9 17:40:42 2012 -0800

    minor updates

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex
Docs/Introduction/Introduction.tex
Docs/UsersGuide.tex

commit 99ebd701c0bca8465ae1a98cd4cf4a193c6193d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 9 17:35:14 2012 -0800

    It works for the simple problem now.  Cleanup is needed.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 8c1609efeb54e066e019834f3cb0e54a61ebe2ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 9 14:30:52 2012 -0800

    Turn on do_diagnostics when mg.v >= 4.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 47e65e8337086a8a7889fb293cf787a0a7b910bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 9 14:26:40 2012 -0800

    Allow MGT_Solver change smoother.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 87cb5aea00f0da2484f8df4b2bd7200902c67820
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 9 13:59:18 2012 -0800

    There are cases that err = ml_residual is zero while err = ml_cycle is not.

Src/LinearSolvers/C_NodalMG/amr_multi.cpp

commit 6ae218541e731fac4d451b7850f2c3b91f8713a8
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sat Jan 7 17:09:52 2012 -0500

    add bender

Tools/F_mk/GMakeMPI.mak

commit b52861c17cac9da9ce4954d03fe407c78e93e5d1
Merge: df5956911 78827113d
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sat Jan 7 15:43:38 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit df595691115874800870972f1b3c684700c8874f
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sat Jan 7 15:41:36 2012 -0500

    update with separate web directory

Tools/C_util/regtests/Maestro-tests.ini

commit 78827113d0b5ebb97da817d3c86a12c718bff8ac
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 6 14:46:15 2012 -0800

    1) Fix the mini_cycle routine which is used only for factor 4 refinement
       between AMR levels.
    2) Adjust the print statements which are used for verbosity > 3

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit b5586b6b66a9369d8c0b3ebcbe98c9f20f26e158
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 6 13:22:13 2012 -0800

    Modify how we set do_diag so that it matches how it is set in the F_MG stuff;
    i.e. if verbosity >= 4 then do_diag = 1 (before it was hard-wired to 0)

Src/LinearSolvers/F_MG/cc_mg_cpp.f90

commit 52850887c98c011458afa12c2c9d5349b5d84e82
Merge: 8053a2fd7 ac3326c31
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 5 17:21:17 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8053a2fd79e7a16d6a3cd715b4ee1d59e92944f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 5 17:20:01 2012 -0800

    Fixed a bug. one_sided_ss should be built with stencil=.true.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit ac3326c310457ea24fcc0f0455614db03d59e4c7
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 5 16:10:10 2012 -0800

    added rodan.

Tools/C_mk/Make.mpi

commit 48b8c80053cb4a2e18d68d430025373ea9c2a3d4
Merge: 7927830f1 98b28c80e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jan 4 14:07:59 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 7927830f195c8e365749a621684859e99f17b95d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jan 4 14:07:41 2012 -0800

    GNUmakefile for use with DUMPI trace package on hopper.

Tests/LinearSolvers/C_CellMG/GNUmakefile.dumpi

commit 98b28c80e26c927517c7f57f79c3064121f77c1b
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jan 4 13:52:42 2012 -0500

    Add mpi stuff for LENS at ORNL

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 79daab5aa421244e930fd5f5c1daec5769d849fb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 3 14:42:36 2012 -0800

    Change verbosity test in Amr.cpp to verbose>0 instead of verbose>1
    when use_efficient_regrid=1.

Src/C_AMRLib/Amr.cpp

commit 744d0d069a9c577be423028d48136af860aceb4d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 3 13:13:16 2012 -0800

    Add use_efficient_regrid flag which allows us to not recreate existing AmrLevels when
    the regridding process does not change the boxArray.

Src/C_AMRLib/Amr.cpp

commit b8bd868a12e2732cda1bee75aa750c5568493e1a
Author: Matthew Emmett <memmett@unc.edu>
Date:   Sat Dec 31 21:10:30 2011 -0500

    PyBoxLib: Add "read" and "copy" methods to multifab class.

Src/Python/pyboxlib/base.py
Src/Python/pyboxlib/multifab.py
Src/Python/src/fboxlib.f90
Src/Python/test.py

commit 3b4caaa07e5a6b2abd92c1c33731a84fb0758ec1
Author: Matthew Emmett <memmett@unc.edu>
Date:   Sat Dec 31 01:37:28 2011 -0500

    PyBoxLib: Add "write" method to multifab class.

Src/Python/pyboxlib/multifab.py
Src/Python/src/fboxlib.f90

commit 6aa39f19ca4cd5ab0faa717b364691853d7796ff
Author: Matthew Emmett <memmett@unc.edu>
Date:   Fri Dec 30 23:44:29 2011 -0500

    PyBoxLib: Add "nboxes" and "local_boxes" methods to layout class.

Src/Python/GMakerules.mak
Src/Python/pyboxlib/fab.py
Src/Python/pyboxlib/layout.py
Src/Python/pyboxlib/multifab.py
Src/Python/src/fboxlib.f90

commit f00a7a911c0c315f08a0c44b955d4e0a5b85bd9c
Merge: c2f55abf4 1f50b4c57
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 29 12:26:40 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c2f55abf4674b3e150d43a8bf86d462924175996
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 29 12:26:04 2011 -0800

    Fix the way we set dt_level in Amr.cpp when we restart with max_level > previous max_level
    and no subcycling.

Src/C_AMRLib/Amr.cpp

commit 1f50b4c57b25d64a401b0fedcd684ae38f7a9584
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 26 09:51:18 2011 -0800

    Added code for cims.nye.edu for Aleks.

Tools/C_mk/Make.mpi

commit 57596441009f9deb410800a05c988edfdbbb8c9b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Dec 25 17:47:34 2011 -0800

    Remove unused variable in Particles.H.

Src/C_AMRLib/Particles.H

commit cc966bb833dfb310f97e7609fc3d4671a4f7a7be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 22 11:10:12 2011 -0800

    work in progress

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/CMakeLists.txt
Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 978d1bc738472fe6775332bd8e157e243e1815dc
Merge: e3529e7d8 a414c71a0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 21 08:49:30 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e3529e7d8842f07509055bb3c14cc8f6f259f016
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 21 08:49:10 2011 -0800

    Fix defaults for NReaders and NRedist.

Src/C_AMRLib/Particles.H

commit a414c71a075f6c1a6df77cf1b15a66dc4ce1e501
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Dec 20 17:41:45 2011 -0800

    staggered grid convergence tester complete

Tools/C_util/Convergence/AVGDOWN_2D.F
Tools/C_util/Convergence/AVGDOWN_3D.F
Tools/C_util/Convergence/AVGDOWN_F.H
Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp

commit 4874e94f8e2f92f2702755141b08a2d0d164e796
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Dec 20 16:16:17 2011 -0800

    good progress on the staggered grid convergence utility.  works now for x-direction, need to generalize to all directions and ref_ratios

Tools/C_util/Convergence/AVGDOWN_2D.F
Tools/C_util/Convergence/AVGDOWN_3D.F
Tools/C_util/Convergence/AVGDOWN_F.H
Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp
Tools/C_util/Convergence/GNUmakefile

commit 538bb7c00898b211cfc10572009fe66ee407b97c
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Dec 20 09:50:28 2011 -0800

    fix comments, check in new template for staggered grid convergence testingZ

Tools/C_util/Convergence/DiffSameDomainRefined.cpp
Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp

commit b64b15ee5443dc6e8be514f12bd17a7d3ab41bee
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Dec 19 12:20:33 2011 -0800

    clean this up

Tools/C_util/Convergence/GNUmakefile

commit 2f9eccc8cc25a9383d9d8f54f91de5a4fe39d3e6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 15 09:12:51 2011 -0800

    Added a critical section around the std::cout call in Reset() just to be safe.

Src/C_AMRLib/Particles.cpp

commit 428168ca7f1fa4bef9e5449aa3b90a98c93c6b72
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 14 22:14:26 2011 -0800

    Added a critical section around that part of intersections() that builds the hash table.

Src/C_BaseLib/BoxArray.cpp

commit 27ac052933629a9996c41388a69000e7204a8bc7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 14 13:15:09 2011 -0800

    More mods for Gunther.

Src/C_BaseLib/GNUmakefile

commit 314c7d96d17e102cb68721fce1257220bdafc97d
Merge: 45f62aa0d edc86555f
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Dec 12 18:52:24 2011 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 45f62aa0db528f9cdf20cafb85e03c60e0954194
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Dec 12 18:51:46 2011 -0500

    fix cray path

Tools/F_mk/GMakedefs.mak

commit edc86555f7912c46cfe664cbd7dc56d69b6b2952
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 12 12:46:49 2011 -0800

    Add domlo and domhi to interface for ErrorFunc2.

Src/C_AMRLib/ErrorList.H

commit 9345b7bf52ed19df7ec1ff0c87bc0f4d0d44d0bc
Author: Matthew Emmett <memmett@unc.edu>
Date:   Mon Dec 12 12:01:27 2011 -0500

    PyBoxLib: Add "interleave" flag to multifab create method.
    
    This allows PyBoxLib to create interleaved FABs, which are indexed
    according to (c,i,j,k) instead of (i,j,k,c).

Src/Python/pyboxlib/fab.py
Src/Python/pyboxlib/multifab.py
Src/Python/src/boxlib_numpy.c
Src/Python/src/boxlib_numpy.f90
Src/Python/src/fboxlib.f90

commit 2fc342ef2d7f4dfb30541e0ad7a91170b4d1a062
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 9 18:41:33 2011 -0800

    Add a couple of functions to MGT_Solver.  It now gets a cell center
    mask from Projection.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit f6d28f76507ae7c1eb35832f00d3fa059d32dd8e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 9 16:36:59 2011 -0800

    Inlined some one liners.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 195c52e5dd2b2946d9c76d6d521314ec63a74457
Merge: 56dd11c5a ed8901097
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 9 15:37:54 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 56dd11c5ade2a36a629df28798c4f22b9002578e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 9 15:37:37 2011 -0800

    Mods requested by Gunther for VisIt.

Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/Make.package

commit ed8901097e1d705124bcc65ffaa817a7dc26078a
Merge: 3a644c9ad d2b905afb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 8 17:25:36 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3a644c9ad10752f1385a624de3b4b3f2da3ab1f4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 8 17:25:09 2011 -0800

    undo change in .gitignore

.gitignore

commit 6e2da55db30729823d5180c33050b1ff09161185
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 8 17:22:06 2011 -0800

    If both rhs and v are provided, the nodal solver will use rhs + div v
    as RHS.  If only v is provided, it will use div v as RHS, as before.

.gitignore
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit d2b905afbcd2460018d9687633d6da799e1e242c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 8 14:56:47 2011 -0800

    Remove defined-but-unused "gridloc"

Src/C_AMRLib/Particles.H

commit d9197576fbaeecf8400e9ee6766fb4d2da8f1f68
Merge: e11cbc6fe af0876fa7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 8 14:12:35 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e11cbc6fe63a18d1b502b3016e90595c851c6d2a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 8 14:12:07 2011 -0800

    We do need to call post_regrid from level 0 up, not level "start", after all.

Src/C_AMRLib/Amr.cpp

commit af0876fa787b95a2d0eef1cdd8007b45171f498b
Merge: 21074f94f c3dc0c3d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 8 13:32:58 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 21074f94ffcfd7cc2be5b33c974effda42c63940
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 8 13:32:53 2011 -0800

    Fix a typo/bug when BL_FORT_USE_UPPERCASE

Src/LinearSolvers/F_MG/mg_cpp_f.h

commit c3dc0c3d2338f55aa939540d64d477db7fd7c6ae
Merge: 446b54871 debfc4047
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 8 13:11:35 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 446b5487162292f4017feaf949bfb562ff415f4a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 8 13:10:55 2011 -0800

    Only call post_regrid on the levels where the grids have actually changed;
    previously it was called from level 0 up, even though lbase may have been higher.

Src/C_AMRLib/Amr.cpp

commit 2c8c6c573b4fb32ddd33fa4849ed8a0cc0bd86b7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 8 13:10:05 2011 -0800

    Create new interface for F90 solvers from C++ that just sets the
    coefficients to be -1 off-diagonal and alpha = 0; this process now
    avoids making a bunch of extra arrays which just carried constant values.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit debfc40474e90de4bdbc8a45252078a9e2e69ae1
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Dec 7 20:21:39 2011 -0500

    pretty it up some more

Tools/C_util/regtests/testnew.py

commit adcf1302d5321b160cfe9fad829345475d1e1e7e
Merge: c6853f05d 3fcf8a6ac
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Dec 7 15:41:41 2011 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c6853f05dbead68bdc9d8130d9c4f3dfeb1981a0
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Dec 7 15:40:53 2011 -0500

    allow for the web directory to be specified independently
    
    also update the CSS some

Tools/C_util/regtests/testnew.py

commit 3fcf8a6ac5aa0ee51d99a4e396685b44ce0009f7
Merge: 75a89a0f3 9d5b3e8fb
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Dec 7 00:34:40 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 75a89a0f3f5faef6e4f75f26dd15414a5f1c4655
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Dec 7 00:34:03 2011 -0800

    Combine all calls to setPhysBoundaryVals in FillPatch, allowing one to intercept the default behavior of calling a static to fill bcs

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Tools/C_scripts/gen_release_tarball

commit 9d5b3e8fb19750d6e2686e94247f8c0acadccc2d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 6 10:12:44 2011 -0800

    Change default verbosity of CGSolver.cpp from 1 to 0.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 8cdac197c875314c73fa18ba495e893c9bc42f0b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 6 10:11:31 2011 -0800

    Need to fix NRedist default.

Src/C_AMRLib/Particles.H

commit 9d1641a1eca4af1f3f01e86a961dc7fa96a359a5
Merge: ff84d1fdb 2bedf7c5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 5 14:42:31 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2bedf7c5a0874292c777e6959d6697e59a20e675
Merge: a9aaaa716 a8e0a3026
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Dec 5 14:41:57 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a9aaaa716f48e15809dcecaef3998f6067828536
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Dec 5 14:41:39 2011 -0800

    back out of some of Ann's solvability changes

Src/LinearSolvers/F_MG/ml_cc.f90

commit ff84d1fdb32972da7416e18033fbc1f925d5b1b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 5 14:32:48 2011 -0800

    Fix a bug in deallocating multifabs for the nodal solver with the dense
    stencil.  The one_sided_ss multifab is not allocated in that case.
    
    The communication between MGT_Solver and the underlying F90 solver is
    changed so that the multifabs in the MGT_Solver can have an arbitrary
    number of components.  This saves memory because we do not have to
    copy the state data into the MGT solver.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit a8e0a3026809eda6b295f1672ffc9844fc6f2e34
Merge: 9b5b069d5 c26d20408
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 5 14:31:04 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9b5b069d5679c06800eae4581bafde2cb2c9d784
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 5 14:28:40 2011 -0800

    Fine tune the setup of Hypre AMG solver according to the
    recommendation of Ulrike Meier.

Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp

commit c26d20408b87fdcb2514e751a62489861eb0fd86
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 5 13:15:45 2011 -0800

    Shut up a compiler warning about a possibly unset variable.

Src/C_AMRLib/Particles.H

commit 8bc2c0084d587feb0dab80d8a024c794cd8d2356
Merge: e0876e378 cc2709bb7
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 2 10:11:02 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e0876e378bbb934180e75271c072e30dea8805e3
Merge: 87fcbfc35 021dd8ad2
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 2 10:08:28 2011 -0800

    Merge branch 'master' of /home/marc/src/CCSE/tmp/../BoxLib

commit 021dd8ad2243818051e25e2a904abc82801f330d
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 2 10:06:46 2011 -0800

    Other part of rename

Tools/C_scripts/gen_release_tarball.txt

commit ca2926d21274fa994f1efe2959cdaff3ae8bd965
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 2 10:06:07 2011 -0800

    Make tarball notes into a script

Tools/C_scripts/gen_release_tarball

commit 87fcbfc359d44d6090d339f916ac461238f7bab5
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 2 10:01:56 2011 -0800

    cmake fixes due to Ben Andre

CMakeLists.txt
Tools/CMake/InstallManager.cmake

commit cc2709bb79066fa8fcac737e9e206dc007b927e2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 21:27:52 2011 -0800

    Fix up InitFromAsciiFile.

Src/C_AMRLib/Particles.H

commit 9be027c61b6aa28a04db3d5a354ec890a93d5c48
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 19:27:59 2011 -0800

    This version breaks up the Redistribute calls into chunks
    in InitFromAsciiFile in Particles.H

Src/C_AMRLib/Particles.H

commit 7f02504e1d9e3f0a4bbbf18968e6f10f376a4452
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 28 17:08:05 2011 -0800

    Revert m_id & NextID() back to int.
    Keep num_particles and num_particles_read as longs.
    NextID() now checks if we try to read/initialize more than INT_MAX
    particles per any MPI process.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 806c3b51197d9d319ee2b1430ef2ebd98f874f45
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 15:33:20 2011 -0800

    One more int --> long in Particles.H

Src/C_AMRLib/Particles.H

commit a704ed8d86499604877e752de9b5623a5acd1ed5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 15:32:12 2011 -0800

    One more int --> long in Particles.H

Src/C_AMRLib/Particles.H

commit 80800af66cff83828df20312dd671c9a341102f4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 15:27:54 2011 -0800

    We need m_id and next_id  to be long instead of int for the case when
    we have lots and lots of particles.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 19102747070b8af5f81ebefba8351e1f7b09741e
Merge: 521ec25b6 ab4c2e116
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 15:17:22 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 521ec25b6867479f29a6155d30a3b9f3091d1c0b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 15:17:13 2011 -0800

    Fix error print statement.

Src/C_AMRLib/Particles.H

commit ab4c2e1160ae1cf14607cb6d7a9930c3f33f5ebe
Merge: be92f3ee5 ffc5d7793
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Mon Nov 28 13:59:53 2011 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit be92f3ee508bfcd3bafbd6076ec022e43293862f
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Mon Nov 28 13:59:05 2011 -0500

    if there are no parameters defined, create the namelist anyway,
    with a dummy parameter, just to make sure that things compile.

Tools/F_scripts/write_probin.py

commit ffc5d77934c331d4f536380f7e35a53e05295ab4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Nov 26 08:40:54 2011 -0800

    We don't need to enforce solvability ahead of time when nlevs = 1 because
    we now enforce it each V-cycle when n = 1.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 50c9942a655f1f3f26433c5256c8310f975b7cf6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Nov 26 08:37:50 2011 -0800

    We must pass the coeffs_sum_to_zero from mgt(1) to mgt(1)%bottom_mgt
    in order for the CG or BiCG solver to know the system is singular
    when using bottom_solver = 4.  Change for cell-centered only.

Src/LinearSolvers/F_MG/ml_cc.f90

commit fc7cc64d6a1a7e7398c55f204d271c3794178dcf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Nov 24 09:24:37 2011 -0800

    Added ParticleBase::MaxReaders().  This is the maximum number of readers
    wanted for InitFromAscii().  It's settable via ParmParse as:
    particles.nreaders=N.  It defaults to min(NProcs,64).  Note that
    this number is always std::min()d with itself and NProcs since we can
    never have more readers than MPI processes.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 0fec7466e5edcf39583e3eb714948a1f24ed19ca
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Nov 24 08:46:45 2011 -0800

    New version of InitFromAscii() that tries to cut down on Redistribute() overhead.

Src/C_AMRLib/Particles.H

commit fc405dc6d7a6e8cee2141cf9d5d8db60c869dde1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Nov 23 13:56:14 2011 -0800

    Inlined index().  This is used in BaseFab::operator() for indexing into a
    FAB with an IntVect.  Doing this greatly sped up Particle::InterpDoit()
    and things like GetGravity(), MoveKick(), MoveKickDrift() which call
    InterpDoit() ...

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp

commit 0b0f1ffa846556502923c629010480c2882bc748
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Nov 23 13:54:00 2011 -0800

    Removed the "len" argument to GetGravity().
    Added an intermediate ifrac[n] = (1-frac[n]) n InterpDoit() to force the calculation to
    be done only once. Results in a modest speedup with g++ at least.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit db4d91f3cac5d497bad151fa8c6d3273058f5ce4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 23 10:49:15 2011 -0800

    Fix shifting in domain replication in Particles.H

Src/C_AMRLib/Particles.H

commit 00c9f0e210eb1d6079adb6c7ba5eda9fa3459a04
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 23 10:39:14 2011 -0800

    Remove random debug statement.

Src/C_AMRLib/Particles.H

commit 1949980a5bd7c01507ca45e0bb7318a48b41bd63
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 23 10:38:11 2011 -0800

    Fix test for print statement.

Src/C_AMRLib/Particles.H

commit 9a9380d6476af50d700cf6f9ca4ca4cecbcdcb6d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 23 10:35:25 2011 -0800

    Fix typo with lNrep...

Src/C_AMRLib/Particles.H

commit f0581865a9cd5f1c160a28b822e75c36d9f9e74f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Nov 23 10:23:31 2011 -0800

    Changed the Nrep argument to InitFromAscii() to const IntVect* and defaulted it to zero.

Src/C_AMRLib/Particles.H

commit c6c446e5135ef415835e7d569851c400f0150d86
Merge: ea21a3a0c 10a53f6c0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Nov 23 09:43:26 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ea21a3a0c7aa059362694b76a345c89d150c59e2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Nov 23 09:42:33 2011 -0800

    Use -O1 instead of -O0 for gcc/g++ when DEBUG=TRUE.
    This still gives good debugging info but yields much faster code.

Tools/C_mk/Make.defs

commit 10a53f6c0ce6e546c06f2931e20ffb86b0d84eeb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 23 09:39:43 2011 -0800

    Pass Nrep through the calling sequence instead of hard-wiring it.

Src/C_AMRLib/Particles.H

commit 19ebaf8328b766e977d38aa077805961c66d7084
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Nov 23 08:03:37 2011 -0800

    more progress - wrote parallel jobs section

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/AdvancedTopics/hopper.run
Docs/GettingStarted/GettingStarted.tex
Docs/UsersGuide.tex

commit c485955af611644870ba06a5902421a8f2807e32
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Tue Nov 22 20:41:20 2011 -0500

    frontmatter page numbers should be roman, main page numbers normal

Docs/UsersGuide.tex

commit 6da04ac24e29622a71d7f68437d9f0d501f905e6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 22 14:44:53 2011 -0800

    Change defaults for how far the bottom solver can go -- we now limit
    by keeping the min in any direction to be 8 rather than by number
    of levels.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower.f90

commit 88310dfe7a412f5353a6b87f6c7909721236def6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 22 14:08:41 2011 -0800

    new color scheme.  fixed typo

Docs/GettingStarted/GettingStarted.tex
Docs/Introduction/Introduction.tex
Docs/UsersGuide.tex

commit ed81fd3ef96a523706fa9bb38079872d6fe26414
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 22 11:54:05 2011 -0800

    Allow for the option of replicating the domain in InitFromAsciiFile.

Src/C_AMRLib/Particles.H

commit c3653475edaf7eff7af6dd1c8cdb9bafa551c108
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 22 11:21:25 2011 -0800

    getting started section complete

Docs/GettingStarted/GettingStarted.tex

commit 6ee747ea552b310b271bf8e6bd7fb73c755fdd23
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 22 10:25:04 2011 -0800

     more progress

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex
Docs/UsersGuide.tex

commit 30434223cdac0e8059c7700f87d875d7c5650d56
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 22 08:38:11 2011 -0800

    more progress and some re-org

Docs/GNUmakefile
Docs/GettingStarted/GettingStarted.tex
Docs/Introduction/Introduction.tex
Docs/UsersGuide.tex

commit 44c9130df6087c17eff48cde0ea040630a84c418
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 22 08:37:53 2011 -0800

    new section

Docs/AdvancedTopics/AdvancedTopics.tex

commit a03dd508ac17e1368deb927eee7ff3dcef08e717
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 22 08:06:44 2011 -0800

    turn off MPI by default

Tutorials/WaveEquation_C/GNUmakefile
Tutorials/WaveEquation_F/GNUmakefile

commit 7462cb066a4311c18e7072f38ea7de643804d8f5
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 22 07:19:01 2011 -0800

    clean these up a bit

Docs/GettingStarted/GettingStarted.tex
Docs/Introduction/Introduction.tex
Docs/Introduction/index_grid.odg
Docs/Introduction/index_grid2.eps
Tutorials/WaveEquation_C/GNUmakefile
Tutorials/WaveEquation_C/Make.package
Tutorials/WaveEquation_F/GNUmakefile
Tutorials/WaveEquation_F/GPackage.mak

commit d8b2248aeb9e71ff043836464ea0cdede0231ee0
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 21 15:42:25 2011 -0800

    starting to take shape

Docs/GettingStarted/GettingStarted.tex
Docs/Introduction/Introduction.tex
Docs/Introduction/index_grid.odg
Docs/Introduction/index_grid2.eps
Docs/UsersGuide.tex
Tutorials/WaveEquation_F/main.f90

commit bb93ec51f3f9f4432c1309131bd688429d94ef6c
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 21 14:34:16 2011 -0800

    new fig

Docs/Introduction/AMR.eps
Docs/Introduction/Introduction.tex

commit 9fb9032fa6b22ff29fe1df90978f5010f355f121
Merge: 7a5dd89f2 cc8a90b9c
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 21 13:40:32 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7a5dd89f2866906d588eb187676552b8b0b1da57
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 21 13:40:12 2011 -0800

    fixed to use regular old layouts and boxarrays

Tutorials/WaveEquation_F/advance.f90
Tutorials/WaveEquation_F/init_data.f90
Tutorials/WaveEquation_F/main.f90
Tutorials/WaveEquation_F/write_plotfile.f90

commit cc8a90b9cb825a588960244fe1c38d85215a50e5
Merge: cfde33f44 a478d0399
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 21 12:42:11 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit cfde33f44a07d3a4b4c61c4dcb11e9517ec05a5c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 21 12:41:54 2011 -0800

    Mod to compile with PGI on hopper.

Src/C_BaseLib/CoordSys.cpp

commit a478d039993463b7e514f654a092116a1e877817
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 21 11:25:15 2011 -0800

    saving progress

Docs/GettingStarted/GettingStarted.tex
Docs/Introduction/Introduction.tex
Docs/UsersGuide.tex

commit 5d0c8edaed40183b8b69223d505846e9741e3d98
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 21 09:37:20 2011 -0800

    now this builds again

Docs/Introduction/Introduction.tex

commit 77e494a5cf3e0225d23d42b655721509f0504431
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 21 09:35:37 2011 -0800

    more playing around with git - hope this works

Docs/Overview/Overview.tex
Docs/Overview/boxlib_directory_bw2.eps
Docs/Overview/castro_scaling.eps
Docs/Overview/data_loc.odg
Docs/Overview/data_loc2.eps
Docs/Overview/index_grid.odg
Docs/Overview/index_grid2.eps
Docs/Overview/lmc_scaling.eps
Docs/Overview/maestro_scaling.eps

commit 2539cea70b07ad162fe4f2c86db36d702ebecbc3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 21 09:35:07 2011 -0800

    more playing with git.  hope this works

Docs/GNUmakefile
Docs/GettingStarted/GettingStarted.tex
Docs/Introduction/Introduction.tex
Docs/Introduction/boxlib_directory_bw2.eps
Docs/Introduction/castro_scaling.eps
Docs/Introduction/data_loc.odg
Docs/Introduction/data_loc2.eps
Docs/Introduction/index_grid.odg
Docs/Introduction/index_grid2.eps
Docs/Introduction/lmc_scaling.eps
Docs/Introduction/maestro_scaling.eps
Docs/UsersGuide.tex

commit 80e66de4936530af228b896a580d015f4d641708
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 18 17:33:20 2011 -0800

    lots of comments in code, wrote small section in User's guide.  This could actually be released now

Docs/GettingStarted/GettingStarted.tex
Tutorials/WaveEquation_F/main.f90
Tutorials/WaveEquation_F/write_plotfile.f90

commit c30d3baf3fe084028b5e5571b0c81575455982d3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 18 13:44:22 2011 -0800

    fortran version of WaveEquation_C.  fully working (I think)

Tutorials/WaveEquation_F/GPackage.mak
Tutorials/WaveEquation_F/advance.f90
Tutorials/WaveEquation_F/init_data.f90
Tutorials/WaveEquation_F/inputs_3d
Tutorials/WaveEquation_F/main.f90
Tutorials/WaveEquation_F/write_plotfile.f90

commit a629751a4b96aad37f28560d2f85ddb5797b4e57
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 18 12:31:43 2011 -0800

    remove unused variables

Tutorials/WaveEquation_C/init_data_2d.f90

commit 9731fa67be693a1c12999f392074a63c7ff2962e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 18 12:30:09 2011 -0800

    datalog is now a Managed PArray instead of UnManaged so it gets properly
    cleaned up on exit.

Src/C_AMRLib/Amr.cpp

commit 9567086c28bdf44d55432ab8c045b88b3b16d068
Merge: 41489c15e 4dcea09fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 12:14:32 2011 -0800

    Merge branch 'hypre'

commit 4dcea09fedeb51cdb0d12155f75147641e476fc2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 12:13:36 2011 -0800

    Minor changes in input file

Tests/LinearSolvers/ComparisonTest/inputs.3d

commit 41489c15efd49cc32a79b32e48f053157973113e
Merge: e1fb94758 daac099fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 12:12:02 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e1fb9475804d2e39c83a28a10e300688f272dd81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 12:10:51 2011 -0800

    Collect more timing info.

Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp

commit daac099fed4ba413db21973f833d5bef93a45ad7
Merge: 4a39731a2 f6dd2da64
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 18 10:58:18 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4a39731a2d5d8e27ef698226f9da3637265354cb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 18 10:58:02 2011 -0800

    Minor performance tweak to copyassoc_check().

Src/F_BaseLib/layout.f90

commit 7294c7fca57ba27f42a6074c8deac5314c458e41
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 10:37:56 2011 -0800

    Minor changes for the case when some processors have no grids.

Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp

commit 3b84370d933aca0ecd56ed8837d8385fdcf9d190
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 10:35:32 2011 -0800

    Remove a useless statement.

Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp

commit c66fe8dbb731b2f82e83726d8ed2de3932b08ec0
Merge: cb2c8d4cf f6dd2da64
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 10:19:41 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit cb2c8d4cf4947b358a1ecdb25d3df2a1d2131275
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 10:18:55 2011 -0800

    Fix typo in a variable name.

Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp

commit f6dd2da64ea441b8f84475508e01fa669a15cdfb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 10:08:27 2011 -0800

    delete BndryData objects in the destructor of HypreABecLap

Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp

commit 691b789d6d4d8979177ce2dd02d24227d5439809
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 18 09:44:56 2011 -0800

    Be a little smarter about which cached copyassocs to delete when the cache
    hits the maximum size.
    The max copyassoc cache size now defaults to 25 instead of 50.

Src/F_BaseLib/layout.f90

commit 3e504e4bdb4b0edb9bd9cdfe84c9f518e05df94c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 18 09:21:27 2011 -0800

    Added -lmpl for my machine.

Tools/F_mk/GMakeMPI.mak

commit 940bc24e323367c4a3f02279986091465244da68
Merge: 87cd2e93c 5cf2d086b
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Fri Nov 18 09:51:56 2011 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 87cd2e93c99d0265d556398847f95ebddd9a57a5
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Fri Nov 18 09:51:08 2011 -0500

    shift the gfortran-specific comments into comps/gfortran.mak

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/gfortran.mak

commit 5cf2d086bdce4c230f9e924e56beb8d22b4b70d5
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 18 06:47:56 2011 -0800

    starting new example

Tutorials/WaveEquation_F/GNUmakefile
Tutorials/WaveEquation_F/GPackage.mak
Tutorials/WaveEquation_F/inputs_2d
Tutorials/WaveEquation_F/main.f90

commit 6a7d62d32e4f2aeb8672a4547a834f8ffa76193c
Merge: e9246ca59 0023a3f77
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 17:51:10 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e9246ca59cf7e14fea7827770516b194421d035d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 17:50:49 2011 -0800

    tidy this tutorial up a biZ

Tutorials/WaveEquation_C/GNUmakefile
Tutorials/WaveEquation_C/inputs_2d
Tutorials/WaveEquation_C/inputs_3d

commit 0023a3f77ae93b6552754e2da334db8337ddc9a5
Merge: 8cff4acd3 947045eb3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 17 17:14:10 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 8cff4acd3e8498985f87701d311e3aa6d4786d11
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 17 17:13:39 2011 -0800

    Fix a bug in setBndryConds.  It now uses FabSetIter to loop over local boxes.

Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp

commit 947045eb36dd4c458694d6462036353fea608cff
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:34:58 2011 -0800

    deleting old copies

Docs/BoxLib/Overview.tex
Docs/BoxLib/boxlib.tex
Docs/BoxLib/boxlib_directory_bw2.eps
Docs/BoxLib/castro_scaling.eps
Docs/BoxLib/data_loc.odg
Docs/BoxLib/data_loc2.eps
Docs/BoxLib/index_grid.odg
Docs/BoxLib/index_grid2.eps
Docs/BoxLib/lmc_scaling.eps
Docs/BoxLib/maestro_scaling.eps
Docs/preface/preface.tex

commit f12a8cb248a2bed5064b0ecfb50a44d8e61e876f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Nov 17 15:31:36 2011 -0800

    Added mgt_flush_copyassoc_cache().
    This is now called on Finalize() to remove any cached copyassoc objects.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit e8c68a5d5d8dfcd6f9fca167ff8d3e5d13cc4481
Merge: 170c02e1b ced020f11
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:29:33 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 170c02e1befeaf1b3f62dc3d27a7a74e6a7f9fa8
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:29:17 2011 -0800

    more re-org

Docs/GNUmakefile
Docs/Overview/Overview.tex
Docs/UsersGuide.tex

commit d15ec3edceaf4660427f9fac18c0860d91551350
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:24:24 2011 -0800

    new section

Docs/GettingStarted/GettingStarted.tex

commit fbc7cc038df5e4ddf7cb15f7c603eb3d82f7f060
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:23:02 2011 -0800

    re-org

Docs/GNUmakefile
Docs/UsersGuide.tex

commit e5a8ad66e39529dcb4a0d6ac4adf10ff972ce882
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:22:14 2011 -0800

    re-org

Docs/Preface/Preface.tex

commit a0175e5f85f3fbe774382f920a1477d8d22f4804
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:21:41 2011 -0800

    re-org

Docs/Preface/preface.tex

commit f2e2fb9f7ae56bc91e953a1612234a29c12ab33d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:21:22 2011 -0800

    re-org

Docs/Overview/Overview.tex
Docs/Overview/boxlib_directory_bw2.eps
Docs/Overview/castro_scaling.eps
Docs/Overview/data_loc.odg
Docs/Overview/data_loc2.eps
Docs/Overview/index_grid.odg
Docs/Overview/index_grid2.eps
Docs/Overview/lmc_scaling.eps
Docs/Overview/maestro_scaling.eps

commit 9726b2114027aa24c749c5049a981ba140466f2d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:20:58 2011 -0800

    re-org

Docs/BoxLib/Overview.tex

commit e812d483bd81eed387d025c61c0d0cedd93cd182
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 14:52:06 2011 -0800

    updates

Docs/BoxLib/boxlib.tex

commit ced020f11778901f65071772571035b3c12466c7
Merge: b477712da 4cb57b57d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 17 12:59:37 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b477712dae103e99ea98aa03d9e2f5906c68e69e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 17 12:58:49 2011 -0800

    Add timing information

Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp

commit 4cb57b57dd79bc6c2e71a7e131c8119eebf7196f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 12:19:35 2011 -0800

    updates

Docs/BoxLib/boxlib.tex
Docs/preface/preface.tex

commit a72614f3c8ffaf284acdd2698aeaf20e11ce12a2
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 12:17:52 2011 -0800

    scaling figs

Docs/BoxLib/castro_scaling.eps
Docs/BoxLib/lmc_scaling.eps
Docs/BoxLib/maestro_scaling.eps

commit 101a2afb68c1fcb938ded2458313dac3808d84d4
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 11:06:43 2011 -0800

    moved file

Src/C_AMRLib/OpenSource.txt

commit 8e821376ffc815f95b64a76a568762f1d44c7b45
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 11:05:45 2011 -0800

    boxlib tree figure

Docs/BoxLib/boxlib_directory_bw2.eps

commit f835a4fa42e1b89725d971072e32ae9e552d3402
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 11:05:19 2011 -0800

    updating doc

Docs/BoxLib/boxlib.tex
Docs/GNUmakefile
Docs/README
Docs/UsersGuide.tex
Docs/preface/preface.tex

commit 4097d56af5b1ca9feb6e3883c7371ccd0a4e18a4
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 11:04:12 2011 -0800

    moved license from C_AMRLib

license.txt

commit 8a423e751e7dff9650bc442f6ef6270af7829370
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 10:15:31 2011 -0800

    renamed UsersGuide.tex

Docs/paper.tex

commit 11b523fd2fa901ec1b32ce910c17459c309f0e2c
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 10:11:52 2011 -0800

    updating in progress...

Docs/BoxLib/boxlib.tex
Docs/BoxLib/maestro_directory.odg
Docs/GNUmakefile
Docs/UsersGuide.tex

commit e3f1268666dd9049ad97a7a0d8f7054b7906789f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 09:27:55 2011 -0800

    eliminating option for building sub-directories within the main documentation.  someone can add this back in if they actually see a reason for this

Docs/BoxLib/GNUmakefile

commit 7ad9b38bac2c14d37bf1a8ba5a65f51dc6fc67d4
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 09:27:24 2011 -0800

    git rid of these too

Docs/BoxLib/mac.odg
Docs/BoxLib/mac2.eps

commit 069cb441110b4356ccff020f49a9d252a1d43781
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 09:24:39 2011 -0800

    get rid of this too

Docs/BoxLib/maestro_directory2.eps

commit 147faa639710c94792ce1f67d178b727d930a8d0
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 09:23:27 2011 -0800

    no idea why this was here
    Z

Docs/BoxLib/paper.tex

commit 16a8bb528455de9de1a2154b03f90169d6c058b3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Nov 17 07:44:42 2011 -0800

    Just a little code rearrangement & reformatting in InitFromAscii().

Src/C_AMRLib/Particles.H

commit bac25312b71921638dac357f093f4bc9325fc0af
Author: Michael Zingale <zingale@xrb.astro.sunysb.edu>
Date:   Thu Nov 17 09:18:38 2011 -0500

    add xrb

Tools/F_mk/GMakeMPI.mak

commit bbd689988f4d08238a60820b1790c84438d62eb5
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Nov 16 22:25:03 2011 -0500

    add defaults for the input param strings -- this is needed for CASTRO

Tools/F_scripts/write_probin.py

commit 8447147227cd02c89d94071514e17e5c006dec27
Merge: 12243b211 8b1ce0ac5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 16 18:16:06 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 12243b211085434acfae2f64d0c5691fd5a32422
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 16 18:15:07 2011 -0800

    In InitFromAsciiFile in Particles:H, we now read the file using at most 64 processors;
    this speeds things up dramatically for nprocs > 64.

Src/C_AMRLib/Particles.H

commit 8b1ce0ac5f10096c5acb4dfcf0f09737ef4d6b9c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Nov 16 16:19:32 2011 -0800

    A little optimization & cleanup.

Src/C_AMRLib/Particles.H

commit 6085f0a5042fdc1789efa9c26b438cf573b37f9b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 16 14:41:13 2011 -0800

    We were not calling post_regrid when using regrid_on_restart with finest_level = 0.  Now we are.

Src/C_AMRLib/Amr.cpp

commit fab8a926d3f984aa6a7d16cf4437fbc702aaa9ce
Merge: 80a2041b2 354e7b1bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 16 10:52:57 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 80a2041b2ef24c0c9da792ad657a4d8dd3fd9582
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 16 10:51:26 2011 -0800

    Add Hypre to the comparison test

Tests/LinearSolvers/ComparisonTest/COMP_NORM_1d.f90
Tests/LinearSolvers/ComparisonTest/COMP_NORM_3d.f90
Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H
Tests/LinearSolvers/ComparisonTest/GNUmakefile
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_3D.F
Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_F.H
Tests/LinearSolvers/ComparisonTest/HypreABecLap/Make.package
Tests/LinearSolvers/ComparisonTest/Make.package
Tests/LinearSolvers/ComparisonTest/compute_norm.cpp
Tests/LinearSolvers/ComparisonTest/inputs.3d
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp
Tests/LinearSolvers/ComparisonTest/writePlotFile.H
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp

commit 354e7b1bd3a6370fe56c7b043141a5aff6731c2b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Nov 16 10:25:02 2011 -0800

    Removed some unused variables and some prettification.

Src/C_AMRLib/Particles.H

commit 5c38de3b061f356d8ead8bb80f2a272c2db30f64
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 15 13:48:59 2011 -0800

    added the IOBenchmark.

Tests/IOBenchmark/GNUmakefile
Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/IOBenchmark/README

commit a3edbdafe72006871fba6d7811ac3943bbd9b535
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 15 13:03:19 2011 -0800

    Add new routine -- set_const_gravity_coeffs -- that does not take an array as an argument.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit ad380bacda1918494efc361a667ab64f257399ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 14 10:30:14 2011 -0800

    untrack tag files

.gitignore

commit 82e72ceb19c9ae61597e0e017f02bc94187077ea
Merge: a897c50da 13b86ff7f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 14 10:27:38 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a897c50da7b7859e0946f9625508c54b5f9130f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 14 10:23:20 2011 -0800

    Add 1D case.

Tests/LinearSolvers/ComparisonTest/main.cpp

commit eb8512a1874168a223b292e9daf25115fcf14177
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 14 10:21:15 2011 -0800

    Add 1D test.

Tests/LinearSolvers/ComparisonTest/COEF_1D.F
Tests/LinearSolvers/ComparisonTest/COEF_F.H
Tests/LinearSolvers/ComparisonTest/COMP_NORM_1d.f90

commit 5c0a65d845d8d341cff435c57e685d0cbe8ad008
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 14 10:18:33 2011 -0800

    Minor changes to make it more generic, in case the physical dome is
    not from 0 to 1.

Tests/LinearSolvers/ComparisonTest/COEF_3D.F

commit 930f1a3926adfdd49cbe5ec7455af5092ce5f786
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 14 10:15:41 2011 -0800

    Add 1D case to mg_tower_print.

Src/LinearSolvers/F_MG/mg.f90

commit 6bf0fa264e41303d8b16361a3aa521f5868df873
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 14 10:06:43 2011 -0800

    Fix the subroutines names in the calls to mgt_verify.
    
    Fix the size of arrays in a 1D routine.

Src/LinearSolvers/F_MG/cc_mg_cpp.f90

commit 13b86ff7fe32c7a4591eae0ca3fa944581705a03
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 11 08:37:07 2011 -0800

    1) Modify default stencil_order (sets order of boundary condition stencils) to be 2 instead of 1
    when the F90 solver is called from C++.
    2) Removed commented lines from stencil routine.

Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/cc_stencil.f90

commit e6e909b789982f814a73c15bacbc8bffd876b3fc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 10 10:27:26 2011 -0800

    These are changes for how the Hypre solver is called -- from Rob Falgout.

Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp
Tutorials/MultiGrid_C/inputs.3d

commit 764ea54149ac81fbefe50d9c8e58d54980c75953
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 9 15:42:35 2011 -0800

    Made the test in AmrData.cpp on whether the grids fit in the domain be
    an explicit test rather than a BL_ASSERT.

Src/Extern/amrdata/AmrData.cpp

commit a6970ca22d14fa88a259ea814681c3065f17113b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 7 19:37:16 2011 -0800

    Applied patches supplied by Steffen Klemer.

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 70a53183edc97308101719c3b869b835e77009a2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 4 15:07:26 2011 -0700

    eps from 1.e13 => 1.e-13.

Src/C_AMRLib/Particles.cpp

commit 0e6a5a92743da175d6b4451b21e872b344be92ed
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 4 10:31:33 2011 -0700

    Made some loops more memory-access efficient.

Src/LinearSolvers/F_MG/coarsen_coeffs.f90

commit f4bbaa53654f24c627ae661a575affe3ff97604d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 4 10:15:12 2011 -0700

    1000.0 => 1000.0D0

Src/F_BaseLib/interp.f90

commit 50d17791598f62fa98e28310dcfdabfadcd886d9
Merge: 4a4ce0baf b96cb3c77
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 3 22:12:15 2011 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 4a4ce0bafcc02573fef916eb1daef3f71db4a54a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 3 22:11:34 2011 -0700

    Split subroutine mg_tower_smoother and jac_smoother out of  mg.f90
    and into mg_tower_smoother.f90 in the F_MG directory.

Src/LinearSolvers/F_MG/CMakeLists.txt
Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower_smoother.f90

commit b96cb3c773443efc1e08ae8d79389702cf4c5a51
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Thu Nov 3 21:11:47 2011 -0400

    add a check whether we defined a parameter already in the previous
    set of runtime parameters

Tools/F_scripts/write_probin.py

commit 1101fbcb38828830f8b9095a72a4c9d0e321c861
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Thu Nov 3 20:14:55 2011 -0400

    add the ability to have 2 separate groups of runtime parameters.
    This allows them to be split into different modules.

Tools/F_scripts/write_probin.py

commit a681cca0f28e94a07a363c90b0a55636163767ef
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Thu Nov 3 19:44:06 2011 -0400

    add comments

Tools/F_scripts/findparams.py

commit d96d9229e4cd2b71f4c524868354893d07b7a504
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Thu Nov 3 15:53:02 2011 -0400

    slight prettification

Tools/F_scripts/findparams.py

commit 086f2b63e8ab3781df2f94dfe8cd4fccb123089f
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Nov 2 14:23:06 2011 -0400

    a simple script to search a list of directories for _parameters
    files and print the resulting list to stdout.  This is used by
    makefiles to provide the list of dependencies for write_probin.py

Tools/F_scripts/findparams.py

commit 0f18810afeced831b2dcc53e14457c0864a3a4d8
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Nov 2 10:28:27 2011 -0400

    move the write_probin.py script from the MAESTRO source to here so
    it can be used by other BoxLib codes (like CASTRO)

Tools/F_scripts/write_probin.py

commit 5c9e6f2f8178efb3e6e78a77682d8e609176b715
Author: Matthew Emmett <memmett@unc.edu>
Date:   Sat Oct 29 09:06:56 2011 -0400

    PyBoxLib: Silence some warning, minor tweaks to build system.

Src/Python/GMakerules.mak
Src/Python/mkpyfboxlib
Src/Python/src/boxlib_numpy.c

commit 5e09d3144c7363f68c07056184e0fc1e961510b4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 28 09:33:43 2011 -0700

    Moved the initialization of "ss" in s_minion_full_fill_3d() to before the OMP PARALLEL DO loop.

Src/LinearSolvers/F_MG/cc_stencil.f90

commit d805c660acda187267ddf2dc4a5f3962fa6b92eb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 28 08:53:21 2011 -0700

    A little note explaining why this directory exists.

Tests/LinearSolvers/C_CellMG/dumpi/NOTE

commit df608fe047404c1cb0f7a8754da105495e548b15
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 28 08:44:53 2011 -0700

    A little cleanup.

Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.4096core
Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.512core
Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.64core
Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.8core

commit 7447e8ee92cfe16af6f98d26c5601c0be7456e17
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 28 08:42:24 2011 -0700

    Now accepts n_cells and max_grid_size.
    If n_cells is defined will make a domain that long in each direction
    and then split it up based on max_grid_size.  Otherwise expects to
    read in a file containing the initial BoxArray.

Tests/LinearSolvers/C_CellMG/main.cpp

commit 80b74ba89fd705fcd1f4db192f8e73322db65f48
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 27 14:32:51 2011 -0700

    Renamed the exascale directory -> dumpi since I really used these inputs
    files for the dumpi test with Joe Kenny.

Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.4096core
Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.512core
Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.64core
Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.8core

commit 7d782ba2d3d7ed9c72f0453e06437be4fb58ac6e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 27 14:30:49 2011 -0700

    I meant to put these input files into the exascale directory.

Tests/LinearSolvers/C_CellMG/exascale/inputs.3d.4096core
Tests/LinearSolvers/C_CellMG/exascale/inputs.3d.512core
Tests/LinearSolvers/C_CellMG/exascale/inputs.3d.64core
Tests/LinearSolvers/C_CellMG/exascale/inputs.3d.8core

commit a310b4fdb1393814733a9383c186026cfe719c95
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 27 14:25:29 2011 -0700

    Inputs files I used when running the MG test for dumpi that I passed to Joe Kenny.

Tests/LinearSolvers/C_CellMG/inputs.3d.4096core
Tests/LinearSolvers/C_CellMG/inputs.3d.512core
Tests/LinearSolvers/C_CellMG/inputs.3d.64core
Tests/LinearSolvers/C_CellMG/inputs.3d.8core

commit db724aa293b448ef86e43136df5b41f06b24bcc1
Merge: aa8ac787c 4ab338a4e
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 26 15:35:03 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit aa8ac787c94b9fe3e65c6ed207c386658e8d342f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 26 15:33:29 2011 -0700

    added Amrvis namespace.
    updated files to use the namespace.
    fixed memory leak.

Src/Extern/amrdata/AmrData.H
Src/Extern/amrdata/AmrData.cpp
Src/Extern/amrdata/AmrvisConstants.H
Src/Extern/amrdata/DataServices.H
Src/Extern/amrdata/DataServices.cpp
Tools/C_mk/Make.mpi
Tools/C_util/Convergence/DiffSameDomainRefined.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGrid2.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileNormB.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp
Tools/C_util/Statistics/PltFileFluxAve.cpp
Tools/C_util/Statistics/PltFileList.cpp
Tools/C_util/Statistics/PltFileStat.cpp
Tools/C_util/Statistics/PltFileXAve.cpp

commit 03168769aea413110a56e83e284febc3f207be01
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 26 15:25:57 2011 -0700

    fixed boxlib path.

Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Statistics/GNUmakefile

commit 4ab338a4e10d62d9810a93a326039cf4e360c329
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 26 14:38:56 2011 -0700

    Fix Redistribute so that empty boxes do not generate seg faults.

Src/C_AMRLib/Particles.H

commit 3e70985b8e675820c5a5d66ef0581066b4d9db24
Merge: 4ff705ed4 bf62007d6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 24 14:01:48 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4ff705ed4e94be43e1d76b9ba95096c59c49d6c7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 24 14:01:01 2011 -0700

    Deprecate CrseInit(FArrayBox&,...); spew a warning if used.

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 5c4044f2765be887fae63718391e481cf72aa93a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 24 14:00:24 2011 -0700

    If blocking_factor or max_grid_size are not explicitly defined, use supplied defaults.

Src/C_AMRLib/Amr.cpp

commit bf62007d6ad77a07b363eb079bd68af71a7f2f5f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 24 13:29:11 2011 -0700

    Get this Tests/LinearSolvers/F_MG test code to compile again.  No guarantee that it works correctly.

Tests/LinearSolvers/F_MG/cc_multi.f90
Tests/LinearSolvers/F_MG/cc_single.f90
Tests/LinearSolvers/F_MG/nodal_multi.f90
Tests/LinearSolvers/F_MG/nodal_single.f90

commit 0430b38c754fc7d99d7da879554e5e31ac019eb7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 24 12:23:30 2011 -0700

    Closer to compiling with new GIT layout.

Tests/LinearSolvers/F_MG/GNUmakefile
Tests/LinearSolvers/F_MG/GPackage.mak
Tests/LinearSolvers/F_MG/cc_multi.f90
Tests/LinearSolvers/F_MG/cc_single.f90
Tests/LinearSolvers/F_MG/nodal_multi.f90
Tests/LinearSolvers/F_MG/nodal_single.f90
Tests/LinearSolvers/F_MG/t_smoother.f90
Tests/LinearSolvers/F_MG/t_stencil.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit adb4f1c892b0dceacc055bd1525aad13976df971
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 24 12:22:59 2011 -0700

    Add t/ to ignore list.

.gitignore

commit 59ce88b96fdd393fcc02a6b3bb321fce50718a4c
Merge: c4e458d88 ee5feaf4b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 24 10:42:50 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c4e458d887162b941940ec18eb86ea6fdd7e1acb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 24 10:41:41 2011 -0700

    Replaced saxpy(a,ONE,b) with plus_plus(a,b) calls.
    Replaced saxpy(a,-ONE,b) with sub_sub(a,b) calls.

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_restriction.f90

commit ee5feaf4b2d8b17bfe53b03eaabfc6bc993c161f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 24 10:20:19 2011 -0700

    Fix bug in reading max_grid_size and blocking_factor arrays -- we need to read
    max_level+1 values, but we were only reading max_level values (when number of
    values > 1 in the inputs file)

Src/C_AMRLib/Amr.cpp

commit 20cf71c6b31668a9f7f8aaf6c8b37f5be944c554
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 21 15:57:38 2011 -0700

    Modest speedup to simplify_doit().

Src/C_BaseLib/BoxList.cpp

commit 4f7680ceef24c13b9b56f8d1eb6d230ceb4facfd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 21 14:44:20 2011 -0700

    Got MPI working on my upgraded machine.

Tools/C_mk/Make.mpi

commit 6dabdfb614cdea80f13be8a6626643057594add8
Merge: 48de16eaa ea67ef579
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 21 13:56:20 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 48de16eaac007b1e4c400abd3418321d9adac04f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 21 13:55:43 2011 -0700

    Added .gitignore that ignores d f o directories as well as *o *a and a few
    other things.

.gitignore

commit ea67ef579942da1287eac5d4a790a147b8564500
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 21 13:54:16 2011 -0700

    Add the line
    
    p_n_comp[i].simplify();
    
    inside the grid_places() routine.  This reduces the number of grids
    dramatically when doing regridding with low lbase and high finest_level.
    Saves a factor of over 100 in test with lbase=2 and finest_level=7.

Src/C_AMRLib/Amr.cpp

commit ba0a1ead341fbc6f2b943fd15d3f38742db2610d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 21 13:47:26 2011 -0700

    Use BoxList::catenate() instead of BoxList::join() when possible.
    The former is more memory efficient.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.cpp
Src/Extern/amrdata/AmrData.cpp

commit b0c9b71b4ff2638c4ff15339fdeac64ac85c4dbe
Author: Matthew Emmett <memmett@unc.edu>
Date:   Thu Oct 20 15:35:40 2011 -0400

    PyBoxLib: Add ml_layout wrapper.

Src/Python/GMakerules.mak
Src/Python/pyboxlib/__init__.py
Src/Python/pyboxlib/layout.py
Src/Python/src/blobjects.py
Src/Python/src/fboxlib.f90

commit 4779042149c8ca6e411163c39224c75c9b6a4354
Author: Matthew Emmett <memmett@unc.edu>
Date:   Thu Oct 20 14:26:07 2011 -0400

    PyBoxLib: Change makefile structure to mimic BoxLib, remove extraneous files.

Src/Python/GMakerules.mak
Src/Python/GPackage.mak
Src/Python/Makefile
Src/Python/mkpyfboxlib
Src/Python/src/blobjects.f90
Src/Python/src/boxlib_numpy.c
Src/Python/src/fboxlib.pyf
Src/Python/src/pyfboxlib.m4
Src/Python/src/pyfboxlib.pyf

commit dbe72636e184599609745959c75a762ee0740671
Author: Matthew Emmett <memmett@unc.edu>
Date:   Thu Oct 20 11:36:12 2011 -0400

    PyBoxLib: Add Src/Python.

Src/Python/Makefile
Src/Python/README
Src/Python/pyboxlib/__init__.py
Src/Python/pyboxlib/base.py
Src/Python/pyboxlib/boxarray.py
Src/Python/pyboxlib/fab.py
Src/Python/pyboxlib/layout.py
Src/Python/pyboxlib/multifab.py
Src/Python/src/blobjects.f90
Src/Python/src/blobjects.py
Src/Python/src/boxlib_numpy.c
Src/Python/src/boxlib_numpy.f90
Src/Python/src/fboxlib.f90
Src/Python/src/fboxlib.pyf
Src/Python/src/pyfboxlib.m4
Src/Python/src/pyfboxlib.pyf
Src/Python/test.py

commit 8a813a0175935fbc21a04683732eabaf5d9b8d8e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 19 19:27:05 2011 -0700

    Add options for Zarija's machine, stribog.

Tools/C_mk/Make.mpi

commit 232bf71dda22e7e40db72fc594240688cb2010ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 11:28:19 2011 -0700

    Add a space to the ouput message

Tools/C_util/regtests/testnew.py

commit ff26b7a115c04859c2f07f8f32ea75c67cc2ef6c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 17 14:20:41 2011 -0700

    This has latest greatest InitCosmo from Jan Frederik.

Src/C_AMRLib/Particles.H

commit 4a497e85d94ddebacfefa03a90f9aa064b511c19
Author: gilet <cgilet@lbl.gov>
Date:   Mon Oct 17 12:27:53 2011 -0700

    added -lmpl for orga

Tools/F_mk/GMakeMPI.mak

commit 2e0224ad058c0dddb93e7fc54a4e1f4a5a50ac40
Author: Ryan Orvedahl <orvedahl@sn.astro.sunysb.edu>
Date:   Sat Oct 15 17:59:29 2011 -0400

    add support for sn.astro.sunysb.edu

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 1810cea785b161cbcc90b0fdc29054e6cdb696d3
Merge: b1758478f e765074d3
Author: Michael Zingale <zingale@sn.astro.sunysb.edu>
Date:   Fri Oct 14 15:12:40 2011 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit b1758478f53c6ebad90b941cfac68fdf9ea9e66c
Author: Michael Zingale <zingale@sn.astro.sunysb.edu>
Date:   Fri Oct 14 15:12:06 2011 -0400

    add MPI stuff for sn

Tools/F_mk/GMakeMPI.mak

commit e765074d3d4754cf309eb08cb53a6593caa510ec
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 14 12:11:54 2011 -0700

    Change int to long in i = 0 to truesize in clear (already did this in define).

Src/C_BaseLib/BaseFab.H

commit 5cd85707cc2e84ffcb05f2252044e55f27e79c95
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 14 11:35:09 2011 -0700

    Replace int by long in BaseFab::define so that it can handle very large
    (e.g, 1024^3) boxes.

Src/C_BaseLib/BaseFab.H

commit 9f4efbb09054dd9739babbfd816e899e70d8ee6d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 14 11:34:39 2011 -0700

    Fix mpi for manda.

Tools/C_mk/Make.mpi

commit 2b3ddfea66872833062f1f36a6b74995ab49f4ae
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 13 14:26:03 2011 -0700

    Un-inlined some stuff that didn't need to be inlined.

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/UseCount.cpp

commit e93dcabc5d2f7279d0b83ab9668a64feab30282c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 13 13:59:03 2011 -0700

    Merged the std::stable_sort() and std::reverse() into a static function Sort().

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit e234a263019a7493e1f583a348035faafb8091f3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 13 12:59:39 2011 -0700

    More protected => private for some data members.
    Un-inlined some stuff.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/Orientation.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit d7e0849e1ae7c4261e2adf15d2ae0580b017b4c8
Merge: 78263f806 85433f302
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 12 13:54:36 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 78263f8069a9b03ef79532018036298b4ab1704b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 12 13:53:40 2011 -0700

    Made as much "protected" data "private" as possible.
    Removed unneeded "virtual" on some member functions.

Src/C_AMRLib/AuxBoundaryData.H
Src/C_AMRLib/BCRec.H
Src/C_AMRLib/Derive.H
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateDescriptor.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/RealBox.H
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/FabSet.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/MultiGrid.H

commit 85433f30258a646be57a514a930aaa7f35a0895c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Oct 11 15:08:30 2011 -0700

    Use -O3 instead of -Ofast with PathScale to work-around current 4.0.9 bug in IPA on hopper.

Tools/C_mk/Make.Linux

commit acb8a7143f8e069a49c10bd2a33e514b70638f4e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Oct 11 15:01:01 2011 -0700

    -Ofast no longer works on latest PathScale on hopper.  Use -O3 instead.

Tools/F_mk/comps/Linux_pathscale.mak

commit 3c32e3231a257791c6505a222f7a7a0d79e9e1f0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 10 13:16:59 2011 -0700

    Changes to work around PathScale bug.
    PathScale has problems with file scope C++ standard strings in MPI programs.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Tools/C_mk/Make.Linux

commit e117ae6860ed5327369f5118e3e5e743f1e5e79f
Merge: c80ff4cae 55f0965b5
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Oct 7 16:34:47 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib
    
    Conflicts:
            Tools/C_mk/Make.defs

commit c80ff4caee9e950dbf2c2d028d1a2fa0638c7080
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Oct 7 16:26:22 2011 -0700

    update for ascem with sub-comm in fBox

BoxLib_Version.txt
Tools/C_scripts/gen_release_tarball.txt

commit 55f0965b5809c0bd595bb5f7e14e8711ad1e6233
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 7 15:59:15 2011 -0700

    std::snprintf() => snprintf() to get to compile with PGI.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 2ca9e892ac3e9501a7dc4006d9ebfa38e2671da9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 7 15:12:55 2011 -0700

    Now always calls the mgt_init() that takes a single argument.
    We want to support George Pau who needs the ability to pass in an
    MPI_Communicator that is not MPI_COMM_WORLD.
    Added Finalize() that gets called on BoxLib::Finalize() which'll reset
    initialized to false.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 92ee6be23ab697ade5a76b02375a67592707df94
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 7 15:10:02 2011 -0700

    mgt_init() now takes a single integer argument "comm".
    Removed the saved logical variable that only called parallel_initialize()
    on the first call.
    Instead MGT_Solver only calls mgt_init() when it needs to.

Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 78f6039275d8de2f97ebb03f1a2927f18ae76159
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 7 15:06:21 2011 -0700

    parallel_initialize() now takes an optional integer "comm" argument.
    If it's present we use it instead of MPI_COMM_WORLD as the MPI communicator.

Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit 77f0a22199b530579b2348a42611085b9f7d7786
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Fri Oct 7 15:10:57 2011 -0400

    add the compilation and execution commands to the web output

Tools/C_util/regtests/testnew.py

commit 4ed8bd9c465a26870448a9883941e62dcad50c03
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 6 14:38:59 2011 -0700

    More tweaking on removeOverlap().
    There's got to be a better way to do this but I don't see it just yet.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 2064452d0cf9b05a6cd538c4270fa6c4b2f747b1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 6 12:40:52 2011 -0700

    Instead of just calling std::list<Box>::clear() our version of clear()
    employs the swap() trick to really get rid of any extra memory hanging
    around due to stray Boxes.

Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit e119b641d2ba69a0c448eaf5610e3df32d8321d1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 6 12:30:18 2011 -0700

    removeOverlap() no longer returns a BoxList.
    Instead it's a void function.
    We now though fix up the resultant BoxArray so it doesn't have holes.
    We then can use the boxList() function to get a good non-overlapping list
    of boxes.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.cpp

commit 6671bfab7ee035ce1286876381dd47e00319a383
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 6 11:06:58 2011 -0700

    This has most of the previous tweeks put back in.
    What I broke was something in removeOverlap() which I'm still thinking
    about.  It's weird.

Src/C_BaseLib/BoxArray.cpp

commit 1f46c539e53bd5569a2b1fa4614b47133589a25e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 6 10:34:33 2011 -0700

    I broke BoxArray somehow.
    I'm reverting to this earlier copy from Parallel/BoxLib till I figure out
    what I did.

Src/C_BaseLib/BoxArray.cpp

commit c87f9e17501bafb684ee6e643cddbfac6f64553e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 5 20:03:05 2011 -0700

    Changes to InitCosmo in Particles.H only.

Src/C_AMRLib/Particles.H

commit ca3a12101f670cc452ae24af6685daa246051e75
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 5 16:15:48 2011 -0700

    A little tidying of for() loops.

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 2c4856d89e67cc6210da1240e0512e0164bf4453
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 5 16:07:20 2011 -0700

    Some more tidying of for() loops.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit 6d1066a58a79a487ec88a1f7a3946e7f73181ab4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 5 15:39:01 2011 -0700

    Some tidying up of for() loops.

Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 5d639e8833bca1e4f9e7f00e239979785e7c83be
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 5 15:31:39 2011 -0700

    Some tidying up of for() loops.
    When possible moved function calls from the test portion to the init portion.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.cpp

commit 8bb2cea3204b500b37f05e452ca94db0690ad2cb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 5 14:07:33 2011 -0700

    Merged the guts of the two define() functions into a new function called by both.

Src/C_BaseLib/FabArray.H

commit 3487a95fbd15e557b7902d82f1b567eb6edd1ae3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 5 12:57:09 2011 -0700

    Removed remnant embedded CVS $Id strings.

Src/LinearSolvers/C_TensorMG/DivVis_F.H
Tests/LinearSolvers/C_CellMG/Make.package
Tests/LinearSolvers/C_CellMG/main.cpp
Tools/C_mk/Make.OSF1
Tools/C_scripts/strip72
Tools/C_util/Make.package

commit 7bd56dac285294361c7857d15be56d5518dea6ac
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 5 12:51:43 2011 -0700

    Use <> on include files not "" for consistency.

Src/C_AMRLib/DatasetClient.cpp
Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/COORDSYS_F.H
Src/Extern/amrdata/AmrData.H
Src/Extern/amrdata/AmrData.cpp
Src/Extern/amrdata/DataServices.H
Src/Extern/amrdata/DataServices.cpp
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/hg_cg.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interpolator.H
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Tests/LinearSolvers/C_NodalMG/proj.cpp
Tests/LinearSolvers/ComparisonTest/compute_norm.cpp
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp
Tools/C_util/Convergence/Add.cpp
Tools/C_util/Convergence/ComputeAmrDataNorms.H
Tools/C_util/Convergence/ComputeAmrDataNorms.cpp
Tools/C_util/Convergence/DiffFab.cpp
Tools/C_util/Convergence/DiffSameDomainRefined.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGrid2.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileNormB.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp
Tools/C_util/Statistics/ComputeAmrDataStat.H
Tools/C_util/Statistics/ComputeAmrDataStat.cpp
Tools/C_util/Statistics/PltFileFluxAve.H
Tools/C_util/Statistics/PltFileFluxAve.cpp
Tools/C_util/Statistics/PltFileList.cpp
Tools/C_util/Statistics/PltFileStat.cpp
Tools/C_util/Statistics/PltFileXAve.H
Tools/C_util/Statistics/PltFileXAve.cpp
Tools/C_util/TV_TempWrite.H
Tools/C_util/ViewMF/MFNorm.cpp
Tools/C_util/ViewMF/checkMFghostcells.cpp
Tools/C_util/ViewMF/main.cpp
Tools/C_util/ViewMF/mfMinMax.cpp
Tools/C_util/ViewMF/viewMF.cpp
Tools/C_util/ViewMF/viewMFcol.cpp
Tools/C_util/ViewMF/viewMFdiff.cpp
Tools/C_util/ViewMF/viewMFdiffHardWire.cpp
Tools/C_util/WritePlotFile.H
Tools/C_util/dbgTools/crsGrids.cpp
Tools/C_util/dbgTools/intersectGrids.cpp
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp
Tutorials/MultiGrid_C/main.cpp
Tutorials/WaveEquation_C/main.cpp

commit 54943ca8443aba26a0e1047196c09d9e73d8291d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Oct 4 14:25:51 2011 -0700

    Simplified how AuxBoundary are built.
    We no longer have to explicitly force'm to not use the MinimizeCommCosts
    code.
    That code no longer exists.

Src/C_AMRLib/AuxBoundaryData.cpp
Tests/C_BaseLib/tMinCommCosts.cpp

commit 41b34604968184823a013bb08ee1234f7fb9b400
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 4 11:09:54 2011 -0700

    Move the definition of r1 so that even when we don't need to solve
    the "Solve Time" output is defined.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 271fb8f0b77a75c4604b63893f36c6ec83553768
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 4 09:42:49 2011 -0700

    Replace
             FOPTF += -mp1
             fOPTF += -mp1
    by
             FOPTF += -mp1 -fltconsistency
             fOPTF += -mp1 -fltconsistency
    in Make.defs for Intel verion 11.*   Without the -fltconsistency, the loss
    of precision with Intel optimization causes multigrid to fail.

Tools/C_mk/Make.defs

commit ca1c69b1dcb0b5ff8c40195beebbd359a05768f9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 3 12:58:46 2011 -0700

    Replaced Cray vector merge routines with fortran 90 merge() calls.

Src/Extern/amrdata/FABUTIL_2D.F
Src/Extern/amrdata/FABUTIL_3D.F

commit e053836198f314de905320c1b603dd2a799c7210
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 3 11:04:17 2011 -0700

    I'm changing BL_NOFAST => BL_FAST.
    I'm don't want the "fast" optimization options to be the
    default when DEBUG=FALSE.
    If you want to try using the "fast" optimization options you now
    have to set BL_FAST=TRUE in you GNUmakefile.
    Buyer beware.  This tends to expose bugs in compilers.

Tools/C_mk/Make.Linux

commit 53e049152759675948ca022640c0cfc5478d568f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Oct 1 08:33:25 2011 -0700

    Fix to multi-level AssignDensity().
    We never should have tried to reuse the BoxArray in fmf that way.
    Weird thing is this code used to work.
    I think what happened is that I "fixed" MultiFab::clear() a while back.
    Previously all it did was get rid of the memory.  The new improved
    version also clear()d the BoxArray among a few other things.

Src/C_AMRLib/Particles.H

commit 762f19e25d39a828f010324f050585887fd331b1
Merge: 575b68be1 e40f6a170
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 30 11:43:25 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 575b68be1fe4ee06d59ebf108f1da0a44a1907aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 30 11:35:12 2011 -0700

    If the link files are absolute path, the old version would fail.
    This is now fixed.  The link files can now be either absolute path or
    just basename.
    
    The old version used gmake.  But on some systems the GNU amke is just
    "make".  In the new version, MAKE is a variable that can be changed in
    the input file for the script.  Also, numMakeJobs is added so that
    several make jobs can run simultaneously.

Tools/C_util/regtests/testnew.py

commit e40f6a17089439e23c6da66959845fbdae0adbc2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 29 16:08:02 2011 -0700

    Quiet compiler warning.

Src/C_AMRLib/DatasetClient.cpp

commit 9edd2256f3574b434186750431d3f4f23aa4f272
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 29 13:42:06 2011 -0700

    Removed all the wrappergen stuff.
    This is a third-party library for profiling MPI calls.
    The only reason it was in our original CVS repository was
    because Chuck made some modifications to it.

Tools/C_util/wrappergen/Makefile
Tools/C_util/wrappergen/PROTO
Tools/C_util/wrappergen/README
Tools/C_util/wrappergen/args.c
Tools/C_util/wrappergen/args.h
Tools/C_util/wrappergen/doc.c
Tools/C_util/wrappergen/doc.h
Tools/C_util/wrappergen/driver.c
Tools/C_util/wrappergen/expandingList.h
Tools/C_util/wrappergen/mpifn
Tools/C_util/wrappergen/petsccfg.h
Tools/C_util/wrappergen/prof.c
Tools/C_util/wrappergen/prof_wrapper.c
Tools/C_util/wrappergen/readproto.c
Tools/C_util/wrappergen/sample.c
Tools/C_util/wrappergen/sample.w
Tools/C_util/wrappergen/system.c
Tools/C_util/wrappergen/system.h
Tools/C_util/wrappergen/tools.h
Tools/C_util/wrappergen/wrappergen.c
Tools/C_util/wrappergen/wrappergen.h
Tools/C_util/wrappergen/write_proto.c

commit 6d5b893593d27b6e0495cf1c70045856000bc5c0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 29 09:17:09 2011 -0700

    sprintf() => snprintf()
    This allows us to specify the size of the buffer into which we're writing
    so that we don't overflow the buffer & write arbitrary memory.
    We also can tell when the buffer when the buffer is too small to contain
    everything we wanted to write and abort if necessary.

Src/C_AMRLib/DatasetClient.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Utility.cpp
Src/Extern/amrdata/AmrData.cpp
Src/Extern/amrdata/DataServices.cpp
Src/F_BaseLib/fabio_c.c

commit 4450f4050d07e634a0154f5109870549bceb22e2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 28 15:48:15 2011 -0700

    Oops. Forgot a semi-colon.

Src/C_AMRLib/Particles.H

commit 0642a68626998b9b5d1b49c2ac8a08aa2e530ecf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 28 15:40:36 2011 -0700

    Changed as many sprintf() calls to BoxLib::Concatenate() as possible.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Particles.H
Src/C_AMRLib/StationData.cpp
Src/C_BaseLib/VisMF.cpp
Src/C_BoundaryLib/BndryRegister.cpp
Tests/LinearSolvers/C_CellMG/main.cpp
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp
Tools/C_util/Statistics/PltFileFluxAve.cpp
Tools/C_util/Statistics/PltFileList.cpp
Tools/C_util/Statistics/PltFileStat.cpp
Tools/C_util/Statistics/PltFileXAve.cpp
Tools/C_util/WritePlotFile.cpp
Tutorials/MultiGrid_C/writePlotFile.cpp
Tutorials/WaveEquation_C/writePlotFile.cpp

commit 20d78f69bcba04dd0fbb37d62c4077ef7f375528
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 28 15:40:11 2011 -0700

    Cut at new GNUmakefile for GIT.

Tools/C_util/Statistics/GNUmakefile

commit f7fb52b6ca12860ba5a262381213c036cc8216cf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 28 15:36:08 2011 -0700

    Cut at working GNUmakefile for new GIT repositories.
    Will needs to be fixed a tad once AmrData stuff is in it's correct place.

Tools/C_util/Convergence/GNUmakefile

commit 3d524a4eba9aba0833b3817c718be8a4a16ef656
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 28 15:10:18 2011 -0700

    Change [fF]DEBF from -O0 => -O1 for gfortran.
    Some version of gfortran get internal compiler error with -O0 on some
    hgproj code.

Tools/C_mk/Make.defs

commit fa44de59c67c8e5373f88fb3215d98eec30f1785
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 28 14:56:14 2011 -0700

    Removed some unused variables.

Tutorials/WaveEquation_C/main.cpp

commit 82a5224cb43b60bb00b7091e9b705260f4a231cc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 28 09:16:56 2011 -0700

    -O -> -O0 when debugging. Will produce slower but "truer" code.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit cbd22c57acb6341bf8024962cb71b7c82e8d64c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 16:15:24 2011 -0700

    BoxLib_F with Dirichlet boundary works for both level solve and
    composite solve.
    
    Periodic and Neumann boundaries do not work yet.

Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp

commit f39c92fad3e5f1931b7fdbf4190d01b9f4a9a13f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 16:12:01 2011 -0700

    MGT_Solver::set_vis_coefficients(PArray<MultiFab>& aa,
                                 Array<PArray<MultiFab> >& bb,
                                 const Real& beta,
                                 Array< Array<Real> >& xa,
                                 Array< Array<Real> >& xb,
                                 int index_order=0);
    
    Add an optional argument index_order.
    
    If index_order == 0, bb[dim][level]
    else,                bb[level][dim]
    The second way is consistent with other set_?_coefficients.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit fcd3f86e12e08daa646fd386e0eb8301261d5749
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 14:23:50 2011 -0700

    add routines for computing norms to makefile

Tests/LinearSolvers/ComparisonTest/Make.package
Tests/LinearSolvers/ComparisonTest/main.cpp

commit eb6676d19d1c25edfbcfed31005e36f0db7fe5f3
Merge: b7bceb7eb 21fcaa5ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 14:21:39 2011 -0700

    Merge branch 'boxarray'

commit 21fcaa5ea828ba3e4eed54e8eb7c9fd19993eb2b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 14:20:52 2011 -0700

    compute 2-norm and max-norm

Tests/LinearSolvers/ComparisonTest/COMP_NORM_3d.f90
Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H
Tests/LinearSolvers/ComparisonTest/compute_norm.cpp

commit b7bceb7eb605dc39f98d70bf82f78a5c3021403a
Merge: ed9ac7d2b 4cba38c6a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 27 14:02:34 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ed9ac7d2b421529a54f12e1cb99f3d95292d33f5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 27 14:01:29 2011 -0700

    Removed a couple gfortran warning flags on the f90 debug line that
    weren't supported by gfortran version 4.3.3 or anything earlier.

Tools/C_mk/Make.defs

commit 13612c2e0edd9c5c8fa4dac30ae0dc68f6826e29
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 27 13:58:53 2011 -0700

    Removed some new/deletes and replaced with Array operations.

Src/C_AMRLib/TagBox.cpp

commit d769f319706bd0569219278015fd514bcbc6fc45
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 27 13:58:24 2011 -0700

    Disabled the copy assignment operator and copy constructor.
    We don't want folks copying BaseFabs.

Src/C_BaseLib/BaseFab.H

commit 4cba38c6ab1734ba880cec316fef2f4bce24eb21
Merge: a1958f23d 09ae66c72
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 12:49:41 2011 -0700

    Merge branch 'master' into boxarray

commit a1958f23d47e8458b060ec97d302f2170ae62290
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 12:48:23 2011 -0700

    a file containing calls to BoxLib_F

Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp

commit 09ae66c723770c10c378b2236490c92de7756115
Merge: 5a95abba6 0dc127fac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 12:37:10 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5a95abba693f279cc26bba7dc8801a06c3d7365f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 12:36:50 2011 -0700

    write plotfile

Tutorials/MultiGrid_C/writePlotFile.H
Tutorials/MultiGrid_C/writePlotFile.cpp

commit e868b40f69c327d67ab611682099be04b1748e6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 10:35:16 2011 -0700

    Fix a bug: phys_bc was created by new BCRec, but was deleted.

Tutorials/MultiGrid_C/main.cpp

commit 0dc127fac63182502e924e13e4e96f387aa04b09
Merge: a2c5fa15c fe822a6be
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 27 08:55:49 2011 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit a2c5fa15cebe72f984cf5fb6dac71bf5e2521233
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 27 08:54:25 2011 -0700

    Make_defs: Turns out franklin does not like having two else statements in an "ifeq" sequence.  We have replaced the
    else ... else by a nested if statement inside the first else.

Tools/C_mk/Make.defs

commit 930178f852184489e696fe59d4c8871a09e09aa1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 26 17:26:16 2011 -0700

    Fix a comment about copy constructor and copy assignment operator.

Src/C_BoundaryLib/InterpBndryData.H

commit fe822a6be67230a264f31399bd24cb5a0e8238ed
Merge: cd4ae62d9 d4e1b7f37
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 26 15:55:59 2011 -0700

    Merge branch 'master' into boxarray

commit cd4ae62d9b67f2e3785769a0a5ff1e7c6b4c92bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 26 15:54:59 2011 -0700

    BoxLib_F runs.  But not sure whether or not the boundaries are set correctly.

Tests/LinearSolvers/ComparisonTest/COEF_3D.F
Tests/LinearSolvers/ComparisonTest/COEF_F.H
Tests/LinearSolvers/ComparisonTest/GNUmakefile
Tests/LinearSolvers/ComparisonTest/Make.package
Tests/LinearSolvers/ComparisonTest/inputs.3d
Tests/LinearSolvers/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/writePlotFile.H
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp

commit d4e1b7f37dddf3c7cf3dd864fe7ee5b15f914ff5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 26 13:47:06 2011 -0700

    Changed the way Arenas are allocated.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/FabArray.H
Tests/LinearSolvers/C_NodalMG/proj.cpp

commit 18e302e158866b0d2dc2f1f02a9dac23a6c78f1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 23 18:28:37 2011 -0700

    Started the linear solver comparison test
    
    The setup of multilevel grids, coefficients, rhs and exact solutions
    are done.  It can also write a plotfile.

Tests/LinearSolvers/ComparisonTest/writePlotFile.H
Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp

commit 0d0064cdfea64e0a1b5082262be537a0f7970b00
Merge: bc82cc698 c98917c8a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 23 10:15:21 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit bc82cc69870754a9380dcf55d9b117dea0e93831
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 23 10:14:56 2011 -0700

    We now pass vel_fac into Particles::InitCosmo() instead of computing it inside.

Src/C_AMRLib/Particles.H

commit c98917c8a4aedec04e9b1989454708438056fc6f
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Fri Sep 23 12:09:08 2011 -0400

    add support for link files (link1File, link2File, link3File).  These
    are linked into the run directory instead of copied.

Tools/C_util/regtests/testnew.py

commit a75359f4c40e155023058c193d976fbbd6b32b52
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Fri Sep 23 10:43:06 2011 -0400

    do a symlink for helm_table.dat instead of copying it

Tools/C_util/regtests/testnew.py

commit a470ea6228e2518345d2874babc3d9a6e7480bac
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Sep 22 22:42:45 2011 -0400

    update for testnew.py

Tools/C_util/regtests/Castro-tests.ini

commit 9dae2b1ed543875da392c68f5a46a4c9ec268bf8
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Sep 22 22:14:08 2011 -0400

    update to work with the latest version of the test suite

Tools/C_util/regtests/Maestro-tests.ini

commit d472258203827ee674aa4ea12cbfd4ba28c5e8a2
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Sep 22 22:00:12 2011 -0400

    add git pull and changelogs for the boxlib directory

Tools/C_util/regtests/testnew.py

commit 4b3d3b33c15b12b7571e5d76953db145151a6ee4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 22 14:33:12 2011 -0700

    MG tutorial now writes plotfiles so that they can be read by Visit.

Tutorials/MultiGrid_C/Make.package
Tutorials/MultiGrid_C/main.cpp

commit ffac0acf8f8750ac352798682afdb5a3f091eb35
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 22 14:32:56 2011 -0700

    Make writePlotFile more general for an arbitary number of components.

Tutorials/WaveEquation_C/writePlotFile.cpp

commit e012e685b4c9a9256ebe176bf28635ad12f51646
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 22 13:45:52 2011 -0700

    slight cleanup of the Hypre  driver

Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp
Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F
Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H

commit c2ce66dcc30f5fa60f4c4e59d41b1a5e1fe2d5a9
Merge: a1e25beb5 6a9107e64
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Sep 22 15:20:44 2011 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit a1e25beb56977500f94b56ea09adc5b2a72521d7
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Sep 22 15:20:00 2011 -0400

    add more checks

Tools/C_util/regtests/testnew.py

commit 6a9107e642e9f3d44a08c9bfd3a17bf08f5e69a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 21 16:41:36 2011 -0700

    Give warning when both of the following are true:
    
    ifndef CG_USE_OLD_CONVERGENCE_CRITERIA
    
    mg. use_Anorm_for_convergence = 0.
    
    This appears to be a bad combination at least for the hard test in MG
    tutorial.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Tutorials/MultiGrid_C/GNUmakefile

commit 3b7df33d067889b40b258597aad35a2a5bc6eef6
Merge: 955bdf4cf d08341105
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 21 15:56:53 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 955bdf4cfa80d72c8d8a7eee6115c20293b2c6cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 21 15:53:40 2011 -0700

    It seems too verbose that all the grids are printed out when
    mg.verbose>2.  The threshold is now >4.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 3df724a2e122b3f9f9f64ddd28179dca738b1081
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 21 15:52:49 2011 -0700

    delete a space in write(*,*)

Src/LinearSolvers/F_MG/itsol.f90

commit f4408cc28ae1157c6bd1daa73df546ae5af80488
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 21 15:39:52 2011 -0700

    In the bottom CG solver, A and RHS are rescaled first.  So the initial
    error printed out is different from the error printed out before
    bottom.  To avoid confusion, a note is added.

Src/LinearSolvers/F_MG/itsol.f90

commit 3bee73c44893be673497637a7ded8cdee21b6c47
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 21 15:24:44 2011 -0700

    Add CPPFLAGS += -DCG_USE_OLD_CONVERGENCE_CRITERIA
    
    This makes BoxLib_C bottom CG solver to use the old convergence
    criteria.  Using the new criteria, BoxLIb_C will fail at the hard
    test.

Tutorials/MultiGrid_C/GNUmakefile

commit d08341105b5ecc5f370d5b54822c73618e1698a8
Merge: 89a73d635 a8c40c6ce
Author: Aleks Donev <donev@courant.nyu.edu>
Date:   Wed Sep 21 17:26:17 2011 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 89a73d635e7e5f131dd7cbc85b4ba9d722d5c508
Author: Aleksandar Donev <donev@donev.cims.nyu.edu>
Date:   Wed Sep 21 16:28:33 2011 -0400

    Added Courant systems to Makefile

Tools/F_mk/GMakeMPI.mak

commit a8c40c6ce3262a41076040e33cc1e77372735968
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Sep 21 12:22:57 2011 -0400

    add support for BOXLIB_HOME.  Finish cleaning things up.

Tools/C_util/regtests/testnew.py

commit 2ef7324293435edfcc9ac54d5460477423068cb7
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Sep 21 12:00:08 2011 -0400

    add BOXLIB_DIR to the list of information held by this module.

Tools/F_scripts/make_build_info

commit 03f8a7e9e3b53ade94a35c64983b59cbd1e18cfe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 11:08:18 2011 -0700

    Added SMG solver for Hypre

Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp
Tutorials/MultiGrid_C/inputs.3d

commit dbfd9afea1a273516de53f5b54d4fca4b9807e99
Merge: 2d6f5756c 346fac64e
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Sep 19 17:19:18 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2d6f5756c44812f3ee2a0aca08c5403c2378d1f0
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Sep 19 17:18:55 2011 -0700

    Replace Wall with everything but unused-dummy-arguments

Tools/C_mk/Make.defs

commit e6d5944abc0f57c0b56cadf0c2b14177b249f8c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 19 15:18:40 2011 -0700

    Two parameters are introduced in the setup of problems.  We now can
    run test problems with variable diffusion coefficient.

Tutorials/MultiGrid_C/COEF_3D.F
Tutorials/MultiGrid_C/COEF_F.H
Tutorials/MultiGrid_C/RHS_3D.F
Tutorials/MultiGrid_C/RHS_F.H
Tutorials/MultiGrid_C/inputs.3d
Tutorials/MultiGrid_C/main.cpp

commit 346fac64e24d4ef2681ff7f801c4c36c518cebd8
Merge: 550b78cca 177d4d0b4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 19 13:50:40 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 550b78cca3314487fffa6b8909b7823a98e6aec5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 19 13:49:30 2011 -0700

    Tests/StencilOrder:
    Add this new test program (with accompanying README file) to demonstrate the difference
    in timings that we see by simply modifying the ordering of the indices in multigrid stencils,
    from ss(i,j,k,n) to ss(n,i,j,k) demonstrates a roughly factor 5 speedup for this example
    stencil with 21 entries.

Tests/StencilOrder/README
Tests/StencilOrder/program.f90

commit 177d4d0b493cc5901da8a84295ad9467550e55f2
Merge: b6bb2ef9b 4a5989f96
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 19 13:07:46 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b6bb2ef9b2377786d56ae1d8e59bd4793c45d2a9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 19 13:07:14 2011 -0700

    Some endian test stuff for Darwin from Chris Malone.

Tools/F_mk/GMakedefs.mak

commit 4a5989f9622093fd1e9c79d3793dcb8e23b76d17
Merge: c09ab80de b69d6b480
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Sep 19 15:22:40 2011 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c09ab80decc09a92a909d1a53e5fa1cdd2dd2846
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Sep 19 15:21:54 2011 -0400

    new version of the test suite.  This uses test and suite objects
    to make things clearer and more managable.  Start of the changes
    to get git into things

Tools/C_util/regtests/testnew.py

commit b69d6b480ab0ea6a830e2761131014148bafd0b9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 19 11:48:06 2011 -0700

    Changes in Src/LinearSolvers/F_MG only:
    These files use the new stencil ordering: ss(n,i,j,k) instead of ss(i,j,k,n).  This
    requires a new type of multifab (type stencil) which orders the data this way, but
    this new type does *not* currently support all the regular multifab operations,
    so care must be used.  Only the stencil arrays ("ss") are re-ordered this way.

Src/LinearSolvers/F_MG/cc_interface_stencil.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/nodal_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90

commit 6dbdd1ae374461de4aa776c0e842cd79b56e01d6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Sep 18 07:05:39 2011 -0700

    Add more output so it will be easier to see which test was run.

Tutorials/MultiGrid_C/main.cpp

commit 2bff14bdf3314da78b6fb47ce5a526ce9a0a7011
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 16 18:27:38 2011 -0700

    Add new flag to control BoxLib_C convergence criteria.

Tutorials/MultiGrid_C/inputs.3d

commit 2dda8dc5f6facac56b6296e392a00debb8beb8e1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 16 16:45:14 2011 -0700

    Removed some duplicate code in Make.mpi.
    In vector_i, removed the built data member and use associated() instead.
    Use BUMP=1.5 as the exponential growth factor. Some cleanup as well.

Src/F_BaseLib/vector_i.f90
Tools/C_mk/Make.mpi

commit 7107777ca5c7c2dedfcba999a8dac73b5041bd76
Merge: 66772967e 5deff2267
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 16 16:19:56 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 66772967e4e71940033578cd7093acbdb0d281d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 16 16:12:54 2011 -0700

    fix a problem in inputs

Tutorials/MultiGrid_C/inputs.3d

commit 5deff22675e3e76af5ac3f9ea6027473fc9cc622
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 16 15:38:59 2011 -0700

    Add a flag "use_Anorm_for_convergence" that allows us to control
    whether or not we use the Anorm in the convergence test.  This allows
    us to test convergence against the F90 solver and the Hypre solver.

Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 9c3b83de913a5639debb97e5f5c7f014f7940b5f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 16 15:26:15 2011 -0700

    Fix test for print statements regarding convergence

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 6e8bee67512a04e9a319d4ef4db61e85d2926eb3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 16 15:04:57 2011 -0700

    Clean up print statements for convergence test.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 58acdf886c8966cf224e128669daccbdd28e677a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 16 14:33:24 2011 -0700

    Add additional output (if verbose > 0) so we know what convergence criterion was used.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit fa32f3527ac2725224799c40a2d5b016684a65d7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 16 14:31:23 2011 -0700

    GNUmakefile: Add much more commentary about how to set variables so this will compile.

Tutorials/MultiGrid_C/GNUmakefile

commit 374b87908e80c5c4b2f832a027c674be809f4fc8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 16 13:13:06 2011 -0700

    pass high-order boundary parameter to Fortran

Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F

commit 133cefb6868f06b58a974713290d53e9f8218eb9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 16 12:04:40 2011 -0700

    make the stencil index in hypre consistent with what returned by
    BoxLib bndlib

Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp
Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F
Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H

commit 386964b7a0ce7fa405d360938d6004fc23120e9a
Merge: c7010a1d6 d6044764e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 16 10:45:48 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c7010a1d686afbfef07e25a61a6143e282771c60
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 16 10:45:40 2011 -0700

    minor cleanup

Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp

commit 2cac522671e933846590cd5c141a132550937520
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 16 10:44:38 2011 -0700

    remove redundant soln.setVale(0.)'s

Tutorials/MultiGrid_C/main.cpp

commit d6044764e232d125215adf86588a49e9eaba2210
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 16 10:17:41 2011 -0700

    Separate out the Fortran code for the RHS from the Fortran code for the coefficients.

Tutorials/MultiGrid_C/COEF_3D.F
Tutorials/MultiGrid_C/COEF_F.H
Tutorials/MultiGrid_C/Make.package
Tutorials/MultiGrid_C/RHS_3D.F
Tutorials/MultiGrid_C/RHS_F.H
Tutorials/MultiGrid_C/main.cpp

commit 160d3fd26f6b7a86112e48f9970b83b60b36b17c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 16 10:08:28 2011 -0700

    Explicitly set cg.v = 0 so we don't get CG messages from BoxLib_C solver.

Tutorials/MultiGrid_C/inputs.3d

commit 5db3cfa011e60c28bd21b352bf78d212df92bcf2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 15 21:37:36 2011 -0700

    1) Set solution to zero before each solve.
    2) Wrap one more solve_with_hypre by ifdef USEHYPRE

Tutorials/MultiGrid_C/main.cpp

commit 4ea2d43473eb4bf5c0ac690fa59b45263464bf25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 15 17:40:32 2011 -0700

    fix a typo in a string for output file name

Tutorials/MultiGrid_C/main.cpp

commit f37b356785ae8710cd773ab2d76bcb5bbc9bdc92
Merge: 3c8c721af 8763c6cdc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 15 17:35:53 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib
    
    Conflicts:
            Tutorials/MultiGrid_C/main.cpp

commit 3c8c721af336d4098b6b869b7cbdb8933e2f2be7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 15 15:55:46 2011 -0700

    Make bc_type and solver_type enum type rather than string type.  Using
    string is more error-prone due to typos in the string.
    
    Move to the part that sets boundaries to a function.  Bot BoxLib_C and
    Hypre use it.

Tutorials/MultiGrid_C/main.cpp

commit 8763c6cdc475447b7372e1611edf8c4f384378f2
Merge: 93028fd6b 18d138c28
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 15 15:35:43 2011 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 93028fd6b346ab53ce116edc8094c8af278ebdb2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 15 15:35:25 2011 -0700

    Add solver_type = "All" and additional print statements.

Tutorials/MultiGrid_C/main.cpp

commit 18d138c28a55cd818686e1c2a8df6f77dfaba40e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 15 13:53:35 2011 -0700

    1) Replace 1e40 by 1e200 in test in fillpatch.f90 whether region is completely covered
    2) Modify print statement to be more informative.

Src/F_BaseLib/fillpatch.f90

commit 5b20fe6fd8629c36cebf3650f8036ff1486ab43b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 15 10:37:03 2011 -0700

    The index for dimension was sometimes "n", sometimes "dir", and
    sometimes "i".   It is now changed to "n" for consistency.

Tutorials/MultiGrid_C/main.cpp

commit 765f5b6faa8fb9b5fef0efac8ecb90fbbc898641
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 15 10:25:27 2011 -0700

    Fix a bug.  dx[i] should be dx[n], where i is MFIter index, n is
    dimension index.
    
    update the setup of boundaries before calling hypre

Tutorials/MultiGrid_C/main.cpp

commit 71c926a99daf3f5ef1dedfef830b23a76a407223
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 15 10:15:24 2011 -0700

    Changes from Chris Malone.

Src/F_BaseLib/GPackage.mak
Tools/C_mk/Make.Darwin
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit dd6c3e154402334dab6b60872949374e7f510eb4
Merge: 4d5cd28b8 3d33d18e6
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 15 08:46:57 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4d5cd28b89f47b5fb9c36f593f460bb89b6a6acf
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 15 08:46:44 2011 -0700

    Clean up screen dump during build using C_mk stuff: if the GNUmakefile (or make cmd line) contains VERBOSE=FALSE or VERBOSE=OFF, the build line will not be echoed to the screen.  Added a line to simply say ...Building XXX... , commented out strip72 warning text, removed warning about unused dummy arguments in gfortran.  Comment out silly echo SUCCESS, since it reports success regardless - tests based on the presence of this string should be restructured.

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules
Tools/C_scripts/strip72

commit 3d33d18e690fcca4ffda78d8d235986388eee588
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 15 08:44:40 2011 -0700

    A little simplification; make the swap() call for clearing memory one liners.

Src/C_AMRLib/Particles.H

commit ce3f8101122f9ddc2e19a2857b5f26003798b8f1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 14 21:28:46 2011 -0700

    1) Fix boundary conditions for BoxLib_C solver in Tutorials/Multigrid_C
    2) Change multifab_remote --> remote in all places for consistency

Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_interface_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/coarsen_coeffs.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_newu.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90
Tutorials/MultiGrid_C/main.cpp

commit 67e2adadf4bf64b6265de30a5b22c8f40fe43282
Merge: b8fcdaf7c f24274ced
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 18:20:48 2011 -0700

    merge

commit b8fcdaf7cfe73b7cb64c2efc271cb72393e98bc5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 18:12:03 2011 -0700

    hypre A matrix is no longer symmetric

Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp
Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F
Tutorials/MultiGrid_C/inputs.3d
Tutorials/MultiGrid_C/main.cpp

commit f24274cedeb6001fcde72afadf445563ad13db51
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 14 17:11:11 2011 -0700

    More mods from Chris Malone.

Tools/F_mk/GMakedefs.mak

commit 0c2f5e2857f3610e630858d278683dd4b74eb799
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 14 16:51:48 2011 -0700

    Added Darwin_intel.mak from Chris Malone.

Tools/F_mk/comps/Darwin_intel.mak

commit c66f71a3d3665962cad36cedbb0fc4849b663d8d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 14 14:19:49 2011 -0700

    Add comments about verbosity flags.

Tutorials/MultiGrid_C/inputs.3d

commit f0ba7df0ac2ce7b5d94ced84f9d93fc07a8132f9
Merge: a466011f8 3c236289b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 14 13:29:35 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3c236289b211a773f276f2c93921f8e3bf82d6d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 12:51:39 2011 -0700

    fix default BOXLIB_HOME

Tutorials/MultiGrid_C/GNUmakefile

commit a8dd99a45d594bc49e1797096f6ec21cc86263b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 12:08:01 2011 -0700

    clean up

Tutorials/MultiGrid_C/COEF_3D.F
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp
Tutorials/MultiGrid_C/inputs.3d
Tutorials/MultiGrid_C/main.cpp

commit 80cd5771a15d9c445b7d7a25a182fda8905db0de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 10:19:25 2011 -0700

    add the iostream and iomanip headers to HypreABecLap

Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H

commit ddb68f90d67cce601666e40bb7fbd3c5ad087de6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 10:14:54 2011 -0700

    Add USE_HYPRE to GNUmakefile so that the code can be compiled without hypre.

Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_C/main.cpp

commit a466011f8e0bec42cae37f2829f796ca9d7c7494
Merge: 895f426a9 90b45e11c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 14 08:29:26 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 90b45e11c0a22c9473e5ad910440fc5cfd5f0a07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 06:18:21 2011 -0700

    rename solvers to BoxLib_C and BoxLib_F

Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_C/inputs.3d
Tutorials/MultiGrid_C/main.cpp

commit f9595a74421155c88b6911bef017cd7b1664028e
Merge: f3255977e 82803c556
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 05:38:55 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f3255977e18211ded75d33e45f6b9b6b763a472b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 05:38:15 2011 -0700

    check in hypre driver

Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H
Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp
Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F
Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H
Tutorials/MultiGrid_C/HypreABecLap/Make.package

commit 895f426a99eeff269c6608c0ded4d76864f92361
Merge: e5ded45cb 82803c556
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 13 22:08:12 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1103bccbee3a53451d7d8b84ca10753e75b81135
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 18:12:45 2011 -0700

    8 combinations work.  The one doesn't work is C++ with periodic boundary.

Tutorials/MultiGrid_C/COEF_3D.F
Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_C/inputs.3d
Tutorials/MultiGrid_C/main.cpp

commit 82803c55679f36b57d0c1e8671fe26f702e62de6
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Sep 13 13:40:31 2011 -0700

    modify install procedure to clean up how an external code might link to the libraries

CMakeLists.txt
Src/C_AMRLib/CMakeLists.txt
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/ParmParse.H
Src/C_BoundaryLib/CMakeLists.txt
Src/Extern/amrdata/CMakeLists.txt
Src/Extern/gslib/CMakeLists.txt
Src/F_BaseLib/CMakeLists.txt
Src/LinearSolvers/C_CellMG/CMakeLists.txt
Src/LinearSolvers/C_to_F_MG/CMakeLists.txt
Src/LinearSolvers/F_MG/CMakeLists.txt
Tools/CMake/CCSEConfig-install.cmake.in
Tools/CMake/CCSEConfigReport.cmake
Tools/CMake/CCSEConfigVersion-install.cmake.in
Tools/CMake/CCSELinkLine.cmake
Tools/CMake/CCSEOptions.cmake
Tools/CMake/InstallManager.cmake
Tools/CMake/MakefileConfig.export.in
Tools/CMake/ParseLibraryList.cmake
Tools/CMake/TransformVersion.cmake
Tools/C_scripts/boxlib-build.sh

commit e5ded45cb11f631ba1525ca86e7872d83cc8b17e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 13 13:15:18 2011 -0700

    This now has the working 3d 4th order variable coefficient stencil.

Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90

commit 3af8df5f9f287d0564c57cac5c7616437b9cfe7d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 13 11:05:04 2011 -0700

    Do a maxSize() on the BoxArrays to get more grids.

Tests/C_BaseLib/tMFcopy.cpp

commit cceb168908c23dab03377181b0294ef295b24efc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 13 10:51:34 2011 -0700

    More work on parallel copy test.

Tests/C_BaseLib/tMFcopy.cpp

commit 20afe70790529b9587ccefd6284a218caef75a29
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 13 07:00:35 2011 -0700

    Fix the 3d 4th order variable coefficient stencil.

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 7f39bd501590f08a243085dcab29a0f0e5941868
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 12 18:21:20 2011 -0700

    More trying to get the 3D variable coefficient 4th order solver to work.

Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90

commit 434edf0c6a192b23e9368e0c1cc7b00d23903ce3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 12 16:38:08 2011 -0700

    fixed a couple of bugs.  C++ & F90 solvers work for Dirichlet boundary.

Tutorials/MultiGrid_C/COEF_3D.F
Tutorials/MultiGrid_C/COEF_F.H
Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_C/inputs.3d
Tutorials/MultiGrid_C/main.cpp

commit 312a9b3daf7a5add12c3b3a3c5bd3542d0407f75
Merge: 158146557 4564b07bf
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 12 14:53:52 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 158146557a521f7f3720aaff8e64b7c99719b81d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 12 14:53:00 2011 -0700

    1) Broke cc_stencil.f90 into two files -- cc_stencil.f90 and cc_stencil_apply.f90
    2) Added 4th order stencil for variable coefficients in 3d (61 terms in stencil)

Src/LinearSolvers/F_MG/CMakeLists.txt
Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_apply.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_solve.f90

commit 4564b07bf55d7dfdc9dccd8cfb01e9834b17f9a5
Merge: 34808451d 7873d5fec
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 12 14:31:11 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 34808451dc4a3c653fe50f1b8c69b6f9b637e192
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 12 14:30:59 2011 -0700

    Fixed typo in comment.

Tests/C_BaseLib/tMFcopy.cpp

commit 12880bb7e044f58d6cbab28540a5cd5dd2d5f98e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 12 14:30:02 2011 -0700

    Added SFC_Threshold() functions to set/get the sfc_threshold.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 41c5d33574e27e98f51e03624020740fc8298949
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 12 14:28:23 2011 -0700

    Added new test routine that tests parallel copy between two multifabs
    whose boxarrays cover the same area but have different number of boxes and
    hence different distribution.

Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/tMFcopy.cpp

commit 7873d5fec28af829416466a858545238502b5189
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 12 12:55:35 2011 -0700

    Remove extra arguments so this compiles.

Src/LinearSolvers/F_MG/cc_stencil_fill.f90

commit 37ec61afdb0592a46de314e126d830810e4fada7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 12 12:54:41 2011 -0700

    Need to declare the new variables so this compiles (though still not working)

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 269105e601df000c58af1cc709e0c2a08012b45d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 12 12:06:36 2011 -0700

    1) New improved version of subroutine minion_fill_full_2d
    2) Introduced subroutine minion_fill_full_3d but it is not yet complete.
    3) Modified call to minion_full_fill_3d to test on whether ns = 61, not 125.

Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90

commit b153170d2a1db58790833f7f4323c3fd70e530a5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Sep 10 09:32:52 2011 -0700

    Latest version -- added choice of bc_type -- still not fully working.

Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_C/inputs.3d
Tutorials/MultiGrid_C/main.cpp

commit 2da2316aa8250009a64891daa50cad0f2f82e1e4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 9 21:54:36 2011 -0700

    New Tutorials directory -- a C++ MultiGrid driver that will call the
    C++ solver, the F90 solver and the Hypre solver.

Tutorials/MultiGrid_C/COEF_3D.F
Tutorials/MultiGrid_C/COEF_F.H
Tutorials/MultiGrid_C/GNUmakefile
Tutorials/MultiGrid_C/Make.package
Tutorials/MultiGrid_C/inputs.3d
Tutorials/MultiGrid_C/main.cpp

commit c6eb615f1c91e61b03aa1d808caf2a991c827dbe
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 9 17:25:13 2011 -0700

    No need to copy mf into plotMF

Tutorials/WaveEquation_C/writePlotFile.cpp

commit 98092bb26e12850b94ba27b3b1568be7244e4048
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 8 11:10:30 2011 -0700

    Keep this file here but don't put it in GPackage.mak
    
    Signed-off-by: Ann Almgren <asalmgren@lbl.gov>

Src/F_BaseLib/mt19937ar.f90

commit 329f995ff2adfbd01228e0bb65e50b72ea21e115
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 8 09:49:30 2011 -0700

    Include options for the Gottingen machines.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi
Tools/F_mk/GMakedefs.mak

commit a16fd652bfddc6d5a70d458bd82c4d3d10bac606
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 7 19:15:59 2011 -0700

    version/release info

BoxLib_Version.txt
Tools/C_scripts/gen_release_tarball.txt

commit b322708519e191d37f8594aaddd548dabda6c749
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 7 18:41:58 2011 -0700

    Add gslib files here to simplify distribution for ASCEM

Src/Extern/gslib/CMakeLists.txt
Src/Extern/gslib/acorni.f
Src/Extern/gslib/backtr.f
Src/Extern/gslib/beyond.f
Src/Extern/gslib/blue.f
Src/Extern/gslib/chknam.f
Src/Extern/gslib/chktitle.f
Src/Extern/gslib/cova3.f
Src/Extern/gslib/dlocate.f
Src/Extern/gslib/dpowint.f
Src/Extern/gslib/dsortem.f
Src/Extern/gslib/gauinv.f
Src/Extern/gslib/gcum.f
Src/Extern/gslib/getindx.f
Src/Extern/gslib/getz.f
Src/Extern/gslib/green.f
Src/Extern/gslib/hexa.f
Src/Extern/gslib/ksol.f
Src/Extern/gslib/ktsol.f
Src/Extern/gslib/locate.f
Src/Extern/gslib/nscore.f
Src/Extern/gslib/numtext.f
Src/Extern/gslib/ordrel.f
Src/Extern/gslib/picksupr.f
Src/Extern/gslib/powint.f
Src/Extern/gslib/psfill.f
Src/Extern/gslib/psline.f
Src/Extern/gslib/pstext.f
Src/Extern/gslib/rand.f
Src/Extern/gslib/red.f
Src/Extern/gslib/resc.f
Src/Extern/gslib/scal.f
Src/Extern/gslib/setrot.f
Src/Extern/gslib/setsupr.f
Src/Extern/gslib/sortem.f
Src/Extern/gslib/sqdist.f
Src/Extern/gslib/srchsupr.f
Src/Extern/gslib/strlen.f

commit 00834825b1ceaed39edbf631c20b01ed22fc6f5a
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 7 18:40:50 2011 -0700

    Add some amrdata files here as a temporary measure until amrvis available elsewhere

Src/Extern/amrdata/AmrData.H
Src/Extern/amrdata/AmrData.cpp
Src/Extern/amrdata/AmrvisConstants.H
Src/Extern/amrdata/CMakeLists.txt
Src/Extern/amrdata/DataServices.H
Src/Extern/amrdata/DataServices.cpp
Src/Extern/amrdata/FABUTIL_2D.F
Src/Extern/amrdata/FABUTIL_3D.F
Src/Extern/amrdata/Make.package

commit 35073eb8f00d83637d2c7f1d034d9cd008b51419
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 7 18:38:40 2011 -0700

    Add support for CMake builds

CMakeLists.txt
Src/CMakeLists.txt
Src/C_AMRLib/CMakeLists.txt
Src/C_BaseLib/CMakeLists.txt
Src/C_BoundaryLib/CMakeLists.txt
Src/F_BaseLib/CMakeLists.txt
Src/LinearSolvers/C_CellMG/CMakeLists.txt
Src/LinearSolvers/C_to_F_MG/CMakeLists.txt
Src/LinearSolvers/F_MG/CMakeLists.txt
Tools/CMake/CCSEConfigReport.cmake
Tools/CMake/CCSEOptions.cmake
Tools/CMake/CMakeParseArguments.cmake
Tools/CMake/ExampleBoxLibConfig.cmake
Tools/CMake/ExampleCMakeLists.txt_CCSEApp
Tools/CMake/PreprocessBoxLibFortran.cmake
Tools/CMake/TestManager.cmake
Tools/C_scripts/boxlib-build.sh

commit 5f65fa2a6ccc455e52eaeddff2b2d2a32be73a60
Merge: 25be55a57 1872ad5d5
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 7 18:34:43 2011 -0700

    Merge branch 'master' of /home/marc/src/CCSE/BoxLib

commit 25be55a5720ab3e923c3655d057f7cddc2e73f93
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 7 18:32:09 2011 -0700

    Add Utility.H

Src/C_AMRLib/SlabStat.cpp

commit 1872ad5d5b61ea1bcc98d75a092afba92c2d45b6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 6 09:51:38 2011 -0700

    Got rid of explicit copy constructors and copy assignment operators.
    Use the compiler generated ones.

Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/Orientation.H

commit 6bdd8ca145a028cf0da5ef0ed3f6870cb65507a4
Author: cmalone <malone@ucolick.org>
Date:   Tue Aug 30 15:04:33 2011 -0700

    get rid of all the *.mod files in the CWD
    
    Signed-off-by: lijewski <mjlijewski@lbl.gov>

Tools/C_mk/Make.Darwin

commit 05d6ea6c8518320d9fe0c1d3a98f8fc9f3573583
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 30 13:52:19 2011 -0700

    workd with USE_F90_MG=TRUE

Tests/LinearSolvers/ComparisonTest/GNUmakefile

commit 8c4b2719949fb36bc17c6bf7af213823423ff83e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 30 12:59:41 2011 -0700

    A wad of simplification and consolidation.
    Removed BL_USECLOSE -- always assume true.
    Removed BL_USEOLDREAD -- always assume false.
    Always use the ReadAndBcastFile() stuff whether or not USE_MPI=TRUE.
    Always use the fancy probin reader regardless of whether or not USE_MPI=TRUE.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Particles.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/VisMF.cpp

commit 4fc226e9c37a7661cc820e178a3c343c226edd52
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 30 09:03:02 2011 -0700

    Added Tutorials directory with first example: WaveEquation_C, a simple program that uses
    BoxLib stuff with the C++ make system to run a single-level wave equation evolution routine.

Tutorials/WaveEquation_C/GNUmakefile
Tutorials/WaveEquation_C/Make.package
Tutorials/WaveEquation_C/advance_2d.f90
Tutorials/WaveEquation_C/advance_3d.f90
Tutorials/WaveEquation_C/init_data_2d.f90
Tutorials/WaveEquation_C/init_data_3d.f90
Tutorials/WaveEquation_C/inputs_2d
Tutorials/WaveEquation_C/inputs_3d
Tutorials/WaveEquation_C/main.cpp
Tutorials/WaveEquation_C/writePlotFile.H
Tutorials/WaveEquation_C/writePlotFile.cpp

commit 9c85fdb6ad65d19f5b13369625f7f5e4f25b0902
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 29 14:51:27 2011 -0700

    Added Initialize()/Finalize() functions to ensure static variables are
    initialized properly.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 81cbb868c2e6012b6ab77502b3f668f72209f4fe
Merge: ccf6f7b20 2369ea7c6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Aug 26 16:12:38 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ccf6f7b203c878e2261386fd76527220f74a31e6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Aug 26 16:11:59 2011 -0700

    Chris' mod for macs

Tools/F_mk/GMakeMPI.mak

commit 51a9bfd921ad5d80f15621850cbb3d4927a8eae1
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Aug 26 16:11:37 2011 -0700

    Chris' mod for mac's

Tools/C_mk/Make.Darwin

commit 2369ea7c65aa91ee76cc747e7e0a9dae81c202a1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 26 16:11:27 2011 -0700

    0.0 -> 0.0d0 in a few places.

Src/C_AMRLib/INTERP_1D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/LinearSolvers/C_TensorMG/DV_2D.F

commit 782319319ecff0729dcee2b9a069df8c52558150
Author: Theodore Kisner <tskisner.public@gmail.com>
Date:   Thu Aug 25 15:58:55 2011 -0700

    Had to modify this commit because BoxLib.f90 was named FBoxLib.f90 in Ted's work and boxlib_f.f90 in Ann's work. We kept it as boxlib_f.f90.
    
    Old message: Rename BoxLib.f90 to FBoxLib.f90 to avoid name conflicts in the output object files when building outputs in the top level of the source tree.
    
    Signed-off-by: lijewski <mjlijewski@lbl.gov>

Src/F_BaseLib/GPackage.mak

commit da21ffe648c5028b4309d48ea73c0cd3ec437646
Author: Theodore Kisner <tskisner.public@gmail.com>
Date:   Thu Aug 25 15:15:03 2011 -0700

    Convert Cray vector merge functions to modern fortran merge syntax.
    
    Signed-off-by: lijewski <mjlijewski@lbl.gov>

Src/C_AMRLib/INTERP_1D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/LinearSolvers/C_CellMG/ABec_1D.F
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/LO_1D.F
Src/LinearSolvers/C_CellMG/LO_2D.F
Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/LP_1D.F
Src/LinearSolvers/C_CellMG/LP_2D.F
Src/LinearSolvers/C_CellMG/LP_3D.F
Src/LinearSolvers/C_TensorMG/DV_2D.F
Src/LinearSolvers/C_TensorMG/DV_3D4.F

commit 5de41c7e1794ed6f992b6b6fdd90cbd2a2f61e2f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 26 13:58:49 2011 -0700

    Removed some unused routines.

Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f

commit 2eea0ea5796552380e70cd4fc7222944b90b8063
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 26 10:48:51 2011 -0700

    Wrapped plotfile and checkpoint file timings in (verbose > 0).
    Also removed the probStartTime member from Amr.H.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 9481c869e2c173d5c2b11ff3cb8652b19d8423ec
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 25 15:16:41 2011 -0700

    Before these lines were commented out -- now they have been removed.

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 298a3086de930e3d3c1b293ef8cb9c08bd176016
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 25 15:13:51 2011 -0700

    1) Rename six files so they no longer have name conflicts with the C++ file.
    So ... box.f90 --> box_f.f90
           boxarray.f90 --> boxarray_f.f90
           cluster.f90 --> cluster_f.f90
           BoxLib.f90 --> boxlib_f.f90
           multifab.f90 --> multifab_f.f90
           particles.f90 --> particles_f.f90
    Note that this does not affect other files as these are included by module name, not file name.
    
    2) Also remove from F_MG/FParallelMG.mak the files which are in F_BaseLib/FParallel.mak

Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/box_f.f90
Src/F_BaseLib/boxarray_f.f90
Src/F_BaseLib/boxlib_f.f90
Src/F_BaseLib/cluster_f.f90
Src/F_BaseLib/multifab_f.f90
Src/F_BaseLib/particles_f.f90
Src/LinearSolvers/F_MG/FParallelMG.mak

commit b39c67c43d9bd443667b737eeb9c660998b56645
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 24 12:33:20 2011 -0700

    A simple commit to check that email notices are working.

Docs/GNUmakefile

commit f55d31b00b3e98fc25ab530415cb6e6e407b5f56
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 23 14:04:30 2011 -0700

    Update the GNUmakefile in Tests/LinearSolvers/ComparisonTest

Tests/LinearSolvers/ComparisonTest/GNUmakefile

commit 089a0b50e96ed0fecd703226ea6741a2b54686af
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 23 14:00:08 2011 -0700

    email push test 0.  v.

Tests/C_BaseLib/tVisMF.cpp

commit bc88ee6744323ad929f421326d53b1c2ac52d643
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 18 14:12:34 2011 -0700

    Quieted some warnings.

Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/ErrorList.cpp
Src/C_BaseLib/BoxLib.cpp

commit 4adfaa3b222ac6369cd42ac44b288098571163b3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 18 13:44:14 2011 -0700

    Cleaned up the Make stuff.
    Removed all hints of installing things since we don't do that anymore.

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules
Tools/C_scripts/install-sh

commit d83c6c2c7f4058e237edf893998933d1b9bf6167
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 18 13:23:14 2011 -0700

    Removed all .dsp stuff for generating Microsoft-compatible Makefiles.
    Also got rid of ckread.pl since we no longer generate tranfiles from
    ChemKin itself.

Tools/C_mk/Make.rules
Tools/C_scripts/ckread.pl
Tools/C_scripts/dsp.lib.mak
Tools/C_scripts/dsp.mak

commit f13aa0a7dba2262425f490164be2c56f845ad5ee
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 13:14:08 2011 -0700

    Fixed comments to refer to new directory structure.

Src/F_BaseLib/FParallelMG.mak

commit 97b765e7df9acbc9ca06f3d8f290b477bb19403e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 13:10:37 2011 -0700

    Make Tests/C_BaseLib and Tests/F_BaseLib both up to date.

Tests/C_BaseLib/GNUmakefile
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/mt19937ar.f90

commit 3264097b8e6de6c84a042090bd56c1ae3ec5a0e9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 13:03:39 2011 -0700

    This now compiles.

Tests/LinearSolvers/C_TensorMG/GNUmakefile

commit a79f09e35eeaa83533f011a414e919217457f625
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 13:01:56 2011 -0700

    Remove reference to iamrlib.

Tests/LinearSolvers/C_CellMG/GNUmakefile

commit 17ead3845e4184bc0d9d00358046be3eaac98fa3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 12:59:09 2011 -0700

    No more reference to fboxlib.

Tests/LinearSolvers/C_CellMG/main.cpp

commit 1f1d8621ab85a081d7780eea24f1ae2a1a4014d3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 12:58:13 2011 -0700

    Need a bunch of Mac* files, copied from IAMR/Source, to compile the macproj test.

Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/MACOPERATOR_2D.F
Tests/LinearSolvers/C_CellMG/MACOPERATOR_3D.F
Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H
Tests/LinearSolvers/C_CellMG/MACPROJ_2D.F
Tests/LinearSolvers/C_CellMG/MACPROJ_3D.F
Tests/LinearSolvers/C_CellMG/MacOpMacDrivers.H
Tests/LinearSolvers/C_CellMG/MacOperator.H
Tests/LinearSolvers/C_CellMG/MacOperator.cpp
Tests/LinearSolvers/C_CellMG/Make.package
Tests/LinearSolvers/C_CellMG/macprojTest.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 4a354f72e846fcb8d34ae4de564fbfee22dbffa0
Merge: 9bd48775e 3c6f2d0bc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 12:38:39 2011 -0700

    Merge branch 'master' of almgren@gamera:/usr/local/gitroot/BoxLib

commit 9bd48775efba69a33d0e3f8a993f73de532a47c6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 12:38:23 2011 -0700

    slight clean-up

Tests/LinearSolvers/ComparisonTest/main.cpp

commit 3c6f2d0bcb12c782af3ddd1f8fbdf047f3c163f7
Merge: 1cbd04d30 d49d32a18
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Aug 17 12:37:05 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d49d32a1893f2aa93341655a8e6788823d8e6ab8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 12:36:02 2011 -0700

    Dont need our own copies of MacBndry* -- they're in C_BoundaryLib.

Tests/LinearSolvers/ComparisonTest/MacBndry.H
Tests/LinearSolvers/ComparisonTest/MacBndry.cpp

commit 25f52d0263779327b79bb4aac3ceaa4bc3dea8e6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 12:33:48 2011 -0700

    Now compiles with F90 solvers turned on as well.

Tests/LinearSolvers/ComparisonTest/GNUmakefile
Tests/LinearSolvers/ComparisonTest/main.cpp

commit dfd4431bdea513b306b9f41a6887b3827de33d51
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 12:27:53 2011 -0700

    This now compiles with the new BoxLib format.

Tests/LinearSolvers/ComparisonTest/GNUmakefile
Tests/LinearSolvers/ComparisonTest/main.cpp

commit 305cea277cbb0ae6e8cab964423b275de1382a64
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 12:12:03 2011 -0700

    Changes to try to get this to compile.

Tests/LinearSolvers/ComparisonTest/GNUmakefile

commit 1cbd04d306cad2f598d56ebb2f87e65972a0b541
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Aug 17 11:00:33 2011 -0700

    Remove bibtex command

Docs/GNUmakefile

commit 77c09bc60dd1d14e55135bce9e51d1da2bad0ea3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 17 08:32:12 2011 -0700

    Removed a couple weird Crutchfield scripts.

Tests/LinearSolvers/C_TensorMG/doit
Tests/LinearSolvers/C_TensorMG/dotest

commit 9d3e82d48c27dadf74c2805e1dcff91f4dc6c699
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 17 08:22:21 2011 -0700

    Removed instances of PROFILE={TRUE,FALSE} in GNUmakefiles.
    Left the PROFILE rule in Make.rules.

Tests/C_BaseLib/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_TensorMG/GNUmakefile
Tests/LinearSolvers/ComparisonTest/GNUmakefile
Tools/C_mk/Make.T3E
Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Convergence/GNUmakefile.temp
Tools/C_util/Statistics/GNUmakefile
Tools/C_util/ViewMF/GNUmakefile
Tools/C_util/dbgTools/GNUmakefile

commit 35c472835bf150c2bf1fe47a6337f80767177f96
Merge: 8b5f4329b c55a4fe5f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 17 08:10:59 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c55a4fe5fe536c12605f6adfdc6aeb34a8237404
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 16 20:59:36 2011 -0700

    PBOXLIB_HOME --> BOXLIB_HOME

Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_TensorMG/GNUmakefile
Tests/LinearSolvers/ComparisonTest/GNUmakefile

commit fd66beae8f556694c3022baceb25568439f0f25f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 16 20:58:33 2011 -0700

    1) PBOXLIB_HOME --> BOXLIB_HOME
    2) Get rid of ComparisonTest from Src/LinearSolvers/C_CellMG  -- it is already in Tests/LinearSolvers/C_CellMG

Src/LinearSolvers/C_CellMG/ComparisonTest/COEF_3D.F
Src/LinearSolvers/C_CellMG/ComparisonTest/COEF_F.H
Src/LinearSolvers/C_CellMG/ComparisonTest/GNUmakefile
Src/LinearSolvers/C_CellMG/ComparisonTest/MacBndry.H
Src/LinearSolvers/C_CellMG/ComparisonTest/MacBndry.cpp
Src/LinearSolvers/C_CellMG/ComparisonTest/Make.package
Src/LinearSolvers/C_CellMG/ComparisonTest/inputs.3d
Src/LinearSolvers/C_CellMG/ComparisonTest/main.cpp

commit 615dc20009304dbfe967a1a5a9d09e884ebbda3f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 16 20:53:16 2011 -0700

    PBOXLIB_HOME --> BOXLIB_HOME

Tests/C_BaseLib/GNUmakefile

commit 462d9e780160e396f564e856fe8ab374ba4d3a7d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 16 20:51:40 2011 -0700

    Change PBOXLIB_HOME --> BOXLIB_HOME

Src/LinearSolvers/F_MG/GPackage.mak
Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Convergence/GNUmakefile.temp
Tools/C_util/Statistics/GNUmakefile
Tools/C_util/ViewMF/GNUmakefile
Tools/C_util/dbgTools/GNUmakefile

commit 5db4f008d15744ac3129d520154bc420c1bc5513
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 16 20:48:37 2011 -0700

    PBOXLIB_HOME --> BOXLIB_HOME.

Tools/C_mk/Make.IRIX64
Tools/C_mk/Make.T3E
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 9efd70f60e9aacb6546b7cb575f1b123d8846777
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 16 18:18:00 2011 -0700

    Better for new BoxLib structure...

Tools/F_mk/GMakedefs.mak

commit 8b5f4329bfb9a046bfcd4aaab7653040c7dce06f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 16 16:34:11 2011 -0700

    No longer keeping around the POSIX Pthread stuff.

Src/C_BaseLib/Thread.H

commit 43b1440f7c8003b3d2e9920ba7f4b6475b4b3c57
Merge: a735b5a94 2b05c2450
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 16 16:25:05 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a735b5a940f301744fde675f7834da76ce20d6e3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 16 16:24:09 2011 -0700

    Removed all BL_PROFILE stuff.
    Left a bare-boned Profiling.H so code that still have BL_PROFILE stuff
    in them will compile.
    Also got rid of the POSIX Pthread stuff.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/BLMpi.cpp
Src/C_BaseLib/BLMpi.w
Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.cpp
Src/C_BoundaryLib/FabSet.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp
Tests/C_BaseLib/tMinCommCosts.cpp

commit 2b05c2450554b1ebe1ab9aa01c26afba0cfe69a7
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Aug 16 15:36:49 2011 -0700

    progress toward getting fParallel stuff to compile

Tools/F_mk/GMakedefs.mak

commit d58c411426abb80c2b6083d442920581f7a7d4f2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 16 15:06:03 2011 -0700

    Removed all references to fParallel/extern/mpi, BL_USE_FARG, etc -- these were only
    needed for hive and harmonic.

Tools/F_mk/GMakeMPI.mak

commit 2d43f80b3fc47cf8f38521bbef01b24941f294f8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 16 14:11:51 2011 -0700

    Change FPARALLEL --> . or ..  (i.e. fix paths)

Tools/F_mk/GMakedefs.mak

commit 0134d9bbb811e0d502dfd41e0ee151baf2da6330
Author: mjlijewski@lbl.gov <lijewski@lijewski.lbl.gov>
Date:   Tue Aug 16 08:56:28 2011 -0700

    Cleaned up some header file comments.
    Removed some embedded TeX and turned it into text.

Src/C_BoundaryLib/InterpBndryData.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_TensorMG/DivVis.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H

commit d030d176dcabe00887e9c0f0950c2905861ce0e1
Author: mjlijewski@lbl.gov <lijewski@lijewski.lbl.gov>
Date:   Mon Aug 15 15:51:28 2011 -0700

    Removed all .cvsignore files.
    Use .git/info/exclude instead.

Src/C_AMRLib/.cvsignore
Src/C_BaseLib/.cvsignore
Src/C_BoundaryLib/.cvsignore
Src/LinearSolvers/C_CellMG/.cvsignore
Src/LinearSolvers/C_NodalMG/.cvsignore
Tests/C_BaseLib/.cvsignore
Tests/F_BaseLib/.cvsignore
Tests/LinearSolvers/C_CellMG/.cvsignore
Tests/LinearSolvers/F_MG/.cvsignore
Tools/C_util/wrappergen/.cvsignore

commit e941baef6a423134827309678c40e7578acf23c9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Aug 15 15:32:10 2011 -0700

    Moved these to Tests/LinearSolvers/C_NodalMG/test_grids.

Src/LinearSolvers/C_NodalMG/tests/3d_4_level.grids
Src/LinearSolvers/C_NodalMG/tests/gr.11
Src/LinearSolvers/C_NodalMG/tests/gr.15
Src/LinearSolvers/C_NodalMG/tests/gr.16
Src/LinearSolvers/C_NodalMG/tests/gr.19
Src/LinearSolvers/C_NodalMG/tests/gr.19l3
Src/LinearSolvers/C_NodalMG/tests/gr.19s2
Src/LinearSolvers/C_NodalMG/tests/gr.19s2.4
Src/LinearSolvers/C_NodalMG/tests/gr.19s4
Src/LinearSolvers/C_NodalMG/tests/gr.19s4.1
Src/LinearSolvers/C_NodalMG/tests/gr.292.11
Src/LinearSolvers/C_NodalMG/tests/gr.292.25
Src/LinearSolvers/C_NodalMG/tests/gr.7
Src/LinearSolvers/C_NodalMG/tests/gr.8
Src/LinearSolvers/C_NodalMG/tests/gr.8a
Src/LinearSolvers/C_NodalMG/tests/gr.ann.1
Src/LinearSolvers/C_NodalMG/tests/gr.sstanley.1
Src/LinearSolvers/C_NodalMG/tests/gr0
Src/LinearSolvers/C_NodalMG/tests/gr0a
Src/LinearSolvers/C_NodalMG/tests/gr0b
Src/LinearSolvers/C_NodalMG/tests/gr1
Src/LinearSolvers/C_NodalMG/tests/gr1mike.thin
Src/LinearSolvers/C_NodalMG/tests/gr1rick2
Src/LinearSolvers/C_NodalMG/tests/gr2
Src/LinearSolvers/C_NodalMG/tests/gr2.0
Src/LinearSolvers/C_NodalMG/tests/gr2.1
Src/LinearSolvers/C_NodalMG/tests/gr2.inf
Src/LinearSolvers/C_NodalMG/tests/gr2a2
Src/LinearSolvers/C_NodalMG/tests/gr2a4
Src/LinearSolvers/C_NodalMG/tests/gr2ann
Src/LinearSolvers/C_NodalMG/tests/gr2ann.l0
Src/LinearSolvers/C_NodalMG/tests/gr2ann.l1
Src/LinearSolvers/C_NodalMG/tests/gr2ann.l2
Src/LinearSolvers/C_NodalMG/tests/gr2ann.p1
Src/LinearSolvers/C_NodalMG/tests/gr2ann.p2
Src/LinearSolvers/C_NodalMG/tests/gr2ann.p3
Src/LinearSolvers/C_NodalMG/tests/gr2ann.p4
Src/LinearSolvers/C_NodalMG/tests/gr2ann.p5
Src/LinearSolvers/C_NodalMG/tests/gr2ann.p6
Src/LinearSolvers/C_NodalMG/tests/gr2b
Src/LinearSolvers/C_NodalMG/tests/gr2c
Src/LinearSolvers/C_NodalMG/tests/gr2cross
Src/LinearSolvers/C_NodalMG/tests/gr2d
Src/LinearSolvers/C_NodalMG/tests/gr2d2
Src/LinearSolvers/C_NodalMG/tests/gr2d4
Src/LinearSolvers/C_NodalMG/tests/gr2dave
Src/LinearSolvers/C_NodalMG/tests/gr2e
Src/LinearSolvers/C_NodalMG/tests/gr2f
Src/LinearSolvers/C_NodalMG/tests/gr2g
Src/LinearSolvers/C_NodalMG/tests/gr2h
Src/LinearSolvers/C_NodalMG/tests/gr2mike
Src/LinearSolvers/C_NodalMG/tests/gr2mike1
Src/LinearSolvers/C_NodalMG/tests/gr2mike2
Src/LinearSolvers/C_NodalMG/tests/gr2mike3
Src/LinearSolvers/C_NodalMG/tests/gr2r1
Src/LinearSolvers/C_NodalMG/tests/gr2r2
Src/LinearSolvers/C_NodalMG/tests/gr2r3
Src/LinearSolvers/C_NodalMG/tests/gr3.rz
Src/LinearSolvers/C_NodalMG/tests/gr3a
Src/LinearSolvers/C_NodalMG/tests/gr3ann
Src/LinearSolvers/C_NodalMG/tests/gr3ann2
Src/LinearSolvers/C_NodalMG/tests/gr3b
Src/LinearSolvers/C_NodalMG/tests/gr3c
Src/LinearSolvers/C_NodalMG/tests/gr3mike
Src/LinearSolvers/C_NodalMG/tests/gr3mike.3
Src/LinearSolvers/C_NodalMG/tests/gr3rick
Src/LinearSolvers/C_NodalMG/tests/gr3rick2
Src/LinearSolvers/C_NodalMG/tests/gr4
Src/LinearSolvers/C_NodalMG/tests/gr4level
Src/LinearSolvers/C_NodalMG/tests/gt.32
Src/LinearSolvers/C_NodalMG/tests/gt.bill1
Src/LinearSolvers/C_NodalMG/tests/gt.inputs.3d.spin.grids
Src/LinearSolvers/C_NodalMG/tests/gt.jbb.1
Src/LinearSolvers/C_NodalMG/tests/gt.sas
Src/LinearSolvers/C_NodalMG/tests/gt.scott.1
Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_2.32
Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_2.64
Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_3
Src/LinearSolvers/C_NodalMG/tests/gt0
Src/LinearSolvers/C_NodalMG/tests/gt010
Src/LinearSolvers/C_NodalMG/tests/gt012
Src/LinearSolvers/C_NodalMG/tests/gt016
Src/LinearSolvers/C_NodalMG/tests/gt05
Src/LinearSolvers/C_NodalMG/tests/gt1
Src/LinearSolvers/C_NodalMG/tests/gt12
Src/LinearSolvers/C_NodalMG/tests/gt12.2
Src/LinearSolvers/C_NodalMG/tests/gt12.3
Src/LinearSolvers/C_NodalMG/tests/gt2
Src/LinearSolvers/C_NodalMG/tests/gt2t1
Src/LinearSolvers/C_NodalMG/tests/gt2t3
Src/LinearSolvers/C_NodalMG/tests/gt2t4
Src/LinearSolvers/C_NodalMG/tests/gt3
Src/LinearSolvers/C_NodalMG/tests/gt3ann
Src/LinearSolvers/C_NodalMG/tests/gt3ann2
Src/LinearSolvers/C_NodalMG/tests/gt4
Src/LinearSolvers/C_NodalMG/tests/gt4s2
Src/LinearSolvers/C_NodalMG/tests/gt4s2.4.4
Src/LinearSolvers/C_NodalMG/tests/gt4s2a
Src/LinearSolvers/C_NodalMG/tests/gt4s4
Src/LinearSolvers/C_NodalMG/tests/gt4s4.2.4
Src/LinearSolvers/C_NodalMG/tests/gt4s4.4.2
Src/LinearSolvers/C_NodalMG/tests/gt5
Src/LinearSolvers/C_NodalMG/tests/gt5s2
Src/LinearSolvers/C_NodalMG/tests/gt5s4
Src/LinearSolvers/C_NodalMG/tests/gt6
Src/LinearSolvers/C_NodalMG/tests/gt6s
Src/LinearSolvers/C_NodalMG/tests/gt6s2
Src/LinearSolvers/C_NodalMG/tests/gt6s4
Src/LinearSolvers/C_NodalMG/tests/gt7a
Src/LinearSolvers/C_NodalMG/tests/gt7aa
Src/LinearSolvers/C_NodalMG/tests/gt8
Src/LinearSolvers/C_NodalMG/tests/gt8a
Src/LinearSolvers/C_NodalMG/tests/gt8b
Src/LinearSolvers/C_NodalMG/tests/gt8c
Src/LinearSolvers/C_NodalMG/tests/gt8ms2
Src/LinearSolvers/C_NodalMG/tests/gtbig
Src/LinearSolvers/C_NodalMG/tests/gtbig2
Src/LinearSolvers/C_NodalMG/tests/gtbig3
Src/LinearSolvers/C_NodalMG/tests/gtbig4
Src/LinearSolvers/C_NodalMG/tests/gtbig5
Src/LinearSolvers/C_NodalMG/tests/gtclearlarge
Src/LinearSolvers/C_NodalMG/tests/gtclearsmall
Src/LinearSolvers/C_NodalMG/tests/gtgrav2
Src/LinearSolvers/C_NodalMG/tests/gtgrav4
Src/LinearSolvers/C_NodalMG/tests/gtjbb
Src/LinearSolvers/C_NodalMG/tests/gtjbb2
Src/LinearSolvers/C_NodalMG/tests/gtpfail
Src/LinearSolvers/C_NodalMG/tests/gtrick

commit 50a44ca32be5e074daacc3ff28db8d4fcbfa13a0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Aug 15 15:29:05 2011 -0700

    Move test directories out of Src.

Src/LinearSolvers/C_CellMG/Test/.cvsignore
Src/LinearSolvers/C_CellMG/Test/COEF_2D.F
Src/LinearSolvers/C_CellMG/Test/COEF_3D.F
Src/LinearSolvers/C_CellMG/Test/COEF_F.H
Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/Make.package
Src/LinearSolvers/C_CellMG/Test/Palette
Src/LinearSolvers/C_CellMG/Test/amrvis.defaults
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_19boxes
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_256squared
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_b
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_c
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_b
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_c
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3x2
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_big
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_b
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_c
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_d
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_e
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_small_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_small_b
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_b
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_c
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_d
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_128cubed
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_256cubed
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_2boxes_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_2x3x4
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_512cubed
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_big
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_b
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_c
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_mac_tst
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_shiftedUp
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_small_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_stack_a
Src/LinearSolvers/C_CellMG/Test/grids/grids.15456.REMOVED.git-id
Src/LinearSolvers/C_CellMG/Test/grids/grids.213
Src/LinearSolvers/C_CellMG/Test/grids/grids.25600.REMOVED.git-id
Src/LinearSolvers/C_CellMG/Test/grids/grids.5034
Src/LinearSolvers/C_CellMG/Test/grids/in.2_19boxes
Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared
Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3x2
Src/LinearSolvers/C_CellMG/Test/grids/in.2_big
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_d
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_e
Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_d
Src/LinearSolvers/C_CellMG/Test/grids/in.2per_2x2_c
Src/LinearSolvers/C_CellMG/Test/grids/in.3_128cubed
Src/LinearSolvers/C_CellMG/Test/grids/in.3_256cubed
Src/LinearSolvers/C_CellMG/Test/grids/in.3_2boxes_a
Src/LinearSolvers/C_CellMG/Test/grids/in.3_2x3x4
Src/LinearSolvers/C_CellMG/Test/grids/in.3_512cubed
Src/LinearSolvers/C_CellMG/Test/grids/in.3_big
Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_a
Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_b
Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_c
Src/LinearSolvers/C_CellMG/Test/grids/in.3_mac_tst
Src/LinearSolvers/C_CellMG/Test/grids/in.3_shiftedUp
Src/LinearSolvers/C_CellMG/Test/grids/in.3_small_a
Src/LinearSolvers/C_CellMG/Test/grids/in.3_stack_a
Src/LinearSolvers/C_CellMG/Test/grids/in.3per_2x3x4
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.15456
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.25600
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034
Src/LinearSolvers/C_CellMG/Test/inputs.2d
Src/LinearSolvers/C_CellMG/Test/inputs.3d
Src/LinearSolvers/C_CellMG/Test/macprojTest.cpp
Src/LinearSolvers/C_CellMG/Test/main.cpp
Src/LinearSolvers/C_CellMG/Test/vpramps.dat
Src/LinearSolvers/C_NodalMG/Test/files.2d
Src/LinearSolvers/C_NodalMG/Test/files.3d
Src/LinearSolvers/C_NodalMG/Test/gt_breaks_27pt
Src/LinearSolvers/C_NodalMG/Test/inputs
Src/LinearSolvers/C_NodalMG/Test/proj.cpp
Src/LinearSolvers/C_TensorMG/Test/GNUmakefile
Src/LinearSolvers/C_TensorMG/Test/Make.package
Src/LinearSolvers/C_TensorMG/Test/Palette
Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.H
Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp
Src/LinearSolvers/C_TensorMG/Test/amrvis.defaults
Src/LinearSolvers/C_TensorMG/Test/doit
Src/LinearSolvers/C_TensorMG/Test/dotest
Src/LinearSolvers/C_TensorMG/Test/grids/gr.3_2x3x4
Src/LinearSolvers/C_TensorMG/Test/grids/gr16.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr16x8.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr2D
Src/LinearSolvers/C_TensorMG/Test/grids/gr32.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr32x8.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr64.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr8.dog
Src/LinearSolvers/C_TensorMG/Test/inputs
Src/LinearSolvers/C_TensorMG/Test/inputs2D
Src/LinearSolvers/C_TensorMG/Test/inputs3D
Src/LinearSolvers/C_TensorMG/Test/inputs8
Src/LinearSolvers/C_TensorMG/Test/main_2D.F
Src/LinearSolvers/C_TensorMG/Test/main_3D.F
Src/LinearSolvers/C_TensorMG/Test/main_F.H
Src/LinearSolvers/C_TensorMG/Test/probin
Src/LinearSolvers/C_TensorMG/Test/testVI.cpp
Src/LinearSolvers/C_TensorMG/Test/vpramps.dat

commit 54ed991765c9d5afcbaa157f7d90c9fc369cae64
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Aug 15 15:27:19 2011 -0700

    This test directory is now in Tests/F_BaseLib.

Src/F_BaseLib/test/.cvsignore
Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/ball_def.14656
Src/F_BaseLib/test/conn_defs
Src/F_BaseLib/test/def_knapsack.out
Src/F_BaseLib/test/fornberg_weights.f90
Src/F_BaseLib/test/inputs.domain
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/makefile
Src/F_BaseLib/test/t_bl_prof.f90
Src/F_BaseLib/test/t_bx.f90
Src/F_BaseLib/test/t_bxasc.f90
Src/F_BaseLib/test/t_cls.f90
Src/F_BaseLib/test/t_knapsack.f90
Src/F_BaseLib/test/t_main.f90
Src/F_BaseLib/test/t_particles.f90

commit 754866e8bb1152b0f6a10a5e2c369b887474d994
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Aug 15 15:26:16 2011 -0700

    This test directory is now in Tests/C_BaseLib.

Src/C_BaseLib/test/.cvsignore
Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/ba.15456.REMOVED.git-id
Src/C_BaseLib/test/ba.15784.REMOVED.git-id
Src/C_BaseLib/test/ba.213
Src/C_BaseLib/test/ba.23925.REMOVED.git-id
Src/C_BaseLib/test/ba.25600.REMOVED.git-id
Src/C_BaseLib/test/ba.3865
Src/C_BaseLib/test/ba.5034
Src/C_BaseLib/test/ba.60
Src/C_BaseLib/test/ba.95860.REMOVED.git-id
Src/C_BaseLib/test/ba.mac.294
Src/C_BaseLib/test/mt19937int.out
Src/C_BaseLib/test/t8BIT.cpp
Src/C_BaseLib/test/tBA.cpp
Src/C_BaseLib/test/tCArena.cpp
Src/C_BaseLib/test/tDM.cpp
Src/C_BaseLib/test/tDir.cpp
Src/C_BaseLib/test/tFAC.cpp
Src/C_BaseLib/test/tFB.cpp
Src/C_BaseLib/test/tMF.cpp
Src/C_BaseLib/test/tMinCommCosts.cpp
Src/C_BaseLib/test/tParmParse.cpp
Src/C_BaseLib/test/tRan.cpp
Src/C_BaseLib/test/tVisMF.cpp
Src/C_BaseLib/test/tVisMF2.cpp
Src/C_BaseLib/test/tread.cpp

commit 577d5fbad921db7ba48c60fcac3e12350983b17e
Author: mjlijewski@lbl.gov <lijewski@lijewski.lbl.gov>
Date:   Mon Aug 15 14:56:47 2011 -0700

    Removed all Doc++ junk.
    Also removed some extraneous GNUmakefiles.
    Reformatted some stuff to make it easier to read.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/BCRec.H
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/Derive.H
Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/LevelBld.H
Src/C_AMRLib/SlabStat.H
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StationData.cpp
Src/C_AMRLib/TagBox.H
Src/C_BaseLib/Arena.H
Src/C_BaseLib/Array.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BLassert.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/CArena.H
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FPC.H
Src/C_BaseLib/FPC.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/Looping.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/REAL.H
Src/C_BaseLib/RealBox.H
Src/C_BaseLib/SPACE.H
Src/C_BaseLib/SPACE_F.H
Src/C_BaseLib/Thread.H
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/docxx_squish.sty
Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BoundCond.H
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/Mask.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/GNUmakefile
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_TensorMG/DivVis.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H

commit f473c0d8b25cee54246f1646706325f4ccfd59c5
Author: mjlijewski@lbl.gov <lijewski@lijewski.lbl.gov>
Date:   Mon Aug 15 12:11:54 2011 -0700

    Removed old CVS embedded version strings.

Src/C_AMRLib/FLUXREG_2D.F
Src/C_BaseLib/BLParmParse_F.f
Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/t8BIT.cpp
Src/C_BaseLib/test/tCArena.cpp
Src/C_BaseLib/test/tDir.cpp
Src/C_BaseLib/test/tFAC.cpp
Src/C_BaseLib/test/tFB.cpp
Src/C_BaseLib/test/tMF.cpp
Src/C_BaseLib/test/tParmParse.cpp
Src/C_BaseLib/test/tVisMF.cpp
Src/C_BaseLib/test/tread.cpp
Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/ppm_util_c.c
Src/F_BaseLib/timer_c.c
Src/LinearSolvers/C_CellMG/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/Make.package
Src/LinearSolvers/C_CellMG/Test/macprojTest.cpp
Src/LinearSolvers/C_CellMG/Test/main.cpp
Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 0f525b53e52c5e7eeda826d7f736525c905b5e74
Author: mjlijewski@lbl.gov <lijewski@lijewski.lbl.gov>
Date:   Mon Aug 15 11:26:00 2011 -0700

    Removed BLVERSION.H file.

Src/C_BaseLib/BLVERSION.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/Make.package

commit 2af0139f0dd53013343b205900ab6abf1d7f513b
Author: mjlijewski@lbl.gov <lijewski@lijewski.lbl.gov>
Date:   Mon Aug 15 11:18:02 2011 -0700

    Removed some WorkQueue and Thread stuff.
    All the WorkQueue stuff is gone.
    Most of the POSIX Thread stuff is gone, but not the files themselves.
    BLProfiler still used the THread stuff.

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/BLWorkQueue.cpp
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/WorkQueue.H
Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/tProfiler.cpp
Src/C_BaseLib/test/tWorkQueue.cpp
Src/LinearSolvers/C_CellMG/ComparisonTest/main.cpp
Src/LinearSolvers/C_CellMG/Test/macprojTest.cpp
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/tProfiler.cpp
Tests/C_BaseLib/tWorkQueue.cpp

commit ae458c259904afec5ea81bebbcc3124f170b49d0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:55:47 2011 -0700

    Remove all Banner.html

commit f70616485b4c1ca10a7f40a0e93814e7e114cb01
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:54:32 2011 -0700

    Remove cvs tags.

Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/t8BIT.cpp
Tests/C_BaseLib/tCArena.cpp
Tests/C_BaseLib/tDir.cpp
Tests/C_BaseLib/tFAC.cpp
Tests/C_BaseLib/tFB.cpp
Tests/C_BaseLib/tMF.cpp
Tests/C_BaseLib/tParmParse.cpp
Tests/C_BaseLib/tVisMF.cpp
Tests/C_BaseLib/tread.cpp

commit aed27a28da2f426b20b50122e1c621c3ef87a8b3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:52:51 2011 -0700

    Removed cvs tags.

Src/C_BaseLib/Arena.H
Src/C_BaseLib/Arena.cpp
Src/C_BaseLib/Array.H
Src/C_BaseLib/ArrayLim.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BArena.cpp
Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BLVERSION.H
Src/C_BaseLib/BLWorkQueue.cpp
Src/C_BaseLib/BLassert.H
Src/C_BaseLib/BLutil_F.f
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/CONSTANTS.H
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FPC.H
Src/C_BaseLib/FPC.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/Looping.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/Orientation.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/REAL.H
Src/C_BaseLib/RealBox.H
Src/C_BaseLib/RealBox.cpp
Src/C_BaseLib/SPACE.H
Src/C_BaseLib/SPACE_F.H
Src/C_BaseLib/Thread.H
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/UseCount.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/WorkQueue.H
Src/C_BaseLib/ccse-mpi.H

commit c0afd4c2f8f63c6ca97e233e08fe7e59be45bdf2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:47:39 2011 -0700

    Remove cvs tags.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/BoundCond.H
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp
Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F
Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F
Src/C_BoundaryLib/INTERPBNDRYDATA_F.H
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp
Src/C_BoundaryLib/LO_BCTYPES.H
Src/C_BoundaryLib/LO_UTIL.F
Src/C_BoundaryLib/MacBndry.cpp
Src/C_BoundaryLib/Mask.H
Src/C_BoundaryLib/Mask.cpp

commit b99c93e70f30e9030966c18c080ab691b01ef9f0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:45:28 2011 -0700

    Remove cvs tags.

Src/C_AMRLib/ARRAYLIM_1D.F
Src/C_AMRLib/ARRAYLIM_2D.F
Src/C_AMRLib/ARRAYLIM_3D.F
Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/AuxBoundaryData.cpp
Src/C_AMRLib/BCRec.H
Src/C_AMRLib/BCRec.cpp
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/DatasetClient.H
Src/C_AMRLib/DatasetClient.cpp
Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/ErrorList.cpp
Src/C_AMRLib/FILCC_1D.F
Src/C_AMRLib/FILCC_2D.F
Src/C_AMRLib/FILCC_3D.F
Src/C_AMRLib/FLUSH_F.H
Src/C_AMRLib/FLUXREG_1D.F
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/LevelBld.H
Src/C_AMRLib/MAKESLICE_3D.F
Src/C_AMRLib/MAKESLICE_F.H
Src/C_AMRLib/Make.package
Src/C_AMRLib/PROB_AMR_F.H
Src/C_AMRLib/SLABSTAT_1D.F
Src/C_AMRLib/SLABSTAT_2D.F
Src/C_AMRLib/SLABSTAT_3D.F
Src/C_AMRLib/SLABSTAT_F.H
Src/C_AMRLib/SlabStat.H
Src/C_AMRLib/SlabStat.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp
Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 0f2ddc8ed078ebf4edf06f5ce11aec511e3b6eae
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:39:15 2011 -0700

    Removing cvs tags.

Src/LinearSolvers/C_TensorMG/DivVis.H
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/DivVis_F.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLO_2D.F
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp
Src/LinearSolvers/C_TensorMG/Make.package

commit d5a76c45c1d62123180f13c03c634d573e029f3b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:28:11 2011 -0700

    Remove cvs tags.

Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/ABec_1D.F
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/ABec_F.H
Src/LinearSolvers/C_CellMG/ABec_UTIL.F
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/CG_2D.F
Src/LinearSolvers/C_CellMG/CG_3D.F
Src/LinearSolvers/C_CellMG/CG_F.H
Src/LinearSolvers/C_CellMG/LO_2D.F
Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/LO_F.H
Src/LinearSolvers/C_CellMG/LP_2D.F
Src/LinearSolvers/C_CellMG/LP_3D.F
Src/LinearSolvers/C_CellMG/LP_F.H
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MG_2D.F
Src/LinearSolvers/C_CellMG/MG_3D.F
Src/LinearSolvers/C_CellMG/MG_F.H
Src/LinearSolvers/C_CellMG/Make.package
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_CellMG/lo_bctypes.fi
Src/LinearSolvers/C_NodalMG/Make.package

commit 0913989631f878eb8f302c8dac508f3636ded639
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:26:58 2011 -0700

    Deleted Banner and  removed CVS Id's from other files.

commit fd67c03dcf1a0e696f0d3e6c30da84876bfd23fc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:18:45 2011 -0700

    Remove reference to FBOXLIB_HOME.

Src/LinearSolvers/C_to_F_MG/Make.package

commit df8ccd217cf847d659ccffa89003e218a11f99d1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 14:51:36 2011 -0700

    Fix $(TOP) --> $(PBOXLIB_HOME) for Tools/...

Tools/C_mk/Make.rules

commit 8cf56858f1ac3a21866829e1f8dd226d22f2538e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 14:48:42 2011 -0700

    Fix the paths and names of mk and scripts

Tools/C_mk/Make.IRIX64
Tools/C_mk/Make.T3E
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit cfb2885f4d45045397346476b244d7f087a0e93f
Author: Ann Almgren <almgren@gamera.lbl.gov>
Date:   Fri Aug 12 19:32:57 2011 -0700

    changed script

Tools/C_mk/Make.rules

commit 448215f1a389a95a35b9cd1f050d92a061879f47
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 12 19:28:33 2011 -0700

    changed script location

Tools/C_mk/Make.rules

commit 1a787ad15cc9f726db9ccff460503726efdab63e
Author: Ann Almgren <almgren@gamera.lbl.gov>
Date:   Fri Aug 12 18:57:18 2011 -0700

    Needed to fix the paths for mk and scripts.

Tools/C_mk/Make.IRIX64
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 7c211b6efd1d285c98f8ef98ad626fbeb22028bc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 12 18:17:15 2011 -0700

    Modifying C_mk/Make* to reflect the new path for C_mk

Tools/C_mk/Make.IRIX64
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 746e104f29eafbfe5a60074748de932ba2804872
Author: almgren <almgren>
Date:   Thu Aug 11 13:47:16 2011 +0000

    This now includes the particles.

Src/C_AMRLib/Make.package

commit b03c56306bfe14888b8430f4a6ccb19cfc4c769f
Author: almgren <almgren>
Date:   Wed Aug 10 22:11:31 2011 +0000

    Fix oops.

Src/C_BaseLib/Make.package

commit 5d9abf01a75ed8d085475879512dbeb3620b3716
Author: ajnonaka <ajnonaka>
Date:   Wed Aug 10 20:33:52 2011 +0000

    added support for Intel12 on hopper

Tools/F_mk/comps/Linux_intel.mak

commit 7e325f4ec111937a02367406f118da46617b8268
Author: almgren <almgren>
Date:   Wed Aug 10 20:19:41 2011 +0000

    Remove RealBox, CoordSys and Geometry stuff.

Src/C_BoundaryLib/Make.package

commit ce4223dc5a93853a220423968e0a80925da9661d
Author: almgren <almgren>
Date:   Wed Aug 10 20:18:57 2011 +0000

    Added RealBox, CoordSys, Geometry stuff.

Src/C_BaseLib/Make.package

commit 796921e14c27405afcfe87afb910952420679076
Author: almgren <almgren>
Date:   Wed Aug 10 19:40:14 2011 +0000

    Remove reference to Minion stencil in nodal stencil.

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 1c30afd90d6c7cb41edcc0094fe4be596df45231
Author: almgren <almgren>
Date:   Wed Aug 10 19:27:09 2011 +0000

    Comment out all SPARSKIT files since we no longer build in the sparse solver capability.

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 4fbebe8a2bba7917dcc459d09626482fb30eaeb5
Author: lijewski <lijewski>
Date:   Tue Aug 9 21:47:18 2011 +0000

    more Initialize()/Finalize() foo fah

Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit a84a627647a350b9e41b9cfba137d939bd22ae86
Author: lijewski <lijewski>
Date:   Tue Aug 9 21:32:45 2011 +0000

    added clear() to DeriveList

Src/C_AMRLib/Derive.H

commit 052a82345c32cf5cacfef7fa47edf666172e8591
Author: lijewski <lijewski>
Date:   Tue Aug 9 16:36:54 2011 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp

commit 2f343ae655cd49c2e5f83605dc05fa1bb0d08638
Author: lijewski <lijewski>
Date:   Tue Aug 9 16:30:16 2011 +0000

    fix to clear(); have to also do a resize(0) to fully clear a StateDescriptorList

Src/C_AMRLib/StateDescriptor.cpp

commit dfce75119ac2c3acb9a9b06cf495dd6f71bbee7a
Author: lijewski <lijewski>
Date:   Tue Aug 9 15:51:53 2011 +0000

    yet more work on Initialize()/Finalize()

Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit 70b700c75802f5335e7f0c6f85375a19cc63c700
Author: lijewski <lijewski>
Date:   Tue Aug 9 00:00:01 2011 +0000

    yet more work on Initialize()/Finalize()

Src/C_BaseLib/Arena.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp

commit aa25a6789e0a22b92fd55a9576edae09d886e457
Author: lijewski <lijewski>
Date:   Mon Aug 8 21:23:34 2011 +0000

    more work on Initialize()/Finalize()

Src/C_BaseLib/BLWorkQueue.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp

commit 3576dd57b123a14aa1721e64ac737bf2e19c0ca0
Author: lijewski <lijewski>
Date:   Mon Aug 8 20:47:45 2011 +0000

    more work on Initialize()/Finalize()

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 0a185b8eea4f1d4347f9f2abe87607dce9be9ed5
Author: lijewski <lijewski>
Date:   Mon Aug 8 20:37:25 2011 +0000

    more work on Initialize()/Finalize()

Src/C_AMRLib/Amr.cpp

commit 59c2fffcebec595aeed8b6469d85f6776bb51e37
Author: lijewski <lijewski>
Date:   Mon Aug 8 17:24:24 2011 +0000

    put 'initialized' into unnamed namespace instead of static member

Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 64758c4cb5cf444646a4336459d2e23dae4d7cdd
Author: lijewski <lijewski>
Date:   Mon Aug 8 16:58:44 2011 +0000

    add clear() to ErrorList

Src/C_AMRLib/ErrorList.H

commit ecec93f42d402a179cd944a41538751b2a439f92
Author: lijewski <lijewski>
Date:   Sat Aug 6 02:57:14 2011 +0000

    turn on/off cache statistics with geometry.verbose

Src/C_BaseLib/Geometry.cpp

commit 39f08d3e873e3a03551de0c0f192c6da628de33a
Author: lijewski <lijewski>
Date:   Sat Aug 6 02:56:31 2011 +0000

    turn on/off cache statistics with fabarray.verbose

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit e6ad17efeb528c7af9f8c40259a52ff514e15e93
Author: almgren <almgren>
Date:   Sat Aug 6 00:34:08 2011 +0000

    Allow us to use DistributionMapping.v as well as DistributionMapping.verbose to control the verbosity.

Src/C_BaseLib/DistributionMapping.cpp

commit 8aec9a5c8c993a62489b337b05c024fd1c983e7a
Author: lijewski <lijewski>
Date:   Fri Aug 5 23:14:10 2011 +0000

    new way of doing Finalize()

Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit 9b50a56e40b735729ffc7c323c2f375ffa7ffd84
Author: lijewski <lijewski>
Date:   Fri Aug 5 22:56:49 2011 +0000

    new way of doing Finalize()

Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 55626e797bbf530e459372e02d17670998f5add4
Author: almgren <almgren>
Date:   Fri Aug 5 22:28:02 2011 +0000

    Needed ParmParse.H ...

Src/C_AMRLib/Particles.H

commit 419cac73379b4e7fad5a3e14440fad4ed2f0c75d
Author: lijewski <lijewski>
Date:   Fri Aug 5 22:21:16 2011 +0000

    some cleanup

Src/C_BoundaryLib/InterpBndryData.cpp

commit 6d7c94cb0d9336b4f0a65455265bafa5f91e12cf
Author: lijewski <lijewski>
Date:   Fri Aug 5 22:21:05 2011 +0000

    new way of doing BoxLib::Finalize()

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 419d3a60b8b3f2583d1d1a1bbdfa0d22d5997cd2
Author: lijewski <lijewski>
Date:   Fri Aug 5 22:20:28 2011 +0000

    BoxLib now maintains a stack of functions that should be called on BoxLib::Finalize().
    Initialization functions that set defaults or that build global data that needs to be
    cleared out on BoxLib::Finalize() should define a function of the form:
    void (fp) () that performs necessary cleanup, and then register those
    functions via BoxLib::ExecOnFinalize(fp).

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParmParse.cpp

commit ce8f5af4e8141aae67bffed6a6171e4b849bf681
Author: almgren <almgren>
Date:   Fri Aug 5 22:04:38 2011 +0000

    Allow a new type of ErrorFunc so that we can have different argument lists for the error tagging functions.

Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/ErrorList.cpp

commit c62073e5401f8f5ce541d2d10517f575acb28454
Author: lijewski <lijewski>
Date:   Thu Aug 4 21:13:49 2011 +0000

    more Initialize()/Finalize() foo fah

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.cpp

commit dabc57be25d4483e925ba3f667f8d96df110feb2
Author: lijewski <lijewski>
Date:   Thu Aug 4 20:25:44 2011 +0000

    Added Initialize()/Finalize() but not yet integrated into BoxLib.cpp

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 4e1a554eac7e0815dc981a4060053301128b0290
Author: lijewski <lijewski>
Date:   Thu Aug 4 19:36:57 2011 +0000

    flush the CPC cache in Finalize()

Src/C_BaseLib/FabArray.cpp

commit 241873b4d01708f140ff93264b2e060012d0592e
Author: almgren <almgren>
Date:   Tue Aug 2 18:47:14 2011 +0000

    Put central copy of MacBndry.{H,cpp} here instead of all applications carrying
    their own copy.

Src/C_BoundaryLib/MacBndry.H
Src/C_BoundaryLib/MacBndry.cpp
Src/C_BoundaryLib/Make.package

commit 04ce8dd1f72debbbff51d3d1b74ee5a50e382eb2
Author: lijewski <lijewski>
Date:   Mon Aug 1 20:32:12 2011 +0000

    more regularization of Initialize()/Finalize() calls

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParmParse.cpp

commit 66320a05be8f0c31b057e655267ef37042f1500c
Author: lijewski <lijewski>
Date:   Thu Jul 28 18:10:15 2011 +0000

    MultiFabs can now be clear()d and define()d again

Src/C_BaseLib/FabArray.H

commit 7c5e157151183a1aedf8efd6cd1d7d1dc68e0c08
Author: almgren <almgren>
Date:   Thu Jul 28 05:39:50 2011 +0000

    get rid of minion_stencil_fill  routines, they were identical to the
    s_simple_2d_cc and s_simple_3d_cc but with order hard-wired to 2.

Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90

commit da7ad8a3c3dea9e08a379de703829a938a44b683
Author: almgren <almgren>
Date:   Thu Jul 28 01:29:08 2011 +0000

    Fix loop indices in Minion 4th order variable density stencil.

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 353d37da6260b72d21898f70599a3700cb054501
Author: lijewski <lijewski>
Date:   Wed Jul 27 19:48:05 2011 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/ComparisonTest/GNUmakefile
Tests/LinearSolvers/ComparisonTest/GNUmakefile

commit 5d9f92c1ce5d87cfb0d810f34e1483e2d651f362
Author: marc <marc>
Date:   Mon Jul 25 18:10:11 2011 +0000

    Add ability to augment pp table externally, used in Amanzi, for example to init via Teuchos::ParameterList

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit dd800052673cc8fe96995e77ee292fd3f4500207
Author: lijewski <lijewski>
Date:   Wed Jul 20 23:17:44 2011 +0000

    Added "stencil" optional logical that implies this multifab is to be used
    as a stencil.  This puts the "ncomps" components of the stencil into the
    first component of the multifab instead of the fourth component.  Use this
    at your own risk.  Almost all of the multifab routines will fail on such a
    multifab.

Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab.f90

commit bdddafdee2c5fb3c695814f0687807c231d3310e
Author: mzingale <mzingale>
Date:   Wed Jul 20 15:33:44 2011 +0000

    local declarations of ZERO and ONE conflict with versions coming in
    from a module.  Explicitly include bl_constants_module now.  Some
    other module needs a private statement somewhere...

Src/LinearSolvers/F_MG/itsol.f90

commit 9a33fbc94bd4c42730fedb4429a31af33a864d5e
Author: lijewski <lijewski>
Date:   Wed Jul 20 15:28:28 2011 +0000

    defined some constants to get code to compile

Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90

commit d3eb8955e35333789bb22c86c96c3234d5fe2a7a
Author: mzingale <mzingale>
Date:   Wed Jul 20 15:21:02 2011 +0000

    use bl_constants_module to get this compiling

Src/LinearSolvers/F_MG/cc_stencil.f90

commit a3def08adb8684317efc2386f9e3c511f50aadaf
Author: almgren <almgren>
Date:   Wed Jul 20 14:50:08 2011 +0000

    Don't need to define these here.

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 1f41b218ed43a202b789d2ffeaeb5508582e80b6
Author: almgren <almgren>
Date:   Wed Jul 20 14:40:03 2011 +0000

    Move definition of BC_GEOM from cc_stencil.f90 to bc_functions.f90

Src/LinearSolvers/F_MG/bc_functions.f90
Src/LinearSolvers/F_MG/cc_stencil.f90

commit f198d1cab607ec25f176ec1154c9e0172591f42a
Author: almgren <almgren>
Date:   Wed Jul 20 14:37:52 2011 +0000

    Add BC_GEOM.

Src/LinearSolvers/F_MG/bc_functions.f90

commit c181c1f2ca3373cc8a1bd1f92fdf81f5d510615f
Author: mzingale <mzingale>
Date:   Wed Jul 20 14:10:56 2011 +0000

    add missing "implicit none".  No longer compiles.

Src/LinearSolvers/F_MG/bc_functions.f90
Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90

commit f34c61898782cac30eb5eb1a1d723628d185bdaf
Author: almgren <almgren>
Date:   Wed Jul 20 05:25:44 2011 +0000

    Separate restriction modules.

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/cc_restriction.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/nodal_restriction.f90

commit 640106ca7bea598e94db57ee68e65bdf462cfe50
Author: almgren <almgren>
Date:   Wed Jul 20 05:20:47 2011 +0000

    Add edge_restriction file.

Src/LinearSolvers/F_MG/edge_restriction.f90

commit 7216cf41026662cf1d2a6df3e586627a17794d15
Author: almgren <almgren>
Date:   Wed Jul 20 05:06:12 2011 +0000

    Fix some modules...now compiles with CASTRO.

Src/LinearSolvers/F_MG/cc_mg_cpp.f90

commit d1afee040022dd602c1ea1f9ef50cfaa08ec43a8
Author: almgren <almgren>
Date:   Wed Jul 20 04:44:52 2011 +0000

    Extracting ml_resid type stuff from ml_cc.f90

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit b5d476f15f4f428c647cefdab5665922f20ddd50
Author: almgren <almgren>
Date:   Wed Jul 20 04:32:44 2011 +0000

    Move applyop stuff into separate file.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 6ae50d8274975d577c3d471354bd3404c1a6504b
Author: almgren <almgren>
Date:   Wed Jul 20 04:23:58 2011 +0000

    Add cc_applyop.f90

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/cc_applyop.f90

commit 6e4356c4f6aac45fadf104d3c7adfb5a10b8d120
Author: almgren <almgren>
Date:   Wed Jul 20 04:06:00 2011 +0000

    Forgot multifab_module.

Src/LinearSolvers/F_MG/ml_norm.f90

commit 09a35a6053729bc89cb3bfd4758a1f3dc86f9cf5
Author: almgren <almgren>
Date:   Wed Jul 20 04:04:35 2011 +0000

    Catch these up with other changes.

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_divu.f90

commit fd6be8ba1bcd5bd47c2d4e39b3075425d322a1ba
Author: almgren <almgren>
Date:   Wed Jul 20 04:04:08 2011 +0000

    ml_util.f90 --> ml_norm.f90

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/ml_norm.f90
Src/LinearSolvers/F_MG/ml_util.f90

commit d433a62c5052656bce51c464f5c7aa6bf3acf52a
Author: almgren <almgren>
Date:   Wed Jul 20 03:54:05 2011 +0000

    Keep up with new files.

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak

commit 44fd970a900fa132c5930b34ef2622241d934b49
Author: almgren <almgren>
Date:   Wed Jul 20 03:53:53 2011 +0000

    Break up ml_interface_stencil.f90 into nodal and cc.

Src/LinearSolvers/F_MG/cc_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_interface_stencil.f90

commit 52300e8e6741fc741e97cb1dd6a318dee9c4542d
Author: almgren <almgren>
Date:   Wed Jul 20 01:51:56 2011 +0000

    Get ml_prolongation started to separate.

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 9253b80cd88b0d12e7c8722d0d428d75760b7649
Author: almgren <almgren>
Date:   Wed Jul 20 01:43:24 2011 +0000

    mg_nodal_cpp --> nodal_mg_cpp

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak

commit 025b18c03557e5294c72f483cba519b99d1159cc
Author: almgren <almgren>
Date:   Wed Jul 20 01:42:44 2011 +0000

    Changed name.

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit d187360580ad86cbd35a43c467955dbb0caa96d5
Author: almgren <almgren>
Date:   Wed Jul 20 01:40:31 2011 +0000

    add bl_error_module...

Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/nodal_mask.f90
Src/LinearSolvers/F_MG/tridiag.f90

commit bc2b7586c0f846f26512bcf21d69d0b1963df0a8
Author: almgren <almgren>
Date:   Wed Jul 20 01:36:49 2011 +0000

    Fix nodal_newu...

Src/LinearSolvers/F_MG/GPackage.mak

commit 7fe9caeb434a20be7a0176fecbe7c10dd3119dfe
Author: almgren <almgren>
Date:   Wed Jul 20 01:34:45 2011 +0000

    Clean up ...

Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 55a4243d588cc6be0147224fa7baf40ba964d08c
Author: almgren <almgren>
Date:   Wed Jul 20 01:32:31 2011 +0000

    Remove ST_FILL... they were never used.

Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90

commit 326fa0d658de6f3d9384783aa197a8a6e4c5dd93
Author: almgren <almgren>
Date:   Wed Jul 20 01:29:44 2011 +0000

    stencil --> ...

Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit c6ca04f98d29aa5b3e3834cabc9c4807e3d90808
Author: almgren <almgren>
Date:   Wed Jul 20 01:29:18 2011 +0000

    stencil_module --> ...

Src/LinearSolvers/F_MG/mg_tower.f90

commit 7ee88d7e420e901188d0b1e212e0cf6192c5bfe5
Author: almgren <almgren>
Date:   Wed Jul 20 01:28:43 2011 +0000

    stencil -->...

Src/LinearSolvers/F_MG/ml_util.f90

commit 1afe4e3bd0f8a588663175afc8450a48fa01cbd8
Author: almgren <almgren>
Date:   Wed Jul 20 01:27:28 2011 +0000

    fix oops.

Src/LinearSolvers/F_MG/bc_functions.f90

commit bda2966d589eb9c63ff32cd70a14760f1a912715
Author: almgren <almgren>
Date:   Wed Jul 20 01:26:43 2011 +0000

    add bl_spacedim.

Src/LinearSolvers/F_MG/bc_functions.f90

commit cb83d9545768a27bd38780e3c31643578add34d0
Author: almgren <almgren>
Date:   Wed Jul 20 01:25:21 2011 +0000

    move BC_BIT...

Src/LinearSolvers/F_MG/bc_functions.f90
Src/LinearSolvers/F_MG/cc_stencil.f90

commit d5488a87cec8cbed4ad698e7c795df7fcb2afc51
Author: almgren <almgren>
Date:   Wed Jul 20 01:23:43 2011 +0000

    Extra bc_neumann, bc_dirichlet, etc, from cc_stencil.f90

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/bc_functions.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90

commit b7a8dc1c43c06925bdd2a9c75c18fc085ff6461e
Author: almgren <almgren>
Date:   Wed Jul 20 01:11:02 2011 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90

commit b3991c0530077171b4a3a6da083804ce2e12b4ae
Author: almgren <almgren>
Date:   Wed Jul 20 01:10:22 2011 +0000

    stencil_module --> cc_stencil_module or nodal_stencil_module

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 1e965085e004180de91eb465ac9e5546b1492a36
Author: almgren <almgren>
Date:   Wed Jul 20 00:59:59 2011 +0000

    impose_neumann_bcs.f90 --> nodal_neumann_bcs.f90

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90
Src/LinearSolvers/F_MG/tridiag.f90

commit 3e94d9580d74ac4c7420f9e14b1a62604fa9f6dd
Author: almgren <almgren>
Date:   Wed Jul 20 00:56:30 2011 +0000

    Separate cc from nodal in the stencil* files.

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/cc_mg_cpp.f90
Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/cc_stencil.f90
Src/LinearSolvers/F_MG/cc_stencil_fill.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/nodal_mg_cpp.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90
Src/LinearSolvers/F_MG/nodal_stencil_fill.f90
Src/LinearSolvers/F_MG/sparse_solve.f90

commit e3031b86e7ac4a08a25ae1d1f188810e6bceb01c
Author: almgren <almgren>
Date:   Wed Jul 20 00:44:13 2011 +0000

    Clean up from previous changes.. this now compiles with CASTRO...

Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90
Src/LinearSolvers/F_MG/tridiag.f90

commit 0f08304627f6cdd60c3da28bef29b4bec1f9c63f
Author: almgren <almgren>
Date:   Wed Jul 20 00:36:27 2011 +0000

    Forgot to fix module name.

Src/LinearSolvers/F_MG/cc_smoothers.f90

commit f14ba5418681b353ec5ef553c5ed52c3607c2de4
Author: almgren <almgren>
Date:   Wed Jul 20 00:36:06 2011 +0000

    Include cc_smoothers_module and nodal_smoothers_module instead of mg_smoother_module

Src/LinearSolvers/F_MG/mg.f90

commit 19bc810d73d496d6b001c195de11c95523f6b5ee
Author: almgren <almgren>
Date:   Wed Jul 20 00:35:38 2011 +0000

    Separate mg_smoother.f90 into separate files -- cc_smoothers.f90 and nodal_smoothers.f90

Src/LinearSolvers/F_MG/cc_smoothers.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit 9e9b9898540e9e129e769fb740a12248bd5afb96
Author: almgren <almgren>
Date:   Wed Jul 20 00:32:58 2011 +0000

    Separate mg_smoother.f90 into nodal_smoothers.f90 and cc_smoothers.f90, and
    separate tridiag.f90 into a separate file.

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/tridiag.f90

commit 82049104a2c467b633de1db40056b759e0c56bfb
Author: lijewski <lijewski>
Date:   Tue Jul 19 21:12:32 2011 +0000

    use -O3 for optimizing with gfortran instead of -O2

Tools/C_mk/Make.defs

commit 3c5bcb5b1652bd7b3cf50298b30ca1aeb9638f36
Author: almgren <almgren>
Date:   Tue Jul 19 17:17:29 2011 +0000

    These are the files I'm using to compare C++ to F90 solvers.

Src/LinearSolvers/C_CellMG/ComparisonTest/COEF_3D.F
Src/LinearSolvers/C_CellMG/ComparisonTest/COEF_F.H
Src/LinearSolvers/C_CellMG/ComparisonTest/GNUmakefile
Src/LinearSolvers/C_CellMG/ComparisonTest/MacBndry.H
Src/LinearSolvers/C_CellMG/ComparisonTest/MacBndry.cpp
Src/LinearSolvers/C_CellMG/ComparisonTest/Make.package
Src/LinearSolvers/C_CellMG/ComparisonTest/inputs.3d
Src/LinearSolvers/C_CellMG/ComparisonTest/main.cpp
Tests/LinearSolvers/ComparisonTest/COEF_3D.F
Tests/LinearSolvers/ComparisonTest/COEF_F.H
Tests/LinearSolvers/ComparisonTest/GNUmakefile
Tests/LinearSolvers/ComparisonTest/MacBndry.H
Tests/LinearSolvers/ComparisonTest/MacBndry.cpp
Tests/LinearSolvers/ComparisonTest/Make.package
Tests/LinearSolvers/ComparisonTest/inputs.3d
Tests/LinearSolvers/ComparisonTest/main.cpp

commit ef882f8c1bee54c84bb22418866d64d69593c990
Author: marc <marc>
Date:   Tue Jul 19 17:11:07 2011 +0000

    Fix up fParallel calls

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/main.cpp

commit 7090ad431ac3afdd46bbe3d862af8400f71bc92a
Author: almgren <almgren>
Date:   Tue Jul 19 00:07:05 2011 +0000

    Remove unused variables in George's new stencils to quiet warnings...

Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_fill.f90

commit 4133b3bd3c9591f4c37c4e023776f16e0a1573e8
Author: almgren <almgren>
Date:   Mon Jul 18 23:45:01 2011 +0000

    Remove unused variables.

Src/LinearSolvers/F_MG/stencil.f90

commit 7d7c56e3164869afa8655b8da9efff67df60fe14
Author: lijewski <lijewski>
Date:   Mon Jul 18 20:51:17 2011 +0000

    substitute istringstream for deprecated istrstream

Src/C_AMRLib/Amr.cpp

commit fc95967cccfde8652c8d2a69e338b60bc62ee20a
Author: lijewski <lijewski>
Date:   Mon Jul 18 19:52:05 2011 +0000

    substitute istringstream for deprecated istrstream

Src/C_BaseLib/VisMF.cpp

commit 78e07f1b626239c610d4c9ef828cd5d2f88e9cbb
Author: lijewski <lijewski>
Date:   Mon Jul 18 16:39:54 2011 +0000

    deal with losing an AmrLevel on a regrid() in Redistribute()

Src/C_AMRLib/Particles.H

commit 5689e17209ae7c928c7f7416cea4de06d4f3aa06
Author: lijewski <lijewski>
Date:   Sat Jul 16 16:02:14 2011 +0000

    in Redistribute() must remove from the level map empty particle containers

Src/C_AMRLib/Particles.H

commit 577f3254f932bf38006b09ba16c45d48508ff59c
Author: lijewski <lijewski>
Date:   Sat Jul 16 04:10:21 2011 +0000

    added m_particles.reserve() calls to the various init routines

Src/C_AMRLib/Particles.H

commit de40cfb1e43dd275a6356332530da5068adfd87a
Author: almgren <almgren>
Date:   Sat Jul 16 04:01:36 2011 +0000

    Change tcmf -> new_cmf so that we dont re-use MultiFab after clear -- turns out that
    clear does not delete the boxarray...

Src/C_AMRLib/Particles.H

commit a3b610e79ed2325b991d28b64b6178606911eb7d
Author: almgren <almgren>
Date:   Sat Jul 16 03:50:17 2011 +0000

    Add m_particles.resize() in Redistribute if m_particles.size() < m_amr.finestLevel()+1.

Src/C_AMRLib/Particles.H

commit 34e3f8ffc1fa2134da4de05f9dd83cf78ace7aa7
Author: lijewski <lijewski>
Date:   Thu Jul 14 23:32:18 2011 +0000

    cut scalar time in Redistribute() by roughly a factor of two

Src/C_AMRLib/Particles.H

commit 12dd6593fea6619bdaefe59e24f384b736b019bf
Author: gilet <gilet>
Date:   Thu Jul 14 22:13:07 2011 +0000

    add note that this script is not for use on Jaguar

Tools/F_scripts/extract.parallel

commit 7565e65ca405ed5d9500a54c51ebcb7e059d6264
Author: almgren <almgren>
Date:   Thu Jul 14 21:24:35 2011 +0000

    Move LO_UTIL.F to bndrylib.

Src/LinearSolvers/C_CellMG/Make.package

commit 95cb2ad19bdf6752c52a94996a0deafc886ffd27
Author: almgren <almgren>
Date:   Thu Jul 14 21:24:11 2011 +0000

    Add LO_UTIL.F

Src/C_BoundaryLib/Make.package

commit 36e082819ca48c8e7fd88cee0e111d13754f20ba
Author: lijewski <lijewski>
Date:   Thu Jul 14 16:53:26 2011 +0000

    ByteSpread() now also prints out total particle count.

Src/C_AMRLib/Particles.H

commit 4a44a3d222a6eeb7ce0cba4b61fe33cb2937dabf
Author: lijewski <lijewski>
Date:   Wed Jul 13 22:42:01 2011 +0000

    Bypass the MPI_Alltoall() calls in Redistribute() if there's no parallel
    work to do by doing a ReduceLongMax() on the number of particles I have
    that aren't mine.

Src/C_AMRLib/Particles.H

commit 021624fe281153b1c5414e73f83fb5d6152a1330
Author: mzingale <mzingale>
Date:   Wed Jul 13 21:31:22 2011 +0000

    have the timestamp routine that an optional argument, vel_mf, which
    contains the velocites.  If this mf is present, then output the
    velocity of the zone where the particle lives along with the other
    data

Src/F_BaseLib/particles.f90

commit bc864535a7f6281f8bd5f1dbc74fbd2889cdd943
Author: almgren <almgren>
Date:   Wed Jul 13 21:28:03 2011 +0000

    No longer need Make_nyx.package since we've moved those files into bndrylib.

Src/LinearSolvers/C_CellMG/Make_nyx.package

commit 15050de7169c681f45426d87527443c633a10bd1
Author: almgren <almgren>
Date:   Wed Jul 13 21:27:31 2011 +0000

    Move files from mglib to here.

Src/C_BoundaryLib/Make.package

commit d3201d2d9394396bff1d0ed47be5737a9828cc7e
Author: almgren <almgren>
Date:   Wed Jul 13 21:26:24 2011 +0000

    Revised Make.package since we moved a bunch of files into bndrylib.

Src/LinearSolvers/C_CellMG/Make.package

commit aa9c9b3a9daae813b272b6bb346c945c459fd2b1
Author: lijewski <lijewski>
Date:   Wed Jul 13 21:16:48 2011 +0000

    now output time spent in scalar and parallel parts of Redistribute()

Src/C_AMRLib/Particles.H

commit fe349bc59a8e791fa436e499777796a0a92ee0b4
Author: gpau <gpau>
Date:   Wed Jul 13 00:17:26 2011 +0000

    added the general stencil for DIM=3: look for simpleg

Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_fill.f90

commit 669681cbdd024e8f1b37cbcca89c124ed0f1f292
Author: lijewski <lijewski>
Date:   Tue Jul 12 18:02:55 2011 +0000

    use memory a bit more efficiently in Redistribute()

Src/C_AMRLib/Particles.H

commit 3d98131dccdef5a2250aaa3fa7784036ed09c01c
Author: lijewski <lijewski>
Date:   Tue Jul 12 16:54:30 2011 +0000

    beefed up OK() a bit more

Src/C_AMRLib/Particles.H

commit 3dda83c309cab3500d95cd1ed6983f78d4a46715
Author: lijewski <lijewski>
Date:   Mon Jul 11 20:29:08 2011 +0000

    Modest speedup to Redistribute().
    Previously we only passed m_cpu and m_id via MPI and recalculated m_lev,
    m_grid and m_cell using Where().  Now Redistribute() sends all the
    integral data via MPI and recalculates nothing.  For large numbers of
    particles this is a modest speedup.

Src/C_AMRLib/Particles.H

commit aeeb49285c32f1eb7cc3df8f46228de40458491e
Author: lijewski <lijewski>
Date:   Fri Jul 8 21:34:26 2011 +0000

    modest speedups and simplifications to estTimestep()

Src/C_AMRLib/Particles.H

commit d737696a38e6d4799801c154cfe8923a501ec662
Author: lijewski <lijewski>
Date:   Fri Jul 8 20:20:49 2011 +0000

    figured out issue with MoveRandom(); should now scale perfectly with threads

Src/C_AMRLib/Particles.H

commit 41510f9f612b55feb7aeb312434181ad482c2a89
Author: lijewski <lijewski>
Date:   Fri Jul 8 19:59:06 2011 +0000

    added parallel keyword to pragma omp so estTimestep() and MoveRandom() really threads

Src/C_AMRLib/Particles.H

commit 30afb773a25c4c0019e171e4f909b62f088ea603
Author: lijewski <lijewski>
Date:   Fri Jul 8 17:15:56 2011 +0000

    quiet some compiler warnings

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 49a670cffb77ff978bced9546cf0c23e0508f737
Author: lijewski <lijewski>
Date:   Fri Jul 8 16:42:38 2011 +0000

    quiet some compiler warnings

Src/C_BaseLib/Looping.H

commit a5e99816663634e16b422bc9797b2fda70a0a479
Author: lijewski <lijewski>
Date:   Fri Jul 8 16:19:06 2011 +0000

    quiet some compiler warnings

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 5d9235910482d035c88de86c91df6b27dd74fe8b
Author: lijewski <lijewski>
Date:   Fri Jul 8 16:03:40 2011 +0000

    removed some unused variables

Src/C_BaseLib/BaseFab.H

commit 4776a48626e6d1d36e72b982b74360e7083feeb7
Author: lijewski <lijewski>
Date:   Fri Jul 8 16:02:51 2011 +0000

    cut number of random number calls in MoveRandom() by half

Src/C_AMRLib/Particles.H

commit c412077965943bb11cf02b7ef80480f2f4b1149e
Author: mzingale <mzingale>
Date:   Fri Jul 8 15:54:28 2011 +0000

    add a function particle_global_numparticles to return the
    total number of active particles -- for diagnostics

Src/F_BaseLib/particles.f90

commit 4b4dc85f703e49b30e6acf72cbf267680baa60aa
Author: marc <marc>
Date:   Wed Jul 6 23:19:58 2011 +0000

    Add + and - to allowed characters in identifiers

Src/C_BaseLib/ParmParse.cpp

commit 3c5253a1ffcb74df9049104b9905109923a32f95
Author: almgren <almgren>
Date:   Wed Jul 6 22:37:55 2011 +0000

    Make sure to do a copyplus instead of a pure copy for the case of a particle
    on a fine grid next to another fine grid -- without this a zero ghost cell
    could overwrite a non-zero ghost cell.

Src/C_AMRLib/Particles.H

commit 537fcdc119791628537ef0714d233e9f3bc428ef
Author: lijewski <lijewski>
Date:   Wed Jul 6 22:27:53 2011 +0000

    The parallel multifab -> multifab copy() can now also do add.
    
    The default is as before; i.e. if you want to copy src to dst:
    
      dst.copy(src)
    
    If you want you want to add src into dst:
    
      dst.copy(src,FabArrayBase::ADD);

Src/C_BaseLib/FabArray.H

commit c01b4323dfa10eb9052f51433a2de16878ecfd46
Author: almgren <almgren>
Date:   Wed Jul 6 21:31:14 2011 +0000

    Fix periodic wraparound in multilevel AssignDensity.

Src/C_AMRLib/Particles.H

commit 34b8c297619084b8ffec0e763eac417b6602803f
Author: almgren <almgren>
Date:   Wed Jul 6 17:13:28 2011 +0000

    Fix the case in AssignDensity where we need to copy from fine ghost cells onto
    coarse valid regions.

Src/C_AMRLib/Particles.H

commit 92ccde940a30e2a623aaf7ef05a99319ed3c43f9
Author: almgren <almgren>
Date:   Wed Jul 6 07:31:34 2011 +0000

    Allow us to enforce solvability even for multilevel solves -- just enforce it at
    amr level = 0, not the higher levels.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 64eac4b7236ee88d9a74c9e0acca4a8d89a6f452
Author: almgren <almgren>
Date:   Wed Jul 6 02:59:40 2011 +0000

    Eliminate GetRhoFromParticles -- this was replaced by AssignDensity and
    other source in CastroParticles.cpp

Src/C_AMRLib/Particles.H

commit 3b2e8648a8ecea9b149e9022e04b8a96819dc846
Author: almgren <almgren>
Date:   Wed Jul 6 02:58:57 2011 +0000

    Add new routine -- MultiplyParticleMass -- used in SantaBarbara initialization.

Src/C_AMRLib/Particles.H

commit 898f35a0ce9cd2270c140a1168e2e9842bd9c870
Author: almgren <almgren>
Date:   Tue Jul 5 20:43:16 2011 +0000

    Fix to GetRhoFromParticles when lev > 1 -- we need to count the contributions from particles
    at level lev-1 which might contribute to the density at level lev.

Src/C_AMRLib/Particles.H

commit 6c068f68a5341599677549202b7c58c001c971e2
Author: almgren <almgren>
Date:   Tue Jul 5 20:41:01 2011 +0000

    Add new subroutine part_sumdensup, which is just like subroutine part_summassup,
    but differs in that it does not multiply the coarse contributions by volfrac
    since it works with density instead of mass.

Src/C_AMRLib/Particles_1D.F
Src/C_AMRLib/Particles_2D.F
Src/C_AMRLib/Particles_3D.F
Src/C_AMRLib/Particles_F.H

commit 3b643baeb26e324dd3a08884d606ec726f823e10
Author: almgren <almgren>
Date:   Mon Jul 4 18:48:19 2011 +0000

    Fix initialization of multilevel Santa Barbara problem

Src/C_AMRLib/Particles.H

commit f8f29b6c6060f1f9f57475626a0963907f18721b
Author: gpau <gpau>
Date:   Sat Jul 2 14:09:47 2011 +0000

    added a generic stencil that constructs the entries to matrix directly.

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_fill.f90

commit 632cff8cfff09779165811f284b7fd38ea1443e9
Author: gpau <gpau>
Date:   Sat Jul 2 13:54:39 2011 +0000

    changes made to handle a generic linear system solve.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 1b32b7b9a2cc99b0f078e43063364572985ffe81
Author: marc <marc>
Date:   Fri Jul 1 23:10:54 2011 +0000

    to facilitate derivation, if necessary

Src/C_BaseLib/ParmParse.H

commit 4a0efd0239cff7d81fce9a7793949b59d1f24a2d
Author: marc <marc>
Date:   Fri Jul 1 22:50:54 2011 +0000

    add hedorah to the list of special cases

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit a7e0ae177f6afe5cfe91203fd6a26c7a33150491
Author: almgren <almgren>
Date:   Fri Jul 1 19:11:24 2011 +0000

    Fix ml_layout_build_la_array so instead of copying the entire mba, we only copy
    nlevel levels of it (as is done in ml_layout_build_n).

Src/F_BaseLib/ml_layout.f90

commit c8a7b55aedc22266db5652213e3ed8aff73ed4de
Author: almgren <almgren>
Date:   Fri Jul 1 06:06:03 2011 +0000

    Don't print all the particles in InitFromAscii.

Src/C_AMRLib/Particles.H

commit 41c7e4ddb223386fedbaa1e20d64c00474b96fdf
Author: almgren <almgren>
Date:   Thu Jun 30 21:59:46 2011 +0000

    Add new way of building ml_layout --  ml_layout_build_la_array -- which allows us to copy
    existing la_array(n) instead of making new ones.

Src/F_BaseLib/ml_layout.f90

commit 0f1ea092b3edfb9e5fc5753fa084948460a536c5
Author: almgren <almgren>
Date:   Thu Jun 30 21:24:09 2011 +0000

    Destroy ba_new once we're done with it (elminated leftover layout in MEMORY STATS)

Src/F_BaseLib/make_new_grids.f90

commit 43eb61dcba569767b6ec2eba8f125760500f8435
Author: lijewski <lijewski>
Date:   Wed Jun 29 16:10:50 2011 +0000

    Fixed bug in InitFromAscii() when running in parallel.
    There was in essence an off-by-one counting bug which caused the last
    particle read in by cpu 0 to be the first particle read in by cpu 1, and
    the last particle in the file to not be read in by cpu N was not read in at all.

Src/C_AMRLib/Particles.H

commit ce3b584f3a3d08b0e9a4e7f78ffb8b1f386aa9f5
Author: lijewski <lijewski>
Date:   Wed Jun 29 15:10:42 2011 +0000

    got rid of some unused variables in Timestamp()

Src/C_AMRLib/Particles.H

commit 96fd03a37fbc65e4a21f965e57606b8d36da6eda
Author: mzingale <mzingale>
Date:   Wed Jun 29 13:31:30 2011 +0000

    store .mod files in o/ on nan

Tools/C_mk/Make.Linux

commit d3b342ab5ac906ba3e2cb6656a355a1c29fdb95c
Author: mzingale <mzingale>
Date:   Wed Jun 29 13:12:13 2011 +0000

    switch to latest MPI for nan

Tools/C_mk/Make.mpi

commit 9934f9e8eabec309790cea31ca40ffa8d599e4d6
Author: lijewski <lijewski>
Date:   Wed Jun 29 05:23:51 2011 +0000

    remove some debugging I/O

Src/C_AMRLib/TagBox.cpp

commit 02f62ac286a358d1841913f24efefafd4239f540
Author: lijewski <lijewski>
Date:   Wed Jun 29 05:21:17 2011 +0000

    fix to previous mod when USE_MPI=FALSE

Src/C_AMRLib/TagBox.cpp

commit 64e791dcacc298cdcd0c2a0e38d5badcea37b4f8
Author: lijewski <lijewski>
Date:   Wed Jun 29 04:40:38 2011 +0000

    remove potential problem with send/recv args to MPI_Gatherv() being the same on the root processor

Src/C_AMRLib/TagBox.cpp

commit b5c6b68fb6eb34e41ddb944c50effd338b0cdc04
Author: mzingale <mzingale>
Date:   Tue Jun 28 21:51:33 2011 +0000

    no -module flag for nan

Tools/C_mk/Make.Linux

commit 3b1e7ee5222a5553ca862772c608ff28b8bcc73c
Author: mzingale <mzingale>
Date:   Tue Jun 28 21:15:01 2011 +0000

    add MPI instructions for nan.  Need -DMPICH_SKIP_MPICXX to make things
    happy

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit c27b9ca88972109d520c02e944fe6dc26633ad6b
Author: almgren <almgren>
Date:   Tue Jun 28 19:09:34 2011 +0000

    Remove characters from word.

Src/F_BaseLib/tag_boxes.f90

commit bb5ff56052a689bf9ae0cd32147248276e0c461b
Author: marc <marc>
Date:   Fri Jun 24 23:13:09 2011 +0000

    Add some arguments for parallel stuff

Src/C_BaseLib/.cvsignore
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ParmParse.H

commit 58b0d0437d79cedac481064c5e6396e4cfb9059c
Author: marc <marc>
Date:   Fri Jun 24 22:59:07 2011 +0000

    add hg file to list

Src/C_BoundaryLib/.cvsignore

commit 0e14ea0ef970ec927ae5b656b9f58458a01f979f
Author: marc <marc>
Date:   Fri Jun 24 22:40:28 2011 +0000

    stupid cast that seems to be needed for idiotic GNU compiler

Src/C_BoundaryLib/BndryData.cpp

commit 83e5754447b14b92e0cd9b7f248b5361d834a105
Author: lijewski <lijewski>
Date:   Fri Jun 24 21:03:23 2011 +0000

    more OMPing

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit ae2cdea752e158a0accb067bfd078a3004769ae9
Author: lijewski <lijewski>
Date:   Fri Jun 24 21:01:36 2011 +0000

    some more OMPing

Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit c0f3c9107b6566c77ac526780bc54cff4d4bbdbc
Author: lijewski <lijewski>
Date:   Fri Jun 24 21:01:02 2011 +0000

    some more OMPing and moved temp from stack to allocatable

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 56e13a67d92a70d53ce349b12c073c6882a09dc2
Author: lijewski <lijewski>
Date:   Fri Jun 24 21:00:21 2011 +0000

    make lr, tb and fb allocatable instead of building on the stack

Src/LinearSolvers/F_MG/mg_smoother.f90

commit beaf25a00f9a74d7c892cc466f7317b5ad8933b6
Author: lijewski <lijewski>
Date:   Thu Jun 23 23:42:44 2011 +0000

    little more OMPing

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit f64e983f2f6e3fdc6e1b4a44ef4cdf499553ed13
Author: lijewski <lijewski>
Date:   Thu Jun 23 20:10:33 2011 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_restriction.f90

commit d818f94223b04b83cf6ea87360210be09cbd135e
Author: lijewski <lijewski>
Date:   Wed Jun 22 23:13:49 2011 +0000

    single-precision constants -> double-precision constants

Src/F_BaseLib/fourth_order_interp_coeffs.f90

commit f648dc3534a685c1d016ffe40d5d323185d1e6aa
Author: lijewski <lijewski>
Date:   Wed Jun 22 22:11:27 2011 +0000

    0 -> 0.0_dp_t in a few places

Src/F_BaseLib/multifab.f90

commit d149b7e11ac11c278792a5689da7521dc7e63169
Author: lijewski <lijewski>
Date:   Wed Jun 22 21:19:15 2011 +0000

    More work on periodic_add_copy():
    Replace array assignments w/ calls to cpy_d() and additions with calls to
    cpy_d() using ml_restrict_copy_sum() as a filter.
    Likewise replace saxpy() calls with multifab_copy() calls using ml_restrict_copy_sum()
    as a filter.

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 6de0035cbbc259e9a107b0b1e3ea9205ebbce261
Author: lijewski <lijewski>
Date:   Wed Jun 22 18:11:33 2011 +0000

    little more simplificaton to periodic_add_copy(); can't be readily cached due to synced argument

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 38e5bad88b05a92c7a4877d3593e9ce01f04a1d3
Author: almgren <almgren>
Date:   Wed Jun 22 01:27:02 2011 +0000

    max --> std::max

Src/C_AMRLib/Particles.H

commit dafa932e266711554c97e64f9d0c034ac89811cd
Author: almgren <almgren>
Date:   Wed Jun 22 01:24:55 2011 +0000

    Fix typo.

Src/C_AMRLib/Particles.H

commit 2ae51226a26b44e4fe2195aa04a3a7c02049e515
Author: almgren <almgren>
Date:   Wed Jun 22 01:20:58 2011 +0000

    Change estTimestep so that we satisfy dt = cfl * a * dx / mag_vel where
    mag_vel is the maximum of a component in any one direction,
    not the magnitude of the velocity.

Src/C_AMRLib/Particles.H

commit ae91d6ee3d5a8e0c7c05b1cf66dfb010c53bbc0c
Author: almgren <almgren>
Date:   Wed Jun 22 00:51:11 2011 +0000

    estTimestep now takes a CFL in the argument list which specifies what
    maximum fraction of a cell the particle can cross in a timestep.

Src/C_AMRLib/Particles.H

commit bd13bb01d7b74c6ebf653561fab29ce7c7033cbe
Author: lijewski <lijewski>
Date:   Wed Jun 22 00:01:51 2011 +0000

    use O2 when optimizing

Tools/F_mk/comps/gfortran.mak

commit c9392e1affcccd3132615017158f5cb29e07bf77
Author: gilet <gilet>
Date:   Tue Jun 21 19:16:42 2011 +0000

    add script to extract multiple files from HSI at a time

Tools/F_scripts/extract.parallel

commit 616924dfa3e77bd9893d9db91616aed53834a1cb
Author: lijewski <lijewski>
Date:   Tue Jun 21 19:05:17 2011 +0000

    early exit from periodic_add_copy() when not periodic

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 827380be8ccd698cb39879e6bb3a85cab5ab33f7
Author: lijewski <lijewski>
Date:   Tue Jun 21 19:04:51 2011 +0000

    removed comment

Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/nodal_divu.f90

commit 7b3adfd8f8ff1fcf5304b74ab6f47f019ca745c0
Author: celdred <celdred>
Date:   Tue Jun 21 18:25:32 2011 +0000

    added gojira entry

Tools/F_mk/GMakeMPI.mak

commit 6e58d0ea603a72403de9e2d96f31aec9f22ec1b3
Author: lijewski <lijewski>
Date:   Thu Jun 16 16:30:26 2011 +0000

    removed some unused code

Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 5a794d5a88c797935956c0c69434600335a65492
Author: lijewski <lijewski>
Date:   Thu Jun 16 15:51:30 2011 +0000

    removed some XT3 junk

Src/C_BaseLib/Utility.cpp

commit 07e71c29483d3f4619d0f948ee8ef39a835b1ede
Author: lijewski <lijewski>
Date:   Tue Jun 14 20:35:53 2011 +0000

    remove option for calling bicubic interp on state data

Src/C_AMRLib/Particles.H

commit 727675e50de4500d8f616fea30e7b84ffc77c9ba
Author: lijewski <lijewski>
Date:   Tue Jun 14 20:35:35 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles_2D.F

commit da656a839af41494237b65a2203b03d4cc46bcb8
Author: ajnonaka <ajnonaka>
Date:   Tue Jun 14 16:44:03 2011 +0000

    now printing lo/hi/avg FAB byte spread

Src/F_BaseLib/fab.f90

commit 1d37f3052cca0bd7a80a43c8c45c86631d4721bf
Author: almgren <almgren>
Date:   Mon Jun 13 20:20:35 2011 +0000

    Need more files than we thought.

Src/LinearSolvers/C_CellMG/Make_nyx.package

commit 8fd27b25e3bd44ecb15555e08b35b8741364adfb
Author: almgren <almgren>
Date:   Mon Jun 13 20:03:47 2011 +0000

    Only include what we need for running NYX.

Src/LinearSolvers/C_CellMG/Make_nyx.package

commit b15a456c11b299a679ede5485ce7249f581a46b8
Author: lijewski <lijewski>
Date:   Fri Jun 10 23:48:03 2011 +0000

    quiet some unsed variable warnings

Src/C_AMRLib/Particles.H

commit 36f82ffb08dc1463b38a628a03e66cb7d2a1fad6
Author: lijewski <lijewski>
Date:   Fri Jun 10 23:45:29 2011 +0000

    we store the average advected velocity in particles that use AdvectWithUmac() for LMC

Src/C_AMRLib/Particles.H

commit e23e26ca206ccbf67677238dd043ad7235199ac0
Author: lijewski <lijewski>
Date:   Fri Jun 10 23:39:54 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles_2D.F

commit 7f7bd95300cdbe9d52bea3db0ce215d63e98b84a
Author: lijewski <lijewski>
Date:   Fri Jun 10 17:43:22 2011 +0000

    make it explicit that we are using cell-centered data in bicubic

Src/C_AMRLib/Particles_2D.F

commit 1ee40d60598d67620c60e7ca9417fcc790ab1a82
Author: wqzhang <wqzhang>
Date:   Fri Jun 10 16:23:59 2011 +0000

    more radiation benchmarks added

Tools/C_util/regtests/radiation-tests.ini
Tools/C_util/regtests/test-Ubuntu.py

commit 1b4385464790db152b9187abecf5401cad7a4007
Author: lijewski <lijewski>
Date:   Thu Jun 9 23:25:54 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles_2D.F
Src/C_AMRLib/Particles_F.H

commit 74fb42d05ac95127ab32edfc2db4266cdcd7ff83
Author: lijewski <lijewski>
Date:   Wed Jun 8 21:40:33 2011 +0000

    more work on AdvectWithUmac(); now Redistribute between predictor and corrector

Src/C_AMRLib/Particles.H

commit efce3be00b153b400aa80390824c297291613af1
Author: lijewski <lijewski>
Date:   Wed Jun 8 19:50:12 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles.cpp

commit f769638176c85ab916a3f95dd79ab563564994fc
Author: mzingale <mzingale>
Date:   Wed Jun 8 17:46:17 2011 +0000

    add a generic catch for a linux machine with the generic localhost
    name (like a typical laptop), with an MPIHOME defined to an mpich
    directory.

Tools/F_mk/GMakeMPI.mak

commit 32c25b24858b8a704d3b6c548c657670c332ab05
Author: lijewski <lijewski>
Date:   Tue Jun 7 21:53:57 2011 +0000

    just a little tidying up of things ...

Src/C_AMRLib/Particles.H

commit c1d348773be0fd2a5208a7730f8da7ad7b0e3571
Author: gilet <gilet>
Date:   Mon Jun 6 23:49:26 2011 +0000

    module name was too long for PathScale on hopper

Src/F_BaseLib/fourth_order_interp_coeffs.f90
Src/F_BaseLib/interp.f90

commit 102bc876c1c36fc22657967baef22457c95981f4
Author: lijewski <lijewski>
Date:   Mon Jun 6 22:39:17 2011 +0000

    added optional finalize_parallel arg to Finalize() for George

Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp

commit 2e36c8f7a7e48c2c24d160e30038cc3a8ea3b4b6
Author: almgren <almgren>
Date:   Mon Jun 6 22:15:21 2011 +0000

    oops.

Src/F_BaseLib/interp.f90

commit 86279bbb4514725add330ce5c6445ad3d60e19bd
Author: almgren <almgren>
Date:   Mon Jun 6 22:13:37 2011 +0000

    fix name of interp_coeffs_module -> fourth_order_interp_coeffs_module.

Src/F_BaseLib/interp.f90

commit f028adbb6f5072891e6d2b3886c0b7eb0f355ee9
Author: lijewski <lijewski>
Date:   Mon Jun 6 21:38:58 2011 +0000

    didn't have vel interp quite right in AdvectWithUmac()

Src/C_AMRLib/Particles.H

commit 01d188c7fd2dd1ea27709fc46e0f174b3b320183
Author: lijewski <lijewski>
Date:   Mon Jun 6 19:51:29 2011 +0000

    Pulled the core of Interp() into InterpDoIt() which is now called by AdvectWithUmac().

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 057f981fb0e25be2b755f65e03dc4d4fa818b394
Author: almgren <almgren>
Date:   Mon Jun 6 18:52:27 2011 +0000

    Add fourth_order_interp_coeffs.f90

Src/F_BaseLib/GPackage.mak

commit ae419e2f6bae513124896d38fce230f5fdd0c146
Author: almgren <almgren>
Date:   Mon Jun 6 18:51:45 2011 +0000

    Change name of module

Src/F_BaseLib/fourth_order_interp_coeffs.f90

commit 9c5902239e5165322e597b9577ab7d59d1199f1d
Author: almgren <almgren>
Date:   Mon Jun 6 18:51:27 2011 +0000

    Add Matt's implementation of fourth-order interpolation, which requires fourth_order_interp_coeffs_module

Src/F_BaseLib/fourth_order_interp_coeffs.f90
Src/F_BaseLib/interp.f90

commit 4c2c6b5897c2d2545d801ea843dbefbda38b0c3a
Author: almgren <almgren>
Date:   Mon Jun 6 18:46:27 2011 +0000

    Fix calling sequence for fourth_order_interp_2d, and replace calls by bl_error calls
    for 1d and 3d.

Src/F_BaseLib/fillpatch.f90

commit 2854b6a2e0d07e119a9b9c317b1415659c259691
Author: lijewski <lijewski>
Date:   Fri Jun 3 22:45:13 2011 +0000

    use scientific notation in Timestamp() and force 10 digits of accurracy

Src/C_AMRLib/Particles.H

commit e293e0cab1ab1a3f0a54c9b41f67a6b1d8154dc8
Author: ajnonaka <ajnonaka>
Date:   Fri Jun 3 17:45:41 2011 +0000

    rennamed a bl_prof_timer to avoid conflict

Src/LinearSolvers/F_MG/stencil.f90

commit 9876f01f8d2d37ccf78ac73263379fc6703f01a4
Author: ajnonaka <ajnonaka>
Date:   Thu Jun 2 21:44:31 2011 +0000

    fix error in ghost cell checking in multifab_sub_sub_c

Src/F_BaseLib/multifab.f90

commit 3108c3cb97e81cc2af46b2f1f4bacc8ec95717bf
Author: mzingale <mzingale>
Date:   Tue May 31 21:40:20 2011 +0000

    add .SDC to the suffix -- this way the build system uses separate files
    for the SDC and non-SDC versions of the code, and doesn't confuse
    object files if you switch.

Tools/F_mk/GMakedefs.mak

commit 55d10eea9e337d83da44b150b5e0e8791ad8e55c
Author: lijewski <lijewski>
Date:   Fri May 27 17:41:13 2011 +0000

    a little simplification

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/ml_solve.f90

commit 95c7f354360bcdec07a0ff46301e4214481d3ae7
Author: lijewski <lijewski>
Date:   Thu May 26 21:11:27 2011 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit da99b8611851fcb02b417aa0aa1b1791717ad2ba
Author: lijewski <lijewski>
Date:   Thu May 26 20:57:34 2011 +0000

    don't build lasrctmp in fluxassoc_build() if not really needed

Src/F_BaseLib/layout.f90

commit e3576a97ad2597bc421da8348b1ba2fc259afcc7
Author: lijewski <lijewski>
Date:   Thu May 26 20:30:27 2011 +0000

    don't build latmp in boxassoc_build() if not really needed

Src/F_BaseLib/layout.f90

commit b8260b5b7f8b843fdd471a895f1b0b365dfad381
Author: lijewski <lijewski>
Date:   Thu May 26 19:29:57 2011 +0000

    multifab_sum_boundary() now used layout_get_box_intersector() stuff

Src/F_BaseLib/multifab.f90

commit cacfaca645e18ce3c2d8421805744571e26edc6a
Author: lijewski <lijewski>
Date:   Thu May 26 17:01:35 2011 +0000

    initial cut at multifab_sum_boundary()

Src/F_BaseLib/multifab.f90

commit bfda22d0c685713af39448cdee5e262b8a6bf24e
Author: lijewski <lijewski>
Date:   Wed May 25 21:59:17 2011 +0000

    Don't forget to call set_particle_id() in checkpoint() after
    get_particle_id().  The latter increments our internal particle_id counter
    and the former sets it back to where it should be.  Otherwise we "lose" a
    particle_id every time we write a checkpoint file.

Src/F_BaseLib/particles.f90

commit c1f9dd5cbc452570d46d657216ca077b2446ea3c
Author: almgren <almgren>
Date:   Mon May 23 22:33:00 2011 +0000

    Add new subroutine make_particle_count which fills a multilevel multifab with the number of particles per cell.

Src/F_BaseLib/particles.f90

commit ef60a2fe01fb6e59b29fb589f75ed0f141f80414
Author: almgren <almgren>
Date:   Mon May 23 20:52:14 2011 +0000

    Fix error message.

Src/F_BaseLib/particles.f90

commit a781a22b0eafe7b621defeeecbcc39108d9b15d6
Author: lijewski <lijewski>
Date:   Mon May 23 20:30:21 2011 +0000

    added Tokenize()

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 01641db35e5adc86a2f188ce7456b74f6f19ff07
Author: almgren <almgren>
Date:   Mon May 23 18:42:30 2011 +0000

    Add comment.

Src/F_BaseLib/particles.f90

commit 64f8ae8c8629deeb6e36f3258b94e446421c9966
Author: almgren <almgren>
Date:   Thu May 19 19:47:51 2011 +0000

    Added some debugging to InitCosmo.

Src/C_AMRLib/Particles.H

commit 0c514b84e3899e8b8109bd3d6166fcc0acae0804
Author: almgren <almgren>
Date:   Thu May 19 18:21:52 2011 +0000

    New version of InitCosmo().

Src/C_AMRLib/Particles.H

commit 549eacb04ed385efd02e054193b283ae2952d1e5
Author: lijewski <lijewski>
Date:   Wed May 18 20:49:11 2011 +0000

    IncrementWithTotal() now returns a long not an int.  Ints are only
    guaranteed to hold numbers up to 2^31-1.  All callers of this routine
    should change their return value from int to long as well.

Src/C_AMRLib/Particles.H

commit 9165a3e939f50b7eea7c02073ef6969394fbab71
Author: almgren <almgren>
Date:   Wed May 18 19:19:22 2011 +0000

    Make a version of MoveRandom that takes level as an argument.

Src/C_AMRLib/Particles.H

commit 4cea52d9d5e36a8e84c6ad57ac05c80fd7899cd2
Author: lijewski <lijewski>
Date:   Wed May 18 16:07:38 2011 +0000

    AdvectWithUmac() now assumes we have at least one ghost cell in umac.
    This means we only have to do one Redistribute() per call instead of two.
    It also means that particles that cross a periodic boundary work properly.

Src/C_AMRLib/Particles.H

commit 986a600d2c1408b2c3c7cfb27e0581580873b6f6
Author: lijewski <lijewski>
Date:   Mon May 16 22:54:34 2011 +0000

    delta in move_advect() didn't take into account a non-zero problo

Src/F_BaseLib/particles.f90

commit 081540255269208e362f5bc560c75f2b9c51ac6f
Author: lijewski <lijewski>
Date:   Mon May 16 22:47:19 2011 +0000

    delta in MoveKick[Drift] routines didn't take account of possibility of non-zero problo

Src/C_AMRLib/Particles.H

commit e70ec87c64f4db29405928f4a5fcecdeb89b950e
Author: lijewski <lijewski>
Date:   Mon May 16 21:48:02 2011 +0000

    fixed my typo

Src/C_AMRLib/Particles.H

commit b06d7409a6f36ef29ab97b1c669dba525d22407c
Author: almgren <almgren>
Date:   Mon May 16 21:13:58 2011 +0000

    Remove unused "grid"

Src/C_AMRLib/Particles.H

commit c67c9a01ce7f9d1a72c7c3794502fc2d1a2ab40b
Author: lijewski <lijewski>
Date:   Mon May 16 17:25:21 2011 +0000

    removed unused variable

Src/C_AMRLib/Particles.H

commit 561f36801c8e033dd679f8ede6d2a947f3033316
Author: lijewski <lijewski>
Date:   Sun May 15 18:29:36 2011 +0000

    added assert that DeriveFunc != 0 in derive()

Src/C_AMRLib/AmrLevel.cpp

commit 3de83c6c1ffd8c29c8407d2629af186d9e30f389
Author: lijewski <lijewski>
Date:   Sun May 15 17:08:14 2011 +0000

    removed some crufty KCC and Cfront stuff

Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/winstd.H
Tools/C_mk/Make.AIX
Tools/C_mk/Make.CRAY
Tools/C_mk/Make.CYGWIN_NT
Tools/C_mk/Make.IRIX64
Tools/C_mk/Make.Linux
Tools/C_mk/Make.OSF1
Tools/C_mk/Make.T3E
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit e234707f011f2102bf09f4a07a3897ec89aee6dd
Author: lijewski <lijewski>
Date:   Sun May 15 15:24:12 2011 +0000

    think I've finally got Timestamp doing what I want

Src/C_AMRLib/Particles.H

commit 4ab15b16b4ebee457a49cd0cb32d776c8524b455
Author: almgren <almgren>
Date:   Fri May 13 21:54:27 2011 +0000

    Make the two Increment routines have separate names.

Src/C_AMRLib/Particles.H

commit ec049a0d4aa8ed8b45a1a11cbcf3ca09814cf7b5
Author: almgren <almgren>
Date:   Fri May 13 21:46:06 2011 +0000

    Add a version of Particles that return the total number of particles in the domain at this level.

Src/C_AMRLib/Particles.H

commit 257ac64428d3f40f03073e21f8937cd5c8dd303d
Author: almgren <almgren>
Date:   Fri May 13 20:58:31 2011 +0000

    Clean up the Fortran-less Derive stuff.

Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp

commit 4502e8a3afcb41c1369bc606aaf33e84821315c6
Author: almgren <almgren>
Date:   Fri May 13 20:35:05 2011 +0000

    Allow us to defined derived quantities without associated Fortran functions -- these must be defined
    entirely in the C++.

Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp

commit 1fe503fa451aa15b4f5113f976ab6ae2ec7fef27
Author: almgren <almgren>
Date:   Fri May 13 17:52:25 2011 +0000

     If particle is right on a domain boundary then move it just inside the boundary.  Also add
    print statements about bad particle if initialization fails.

Src/C_AMRLib/Particles.H

commit 111dcd634de9529e6485ae15b4f95276c188216b
Author: lijewski <lijewski>
Date:   Thu May 12 22:20:33 2011 +0000

    removed names from Timestamp

Src/C_AMRLib/Particles.H

commit 0cc3c0ce723e85794c7f865a2b8033884e376f47
Author: lijewski <lijewski>
Date:   Thu May 12 20:58:44 2011 +0000

    close() Timestamp file after flush()

Src/C_AMRLib/Particles.H

commit e3306725292a3903f64cab8b9ecfcccad0ea9910
Author: lijewski <lijewski>
Date:   Wed May 11 17:55:40 2011 +0000

    exist ASAP from Timestamp() if no work to do

Src/C_AMRLib/Particles.H

commit 8483ac48a9b9c65b3e1acd81e585735699281e53
Author: lijewski <lijewski>
Date:   Tue May 10 22:36:04 2011 +0000

    make AssignDensityDoIt() work with non zero-based prob domain like Interp()

Src/C_AMRLib/Particles.H

commit ca9ef50163a7be357801cce99b525f090646832a
Author: lijewski <lijewski>
Date:   Tue May 10 22:34:35 2011 +0000

    make sure frac is in [0,1] in a floating-point way

Src/C_AMRLib/Particles.cpp

commit 0d423ba5921ef1713aade3b773abe23ac9c1f7e0
Author: lijewski <lijewski>
Date:   Tue May 10 18:56:30 2011 +0000

    frac calculation in Interp now works with non zero-based prob domain

Src/C_AMRLib/Particles.cpp

commit f5b2a5b865fee47a54e2e9807d5f8df6fda3348e
Author: lijewski <lijewski>
Date:   Tue May 10 04:55:21 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles.H

commit 2fa73845aec986aa253870e7624163d8ac8f9d9a
Author: lijewski <lijewski>
Date:   Mon May 9 20:03:29 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles.cpp

commit d62424634f2e2920128a3d3f1868f356a1525931
Author: lijewski <lijewski>
Date:   Mon May 9 19:48:36 2011 +0000

    just use MyProc when setting initial m_cpu

Src/C_AMRLib/Particles.H

commit 14b0c8b112245a0412bf6654a9ff10dcb4cab4f1
Author: lijewski <lijewski>
Date:   Mon May 9 17:27:45 2011 +0000

    removed lev argument from Interp()

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit cfc92c2b00f6546ca75ebe23161c8e53ca20bd89
Author: lijewski <lijewski>
Date:   Mon May 9 16:43:30 2011 +0000

    Timestamp() must now be passed the MultiFab to be sampled

Src/C_AMRLib/Particles.H

commit e8dd76fc105e5c41d77729de990aa4ca16e970ba
Author: lijewski <lijewski>
Date:   Mon May 9 05:51:58 2011 +0000

    some I/O mods

Src/C_AMRLib/Particles.H

commit e0f2191a4c7d55b8d0a80f31e2aae27b02860ebe
Author: lijewski <lijewski>
Date:   Mon May 9 05:51:03 2011 +0000

    removed some I/O

Src/C_AMRLib/Particles.cpp

commit e127fcee11e9646465e7d23705d72037ec0d24af
Author: lijewski <lijewski>
Date:   Mon May 9 04:35:50 2011 +0000

    print count of particles removed in RemoveParticlesNotAtFinestLevel()

Src/C_AMRLib/Particles.H

commit c65a387b0319380846baa4c397c89f17042b341f
Author: lijewski <lijewski>
Date:   Mon May 9 02:02:41 2011 +0000

    no longer remove zero length files in Timestamp; can't happen since each file gets a header

Src/C_AMRLib/Particles.H

commit 2d310c38011c6c7636ef6e33146936a7584f7b70
Author: lijewski <lijewski>
Date:   Mon May 9 01:25:38 2011 +0000

    fixed some debug output when DIM=2

Src/C_AMRLib/Particles.H

commit 635258f02972b40893e0232233c0c7beaa57bb8c
Author: lijewski <lijewski>
Date:   Mon May 9 00:09:20 2011 +0000

    refinement to Timestamp()

Src/C_AMRLib/Particles.H

commit bd88647ca029ad8c3f80e6386c73be9908a7568c
Author: lijewski <lijewski>
Date:   Sun May 8 20:04:49 2011 +0000

    Undefaulted the second argument to InitFromAsciiFile().
    This way is someone updates to the latest code and tries to use it, they'll
    get an error, until I've gotten around to fixing all calling sequences.

Src/C_AMRLib/Particles.H

commit 2d75d5171cb2901a97c96e32f2bbe0f539321627
Author: lijewski <lijewski>
Date:   Sun May 8 19:37:15 2011 +0000

    Apparently InitFromAsciiFile() has changed since I wrote it. Instead of
    just reading in the position data, N bytes of m_data where also being read it.
    Not sure how reading in all those bytes could possibly make sense since
    some of those bytes are there only to hold temporary position data in
    AdvectWithUmac(), but I
    had to change it a bit in order to make the routine work when I only want to
    read in positions: I added a default integer argument "extradata", that
    defaults to zero, which is the number of bytes of data in m_data to read
    in for each particle.  It MUST be <= N.
    The default way to use InitFromAsciiFile() is now to read in just
    positions. If you want to get "extra" data read in for each particle, you
    must specify the count as the second argument of the call.

Src/C_AMRLib/Particles.H

commit b984fa5c9c9835dde13cc093efdfbd69ecd86a5a
Author: lijewski <lijewski>
Date:   Sun May 8 19:02:58 2011 +0000

    remainder of particles in InitFromAscii() needs to go to last CPU not IOProc

Src/C_AMRLib/Particles.H

commit 7fd55e972cda178b5c5ad7d9969535d0ee07a863
Author: lijewski <lijewski>
Date:   Sat May 7 00:16:22 2011 +0000

    InitFromAsciiFile() is now much faster in parallel

Src/C_AMRLib/Particles.H

commit 12ed44dfbb5445ac7d8d146153463d4d6ce87903
Author: lijewski <lijewski>
Date:   Fri May 6 21:52:07 2011 +0000

    changed AdvectWithUmac() to John's satisfaction

Src/C_AMRLib/Particles.H

commit 34ef9ff6b49c43b9b2ade4e5c7b6ed0ca04091a9
Author: lijewski <lijewski>
Date:   Fri May 6 21:21:07 2011 +0000

    modest speedup to InitFromAsciiFile(); more to come ...

Src/C_AMRLib/Particles.H

commit 5758965ae597e044af1384e7ac668a39ec60c40f
Author: almgren <almgren>
Date:   Fri May 6 21:03:11 2011 +0000

    Add new routine -- GetRhoFromParticles which defines a grid-based density and
    modifies the mass of the particles so that the total mass of grid+particles
    remains the same.

Src/C_AMRLib/Particles.H

commit 54be97ea6599ef8bd8b7630d49f6704554a146f3
Author: almgren <almgren>
Date:   Fri May 6 00:06:04 2011 +0000

    If we call AssignDensity, then now allow domains that have no periodic boundaries
    as long as none of the particles are within one cell of the domain boundary.

Src/C_AMRLib/Particles.H

commit 1d29c22ec266497ab71d619f169c265edbc06cd5
Author: lijewski <lijewski>
Date:   Thu May 5 22:49:45 2011 +0000

    GetGravity() now calls Interp()

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 84c10585cb069b75e6b2b34676a588445fe52ec2
Author: lijewski <lijewski>
Date:   Thu May 5 17:35:39 2011 +0000

    added ParticleBase::Interp() -- called by Timestamp()

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit b55b5fedda6ac452d418dc1839c8e4501921fd01
Author: lijewski <lijewski>
Date:   Wed May 4 19:46:04 2011 +0000

    early exit from Increment()

Src/C_AMRLib/Particles.H

commit 110b4b10ff81121bfcca5c03144aab5d30a8f30b
Author: lijewski <lijewski>
Date:   Wed May 4 17:10:37 2011 +0000

    added RemoveParticlesNotAtFinestLevel() needed by HeatTransfer

Src/C_AMRLib/Particles.H

commit 52bde8ac565d7e6602be41dba3c1d0c1691ce649
Author: lijewski <lijewski>
Date:   Tue May 3 21:01:37 2011 +0000

    removed some excess whitespace when printing in verbose

Src/C_AMRLib/Particles.H

commit 5bf196e35f12467c3df6b4b894d36d065a5f894b
Author: lijewski <lijewski>
Date:   Tue May 3 20:00:00 2011 +0000

    no longer force Timestamp() to have non-empty names and indices

Src/C_AMRLib/Particles.H

commit a28e619171853bc4bee64c52399bce2938077421
Author: lijewski <lijewski>
Date:   Tue May 3 19:21:09 2011 +0000

    refinement to how we reset NextID()

Src/C_AMRLib/Particles.H

commit 5264abb3c3ae3672ca390f07e953fabc125a6a03
Author: almgren <almgren>
Date:   Mon May 2 18:45:30 2011 +0000

    Only enforce periodicty in AssignDensity if there are actually particles present.

Src/C_AMRLib/Particles.H

commit de52900600575a74b978497e2e4f96fb13ef3e5f
Author: almgren <almgren>
Date:   Fri Apr 29 22:24:46 2011 +0000

    Modify fill_boundary so that it doesn't kick out if ng = 0.

Src/F_BaseLib/multifab.f90

commit 4d178a6a1951e240a2bda182fa41097d2bcfb9f8
Author: lijewski <lijewski>
Date:   Fri Apr 29 17:57:19 2011 +0000

    slightly different rules for libraries from Gunther for VisIt usage

Tools/C_mk/Make.rules

commit abb81b4a3ff6f2fbe446a0776509b961dd62bd90
Author: almgren <almgren>
Date:   Thu Apr 28 21:59:53 2011 +0000

    Correct criterion for destroying gcrse.

Src/F_BaseLib/fillpatch.f90

commit 5d33678f63cd2f0006fc71d2abb8445aedf5c7a2
Author: almgren <almgren>
Date:   Thu Apr 28 20:56:38 2011 +0000

    Changes by Ann & Mike L. which hopefully fix the problems we were seeing.  Still not clear if this will
    work in all cases; we are assuming that proper nesting covers situations.

Src/F_BaseLib/fillpatch.f90

commit 9060a21d7b17fdf9ba93c641c4fc2410d8d578b9
Author: almgren <almgren>
Date:   Thu Apr 28 19:33:36 2011 +0000

    If ng = 0 define ncomp(crse) components of gcrse (used to default to 1).

Src/F_BaseLib/fillpatch.f90

commit 56d3e69141ce3e750b1bf7712af4b4dfef6aa215
Author: almgren <almgren>
Date:   Sun Apr 24 21:17:11 2011 +0000

    Allow for fourth order stencil with stencil_width = 2.

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 88c932351e3fbc9c0db117ffba3c8c3c49766d0c
Author: almgren <almgren>
Date:   Sun Apr 24 21:09:14 2011 +0000

    If fourth_order = .true. then call fourth_order_interp instead of lin_cc_interp.

Src/F_BaseLib/fillpatch.f90

commit 524d5a0a5c082b21476548702f89c4f195d6610e
Author: almgren <almgren>
Date:   Sun Apr 24 21:08:15 2011 +0000

    Add stubs for fourth order interpolation routines.

Src/F_BaseLib/interp.f90

commit 041917e70f7d9a5b76bf5c7d3c223bf66b837399
Author: lijewski <lijewski>
Date:   Fri Apr 22 23:05:21 2011 +0000

    a little more OMP work

Src/LinearSolvers/F_MG/coarsen_coeffs.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/nodal_mask.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 013ece29e83aff808a949b1adc9ecbed65e0ff61
Author: lijewski <lijewski>
Date:   Fri Apr 22 21:37:17 2011 +0000

    changed some 0 -> ZERO

Src/LinearSolvers/F_MG/stencil.f90

commit cca17799f6362ba521bbcaaf2f29b384e2dff3ec
Author: almgren <almgren>
Date:   Fri Apr 22 21:35:20 2011 +0000

    1) Pass through optional argument stencil_width_input.
    2) Send ng=0 to fillpatch -- no need to create ghost cells of the buffer region mf's around the fine grids.

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit c1183891ac6c24dafaa65a92397ffc7e0bb1793e
Author: almgren <almgren>
Date:   Fri Apr 22 21:29:06 2011 +0000

    Allow for a more general stencil_width (still defaults to one)

Src/F_BaseLib/fillpatch.f90

commit b68e06f67b2b3e10bf705cfcd5c67abfb5246d54
Author: almgren <almgren>
Date:   Fri Apr 22 20:18:52 2011 +0000

    Fix test on whether coeffs sum to zero (used for whether we enforce solvability)

Src/LinearSolvers/F_MG/ml_cc.f90

commit d034d7be7616b55df6db196b8cf1e26912b14676
Author: almgren <almgren>
Date:   Fri Apr 22 20:07:27 2011 +0000

    Add new function -- "max_of_stencil_sum" that looks just like stencil_norm but
    doesn't take the absolute value of each component before summing.

Src/LinearSolvers/F_MG/stencil.f90

commit dd3d3cee2912f9f30ebceb8a1e0d5c4e7ac099c9
Author: almgren <almgren>
Date:   Fri Apr 22 18:49:40 2011 +0000

    Adding additional print statement.

Src/LinearSolvers/F_MG/ml_cc.f90

commit d34370b6f07baf8bbf2c0d50d646a1a75a4624a6
Author: ajnonaka <ajnonaka>
Date:   Thu Apr 21 20:12:24 2011 +0000

    prevent the grid iteration code from running during initialization if you have supplied a grid file.  This prevents multiple redundant calls to initData at level 1 and greater if you have supplied a fixed grid file

Src/C_AMRLib/Amr.cpp

commit 46e3c4397cc060e34cfd4cbb3a0cde3ecf597dc7
Author: lijewski <lijewski>
Date:   Wed Apr 20 20:08:44 2011 +0000

    use CC wrapper instead of crayc++ for Cray

Tools/C_mk/Make.Linux

commit a0beb4049f3a5e6d223d37541f7bb6427c0cc5e1
Author: lijewski <lijewski>
Date:   Mon Apr 18 16:43:03 2011 +0000

    now print out number of OMP threads if BL_USE_OMP=TRUE

Src/C_BaseLib/BoxLib.cpp

commit a9135de36ea88c01344ca626a7a9016896f5dfa8
Author: marc <marc>
Date:   Thu Apr 14 22:25:22 2011 +0000

    Fix up the logic for BL_NO_FORT

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp

commit 6045aceba361a9e4a089bf4fd2198f5c87532968
Author: lijewski <lijewski>
Date:   Wed Apr 13 21:15:20 2011 +0000

    some OMP

Src/C_AMRLib/FLUXREG_3D.F

commit 8aac6a4ec330e49f2e43c7b7e07ec2e662bb05d0
Author: lijewski <lijewski>
Date:   Wed Apr 13 21:03:26 2011 +0000

    minor performance improvement

Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F

commit b32c306f3f8a64d35e35e823e71ae82e63e11f3a
Author: almgren <almgren>
Date:   Fri Apr 8 18:46:32 2011 +0000

    Get rid of extra characters.

Src/F_BaseLib/make_new_grids.f90

commit 8574335147d76ba18c1a5845333ff8de12ad1389
Author: marc <marc>
Date:   Fri Apr 8 01:34:01 2011 +0000

    *** empty log message ***

Tools/C_util/ViewMF/viewMFcol.cpp

commit c6229704b14dd4ac5170a1f79474500f409b0124
Author: lijewski <lijewski>
Date:   Thu Apr 7 21:18:19 2011 +0000

    removed all references to USE_THREADS

Src/C_BaseLib/test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Tests/C_BaseLib/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tools/C_mk/Make.AIX
Tools/C_mk/Make.OSF1
Tools/C_mk/Make.defs

commit e93c256015e86da9263de88a6c43b5367820a682
Author: lijewski <lijewski>
Date:   Sat Apr 2 23:26:07 2011 +0000

    minor simplification of AssignDensity()

Src/C_AMRLib/Particles.H

commit 9ef548b36e08aebf25d10ba35acac2cc2a57c936
Author: lijewski <lijewski>
Date:   Fri Apr 1 23:15:23 2011 +0000

    *** empty log message ***

Tools/C_mk/Make.mpi

commit ba907cfbf64a8903c3ba92cd6112fe6860c6eb94
Author: lijewski <lijewski>
Date:   Fri Apr 1 17:36:21 2011 +0000

    added GPROF stuff

Tools/F_mk/comps/gfortran.mak

commit cd14ba9a71fe938ed2b00d92214126c11d79c818
Author: almgren <almgren>
Date:   Thu Mar 31 18:03:47 2011 +0000

    Add comments about which MoveKick or MoveKickDrift function we're calling -- the one
    with gravity at cell centers or the one with the normal components of gravity on faces.

Src/C_AMRLib/Particles.H

commit 4b70af736f7d76c2f965c65134d6c604df02fbe8
Author: lijewski <lijewski>
Date:   Thu Mar 31 16:59:12 2011 +0000

    added a little commented out debugging code

Src/C_BaseLib/Geometry.cpp

commit c88db5d9b7107b46aa77a896c367a2a1d447d320
Author: lijewski <lijewski>
Date:   Thu Mar 31 16:17:04 2011 +0000

    got to call new SumPeriodicBoundary() with correct Geom

Src/C_AMRLib/Particles.H

commit 614af5d6c9f0fe31a69471fd15fbef5de1f4cce0
Author: lijewski <lijewski>
Date:   Wed Mar 30 23:59:27 2011 +0000

    integrated in new SumPeriodicBoundary(dstmf,srcmf)

Src/C_AMRLib/Particles.H

commit ee1b80d10263a38252c6a4d845bcb9b6ffd6b424
Author: lijewski <lijewski>
Date:   Wed Mar 30 23:58:51 2011 +0000

    Wrote SumPeriodicBndry() taking a srcmf and dstmf.  Still needs to be tested.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 4419c69a20a9dbe8b617c4bcef08a4425f9c488b
Author: lijewski <lijewski>
Date:   Wed Mar 30 21:42:56 2011 +0000

    more work on AssignDensity(); still not right for level 1 grid abutting periodic boundary

Src/C_AMRLib/Particles.H

commit 1333972a72ffe5d48693e2818729f6f5537f603d
Author: almgren <almgren>
Date:   Wed Mar 30 19:27:13 2011 +0000

    1) Change verbosity threshhold.
    2) If there are no particles at a level then return a negative est_dt for that level.

Src/C_AMRLib/Particles.H

commit f8b12073a406c043747f8be29bf65eac7f9d3a9a
Author: almgren <almgren>
Date:   Wed Mar 30 18:28:55 2011 +0000

    if particles.verbose > 0 then print out total number of particles when reading from ascii file.

Src/C_AMRLib/Particles.H

commit 5d7de367133f32b4298ce027a8453e31ac96ef7e
Author: lijewski <lijewski>
Date:   Wed Mar 30 18:16:59 2011 +0000

    modest improvement to bndry_reg_copy()

Src/F_BaseLib/bndry_reg.f90

commit 716631ab0f0ae4ae6815fdad9d9c4734527ccb0b
Author: almgren <almgren>
Date:   Wed Mar 30 17:44:22 2011 +0000

    Add setval of tcmf.

Src/C_AMRLib/Particles.H

commit 7b9dfdfdf697536b0f1ada09a065f83a66227df4
Author: almgren <almgren>
Date:   Wed Mar 30 17:08:00 2011 +0000

    Make sure to call multifab_fill_boundary on crse mf when filling bndry_reg.

Src/F_BaseLib/bndry_reg.f90

commit 6e605c640b88c217c46e86222a29178ef4d0f88f
Author: lijewski <lijewski>
Date:   Tue Mar 29 20:48:25 2011 +0000

    yet more work on multi-level AssignDensity()

Src/C_AMRLib/Particles.H

commit 97e565ff3ed983f36016f16f86b8d8b72a10dab4
Author: lijewski <lijewski>
Date:   Tue Mar 29 20:35:46 2011 +0000

    more work on multi-level AssignDensity()

Src/C_AMRLib/Particles.H

commit a4db7937acde2720565d9192be6bba8fe7812e7d
Author: lijewski <lijewski>
Date:   Tue Mar 29 20:24:20 2011 +0000

    more work on multi-level AssignDensity()

Src/C_AMRLib/Particles_1D.F
Src/C_AMRLib/Particles_2D.F
Src/C_AMRLib/Particles_3D.F

commit 4457897b2873c7151e7de540d8eb93bedfeeee4f
Author: lijewski <lijewski>
Date:   Tue Mar 29 17:43:39 2011 +0000

    more work on multi-level AssignDensity()

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles_F.H

commit 81d8358487c7aa069c4b95f70fd4b85a2d459aa3
Author: lijewski <lijewski>
Date:   Tue Mar 29 17:28:13 2011 +0000

    some work on multi-level AssignDensity()

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles_1D.F
Src/C_AMRLib/Particles_2D.F
Src/C_AMRLib/Particles_3D.F
Src/C_AMRLib/Particles_F.H

commit 2c92cf131d544fc50bacf24e9ea57698fd9386de
Author: lijewski <lijewski>
Date:   Mon Mar 28 23:00:26 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles_3D.F

commit 2f5dea77a020749b1baabb010dd426a1c0664e4f
Author: lijewski <lijewski>
Date:   Mon Mar 28 23:00:13 2011 +0000

    added AssignDensityDoIt()

Src/C_AMRLib/Particles.H

commit 1db4bdea075d95ab374e617437ddd88bb0450b73
Author: lijewski <lijewski>
Date:   Mon Mar 28 22:37:45 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles_1D.F
Src/C_AMRLib/Particles_2D.F

commit 5ae45db8c61006f07600dd7bf3ad614e187d8a37
Author: lijewski <lijewski>
Date:   Mon Mar 28 22:20:08 2011 +0000

    added part_summassup()

Src/C_AMRLib/Particles_3D.F
Src/C_AMRLib/Particles_F.H

commit 9ea1c8eb6c5abb5b5d53128ad2963ae23553c030
Author: lijewski <lijewski>
Date:   Mon Mar 28 20:32:42 2011 +0000

    added part_sumdown()

Src/C_AMRLib/Particles_3D.F
Src/C_AMRLib/Particles_F.H

commit 017cd78c7014c27a706251c4f1365239022108a7
Author: lijewski <lijewski>
Date:   Mon Mar 28 16:19:35 2011 +0000

    mod to quiet g++

Src/C_AMRLib/Particles.H

commit 1503348ff3228c0203c504c96f8a3519bfcd0ba3
Author: lijewski <lijewski>
Date:   Fri Mar 25 18:01:48 2011 +0000

    some OMP refinement

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 0f5999c1322522f3d84db5a70bd7a25961ecf311
Author: lijewski <lijewski>
Date:   Fri Mar 25 17:11:38 2011 +0000

    some OMP refinement

Src/F_BaseLib/fab.f90
Src/F_BaseLib/interp.f90
Src/F_BaseLib/multifab.f90

commit 731234bf48973e8200bb7d7867e72a1964b471a6
Author: lijewski <lijewski>
Date:   Thu Mar 24 21:27:31 2011 +0000

    some OMP refinement

Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/CG_3D.F
Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/LP_3D.F

commit eecf6c81d397e512d3f20b8734027be767a16be8
Author: lijewski <lijewski>
Date:   Thu Mar 24 20:50:43 2011 +0000

    some OMP refinement

Src/C_AMRLib/INTERP_3D.F

commit 0f244370fb7979854900797701a0872e94c10113
Author: lijewski <lijewski>
Date:   Thu Mar 24 20:37:37 2011 +0000

    some OMP refinement

Src/C_BaseLib/SPECIALIZE_3D.F

commit 2c3839d4b0c86f6b22973fd290cdcbd6b099ee44
Author: lijewski <lijewski>
Date:   Tue Mar 22 20:24:56 2011 +0000

    some cleanup

Src/C_AMRLib/Amr.cpp
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/interface.cpp

commit 049b34833ba5b2c3843879d913959eef82a8477d
Author: lijewski <lijewski>
Date:   Tue Mar 22 20:02:48 2011 +0000

    No longer need to call AddToCache() to recache some MultiFabs.
    DistributionMapping::FlushCache() now only removes DMs that are not
    referenced by any MultiFabs.

Src/C_AMRLib/Amr.cpp

commit d781e4d7264c5e46d2ae1944c90f7ae0020ee358
Author: lijewski <lijewski>
Date:   Tue Mar 22 20:01:39 2011 +0000

    The cache is now a std::map instead of a std::vector.
    FlushCache() now only removes DMs that are not referenced by any MultiFabs.
    Removed AddToCache().

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 373d14eb15a5b8f8fac1b4e0579a8c87a692e494
Author: almgren <almgren>
Date:   Sun Mar 20 17:42:38 2011 +0000

    Make the minion smoother be GSRB, for now anyway.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_smoother.f90

commit b759a8fb43b7adf4ecd4df0ed6a65e68de9ef732
Author: almgren <almgren>
Date:   Sun Mar 20 15:36:34 2011 +0000

    Add crse flux construction for Minion's 2D cross stencil (ns = 9 as opposed to 7).

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 92b106b4ed8c7f76be78bed45bd4af0894057aab
Author: almgren <almgren>
Date:   Sun Mar 20 15:35:56 2011 +0000

    Add flux construction for Minion's 2D cross stencils (ns = 9 as opposed to 7)

Src/LinearSolvers/F_MG/stencil.f90

commit 8f2d33ef89c58e0a977c78e4afc2c1fffd6a22e5
Author: almgren <almgren>
Date:   Sun Mar 20 15:29:42 2011 +0000

    Fix typo.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 0a9c55df74c4b3e27248f951078820952a4fa386
Author: almgren <almgren>
Date:   Sun Mar 20 15:26:43 2011 +0000

    Clean up how we test whether we should enforce solvability.

Src/LinearSolvers/F_MG/mg.f90

commit 856ff3d37e09393e0ef64c4c172b302d3d03cfe7
Author: almgren <almgren>
Date:   Sun Mar 20 15:25:59 2011 +0000

    Use new coeffs_sum_to_zero flag to decide whether to enforce solvability.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 579594a99b1aff4269b9f61ccff72993d5a2fc2d
Author: almgren <almgren>
Date:   Sun Mar 20 15:25:33 2011 +0000

    Add coeffs_sum_to_zero flag in mgt

Src/LinearSolvers/F_MG/mg_tower.f90

commit 383000cd5b40e4856c1075b3daaf309f719a02fd
Author: almgren <almgren>
Date:   Sun Mar 20 02:51:00 2011 +0000

    Need to allow for nghost > 1.

Src/F_BaseLib/create_umac_grown.f90

commit 3ed535aa9b96eb0a1026180fa7d0c1eb1a9fc46f
Author: almgren <almgren>
Date:   Sat Mar 19 20:15:17 2011 +0000

    Grow the fine region by ng_fill instead of 1 so that we fill the right zone
    of ghost cells.

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90

commit c9549dcafd368fad05744ecb93a6fc23cb4a4385
Author: almgren <almgren>
Date:   Sat Mar 19 01:24:04 2011 +0000

    Remove unused variable.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 665f09d440ae25c09eae97e7357f01ff10eb54f9
Author: almgren <almgren>
Date:   Fri Mar 18 23:59:32 2011 +0000

    Comment out the making of bottom_singular until I figure out how to differentiate
    MAC solves from viscous/diffusive solves.

Src/LinearSolvers/F_MG/mg.f90

commit ae8a745513d5bfcd6276b576fa627a0dc7da3322
Author: lijewski <lijewski>
Date:   Fri Mar 18 16:40:29 2011 +0000

    removed some too-little-work OMP loops

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 8fd8622d0e66d03975ef1b907b9fbd69adbe2728
Author: lijewski <lijewski>
Date:   Fri Mar 18 16:03:41 2011 +0000

    removed some too-little-work OMP loops

Src/F_BaseLib/fab.f90
Src/F_BaseLib/interp.f90
Src/F_BaseLib/multifab.f90

commit 36683cda860921c3cb8c0ba85cbea36fcf5d15d8
Author: lijewski <lijewski>
Date:   Thu Mar 17 22:11:14 2011 +0000

    removed some too-little-work OMP loops

Src/LinearSolvers/C_NodalMG/amr_real3d.f
Src/LinearSolvers/C_NodalMG/hg_avg3d.f

commit 90fca2c8a777de4149f2e99e4f70274f96fe6352
Author: lijewski <lijewski>
Date:   Thu Mar 17 21:13:01 2011 +0000

    removed some too-little-work OMP loops

Src/C_BaseLib/COORDSYS_3D.F

commit a4fda83f9393b888179438715b2cb9c8d5ec0b15
Author: lijewski <lijewski>
Date:   Thu Mar 17 21:00:23 2011 +0000

    removed some too-little-work OMP loops

Src/C_AMRLib/FILCC_3D.F
Src/C_AMRLib/INTERP_3D.F

commit 7a11c523d6770ecb71b7a654ecb8b294d985f36c
Author: lijewski <lijewski>
Date:   Thu Mar 17 20:52:50 2011 +0000

    removed some too-little-work OMP loops

Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/CG_3D.F
Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/LP_3D.F

commit 2cc3c2606cb200ae5c5d28e5c6aa43802ea4ebc9
Author: almgren <almgren>
Date:   Wed Mar 16 19:50:38 2011 +0000

    We now allow crse to have more than one ghost cell (before required exactly one) and
    we only copy what is needed for interpolation.

Src/F_BaseLib/create_umac_grown.f90

commit e9bb87ebdfa4cf82e2cfff48a1d871393a752139
Author: almgren <almgren>
Date:   Wed Mar 16 17:56:35 2011 +0000

    Convert is_singular from integer to logical.

Src/LinearSolvers/F_MG/mg.f90

commit 723ffd9c624b77a2c2366fb62f8cfc1e7c88e1ae
Author: almgren <almgren>
Date:   Wed Mar 16 17:34:59 2011 +0000

    Add "is_singular" optional argument to mg_tower_build so that you can over-ride the local test for solvability.

Src/LinearSolvers/F_MG/mg.f90

commit a1f709cc893818d09af1e34280b9921ffa834890
Author: nazgul <nazgul>
Date:   Tue Mar 15 23:56:12 2011 +0000

    Adding ability to specify DistributionMapping when defining
    FluxRegisters.

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 2f91d691bbc009969e6e136a271c508f536ff33e
Author: nazgul <nazgul>
Date:   Tue Mar 15 23:55:15 2011 +0000

    Adding ability to specify DistributionMapping when defining these
    objects, in case the correct map has been flushed from the cache.

Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit c4172d61a8b89742f8cd6b60ab93fcbe848fbccd
Author: almgren <almgren>
Date:   Thu Mar 10 23:42:04 2011 +0000

    Add pleiades stuff.

Tools/C_mk/Make.mpi

commit 0dca7de44729be768e002ce2d61554961361b17e
Author: wqzhang <wqzhang>
Date:   Wed Mar 9 23:54:05 2011 +0000

    Some new features.
    
    If one types "touch dump_and_continue" in the run directory, a
    checkpoint file and a plot file will be generated and then the run
    will continue.  The "dump_and_continue" file will be deleted.
    
    If one types "touch stop_run" in the run directory, the run will stop
    without generating a checkpoint.  The "stop_run" file will be deleted.
    
    If one types "touch dump_and_stop" in the run directory, a checkpoint
    file and a plot file will be generated and then the run will stop.
    The "dump_and_stop" file will be deleted.

Src/C_AMRLib/Amr.cpp

commit fbeca23a12ef5502590cd5bd84972fd3bdb7e5bf
Author: ajnonaka <ajnonaka>
Date:   Wed Mar 9 13:32:07 2011 +0000

    typo in output string

Src/F_BaseLib/fab.f90

commit c2661dfa951b3a355896a8d9d975e4d7ebfab51f
Author: almgren <almgren>
Date:   Tue Mar 8 21:04:50 2011 +0000

    Modify the verbosity tests so that the "particles added per processor" print only happens
    if verbosity > 1.

Src/C_AMRLib/Particles.H

commit ae0874d88fe6c8bc901460b6d2076281ddda75dd
Author: marc <marc>
Date:   Tue Mar 8 18:47:47 2011 +0000

    *** empty log message ***

Tools/C_util/ViewMF/GNUmakefile
Tools/C_util/ViewMF/mfMinMax.cpp

commit dc69ba3831b51fceccb093fe371ae5d49ad0b865
Author: lijewski <lijewski>
Date:   Tue Mar 8 02:09:14 2011 +0000

    little mod to previous OMP reorg of estTimestep()

Src/C_AMRLib/Particles.H

commit 3f6b1b01ac7f8a62d7dbdf3de125aad9931257e2
Author: almgren <almgren>
Date:   Tue Mar 8 01:32:18 2011 +0000

    Mike L's fixes to estTimestep make this work with PGI + OMP.

Src/C_AMRLib/Particles.H

commit 48107b8f1d2a698e81b9ff19ed9c2edf12269604
Author: almgren <almgren>
Date:   Mon Mar 7 03:39:11 2011 +0000

    Add additional solvability enforcement -- *before* we start the V-cycle.
    We might even be able to use this only and eliminate the tests inside the V-cycles ....
    but for now we'll leave them in.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 9bb23368b351065bd3c5e2b10e1e3cc62024be0e
Author: almgren <almgren>
Date:   Sun Mar 6 16:20:48 2011 +0000

    Move ParallelReduceMin call out of verbose test.

Src/C_AMRLib/Particles.H

commit adf4672587f1898240287fb163195d82576d8226
Author: lijewski <lijewski>
Date:   Sat Mar 5 00:18:09 2011 +0000

    version of contains_nan() and contains_inf() that take scomp ncomp and ngrow

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 7a5147b4455256acbfb7b70700c9e0799d7cc43b
Author: almgren <almgren>
Date:   Fri Mar 4 02:03:50 2011 +0000

    Add Amr::NumDataLogs to tell you how many data streams you have opened.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 4ed5a936c975a3cc2af9d557cf3f49b6214b066a
Author: almgren <almgren>
Date:   Thu Mar 3 23:19:38 2011 +0000

    Verbose --> SetVerbose

Src/C_AMRLib/Particles.H

commit b493d19bb0c55d74c52db604f4d3c471e016a4b4
Author: lijewski <lijewski>
Date:   Thu Mar 3 21:49:55 2011 +0000

    some simplification

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 7653303114c4343c66fe40fb19167207506856ec
Author: lijewski <lijewski>
Date:   Thu Mar 3 17:57:22 2011 +0000

    added minIndex() and maxIndex()

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit a9c0ca7690c9e15188cc6962f29ff9bac8380f8c
Author: almgren <almgren>
Date:   Wed Mar 2 23:21:49 2011 +0000

    Comment out print statement.

Src/LinearSolvers/F_MG/mg.f90

commit c59081121057e589ba9609b881c3955673f0e2f0
Author: almgren <almgren>
Date:   Wed Mar 2 23:21:08 2011 +0000

    Make the cell-centered single-level solver solvable if singular -- EACH V-cycle.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 7af67a0bdbbaf968feffc03dc6d910d9b0e787d0
Author: almgren <almgren>
Date:   Wed Mar 2 23:20:11 2011 +0000

    Fix print statement.

Src/LinearSolvers/F_MG/itsol.f90

commit f75c7ed57f3052b5beea317c54434e8cf42bb663
Author: lijewski <lijewski>
Date:   Tue Mar 1 17:12:29 2011 +0000

    simplified AdvectWithUMac()

Src/C_AMRLib/Particles.H

commit e9f7644949a578bfecf1e39b4fee1d71830c7aed
Author: lijewski <lijewski>
Date:   Tue Mar 1 17:09:07 2011 +0000

    simpler but equivalent formulas for delta and vel in move_advect

Src/F_BaseLib/particles.f90

commit 72d738b23c63c6848f6ff182cd278e78963a535c
Author: wqzhang <wqzhang>
Date:   Mon Feb 28 23:10:19 2011 +0000

    test.py does not work on Ubuntu (at least 10.04 LTS) because os.system calls dash instead of bash

Tools/C_util/regtests/test-Ubuntu.py

commit ccb86d391ca8b63bd5420aa0f3a9dd8cff03d69f
Author: wqzhang <wqzhang>
Date:   Mon Feb 28 23:05:34 2011 +0000

    *** empty log message ***

Tools/C_util/regtests/radiation-tests.ini

commit 012fe5a155e87f1f0f5ec3fc555c3daa5702cd3f
Author: lijewski <lijewski>
Date:   Mon Feb 28 21:17:26 2011 +0000

    removed an assertion

Src/C_AMRLib/Particles.H

commit 25296e269faa327cfca3f0cbbaf9711e346a222b
Author: mzingale <mzingale>
Date:   Mon Feb 28 21:06:53 2011 +0000

    the predictor and corrector in the advection were both doing almost
    the same thing -- remove redundant code by looping over the velocity
    interpolation and redistribution

Src/F_BaseLib/particles.f90

commit 496491c2adc369c457dedab74d488d6dbf06f549
Author: lijewski <lijewski>
Date:   Mon Feb 28 19:03:52 2011 +0000

    bit more simplification

Src/C_AMRLib/Particles.H

commit f0454b82806cd98bc5aa8b79b8b391077e54c947
Author: lijewski <lijewski>
Date:   Mon Feb 28 18:29:09 2011 +0000

    made AdvectWithUMac mirror the one in fParallel

Src/C_AMRLib/Particles.H

commit a53786d8446ff7637d134aadf78ea5566772c5d5
Author: lijewski <lijewski>
Date:   Mon Feb 28 18:23:43 2011 +0000

    some cleanup & speedups

Src/C_AMRLib/Particles.H

commit 62999c433ee108a5bbc4263bd684f05ce47e0565
Author: lijewski <lijewski>
Date:   Mon Feb 28 17:49:31 2011 +0000

    added code to check to infs mirroring nan code

Src/F_BaseLib/fab.f90
Src/F_BaseLib/fabio_c.c

commit ad98b2fe441be68c89326fdb061d0e116fcc68d7
Author: almgren <almgren>
Date:   Sat Feb 26 01:59:18 2011 +0000

    Remove extraneous definition.

Src/C_AMRLib/Particles.H

commit d986f63e1fe93242fb83d85f7a3f4af8035a032c
Author: almgren <almgren>
Date:   Sat Feb 26 01:50:11 2011 +0000

    Change default in estTimeStep to be 0.5 rather than 0.1

Src/C_AMRLib/Particles.H

commit 6a23aa0bcd43ae6c2398211b31d67f75d48101d8
Author: almgren <almgren>
Date:   Sat Feb 26 01:45:33 2011 +0000

    Added another version of moveKick and moveKickDrift that takes edge-based gravity components
    rather than cell-based.

Src/C_AMRLib/Particles.H

commit da3432de0b624308e46e13f8bca8701351480567
Author: almgren <almgren>
Date:   Sat Feb 26 00:03:02 2011 +0000

    Remove print statement.

Src/LinearSolvers/F_MG/itsol.f90

commit aae3d367a865a9bbcb9bb31b100523fe69cf6c31
Author: lijewski <lijewski>
Date:   Fri Feb 25 22:39:33 2011 +0000

    FAB_CONTAINS_NAN now works for gcc; need to test on __GNUC__ macro

Src/F_BaseLib/fabio_c.c

commit 068e39a15556a5cb57cf341ab854571a14b0c8d2
Author: lijewski <lijewski>
Date:   Fri Feb 25 22:13:25 2011 +0000

    contains_nan_bx_c()

Src/F_BaseLib/fab.f90

commit 668db550a17db4460b9200345a4e87fce31f82de
Author: lijewski <lijewski>
Date:   Fri Feb 25 21:17:51 2011 +0000

    contains_nan_allc() calls contains_nan_c()

Src/F_BaseLib/fab.f90

commit 2155523d6aba608219458be4fda3c668dc2a00aa
Author: lijewski <lijewski>
Date:   Fri Feb 25 21:10:52 2011 +0000

    added contains_nan_c()

Src/F_BaseLib/fab.f90

commit bca9b562f8d2de1e7a4ca95eb78827ddb9c99d88
Author: lijewski <lijewski>
Date:   Fri Feb 25 18:47:10 2011 +0000

    some simplification of add_point()

Src/F_BaseLib/particles.f90
Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit e0321505d84e5262fd3ce3bc86c6b3a5f0dd4412
Author: mzingale <mzingale>
Date:   Fri Feb 25 16:52:21 2011 +0000

    remove the conditional_add routine -- it required that all processors
    call it at the same time -- this is not how we do the particle adds
    in MAESTRO.  Instead, implement a less ambitious version by adding
    the "conditional" logical optional argument to the normal
    pointwise add routine.  If true, then this will only add the particle
    if there is not already one in the same zone/level.

Src/F_BaseLib/particles.f90

commit b69a93965713cc66a755dc053ecc73caa152c2b0
Author: marc <marc>
Date:   Thu Feb 24 01:06:52 2011 +0000

    *** empty log message ***

Tools/C_util/ViewMF/viewMF.cpp

commit 21eb835bb344e18212015ec8f8799d7b76bf8393
Author: almgren <almgren>
Date:   Tue Feb 22 23:53:07 2011 +0000

    Make sure to do singular adjustment *before* diagonal preconditioning.

Src/LinearSolvers/F_MG/itsol.f90

commit 0c595a1680fede756ee51e4c28cfb4c1168dc0d9
Author: almgren <almgren>
Date:   Tue Feb 22 23:35:14 2011 +0000

    Fix test for mgt%bottom_singular.

Src/LinearSolvers/F_MG/mg.f90

commit b804f7e779129cdd0fb81ccfa02bf82a00ac0545
Author: almgren <almgren>
Date:   Tue Feb 22 21:48:34 2011 +0000

    Change Init --> InitFromAsciiFile

Src/C_AMRLib/Particles.H

commit f15497b2a4a416aa7195d2bda362782c2f695e91
Author: mzingale <mzingale>
Date:   Sun Feb 20 15:45:19 2011 +0000

    first cut at a "conditional add" routine -- only add a particle if it
    is some distance (dr) away from any existing particle.  Needs more
    testing, but seems to work.

Src/F_BaseLib/particles.f90

commit 51ea5ec9ceefb180774a87271c113cf2ae991083
Author: almgren <almgren>
Date:   Fri Feb 18 21:28:34 2011 +0000

    1) Wrapped printing of read time for PROBINIT inside verbose>1 test.
    2) Added sanity checks when restarting to check n_cell and ref_ratio from inputs file against what is in checkpoint file.
    If the index-space domains at all levels don't match then the code aborts on restart.

Src/C_AMRLib/Amr.cpp

commit b44a287f155f549aae05205926f028cc005c3db3
Author: lijewski <lijewski>
Date:   Thu Feb 17 17:14:24 2011 +0000

    more specialized versions of contains_nan() and contains_inf()

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp

commit 35d118157d232b51a17c3dcaf03884fb05002d58
Author: lijewski <lijewski>
Date:   Thu Feb 17 00:02:18 2011 +0000

    changes to debugging interface

Src/F_BaseLib/particles.f90

commit b7a2de5af9a4d3f57577b90c15cad04b70bc81bd
Author: almgren <almgren>
Date:   Tue Feb 15 22:38:43 2011 +0000

    Forgot commas.

Src/C_AMRLib/Particles.H

commit bf5e15b97908259d7a7105bb3a150952cf951d40
Author: almgren <almgren>
Date:   Tue Feb 15 22:33:16 2011 +0000

    Fix typos.

Src/C_AMRLib/Particles.H

commit 6b648d6a8f1c06149a5dd245b833a8cb764a472e
Author: almgren <almgren>
Date:   Tue Feb 15 20:55:18 2011 +0000

    This has the correct time stepping now (fingers crossed)

Src/C_AMRLib/Particles.H

commit eac71640515973573f2ad770bc4eaf435d03d0a7
Author: almgren <almgren>
Date:   Mon Feb 14 22:54:12 2011 +0000

    Add adot/a term to velocity update.

Src/C_AMRLib/Particles.H

commit d24109c37d3330bc1291ab386c516c9aeb396da3
Author: almgren <almgren>
Date:   Mon Feb 14 02:48:02 2011 +0000

    This version includes new options for JFE's machine (Jan Frederik Engels).

Tools/C_mk/Make.defs

commit e397d0aef3fbc7b718fbff16ab157497195b3861
Author: almgren <almgren>
Date:   Sat Feb 12 03:17:19 2011 +0000

    Integrate changes from Test_90Mpc version.

Src/C_AMRLib/Particles.H

commit 65b34564bf63e0f2c610c7392bb5fdacf3f9a337
Author: lijewski <lijewski>
Date:   Fri Feb 11 22:30:02 2011 +0000

    some cleanup

Src/C_AMRLib/Particles.H

commit bcc4cd903dc842c81890fa37ab8ca89ff02e7900
Author: lijewski <lijewski>
Date:   Fri Feb 11 21:50:34 2011 +0000

    added WriteAsciiFile()

Src/C_AMRLib/Particles.H

commit 6ee908d8f35084b203f446213f51edc82e7b1d29
Author: marc <marc>
Date:   Thu Feb 10 19:15:21 2011 +0000

    adjust usage of numLevelsMAX to be consistent with its name, was allowing one extra level

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit c07bbd987f7a67b07b23ebc78260293e0e35e003
Author: lijewski <lijewski>
Date:   Thu Feb 10 00:06:50 2011 +0000

    fixed issue with Timestamp()

Src/C_AMRLib/Particles.H

commit 83a340e632ced515920385460ca9e0d3b417ce37
Author: lijewski <lijewski>
Date:   Wed Feb 9 23:42:03 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles.H

commit 45ee144c1242efd02f4ebcd453b9aef321677b0e
Author: lijewski <lijewski>
Date:   Wed Feb 9 23:21:15 2011 +0000

    some work on advectWithUMac()

Src/C_AMRLib/Particles.H

commit a5035b6e157da7af51d318d8bf1373efc16199c6
Author: lijewski <lijewski>
Date:   Tue Feb 8 23:01:50 2011 +0000

    bit more work on Timestamp() -- appears to be working

Src/C_AMRLib/Particles.H

commit 4a6ffacd2f3455767cb842c166269e08b92d7a4b
Author: lijewski <lijewski>
Date:   Tue Feb 8 22:17:50 2011 +0000

    redistribute() now also does the origpos member

Src/F_BaseLib/particles.f90

commit e91c4b7dab6924e8073b11753206ed02a0ff1568
Author: lijewski <lijewski>
Date:   Tue Feb 8 19:19:01 2011 +0000

    more work on Timestamp()

Src/C_AMRLib/Particles.H

commit 678e89fa59ba47e894cf4e509ac389f31b84f6e7
Author: lijewski <lijewski>
Date:   Tue Feb 8 19:05:22 2011 +0000

    some work on Timestamp()

Src/C_AMRLib/Particles.H

commit 09d8d31009ebaf8d68a78e2f95604f096ede2873
Author: mzingale <mzingale>
Date:   Sun Feb 6 03:07:39 2011 +0000

    first attempt at doing second-order in time advection of the particles.
    A new field, origpos(), was added to the particle datatype to store
    the position of the particle at the start of the time integration.
    Redistribution is now done twice -- once at the half-time and then
    after the final movement of the particle.

Src/F_BaseLib/particles.f90

commit 6a807169af16243cde1b1ee6c665022adcf88a62
Author: lijewski <lijewski>
Date:   Fri Feb 4 23:20:33 2011 +0000

    we now checkpoint/restart the max value of particle_id

Src/F_BaseLib/particles.f90

commit 9a9cbc5e193b0ce79889bfd719a521fa446407b5
Author: lijewski <lijewski>
Date:   Fri Feb 4 22:46:21 2011 +0000

    we now checkpoint/restart the max value of NextID()

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit eff3d8f2a2d034ab1d657ec69597f74c1ff5e926
Author: lijewski <lijewski>
Date:   Fri Feb 4 22:30:24 2011 +0000

    Init() can now be called on restart too - doesn't assume there are no existing particles in container

Src/C_AMRLib/Particles.H

commit 398c68202ecffc3a8ff9a08022294c72d6bdf12c
Author: lijewski <lijewski>
Date:   Fri Feb 4 21:32:06 2011 +0000

    do NOT use the update arg to Where() after PeriodicShift()

Src/C_AMRLib/Particles.H

commit e3e18fc5fd320b2721a6bca249deb102b5f3a225
Author: lijewski <lijewski>
Date:   Fri Feb 4 21:31:25 2011 +0000

    PeriodicShift() now only tries a particular dir if you're periodic in that dir

Src/C_AMRLib/Particles.cpp

commit 35fc616c11226a2e36001fcdb7855299ca5d02f2
Author: lijewski <lijewski>
Date:   Fri Feb 4 20:25:50 2011 +0000

    deal with N==0 in InitRandom()

Src/C_AMRLib/Particles.H

commit 03ee8e1f8a0f49885a76b3af6cecbe06495f5e87
Author: lijewski <lijewski>
Date:   Fri Feb 4 19:08:15 2011 +0000

    integrated in ParticleBase::NextID()

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 212f9409ff3c61299a0671f6fbb023826b74c9fb
Author: lijewski <lijewski>
Date:   Fri Feb 4 18:47:34 2011 +0000

    Particles can now be invalidated.
    Their ID is negated.
    Algorithms must ignore invalid particles.
    Redistribute() gets rid of them.
    Checkpoint() doesn't write'm to disk.

Src/C_AMRLib/Particles.H

commit 3c28a31fd8de658bce72477e9209963e6f675417
Author: lijewski <lijewski>
Date:   Fri Feb 4 16:44:00 2011 +0000

    added a BL_ASSERT()

Src/C_AMRLib/Particles.H

commit 61ec0ffd7461c3aee2b8efceb27c2f699cd3f6fe
Author: lijewski <lijewski>
Date:   Wed Feb 2 22:15:45 2011 +0000

    removed do_not_minimize_comcost stuff

Src/C_BaseLib/DistributionMapping.cpp

commit 31368e35fc04faaeb60507dfda3a6476be778317
Author: marc <marc>
Date:   Wed Feb 2 01:42:16 2011 +0000

    *** empty log message ***

Tools/C_mk/Make.mpi

commit 2aefc92ff5fc85ba4c6d1545f18e545b323386c2
Author: mzingale <mzingale>
Date:   Sun Jan 30 02:45:07 2011 +0000

    change the header names to contain no spaces so it is easier to parse

Src/F_BaseLib/particles.f90

commit ec0adc991c15bda05933cde9b1fa5e9668317c26
Author: mzingale <mzingale>
Date:   Sat Jan 29 20:13:12 2011 +0000

    add a header to the top of the timestamp files that lists the name of
    each column.  This requires that a names() array is passed through
    giving the name of each data field.

Src/F_BaseLib/particles.f90
Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit bb4541229038fc5273b75bed51b90a1539e6866f
Author: ajnonaka <ajnonaka>
Date:   Sat Jan 29 01:59:27 2011 +0000

    created a tidy interface for adding a single particle at a point

Src/F_BaseLib/particles.f90

commit e11a6d4091d9c8bff2682696eedef2b5ad99be80
Author: ajnonaka <ajnonaka>
Date:   Fri Jan 28 18:12:27 2011 +0000

    generalized piecewise bilinear advection of particles using mac velocities to 1d/2d/3d

Src/F_BaseLib/particles.f90

commit 5b2aec51b77be75c33394fe5bd02eada3767250c
Author: ajnonaka <ajnonaka>
Date:   Fri Jan 28 00:41:26 2011 +0000

    bilinear advection using MAC velocities (2d only)

Src/F_BaseLib/particles.f90

commit ffabe8eee93e25737daf52c05b8d2683e66320d2
Author: ajnonaka <ajnonaka>
Date:   Fri Jan 28 00:23:49 2011 +0000

    particle_move_advect now takes mac velocities as input.  Still using 1st order approximation to velocity at a point, which will be upgraded soon.
    
    moved advection of particles to advance.f90, immediately following the second call to macproject

Src/F_BaseLib/particles.f90

commit 34670e4bf4216be0e45542987f5c2983b7d61d85
Author: lijewski <lijewski>
Date:   Thu Jan 27 23:39:44 2011 +0000

    *** empty log message ***

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit 1098ba2a72c47700a46ac75e487f31d805037045
Author: ajnonaka <ajnonaka>
Date:   Thu Jan 27 23:38:52 2011 +0000

    made particle_id a saved variable
    added global accessor for particle_id

Src/F_BaseLib/particles.f90

commit 85084dfa4e3e028bac86ec84a84dd60bad727569
Author: lijewski <lijewski>
Date:   Thu Jan 27 23:19:50 2011 +0000

    more error checking

Src/F_BaseLib/vector_i.f90

commit 3deda67ed26709146ea51e0cc93fdde5e8e6e935
Author: ajnonaka <ajnonaka>
Date:   Thu Jan 27 22:53:08 2011 +0000

    changed problo/hi -> prob_lo/hi to make consistent with VARDEN and MAESTRO

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/particles.f90

commit 95903767f1397d839a30a194d3670045034f9a28
Author: ajnonaka <ajnonaka>
Date:   Thu Jan 27 22:46:20 2011 +0000

    added an advect function

Src/F_BaseLib/particles.f90

commit 709e44dc7ad9846a89ec24a262e10819ee8c0094
Author: lijewski <lijewski>
Date:   Thu Jan 27 22:31:22 2011 +0000

    more error checking

Src/F_BaseLib/particles.f90

commit 072082e9f81dc41fcbad6797ea710ae1b92d01f2
Author: lijewski <lijewski>
Date:   Thu Jan 27 22:13:30 2011 +0000

    brought up-to-date with latest particle changes

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit cd06bbad69c79ac3269559836cfd41a14258290a
Author: lijewski <lijewski>
Date:   Thu Jan 27 21:27:57 2011 +0000

    mods for MAESTRO

Src/F_BaseLib/particles.f90

commit 284f34ccefaf84b7594205c133dabba34cdec835
Author: lijewski <lijewski>
Date:   Wed Jan 26 22:51:02 2011 +0000

    now used PARTICLES

Src/F_BaseLib/test/GNUmakefile
Tests/F_BaseLib/GNUmakefile

commit 089aa9a988b70d9001146417ed964e74fd751671
Author: lijewski <lijewski>
Date:   Wed Jan 26 22:47:07 2011 +0000

    added PARTICLES macro to get particles.f90

Src/F_BaseLib/GPackage.mak

commit cad9ef451f9da5865f993cce474a3d17004b92df
Author: ajnonaka <ajnonaka>
Date:   Wed Jan 26 21:12:13 2011 +0000

    add f90sources += particles.f90

Src/F_BaseLib/GPackage.mak

commit 671a40933dab97b9c6c4ed72daa0a69338edbe14
Author: lijewski <lijewski>
Date:   Wed Jan 26 17:11:47 2011 +0000

    added dataptr()

Src/F_BaseLib/particles.f90
Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit dd2a8fc2d82f19f4758f1d30528523ec3d6842b8
Author: marc <marc>
Date:   Tue Jan 25 23:50:22 2011 +0000

    Add placeholder for max_order...ordre of tangential interpolant...supporting only 1 and 3 at the moment

Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F
Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F
Src/C_BoundaryLib/INTERPBNDRYDATA_F.H
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp

commit ce2ac33663ffbaf08d909b3de58843db66ecddd0
Author: lijewski <lijewski>
Date:   Tue Jan 25 23:26:33 2011 +0000

    some simplification

Src/F_BaseLib/particles.f90
Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit cc93ac78488aad402454bd5f0fbb891224333f49
Author: lijewski <lijewski>
Date:   Tue Jan 25 22:26:54 2011 +0000

    2D now appears to work also

Src/F_BaseLib/particles.f90
Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit d73b353da95d42b040632e716b6cda6f7d2bf7c9
Author: lijewski <lijewski>
Date:   Tue Jan 25 18:44:57 2011 +0000

    some simplification

Src/F_BaseLib/particles.f90

commit 35329ed0d7a6d9c62714846067638c82a39e6c70
Author: lijewski <lijewski>
Date:   Tue Jan 25 17:16:44 2011 +0000

    particle_vector -> particle_container

Src/F_BaseLib/particles.f90
Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit 5d4604190b8fa85c1cc8e139c47a1f84da57e6be
Author: lijewski <lijewski>
Date:   Tue Jan 25 00:04:21 2011 +0000

    little more cleanup

Src/F_BaseLib/particles.f90

commit 4872091dd1f9e730cb110597104f8e3db4cc1227
Author: lijewski <lijewski>
Date:   Mon Jan 24 23:56:30 2011 +0000

    remove empty timestamp files after each series of writes

Src/F_BaseLib/particles.f90
Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit fe747390417ec3a0ba9f40dad831c2012228a986
Author: lijewski <lijewski>
Date:   Mon Jan 24 23:55:59 2011 +0000

    added some unlink() code for empty files used by particle code

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c

commit f41cce267b76f6f44f96cd1834133753a0aa4b90
Author: lijewski <lijewski>
Date:   Mon Jan 24 23:08:26 2011 +0000

    can now set/unset verbosity and debugging via function calls

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit 807b15c1b35c52b1824daa52e6674383ca8ab573
Author: lijewski <lijewski>
Date:   Mon Jan 24 23:07:58 2011 +0000

    some cleanup

Src/F_BaseLib/particles.f90

commit 50bb96c0e17d6e4124639ace729e92d07e40e731
Author: lijewski <lijewski>
Date:   Mon Jan 24 22:36:05 2011 +0000

    added some timestamp() tests

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit d9db99ce329fa848f32cdf234c30ee3006aeed8c
Author: lijewski <lijewski>
Date:   Mon Jan 24 22:35:42 2011 +0000

    timestamp() appears to be working

Src/F_BaseLib/particles.f90

commit c7cf0b46b3e409d4678a4778b3ba3ad48dd0e2c1
Author: lijewski <lijewski>
Date:   Mon Jan 24 22:22:58 2011 +0000

    timestamp() closer to working

Src/F_BaseLib/particles.f90

commit db5904c26d33d4eac959aca7d32ee20b1b375f81
Author: lijewski <lijewski>
Date:   Mon Jan 24 21:06:56 2011 +0000

    *** empty log message ***

Src/F_BaseLib/fabio_c.c

commit 911e4a3c6cfb2b4bf5cfd85b8289e45922957a97
Author: lijewski <lijewski>
Date:   Mon Jan 24 21:06:42 2011 +0000

    some work on timestamp()

Src/F_BaseLib/particles.f90

commit 43b2304595deb07abe77dfe1a48f20776a74c1a2
Author: lijewski <lijewski>
Date:   Fri Jan 21 21:23:59 2011 +0000

    added couple more functions needed by particle code

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c

commit 3eb3d9e01aba89b650d46ae75ac48555119f5037
Author: lijewski <lijewski>
Date:   Fri Jan 21 21:22:03 2011 +0000

    some cleanup

Src/F_BaseLib/particles.f90

commit 38cfb2358c6f068123668aca9c2a6cec95de928e
Author: lijewski <lijewski>
Date:   Fri Jan 21 20:59:15 2011 +0000

    *** empty log message ***

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit f2d3a04c1ac86b62094b3789af198e431b75156a
Author: lijewski <lijewski>
Date:   Fri Jan 21 20:52:04 2011 +0000

    some code to test restart()

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit a13abc933aedba82806aa393abe602a58a9b08da
Author: lijewski <lijewski>
Date:   Fri Jan 21 20:51:52 2011 +0000

    restart appears to be working

Src/F_BaseLib/particles.f90

commit c5d4d351caba94ae4e6fd4eaeb2b272fd31fa07c
Author: lijewski <lijewski>
Date:   Fri Jan 21 01:21:27 2011 +0000

    *** empty log message ***

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit 8d1e0d408591fddbe9bc0f3acd543aabbbf4dad7
Author: lijewski <lijewski>
Date:   Fri Jan 21 01:21:16 2011 +0000

    some work on restart()

Src/F_BaseLib/particles.f90

commit a1741c876cb3b0ac672ec9f45be1eb84aee70f49
Author: lijewski <lijewski>
Date:   Thu Jan 20 21:35:32 2011 +0000

    checkpoint() appears to work; on to restart()

Src/F_BaseLib/particles.f90

commit b486092867b7b47f4e0a72f310b2ec82deceb5e0
Author: lijewski <lijewski>
Date:   Thu Jan 20 17:45:26 2011 +0000

    checkpoint() is that much closer to working

Src/F_BaseLib/particles.f90

commit b5947b9cee06b1d629ac53311f38e60faa7111de
Author: lijewski <lijewski>
Date:   Wed Jan 19 23:51:18 2011 +0000

    yet more work on checkpoint()

Src/F_BaseLib/particles.f90

commit 454b5a39277aa8e3965eb922dec500717b40fdf8
Author: lijewski <lijewski>
Date:   Wed Jan 19 23:50:27 2011 +0000

    moved interface for particle write routines from particles.f90 to here

Src/F_BaseLib/fabio.f90

commit b1d6b2348f08704c4165b8cb979f8a7aaaf36a3a
Author: lijewski <lijewski>
Date:   Wed Jan 19 23:37:33 2011 +0000

    added couple C I/O functions needed by particle code

Src/F_BaseLib/fabio_c.c

commit e8650168165eff1286f5fb5fbb42b1ad7aab24bd
Author: lijewski <lijewski>
Date:   Wed Jan 19 23:37:09 2011 +0000

    yet more work on checkpoint()

Src/F_BaseLib/particles.f90

commit 2f2f2379c8571ca08cd8cf8e096a2bc793b1a0c3
Author: lijewski <lijewski>
Date:   Wed Jan 19 22:26:51 2011 +0000

    some more work on checkpoint()

Src/F_BaseLib/particles.f90

commit c7c397455c482f4373e8b671a86b0734941b6046
Author: lijewski <lijewski>
Date:   Wed Jan 19 21:43:22 2011 +0000

    some work on checkpoint()

Src/F_BaseLib/particles.f90

commit aee91af68d949710c4bdd9639add89620345485f
Author: lijewski <lijewski>
Date:   Fri Jan 14 21:25:30 2011 +0000

    comment out particles.f90 for the moment

Src/F_BaseLib/GPackage.mak

commit 3cef6e5a7475bc89cf2975a0f470b0e5de96ab44
Author: lijewski <lijewski>
Date:   Thu Jan 13 19:13:20 2011 +0000

    redistribute() appears to be working

Src/F_BaseLib/particles.f90

commit 8b364887455ae1bc2f033bd82e437864d63bfaa7
Author: lijewski <lijewski>
Date:   Thu Jan 13 19:12:58 2011 +0000

    *** empty log message ***

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit 61fbbbb8a14b2fb87091425eb123ee4c1185d088
Author: lijewski <lijewski>
Date:   Thu Jan 13 18:15:16 2011 +0000

    redistribute() is closer to being working code ...

Src/F_BaseLib/particles.f90

commit 39f168a93fd3e2b7689684233bb8768da2605093
Author: lijewski <lijewski>
Date:   Thu Jan 13 18:14:54 2011 +0000

    more testing for redistribute()

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit bdfa002e10c9249448a5675764c50a4da9534037
Author: lijewski <lijewski>
Date:   Thu Jan 13 00:18:13 2011 +0000

    some work on redistribute() - not finished

Src/F_BaseLib/particles.f90

commit 7ba867837db22e1e670b9f130d4f580f4bf1f660
Author: lijewski <lijewski>
Date:   Wed Jan 12 22:12:29 2011 +0000

    Figured out the Intel -vs- gfortran issue.
    I wasn't setting the rr(n,:) component of the ml_boxarray.
    That should really be passed as part of build_n().

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit c5d47669764012c60b5f468cb410230fe2d46e7a
Author: lijewski <lijewski>
Date:   Wed Jan 12 21:49:57 2011 +0000

    move_randomo() implemented; works with gfortran but not Intel 11.1 ???

Src/F_BaseLib/particles.f90

commit 5df1388eca23b3c4f9af0d5f7e401ca67e389643
Author: lijewski <lijewski>
Date:   Wed Jan 12 21:49:24 2011 +0000

    test code for move_random()

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit cc5b4593be664d9b5858bd8c498ee1c64b8d8867
Author: lijewski <lijewski>
Date:   Wed Jan 12 17:55:14 2011 +0000

    multi-level mla's appear to work OK

Src/F_BaseLib/particles.f90

commit c4272b91797f1119fa3387801160d54bd39f3d0f
Author: lijewski <lijewski>
Date:   Wed Jan 12 17:54:41 2011 +0000

    added test for multi-level mla

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit 150b06d94fe1c76094288bc6fb89dda289f1aef1
Author: lijewski <lijewski>
Date:   Wed Jan 12 03:09:37 2011 +0000

    fixed bug -- how did it work for me before?

Src/F_BaseLib/particles.f90

commit 6062518c92d6404f91031636fa45f3cf73ca2f4c
Author: lijewski <lijewski>
Date:   Wed Jan 12 00:27:26 2011 +0000

    init_random() seems OK in serial

Src/F_BaseLib/particles.f90

commit 94a623cff0a1621c917b8a044c8644402c0c0980
Author: lijewski <lijewski>
Date:   Wed Jan 12 00:26:52 2011 +0000

    testing init_random()

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit f8124f2b76abde7e6c3183883f4973c3a522fb7f
Author: lijewski <lijewski>
Date:   Tue Jan 11 23:56:23 2011 +0000

    wrote init_random() -- untested yet

Src/F_BaseLib/particles.f90

commit 3f2f9c28d8ea2f5738247d7d74ad192feb4b6649
Author: lijewski <lijewski>
Date:   Tue Jan 11 22:24:08 2011 +0000

    wrote particle_index() and particle_where(); now to test ...

Src/F_BaseLib/particles.f90

commit 41eb3592aab5b8e3fea66e3858e09f72ce93d7fd
Author: lijewski <lijewski>
Date:   Tue Jan 11 20:30:22 2011 +0000

    particle_vector knows about valid/invalid particles

Src/F_BaseLib/particles.f90

commit 223ffc6eabf384a31ad9641a949ed5c056d50a2e
Author: lijewski <lijewski>
Date:   Tue Jan 11 20:30:01 2011 +0000

    *** empty log message ***

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit 6d26eef25be786fc1af0aeecad12341dfb837945
Author: lijewski <lijewski>
Date:   Tue Jan 11 18:25:28 2011 +0000

    added particle_vector

Src/F_BaseLib/particles.f90

commit e64deb07f9d85a3ca819fbb10f6d62e4ef928174
Author: lijewski <lijewski>
Date:   Tue Jan 11 17:02:19 2011 +0000

    added particles stuff

Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/main.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/main.f90

commit 4ab911788d8c8183988f3640c19f607f4af4f1a9
Author: lijewski <lijewski>
Date:   Tue Jan 11 17:01:50 2011 +0000

    particles test code

Src/F_BaseLib/test/t_particles.f90
Tests/F_BaseLib/t_particles.f90

commit 37e7fdcf9b3eb3d97161bdfb7e029e4d6021bfb8
Author: lijewski <lijewski>
Date:   Tue Jan 11 17:01:11 2011 +0000

    added particles.f90

Src/F_BaseLib/GPackage.mak

commit 2b7bd76ac6865fd440aa9292ff019138b86e7341
Author: lijewski <lijewski>
Date:   Tue Jan 11 17:00:47 2011 +0000

    Just getting started ...

Src/F_BaseLib/particles.f90

commit 94ed7421e9fbea49676e18e6d360825668b4ddcd
Author: almgren <almgren>
Date:   Thu Jan 6 23:05:44 2011 +0000

    Add JFE's InitCosmo() routine which sets up initial conditions a la Martin White.

Src/C_AMRLib/Particles.H

commit a1398f84a3f5df10890e14579191771959855b2a
Author: almgren <almgren>
Date:   Mon Jan 3 21:35:05 2011 +0000

    Add a to estTimestep.

Src/C_AMRLib/Particles.H

commit 550be76fa9a6587cb60b73ebe86a8f8a157154db
Author: almgren <almgren>
Date:   Mon Jan 3 20:49:31 2011 +0000

    Fix...

Src/C_AMRLib/Particles.H

commit 8bc34dede449830a0398da207112491b4e99c15c
Author: almgren <almgren>
Date:   Mon Jan 3 20:48:00 2011 +0000

    Add versions of moveKick and moveKickDrift that include the comoving coordinate stuff.

Src/C_AMRLib/Particles.H

commit 7efe4e360feef4cd0e6d09d3a54ae89cf8b995cd
Author: almgren <almgren>
Date:   Mon Jan 3 20:26:30 2011 +0000

    This doesn't compile.

Src/C_AMRLib/Particles.H

commit 4dea81541ab142460efca12278c4d3c7b80a2cc1
Author: gpau <gpau>
Date:   Wed Dec 22 23:46:58 2010 +0000

    *** empty log message ***

Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/GNUmakefile

commit 31f5c0dde6ea182d5f12a5a4d3776e8aeedb1a8c
Author: ajnonaka <ajnonaka>
Date:   Tue Dec 21 18:38:02 2010 +0000

    added ability to pass in aux multifab to tagging routines

Src/F_BaseLib/make_new_grids.f90
Src/F_BaseLib/tag_boxes.f90

commit 057b35332743b620cd9ec03baf6e6a9de52d15fe
Author: mzingale <mzingale>
Date:   Tue Dec 21 15:08:41 2010 +0000

    add toy_convect, diffusion tests

Tools/C_util/regtests/Maestro-tests.ini

commit e30646f4460726be9fda154612686a1bfd92c429
Author: ajnonaka <ajnonaka>
Date:   Mon Dec 20 20:34:35 2010 +0000

    fixed bug in calls to multifab_fill_boundary and multifab_physbc_edgevel for problems where nlevs > 2

Src/F_BaseLib/create_umac_grown.f90

commit 4032ed90a05cbcf8d8f9ff89386485b8ce18a434
Author: mzingale <mzingale>
Date:   Wed Dec 15 03:30:51 2010 +0000

    trap uninitalized variables in debug mode

Tools/F_mk/comps/gfortran.mak

commit d7402f076dbc81b7538f5aaca760ba69033678fd
Author: mzingale <mzingale>
Date:   Tue Dec 14 03:23:35 2010 +0000

    add support for MPI for fParallel-based runs

Tools/C_util/regtests/test.py

commit 9b4094cdbc4481b7d1cb1eda03d160b62c5d8b5a
Author: gpau <gpau>
Date:   Thu Dec 9 00:53:21 2010 +0000

    fix for pgCC oddity

Src/C_BaseLib/BaseFab.cpp

commit 033dc34047f66366ad548e1ca9a63f291235edd5
Author: lijewski <lijewski>
Date:   Wed Dec 8 23:07:06 2010 +0000

    mods for compiling VisIt with Microsoft

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/winstd.H

commit 950f94545746286486f9e6619afffe0cdbbd6a9d
Author: lijewski <lijewski>
Date:   Wed Nov 24 02:50:25 2010 +0000

    Yet another downgrade of the Cray optimization options.
    I've finally managed to get Castro/ParticleTest working with the Cray compiler on grace.
    The C++ used "-O 1 -h noexceptions" and the Fortran "-O 1,vector0 -h noomp".
    This is strictly with MPI not with OMP.
    It takes roughly twice as long per timestep as does PGI.

Tools/C_mk/Make.Linux

commit 6962caea5fb723674cc6c246b84f33e3e5008bc1
Author: lijewski <lijewski>
Date:   Sat Nov 20 21:50:29 2010 +0000

    Downgrade Cray optimization from -O 2 -> -O 1.
    Still can't get Castro/ParticleTest to run.
    It's dying in the first gravity solve.
    Weird since MAESTRO/wdconvect works with -O 1.

Tools/C_mk/Make.Linux

commit 0e4dbd8b468a5f96c3abf8925fce4f605c1ca333
Author: lijewski <lijewski>
Date:   Sat Nov 20 20:21:26 2010 +0000

    Downgrade optimization from -O2 -> -O1.
    -O2 hits an OMP bug though -O2 works fine with just MPI.
    Weirdly -O1 appears to produce slight faster code (just a few percent).

Tools/F_mk/comps/Linux_cray.mak

commit 8a61abad95f56d977d43af121b2e97f0c2eff5e5
Author: mzingale <mzingale>
Date:   Sat Nov 20 01:42:58 2010 +0000

    add a 1-d version to get flame_1d running again

Src/F_BaseLib/multifab_physbc_edgevel.f90

commit 03ed0297ce3835f2c423ae6bef945e6f3713a852
Author: lijewski <lijewski>
Date:   Fri Nov 19 18:06:59 2010 +0000

    dm wasn't being initialized

Src/F_BaseLib/test/t_bxasc.f90
Tests/F_BaseLib/t_bxasc.f90

commit 2ff3e01c168ebe3312726b3303d8a5c8fb6b621c
Author: lijewski <lijewski>
Date:   Thu Nov 18 20:14:12 2010 +0000

    tweaks to Cray options to work around a bug

Tools/C_mk/Make.Linux

commit 990052328ce02c7ba2e7f4578edfaf32d8ccd267
Author: ajnonaka <ajnonaka>
Date:   Mon Nov 15 20:50:51 2010 +0000

    default max_bottom_nlevel=3 instead of 1024

Src/LinearSolvers/F_MG/mg_tower.f90

commit def1f343d24768d9f03ba01e40a571b308f1bbf1
Author: lijewski <lijewski>
Date:   Mon Nov 15 19:23:57 2010 +0000

    speedup to InitRandom()

Src/C_AMRLib/Particles.H

commit f854c9188d19620c2dea43f94871a4f16dd7f222
Author: vince <vince>
Date:   Mon Nov 15 19:13:37 2010 +0000

    couts.

Src/C_AMRLib/StationData.cpp

commit f94798eca8a6f9b9e4d1cb69ff68adae23e902da
Author: lijewski <lijewski>
Date:   Thu Nov 11 21:08:56 2010 +0000

    parallel_abort() was ignoring the optional string argument

Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit ed4ff64e0c166e71c3e3f9daf28a2a5a700531f7
Author: ajnonaka <ajnonaka>
Date:   Thu Nov 11 17:54:39 2010 +0000

    fixed USE_OLDPLOTPER

Tools/C_mk/Make.defs

commit a8e291ad7e133fd5a4cd9af7dd7d32725417f65d
Author: ajnonaka <ajnonaka>
Date:   Thu Nov 11 17:48:44 2010 +0000

    add support for USE_OLDPLOTPER=TRUE in makefile

Tools/C_mk/Make.defs

commit 3ee111ca09ad657e7d572cb10f4e2ed5dcd25057
Author: ajnonaka <ajnonaka>
Date:   Thu Nov 11 17:48:24 2010 +0000

    change "BL_USEOLDPLOT_PER" to "BL_USE_OLDPLOTPER" to be consistent with other cases

Src/C_AMRLib/Amr.cpp

commit 25aa4e267ad91619b09b7b67887249f5d23fcd9b
Author: lijewski <lijewski>
Date:   Wed Nov 10 23:46:48 2010 +0000

    tweaked g++ and gfortran debug options

Tools/C_mk/Make.defs

commit 1be67525fcaba9a04e19aced0b79248e0d09bc15
Author: lijewski <lijewski>
Date:   Wed Nov 10 23:46:09 2010 +0000

    quiet -Wall warnings

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/MAKESLICE_3D.F
Src/C_BaseLib/COORDSYS_3D.F

commit 4296cdee4e648908100f22e4b12e2a0d5f84ea83
Author: lijewski <lijewski>
Date:   Wed Nov 10 22:10:08 2010 +0000

    more IPM tweaks for hopper and franklin

Tools/C_mk/Make.Linux

commit 97d94a64a641e98968547a5ebb7660a501b25dfc
Author: lijewski <lijewski>
Date:   Tue Nov 9 21:16:51 2010 +0000

    short-circuited some parallel routines when nprocs()==1

Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 70d605cd12bb721255d16fb5145e26877f50321c
Author: lijewski <lijewski>
Date:   Tue Nov 9 20:37:41 2010 +0000

    added MPI_Gatherv() capability to parallel_gather()

Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit e3b107317186363d249ff5eed58c6dde1277db1b
Author: lijewski <lijewski>
Date:   Tue Nov 9 20:36:44 2010 +0000

    added simple parallel_gather() test

Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_main.f90

commit a8aa41270e527e3bd6f6f57661082169c15b7cab
Author: almgren <almgren>
Date:   Tue Nov 9 20:08:24 2010 +0000

    Cleanup...

Src/C_BaseLib/COORDSYS_2D.F
Src/C_BaseLib/COORDSYS_3D.F
Src/C_BaseLib/COORDSYS_F.H

commit 56e798f2d72dfd7545c7a1fe1d181b9cb587e6d6
Author: lijewski <lijewski>
Date:   Tue Nov 9 17:16:07 2010 +0000

    compiles again

Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_bx.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_bx.f90
Tests/F_BaseLib/t_main.f90

commit 716cff18a6b869352010969245c5f344932f7520
Author: almgren <almgren>
Date:   Tue Nov 9 16:56:07 2010 +0000

    Replace 1e-20 by 1d-50 -- we were bumping into this limit in very
    low density astrophysics problems.

Src/C_AMRLib/INTERP_1D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F

commit a5b578b8d3fd9659015dfa8a6d7199a849255d5b
Author: vince <vince>
Date:   Mon Nov 8 20:19:22 2010 +0000

    fix for stationdata with capped finest level.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp

commit ac8af0fdd83b7380c483053376d4749b35472b12
Author: vince <vince>
Date:   Fri Nov 5 21:22:19 2010 +0000

    fixed station bug.
    modified plot_per to adjust timestep.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp

commit c764015ca52678c9ca909f72645d494a725859a6
Author: lijewski <lijewski>
Date:   Fri Nov 5 21:00:44 2010 +0000

    fixed bug I just introduced

Src/C_AMRLib/Particles.H

commit 415f008f4ead783ad011b3632dc1535815a6d5eb
Author: lijewski <lijewski>
Date:   Fri Nov 5 20:13:53 2010 +0000

    trimmed memory use in Redistribute() a tad

Src/C_AMRLib/Particles.H

commit a4b653f41f510ccc0363eb36888eb8149e7aa0de
Author: lijewski <lijewski>
Date:   Fri Nov 5 18:04:54 2010 +0000

    call mgt_use_alltoallv() if fabarray.do_alltoallv is true

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 12e65418b40105ff9358af648499244762301952
Author: lijewski <lijewski>
Date:   Fri Nov 5 18:04:09 2010 +0000

    added mgt_use_alltoallv() which sets Do_AllToAllV in multifab_module to true

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 013be99bb28620dd7a76a4f6e2c4444bbcc629f6
Author: lijewski <lijewski>
Date:   Fri Nov 5 16:47:15 2010 +0000

    Twiddle particles by some epsilon in PeriodicShift() in the case where
    they lie exactly on the domain boundary.  We do this to make sure the
    particles when periodically shifted is back in the domain.  I don't trust
    floating point arithmetic to always do the right thing.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 18cc719270cbe8a2e086d81f2fe82e8fab8346ce
Author: lijewski <lijewski>
Date:   Thu Nov 4 16:53:00 2010 +0000

    wrapped some stray I/O statements in m_verbose > 0

Src/C_AMRLib/Particles.H

commit d7d12fe342effbcbb35628b9f60a3df3df904e90
Author: lijewski <lijewski>
Date:   Thu Nov 4 16:24:40 2010 +0000

    some more error checking

Src/C_AMRLib/Particles.H

commit 75871fa48db802c9e7dc7c92629907c6c6b18a4f
Author: lijewski <lijewski>
Date:   Wed Nov 3 06:01:07 2010 +0000

    changed the byte spread output to refer to MPI processes instead of CPUs

Src/F_BaseLib/fab.f90

commit ed569a9a2267feabbfb5e660ca180a9c5e5ebe04
Author: almgren <almgren>
Date:   Tue Nov 2 16:05:37 2010 +0000

    oops -- still need variable "vol"

Src/LinearSolvers/F_MG/mg.f90

commit b43f6b7c28840b46a83b933e41e04b700f96ef59
Author: almgren <almgren>
Date:   Tue Nov 2 16:00:35 2010 +0000

    Change box_volume to box_dvolume so we can handle really big
    numbers (too big for an integer)

Src/LinearSolvers/F_MG/mg.f90

commit af4b464e0d8736fe321f4037c989853ea9e90809
Author: lijewski <lijewski>
Date:   Mon Nov 1 23:01:49 2010 +0000

    Added timer to InitRandom().
    Added some more error checking.
    Unroll the last of simple BL_SPACEDIM loops.

Src/C_AMRLib/Particles.H

commit 545021dc840810b2b9f8235df3a448dac4fbb8ef
Author: lijewski <lijewski>
Date:   Mon Nov 1 21:26:59 2010 +0000

    we no longer send/recv m_lev, m_grid or m_cell -- the receiving MPI process just recalculates

Src/C_AMRLib/Particles.H

commit 127ecb6a5fb89cd63fcace209c9986032096e27b
Author: lijewski <lijewski>
Date:   Mon Nov 1 20:57:00 2010 +0000

    some performance tweaks

Src/C_AMRLib/Particles.H

commit 62ec42d2cece7915dd88b767bb9727c7f0f6b470
Author: lijewski <lijewski>
Date:   Mon Nov 1 18:04:36 2010 +0000

    no longer write p.m_lev and p.m_grid to disk -- they can be easily recreated given how we write checkpoint files

Src/C_AMRLib/Particles.H

commit 46c2b8f4c6d077b4554150089d202c92d379e3a3
Author: lijewski <lijewski>
Date:   Mon Nov 1 17:22:41 2010 +0000

    I've redone how particles are stored.  Instead of a single deque we now
    have a deque per grid per level.  This makes most of the algorithms that
    operate on particles containers more memory efficient since they almost
    always work on a level by level and grid by grid basis.

Src/C_AMRLib/Particles.H

commit b7ed5d0ba8846314edc8dd1ff3d09e4757702277
Author: lijewski <lijewski>
Date:   Mon Nov 1 17:16:55 2010 +0000

    some IPM stuff for hopper

Tools/C_mk/Make.Linux

commit c4e8ce23c67943cf2beaaf9a6926c9e09255f2ae
Author: lijewski <lijewski>
Date:   Fri Oct 29 22:50:41 2010 +0000

    added ability to sort particles -- not yet used

Src/C_AMRLib/Particles.H

commit eea5383c38e730f6c1b0950b2c7ca49fb580f622
Author: lijewski <lijewski>
Date:   Fri Oct 29 21:39:15 2010 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_cc.f90

commit 55e74ccd0cafe8c6111e2e8be54e02a0507573c9
Author: almgren <almgren>
Date:   Fri Oct 29 21:16:41 2010 +0000

    Add code to print "sum of rhs" *only* for all periodic bc's and cell-centered.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 2cc61686ef3da8b78e23f0d11eb6f9d4dc21bd68
Author: lijewski <lijewski>
Date:   Fri Oct 29 20:36:14 2010 +0000

    added serialize option to InitRandom()

Src/C_AMRLib/Particles.H

commit 754200a895dfe5ec209b0861297504194479cc2d
Author: lijewski <lijewski>
Date:   Fri Oct 29 17:22:04 2010 +0000

    *** empty log message ***

Src/C_AMRLib/Particles.cpp

commit 15721de0e0a9dad08da6ca8280a212cf879ddc17
Author: lijewski <lijewski>
Date:   Thu Oct 28 15:56:43 2010 +0000

    AssignDensity() wasn't quite right for 3D

Src/C_AMRLib/Particles.H

commit 944e7d0e90a571d1e032928f9a32f404d22c45a2
Author: lijewski <lijewski>
Date:   Wed Oct 27 22:11:54 2010 +0000

    tweak to OMP in sumParticleMomentum() to satisfy PathScale

Src/C_AMRLib/Particles.H

commit 551331575feb4429104d0556dd7e98a04f10ae05
Author: lijewski <lijewski>
Date:   Wed Oct 27 22:04:34 2010 +0000

    simplified the OMP scheme for sumParticleMomentum()

Src/C_AMRLib/Particles.H

commit 54fb4499a48ba4b0272f977bfff8e110d480824a
Author: lijewski <lijewski>
Date:   Wed Oct 27 21:56:03 2010 +0000

    OMPd sumParticleMomentum()

Src/C_AMRLib/Particles.H

commit c9a81e72d1e8b44f2da18a1d956df1ed97045a6d
Author: lijewski <lijewski>
Date:   Wed Oct 27 21:25:55 2010 +0000

    came up with a way to OMP AssignDensity()

Src/C_AMRLib/Particles.H

commit dce5d5e3f2372d2ce12f4ed9bf189d9247a5289d
Author: lijewski <lijewski>
Date:   Wed Oct 27 20:45:39 2010 +0000

    sumParticleMomentum() now calculates all BL_SPACEDIM momemtums at once

Src/C_AMRLib/Particles.H

commit fcbd1ebfad975f80a280143f449503411f19fdc4
Author: lijewski <lijewski>
Date:   Wed Oct 27 19:41:04 2010 +0000

    mods for PathScale

Tools/C_mk/Make.Linux

commit 471aed64db6172faaef31a778f56121484d3ae7b
Author: lijewski <lijewski>
Date:   Wed Oct 27 17:44:22 2010 +0000

    added -h noexceptions to CXXFLAGS for Cray

Tools/C_mk/Make.Linux

commit 9b59dd4bdfcba87ba23161dfbe150f388b10a629
Author: lijewski <lijewski>
Date:   Tue Oct 26 23:25:02 2010 +0000

    Decreased the optimization in BL_NOFAST for PathScale to just -O.
    Looks like I have to use BL_NOFAST on the current version of hopper.
    Else I get Bottom solver failures in the gravity solve.

Tools/C_mk/Make.Linux

commit 8b5839d99adc87cd11ee4a1a168a92d42e4285b3
Author: lijewski <lijewski>
Date:   Tue Oct 26 22:09:17 2010 +0000

    decrease Cray optimization intensity

Tools/F_mk/comps/Linux_cray.mak

commit 22c3c5f646e61a4fb0c2d186ef92dae92ab8994b
Author: lijewski <lijewski>
Date:   Tue Oct 26 20:32:29 2010 +0000

    decreased Cray optimization strenght a bit

Tools/C_mk/Make.Linux

commit 945075534541e153555bf4f56af74c2b5f678cfa
Author: lijewski <lijewski>
Date:   Tue Oct 26 20:21:33 2010 +0000

    mods to quiet Cray compiler

Src/C_AMRLib/Particles.H

commit 98d67453f686d7479181c1c8d8bf65ddea62864c
Author: lijewski <lijewski>
Date:   Mon Oct 25 23:36:18 2010 +0000

    OMPd estTimestep()

Src/C_AMRLib/Particles.H

commit 8d550d3d86dea3b2bd7f1ed9dce2e6f60e00225d
Author: almgren <almgren>
Date:   Mon Oct 25 22:10:07 2010 +0000

    Fix indexing of cell vs csect in AssignDensity...

Src/C_AMRLib/Particles.H

commit 31275dbab36d2079dfa350fbf1020b8f6367f20e
Author: almgren <almgren>
Date:   Mon Oct 25 22:01:54 2010 +0000

    Fix up getGravity

Src/C_AMRLib/Particles.cpp

commit 57411ae0f65f918b3d138375cd9a74d7a884c226
Author: lijewski <lijewski>
Date:   Mon Oct 25 20:06:33 2010 +0000

    getParticleGrav() -> ParticleBase::GetGravity()

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit e2a004d4986a88609c9662cd31354b9b1cc087d1
Author: almgren <almgren>
Date:   Mon Oct 25 18:47:48 2010 +0000

    This now includes Jan's updates which use getParticleGrav to interpolate the
    gravity onto particle locations instead of using the cell-centered value.

Src/C_AMRLib/Particles.H

commit 176e0b4cace3e6151a1c3b05224b805ed786dcce
Author: lijewski <lijewski>
Date:   Mon Oct 25 03:43:11 2010 +0000

    little cleanup

Src/C_AMRLib/Particles.H

commit 2d221cf1dee7d4b183d752444b6f19f9730f6738
Author: lijewski <lijewski>
Date:   Mon Oct 25 01:59:43 2010 +0000

    std::list -> std::deque as the latter is more amenable to OMPing

Src/C_AMRLib/Particles.H

commit 56ff56e51736f21b0c673246676dfaae48080bbd
Author: lijewski <lijewski>
Date:   Sun Oct 24 23:41:46 2010 +0000

    some OMPing

Src/C_AMRLib/Particles.H

commit 3355039a9d33c026fc56e56c35e1f20beb083256
Author: lijewski <lijewski>
Date:   Sun Oct 24 22:45:29 2010 +0000

    minor performance tweaks

Src/C_AMRLib/Particles.H

commit 35a31c1cde9e8383d0915967689df83b90b33f7a
Author: lijewski <lijewski>
Date:   Sun Oct 24 22:07:10 2010 +0000

    add some more timers

Src/C_AMRLib/Particles.H

commit c25c23d11faddae30a9995074b089fd4b2d3426d
Author: lijewski <lijewski>
Date:   Fri Oct 22 23:25:30 2010 +0000

    more Cray tweaks

Tools/C_mk/Make.Linux

commit ce42be1b5a80229d079faf9d29d226145192febe
Author: lijewski <lijewski>
Date:   Fri Oct 22 22:26:31 2010 +0000

    fixed bug in AssignDensity() when DIM=3 - be good if Jhon could confirm

Src/C_AMRLib/Particles.H

commit eb2bbd75e48c3f9ff790ac8650fe73d340eca789
Author: wqzhang <wqzhang>
Date:   Fri Oct 22 21:10:12 2010 +0000

    added my desktop baragon

Tools/C_mk/Make.defs

commit 816c636f18a1ee149d79fcc5b1bf82ea1dccd24c
Author: ajnonaka <ajnonaka>
Date:   Fri Oct 22 20:31:36 2010 +0000

    if USE_LEVELSET=T, at .LevelSet suffix to executable name

Tools/C_mk/Make.defs

commit 1bd6264156584ce28a37929be977b175b1883517
Author: lijewski <lijewski>
Date:   Fri Oct 22 20:26:10 2010 +0000

    more Cray stuff

Tools/C_mk/Make.Linux

commit 8fa04dd8d1fc4001df945ef6da2e4ab1c450d0f8
Author: lijewski <lijewski>
Date:   Fri Oct 22 16:48:51 2010 +0000

    some work adding Cray

Tools/C_mk/Make.Linux

commit e8eec6dba102548db2a6386b4093caae42100e4b
Author: lijewski <lijewski>
Date:   Fri Oct 22 15:34:29 2010 +0000

    added -Minline flag

Tools/F_mk/comps/Linux_pgi.mak

commit af9b83e866c26c2767955df18855e92659345218
Author: lijewski <lijewski>
Date:   Thu Oct 21 20:59:14 2010 +0000

    for Cray compilers

Tools/F_mk/comps/Linux_cray.mak

commit 980fa4ba43088597c7ee05a0e50b4c058f1e0073
Author: lijewski <lijewski>
Date:   Thu Oct 21 20:58:15 2010 +0000

    some work for Cray compiler suite

Tools/F_mk/GMakedefs.mak

commit 95efbdb385cd47b44812b72f24dbb281b0c02945
Author: lijewski <lijewski>
Date:   Thu Oct 21 18:21:39 2010 +0000

    added grace

Tools/F_mk/GMakeMPI.mak

commit 4bfb8680a9702744650520cc6a22acc6ceeac803
Author: lijewski <lijewski>
Date:   Wed Oct 20 23:17:09 2010 +0000

    tweaked the PGI optimization flags

Tools/C_mk/Make.Linux

commit e52a73ea1102af26b5a8b0a287489577f05435e3
Author: lijewski <lijewski>
Date:   Wed Oct 20 23:15:22 2010 +0000

    added GRACE

Tools/C_mk/Make.defs

commit 4e6f9e04d29292305b855ffdfc5ec2f3027b2bca
Author: ajnonaka <ajnonaka>
Date:   Wed Oct 20 13:58:53 2010 +0000

    mpi for my home machine

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 6322fc185db0eac690b9669518063014fefa3a54
Author: mzingale <mzingale>
Date:   Wed Oct 20 13:54:55 2010 +0000

    add support for kraken

Tools/F_mk/GMakeMPI.mak

commit 3a44d87c42bec8809de74b3c2b8185afdcbe93d4
Author: wqzhang <wqzhang>
Date:   Tue Oct 19 22:48:32 2010 +0000

    *** empty log message ***

Tools/C_mk/Make.rules

commit 353a919764eaa4f9b370579901be4193ef0598b8
Author: ajnonaka <ajnonaka>
Date:   Tue Oct 19 00:04:05 2010 +0000

    MPI for ebirah

Tools/F_mk/GMakeMPI.mak

commit e6958bfef8b4822e41a86685f25326be762a469e
Author: almgren <almgren>
Date:   Mon Oct 18 21:48:52 2010 +0000

    We do not need those lines for compiling with intel on ranger.

Tools/C_mk/Make.mpi

commit e884ce44abc6cb83c6e10417a355227a1e6dd06f
Author: lijewski <lijewski>
Date:   Mon Oct 18 21:09:32 2010 +0000

    introduced  version string for checkpoint/restart files

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit b18c0b7cb88439325a30b68ead22879a9b2fc277
Author: lijewski <lijewski>
Date:   Mon Oct 18 20:02:18 2010 +0000

    some performance tweaking

Src/C_AMRLib/Particles.H

commit 806338863d9c02be68187bbbb43707104dea05f6
Author: lijewski <lijewski>
Date:   Mon Oct 18 19:18:49 2010 +0000

    a little cleanup

Src/C_AMRLib/Particles.H

commit 9f26609da780754e20bb4ffc0699644f6fcd2f73
Author: lijewski <lijewski>
Date:   Mon Oct 18 18:26:32 2010 +0000

    now unlink() zero-length data files but not directories

Src/C_AMRLib/Particles.H

commit e5cffd200820c1bec4a5d6950827b11f0f60ddf6
Author: lijewski <lijewski>
Date:   Mon Oct 18 17:14:17 2010 +0000

    non-backward compatible performance change to particle checkpoint/restart files

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit e5bd5964223759b9a4d1515214e62c5fee5a5456
Author: almgren <almgren>
Date:   Fri Oct 15 22:55:19 2010 +0000

    Add orion.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 28138ffc67b0f89eb12ca891e8002612c00ffb3a
Author: lijewski <lijewski>
Date:   Fri Oct 15 21:33:53 2010 +0000

    some cleanup and additional error checking

Src/C_AMRLib/Particles.H

commit ea094d1748f061a33d9500da8c96f353702c5d0e
Author: ajnonaka <ajnonaka>
Date:   Fri Oct 15 20:45:02 2010 +0000

    bugfix - using && instead of .and. didn't work with my gfortran

Src/LinearSolvers/F_MG/mg.f90

commit 85a9f0f467f03c68b9fa56a16edd73fb991ae26f
Author: lijewski <lijewski>
Date:   Fri Oct 15 20:42:51 2010 +0000

    Restart() appears to be working.
    Will need to be updated when Vince's IntRealDescriptor-style stuff is ready.

Src/C_AMRLib/Particles.H

commit 8e96f5615e8ae0e76848e395358d5f431077677b
Author: almgren <almgren>
Date:   Fri Oct 15 20:35:40 2010 +0000

    Add "if verbose > 1" before print statement re bottom_solver=4 coarse domain size

Src/LinearSolvers/F_MG/mg.f90

commit c1f14a8083dfaa1da5574a0c6c970a1c6a220747
Author: adonev <adonev>
Date:   Fri Oct 15 20:21:27 2010 +0000

    Added flag BL_FAST_COMP

Tools/F_mk/comps/Linux_intel.mak

commit 9e6c485130c9a653ef80d8248a0006c6673f93d1
Author: lijewski <lijewski>
Date:   Fri Oct 15 17:03:47 2010 +0000

    Now writing out particles in native binary.
    Needs to eventually to brought up to date with Vince's IntDescriptor stuff
    when he's done with it.

Src/C_AMRLib/Particles.H

commit 5da107bf47d9e8f27768de0a37cc270285112fe3
Author: lijewski <lijewski>
Date:   Thu Oct 14 23:50:37 2010 +0000

    a little cleanup

Src/C_AMRLib/Particles.H

commit 5bb69d9f86498ef909abc58d51487d628b8fb39a
Author: lijewski <lijewski>
Date:   Thu Oct 14 23:34:34 2010 +0000

    OK() is now more thorough

Src/C_AMRLib/Particles.H

commit 002cdbbc30edef26294a71f4f584d56ad9403ba9
Author: lijewski <lijewski>
Date:   Thu Oct 14 23:13:04 2010 +0000

    yet more work on Checkpoint()

Src/C_AMRLib/Particles.H

commit 668a45595796d8f6dae6bd70b12edec0564643be
Author: lijewski <lijewski>
Date:   Thu Oct 14 22:37:31 2010 +0000

    more work on Checkpoint()

Src/C_AMRLib/Particles.H

commit 4ecb3abc6cc1f49ee3c9321cfc2af1981968b5ae
Author: lijewski <lijewski>
Date:   Thu Oct 14 21:51:03 2010 +0000

    initial work on Checkpoint(); more needed

Src/C_AMRLib/Particles.H

commit 67ed9bd8bb3e078971d6aa5f4584b26f08790831
Author: lijewski <lijewski>
Date:   Thu Oct 14 17:34:43 2010 +0000

    some optimization

Src/C_AMRLib/Particles.H

commit 0f0eb8fb5268c3e006327ef938fa209f211af975
Author: lijewski <lijewski>
Date:   Wed Oct 13 23:11:33 2010 +0000

    some cleanup and more error checking

Src/C_AMRLib/Particles.H

commit ec649a3cf333076e4388aa408cfa4dd9942f9ac8
Author: almgren <almgren>
Date:   Sat Oct 9 19:16:31 2010 +0000

    Add verbose to test for output...

Src/C_AMRLib/Particles.H

commit 29ef6f8de26fc66cd302977d7f389294a4d44a2b
Author: almgren <almgren>
Date:   Sat Oct 9 16:31:01 2010 +0000

    Make sure to set bottom_singular = .true. if the boundary conditions for the
    current solve are all periodic.

Src/LinearSolvers/F_MG/mg.f90

commit 0c937af5e164e2ac1c0a2d0f0317fcd1aa8cc33b
Author: almgren <almgren>
Date:   Fri Oct 8 20:50:57 2010 +0000

    These appear to actually work with clumping particles in 2d.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 3c0a480080c35c18b6ee1e305a786d67cffb4338
Author: almgren <almgren>
Date:   Fri Oct 8 17:03:28 2010 +0000

    Latest updates from JF.

Src/C_AMRLib/Particles.H

commit 429daf4af9ba5276e0f8f72b6d5c8cf655527a38
Author: almgren <almgren>
Date:   Thu Oct 7 16:49:54 2010 +0000

    Change the default particle to have the first real component have value = 1
    (and all the others are zero).

Src/C_AMRLib/Particles.H

commit b7c9b3e4b6e4e3bda5efd3acb7170d0b97e393f8
Author: almgren <almgren>
Date:   Wed Oct 6 22:05:14 2010 +0000

    Add Particles_F.H

Src/C_AMRLib/Particles_F.H

commit cd581f37de87a765ec222a8fbb08cb320ccdd113
Author: almgren <almgren>
Date:   Wed Oct 6 21:14:44 2010 +0000

    This is a merge of Mike's latest and Jan's latest -- it has everything as of now.

Src/C_AMRLib/Particles.H

commit 2dcab77f432c15b38282066e7a3233eb6f2102a8
Author: almgren <almgren>
Date:   Wed Oct 6 20:17:48 2010 +0000

    Moved Particles.* from amrlib to particles directory.

Src/C_AMRLib/Make.package
Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit a4a51da96ba6f3ffea4c00c501e136d0494ebf7b
Author: vince <vince>
Date:   Wed Oct 6 20:01:22 2010 +0000

    added new machines.

Tools/C_mk/Make.mpi

commit 0ed17248de77ba5d954f58b4531244f80674550c
Author: lijewski <lijewski>
Date:   Wed Oct 6 15:44:20 2010 +0000

    little code rearrangement

Src/C_BaseLib/FabArray.H

commit 35b6b8a4093164fd1cb95ca2a822a69373ff05ec
Author: lijewski <lijewski>
Date:   Wed Oct 6 15:38:30 2010 +0000

    little code rearrangement in SumPeriodicBoundary()

Src/C_BaseLib/Geometry.cpp

commit ef7a4a9f9daa1c33dea2c4b8fff0613a49eee8bd
Author: lijewski <lijewski>
Date:   Wed Oct 6 15:31:30 2010 +0000

    use intersections() in SumBoundary()

Src/C_BaseLib/MultiFab.cpp

commit 7ab858e9481089a76b1da2cc4fc549e4821245d9
Author: lijewski <lijewski>
Date:   Wed Oct 6 15:14:27 2010 +0000

    minor code motion

Src/C_BoundaryLib/BndryData.cpp

commit 41d7df28cd5da797c8a4e897caa931af8c90cdc5
Author: lijewski <lijewski>
Date:   Wed Oct 6 15:14:27 2010 +0000

    minor code motion

Src/C_AMRLib/FluxRegister.cpp
Src/C_BoundaryLib/FabSet.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 062b0c6cc9e2a6d2cd82886d881d1847d4e6a0b5
Author: lijewski <lijewski>
Date:   Tue Oct 5 23:00:00 2010 +0000

    added initial cut of SumBoundary()

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 696fc700323c502ad7afa4d3e44ab676bb7e7e2d
Author: lijewski <lijewski>
Date:   Tue Oct 5 21:40:47 2010 +0000

    added SumPeriodicBoundary()

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit b197069a44d76214ca25caf3ef6214bd3097840f
Author: lijewski <lijewski>
Date:   Mon Oct 4 16:47:42 2010 +0000

    ParmParse can now deal with longs

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit ead690e1c43b5289aa54b62d917d8180645f69fb
Author: adonev <adonev>
Date:   Sun Oct 3 23:32:29 2010 +0000

    donev in Makefile

Tools/C_mk/Make.mpi

commit 5388e4e556820030d821ceaabdb706a4b1031d19
Author: ajnonaka <ajnonaka>
Date:   Fri Oct 1 23:13:06 2010 +0000

    more makefile hacking

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/multifab_physbc_edgevel.f90

commit 627f8e56293246ffcb21e25744e8cabdec57864e
Author: ajnonaka <ajnonaka>
Date:   Fri Oct 1 22:41:37 2010 +0000

    in progress hacking to get the initial model stuff to compile

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/multifab_physbc_edgevel.f90

commit d5aef03c8bdeca3b9ae50c327e3b4dea87b0df65
Author: marc <marc>
Date:   Fri Oct 1 21:55:40 2010 +0000

    Add win include

Src/C_BaseLib/IntVect.H

commit f23b7b9764a6ee47da36aae1df27b2f6321cca2a
Author: marc <marc>
Date:   Fri Oct 1 21:54:57 2010 +0000

    Rename macro for excluding fortran functions from boxlib build

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/Make.package

commit 2f9722a46e6cee3417836fa6c458e9451b27dcaa
Author: ajnonaka <ajnonaka>
Date:   Fri Oct 1 21:54:18 2010 +0000

    moved MAESTRO/Source/impose_phys_bcs_on_edge_vels into /boxlib/ and rennamed it multifab_physbc_edgevel.
    
    create_umac_grown.f90 now calls multifab_physbc_edgevel on the coarsest and the current fine level

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/create_umac_grown.f90
Src/F_BaseLib/multifab_physbc_edgevel.f90

commit 116bab0663f725d7c56cf1c9ca12367de1c5e172
Author: lijewski <lijewski>
Date:   Fri Oct 1 21:44:47 2010 +0000

    brought back from the dead

Src/C_BaseLib/GNUmakefile

commit 8bcf8dc9c8f0e6cbaf183554e0b69f0d30cd2bd8
Author: ajnonaka <ajnonaka>
Date:   Fri Oct 1 21:14:33 2010 +0000

    need to pass the_bc_level into create_umac_grown so we can call impose_phys_bcs_on_edges

Src/F_BaseLib/create_umac_grown.f90

commit d19c785753689c6db8c760f356f1082a7f512ba3
Author: ajnonaka <ajnonaka>
Date:   Fri Oct 1 20:40:21 2010 +0000

    it would help if i actually added this file to the repository

Src/F_BaseLib/create_umac_grown.f90

commit 45ed05189fa130b54d69811888cefcd93a1dd0ae
Author: ajnonaka <ajnonaka>
Date:   Fri Oct 1 19:34:31 2010 +0000

    move create_umac_grown.f90 into /boxlib/ and removed these local copies

Src/F_BaseLib/GPackage.mak

commit ad64007e090db8073b6a6bf8937d314663bb3832
Author: almgren <almgren>
Date:   Fri Oct 1 17:40:07 2010 +0000

    We need to back out this change from v1.36 to v1.37 or the CASTRO codes don't build anymore

Tools/C_mk/Make.rules

commit ed8da9f3dd2653c5d72ef1ac93770f40c25cfe80
Author: lijewski <lijewski>
Date:   Thu Sep 30 22:41:03 2010 +0000

    some VisIt changes from Gunther

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/FPC.cpp
Src/C_BaseLib/Make.package
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 6f3cf23ca034db3dd50a10dba8518e2ed5fc69e1
Author: ajnonaka <ajnonaka>
Date:   Thu Sep 30 05:00:39 2010 +0000

    remove unused variables

Src/F_BaseLib/fab.f90
Src/LinearSolvers/F_MG/ml_solve.f90

commit 04acb3dc767c634f2a14a8dd558225f2a17da2bf
Author: ajnonaka <ajnonaka>
Date:   Thu Sep 30 01:08:20 2010 +0000

    turn on gfortran compiler warnings if you are in debug mode.  it will warn you about uninitialize and unused variables

Tools/F_mk/comps/gfortran.mak

commit c81c74a6bda85a8821ce3eef0894ef6913b33861
Author: marc <marc>
Date:   Wed Sep 29 23:16:18 2010 +0000

    removing files that were renamed to avoid name collisions

Src/LinearSolvers/C_NodalMG/cg.cpp
Src/LinearSolvers/C_NodalMG/cg_2d.f
Src/LinearSolvers/C_NodalMG/cg_3d.f

commit 77e2721a80c22bfc5539f8dd57d2bab22077b987
Author: marc <marc>
Date:   Wed Sep 29 23:14:21 2010 +0000

    Incorporate name changes into filelist

Src/LinearSolvers/C_NodalMG/Make.package

commit 20de950baca4681a5f1391eafafbb9bf5ed2db19
Author: marc <marc>
Date:   Wed Sep 29 23:13:40 2010 +0000

    Renamed from cg_3d.f to avoid name collision in case-insensitive environments

Src/LinearSolvers/C_NodalMG/hg_cg3d.f

commit d59ab580c9ac5b38e49c4f5920b676fb5c90accf
Author: marc <marc>
Date:   Wed Sep 29 23:12:54 2010 +0000

    Renamed from cg_2d.f to avoid name collision in case-insensitive environments

Src/LinearSolvers/C_NodalMG/hg_cg2d.f

commit 9e832b00e19ba99406dcb0273edd889c05c8ebe0
Author: marc <marc>
Date:   Wed Sep 29 23:11:30 2010 +0000

    Renamed from cg.cpp to avoid name collision in case-insensitive environments

Src/LinearSolvers/C_NodalMG/hg_cg.cpp

commit 78ca7d97fb4343145709ccf6cc70785967bf02c8
Author: marc <marc>
Date:   Wed Sep 29 03:46:35 2010 +0000

    *** empty log message ***

Tools/C_mk/Make.CYGWIN_NT

commit 9c9b0172961b3fe4edd250203e56364cb553f49e
Author: adonev <adonev>
Date:   Mon Sep 27 23:28:22 2010 +0000

    Added host donev

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit a14c34f0ed4f5cc3a29b268e03a5c10063ce4a74
Author: adonev <adonev>
Date:   Mon Sep 27 21:22:18 2010 +0000

    Added host donev

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit c8c0c53f76e4dd6e9d7feb6251c52741a9ecb2da
Author: lijewski <lijewski>
Date:   Mon Sep 27 21:11:33 2010 +0000

    more particle stuff

Src/C_AMRLib/Make.package

commit 8ecd29c99534af0f8eb9ff9edd5c11fa86ee0f63
Author: gpau <gpau>
Date:   Wed Sep 22 04:47:04 2010 +0000

    Doing function provided by ViscBndry differently: do not need ViscBndry in solve.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit c5b1ac310b2b9736052602ee087a83aff18ff641
Author: gpau <gpau>
Date:   Tue Sep 21 22:01:10 2010 +0000

    *** empty log message ***

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 1c92891c28a49ff750ef592169e3563f43fc7e7d
Author: wqzhang <wqzhang>
Date:   Thu Sep 16 21:29:17 2010 +0000

    Fixed a comment

Src/C_BaseLib/IntVect.H

commit f40d8a7edb38714e7f650b383ffc52a1e91b574b
Author: ajnonaka <ajnonaka>
Date:   Thu Sep 16 17:56:36 2010 +0000

    Chris' fix to get PathScale working on atlas

Tools/F_mk/GMakeMPI.mak

commit 0d83a8a33e207b1dc64a065b11f13feba10ecfa7
Author: marc <marc>
Date:   Mon Sep 13 20:33:30 2010 +0000

    fix PathScale second underscore thing

Tools/C_mk/Make.Linux

commit 30aea3be16d352aa08af49b3a2250f99f081a04f
Author: lijewski <lijewski>
Date:   Fri Sep 10 23:05:34 2010 +0000

    beefed up FULLWARN for g++

Tools/C_mk/Make.defs

commit 7f716bb081b5f418c89fecf20dcf4010fe3e9265
Author: lijewski <lijewski>
Date:   Fri Sep 10 22:34:20 2010 +0000

    now passes g++ -pedantic -Wall

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BoundaryLib/BndryData.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 1460228a1e0690fa19135fbc68053590d48fcda9
Author: lijewski <lijewski>
Date:   Fri Sep 10 20:24:52 2010 +0000

    added -fbacktrace flag when debugging with gfortran

Tools/F_mk/comps/gfortran.mak

commit 2cb89b71f6708672ea7073b357b7dfcc76667c12
Author: lijewski <lijewski>
Date:   Thu Sep 9 16:47:29 2010 +0000

    unOMPd setval()

Src/F_BaseLib/fab.f90

commit 6f4170bdcefa76e259473558eb8bb038d2f60268
Author: lijewski <lijewski>
Date:   Thu Sep 9 16:27:10 2010 +0000

    removed some unused dummy arguments and unOMPd SETVAL

Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/SPECIALIZE_1D.F
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H

commit a2c182ce998082f668fdb3ae398c2806bd40413e
Author: almgren <almgren>
Date:   Wed Sep 8 16:47:35 2010 +0000

    Add kraken stuff.

Tools/C_mk/Make.Linux

commit f480a1a50715280b79de525defd18ce6681d7504
Author: almgren <almgren>
Date:   Wed Sep 8 16:46:48 2010 +0000

    Add kraken info.

Tools/C_mk/Make.defs

commit 27cbcc3b59f99cb695776c65b0a49c3c549106e3
Author: gpau <gpau>
Date:   Tue Sep 7 18:03:14 2010 +0000

    *** empty log message ***

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 4e0ec6f19f2e4030d5f0b8f7ff02a6844d4cf916
Author: almgren <almgren>
Date:   Thu Sep 2 23:35:06 2010 +0000

    Fix bug in stencil_norm inside if present(mask) test.

Src/LinearSolvers/F_MG/stencil.f90

commit 7c3b7406e900c2be914e4e4c8a01427dbe8b0749
Author: ajnonaka <ajnonaka>
Date:   Tue Aug 31 15:21:08 2010 +0000

    MPI on my home machine

Tools/F_mk/GMakeMPI.mak

commit 6e5b85fb04c5ba50afdcb0b779d40263a82ec4fd
Author: ajnonaka <ajnonaka>
Date:   Tue Aug 31 15:21:01 2010 +0000

    MPI on my home machin

Tools/C_mk/Make.mpi

commit f7ccb72d04eb349cece0193d8f9f4fa6b6d8e047
Author: ajnonaka <ajnonaka>
Date:   Fri Aug 27 23:02:54 2010 +0000

    added -fno-range-check for gfortran to get the fParallel/extern/random/mt19937ar.f90 stuff to compile

Tools/C_mk/Make.defs

commit f15f10b6db6f843da4941f912975fe36d8058474
Author: ajnonaka <ajnonaka>
Date:   Fri Aug 27 22:43:02 2010 +0000

    new install of mpi.  Fixed to work with gfortran on atragon

Tools/C_mk/Make.mpi

commit d2e0b9a0d7196be0fa25d4d9ac903555b2f74622
Author: ajnonaka <ajnonaka>
Date:   Fri Aug 27 22:32:11 2010 +0000

    new install of mpi.  Fixed to work with gfortran on atragon

Tools/F_mk/GMakeMPI.mak

commit 9d02c3d103733af067174ed46aab973b8569c746
Author: almgren <almgren>
Date:   Fri Aug 27 21:54:47 2010 +0000

    This modifies the convergence criterion for the solver in ml_cc so that
    it stops when res < eps * MAX(bnorm,tres0) instead of res < eps * bnorm.
    Here bnorm = norm(rhs) and tres0 = norm(resid0).

Src/LinearSolvers/F_MG/ml_cc.f90

commit 75f8f1c32caee746d9bb21eab588ab903055f708
Author: ajnonaka <ajnonaka>
Date:   Thu Aug 26 21:33:27 2010 +0000

    printing out fancy bottom solver grids even when mg_verbose=0

Src/LinearSolvers/F_MG/mg.f90

commit 0ffdf6f243ef0635f199f699624d138dd2d6d561
Author: nazgul <nazgul>
Date:   Thu Aug 26 00:15:56 2010 +0000

    Commenting out iters.f, as it causes build problems for Castro
    and does not appear to be used.
    
    Louis

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 977e74398b627a5673c2cd402c4c052f46e20354
Author: lijewski <lijewski>
Date:   Wed Aug 25 21:40:17 2010 +0000

    no longer include sparse_solve.f90

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 878ff03a602a4bd30c8a7126624b1dfc5c1ee945
Author: lijewski <lijewski>
Date:   Wed Aug 25 20:37:51 2010 +0000

    removed some dubiously useful OMP constructs

Src/LinearSolvers/F_MG/ml_util.f90

commit c66a102082b733c1823c1b0599cb5a6bd00811ee
Author: lijewski <lijewski>
Date:   Wed Aug 25 19:51:11 2010 +0000

    remove OMP stuff on faces -- not enough work

Src/LinearSolvers/F_MG/impose_neumann_bcs.f90

commit 43d9d681b8410a9eab71e8f7eda06e71d062915c
Author: lijewski <lijewski>
Date:   Wed Aug 25 19:35:15 2010 +0000

    OMP'd stencil_norm() when present(mask)

Src/LinearSolvers/F_MG/stencil.f90

commit 3f636502de11d6a63787d685a40a9deb48495c59
Author: lijewski <lijewski>
Date:   Tue Aug 24 23:08:25 2010 +0000

    some cleanup

Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_mask.f90

commit 1c5fd530ede896aa4b939de9a57aadf3ac6916a2
Author: ajnonaka <ajnonaka>
Date:   Tue Aug 24 21:41:34 2010 +0000

    fixed the 12 thread multilevel bug.  now it gives the same answer as 6 threads to machine precision

Src/LinearSolvers/F_MG/stencil.f90

commit 4c6ecaa9d5406d25db2da8dcddd198a5f4cd3314
Author: almgren <almgren>
Date:   Tue Aug 24 20:30:31 2010 +0000

    end if --> endif

Src/C_BaseLib/BoxLib.cpp

commit 67bdbd7159578d9f28d74dac685cf2e9bb4f7546
Author: almgren <almgren>
Date:   Tue Aug 24 20:12:38 2010 +0000

    Print out many MPI processes even if only one.

Src/C_BaseLib/BoxLib.cpp

commit 6d99f244be8acba98719526a3cd59453a371b799
Author: lijewski <lijewski>
Date:   Tue Aug 24 20:12:00 2010 +0000

    removed all nocomm stuff and some OMP loops of dubious usefulness

Src/F_BaseLib/multifab.f90

commit 4c113f1c7a900c76f07b545fdfa15bdc4c844f17
Author: almgren <almgren>
Date:   Tue Aug 24 20:08:19 2010 +0000

    Wrap the statement "MPI initialized..." with
    #ifdef BL_USE_MPI

Src/C_BaseLib/BoxLib.cpp

commit 3490e3861204069e41bcc5787540cae081187ae7
Author: lijewski <lijewski>
Date:   Tue Aug 24 17:46:28 2010 +0000

    removed ml_layout_build_la() -- not used by any current code

Src/F_BaseLib/ml_layout.f90

commit 333fba55dc9d6bf703460fb7fa8c7561065b0726
Author: lijewski <lijewski>
Date:   Tue Aug 24 17:31:57 2010 +0000

    Added destroy_all_layouts member to ml_layout.
    This is so we can distinguish between the two main ways of building
    ml_layouts.
    In most f90 code we use build() which forces the layouts of higher levels
    to be owned by the one at the coarsest level, via proper nesting.
    In the MGT code however the layouts are build level by level and hence in
    destroy() we must destroy all of them, not just the one at the coarsest
    level.

Src/F_BaseLib/ml_layout.f90

commit f36b4162d5ee3d361a5340501c5a60bf846850a3
Author: ajnonaka <ajnonaka>
Date:   Mon Aug 23 23:36:14 2010 +0000

    upgraded the fancy bottom_solver_type 4 to allow an even coarsen bottom solve for this bottom solver.  ultra complicated and will get some details in the user's guide when I figure out a clean way of describing it

Src/LinearSolvers/F_MG/mg.f90

commit 4c9018aeb100c0e69eaaa5c73a5e905570968811
Author: lijewski <lijewski>
Date:   Mon Aug 23 23:30:51 2010 +0000

    got rid of OMP shared variable warnings via firstprivate

Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 5a9c0857cdc686c7466574db4921ae00340fbe44
Author: ajnonaka <ajnonaka>
Date:   Mon Aug 23 20:35:00 2010 +0000

    some cleanup - preparing to make the new bottom solver more robust by allowing more levels in certain cases.  Example:  we would like a 20^3 problem to be able to go down to a 5^3 rather than the 10^3 it would currently do.

Src/LinearSolvers/F_MG/mg.f90

commit cf0b5fc486e5f1c50e95b6065ccb71bf4f6a0d8b
Author: lijewski <lijewski>
Date:   Fri Aug 20 17:30:30 2010 +0000

    some cleanup

Src/LinearSolvers/F_MG/ml_solve.f90

commit ac9658e952dc9ccecd62c9dc8bb923f0178c58c1
Author: lijewski <lijewski>
Date:   Fri Aug 20 17:03:27 2010 +0000

    unOpenMPd set_faces_edges_corners_3d - probably not a win

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit f041aff891e8b9d591e3e56154fd5d765d108c02
Author: lijewski <lijewski>
Date:   Fri Aug 20 16:46:50 2010 +0000

    some more OpenMPing

Src/LinearSolvers/F_MG/stencil.f90

commit 7e000bffccf7e375183abe8dd031a97a395e64b4
Author: lijewski <lijewski>
Date:   Thu Aug 19 23:45:25 2010 +0000

    removed some unused routines & made some private

Src/LinearSolvers/F_MG/stencil.f90

commit 4e8d9b5366e29ed7620925c23e8e9ec0f621dd99
Author: lijewski <lijewski>
Date:   Thu Aug 19 22:56:32 2010 +0000

    refined public interface

Src/LinearSolvers/F_MG/nodal_mask.f90

commit 672c09741d6a1866d3e28a6b9b8d1c83b01a29f5
Author: lijewski <lijewski>
Date:   Thu Aug 19 22:36:40 2010 +0000

    fixed up public/private stuff

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 43cf26a01e81ac1c3f3f4ecf5c22e0e753cd5f9a
Author: lijewski <lijewski>
Date:   Thu Aug 19 22:29:44 2010 +0000

    made only those routines that need to be public

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 109737e73a596f4fbdfe5f3dfe2d740982184302
Author: lijewski <lijewski>
Date:   Thu Aug 19 22:20:46 2010 +0000

    made only those functions used outside this module public

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 311e51850a88f017e4cf80382c17957a7afcc36b
Author: lijewski <lijewski>
Date:   Thu Aug 19 22:12:30 2010 +0000

    make scale_residual_[123]d private

Src/LinearSolvers/F_MG/ml_cc.f90

commit 77cf804cc67e37103f9a7b5ac7fbd40bcce6e5b3
Author: ajnonaka <ajnonaka>
Date:   Thu Aug 19 21:51:52 2010 +0000

    output number of threads and MPI processes to job_info and at the beginning of each run

Src/F_BaseLib/BoxLib.f90
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/omp.f90
Src/F_BaseLib/omp_stubs.f90

commit a64875a56a0bf77a312e1d62ec94fbea56b03ec2
Author: lijewski <lijewski>
Date:   Thu Aug 19 21:30:06 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/itsol.f90

commit a15eb4a8da49eb3674c9e540e02faec2531006a0
Author: lijewski <lijewski>
Date:   Thu Aug 19 21:19:17 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/nodal_newu.f90

commit 2b18dc3a3cf43c5054d6cb6c99c5c7edca24f930
Author: almgren <almgren>
Date:   Thu Aug 19 00:37:34 2010 +0000

    Modified the nodal solver output to more closely match the MAC solver --
    specifically, it now prints
    
    F90mg: Final Iter.   7 resid/resid0 =  0.33106928E-11
    
    rather than
    
    MG finished at   7 iterations
    
    at the end of the solve.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 75a0bb3429421e6dd8594a0cf054fae37f868389
Author: lijewski <lijewski>
Date:   Wed Aug 18 22:10:12 2010 +0000

    attempt to shut up 'possible uninitialized variable' msgs

Src/F_BaseLib/multifab.f90
Src/F_BaseLib/plotfile.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 5507c1419343ef8d160678242dcb2bc238ee2341
Author: lijewski <lijewski>
Date:   Wed Aug 18 20:15:12 2010 +0000

    0 -> 0_dp_t and removed a print statement

Src/F_BaseLib/multifab.f90

commit 84b59d00d1d4e5af8a292bac01ff1cce7f296b96
Author: ajnonaka <ajnonaka>
Date:   Tue Aug 17 13:44:07 2010 +0000

    in MAESTRO/Source/ rennamed cluster_min_width to minwidth so it matches what's in boxlib/cluster.f90
    
    now you can set blocking_factor in the inputs file
    
    both blocking_factor and minwidth default to 8 in both MAESTRO and cluster.f90

Src/F_BaseLib/cluster.f90

commit cbf4965300053c747a3ba0cdad41bcd8a9c53160
Author: ajnonaka <ajnonaka>
Date:   Tue Aug 17 13:09:04 2010 +0000

    output says "MPI initialized with  XXXX  MPI processes" instead of CPUs

Src/F_BaseLib/BoxLib.f90

commit a79632c38697af60da5ee7842c68f94dae52bf59
Author: lijewski <lijewski>
Date:   Mon Aug 16 20:02:11 2010 +0000

    plugged memory leak

Src/F_BaseLib/fabio.f90

commit 7eb887eb0f1265f82c69b5f5e3c4454e0166403f
Author: lijewski <lijewski>
Date:   Mon Aug 16 19:26:22 2010 +0000

    shut up some valgrind warnings

Src/F_BaseLib/bndry_reg.f90

commit 50c2eb9b115ed6cb900957fb7ff29a01dd8e9b5c
Author: mzingale <mzingale>
Date:   Mon Aug 16 13:22:09 2010 +0000

    get make_benchmarks working again if there are self-tests defined

Tools/C_util/regtests/test.py

commit 44dc6d1e985cd8015dcf95a9c42f6e75eff01f41
Author: lijewski <lijewski>
Date:   Fri Aug 13 21:44:26 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 66e740cfd836168e56a84728eb7a4fa98cc6f899
Author: lijewski <lijewski>
Date:   Fri Aug 13 20:30:07 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 6bd7744d6450b1457bed28d4eb553cbdc2327cb7
Author: lijewski <lijewski>
Date:   Fri Aug 13 20:18:08 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 47fb4ce512f7426cbd4e851dbd31389d3e4e84ec
Author: lijewski <lijewski>
Date:   Fri Aug 13 17:21:51 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/mg_restriction.f90

commit 5b59025c16170f3ca46fc0f13791bd492c321163
Author: lijewski <lijewski>
Date:   Fri Aug 13 17:05:32 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/coarsen_coeffs.f90

commit 838e620a7131d60f822b3eb5d0a15cfe57f9876e
Author: lijewski <lijewski>
Date:   Fri Aug 13 16:33:13 2010 +0000

    some code rearrangement

Src/F_BaseLib/sort_box.f90

commit c34c05e31f8964c9a3a58118a0e9251c443242ff
Author: lijewski <lijewski>
Date:   Fri Aug 13 16:24:31 2010 +0000

    some OpenMPing

Src/F_BaseLib/interp.f90

commit 2a4a01b1833bf72891f30a5278c5b3c2dac361e9
Author: ajnonaka <ajnonaka>
Date:   Fri Aug 13 15:16:41 2010 +0000

    test commit for cvs email notifications

Src/F_BaseLib/make_new_grids.f90

commit fb65c719648c53128589828e2329c990048a7a93
Author: ajnonaka <ajnonaka>
Date:   Fri Aug 13 14:38:54 2010 +0000

    New probin variables that let you set max_grid_size as a function of level.  They are max_grid_size_1, max_grid_size_2, and max_grid_size_3.
    
    Note max_grid_size_base has been replaced by max_grid_size_1.
    
    These default to max_grid_size if they are not set.
    
    max_grid_size_1 is max_grid_size for the coarsest level, "level 1"
    max_grid_size_2 is max_grid_size for the first level of refinement, "level 2"
    max_grid_size_3 is max_grid_size for the second level of refinement and beyond, "level 3 and beyond"
    
    Modified inputs files to reflect this.
    
    Also, setting the default value of cluster_min_width to 8.  16 gave horrifically blocky looking grid structures, even for very hi-res problems.  The averaging procedure just works better if you get more form-fitting grids.
    
    Still need to update local copies of initialize.f90, regrid.f90, and make_new_grids.f90

Src/F_BaseLib/make_new_grids.f90

commit 83cd9088ab59f476327b4e5176aa4670b889a201
Author: lijewski <lijewski>
Date:   Thu Aug 12 23:36:20 2010 +0000

    removed pc_cc_interp and pr_cc_interp routines

Src/F_BaseLib/interp.f90

commit f4ec43b3934c3ba7385c7a2862e19b8d19d2bc8a
Author: lijewski <lijewski>
Date:   Thu Aug 12 23:18:05 2010 +0000

    removed bl_nd_interp_[23]d

Src/F_BaseLib/interp.f90

commit af6dd476b806094949f51e20164ad761b55e43df
Author: ajnonaka <ajnonaka>
Date:   Thu Aug 12 22:23:27 2010 +0000

    use lbound/ubound instead of 1,size for fab/multifab loops

Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab.f90

commit b53ab2beb8c1c18b814eb368975a89535564624f
Author: lijewski <lijewski>
Date:   Thu Aug 12 21:04:28 2010 +0000

    workaround for dumb IBM xlf bug

Src/F_BaseLib/fillpatch.f90

commit 93ae903df568769b8122ac1b4a36df21d6ee23d5
Author: almgren <almgren>
Date:   Thu Aug 12 19:45:38 2010 +0000

    Anything to do with the sparse solver is now commented out in mg.f90 and mg_tower.f90
    and we no longer include sparse_solve.f90 in GPackage.mak

Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_tower.f90

commit 66d8e047f2b7d9a5913631f6ee4814a21c74e1fc
Author: lijewski <lijewski>
Date:   Thu Aug 12 19:33:22 2010 +0000

    OpenMP'd min_val and max_val routines

Src/F_BaseLib/fab.f90

commit 07514d755ad217cf90d02a4b5640b9dfdcc7b4d1
Author: lijewski <lijewski>
Date:   Thu Aug 12 17:41:18 2010 +0000

    OpenMP'd sub_sub and plus_plus routines

Src/F_BaseLib/multifab.f90

commit de0c9af114b22b5d78e44eccc58409803e2b31be
Author: lijewski <lijewski>
Date:   Thu Aug 12 17:27:38 2010 +0000

    OpenMP'd mult_mult routines

Src/F_BaseLib/multifab.f90

commit 2a022aeeecf4543c69035304c52e15d60cd1322c
Author: lijewski <lijewski>
Date:   Thu Aug 12 17:18:03 2010 +0000

    OpenMP'd div_div routines

Src/F_BaseLib/multifab.f90

commit dd061d14688fb697331dad4326dad3e1d1372e17
Author: lijewski <lijewski>
Date:   Thu Aug 12 16:06:17 2010 +0000

    some code simplification

Src/F_BaseLib/multifab.f90

commit d0b938b646b8f792e12a847850df1039e9a5df28
Author: ajnonaka <ajnonaka>
Date:   Thu Aug 12 13:47:07 2010 +0000

    -O for franklin, -Ofast for everyone else, regardless of what the OMP flag is set to

Tools/F_mk/comps/Linux_pathscale.mak

commit d311f9fdd6c8bacfafd15b44d2aec9ae30040db1
Author: gpau <gpau>
Date:   Thu Aug 12 00:12:50 2010 +0000

    *** empty log message ***

Tools/C_util/Convergence/ComputeAmrDataNorms.H
Tools/C_util/Convergence/ComputeAmrDataNorms.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Convergence/PltFileNorm.cpp

commit 36dda58ddc03e71b0de2da4f333fef607b7bb782
Author: gpau <gpau>
Date:   Wed Aug 11 22:46:45 2010 +0000

    added multilevel support for visc_coefficients

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 32e16bbd4486b6677142ad7ee0d37a6ab808ac95
Author: mzingale <mzingale>
Date:   Fri Aug 6 19:31:13 2010 +0000

    update to new file and dir locations

Tools/C_util/regtests/Maestro-tests.ini

commit 9f4f4f239e9932cfc149559e36206111bdc4e97d
Author: lijewski <lijewski>
Date:   Thu Aug 5 15:53:24 2010 +0000

    compiles now

Tools/C_util/Convergence/DiffSameGrid2.cpp

commit 1ddaf92208e99c4d246283ad92cb933cd98ce7e8
Author: mzingale <mzingale>
Date:   Tue Aug 3 15:32:19 2010 +0000

    add support for NYBlue -- note, now we do COMP=xlf

Tools/F_mk/comps/xlf.mak

commit 05305f69f88463b70fe38864d8847c332d0c975d
Author: almgren <almgren>
Date:   Fri Jul 30 23:25:33 2010 +0000

    rho_xy,rho_yz,rho_xz were not being used.

Src/LinearSolvers/C_CellMG/ABec_3D.F

commit 0b47a14740f9bc5e706da0a019e2fb986297c057
Author: almgren <almgren>
Date:   Fri Jul 30 21:41:06 2010 +0000

    Fix an oops.

Src/C_AMRLib/INTERP_1D.F

commit 8ba0e33ed5ae2492c8ac7974e82b51637cae5535
Author: almgren <almgren>
Date:   Thu Jul 29 16:33:28 2010 +0000

    Reused "actual_state" twice, first should have been "actual_comp"

Src/C_AMRLib/INTERP_F.H

commit 63ebb521ed0627e1d9be9bb97303da6a50c499f1
Author: almgren <almgren>
Date:   Wed Jul 28 01:21:08 2010 +0000

    Fix another oops.

Src/C_AMRLib/INTERP_2D.F

commit 0a5212ffa665ddcbc3e59f605bfe0467b427d2bc
Author: almgren <almgren>
Date:   Wed Jul 28 01:17:57 2010 +0000

    Typo before.

Src/C_AMRLib/INTERP_2D.F

commit 5da7ef1415421455932c77088b9054e1a141e91c
Author: almgren <almgren>
Date:   Wed Jul 28 01:07:23 2010 +0000

    Pass actual_comp and actual_state to the Fortran interp routines,
    through the Interpolater::interp(...) routines.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/INTERP_1D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp

commit 7eef840d7ff3be3d0735e74897ca43c7717e5adc
Author: gilet <gilet>
Date:   Wed Jul 28 00:50:55 2010 +0000

    Change MPIHOME for orga so things work again

Tools/F_mk/GMakeMPI.mak

commit 182ad6ea343867e02823686becc9856f75d769c2
Author: almgren <almgren>
Date:   Mon Jul 26 23:56:09 2010 +0000

    Moved ml_fill_all_fluxes back from mg_cpp.f90 into stencil.f90

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 7149216fbe4d7a9597a2b1b695a7bb118ea4f507
Author: almgren <almgren>
Date:   Mon Jul 26 16:54:04 2010 +0000

    Start to put use_hypre option in.

Src/LinearSolvers/F_MG/mg.f90

commit 740eec39971ac2c72f42d20ad4bbfcb7f1bf2d3c
Author: lijewski <lijewski>
Date:   Fri Jul 23 23:14:46 2010 +0000

    some g++ and gfortran mods

Tools/C_mk/Make.defs

commit 5e2d59fbbe28cfe3237c5f0da7f2c2dfbf3f594b
Author: lijewski <lijewski>
Date:   Fri Jul 23 18:21:28 2010 +0000

    some cleanup prompted by gfortran -Wall

Src/F_BaseLib/interp.f90
Src/F_BaseLib/list_box.f90
Src/LinearSolvers/F_MG/mg_restriction.f90

commit 0f17e775671c71478b23a2db32886619ac78605e
Author: lijewski <lijewski>
Date:   Fri Jul 23 17:00:40 2010 +0000

    add -fopenmp if OMP

Tools/F_mk/comps/gfortran.mak

commit 79a1001d7e973e427167b3737477a50c8e3b1c1c
Author: almgren <almgren>
Date:   Fri Jul 23 16:31:01 2010 +0000

    Modify to let this work on hicegate0, Wolfram Schmidt's machine.

Tools/C_mk/Make.mpi

commit 7a8a2bee16c07b604a1399597efd8633f8952293
Author: almgren <almgren>
Date:   Fri Jul 23 16:24:28 2010 +0000

    Fix the eps stuff we pass in to ml_nd_solve and ml_cc_solve.

Src/LinearSolvers/F_MG/ml_solve.f90

commit 2f7936a18bf2653cfd0dd9b630cb02f98261e841
Author: almgren <almgren>
Date:   Fri Jul 23 03:19:20 2010 +0000

    Fix oops in previous commit.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 7c05054a6adb8f5a92c03024bfcef8ba944308c3
Author: almgren <almgren>
Date:   Fri Jul 23 03:15:47 2010 +0000

    Add print statement if already converged

Src/LinearSolvers/F_MG/ml_nd.f90

commit ed11557ec2c1aec65bf9d23aee9c7a80dbab87d9
Author: almgren <almgren>
Date:   Thu Jul 22 23:49:52 2010 +0000

    Don't force the Intel compilers when MPI is defined.

Tools/F_mk/GMakeMPI.mak

commit 3123b1083603e4a3dbe32400c66d1e30367e7136
Author: almgren <almgren>
Date:   Thu Jul 22 14:34:43 2010 +0000

    Removed quotes around included files.

Tools/F_mk/GMakedefs.mak

commit 49ff4250a5178c834a5d92e6c28c9c3c3f4e742f
Author: almgren <almgren>
Date:   Wed Jul 21 21:46:16 2010 +0000

    Put each compiler's options into a separate file in comps/*.mak

Tools/F_mk/GMakedefs.mak

commit e1f97d7535667320584b6d065453c7efde4bdce2
Author: almgren <almgren>
Date:   Wed Jul 21 21:44:11 2010 +0000

    Use this to simplify the makefile system -- these are included in Gmakedefs.mak

Tools/F_mk/comps/Darwin_ibm.mak
Tools/F_mk/comps/Linux_catamount.mak
Tools/F_mk/comps/Linux_intel.mak
Tools/F_mk/comps/Linux_lahey.mak
Tools/F_mk/comps/Linux_nag.mak
Tools/F_mk/comps/Linux_pathscale.mak
Tools/F_mk/comps/Linux_pgi.mak
Tools/F_mk/comps/Linux_sunstudio.mak
Tools/F_mk/comps/Linux_xt4.mak
Tools/F_mk/comps/aix.mak
Tools/F_mk/comps/crayx1.mak
Tools/F_mk/comps/g95.mak
Tools/F_mk/comps/gfortran.mak
Tools/F_mk/comps/irix64.mak
Tools/F_mk/comps/osf1.mak
Tools/F_mk/comps/xlf.mak

commit 1999fb539f31adce58de402946fcd8fdaa24eb53
Author: lijewski <lijewski>
Date:   Wed Jul 21 19:28:28 2010 +0000

    fix where to find mpi stuff for my machine

Tools/F_mk/GMakeMPI.mak

commit 728aab835dc53c1a932cb0af89b01b4277d677cc
Author: lijewski <lijewski>
Date:   Wed Jul 21 19:03:55 2010 +0000

    fix for when not all levels defined

Src/F_BaseLib/ml_layout.f90

commit fb82cda7c5fe551dd0a939b07b9f00da4cf8ac27
Author: almgren <almgren>
Date:   Tue Jul 20 21:35:12 2010 +0000

    Need this to compile from C++

Src/LinearSolvers/F_MG/mg_cpp.f90

commit ce298b90068d9c966f3c75d68cfe5711c78d777f
Author: almgren <almgren>
Date:   Tue Jul 20 20:59:33 2010 +0000

    Use local form of dnrm2 so we don't have to link with LAPACK.

Src/LinearSolvers/F_MG/sparse_solve.f90

commit 8ddfbabbaca025cdf1fd2c2223d4f69dde378afd
Author: almgren <almgren>
Date:   Tue Jul 20 19:58:40 2010 +0000

    More clean-up of use modules...

Src/LinearSolvers/F_MG/ml_solve.f90

commit 2d387426775bca1f50399c5ce24cc0995197390a
Author: almgren <almgren>
Date:   Tue Jul 20 19:56:50 2010 +0000

    More clean-up...

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_solve.f90

commit e16c8a885900e2023206bf6ceb220a7db5836c14
Author: almgren <almgren>
Date:   Tue Jul 20 19:54:26 2010 +0000

    Clean up "use" statements.

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/nodal_divu.f90

commit 4125108dff9cd5739b3db75e666048d983e14888
Author: almgren <almgren>
Date:   Tue Jul 20 19:35:22 2010 +0000

    Moved ml_fill_all_fluxes from ml_util into mg_cpp.f90

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/ml_util.f90

commit bdd0edb444d759ab87b61beee8bc0886382d2d75
Author: almgren <almgren>
Date:   Tue Jul 20 19:32:44 2010 +0000

    No more mlmg.f90

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak

commit fa20e42e02fad65a211a2b3c8eaddaef207d9690
Author: almgren <almgren>
Date:   Tue Jul 20 19:22:48 2010 +0000

    Fix oops.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 2c17475397fd126f44e3bc29b26232c114c7a8e0
Author: almgren <almgren>
Date:   Tue Jul 20 19:03:17 2010 +0000

    Fix oops...

Src/LinearSolvers/F_MG/ml_nd.f90

commit 9c51d17459012909715cbea09ca212312b357cdf
Author: almgren <almgren>
Date:   Tue Jul 20 19:00:09 2010 +0000

    Moved grid_res into ml_nd.

Src/LinearSolvers/F_MG/mg.f90

commit 8540e67fbd021a9ceb69c19a3fbbb6d704548730
Author: almgren <almgren>
Date:   Tue Jul 20 18:59:07 2010 +0000

    Move files from mg_defect.f90 (which no longer exists) into ml_nd.f90

Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/ml_nd.f90

commit af62c2a6625b9cb26c5d163fa84bd4247f5f3e84
Author: almgren <almgren>
Date:   Tue Jul 20 17:59:52 2010 +0000

    Renamed eps --> rel_eps

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 7df677b2803601d99b44ee103f6bf3b0dd744a23
Author: almgren <almgren>
Date:   Tue Jul 20 03:31:20 2010 +0000

    Add eps_in as optional argument to ml_cc_solve.

Src/LinearSolvers/F_MG/ml_solve.f90

commit 3ebe992b7dd776ec7294870ae59f27d272e4829d
Author: almgren <almgren>
Date:   Mon Jul 19 22:11:17 2010 +0000

    Need to remove "pure" to compile with Intel 10.1

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab.f90

commit 6cbff8c358d94e48e0519098183c84f76a12fc71
Author: almgren <almgren>
Date:   Mon Jul 19 20:46:04 2010 +0000

    Change the print statement:
    
    MPI initialized with xx CPUs
    
    to
    
    MPI initialized with xx MPI Processes
    
    since they are no longer the same with threading.

Src/C_BaseLib/BoxLib.cpp

commit 0e986e3f27f686607701c6e86fd84f70f52bf19d
Author: lijewski <lijewski>
Date:   Mon Jul 19 20:09:44 2010 +0000

    some cleanup including making functions with no side-effects pure

Src/F_BaseLib/bl_IO.f90
Src/F_BaseLib/bl_stream.f90
Src/F_BaseLib/bl_string.f90
Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/sort_d.f90
Src/F_BaseLib/sort_i.f90
Src/F_BaseLib/tag_boxes.f90
Src/F_BaseLib/vector_i.f90

commit d52881e16017bfdc509c0ba15290fe209a30d9ae
Author: almgren <almgren>
Date:   Mon Jul 19 19:40:08 2010 +0000

    Change default for max_iter from 20 to 50.

Src/LinearSolvers/F_MG/mg_tower.f90

commit 73921a01dbb428b4b2b377cb9198c35ae4fe0d74
Author: almgren <almgren>
Date:   Mon Jul 19 18:14:02 2010 +0000

    Make the default for RANGER be for PGI so we don't need the special intel stuff.

Tools/C_mk/Make.mpi

commit 5bf1381b920178417acaddc5163a4d9d3cfbd992
Author: almgren <almgren>
Date:   Mon Jul 19 18:10:08 2010 +0000

    Works now for ranger.

Tools/C_mk/Make.Linux

commit f19073ec4aaff4052066d1301442dee4325cadc7
Author: lijewski <lijewski>
Date:   Mon Jul 19 16:56:47 2010 +0000

    mods in preparation for making the components of multifabs private

Src/LinearSolvers/F_MG/ml_nd.f90

commit dee2a81b165036d7866b19608f111a55df4e908b
Author: lijewski <lijewski>
Date:   Sat Jul 17 00:51:01 2010 +0000

    mods to quiet gfortran std=f95 warnings

Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/ppm_util_c.c
Src/F_BaseLib/system_util_c.c
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit d30ef740088d89f5b9b9602f9a380485bcb56c81
Author: lijewski <lijewski>
Date:   Sat Jul 17 00:05:27 2010 +0000

    mods in preparation of making the components of multifabs private

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/cluster.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/make_new_grids.f90
Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/multifab.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90
Src/LinearSolvers/F_MG/coarsen_coeffs.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_mask.f90
Src/LinearSolvers/F_MG/sparse_solve.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_fill.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 6e573cd66d5e190975f813d7af470da3639383aa
Author: lijewski <lijewski>
Date:   Thu Jul 15 20:29:51 2010 +0000

    the components of type fab are now private and only accessible via function calls

Src/F_BaseLib/fab.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 34135e109867778279a34943dcd97cc4ba52a572
Author: almgren <almgren>
Date:   Thu Jul 15 04:01:29 2010 +0000

    Add Amr::blockingFactor (int lev) which returns blocking_factor[lev].

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 788d861073f285ad4231fff8aa5b6c2418605cf0
Author: lijewski <lijewski>
Date:   Wed Jul 14 23:27:45 2010 +0000

    the components of type boxarray are now private and only accessible via function calls

Src/F_BaseLib/box.f90
Src/F_BaseLib/box_util.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/list_box.f90
Src/F_BaseLib/make_new_grids.f90
Src/F_BaseLib/ml_boxarray.f90
Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_fill.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 42828dd5975ec1c33c9590fdd58ff2782d3be001
Author: lijewski <lijewski>
Date:   Wed Jul 14 20:16:18 2010 +0000

    made get_dim() a pure function

Src/F_BaseLib/box.f90

commit 8711b2bbe9cc4d0d72ed102b4e1377392bd0c02f
Author: lijewski <lijewski>
Date:   Tue Jul 13 22:16:48 2010 +0000

    made component types private

Src/F_BaseLib/bl_stream.f90

commit 5c7264fa69d3257cab3163d2b6144a6c1fbae54c
Author: lijewski <lijewski>
Date:   Tue Jul 13 21:22:53 2010 +0000

    made a couple module variables private

Src/F_BaseLib/plotfile.f90

commit cee2ecb7f6caef452c7a79ca88f7f9ebe1e2cb43
Author: lijewski <lijewski>
Date:   Tue Jul 13 21:22:33 2010 +0000

    removed pingpong.f90

Src/F_BaseLib/GPackage.mak

commit 0cef45f0bdaefdd7b2d34466607c43f35027e3d5
Author: lijewski <lijewski>
Date:   Tue Jul 13 21:15:56 2010 +0000

    made sfc_greater_i() private

Src/F_BaseLib/knapsack.f90

commit 08ab0e512d3d5df3ded07a0af3bd103899a5f577
Author: lijewski <lijewski>
Date:   Tue Jul 13 21:04:17 2010 +0000

    made a module variable private

Src/F_BaseLib/bl_timer.f90

commit fa588b7c587d85f524d621b2c70c8fee733bfb85
Author: lijewski <lijewski>
Date:   Tue Jul 13 20:58:19 2010 +0000

    removed unused module variables and made others private

Src/F_BaseLib/bl_IO.f90

commit 7bdfb9ebed8aa8eb2f38073d02bae45b6cb77dc7
Author: lijewski <lijewski>
Date:   Tue Jul 13 20:50:49 2010 +0000

    removed unused module variable

Src/F_BaseLib/box.f90

commit c7ef4b2c7f66ea61ab7eedad817589ed6f5ebe99
Author: lijewski <lijewski>
Date:   Wed Jun 30 22:50:53 2010 +0000

    only call simplify() if too few grids

Src/C_AMRLib/AuxBoundaryData.cpp

commit 0b9ee5106f014b9c8371646853bbbfb001bf73f8
Author: lijewski <lijewski>
Date:   Wed Jun 30 22:35:46 2010 +0000

    add back in KnapSack to initialize()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 850d35968b9ed22d987c643f1e390a0f7fc2cb4c
Author: lijewski <lijewski>
Date:   Wed Jun 30 22:16:36 2010 +0000

    do a maxSize() after the simplify() in initialize()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 76606b0813833eb10ae279f445875a49bce2dc05
Author: lijewski <lijewski>
Date:   Tue Jun 29 20:19:45 2010 +0000

    sped up boxlist_simplify() and boxarray_simplify()

Src/F_BaseLib/list_box.f90

commit bbddffd6bbebb7f196e9f23dba8942d58c829a2c
Author: ajnonaka <ajnonaka>
Date:   Tue Jun 29 15:25:44 2010 +0000

    changed the plot_per functionality to print the plotfile *after* you pass plot_per, rather than before.  This matches the MAESTRO functionality and also prevents the code from printing two plotfiles in a row at the end of a simulation.

Src/C_AMRLib/Amr.cpp

commit 79e7714a5caf9a7097c45df7e73b56bcdead2c71
Author: lijewski <lijewski>
Date:   Mon Jun 28 20:44:24 2010 +0000

    do NOT force the use of KnapSack in initialize()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 2a0d24c3f3b363f951865f372effe0f99f35d38a
Author: lijewski <lijewski>
Date:   Mon Jun 28 18:25:12 2010 +0000

    initialize() now calls GetBndryCells()

Src/C_AMRLib/AuxBoundaryData.cpp

commit e84a86abf8d94442f1465db3d443395477eb80ec
Author: lijewski <lijewski>
Date:   Mon Jun 28 18:24:45 2010 +0000

    make better use of faster simplify() in GetBndryCells()

Src/C_BaseLib/BoxArray.cpp

commit e4b3a2caf580e875be5b71f2bdc689cc54dec2ee
Author: lijewski <lijewski>
Date:   Mon Jun 28 17:43:50 2010 +0000

    call simplify() at end of GetBndryCells()

Src/C_BaseLib/BoxArray.cpp

commit d787f94e3ac07470a191e54f04415f374e7fed76
Author: lijewski <lijewski>
Date:   Mon Jun 28 17:33:48 2010 +0000

    users can choose the best simplify() or the fast one

Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit 339b28e070357b83c4a849f93a175069514a0807
Author: lijewski <lijewski>
Date:   Mon Jun 28 16:17:48 2010 +0000

    limit how far afield we look for abutting boxes in simplify_doit()

Src/C_BaseLib/BoxList.cpp

commit 8ba9c0df4372ca74331606af276308a88cad4f86
Author: vince <vince>
Date:   Fri Jun 25 22:36:07 2010 +0000

    added some diagnostics and a sync.

Src/C_BaseLib/VisMF.cpp

commit 57ebb28de9210a20404206623e722c3b0a5f6b85
Author: lijewski <lijewski>
Date:   Wed Jun 23 22:02:06 2010 +0000

    use std::fabs() instead of std::abs() in a couple places

Src/C_BaseLib/FArrayBox.cpp

commit b9225915e5a080d13588e44408bf26d1f4c9f212
Author: almgren <almgren>
Date:   Sun Jun 20 00:47:24 2010 +0000

    Get rid of daxpy.f and ddot -- these are in BLAS...

Src/LinearSolvers/F_MG/FParallelMG.mak

commit bddf8a447488b83e742000ddbca6bbb7f9eec011
Author: almgren <almgren>
Date:   Sun Jun 20 00:23:19 2010 +0000

    Change the interface for set_mac_coefficients, set_visc_coefficients, set_porous_coefficients
    so we don't have to pass a MacBndry, instead we pass xa and xb directly.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 4e14c2a0485e7df56a72fedc8a399f0ea5a7c350
Author: almgren <almgren>
Date:   Sun Jun 20 00:15:07 2010 +0000

    Add these files so we can stop including the Make.package from LAPACK,
    SPARSKIT and BLAS.  Hope this works!

Src/LinearSolvers/F_MG/FParallelMG.mak

commit d693dae62f40e12cda0ad013ef2519b055b168ef
Author: lijewski <lijewski>
Date:   Fri Jun 18 22:22:05 2010 +0000

    more refinement of refine_grid_layout

Src/C_AMRLib/Amr.cpp

commit 7ad1715ec5a91c653119bbf088fc1ee3ad06edfb
Author: lijewski <lijewski>
Date:   Wed Jun 16 20:49:27 2010 +0000

    Attempt to minimize the number of new grids built in refine_grid_layout by
    refining each dimension at a time until we've got more than NProcs
    grids.

Src/C_AMRLib/Amr.cpp

commit 348af522e515bd8218f6907706c599a2c47ff527
Author: lijewski <lijewski>
Date:   Wed Jun 16 20:17:55 2010 +0000

    added version of maxSize() taking an IntVect to mirror the version in BoxList

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 046b1e51d79b801856f1252cb52a770e889f7cc8
Author: almgren <almgren>
Date:   Fri Jun 11 19:48:58 2010 +0000

    Add kiryu.

Tools/F_mk/GMakeMPI.mak

commit c2a8bbd3c8a3a557b2a6c76b2b3a2d08ec6810f5
Author: marc <marc>
Date:   Thu Jun 10 20:29:13 2010 +0000

    Mods for marcs account on the TUe computer

Tools/C_mk/Make.mpi

commit f6c9308127ccd617425a1efec151a868454b244b
Author: almgren <almgren>
Date:   Thu Jun 10 00:34:46 2010 +0000

    Remove unused variable.

Src/LinearSolvers/F_MG/ml_cc.f90

commit cbb0f20b8aeb80bc98cf1678d19160b1073106d0
Author: almgren <almgren>
Date:   Wed Jun 9 19:59:36 2010 +0000

    Modified amr.regrid_int so that we only need max_level values
    of it (instead of max_level+1), and we don't need it at all if
    max_level = 0.   Also add print statement that says
    "Successfully read inputs file" (analogous to "Successfully read probin...")

Src/C_AMRLib/Amr.cpp

commit 38ac663f514bd375a83b3d7da9bf45ac3759ae5e
Author: mzingale <mzingale>
Date:   Wed Jun 9 16:57:12 2010 +0000

    update to allow for the cvs updates to work when fParallel is not in
    the top level directory

Tools/C_util/regtests/test.py

commit 6e8f1870bca3c285092dac67156d38f94dc6283c
Author: gpau <gpau>
Date:   Wed Jun 9 16:56:26 2010 +0000

    added an optional argument for Reflux function that allows the flux to be multiplied by a fixed value regardless of the face direction.

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit ca00a6b5496c068199be318ca81ee13961aa50fc
Author: mzingale <mzingale>
Date:   Wed Jun 9 00:48:16 2010 +0000

    remove the old NMake stuff

Tools/F_mk/NMakedefs.mak
Tools/F_mk/NMakerules.mak

commit 64039fdd74a70df9e56e160a5f2793fa5b512ba9
Author: almgren <almgren>
Date:   Tue Jun 8 21:34:32 2010 +0000

    Dont maintain NPackage.mak anymore.

Src/F_BaseLib/NPackage.mak

commit 8e364fda454711bf4a13e39ff0f44bef9aa808ce
Author: ajnonaka <ajnonaka>
Date:   Tue Jun 8 20:05:38 2010 +0000

    back of compiler optimization for franklin with pathscale and openmp.  -Ofast won't even compile so going back to -02

Tools/F_mk/GMakedefs.mak

commit 8f0d8ce7c287f3b5da43813c7e077ea36da52d8b
Author: almgren <almgren>
Date:   Mon Jun 7 19:59:39 2010 +0000

    Remove unused variable.

Src/LinearSolvers/F_MG/stencil.f90

commit dc30d85e35f0b756d44eccd8e93fa323f5c2141d
Author: ajnonaka <ajnonaka>
Date:   Mon Jun 7 19:41:23 2010 +0000

    added a .MAESTRO to the executable suffix list if we are building with USE_MAESTR_INIT=TRUE

Tools/C_mk/Make.defs

commit b0a7103432e1c2d4ba250704a816ede089361d2f
Author: almgren <almgren>
Date:   Sun Jun 6 20:07:22 2010 +0000

    Fix this.

Src/LinearSolvers/F_MG/FParallelMG.mak

commit d8c278dbe35f429eb0bd90c6d8981a5c9cf47503
Author: gpau <gpau>
Date:   Sat Jun 5 02:10:53 2010 +0000

    updated to handle new operator

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_fill.f90

commit fb7fd70eda0e8febae4218e68f5ca902ac40ae1b
Author: gpau <gpau>
Date:   Sat Jun 5 02:06:46 2010 +0000

    updated to handle new operator.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit d496158231ce305b9ead559f82d9cf3b0c25412a
Author: adonev <adonev>
Date:   Fri Jun 4 23:16:23 2010 +0000

    Added host angilas

Tools/F_mk/GMakeMPI.mak

commit baf8ffd5b2ce0af830890f70899bf2e23224c288
Author: almgren <almgren>
Date:   Fri Jun 4 21:42:45 2010 +0000

    Latest ...

Docs/BoxLib/boxlib.tex
Docs/paper.tex

commit 5dca9c30819f24ef328b9191f4b4572adaac77f6
Author: almgren <almgren>
Date:   Fri Jun 4 21:39:28 2010 +0000

    We just keep making it better...

Docs/BoxLib/boxlib.tex

commit 3a80fcf4c01f88457385838a8c62418c3acb5884
Author: almgren <almgren>
Date:   Fri Jun 4 21:39:15 2010 +0000

    These are just the framework for building the docs.

Docs/GNUmakefile
Docs/paper.tex

commit cc1d3f4793c64394494f2a44cb251c0f52ed4180
Author: almgren <almgren>
Date:   Fri Jun 4 21:16:00 2010 +0000

    Copied from MAESTRO/docs/architecture then modified.

Docs/BoxLib/GNUmakefile
Docs/BoxLib/boxlib.tex
Docs/BoxLib/data_loc.odg
Docs/BoxLib/data_loc2.eps
Docs/BoxLib/index_grid.odg
Docs/BoxLib/index_grid2.eps
Docs/BoxLib/mac.odg
Docs/BoxLib/mac2.eps
Docs/BoxLib/maestro_directory.odg
Docs/BoxLib/maestro_directory2.eps
Docs/BoxLib/paper.tex

commit 5dd18f376cbd9ef04222947facef95d306c161ac
Author: almgren <almgren>
Date:   Fri Jun 4 21:15:33 2010 +0000

    For now this holds the copyright info.

Docs/preface/preface.tex

commit 099cdb05068cf6e5e17ca9ab4c862cf5661cce7f
Author: ajnonaka <ajnonaka>
Date:   Fri Jun 4 17:14:31 2010 +0000

    works now for array of regrid_int's

Src/C_AMRLib/Amr.cpp

commit 0c4fe056d1bcc53ac4bb657966a268464eb00489
Author: almgren <almgren>
Date:   Thu Jun 3 20:22:07 2010 +0000

    Turns out regrid_int was being stored as an array over nlevels but
    was only being read in as a single integer which was assigned to all levels.
    Now we have the option of reading in a single integer for all levels or
    an array (nlevels long) of values.

Src/C_AMRLib/Amr.cpp

commit 67364655bf30582d19ba4534217b2ad21ec9443d
Author: lijewski <lijewski>
Date:   Wed Jun 2 19:49:57 2010 +0000

    added stuff for ORANGE

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 796f5be1eff57f06e8653144fa1e5d03c9ecfa4f
Author: lijewski <lijewski>
Date:   Wed Jun 2 02:59:42 2010 +0000

    removed some unused variables

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90

commit d24636fef3e83adb3624b5782d317f3a6cec6aba
Author: lijewski <lijewski>
Date:   Wed Jun 2 02:43:50 2010 +0000

    removed some unused variables

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_smoother.f90

commit da3dbedefc31eefb290739a16bdbe25a30731b9c
Author: lijewski <lijewski>
Date:   Wed Jun 2 02:33:28 2010 +0000

    removed some unused variables

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 093e73801ef65ce0f8ff4f1051e1f9422a0284e1
Author: lijewski <lijewski>
Date:   Wed Jun 2 02:15:41 2010 +0000

    removed some unused variables

Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_fill.f90

commit 1bc676136872c55ad99cdb8971705757e07627ee
Author: lijewski <lijewski>
Date:   Wed Jun 2 02:00:01 2010 +0000

    removed some unused variables

Src/LinearSolvers/F_MG/mg.f90

commit 7da8fcc38530241f5fc22c91078956dae50d3a3e
Author: lijewski <lijewski>
Date:   Wed Jun 2 01:49:57 2010 +0000

    removed some unused variables

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/sparse_solve.f90
Src/LinearSolvers/F_MG/stencil_fill.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 6c9509ea865fb99824aaea604a5b6f9f92e82499
Author: lijewski <lijewski>
Date:   Wed Jun 2 01:25:23 2010 +0000

    removed some unused variables

Src/LinearSolvers/F_MG/mg.f90

commit d9ee3cde690bde9a8c6bff3efe06172673385d48
Author: ajnonaka <ajnonaka>
Date:   Wed Jun 2 00:53:13 2010 +0000

    backing out of a previous change which mysteriously breaks the multigrid on Ann's and my machine

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/sparse_solve.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_fill.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit b17daf618a518c4d784a97ebe338ddbc6973fa3c
Author: vince <vince>
Date:   Tue Jun 1 21:50:06 2010 +0000

    paths for kiryu.

Tools/C_mk/Make.mpi

commit 97c00579d2800134e8f6c61075035a35f5cce3d7
Author: almgren <almgren>
Date:   Mon May 31 19:40:23 2010 +0000

    Modify the amr.verbose > 1 option so that it calls printGridSummary
    instead of not printing any grid info.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit d861b22d9b94cfb924ceb8c866408c60bae2ba6d
Author: almgren <almgren>
Date:   Mon May 31 18:33:06 2010 +0000

    Replace "verbose" by
    "verbose > 0" in most cases, but
    "verbose > 1" in cases which controlled a call to printGridInfo.

Src/C_AMRLib/Amr.cpp

commit 4b4a0325a4f3bcf5b4bb6dfd12ef983e6e9fe51d
Author: lijewski <lijewski>
Date:   Mon May 31 15:52:09 2010 +0000

    plugged memory leak

Src/F_BaseLib/cluster.f90

commit 30108129b510a6809d3f4e701bd229a0c77eae10
Author: almgren <almgren>
Date:   Mon May 31 03:38:54 2010 +0000

    Add checkpoint_on_restart flag which only happens if
    doing regrid_on_restart.

Src/C_AMRLib/Amr.cpp

commit 93687b24aad98b03afc9d47818c1a0ed1ee6f245
Author: almgren <almgren>
Date:   Mon May 31 03:29:16 2010 +0000

    Fix indentation.

Src/C_AMRLib/Amr.cpp

commit 4e70f27ab274d4d55330fc0545cc0eeaf047368b
Author: almgren <almgren>
Date:   Sun May 30 23:07:43 2010 +0000

    I believe that this version of cluster correctly uses blocking_factor
    when making grids, both in serial and in parallel.  It works for a simple
    2d test in varden anyway.

Src/F_BaseLib/cluster.f90

commit e3b3f021e2bdc6da304dfeefc5481e4a4a7bbc82
Author: lijewski <lijewski>
Date:   Fri May 28 23:39:28 2010 +0000

    removed some unused variables

Src/F_BaseLib/pingpong.f90

commit 7c184483c573ea7e3d65c5028e1602d3d8de9492
Author: lijewski <lijewski>
Date:   Fri May 28 23:31:09 2010 +0000

    cleaned up some unused variables

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/sparse_solve.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_fill.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 8977241f6d3f6ec5920550e170dedcd2e6ed8bb6
Author: lijewski <lijewski>
Date:   Fri May 28 21:58:13 2010 +0000

    removed some unused variables

Src/F_BaseLib/box_util.f90
Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/multifab.f90
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_bx.f90
Src/F_BaseLib/test/t_bxasc.f90
Src/F_BaseLib/test/t_cls.f90
Src/F_BaseLib/test/t_knapsack.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_bx.f90
Tests/F_BaseLib/t_bxasc.f90
Tests/F_BaseLib/t_cls.f90
Tests/F_BaseLib/t_knapsack.f90
Tests/F_BaseLib/t_main.f90

commit 7a0e000e6374bba9e58677ad878e2526505fe083
Author: lijewski <lijewski>
Date:   Thu May 27 22:23:32 2010 +0000

    moved tagboxes_coarsen() from tag_boxes.f90 -> cluster.f90

Src/F_BaseLib/cluster.f90
Src/F_BaseLib/tag_boxes.f90

commit 33756cc9b71e6af0a5a7e4b4685270f69c4aabfd
Author: lijewski <lijewski>
Date:   Thu May 27 22:16:30 2010 +0000

    bit more cleanup

Src/F_BaseLib/tag_boxes.f90

commit 27bd8a1f1616fb8c8ec118cd75d524550ea274d6
Author: lijewski <lijewski>
Date:   Thu May 27 22:15:02 2010 +0000

    got rid of some unused variables

Src/F_BaseLib/make_new_grids.f90

commit fd083b1c8b22932792754427fad135a65e73d76d
Author: lijewski <lijewski>
Date:   Thu May 27 22:13:57 2010 +0000

    tagboxes_coarsen() appears to work

Src/F_BaseLib/tag_boxes.f90

commit 5744a7408e36a7d67b954dfff43ec34891ab7f7e
Author: lijewski <lijewski>
Date:   Thu May 27 21:37:55 2010 +0000

    initial cut of tagboxes_coarsen(); compiles but hasn't been tested

Src/F_BaseLib/tag_boxes.f90

commit c43127d3118b5c4583fd97e49c590b239ca6ff03
Author: lijewski <lijewski>
Date:   Thu May 27 16:32:50 2010 +0000

    now compiles again after recent code changes

Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_bxasc.f90
Src/F_BaseLib/test/t_cls.f90
Src/F_BaseLib/test/t_knapsack.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_bxasc.f90
Tests/F_BaseLib/t_cls.f90
Tests/F_BaseLib/t_knapsack.f90
Tests/F_BaseLib/t_main.f90

commit 0ca1a46d70ad73a80ccb2ba1595ecdb27c5ef53e
Author: almgren <almgren>
Date:   Wed May 26 03:25:12 2010 +0000

    SPARSKIT stuff needs ddot which is  now in BLAS.

Src/LinearSolvers/F_MG/GPackage.mak

commit 9e1e9456d505b48241cc1575031799b770506e7a
Author: almgren <almgren>
Date:   Wed May 26 00:47:58 2010 +0000

    Replace a comma by a semicolon so we now compile again with USE_MPI = TRUE.

Tools/C_util/Convergence/DiffSameDomainRefined.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGrid2.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp

commit 52c132c39accd505eed78a930e224a25817fab0f
Author: almgren <almgren>
Date:   Tue May 25 21:56:21 2010 +0000

    One more fix...

Tools/C_util/Convergence/DiffSameDomainRefined.cpp

commit 21c3832b996919c9d8960e21598c32ef80b07402
Author: almgren <almgren>
Date:   Tue May 25 21:47:45 2010 +0000

    Try again...

Tools/C_util/Convergence/DiffSameDomainRefined.cpp

commit 8e63620e554cd3f95d2a99dc9944f92be90e05e4
Author: almgren <almgren>
Date:   Tue May 25 21:39:24 2010 +0000

    Fix mistakes.

Tools/C_util/Convergence/DiffSameDomainRefined.cpp

commit 3db71d39d3a3da01daefa3945ce091e0e418608c
Author: almgren <almgren>
Date:   Tue May 25 21:24:14 2010 +0000

    Allow different number of state variables.

Tools/C_util/Convergence/DiffSameDomainRefined.cpp

commit 2e9a4eb810b7b665af19ce7c712b832e96f90d4b
Author: almgren <almgren>
Date:   Tue May 25 21:12:18 2010 +0000

    If nComp differs then choose the min of the two files.

Tools/C_util/Convergence/DiffSameDomainRefined.cpp

commit e2d9b789aa3ac9ebbd2b9b55f3a56c9f0f07a6fc
Author: almgren <almgren>
Date:   Tue May 25 19:09:30 2010 +0000

    Fix countval arguments.

Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/DiffUniform.cpp

commit ecd832be75d8779c842549b6553440d3262f9cc5
Author: almgren <almgren>
Date:   Tue May 25 19:08:24 2010 +0000

    This version is derived from DiffSameGridRefined but does *not* require that the
    two plotfiles have the same boxarray at each level being compared, only that they
    have the same region of space covered.  We do a multifab copy to fill a boxarray
    at the coarse resolution instead of comparing directly to the multifab in the plotfile.

Tools/C_util/Convergence/DiffSameDomainRefined.cpp

commit 692e6f93bea1d3e4586231b3bd49afb72d316ea9
Author: mzingale <mzingale>
Date:   Tue May 25 00:28:36 2010 +0000

    also store the compilation flags in the job_info file.  That should
    pretty much cover it all.

Tools/F_scripts/make_build_info

commit a3013dd3d1190b95820ab62310f7579292a26f5a
Author: mzingale <mzingale>
Date:   Sat May 22 18:26:58 2010 +0000

    allow for the list of modules to be longer, but we need to break it over
    2 lines in the source to get it to compile.

Tools/F_scripts/make_build_info

commit 37aebea02f2959bf72452e03a4d87034c5c554e2
Author: mzingale <mzingale>
Date:   Fri May 21 23:13:57 2010 +0000

    get Castro building again -- daxpy and ddot are not in this directory

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 9bdffb47f8122b40d6206d52f01d3a3074140c06
Author: almgren <almgren>
Date:   Fri May 21 22:36:02 2010 +0000

    Remove unused variable.

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit 4a912254ab8a6ae5d60ee11dcea3ee4583cc88f2
Author: mzingale <mzingale>
Date:   Fri May 21 18:59:26 2010 +0000

    comment tweaks

Tools/F_scripts/make_build_info

commit 06547fc74e444188e92fdc27b8dab05478b2f53a
Author: mzingale <mzingale>
Date:   Fri May 21 17:20:07 2010 +0000

    change how build_info works.  It is now a module (which is safer for
    the string length matching) and therefore, it now needs to be detected
    by the moddep.pl script, so the dependences in GMaestro.mak are updated.
    This seems to work.  When you recompile, it rewrites build_info.f90 and
    recompiles it (as we want).  Note that now build_info.f90 is deleted
    once it is built.

Tools/F_scripts/make_build_info

commit 9eab2efdd162a158c18272639e9af3c3328da823
Author: mzingale <mzingale>
Date:   Thu May 20 23:50:48 2010 +0000

    fix a line-length issue -- should really wrap the modules line

Tools/F_scripts/make_build_info

commit 5d871a112220ba873e969ac4fca951cdf1d9a35d
Author: mzingale <mzingale>
Date:   Thu May 20 22:10:41 2010 +0000

    store the list of "modules" (e.g. reaction network, EOS, ...) compiled
    into the code in the job_info file.

Tools/F_scripts/make_build_info

commit b14bf4c6b2afca87359ca4386985f010faf8dd3a
Author: mzingale <mzingale>
Date:   Thu May 20 19:52:54 2010 +0000

    move the stuff that makes build_info.f90 out of the general mk/ stuff
    and into GMaestro.mak, since this is only used by Maestro.  This will
    give us more control over it.

Tools/F_mk/GMakerules.mak

commit 398f8bc1d404af9d4dc886e4caa02fdf47a47720
Author: ajnonaka <ajnonaka>
Date:   Mon May 17 22:46:49 2010 +0000

    OMP fix

Src/LinearSolvers/F_MG/itsol.f90

commit d4f3cd5e7ed10651d26ced1f38e3ccc1312970f4
Author: almgren <almgren>
Date:   Sat May 15 01:12:56 2010 +0000

    Fix the way max_bottom_nlevel is handled.

Src/LinearSolvers/F_MG/mg.f90

commit 9b8352d8e8bec1df997a95694f82972f0632591e
Author: lijewski <lijewski>
Date:   Fri May 14 18:06:17 2010 +0000

    intel icc does not support -fltconsistency :-(

Tools/F_mk/GMakedefs.mak

commit 333ec4ce7edf27030c569f2a932fe50a2a5cfb21
Author: ajnonaka <ajnonaka>
Date:   Thu May 13 17:00:07 2010 +0000

    amr.plot_per and amr.check_per now do not alter the time step, and print the plot/check file immediately before you hit the period you specify

Src/C_AMRLib/Amr.cpp

commit 662f7d6b96f62a70aaea4bf03e20262877a14f36
Author: lijewski <lijewski>
Date:   Wed May 12 22:19:16 2010 +0000

    removed omp.f90 and omp_stubs.f90

Tests/LinearSolvers/F_MG/cc_single.f90
Tests/LinearSolvers/F_MG/nodal_single.f90

commit 4ec2f8ae6d196d231f9efe0799ccc0695c0808a4
Author: lijewski <lijewski>
Date:   Wed May 12 22:19:08 2010 +0000

    removed omp.f90 and omp_stubs.f90

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/NPackage.mak
Src/F_BaseLib/make_new_grids.f90
Src/F_BaseLib/tag_boxes.f90

commit 97a509648d7e119224eab8e02fc249eec72b08a8
Author: lijewski <lijewski>
Date:   Wed May 12 22:16:08 2010 +0000

    not needed

Src/F_BaseLib/omp.f90
Src/F_BaseLib/omp_stubs.f90

commit 6853a906811534207243f11d714043121c0371e7
Author: lijewski <lijewski>
Date:   Wed May 12 21:18:43 2010 +0000

    removed boxlist_intersection() for boxes and boxlists -- not needed anywhere

Src/F_BaseLib/list_box.f90
Src/F_BaseLib/test/t_knapsack.f90
Tests/F_BaseLib/t_knapsack.f90

commit feba6340057cf6285ae731850f77b987d24127e4
Author: lijewski <lijewski>
Date:   Wed May 12 20:48:04 2010 +0000

    removed some unused drek

Src/F_BaseLib/box.f90

commit f0150d03bbd42c88f96056f255b4bc6eb59ad3d1
Author: lijewski <lijewski>
Date:   Wed May 12 20:35:26 2010 +0000

    removed some unused drek

Src/F_BaseLib/boxarray.f90

commit 8373fbf06a8ce92be1a2c3aec7e4cc88209e4d62
Author: almgren <almgren>
Date:   Wed May 12 18:05:46 2010 +0000

    Put print statements before and after reading probin so that
    we can tell if we die there -- dying while reading probin always
    just gives an Abort with no error message, so this at least lets
    you know you are there.  Only prints with amr.v >= 1.

Src/C_AMRLib/Amr.cpp

commit da24461fca0b3f91e0e9ff30dc2607fec2767df0
Author: lijewski <lijewski>
Date:   Wed May 12 16:45:22 2010 +0000

    removed aveassoc stuff - no longer used by average.f90

Src/F_BaseLib/layout.f90

commit 7fb05cd8e80a614a87630455bca148480783e17e
Author: lijewski <lijewski>
Date:   Wed May 12 16:29:17 2010 +0000

    removed mcc stuff -- SFC is the way to go

Src/F_BaseLib/knapsack.f90

commit a3dfadda908b890441df9f81af05042e4dc2da97
Author: almgren <almgren>
Date:   Tue May 11 02:16:20 2010 +0000

    Fix comment for subroutine mg_defect.

Src/LinearSolvers/F_MG/mg.f90

commit 24c42c0cd5f53e6ddbfb83fef2f37657e12b04d8
Author: marc <marc>
Date:   Fri May 7 22:19:03 2010 +0000

    Add support for euclid at nersc

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit c8fd80077ee1bf65a9323e6dd3900ced383bc44d
Author: almgren <almgren>
Date:   Fri May 7 20:44:26 2010 +0000

    Add one line of comment...

Src/LinearSolvers/F_MG/mg.f90

commit cd3c9b4a8fccbe5ca7ee54a2251e6331ad5adc0d
Author: almgren <almgren>
Date:   Fri May 7 20:13:52 2010 +0000

    Fix print statement for convergence.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 5b8bcbd632c01564c9197eb8c8900e0e0cee44f5
Author: almgren <almgren>
Date:   Fri May 7 20:04:03 2010 +0000

    Change in what is printed, not what is done.

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 16ce697823de7423dce3408e1d278e8355fc8a4d
Author: lijewski <lijewski>
Date:   Fri May 7 16:31:20 2010 +0000

    added assert to make sure folks don't ask for more grow cells than they have valid region

Src/C_BaseLib/Geometry.H

commit c87e04fd013c3d0e60924dac339dc85a47661688
Author: almgren <almgren>
Date:   Thu May 6 20:31:13 2010 +0000

    1) Do singular adjustment for cell-centered as well as nodal.
    2) Set solution to zero if rnorm > bnorm at end of bicg.

Src/LinearSolvers/F_MG/itsol.f90

commit ec2ec4df21b39851c5d58a7875838d04e70f798c
Author: almgren <almgren>
Date:   Thu May 6 01:59:20 2010 +0000

    More clean up -- also adding mgt%st_type as a member of mg_tower,
    so we can test on that instead of on ns.

Src/LinearSolvers/F_MG/mg.f90

commit 45f3e0df05143d0247adf7028e7dde6970564b7d
Author: almgren <almgren>
Date:   Thu May 6 01:58:28 2010 +0000

    Fix definitions of hi.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit a27b9c19ba61ed452f3b239c782f2308c42de781
Author: almgren <almgren>
Date:   Thu May 6 01:58:04 2010 +0000

    Add st_type as a member of mg_tower.

Src/LinearSolvers/F_MG/mg_tower.f90

commit 61a962dcd4a897e9de6c12c96d0454cc5f472ae5
Author: almgren <almgren>
Date:   Thu May 6 01:38:58 2010 +0000

    Fixes for minion routines plus getting rid of more "stencil" stuff.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/stencil.f90

commit a90cf6261c50c2cf79421a5e142cd67900626436
Author: almgren <almgren>
Date:   Wed May 5 21:38:45 2010 +0000

    AmrLevel::computeNewDt now takes post_regrid_flag as a final argument.

Src/C_AMRLib/AmrLevel.H

commit 1859ac414a9658456724460e52611f7e4d04065a
Author: almgren <almgren>
Date:   Wed May 5 21:38:24 2010 +0000

    1) Amr::timeStep now takes stop_time as the final argument.
    2) There is a new flag, compute_new_dt_on_regrid (default=0) which, if true, tells the
    code to call computeNewDt after a regrid with base level 0.   This is needed in particular
    in codes like CASTRO which call an EOS routine to compute the sound speed which is used
    in computing dt.
    3) AmrLevel::computeNewDt now takes an integer flag, post_regrid_flag, which tells the routine
    whether it is being called after a regrid.  If so, then dt_min[i] is "minned" with dt_level[i], rather
    than change_max*dt_level[i].

Src/C_AMRLib/Amr.cpp

commit 431b5542a4f2b3019c1a0c82f1ed689e6c6da4d9
Author: almgren <almgren>
Date:   Wed May 5 21:36:11 2010 +0000

    Amr::timeStep now takes stop_time as the final argument.

Src/C_AMRLib/Amr.H

commit c059da7481a52e418ae1da445156223baca40bf0
Author: lijewski <lijewski>
Date:   Wed May 5 20:17:25 2010 +0000

    got rid of some duplicate printing

Src/C_AMRLib/Amr.cpp

commit 5967f6876766371abb13791077b4b990f58125ab
Author: almgren <almgren>
Date:   Sat May 1 02:54:58 2010 +0000

    Add hypre_libraries to the link line in the right way.

Tools/F_mk/GMakedefs.mak

commit 41e5d5e58a6f378c869afdfbea668ab9b62f1727
Author: almgren <almgren>
Date:   Fri Apr 30 19:48:04 2010 +0000

    Need mg_tower.f90 as well as mg.f90

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 1584ec78b9365a6c2bb1ad37162658ce72fdcfdc
Author: almgren <almgren>
Date:   Fri Apr 30 19:07:19 2010 +0000

    Change the print statements for bottom_solver = 4

Src/LinearSolvers/F_MG/mg.f90

commit 41f46e7eaad43ddf827fece865041c753912443f
Author: almgren <almgren>
Date:   Fri Apr 30 17:37:46 2010 +0000

    Move mg_tower type definition into mg_tower.f90

Src/LinearSolvers/F_MG/mg.f90

commit 8592d1c17f2a5a5a2efe8173d25e4b47b4c85711
Author: almgren <almgren>
Date:   Fri Apr 30 17:37:01 2010 +0000

    Remove unused mg_tower_v_cycle_c.

Src/LinearSolvers/F_MG/mg.f90

commit e1d6094400278ba7b2d16925a8e3737b1a322c8f
Author: almgren <almgren>
Date:   Fri Apr 30 17:34:52 2010 +0000

    Move the definition of mg_tower out of mg.f90 so that we
    don't have to remake as many files when we play with mg.

Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/mg_tower.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/stencil_fill.f90

commit 7c6321fbca7c362685b2ef33952ea181132455da
Author: mzingale <mzingale>
Date:   Fri Apr 30 15:05:03 2010 +0000

    no, really add inf...

Tools/F_mk/GMakeMPI.mak

commit 2498600a6ee5fe904dfb843da69652cfc6f4893a
Author: mzingale <mzingale>
Date:   Fri Apr 30 15:03:55 2010 +0000

    add inf

Tools/F_mk/GMakeMPI.mak

commit e87c6b6e9ec3033352475c363043e0821a1411d6
Author: almgren <almgren>
Date:   Thu Apr 29 21:38:05 2010 +0000

    Modify print statement to be more similar to Initial error print.

Src/LinearSolvers/F_MG/mg.f90

commit b12c4c6c5fc813f1f549a022d389c3ed6aba2be3
Author: almgren <almgren>
Date:   Thu Apr 29 21:34:40 2010 +0000

    Fix typo in previous commit.

Src/LinearSolvers/F_MG/itsol.f90

commit c0fb2504a2bbc58410025b61699326906c9bf879
Author: almgren <almgren>
Date:   Thu Apr 29 21:33:37 2010 +0000

    Add diagonal preconditioning to the CG solve as well.

Src/LinearSolvers/F_MG/itsol.f90

commit 2658461e42b519513ae7deedf3cece1deb8dde79
Author: almgren <almgren>
Date:   Thu Apr 29 21:31:45 2010 +0000

    1) Add diagnoal preconditioning to the BiCG so that we set a = a/a(:,0)
    and res = res/a(:,0) before starting to solve -- this reduces the number
    of BiCG iterations needed.
    2) Change convergence test to *only* return true if res < eps*bnorm

Src/LinearSolvers/F_MG/itsol.f90

commit 9eb962034101c0c4305f477cc4415adcc7a88edd
Author: almgren <almgren>
Date:   Thu Apr 29 21:30:27 2010 +0000

    Change convergence test to *only* return true if res < eps*bnorm

Src/LinearSolvers/F_MG/ml_cc.f90

commit 4346d7728f8e7885757969af12422b5ab7a9a335
Author: almgren <almgren>
Date:   Thu Apr 29 21:30:17 2010 +0000

    1) Add print statement for Initial(rhs) and Initial(error)
    2) Change convergence test to *only* return true if res < eps*bnorm

Src/LinearSolvers/F_MG/ml_nd.f90

commit bb677be3aff5b5dbfaffaf9286b25eb8b5a594a0
Author: almgren <almgren>
Date:   Thu Apr 29 19:11:16 2010 +0000

    Remove itsol_BiCGStab_solve_st, itsol_CG_solve_st, itsol_precon_st -- no one was
    using these...

Src/LinearSolvers/F_MG/itsol.f90

commit b1ca7d3e110d79dcd704938235c6435255a9971c
Author: mzingale <mzingale>
Date:   Wed Apr 28 23:34:43 2010 +0000

    mgt_bottom_solver -> mgt%bottom_solver
    
    line-wrap some comments

Src/LinearSolvers/F_MG/mg.f90

commit 550d8d7a1912717809a4c1223c7e690dc7ffa833
Author: almgren <almgren>
Date:   Wed Apr 28 21:47:32 2010 +0000

    If we're at a higher AMR level don't create all the bottom_solver stuff.

Src/LinearSolvers/F_MG/mg.f90

commit a3a730fe7bc7e3d125dd6c64ededc4fa08261099
Author: ajnonaka <ajnonaka>
Date:   Wed Apr 28 13:57:29 2010 +0000

    now testing the new email list...

Src/LinearSolvers/F_MG/stencil_fill.f90

commit 0903180d7919dedadca00dbe85c889a3068108d4
Author: ajnonaka <ajnonaka>
Date:   Wed Apr 28 13:53:36 2010 +0000

    FINAL TEST COMMIT

Src/LinearSolvers/F_MG/stencil_fill.f90

commit f69567dd24ae4fb063af4626e21fea50b8b188a9
Author: ajnonaka <ajnonaka>
Date:   Wed Apr 28 13:52:00 2010 +0000

    TEST COMMIT 3

Src/LinearSolvers/F_MG/stencil_fill.f90

commit 3a68e13b4cb0998e84febc72d09e3746d1196d81
Author: ajnonaka <ajnonaka>
Date:   Wed Apr 28 13:49:48 2010 +0000

    TEST COMMIT 2 (almost done - sorry for the spam)

Src/LinearSolvers/F_MG/stencil_fill.f90

commit 6096481bdc8ac01a0ec471e42a1a8d40d70e7ad4
Author: ajnonaka <ajnonaka>
Date:   Wed Apr 28 13:46:45 2010 +0000

    TEST COMMIT

Src/LinearSolvers/F_MG/stencil.f90

commit 3f1915958f73a767c778646dba2bd68119276df8
Author: ajnonaka <ajnonaka>
Date:   Wed Apr 28 13:40:49 2010 +0000

    commit to test log messages - no changes

Src/LinearSolvers/F_MG/stencil.f90

commit 55f4281a2d4fa307fdd1f92995ba4aeb7d9221e0
Author: almgren <almgren>
Date:   Wed Apr 28 00:01:43 2010 +0000

    If doing XGRAPH stuff (1d) then allow Amr::init to call setPlotVariables
    so we can use it in the xgraph stuff.

Src/C_AMRLib/Amr.cpp

commit 83ed0cda0ce522d7ffa84dc9ba702977951d1610
Author: lijewski <lijewski>
Date:   Tue Apr 27 23:01:54 2010 +0000

    plugged memory leaks in bottom_solver==4

Src/LinearSolvers/F_MG/mg.f90

commit e634ad044faa300ea330da6339078533a9105a93
Author: mzingale <mzingale>
Date:   Tue Apr 27 19:18:31 2010 +0000

    add a routine write_a_hgproj_grid to complement read_a_hgproj_grid.
    This is useful for dumping out a grid structure from MAESTRO for
    debugging in the test_average problem.

Src/F_BaseLib/box_util.f90

commit 1cb4db49970a92f921166186e510e1d60701447a
Author: almgren <almgren>
Date:   Mon Apr 26 21:26:15 2010 +0000

    There was duplication of code that didn't need to be there,
    inside the bottom solver stuff.

Src/LinearSolvers/F_MG/stencil_fill.f90

commit 636e58b4a8870f2638ce959b80df838b977e3b2f
Author: gpau <gpau>
Date:   Mon Apr 26 19:13:01 2010 +0000

    updated the porous stuff

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit b826541bb978c2f22d43dbd4a46e6e9bd87e034a
Author: almgren <almgren>
Date:   Mon Apr 26 19:10:26 2010 +0000

    This version compiles...

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 3457b2de9663cb8ca716a96a8a70afa3b5531346
Author: almgren <almgren>
Date:   Mon Apr 26 19:00:08 2010 +0000

    Fix the definition of nlevel -- it's number of mglevels, not amr levels,
    when used for cell_coeffs and edge_coeffs.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 8efed4f50b60bed1b6078c6351c434e94e0ad3b7
Author: almgren <almgren>
Date:   Mon Apr 26 17:23:07 2010 +0000

    st_coeffs --> coarsen_coeffs

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 41039936b0a6ae149d367ad955b5ce3b72b4e42d
Author: almgren <almgren>
Date:   Mon Apr 26 17:21:55 2010 +0000

    edge_coeffs should be (:,:), not (:)

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 7f4471de00cae6a0f5aa679090fd2c8ceeea59dc
Author: mzingale <mzingale>
Date:   Sat Apr 24 13:42:12 2010 +0000

    line wrap error

Src/LinearSolvers/F_MG/stencil.f90

commit f462d96e9b5010a9b47ee2836f9cf04a128daa6d
Author: almgren <almgren>
Date:   Sat Apr 24 05:13:53 2010 +0000

    Fix bug in 3d averaging of x-edge coefficients.

Src/LinearSolvers/F_MG/coarsen_coeffs.f90

commit 200403bf6d5cee425db5582b7544529ea96fcc8b
Author: almgren <almgren>
Date:   Sat Apr 24 01:34:49 2010 +0000

    Remove print statement.

Src/LinearSolvers/F_MG/stencil_fill.f90

commit e3ec8212dc242831c0901ce972b377bb63fb1eb9
Author: almgren <almgren>
Date:   Sat Apr 24 01:16:13 2010 +0000

    We no longer have a single coeffs(:) array, we now have cell_coeffs and edge_coeffs.

Src/LinearSolvers/F_MG/coarsen_coeffs.f90
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_nodal_cpp.f90
Src/LinearSolvers/F_MG/stencil_fill.f90

commit 46574f4c2b51fa824514df16b31897da0ad87f16
Author: almgren <almgren>
Date:   Sat Apr 24 01:08:53 2010 +0000

    Remove unused "cross" in extrap_1d.

Src/LinearSolvers/F_MG/stencil.f90

commit ef0e467b977cd715639454806900a93b0deb5454
Author: almgren <almgren>
Date:   Sat Apr 24 00:59:37 2010 +0000

    Fix calls to ml_restriction to no longer pass "face_type"

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 0b10be5dba5582ee03924717e9a04856c0eecea3
Author: almgren <almgren>
Date:   Sat Apr 24 00:59:16 2010 +0000

    Removed unused variable "face_type" from ml_restriction and ml_nodal_restriction

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 9f6ecafa52414e24511003b7f07e757d644e4f50
Author: almgren <almgren>
Date:   Sat Apr 24 00:27:30 2010 +0000

    Get rid of unused variable "vol"

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit fd8d4f02654ea99eb501b9e7d44228f9f93cec0c
Author: almgren <almgren>
Date:   Sat Apr 24 00:07:01 2010 +0000

    Typo ex --> dx

Src/F_BaseLib/tag_boxes.f90

commit 6adfb5d8b401c8da8cad63ff1bad24827dbd91d0
Author: ajnonaka <ajnonaka>
Date:   Fri Apr 23 23:41:55 2010 +0000

    for intel 9, reverting to a less optimized mode, which actually runs faster (go figure) and is less susceptible to the plotfile pi bug I've been struggling with

Tools/F_mk/GMakedefs.mak

commit 08c5d1d17ce626fa8ecced67c2190092761cec9d
Author: ajnonaka <ajnonaka>
Date:   Fri Apr 23 22:36:32 2010 +0000

    rewritten in gfortran-friendly way

Src/F_BaseLib/layout.f90

commit 9918c8846b8f7769edd3949bbf3d2b8ead6d6871
Author: ajnonaka <ajnonaka>
Date:   Fri Apr 23 22:29:28 2010 +0000

    pass in dx to tag_boxes so you can refine based on location

Src/F_BaseLib/make_new_grids.f90
Src/F_BaseLib/tag_boxes.f90

commit 3ce13fba9c37b8810aab4203690789a1f5ba8930
Author: almgren <almgren>
Date:   Fri Apr 23 21:34:20 2010 +0000

    Add multifab_build_edge routine.

Src/F_BaseLib/multifab.f90

commit ccc2d4c4b8d5097e0c5e9eeec009f27a0f6e698a
Author: lijewski <lijewski>
Date:   Fri Apr 23 20:16:46 2010 +0000

    removed some dead code

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ccse-mpi.H

commit 75ea8460969a7d230976686ba6549dfb4c1f38fc
Author: almgren <almgren>
Date:   Fri Apr 23 18:33:18 2010 +0000

    Renamed st_coeffs.f90 --> coarsen_coeffs.f90

Src/LinearSolvers/F_MG/GPackage.mak

commit 762770eb3a93ae03da7dc3d31b39189e7ec5b681
Author: almgren <almgren>
Date:   Fri Apr 23 18:24:47 2010 +0000

    Rename st_coeffs.f90 --> coarsen_coeffs.f90 and modify it to put
    in more comments and make it work for the porous media stencils.

Src/LinearSolvers/F_MG/coarsen_coeffs.f90

commit e082129eb916b9632925c6c1c4d2d4ce243e7a72
Author: almgren <almgren>
Date:   Fri Apr 23 18:24:00 2010 +0000

    1) Include coarsen_coeffs_module instead of coeffs_module.
    2) Start to make the number of components more general so we can accomodate the
       porous media stuff.

Src/LinearSolvers/F_MG/stencil_fill.f90

commit 2d6025901ea7e5332319e57d52819b59ee60de65
Author: almgren <almgren>
Date:   Fri Apr 23 18:21:05 2010 +0000

    Doesn't need to include coeffs_module.

Src/LinearSolvers/F_MG/nodal_mask.f90

commit 528f54aa36c9d43907ebdc437bd4ae71c52973ba
Author: mzingale <mzingale>
Date:   Fri Apr 23 15:29:17 2010 +0000

    mgt%dh was being indexed incorrectly when initializing coarse_dx

Src/LinearSolvers/F_MG/mg.f90

commit 8d05ad40816bcf474a3b71c2cab571b769551e41
Author: gilet <gilet>
Date:   Wed Apr 21 16:30:17 2010 +0000

    added stuff for orga

Tools/F_mk/GMakeMPI.mak

commit 38940c48a4d74a3abe2e42840796d91109decf25
Author: almgren <almgren>
Date:   Wed Apr 21 04:00:44 2010 +0000

    Pass in bottom_solver

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 8dd4a39059f5a128be3da9c9bdfb50cd7750e0cf
Author: almgren <almgren>
Date:   Wed Apr 21 03:58:56 2010 +0000

    Fix a buggy part.

Src/LinearSolvers/F_MG/stencil_fill.f90

commit 84fdbacb037c17395db58aaffdf56008001d287e
Author: almgren <almgren>
Date:   Wed Apr 21 03:57:48 2010 +0000

    Remove unused statements.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 7fe617e67ffd1db7288fb8de6399b233c8b8a51d
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 20 21:55:41 2010 +0000

    xlf library location mysteriously moved in the last hour

Tools/C_mk/Make.mpi

commit 5a6a23c3839a8d9d05d8e15820c676343ffaea5d
Author: almgren <almgren>
Date:   Tue Apr 20 21:36:42 2010 +0000

    Need to set coeffs%nc equal to coeffs(maxlev)%nc, NOT ss%nc.

Src/LinearSolvers/F_MG/stencil_fill.f90

commit c7e46e6882cdd3088def45d3ed105d7262ef888e
Author: almgren <almgren>
Date:   Tue Apr 20 21:30:33 2010 +0000

    One more call to fix.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit aa1a3229f93cbaa84d5bcd42fe01213dc7955a93
Author: almgren <almgren>
Date:   Tue Apr 20 21:29:35 2010 +0000

    Fix interface for porous...

Src/LinearSolvers/F_MG/mg_cpp_f.h

commit d5d5083ad1659c1133334092dbda4d4ada12678e
Author: almgren <almgren>
Date:   Tue Apr 20 21:26:54 2010 +0000

    Make this work with the C++ interface.

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit f107f19de3602329e5e19310f48828e59dd0dbf4
Author: almgren <almgren>
Date:   Tue Apr 20 21:26:36 2010 +0000

    Make the number of components more general so this will
    work with the multicomponent porous media stencil.

Src/LinearSolvers/F_MG/stencil_fill.f90

commit 72b52cb310eb0cd0e166dff7ec7b01ab07e6eb4d
Author: almgren <almgren>
Date:   Tue Apr 20 20:34:37 2010 +0000

    Also need to include stencil_fill.f90

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 43758a95f037bbf9ffb5947f92537705136959dd
Author: almgren <almgren>
Date:   Tue Apr 20 20:33:14 2010 +0000

    Dont use optional dh to define the dimension of another array.

Src/LinearSolvers/F_MG/mg.f90

commit 6d728269f7bc5f216d6b8f724cbde5c2b406d930
Author: almgren <almgren>
Date:   Tue Apr 20 20:31:06 2010 +0000

    Fix line 157.

Src/LinearSolvers/F_MG/mg.f90

commit 876a80d351eb57375869dd4b2ffce0a74a1bfc1c
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 20 20:22:34 2010 +0000

    forgot to include impose_neumann_bcs.f90

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 8cb0b2ecc2a3d8f4c311b4d212c16aa76f6d33dc
Author: almgren <almgren>
Date:   Tue Apr 20 20:12:56 2010 +0000

    Dont need to pass pd into stencil_fill.

Src/LinearSolvers/F_MG/stencil_fill.f90

commit 445e3dcd52d0da1117cba32094bfb79d2775c1ce
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 20 19:43:52 2010 +0000

    omp now compiles on intrepid with xlf; whether it works or not is currently unknown

Tools/C_mk/Make.mpi

commit 2e21f171a63de21a761edae9233cdafd4bb63051
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 20 19:35:49 2010 +0000

    oops, guess it doesn't work yet, but this fixes one library

Tools/C_mk/Make.mpi

commit 45986cd52dc3008250d13ca5875ae35a8d7a0f49
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 20 19:34:27 2010 +0000

    omp now compiles on intrepid with xlf; whether it works or not is currently unknown

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit af3f696d55a9e9e9051c274576eadee748d935d9
Author: almgren <almgren>
Date:   Tue Apr 20 19:31:59 2010 +0000

    Add stencil_fill_minion_all_mglevels which enables bottom_solver=4
    for the minion stencil as well.

Src/LinearSolvers/F_MG/stencil_fill.f90

commit b9885a9edac4dedab92b1b2d8da10b7db449a03a
Author: almgren <almgren>
Date:   Tue Apr 20 18:59:55 2010 +0000

    Added some new files.

Src/LinearSolvers/F_MG/GPackage.mak

commit c6a07deba1c08682b36985c3b81f234128d9d95f
Author: almgren <almgren>
Date:   Tue Apr 20 18:53:58 2010 +0000

    Changes so that all of the bottom_solver=4 stuff is now created in
    files in this directory rather than needing to be passed in.

Src/LinearSolvers/F_MG/impose_neumann_bcs.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_fill.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 8d72fd9b59dd041f9bcd4d1f848cbb2bd8974bec
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 20 16:42:16 2010 +0000

    added some non-mpi support for interpid

Tools/C_mk/Make.Linux

commit e06744660ae7a989e5354e524675202733d4433d
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 20 16:19:13 2010 +0000

    OMP compiler options for xlf compilers on intrepid

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit 2f46f2b065ded104009b0f38fef5c07ee8a7e941
Author: lijewski <lijewski>
Date:   Mon Apr 19 23:16:09 2010 +0000

    fixed bug in init() -- copy()s weren't correct in parallel

Src/C_BoundaryLib/BndryData.cpp

commit a5923fa5ecf70bc94b37210aad16abbc0cf2c1f7
Author: almgren <almgren>
Date:   Sun Apr 18 18:35:05 2010 +0000

    Fix spelling of error message -- incommesurate --> incommensurate

Src/F_BaseLib/layout.f90

commit dc8483e7d0e0e3a110033247957c0dd12457a4fe
Author: almgren <almgren>
Date:   Sat Apr 17 00:20:12 2010 +0000

    Put a & to break up a long line so hopefully Minion's
    compiler will be ok with it.

Src/F_BaseLib/layout.f90

commit 0b127e3ee9133ac1aa363b26a3b03b54a9876a2d
Author: gpau <gpau>
Date:   Fri Apr 16 19:55:46 2010 +0000

    added some functions to handle multilevel solve for the porous media code

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit e5724fec724f30c817900a7f8889c12e984e2f19
Author: gpau <gpau>
Date:   Fri Apr 16 19:55:04 2010 +0000

    added a subroutine to handle multilevel solve for the porous media code

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 79dd717edb3c77c770814eb15de92f8332f56fbd
Author: lijewski <lijewski>
Date:   Thu Apr 15 21:17:10 2010 +0000

    carver.nersc.gov stuff

Tools/F_mk/GMakeMPI.mak

commit 652edd0b91092131bd2fead15ba09ead26318a44
Author: lijewski <lijewski>
Date:   Thu Apr 15 21:16:38 2010 +0000

    more junk for carver.nersc.gov

Tools/C_mk/Make.Linux

commit 445dc3cb32cedc924c58579c7dfbef77ae57c139
Author: lijewski <lijewski>
Date:   Tue Apr 13 23:16:33 2010 +0000

    now works with full pathname instead of just relative

Tools/C_scripts/moddep.pl

commit 118c249065ae8304db4ba7b701b573758218318d
Author: lijewski <lijewski>
Date:   Tue Apr 13 23:15:30 2010 +0000

    now works with full pathname for FPARALLEL instead of just relative

Tools/F_scripts/moddep.pl

commit d83162a8f1b79b5fe1d5d3f79ccd400f1f7e2983
Author: lijewski <lijewski>
Date:   Tue Apr 13 23:14:54 2010 +0000

    added extern/random stuff

Tests/LinearSolvers/F_MG/GNUmakefile

commit c70e5bc205c2fd5bc8e3d98d072e3c534a6102f0
Author: almgren <almgren>
Date:   Mon Apr 12 18:39:33 2010 +0000

    Move mt19937ar.f90 from boxlib to extern/random so we don't have
    to compile it every time -- it takes a long time.

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/mt19937ar.f90

commit 671158057677ca6013cb1d569a5b693bd233b07e
Author: adonev <adonev>
Date:   Fri Apr 9 22:15:57 2010 +0000

    stochastic_varden now compiles OK

Src/F_BaseLib/GPackage.mak

commit dbd7a6934bd9122596bc72a7f81127f7afa6e807
Author: ajnonaka <ajnonaka>
Date:   Wed Apr 7 19:03:39 2010 +0000

    xlf on interpid with omp now compiles

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak

commit 8a1f397995aa9e16e679a904c41c00cae4f52c6a
Author: vince <vince>
Date:   Tue Apr 6 20:48:05 2010 +0000

    fixed default MPI_HOME.

Tools/C_mk/Make.mpi

commit efc16db5d7e8042990f203079093dc457e270a41
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 6 20:41:44 2010 +0000

    turned of auto threading on intrepid

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak

commit 66866f6516e40b196f7a507e2fb6811beed13419
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 6 20:14:57 2010 +0000

    for some reason the mpi compiler on intrepid needs its own OMP statements

Tools/F_mk/GMakeMPI.mak

commit 535418ea1885479534e9f41bf3e370cbba07c521
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 6 19:45:36 2010 +0000

    OMP flags for xlf compiler on intrepid

Tools/F_mk/GMakedefs.mak

commit ff75457ac562e606b5cc9ad4bbb420c9e51df065
Author: almgren <almgren>
Date:   Fri Apr 2 21:43:37 2010 +0000

    1) Define a RegridOnRestart function that returns regrid_on_restart
       (called only by main.cpp at this point)
    2) Define a RegridOnly(time) function which does regridding only if we
       restart but don't take a timestep.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit fb8d620bad5220b2940d207143b40234d63149f0
Author: almgren <almgren>
Date:   Fri Apr 2 20:29:13 2010 +0000

    Now allow us to have StateData that is not stored in the checkpoint.
    
    If store_in_checkpoint = false then the statedata multifabs will not
    be written to the checkpoint diretory (though the times, domain, etc
    will be written in the header).    We set "nsets" = 0 when we write.
    
    Then when we read, for each statedata we read "nsets" to know whether
    to read 0, 1, or 2 multifabs (1 if only new data, 2 if both old and new data).

Src/C_AMRLib/StateData.cpp

commit 1819a6e12a57febf3e0dfc545dad5729bc0d3296
Author: almgren <almgren>
Date:   Fri Apr 2 20:27:18 2010 +0000

    Undo the previous stuff I added in AmrLevel for controlling
    the StateData::store_in_checkpoint.  This is now entirely used
    inside StateData, in the checkPoint and restart routines.

Src/C_AMRLib/AmrLevel.cpp

commit 4f36613631cb5a5702d365ce9036591358847215
Author: almgren <almgren>
Date:   Wed Mar 31 23:43:33 2010 +0000

    Added Minion 2nd order stencils -- these are identical to the
    standard 2nd order cell-centered stencil except the dimensioning
    of the incoming arrays is different.  Eventually we should merge these
    routines.

Src/LinearSolvers/F_MG/stencil.f90

commit 38ac6a41c8da3d34fbae0d1f57beda92b0f8ff5a
Author: lijewski <lijewski>
Date:   Mon Mar 29 21:01:38 2010 +0000

    got 2D working again

Src/LinearSolvers/C_NodalMG/hg_multi2d.f
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit adb92fafd88e22d4413a2d827b0d7a521572987b
Author: almgren <almgren>
Date:   Fri Mar 26 21:43:08 2010 +0000

    If the desc_lst[i].store_in_checkPoint() is not true then we
    1) dont write this statedata to a checkpoint
    2) dont read this statedata from a checkpoint.
    
    Note that the first StateData must be read/written so that we can get "time" from it.
    We also assume that the StateData being defined has the same TimeType as the first StateData.

Src/C_AMRLib/AmrLevel.cpp

commit f417581e84b768508fc7598613f2859754d6cd70
Author: almgren <almgren>
Date:   Fri Mar 26 21:34:23 2010 +0000

    StateDescriptor now has a member called store_in_checkpoint.  If this is true
    then this StateData will be written to the checkpoint file via AmrLevel::checkPoint
    and will be read from checkpoint via AmrLevel::restart.  If it is false then
    the data will be allocated in restart but set to 0, and it won't be written to
    a checkpoint file.

Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp

commit 1e57d642448a5fc7a9fda9daaf769e930390d3d2
Author: lijewski <lijewski>
Date:   Fri Mar 26 20:33:02 2010 +0000

    fixed parallel bug

Src/LinearSolvers/C_NodalMG/amr_multi.cpp

commit e721ec6ceaed507847cde7958ecf3c385e6d99d5
Author: almgren <almgren>
Date:   Thu Mar 25 21:44:46 2010 +0000

    Allow a "dump_old" flag to be passed through AmrLevel into StateData so we
    have the option not to write both the old and new data.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 164c2519ea4160e9999d7108a6a019051331bc75
Author: lijewski <lijewski>
Date:   Thu Mar 25 20:33:42 2010 +0000

    mods for carver.nersc.gov

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 02a1c52e79251d32edfeff0217f166d09ba0f819
Author: gpau <gpau>
Date:   Wed Mar 24 23:53:44 2010 +0000

    fixed an error with the pressure solve

Src/LinearSolvers/F_MG/stencil.f90

commit 02ec51ef7fdf45c0dce051e76facc92cab34b765
Author: gpau <gpau>
Date:   Wed Mar 24 19:29:43 2010 +0000

    fixed the stencil to loop over ncomp of density

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 0f06e11cdd6d0d46fbe702ef57aed84f1bc0ed3c
Author: gpau <gpau>
Date:   Wed Mar 24 19:28:47 2010 +0000

    updated the porous

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit a563781fff58be4edc9c4cb08bc1853aec3ec689
Author: lijewski <lijewski>
Date:   Tue Mar 23 19:17:33 2010 +0000

    hmmmm

Src/C_BaseLib/BoxList.cpp

commit 70b79786a7f83aeb102b86f4fc1e3ca42d3f7708
Author: gpau <gpau>
Date:   Tue Mar 23 19:10:35 2010 +0000

    removed bad BL_ASSERT()

Src/C_BaseLib/BoxList.cpp

commit 1195a8474503e563236274a0ff9c1ee2c553f0a2
Author: mzingale <mzingale>
Date:   Sun Mar 21 20:55:41 2010 +0000

    add support for self-tests (like Maestro's test_advect).  These are tests
    that diagnose themselves, so no comparison to a benchmark is needed.

Tools/C_util/regtests/Maestro-tests.ini
Tools/C_util/regtests/test.py

commit 12722230aa85297fc5416646689dcde198131fd8
Author: mzingale <mzingale>
Date:   Fri Mar 19 20:21:00 2010 +0000

    add -fltconsistency to the -mp1 for Intel 10 and 11 -- this fixes
    errors that test_advect showed.

Tools/F_mk/GMakedefs.mak

commit 451af8379f7d44e0ad73bffd7d45f5e724841610
Author: ajnonaka <ajnonaka>
Date:   Fri Mar 19 19:23:06 2010 +0000

    mods for PGI and jaguar

Tools/C_mk/Make.Linux

commit c458c7d740ec8bf79455ec0631707870fe6cca2f
Author: gpau <gpau>
Date:   Fri Mar 19 18:05:17 2010 +0000

    fixed a bug in the simplen_2d

Src/LinearSolvers/F_MG/stencil.f90

commit 408f3f68d015b490191422c06cd0173d28138415
Author: mzingale <mzingale>
Date:   Fri Mar 19 14:01:08 2010 +0000

    add some error handling for the visualization if no output file
    is produced

Tools/C_util/regtests/test.py

commit a7a3fb82f5b6606578b7d1261992d492adbce015
Author: almgren <almgren>
Date:   Thu Mar 18 21:48:00 2010 +0000

    Move "finest_level = new_finest_level" to be before the call to amr_level->post_restart
    in Amr::restart.

Src/C_AMRLib/Amr.cpp

commit c77c1f6bc30599fea2d58d11d94bbbbeb06728f1
Author: almgren <almgren>
Date:   Thu Mar 18 21:14:42 2010 +0000

    Fixing spacing in print statements.

Src/LinearSolvers/F_MG/mg.f90

commit b6eee8deb588add635e65e8511c58e476108373d
Author: almgren <almgren>
Date:   Thu Mar 18 20:56:16 2010 +0000

    We now define the stencil terms based on
    (alpha - sum_i beta0_i div dot beta_i grad)

Src/LinearSolvers/F_MG/stencil.f90

commit 22de052bc2b8c4b7290e3c71a7b18fe36f81e4ee
Author: almgren <almgren>
Date:   Thu Mar 18 20:51:02 2010 +0000

    We now pass a cell-centered beta0 in for the porous media stuff -- the new
    stencil is
    (alpha - sum_i beta0_i div dot beta_i grad)

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit d8081503cb84b503a085936cf3f7bc9a17e85f94
Author: almgren <almgren>
Date:   Thu Mar 18 20:47:48 2010 +0000

    1) Pass abs_tol into ml_nd
    2) Need to pass a "nc" argument into coarsen_coeffs now.

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit 8d22f0386ec8e0b348923098da26fab475112384
Author: almgren <almgren>
Date:   Thu Mar 18 20:46:14 2010 +0000

    Pass in abs_eps and use as appropriate.

Src/LinearSolvers/F_MG/ml_nd.f90

commit a3d09c8ec6a4b27a6382837ace0bcf23a9ba3e4d
Author: almgren <almgren>
Date:   Thu Mar 18 20:42:31 2010 +0000

    Modify set_porous_coefficients to take a cell-centered beta0 such that
    the stencil looks like
    (alpha - sum beta0_i del dot beta_i grad).

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 545e627ffb310d2f28351a8337102968d81a4577
Author: mzingale <mzingale>
Date:   Thu Mar 18 16:52:49 2010 +0000

    latest test suite

Tools/C_util/regtests/Maestro-tests.ini

commit 4d0dfe5fb61f43645b7a2054701b84938570c286
Author: mzingale <mzingale>
Date:   Thu Mar 18 16:52:14 2010 +0000

    pretty-up the output (now in color)

Tools/C_util/regtests/test.py

commit deca8d9f59ed8c7631824b1508abc2e592badeff
Author: almgren <almgren>
Date:   Tue Mar 16 23:44:51 2010 +0000

    Wrap BoxLib::Warning inside if IOProcessor test.

Src/C_AMRLib/Amr.cpp

commit abe2c859cc2f61310e925b33f2996b618b55ecf1
Author: almgren <almgren>
Date:   Tue Mar 16 19:38:23 2010 +0000

    Remove unused variables.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_nodal_cpp.f90
Src/LinearSolvers/F_MG/nodal_divu.f90

commit b6bd20c2c4ffc668e21447e632db25c2a774fa9f
Author: almgren <almgren>
Date:   Tue Mar 16 19:23:23 2010 +0000

    Clean up unused variables.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit a536d08c60f6f348e00f214b6a7fc202953244e4
Author: ajnonaka <ajnonaka>
Date:   Tue Mar 16 19:16:12 2010 +0000

    syntax fix

Src/LinearSolvers/F_MG/mg.f90

commit dc6cbda7ea1112c1a2ba271f0b9d6b5f550bef51
Author: almgren <almgren>
Date:   Tue Mar 16 19:10:32 2010 +0000

    Fix bottom_solver_type = 4 so that it now works with PGI on franklin -- problem
    before was that mg_tower_bottom_solve was effectively called recursively from
    mg_tower_cycle --> mg_tower_cycle --> mg_tower_bottom_solve --> mg_tower_cycle --> mg_tower_bottom_solve.
    We have fixed this by renaming the routine that is called when bottom_mgt is present --
    that is now "do_bottom_mgt", and the routine mg_tower_bottom_solve only does
    bottom_solver_type = 1,2 or 3.

Src/LinearSolvers/F_MG/mg.f90

commit fe032b7cc52e584d5d33bafbeddc30b00559da0e
Author: lijewski <lijewski>
Date:   Mon Mar 15 21:24:19 2010 +0000

    removed commented out vestiges of OMP in hgrlxu()

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit e312b0e7595d7a3896ca5443e8d8ef385ec3b8f8
Author: lijewski <lijewski>
Date:   Mon Mar 15 19:56:16 2010 +0000

    added levelCount()

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 85fca65a8f59e39c93f73b964d970772efcdbf60
Author: lijewski <lijewski>
Date:   Mon Mar 15 01:15:22 2010 +0000

    added fredom stuff

Tools/C_mk/Make.Linux

commit 53383a9ffff462a60054a63817ecc0a8c2b52a12
Author: lijewski <lijewski>
Date:   Mon Mar 15 01:13:15 2010 +0000

    removed some OMP stuff that PGI gets wrong

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit 6254d754e8c1a4da868ae44716eeba8208b1e703
Author: lijewski <lijewski>
Date:   Sun Mar 14 22:01:46 2010 +0000

    freedom added

Tools/C_mk/Make.defs

commit 804c69d9c7109e863869e756e40e03a620be4769
Author: lijewski <lijewski>
Date:   Sat Mar 13 01:24:22 2010 +0000

    OMP mods to compile with PGI

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit 043c91c07c737e615e84e79615051fd84f0ab79a
Author: lijewski <lijewski>
Date:   Fri Mar 12 21:07:59 2010 +0000

    changed -O -> -fast for PGI

Tools/F_mk/GMakedefs.mak

commit 332fa9027d5b00f9b38ffaba5169d6f0441936a2
Author: lijewski <lijewski>
Date:   Thu Mar 11 22:28:09 2010 +0000

    remove OMP loop -- Intel didn't like it :-(

Src/LinearSolvers/F_MG/mg_restriction.f90

commit b45819b5bbd78b7c3ae4b1250e2c5c104b2b8eef
Author: mzingale <mzingale>
Date:   Thu Mar 11 03:38:22 2010 +0000

    fix a bug introduced during an optimization

Src/LinearSolvers/F_MG/stencil.f90

commit 9516d785bb68cab154aeaa3883f84417d3bc1cf7
Author: ajnonaka <ajnonaka>
Date:   Wed Mar 10 21:18:08 2010 +0000

    get rid of SMP stuff so nobody gets the (false) impression that it actually works

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak

commit a8d4fee5889ff6609b389ba0046e1743ff413a6f
Author: almgren <almgren>
Date:   Tue Mar 9 18:23:25 2010 +0000

    Remove print statements.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit c4b0308d6077a6a4eda7f58a73018dcd506b5435
Author: lijewski <lijewski>
Date:   Tue Mar 9 17:01:01 2010 +0000

    fixed something I broke

Src/LinearSolvers/F_MG/nodal_mask.f90

commit 0c6c63a77eb69b91fa0105beca915967450d4245
Author: lijewski <lijewski>
Date:   Mon Mar 8 19:02:52 2010 +0000

    *** empty log message ***

Tests/LinearSolvers/F_MG/nodal_multi.f90

commit 5ab18f200e4f6bf1d5ace7abbce5c4f5ede91f02
Author: almgren <almgren>
Date:   Sat Mar 6 22:40:05 2010 +0000

    Now allow multicomponent coefficients.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 163b58e80402168d77a61387e7c08c2d9722bf54
Author: almgren <almgren>
Date:   Sat Mar 6 22:39:38 2010 +0000

    Now allow multicomponent betax, betay.

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/stencil.f90

commit 56112f93857682c39574ef2dbf2bf044b86701ff
Author: almgren <almgren>
Date:   Sat Mar 6 04:25:35 2010 +0000

    Remove unused variables.

Src/F_BaseLib/multifab.f90

commit dce71441378ab3deb9a974271fc9171504cb1e9c
Author: lijewski <lijewski>
Date:   Sat Mar 6 00:15:55 2010 +0000

    use our cpy_[dilz] routines instead of compiler generated ones

Src/F_BaseLib/multifab.f90

commit 3a3b4043a8b337aa5ba386ef8d2ef7bd1635dfa4
Author: lijewski <lijewski>
Date:   Fri Mar 5 23:46:58 2010 +0000

    bit more OMP

Src/F_BaseLib/multifab.f90

commit 15e66cb4c0fb3b4315d47035a06602ba194ff1a5
Author: lijewski <lijewski>
Date:   Fri Mar 5 23:28:10 2010 +0000

    OMPd fab_setval_c()

Src/F_BaseLib/fab.f90

commit e253ed0d364755d55c1ab6f2094c6a53f1c18530
Author: lijewski <lijewski>
Date:   Fri Mar 5 23:05:05 2010 +0000

    OMP'd norm_inf

Src/F_BaseLib/multifab.f90

commit 69194a6d04273835c9355c585becc1390da9e9da
Author: lijewski <lijewski>
Date:   Fri Mar 5 21:52:58 2010 +0000

    more OMPing

Src/F_BaseLib/multifab.f90

commit 31c1478390a76ab0af93740652b59d2959e9b85a
Author: lijewski <lijewski>
Date:   Fri Mar 5 20:40:21 2010 +0000

    little code rearrangement

Src/LinearSolvers/F_MG/stencil.f90

commit b42a0d121e60ab6e7f46dcfec941d5ebc6a261de
Author: lijewski <lijewski>
Date:   Fri Mar 5 18:58:48 2010 +0000

    some code consolidation

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 347e9524425fa75d69a35e476575595bac5f9ca9
Author: lijewski <lijewski>
Date:   Fri Mar 5 18:19:11 2010 +0000

    some more OMPing

Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 286de7a8e4de4edb20533a0d414c24ab134444eb
Author: lijewski <lijewski>
Date:   Fri Mar 5 17:46:01 2010 +0000

    removed some duplicate code

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 8a07f08f92839f10627099e7f559de68fc32c526
Author: lijewski <lijewski>
Date:   Fri Mar 5 00:03:13 2010 +0000

    more OMP tweaking

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_mask.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 0c2afa953d81cbf8e17176fb1c99fa5dd23aa060
Author: lijewski <lijewski>
Date:   Thu Mar 4 22:03:50 2010 +0000

    removed itsol_breakdown() -- not used

Src/LinearSolvers/F_MG/itsol.f90

commit 5e5fd7b7aaf0b21cf88b42aa10479770dce08a35
Author: lijewski <lijewski>
Date:   Thu Mar 4 22:00:53 2010 +0000

    some cleanup

Src/F_BaseLib/multifab.f90

commit 7706e7a7a6ed537ea896b33ed7dee77d260f3c2b
Author: lijewski <lijewski>
Date:   Thu Mar 4 17:35:13 2010 +0000

    Commented out a bunch of OMP directives that Chuck put in.
    They were over boxes which is not the right way to do things.
    Got to eventually go back over these and OMP over the fortran instead.

Src/F_BaseLib/multifab.f90

commit 89ac65a11d84098285a05f261ce6cb1370849bbc
Author: lijewski <lijewski>
Date:   Thu Mar 4 17:33:36 2010 +0000

    OCVS: ----------------------------------------------------------------------
    Removed couple OMP directives on loops over boxes that Chuck put in some time ago.
    It's not the right way to do things.
    It was leading to nested thread calls which was killing PathScale.

Src/LinearSolvers/F_MG/mg.f90

commit 206edffaa77a60c540adcef2916a8944af9ea092
Author: lijewski <lijewski>
Date:   Thu Mar 4 00:05:18 2010 +0000

    more eliding of function calls

Src/LinearSolvers/F_MG/nodal_mask.f90

commit bd6becc7be6f80d59624fcc21b2b349c8e271811
Author: lijewski <lijewski>
Date:   Wed Mar 3 23:59:12 2010 +0000

    some cleanup

Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/nodal_mask.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit ee56089a7c394a8f1a46af20596d373e3e6361af
Author: lijewski <lijewski>
Date:   Wed Mar 3 23:17:39 2010 +0000

    some OMPing

Src/LinearSolvers/F_MG/nodal_divu.f90

commit e6410fc36f2d6c841a4e7235fabe31a5a263a1a6
Author: lijewski <lijewski>
Date:   Wed Mar 3 23:13:07 2010 +0000

    OPM'd

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 5032baf79b86dd69c5b7aeacae33ac94f4589505
Author: lijewski <lijewski>
Date:   Wed Mar 3 21:15:01 2010 +0000

    Removed bunch of duplicate functions by making single module private version.

Src/LinearSolvers/F_MG/itsol.f90

commit dbb9dcd8974cd46bbb9be7b0e87e15c68b17caa8
Author: lijewski <lijewski>
Date:   Wed Mar 3 21:06:03 2010 +0000

    more OMP and cleanup

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/sparse_solve.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 40109797cdfaf5f231d7eec31e9f176c14ebaf96
Author: lijewski <lijewski>
Date:   Wed Mar 3 18:11:03 2010 +0000

    OMP 7-point jacobi

Src/LinearSolvers/F_MG/mg_smoother.f90

commit f6e9a189b7026f984f3f9daf9f99bf22e44baa7c
Author: lijewski <lijewski>
Date:   Wed Mar 3 17:57:28 2010 +0000

    more OMP stuff

Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit fe5593b142f9c79aff56f5bd07be98cd6974d4f1
Author: lijewski <lijewski>
Date:   Tue Mar 2 23:49:03 2010 +0000

    some OPMing

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 39914b8fd38b8299ea3cd6255d31230e21ee3cdd
Author: lijewski <lijewski>
Date:   Tue Mar 2 23:20:41 2010 +0000

    some OMP

Src/LinearSolvers/F_MG/mg_restriction.f90

commit 797d6da6a334a8f80b0eb866f26bd52d7c23c304
Author: lijewski <lijewski>
Date:   Tue Mar 2 23:08:27 2010 +0000

    more function eliding

Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/stencil.f90

commit efd30b24610554ce1eafde6d93c2e93d694d05a1
Author: lijewski <lijewski>
Date:   Tue Mar 2 21:06:00 2010 +0000

    yet more eliding of bc_neumann() and bc_dirichlet()

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 4c5d0fd0dc99dd48e6e5c348bbf726720cca8d31
Author: lijewski <lijewski>
Date:   Tue Mar 2 19:05:19 2010 +0000

    more eliding of bc_neumann() and bc_dirichlet()

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 58c4d32a536750e42e1cd26c72cc231fc92a075f
Author: lijewski <lijewski>
Date:   Tue Mar 2 18:16:47 2010 +0000

    Rearranged code to remove bunch of bc_neumann() calls.  More to be done ...

Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit fcb350bc3dedb9a6d27bb1a69b5c55d9bac316f4
Author: lijewski <lijewski>
Date:   Mon Mar 1 23:45:37 2010 +0000

    removed some OMP loops that crashed Intel

Src/F_BaseLib/multifab.f90

commit c70cc22b777a5ab146811c7c4d5e5fd3c7d87e56
Author: lijewski <lijewski>
Date:   Mon Mar 1 23:10:17 2010 +0000

    some OMP

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 2bbe1d8133cd1e15f7137e20773b92fbcd239bc1
Author: lijewski <lijewski>
Date:   Mon Mar 1 22:43:58 2010 +0000

    yet more OMP

Src/LinearSolvers/F_MG/stencil.f90

commit 2166e1b3505f53a72f09713952cbdb83a039124e
Author: lijewski <lijewski>
Date:   Mon Mar 1 22:22:02 2010 +0000

    some OMP

Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 249014c8f1dcf3cbf90bb8b97ef59eaa22898aef
Author: lijewski <lijewski>
Date:   Mon Mar 1 22:15:57 2010 +0000

    some OMP

Src/LinearSolvers/F_MG/mg_smoother.f90

commit ee4ac73aff413b14268caf3493d203633b5458f2
Author: lijewski <lijewski>
Date:   Mon Mar 1 22:02:03 2010 +0000

    brought up-to-date

Tests/LinearSolvers/F_MG/main.f90
Tests/LinearSolvers/F_MG/wrapper.f90

commit c71cd67454116ac0a8fbdcd4386cb01b60505a7a
Author: lijewski <lijewski>
Date:   Mon Mar 1 22:00:11 2010 +0000

    Got rid of -stand f95 for intel; complains about OMP loops.
    Added appropriate stuff for OMP with Intel.
    Changed -mp --> -mp1

Tools/F_mk/GMakedefs.mak

commit 7b3b4bbdce4ef1af3cf1a1da65a619b0bab07c51
Author: lijewski <lijewski>
Date:   Mon Mar 1 20:12:14 2010 +0000

    speedup to gs_rb_smoother_3d

Src/LinearSolvers/F_MG/mg_smoother.f90

commit e8da78520ed4108a5a8064905c039d80f1b5c1fe
Author: almgren <almgren>
Date:   Fri Feb 26 22:23:37 2010 +0000

    Remove unused variable:
    IntVect b1_length = b1.size();

Src/C_AMRLib/TagBox.cpp

commit 9bc1ed8228fb412e8846542d172d08ccfe83e361
Author: almgren <almgren>
Date:   Fri Feb 26 21:57:04 2010 +0000

    Modify Amr, AmrLevel and Make.package so that we don't generically include
    SlabStat and StationData stuff.   You must now define USE_SLABSTAT or USE_STATIONDATA
    to get those (respectively).

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Make.package

commit f066e95e7bf6828621b7de52e6a739312568aa4f
Author: lijewski <lijewski>
Date:   Fri Feb 26 21:33:58 2010 +0000

    minor efficiency tweaks

Src/C_BaseLib/BoxList.cpp

commit f97aeb710e27e9aa877b6357fba77058c60375a7
Author: lijewski <lijewski>
Date:   Fri Feb 26 21:14:00 2010 +0000

    minor tweaks to add()

Src/C_BaseLib/BoxDomain.cpp

commit 321b38acdf934271f3ea02c938ea62f7dbaa68c6
Author: lijewski <lijewski>
Date:   Thu Feb 25 22:34:34 2010 +0000

    use LnClassPtr instead of CpClassPtr

Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit a8c4cd2d1e576f9353ebd50e37ec5252b8a90f0e
Author: lijewski <lijewski>
Date:   Thu Feb 25 20:59:23 2010 +0000

    undrrelxr now uses LnClassPtr instead of CpClassPtr

Src/LinearSolvers/C_CellMG/LinOp.H

commit b20ab92d21df8f9d0757475d43b3926cb3f516a1
Author: lijewski <lijewski>
Date:   Tue Feb 23 21:37:42 2010 +0000

    minor tweak to how intersections() is used

Src/C_AMRLib/AuxBoundaryData.cpp
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/FabSet.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit c85db87eab07f2d2cf64fa6c39090c9075e4018f
Author: lijewski <lijewski>
Date:   Tue Feb 23 21:08:02 2010 +0000

    remove unused constructor & use reserve() on vector members

Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 008d668f54555e09a72fb4aa8f890b8525fbcf8d
Author: lijewski <lijewski>
Date:   Tue Feb 23 20:09:48 2010 +0000

    use a std::list instead of std::vector for PIRMList type

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit c373ecc11199942b6f1b8abc3baacca979ed70b2
Author: lijewski <lijewski>
Date:   Tue Feb 23 18:36:07 2010 +0000

    added swap()

Src/C_BaseLib/BaseFab.H

commit 2c80ce5e6096489ac77e3da4ac46a2fd24978621
Author: almgren <almgren>
Date:   Mon Feb 22 00:53:12 2010 +0000

    Removed empty loop in Amr::restart

Src/C_AMRLib/Amr.cpp

commit 6f93bfa722676468d4bcf3ec336b3f1d69e19d73
Author: lijewski <lijewski>
Date:   Sun Feb 21 16:28:19 2010 +0000

    efficiency mods to simplify()

Src/C_BaseLib/BoxList.cpp

commit 0c0c5a4709b10da4d50461ffdddd2c6aec575f29
Author: almgren <almgren>
Date:   Fri Feb 19 23:40:10 2010 +0000

    These now compile.

Tools/C_util/Convergence/Add.cpp
Tools/C_util/Convergence/DiffFab.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileNormB.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp

commit 10ddef716b96a49be0f2b17b137df73014353e6d
Author: ajnonaka <ajnonaka>
Date:   Fri Feb 19 23:04:42 2010 +0000

    prints out norms now - that are properly normalized as well (as noted in the output stream)!

Tools/C_util/Convergence/DiffFab.cpp

commit ce1f42e056386570fe875a780510acc816817537
Author: almgren <almgren>
Date:   Fri Feb 19 22:45:04 2010 +0000

    Start to make these compile again.

Tools/C_util/Convergence/Add.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileNormB.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp

commit 273ec2566ffa63b34d82917529c58ad05547b815
Author: almgren <almgren>
Date:   Fri Feb 19 22:44:51 2010 +0000

    Default COMP to Intel, not g++.

Tools/C_util/Convergence/GNUmakefile

commit 8fe144acd66b9be222d06c829e8949cf36c7a3f5
Author: ajnonaka <ajnonaka>
Date:   Fri Feb 19 22:36:05 2010 +0000

    compiles again

Tools/C_util/Convergence/DiffFab.cpp

commit 1affa13cb658e0976532579b745c939f2410d982
Author: lijewski <lijewski>
Date:   Fri Feb 19 21:19:34 2010 +0000

    minor refinement of execute()

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 96c916151dcb2278624b2cf1444b64dbff91493b
Author: lijewski <lijewski>
Date:   Fri Feb 19 18:18:34 2010 +0000

    a bit more const-correctness

Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit 537d266e68039ae8c9da03154b1f9b586106ad3b
Author: almgren <almgren>
Date:   Fri Feb 19 18:16:11 2010 +0000

    Add -DBL_PLEIADES so we know if we are on pleiades.

Tools/C_mk/Make.Linux

commit bd4348f0ccd20e09e8a368decee88ca61778aadc
Author: lijewski <lijewski>
Date:   Fri Feb 19 17:59:07 2010 +0000

    removed BFProxy stuff

Src/C_BaseLib/BaseFab.H

commit 8c900fa9ed7156dff7619d3d79c53230e13184c4
Author: almgren <almgren>
Date:   Thu Feb 18 17:49:08 2010 +0000

    Fix print statements.

Src/LinearSolvers/F_MG/mg.f90

commit effe8cd4bdbc51ecd3bf6fd3bf77f7e30a7744b9
Author: lijewski <lijewski>
Date:   Wed Feb 17 16:49:54 2010 +0000

    integrated back in FORT_HGRESU and FORT_HGRLXU for the time being

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit b4efa0046f0e2a85b8f13ca6cef5c52c8f8d4c97
Author: lijewski <lijewski>
Date:   Tue Feb 16 18:41:07 2010 +0000

    removed some virtuals -- FabArrayBase is a concrete class

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 76a8d5a9439f235c48b8ee7f2b53f8b3fa6fd187
Author: lijewski <lijewski>
Date:   Tue Feb 16 18:15:50 2010 +0000

    remove some temporaries

Src/C_BaseLib/BoxList.cpp

commit 2a27bc7569ba524642e50e62da2a709378fa14b1
Author: lijewski <lijewski>
Date:   Tue Feb 16 18:15:17 2010 +0000

    enforce stricter const-correctness

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/Orientation.H

commit a3321cc4c6b35a2065e2dad67c4637108ac6d472
Author: lijewski <lijewski>
Date:   Tue Feb 16 18:07:00 2010 +0000

    fix for more const-correct BoxLib

Src/LinearSolvers/C_NodalMG/interface.cpp

commit 960d98e4fc7086b647be827baae436b04cb6f522
Author: lijewski <lijewski>
Date:   Tue Feb 16 18:02:58 2010 +0000

    Uninlined constructors/destructor.  Removed "virtual" on destructor.

Src/C_BoundaryLib/Mask.H
Src/C_BoundaryLib/Mask.cpp

commit 94fd978b971dacb92698ae3ca2681c7134d7b8a0
Author: lijewski <lijewski>
Date:   Tue Feb 16 17:54:23 2010 +0000

    uninlined constructors

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp

commit d5276cf2a082d7ed48ade9f0c6e55076d322c12a
Author: lijewski <lijewski>
Date:   Tue Feb 16 17:52:34 2010 +0000

    moved constructor/destructor to .cpp file instead of inlining

Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp

commit 7072ff560908fdcc9f87c8992f3efe96c97206d8
Author: lijewski <lijewski>
Date:   Tue Feb 16 17:42:46 2010 +0000

    *** empty log message ***

Src/C_AMRLib/Cluster.cpp

commit 86f53ef18a111f22381b12ce5d9405a29517146f
Author: lijewski <lijewski>
Date:   Sat Feb 13 23:06:18 2010 +0000

    added cg.cpp

Src/LinearSolvers/C_NodalMG/Make.package

commit 0a8d767d29a66588da01f61648489cf501097199
Author: lijewski <lijewski>
Date:   Sat Feb 13 22:50:17 2010 +0000

    some efficiency mods

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AuxBoundaryData.cpp
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.cpp

commit 2a36501f1969fd3dcfeecb432dfbd1acffc94e6a
Author: almgren <almgren>
Date:   Sat Feb 13 01:41:39 2010 +0000

    Remove unused variables.

Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit aa11fdc528e975ab7a30ef4b427f2ee7fb8b6e04
Author: almgren <almgren>
Date:   Sat Feb 13 01:17:54 2010 +0000

    Moved gt_breaks_27pt to the Test directory.

Src/LinearSolvers/C_NodalMG/Test/gt_breaks_27pt
Tests/LinearSolvers/C_NodalMG/gt_breaks_27pt

commit 3adf9176ff364f48f25af67ae987a5942b207d5a
Author: almgren <almgren>
Date:   Sat Feb 13 01:15:26 2010 +0000

    Moved 3d_4_level.grids to the tests directory.

Src/LinearSolvers/C_NodalMG/tests/3d_4_level.grids
Tests/LinearSolvers/C_NodalMG/test_grids/3d_4_level.grids

commit 2c1575dba8595f031dee012f876ca7cb6009fcde
Author: almgren <almgren>
Date:   Sat Feb 13 01:14:08 2010 +0000

    Moved files.2d and files.3d to the Test directory.

Src/LinearSolvers/C_NodalMG/Test/files.2d
Src/LinearSolvers/C_NodalMG/Test/files.3d
Tests/LinearSolvers/C_NodalMG/files.2d
Tests/LinearSolvers/C_NodalMG/files.3d

commit 3f2e088c43bfdca69cfe28257f0ab18c70de5924
Author: almgren <almgren>
Date:   Sat Feb 13 01:12:33 2010 +0000

    Moved proj.cpp and inputs to the Test directory.

Src/LinearSolvers/C_NodalMG/Test/inputs
Src/LinearSolvers/C_NodalMG/Test/proj.cpp
Tests/LinearSolvers/C_NodalMG/inputs
Tests/LinearSolvers/C_NodalMG/proj.cpp

commit b42a9ddc5e039b1066107f22ede3f383bee59dcf
Author: almgren <almgren>
Date:   Sat Feb 13 01:10:35 2010 +0000

    No clue what hgproj.pg was for.

Src/LinearSolvers/C_NodalMG/hgproj.pg

commit eee1c2e385fbf44f780c96220c43b5519d51283f
Author: almgren <almgren>
Date:   Sat Feb 13 00:53:07 2010 +0000

    Move cgsolve out of hg_multi3.cpp and into a separate file, cg.cpp

Src/LinearSolvers/C_NodalMG/cg.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit bc7e855655e81ccf76eea6bec5810229cbe4cb24
Author: almgren <almgren>
Date:   Sat Feb 13 00:47:47 2010 +0000

    Removed unused subroutines and renamed HGRESUR to HGRES_CROSS.

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 29f7accccc7c0c8f8198429f2c84b6b59d53a3cb
Author: almgren <almgren>
Date:   Sat Feb 13 00:47:07 2010 +0000

    Moving subroutines around to make it easier to keep track of things.
    Created cg_2d.f and cg_3d.f to hold the subroutines used for the CG bottom solve.

Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/cg_2d.f
Src/LinearSolvers/C_NodalMG/cg_3d.f
Src/LinearSolvers/C_NodalMG/hg_multi2d.f
Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f
Src/LinearSolvers/C_NodalMG/hg_multi3d.f
Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f

commit 520bc3588d2ddd93e158275588e4097eea006590
Author: almgren <almgren>
Date:   Fri Feb 12 23:36:42 2010 +0000

    Added more print statements to make it look more like f90 version.
    Doesn't change execution and should be the same with Pcode = 0 or 1.

Src/LinearSolvers/C_NodalMG/amr_multi.cpp

commit 85dcb13ffb334f92abe53f842fcdd582e739db13
Author: almgren <almgren>
Date:   Fri Feb 12 23:34:40 2010 +0000

    Remove unused routines (ones with unrolled loops) and modified
    print statements.

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 155fb0f883515fb5372d66c67908647bacf5fd80
Author: almgren <almgren>
Date:   Fri Feb 12 23:34:04 2010 +0000

    Remove unused variables, unused subroutines, and
    the unrolled versions of the cross-stencil relaxation routines.

Src/LinearSolvers/C_NodalMG/hg_multi2d.f
Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit 98bb50dbb8c70a2518f3cf2bca8199e5194f256f
Author: lijewski <lijewski>
Date:   Thu Feb 11 23:38:05 2010 +0000

    some inlining

Src/C_AMRLib/BCRec.H
Src/C_AMRLib/BCRec.cpp
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp

commit a85e2bb416647af415fe9b962fc5195a0f8d037c
Author: lijewski <lijewski>
Date:   Thu Feb 11 23:15:08 2010 +0000

    some inlining

Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/RealBox.H
Src/C_BaseLib/RealBox.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit b52d6390fca4d7fe72c033e81a4c1e176fb0a0a3
Author: lijewski <lijewski>
Date:   Thu Feb 11 22:22:34 2010 +0000

    some inlining

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/UseCount.cpp

commit 1b922d62c0fcf9723ec6e9672f3ed08d576260a8
Author: almgren <almgren>
Date:   Wed Feb 10 22:19:52 2010 +0000

    1) Back out the introduction of "just_solve"
    2) Add an extra argument (Rhs) to nodal_project.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 014165552476977c2cc6d43695d5473ef81a1cfb
Author: almgren <almgren>
Date:   Wed Feb 10 21:46:57 2010 +0000

    Add additional option for solve which doesn't take a BndryData

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 7deca33ed236961cd853673fb021c7dacacddf13
Author: lijewski <lijewski>
Date:   Wed Feb 10 21:22:23 2010 +0000

    some refinement to Distribute()

Src/C_BaseLib/DistributionMapping.cpp

commit 5367f307867ae0aec20c0086cde5ccafd46bcf6d
Author: almgren <almgren>
Date:   Wed Feb 10 20:44:49 2010 +0000

    Modified print statements to be more aligned with current mglib.

Src/LinearSolvers/F_MG/mg.f90

commit 0386aa07297c2f58590bc692fad4cafb950ef9c4
Author: almgren <almgren>
Date:   Wed Feb 10 20:42:24 2010 +0000

    Modified verbosity controls to make output more similar to that of F90 solvers.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 98040fe40ac5c208084763e105950057276c4052
Author: almgren <almgren>
Date:   Wed Feb 10 20:31:43 2010 +0000

    Remove unused variable.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 63802dbefc1f271a3e7739f55121ccb3037e2d71
Author: lijewski <lijewski>
Date:   Wed Feb 10 17:32:03 2010 +0000

    some simplification

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 30dbd1204d64962b281ed187e5c647fa645448ec
Author: lijewski <lijewski>
Date:   Tue Feb 9 23:04:49 2010 +0000

    added <cstdio> to get sprintf()

Src/C_BoundaryLib/BndryRegister.cpp

commit ed78307b4fa834ae149289d1d587a16a228fdc33
Author: lijewski <lijewski>
Date:   Tue Feb 9 22:15:36 2010 +0000

    shut up some compiler warnings on franklin

Src/C_AMRLib/FluxRegister.cpp

commit 3ad7a098c76ae00dc6f33ed254f5b1f7e50c38f2
Author: aaspden <aaspden>
Date:   Tue Feb 9 21:00:42 2010 +0000

    Hopper

Tools/F_mk/GMakeMPI.mak

commit cd156dfe35b3b82dfb0bb2faa65bcff0e827ca4d
Author: lijewski <lijewski>
Date:   Tue Feb 9 20:29:04 2010 +0000

    use a std::map instead of a std::vector for the cache

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit cc7813fc182f8f4eb681a3075befb2e0594f2a3d
Author: lijewski <lijewski>
Date:   Tue Feb 9 18:22:09 2010 +0000

    removed unused BL_ASSERT()

Src/C_AMRLib/TagBox.cpp

commit 0bb268f5f9ee06e4740ed181791674ce67bb7f51
Author: lijewski <lijewski>
Date:   Tue Feb 9 18:19:35 2010 +0000

    *** empty log message ***

Src/C_AMRLib/FluxRegister.cpp

commit fbe08482f078ccf1b22347cc8261393586f901ba
Author: lijewski <lijewski>
Date:   Tue Feb 9 17:33:59 2010 +0000

    added some reserve() calls

Src/C_BoundaryLib/FabSet.cpp

commit f107790823b87430b10a2e8c5a8c9d0dced10dc0
Author: lijewski <lijewski>
Date:   Tue Feb 9 17:32:44 2010 +0000

    added reserve() call in intersections code

Src/C_BaseLib/BoxArray.cpp

commit 7bcaa91f8ace0a9112afd6c3096ab48f0cec0209
Author: lijewski <lijewski>
Date:   Tue Feb 9 06:32:27 2010 +0000

    some memory consolidation

Src/C_AMRLib/TagBox.cpp

commit 3d33070d37dbe488af42caaa9174b3dc936bfe8f
Author: lijewski <lijewski>
Date:   Tue Feb 9 06:05:55 2010 +0000

    use vector::reserve()

Src/LinearSolvers/C_NodalMG/interface.cpp

commit 152aea1242bd4ff8fd865bd1bb530341b0ab2202
Author: lijewski <lijewski>
Date:   Tue Feb 9 03:59:25 2010 +0000

    removed unused function

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 9b73857b778dc44136f544190833b21338d941b7
Author: lijewski <lijewski>
Date:   Tue Feb 9 01:08:39 2010 +0000

    now use vector::reserve()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 6224af89550833ca1a4b77ec8b828aaaacbcc943
Author: lijewski <lijewski>
Date:   Tue Feb 9 00:50:26 2010 +0000

    use vector::reserve() a bit

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit a9a35f2ddae3a4e4c45a3cc5569e81a7206b9d04
Author: lijewski <lijewski>
Date:   Mon Feb 8 23:39:53 2010 +0000

    use std::vector::reserve() in places

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit bc738d945df42a902f8d31f98f801ede490e29ab
Author: lijewski <lijewski>
Date:   Mon Feb 8 23:39:13 2010 +0000

    some simplification

Src/C_BaseLib/BoxList.cpp

commit e516da4b4b8e6b1557ac478a4daa194ac3d4f379
Author: lijewski <lijewski>
Date:   Mon Feb 8 21:05:04 2010 +0000

    replace std::vector with std::list in a number of places

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 9394cd59eaff1ad4fc30fa671397faeaec559d32
Author: almgren <almgren>
Date:   Mon Feb 8 19:01:38 2010 +0000

    Add shift operator for BoxArray that takes an IntVect.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 59a982acb519b8a4688791d2a917491646441a3f
Author: ajnonaka <ajnonaka>
Date:   Tue Feb 2 19:15:06 2010 +0000

    turn on Ann and Andy's unused variable warnings for C++ and fortran

Tools/C_mk/Make.defs

commit ced34dd8a8aa90413b5de907d211da2a746db26f
Author: ajnonaka <ajnonaka>
Date:   Tue Feb 2 14:45:19 2010 +0000

    turn on unused variable check in debug mode using gfortran

Tools/C_mk/Make.defs

commit beeced10a7fd58bcc94d48eb29d052443bb7c705
Author: ajnonaka <ajnonaka>
Date:   Tue Feb 2 14:10:58 2010 +0000

    when compiling in debug mode with intel 9, you now get unused variable warning messages

Tools/F_mk/GMakedefs.mak

commit 351c159892819d2d450bd280373deca892437445
Author: ajnonaka <ajnonaka>
Date:   Tue Feb 2 13:01:47 2010 +0000

    reverting back to 1/29/10 - otherwise Castro doesn't compile with Intel10 in DEBUG mode

Src/C_BaseLib/CArena.cpp

commit 205544e1b53445cd43dbcaf2f3dbf75944fae0bd
Author: ajnonaka <ajnonaka>
Date:   Tue Feb 2 12:56:23 2010 +0000

    need to declare freeblock before using - was causing compiler error in debug

Src/C_BaseLib/CArena.cpp

commit 9bd9703fe4aec1e9b7cebe382bba09a406c87acd
Author: lijewski <lijewski>
Date:   Fri Jan 29 21:14:02 2010 +0000

    additional optimization options for PathScale

Tools/C_mk/Make.Linux

commit 166763b966b056812dc5d45c6573cf8d31a8cbb8
Author: lijewski <lijewski>
Date:   Fri Jan 29 20:42:04 2010 +0000

    some cleanup

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/VisMF.cpp

commit f4393a701e4d35499e0c8cf597883d34dddf32ae
Author: mzingale <mzingale>
Date:   Thu Jan 21 17:53:51 2010 +0000

    add xmin, ymin, ... to the coordinates vector to account for domains
    that don't start at 0

Tools/F_scripts/idlbl/rawread.pro
Tools/F_scripts/idlbl/rawread3d.pro

commit 6f633b68ae6e15efe6db4668b09df83a574041df
Author: nazgul <nazgul>
Date:   Wed Jan 20 19:21:49 2010 +0000

    Added read and write functions to support FluxRegister checkpoint/restart.
    
    Louis

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 112d83aff147a2f2701d2d96b0fe5a6ff17c8cdb
Author: nazgul <nazgul>
Date:   Wed Jan 20 19:20:11 2010 +0000

    Read and write functions to support flux register checkpoint/restart.
    
    Louis

Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 38c3029c1289ad9f701ac2616b0654fe553d52c3
Author: almgren <almgren>
Date:   Tue Jan 12 22:51:34 2010 +0000

    Make sure to set abs_eps based on what we've defined in the mgt.

Src/LinearSolvers/F_MG/ml_cc.f90

commit a7a22db8be634eef22601e344e695a542cfacc4d
Author: almgren <almgren>
Date:   Tue Jan 12 20:34:42 2010 +0000

    Fix print statement.

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 499e651bac98d43e8d5248095648b5ed9c4f9b41
Author: gilet <gilet>
Date:   Wed Jan 6 01:11:50 2010 +0000

    *** empty log message ***

Tools/C_mk/Make.mpi

commit 385f181838c97ddbf65f90f81a9dd0d93cab1ab5
Author: lijewski <lijewski>
Date:   Wed Dec 23 04:34:56 2009 +0000

    disabled (again) FAST optimization for PathScale

Tools/C_mk/Make.Linux

commit e963bc492280213877d555cb48e00d94de30f3f2
Author: gpau <gpau>
Date:   Mon Dec 21 21:52:11 2009 +0000

    add new files so that we can calculate fluxes at any location and direction

Tools/C_util/Statistics/PltFileFluxAve.H
Tools/C_util/Statistics/PltFileFluxAve.cpp

commit 87fb961f8e4dd3a64b12d2ae97c54ee7935197a5
Author: gpau <gpau>
Date:   Mon Dec 21 21:51:12 2009 +0000

    make changes to flux calculations

Tools/C_util/Statistics/ComputeAmrDataStat.H
Tools/C_util/Statistics/ComputeAmrDataStat.cpp
Tools/C_util/Statistics/GNUmakefile
Tools/C_util/Statistics/PltFileStat.cpp

commit 2d08d3eaa73992f2b006af741e33ad1ee2df4696
Author: lijewski <lijewski>
Date:   Mon Dec 21 20:36:20 2009 +0000

    removed stdnormal_cdf()

Src/C_BaseLib/Utility.cpp

commit 4086842e2392175cfd388ebf6d444dc954eda6f4
Author: lijewski <lijewski>
Date:   Mon Dec 21 20:36:04 2009 +0000

    removed Output_CPU_Comm_Costs()

Src/C_BaseLib/DistributionMapping.cpp

commit 2f421623b49531bce3c7514babd6ab22939c5d63
Author: almgren <almgren>
Date:   Mon Dec 21 17:44:10 2009 +0000

    Added stuff for ranger, a machine that Jason Nordhaus uses.

Tools/C_mk/Make.mpi

commit 8740b09d32c3e8afdeab48c8e319ab467ee389d8
Author: almgren <almgren>
Date:   Mon Dec 21 17:42:40 2009 +0000

    Added ranger (a Texas machine which Jason Nordhaus uses).

Tools/C_mk/Make.defs

commit eed94342cf5300d3c3731462f1a17b5a56d90e15
Author: lijewski <lijewski>
Date:   Mon Dec 21 16:07:03 2009 +0000

    disable fast stuff for PGI -- breaks LLNS

Tools/C_mk/Make.Linux

commit c29c228c32d2e86b8deef6273a1a664247b3b319
Author: lijewski <lijewski>
Date:   Fri Dec 18 19:04:17 2009 +0000

    put back some of the not NOFAST stuff

Tools/C_mk/Make.Linux

commit 36717f3cc7a1257a723c41e54944c694c570161c
Author: lijewski <lijewski>
Date:   Fri Dec 18 18:41:34 2009 +0000

    don't print MFRead::: stuff by default

Src/C_AMRLib/Amr.cpp

commit 3bfaf52ac8d17bf7cbc04e08662775b92ca142d3
Author: lijewski <lijewski>
Date:   Mon Dec 14 21:13:58 2009 +0000

    disable the MFRead:: output

Src/C_BaseLib/VisMF.cpp

commit 96b176bb6558d137fb6d991bac830ca7e3d44907
Author: lijewski <lijewski>
Date:   Fri Dec 11 03:05:08 2009 +0000

    some cleanup of InvNormDistBest()

Src/C_BaseLib/Utility.cpp

commit 0153cfdf92bbff627ee394b674b82c40b2030789
Author: lijewski <lijewski>
Date:   Fri Dec 11 01:06:49 2009 +0000

    Added InvNormDistBest().
    This is used instead of the previous "best" option to InvNormDist().
    The algorithm is from Applied Statistics Algorithm 241 by Michael
    Wichura and the C++ implementation by John Burkardt.  It provides
    machine precision and is much faster than the previous "best" option.
    It's only about 30% slower than InvNormDist().

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit ebd33c4ae4038a11082280ba80ed092c4f6c5ca1
Author: vince <vince>
Date:   Thu Dec 10 22:49:30 2009 +0000

    added code for more file system friendly restarts.

Src/F_BaseLib/fabio.f90

commit 70d4e1fd61d22e65ebea46373125be1b67bf0c4d
Author: almgren <almgren>
Date:   Thu Dec 10 22:18:47 2009 +0000

    We need to delete fluxes which we have created through a call to mgt_compute_flux.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 180e9a6a7baad84652e1865b9da1923038d5ffe7
Author: almgren <almgren>
Date:   Thu Dec 10 22:18:27 2009 +0000

    We need to be able to delete fluxes which are built in mgt_compute_fluxes.

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 4547fab1eb121dfa803dd6fd41748e6ee737ffb7
Author: almgren <almgren>
Date:   Wed Dec 9 19:15:15 2009 +0000

    Allow us to read in a single value for n_error_buf, to be used for
    all levels, or an array for n_error_buf with a distinct value for each level.

Src/C_AMRLib/Amr.cpp

commit 31a965cfc0905107ab17c1cb8ee463cbcf97615d
Author: lijewski <lijewski>
Date:   Wed Dec 9 17:41:57 2009 +0000

    Added d2_value() from latest MT folks.
    Faster implementation of d[12]?_value() according to latest MT stuff.
    Changed names: d1_value -> d_value and d_value -> d1_value to match MT.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit cf56abeb6d856494f10707e39d210d54ad9d77b5
Author: lijewski <lijewski>
Date:   Wed Dec 9 06:37:50 2009 +0000

    modest speedup to mt19937 code

Src/C_BaseLib/Utility.cpp

commit f6fe84224730b4f486322bafe39442ec676f3b86
Author: lijewski <lijewski>
Date:   Tue Dec 8 22:36:42 2009 +0000

    increased a buffer size by a tad

Src/C_BaseLib/VisMF.cpp

commit 8614490a558ae451a1bff4817d77cbd0202a70ff
Author: lijewski <lijewski>
Date:   Tue Dec 8 21:20:35 2009 +0000

    added save()/restore() for mt19937

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit e804a8ae6ec8bf26e326bff98c7509d949abf9e3
Author: lijewski <lijewski>
Date:   Tue Dec 8 19:23:14 2009 +0000

    added blinitrand() entry point

Src/C_BaseLib/Utility.cpp

commit 761d12241090d16ef59607c5069a246e62e088ef
Author: almgren <almgren>
Date:   Fri Dec 4 20:18:50 2009 +0000

    Add empty line after Final Iter print statement for easier readability.

Src/LinearSolvers/F_MG/ml_cc.f90

commit f9d941abab706162186ba7553aab36e56269579d
Author: lijewski <lijewski>
Date:   Fri Dec 4 18:21:56 2009 +0000

    fixed bug I introduced yesterday

Src/C_BaseLib/Geometry.cpp

commit ffcc320685dc325dece0007f38da87d43bf4008c
Author: lijewski <lijewski>
Date:   Fri Dec 4 17:35:13 2009 +0000

    *** empty log message ***

Src/C_AMRLib/Amr.cpp

commit 70af7fd46ff5df6a1f7b9eed8f82cfb8879b5ff0
Author: lijewski <lijewski>
Date:   Thu Dec 3 19:12:28 2009 +0000

    can now set periodicity on construction

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit a322b68ace9a1a1ab133d1b0ee94e4c403d24596
Author: mzingale <mzingale>
Date:   Thu Dec 3 02:25:59 2009 +0000

    fix the C compiler on Atlas, add optimizations for Intel 11

Tools/F_mk/GMakedefs.mak

commit e5fbcb50f579caebc361f6dda4255cd88d80d597
Author: lijewski <lijewski>
Date:   Sat Nov 28 07:27:53 2009 +0000

    up rMAX to 16 from 8

Src/C_AMRLib/INTERP_3D.F

commit 8b8dd3704c9df05249509a9882cdba12d3f9bf30
Author: almgren <almgren>
Date:   Sat Nov 28 04:28:45 2009 +0000

    Should have 1/hx^2 in filling the Minion stencil...

Src/LinearSolvers/F_MG/stencil.f90

commit 3dd4da2ae73ba15dcf1a0073fd85ca555ad08b11
Author: minion <minion>
Date:   Sat Nov 28 00:23:19 2009 +0000

    fixed stencil

Src/LinearSolvers/F_MG/stencil.f90

commit f13af5f49cf75288a958298182f49e00d8927893
Author: minion <minion>
Date:   Wed Nov 25 18:14:11 2009 +0000

    var density mg still not working

Src/LinearSolvers/F_MG/stencil.f90

commit 98789ca5509f52072511f5c4b95ea05f9f4021b6
Author: lijewski <lijewski>
Date:   Wed Nov 25 05:28:18 2009 +0000

    refine_grid_layout yet again defaults to true

Src/C_AMRLib/Amr.cpp

commit 4645679a3d03b5256ae3341873eb067fb18efe3c
Author: lijewski <lijewski>
Date:   Tue Nov 24 18:37:17 2009 +0000

    mods for hopper

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 13fdc62c441b14be936db7d51576bf6781232769
Author: lijewski <lijewski>
Date:   Sat Nov 21 03:46:42 2009 +0000

    Dug up an old version of FORT_NBINTERP that didn't have the "vectorization"
    crap in it and then OpenMP'd it.

Src/C_AMRLib/INTERP_3D.F

commit 673eea439b52d229dd14c0aeaaa255c07894bf7b
Author: lijewski <lijewski>
Date:   Fri Nov 20 21:46:35 2009 +0000

    more OpenMPing

Src/C_AMRLib/FILCC_3D.F
Src/C_AMRLib/INTERP_3D.F

commit c6a51097d6603fa55cc9693a94bb444c151e5965
Author: lijewski <lijewski>
Date:   Fri Nov 20 17:41:11 2009 +0000

    -fno-exceptions doesn't play well with MPICH2 header files at the moment

Tools/C_mk/Make.defs

commit 988546ca88e832807ca52d88369c65177adc9b1e
Author: lijewski <lijewski>
Date:   Thu Nov 19 20:59:26 2009 +0000

    Get rid of the -Ofast stuff for PathScale.
    Now you get same options w/wo BL_NOFAST=TRUE.

Tools/C_mk/Make.Linux

commit 3e6baee96b1db544b2b63d67f4cbf98f3cb93761
Author: lijewski <lijewski>
Date:   Wed Nov 18 17:11:48 2009 +0000

    some cleanup

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 92884feb775d7d4b2c92b7a4811c25012cb687aa
Author: lijewski <lijewski>
Date:   Tue Nov 17 22:14:46 2009 +0000

    yet more OpenMP

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit 34174cefdfc39c01716d83f4c391fe6d222d8f0b
Author: lijewski <lijewski>
Date:   Tue Nov 17 21:52:53 2009 +0000

    yet more OpenMP

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit 112fd8bee555c35fcb2709c75f773854883eb799
Author: lijewski <lijewski>
Date:   Tue Nov 17 21:40:58 2009 +0000

    more OpenMP

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit 304066fd69df64e609c627e384a10d887cb8f7db
Author: lijewski <lijewski>
Date:   Tue Nov 17 21:19:20 2009 +0000

    more OpenMP

Src/LinearSolvers/C_NodalMG/hg_avg3d.f

commit 201843aa24db294695dc5691c138dc92a0d8fa30
Author: lijewski <lijewski>
Date:   Tue Nov 17 18:57:50 2009 +0000

    changed FAB byte string to say MPI nodes not CPUs

Src/C_AMRLib/Amr.cpp

commit c524f74b0d3b40dc0d9fc36d9727ebff8466c10d
Author: mzingale <mzingale>
Date:   Tue Nov 17 04:39:36 2009 +0000

    get create_nodal_mask_1d to compile

Src/LinearSolvers/F_MG/ml_solve.f90

commit d47052d152b813c484572fa8ddc0eeb1ad0ee737
Author: almgren <almgren>
Date:   Tue Nov 17 03:04:27 2009 +0000

    Add 1d versions.

Src/LinearSolvers/F_MG/ml_solve.f90
Src/LinearSolvers/F_MG/nodal_mask.f90

commit 28ca8a09b7717bda8e56ecf8816e5809733e114b
Author: almgren <almgren>
Date:   Tue Nov 17 03:01:00 2009 +0000

    Add 1d version.

Src/LinearSolvers/F_MG/nodal_newu.f90

commit 801b48e79a1bd2b9f2af0c12fdd29008c35e8168
Author: gpau <gpau>
Date:   Mon Nov 16 18:16:27 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/ComputeAmrDataStat.H
Tools/C_util/Statistics/ComputeAmrDataStat.cpp
Tools/C_util/Statistics/GNUmakefile
Tools/C_util/Statistics/PltFileStat.cpp

commit 15e205a90bc76949d229d7b3078494189b89ca72
Author: gpau <gpau>
Date:   Sun Nov 15 17:01:53 2009 +0000

    added functionality to PltFileList: now reads in multifab instead of just plotfiles.

Tools/C_util/Statistics/GNUmakefile
Tools/C_util/Statistics/PltFileList.cpp

commit ddb3c5f2bc96ecb3950218643d094725e535f52d
Author: gpau <gpau>
Date:   Sun Nov 15 00:06:43 2009 +0000

    update the outputfile

Tools/C_util/Statistics/PltFileStat.cpp

commit c4d1def7a2c2763ea276628f9ef01e8ca7bc1672
Author: almgren <almgren>
Date:   Sat Nov 14 01:17:23 2009 +0000

    Hack the mg driver so that in 1d the code calls the line solve at the
    top level and does not enter the V-cycle or call the bottom solver.

Src/LinearSolvers/F_MG/mg.f90

commit 4f7711075a98dadb147348f5b30bdfc8cc58a42f
Author: almgren <almgren>
Date:   Sat Nov 14 01:16:39 2009 +0000

    Fix the Neumann boundary conditions in the nodal_line_solve_1d.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 7394edc051faec682a65144326b583ce0ce2966c
Author: gpau <gpau>
Date:   Fri Nov 13 22:47:04 2009 +0000

    handles multifab variogram

Tools/C_util/Statistics/ComputeAmrDataStat.H
Tools/C_util/Statistics/ComputeAmrDataStat.cpp
Tools/C_util/Statistics/PltFileStat.cpp

commit 8a8cbc220795fc0f8fc5190788d11af2eb4cf77e
Author: gpau <gpau>
Date:   Thu Nov 12 21:57:09 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/ComputeAmrDataStat.H
Tools/C_util/Statistics/ComputeAmrDataStat.cpp
Tools/C_util/Statistics/GNUmakefile
Tools/C_util/Statistics/PltFileStat.cpp

commit b2722597a377b362b3f9d958ecaa97f4e20d7994
Author: almgren <almgren>
Date:   Wed Nov 11 22:26:38 2009 +0000

    Replaced cycle by cycle_type.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_nodal_cpp.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit fad336fb610df0a0d7bca3d7cc1bc24b12a03023
Author: almgren <almgren>
Date:   Wed Nov 11 22:19:52 2009 +0000

    Just a cleanup..

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 50461ff9f9728dbdb7bc1d2fbe92ebbaeb480e23
Author: ajnonaka <ajnonaka>
Date:   Wed Nov 11 21:53:06 2009 +0000

    fixed the pesky bottom_solver=4 once and for all

Src/LinearSolvers/F_MG/mg.f90

commit e96ea9639f14ddc96435efdd65b37b8ab756e52a
Author: lijewski <lijewski>
Date:   Wed Nov 11 20:37:02 2009 +0000

    add -fpconstant to Intel fortran and some simplification

Tools/C_mk/Make.defs

commit 085ae0376bbcedc5cc945422c6439f1ed5201f54
Author: lijewski <lijewski>
Date:   Wed Nov 11 20:20:36 2009 +0000

    decrease Intel optimization -O3 and -ip are buggy

Tools/C_mk/Make.defs

commit 504b171fc94b030761910a93b5fced57efd8d32f
Author: gpau <gpau>
Date:   Tue Nov 10 23:26:05 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/PltFileList.cpp

commit 78a19761f053c4b7fb6addbfad035fda9af252dc
Author: gpau <gpau>
Date:   Tue Nov 10 22:19:48 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/PltFileList.cpp

commit e5322e0c9a9a5d3ceefa52a1171a788b3a24d6d9
Author: lijewski <lijewski>
Date:   Tue Nov 10 21:44:13 2009 +0000

    now use a map instead of a PArray to hold FABs

Src/C_AMRLib/TagBox.cpp
Src/C_BoundaryLib/FabSet.H

commit 6fbab7b061c355811660e2267dc56575a1c4950e
Author: lijewski <lijewski>
Date:   Tue Nov 10 21:43:44 2009 +0000

    now us a map instead of a PArray to hold FABs

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 43371cc6924d0518ee0308cb385e897e97f6f677
Author: gpau <gpau>
Date:   Tue Nov 10 21:39:32 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/PltFileList.cpp

commit 3ac953cbec8df6eeb5f1b31bc11ce1a066e3e765
Author: gpau <gpau>
Date:   Tue Nov 10 21:10:53 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/GNUmakefile
Tools/C_util/Statistics/PltFileList.cpp

commit 2b343d9de01d41cdceb419b08695af7d1ff76446
Author: gpau <gpau>
Date:   Tue Nov 10 20:42:17 2009 +0000

    updated with some GSLIB stuff

Tools/C_util/Statistics/ComputeAmrDataStat.H
Tools/C_util/Statistics/ComputeAmrDataStat.cpp
Tools/C_util/Statistics/GNUmakefile
Tools/C_util/Statistics/PltFileStat.cpp

commit 71d8c1ea67468685c77d176160b4b18f1837b362
Author: nazgul <nazgul>
Date:   Tue Nov 10 19:45:40 2009 +0000

    For della, use mpich by default.  openmpi version commented out.
    
    Louis

Tools/C_mk/Make.mpi

commit 78c1a8ade7f95f727fb14651740b00d9e1bdbe39
Author: almgren <almgren>
Date:   Tue Nov 10 02:32:38 2009 +0000

    This version should now work with della.

Tools/C_mk/Make.mpi

commit e79eebad76ec63a0691f675c8327057e0a6e3bd8
Author: lijewski <lijewski>
Date:   Fri Nov 6 22:51:47 2009 +0000

    added some if clauses to OpenMP directives

Src/LinearSolvers/C_NodalMG/hg_proj3d.f

commit 1c0abed8b4a342aa5c149bc8d6177cc631861213
Author: lijewski <lijewski>
Date:   Fri Nov 6 22:39:49 2009 +0000

    added some if clauses to OpenMP directives

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit 2b501040ca56a93c697a076cd1298bb75329e873
Author: lijewski <lijewski>
Date:   Fri Nov 6 22:03:02 2009 +0000

    added some if clauses to OpenMP directives

Src/LinearSolvers/C_NodalMG/hg_avg3d.f

commit 186bfc89d3d4fd2452c2cb1b937a0bd00f2a3567
Author: lijewski <lijewski>
Date:   Fri Nov 6 21:55:50 2009 +0000

    added some if clauses to OpenMP directives

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit 8e4d07af34a52cf92c68c477dfd95d27e26e418c
Author: lijewski <lijewski>
Date:   Fri Nov 6 21:00:18 2009 +0000

    more OpenMP stuff

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/CG_3D.F

commit 457bc3657c4478489f71ed594b5da6d5ef4b53d3
Author: lijewski <lijewski>
Date:   Fri Nov 6 20:34:20 2009 +0000

    wrapped pragma omp with BL_USE_OMP to shut up warnings

Src/C_AMRLib/FluxRegister.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit d052fc119e39dffaad97e0ef8ce521e42bca061d
Author: lijewski <lijewski>
Date:   Fri Nov 6 20:06:43 2009 +0000

    replaced some usages of MFIter::fabbox()

Src/C_AMRLib/FluxRegister.cpp

commit c604300e6db34c7234c13a2d6eb6e0ca15a2ef5a
Author: lijewski <lijewski>
Date:   Fri Nov 6 18:33:23 2009 +0000

    some cleanup

Src/C_BaseLib/FabArray.cpp

commit 94957e65ee280ced403e03867ba68ba2984da310
Author: lijewski <lijewski>
Date:   Fri Nov 6 16:44:43 2009 +0000

    g++ 4.4.1 thinks strrchr() returns const char*

Src/C_BaseLib/VisMF.cpp

commit 40e39786ee048413df7de0d58a5ec0914c9675ad
Author: lijewski <lijewski>
Date:   Thu Nov 5 23:41:37 2009 +0000

    more OpenMP mumbo-jumbo

Src/LinearSolvers/C_CellMG/LP_3D.F

commit 1f3eea5235342e40d350c9b61ab5975c6d4de943
Author: lijewski <lijewski>
Date:   Thu Nov 5 23:34:18 2009 +0000

    more OpenMP mumbo-jumbo

Src/LinearSolvers/C_CellMG/LO_3D.F

commit 797b2d67656e2e1a6632d2cb0169f19f7c603f13
Author: lijewski <lijewski>
Date:   Thu Nov 5 23:23:24 2009 +0000

    more OpenMP mumbo-jumbo

Src/LinearSolvers/C_CellMG/ABec_3D.F

commit 68ed80f60d7eabbf1e809cfaadc930b0f7954dad
Author: almgren <almgren>
Date:   Thu Nov 5 23:07:06 2009 +0000

    Ann's changes in gridding parameters (blocking_factor, max_grid_size) as
    detailed in an email to CCSE.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit d174236ad755d2d371ad848caabca71385b28923
Author: lijewski <lijewski>
Date:   Thu Nov 5 22:45:37 2009 +0000

    OpenMP'd

Src/C_BaseLib/COORDSYS_3D.F

commit 3a1ae54f5957a26bc5dd629de0bb7f7867b6dbfa
Author: lijewski <lijewski>
Date:   Thu Nov 5 22:33:23 2009 +0000

    OpenMPing FASTCOPY() is a lose

Src/C_BaseLib/SPECIALIZE_3D.F

commit 579bf293c9077ed19af24956c4d3a1744d89bc41
Author: lijewski <lijewski>
Date:   Thu Nov 5 21:30:53 2009 +0000

    more OpenMPing

Src/C_BaseLib/SPECIALIZE_3D.F

commit d0896a0ebf0c1e88d6164f424b8219a894255312
Author: lijewski <lijewski>
Date:   Thu Nov 5 07:50:40 2009 +0000

    commented out one pragma omp that kills PathScale

Src/C_AMRLib/FluxRegister.cpp

commit dda7ea5cebd90b3b0ae5474528acc3b95eb2084a
Author: almgren <almgren>
Date:   Thu Nov 5 04:01:13 2009 +0000

    Modify the test on max_grid_size vs blocking_factor -- we now only
    require that max_grid_size >= blocking_factor, not .
      *not* that max_grid_size >= blocking_factor*ref_ratio

Src/C_AMRLib/Amr.cpp

commit 5d4dbd8800a8a4716f8a2a9dc3d6005b8ee0151d
Author: lijewski <lijewski>
Date:   Wed Nov 4 21:35:24 2009 +0000

    OpenMP the .cpp not the .F when possible

Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/FluxRegister.cpp

commit 3401f654c984dd954cc0a3df69e645b16e10204c
Author: lijewski <lijewski>
Date:   Wed Nov 4 18:50:35 2009 +0000

    now thread across FABS in applyBC()

Src/LinearSolvers/C_TensorMG/DV_3D4.F
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 49f9fc278357261c9298edf44be668b821ee129b
Author: lijewski <lijewski>
Date:   Wed Nov 4 18:14:56 2009 +0000

    now do all faces of given FAB at a time in applyBC()

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit c5953b60934f3f66f6a0ce023edbdc06ecb27ea3
Author: lijewski <lijewski>
Date:   Wed Nov 4 17:11:39 2009 +0000

    now thread applyBC() across FABs

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit df2ff0ce0b479f07b6dc07853b4951739104cfda
Author: lijewski <lijewski>
Date:   Wed Nov 4 16:55:37 2009 +0000

    OpenMP stuff

Src/LinearSolvers/C_CellMG/MG_3D.F
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit f10ede1435960e0112ca6eab585434bf5df33705
Author: lijewski <lijewski>
Date:   Wed Nov 4 02:30:19 2009 +0000

    modified MFITer internals for some OpenMP work to come

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit b5e371533c1ff3a78303a77afe3c3055d949f4a0
Author: lijewski <lijewski>
Date:   Wed Nov 4 02:28:22 2009 +0000

    OpenMP'd solves across FABs and removed advance() and update()

Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 0fa1638f7dc936671528a8920e9b151136471def
Author: lijewski <lijewski>
Date:   Tue Nov 3 21:37:29 2009 +0000

    more OpenMP stuff

Tools/C_mk/Make.defs

commit 84ca88bc14e6881ce17455cf4cafc33532efbe9d
Author: lijewski <lijewski>
Date:   Tue Nov 3 16:35:22 2009 +0000

    OpenMp LinOp::applyBC() over face calls to FORT_APPLYBC()

Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 9e154248980905217fb963cc6f1a5a9d899c775e
Author: nazgul <nazgul>
Date:   Fri Oct 30 23:51:19 2009 +0000

    Using what appears to be the preferred mpi on della.
    
    Louis

Tools/C_mk/Make.mpi

commit 0f3f3ae9302c841bc9db28de7c4ac1334d16b61d
Author: almgren <almgren>
Date:   Wed Oct 28 20:18:31 2009 +0000

    Minor tweaks for 1d.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit a2d8b5477603bea055eda646d37949d6f920b118
Author: mzingale <mzingale>
Date:   Wed Oct 28 00:37:14 2009 +0000

    add support for different compilers for CASTRO

Tools/C_util/regtests/Castro-tests.ini
Tools/C_util/regtests/test.py

commit f59da16728d8c5f1791ec08af81a6f00cc160839
Author: lijewski <lijewski>
Date:   Tue Oct 27 21:05:48 2009 +0000

    more OpenMPing

Src/LinearSolvers/C_NodalMG/hg_proj3d.f

commit dab320250cefc633de1bf5656a6c3cdfcbdb145e
Author: lijewski <lijewski>
Date:   Tue Oct 27 20:45:56 2009 +0000

    some cleanup

Src/LinearSolvers/C_NodalMG/hg_multi2d.f
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.f
Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f

commit 075e2b0ee89977f271120aeeeffb1f3753652303
Author: lijewski <lijewski>
Date:   Tue Oct 27 20:06:01 2009 +0000

    more OpenMPing

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit 1c60f18646eba92cdb53cd186ba67132d33af52a
Author: lijewski <lijewski>
Date:   Tue Oct 27 19:37:59 2009 +0000

    more OpenMPing

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit aab15187414404cf5ab15f88888ae17ea30ef206
Author: lijewski <lijewski>
Date:   Tue Oct 27 19:09:12 2009 +0000

    more OpenMPing

Src/C_AMRLib/FLUXREG_3D.F

commit 34c856816e2f1ba7bf4b77d2edfee5a540570b64
Author: lijewski <lijewski>
Date:   Tue Oct 27 04:55:45 2009 +0000

    some OpenMP

Src/LinearSolvers/C_NodalMG/hg_avg3d.f

commit 9a5fccd6354ed7633ec775f7a9d30cbfa365d240
Author: lijewski <lijewski>
Date:   Tue Oct 27 04:43:04 2009 +0000

    some OpenMPing

Src/C_AMRLib/FLUXREG_3D.F

commit 41aa6723777aa74e39284da1448cbfc6739ccb7d
Author: lijewski <lijewski>
Date:   Mon Oct 26 21:58:40 2009 +0000

    print out size as well as initialize() time

Src/C_AMRLib/AuxBoundaryData.cpp

commit 7661605829bca2af733d2f3939fd5e22d0348095
Author: lijewski <lijewski>
Date:   Mon Oct 26 20:26:53 2009 +0000

    add some PathScale options for when BL_NOFAST=TRUE

Tools/C_mk/Make.Linux

commit bbdaa44ecd0135908f23a450e20e479bd324f04c
Author: lijewski <lijewski>
Date:   Fri Oct 23 20:12:29 2009 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit 16cd2e325016ab14c21eb1c32fff859aa6107f97
Author: lijewski <lijewski>
Date:   Fri Oct 23 19:57:50 2009 +0000

    OpenMP mods for Intel 11

Tools/C_mk/Make.defs

commit 8f8e2678a49d0e32f13c8885f4dda65207bb2ef3
Author: lijewski <lijewski>
Date:   Thu Oct 22 21:00:30 2009 +0000

    removed OpenMP directives from FORT_NBINTERP() - buggy

Src/C_AMRLib/INTERP_3D.F

commit 065d8111437e333b3cb73ffb36e4dca8d7a1c113
Author: vince <vince>
Date:   Thu Oct 22 19:24:32 2009 +0000

    added the new mothra.

Tools/C_mk/Make.mpi

commit 0e08a5277339f1171f5fc8a8bfb3490ab93e08ec
Author: lijewski <lijewski>
Date:   Tue Oct 20 22:47:35 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/MCLO_3D.F

commit 911a6159c2925f1c888f0704cf908540036427d2
Author: lijewski <lijewski>
Date:   Tue Oct 20 02:37:46 2009 +0000

    rearranged OpenMP directives for Intel 11.1

Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F

commit 4fef3d1783abdfb0968f078c9c6d0c9cc13dce16
Author: lijewski <lijewski>
Date:   Fri Oct 16 18:17:21 2009 +0000

    OpenMP mods to quiet PathScale

Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F

commit 18c0203086af329465b2da2c363bb7b2e12283e9
Author: lijewski <lijewski>
Date:   Fri Oct 16 17:04:09 2009 +0000

    OpenMP tweaks to quiet PathScale

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit 2d412fd700f75dc79d85813687ccf58dbfd07475
Author: almgren <almgren>
Date:   Thu Oct 15 21:57:39 2009 +0000

    Remove print statement.

Src/LinearSolvers/F_MG/mg_restriction.f90

commit 228facb311e995a46df665cdde07ef6942b84863
Author: almgren <almgren>
Date:   Thu Oct 15 21:57:21 2009 +0000

    Fix 1d version.

Src/LinearSolvers/F_MG/mg_restriction.f90

commit 46e5242f6c0058666bee240b8ec0ec5bdcb1cff3
Author: almgren <almgren>
Date:   Thu Oct 15 21:57:10 2009 +0000

    Add impose_neumann_bcs_1d.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 6af8a7eb948f63ef86823449b6b74c929bac200a
Author: lijewski <lijewski>
Date:   Mon Oct 12 21:40:17 2009 +0000

    *** empty log message ***

Src/C_BaseLib/BaseFab.H

commit 56dc460619ef85b55b3631a6ec207e060e94aa2d
Author: lijewski <lijewski>
Date:   Mon Oct 12 21:37:41 2009 +0000

    New versions of fortran-specialized functions that can be OpenMP'd in 3D.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/SPECIALIZE_1D.F
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H

commit 98622516503f3bbcc27bb466eaa6ef04ecc0240a
Author: mzingale <mzingale>
Date:   Sat Oct 10 20:54:02 2009 +0000

    add Intel 11, and support for atlas

Tools/F_mk/GMakedefs.mak

commit 7a0b8fac78461a6b206930f32b68a02487a1854d
Author: gpau <gpau>
Date:   Thu Oct 8 22:50:52 2009 +0000

    removed a bug

Tools/C_util/Statistics/PltFileXAve.cpp

commit 30b4f0bbe3dfe8187b9b72690d4a954173de09c7
Author: lijewski <lijewski>
Date:   Thu Oct 8 22:10:56 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit b74ff527da1e19daa4fd9d1aebc4e13ee8ce897f
Author: lijewski <lijewski>
Date:   Thu Oct 8 21:50:46 2009 +0000

    more OpenMP

Src/LinearSolvers/C_NodalMG/hg_proj3d.f

commit 163c226b7ad64c3179b687a906f0617a2a049c33
Author: lijewski <lijewski>
Date:   Thu Oct 8 21:38:47 2009 +0000

    more OpenMP stuff

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit 7afa5d3efcbf4fa26a31e4e8a903ddfd78a5b175
Author: lijewski <lijewski>
Date:   Thu Oct 8 21:05:19 2009 +0000

    redo of OpenMP stuff

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit 7d2876cf51531836b212fb55f6c4195f028d35bc
Author: lijewski <lijewski>
Date:   Thu Oct 8 20:35:29 2009 +0000

    OpenMP

Src/LinearSolvers/C_NodalMG/amr_real3d.f
Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit d602ecfbc352ff7bbeec6ea0482288a417438554
Author: lijewski <lijewski>
Date:   Thu Oct 8 20:29:52 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit d1d6eae0e3b65ce5d371db0dc9347322d9beb1b4
Author: lijewski <lijewski>
Date:   Thu Oct 8 17:58:43 2009 +0000

    mods to work with PGI OpenMP

Src/LinearSolvers/C_TensorMG/DV_3D4.F

commit d3fbff33ab813920f9f4ed072dd6596487b95ea4
Author: lijewski <lijewski>
Date:   Thu Oct 8 17:41:02 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/DV_3D1.F

commit 69017ef9246f277e2a8ef5ebb80513a467b69293
Author: lijewski <lijewski>
Date:   Thu Oct 8 17:40:47 2009 +0000

    more OpenMP

Src/LinearSolvers/C_TensorMG/DV_3D2.F

commit e1de999d814187b9bbaefca8ec1be35afd686524
Author: lijewski <lijewski>
Date:   Wed Oct 7 22:14:01 2009 +0000

    more OpenMP directives

Src/LinearSolvers/C_TensorMG/DV_3D1.F

commit adfb6e008ae7bc6a8aa6389fc978d9b87ee99f9d
Author: gpau <gpau>
Date:   Wed Oct 7 21:24:49 2009 +0000

    updated file reflect variable phi

Tools/C_util/Statistics/GNUmakefile
Tools/C_util/Statistics/PltFileXAve.H
Tools/C_util/Statistics/PltFileXAve.cpp

commit 73cccdc37e4a689fee98d01ad525b3eed7f3135f
Author: lijewski <lijewski>
Date:   Wed Oct 7 21:19:17 2009 +0000

    more OpenMP junk

Src/LinearSolvers/C_TensorMG/DV_3D4.F

commit 5154ba21be0c1510cd777f11e13483920464e8b9
Author: lijewski <lijewski>
Date:   Wed Oct 7 21:00:43 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_TensorMG/DV_3D4.F

commit f081c31654b0b4d2cf32ac023ecabac4f690c000
Author: lijewski <lijewski>
Date:   Wed Oct 7 20:24:37 2009 +0000

    more OpenMP directives

Src/LinearSolvers/C_TensorMG/DV_3D3.F

commit ea6bd912f7b9d26680ba79dda8909559043f4f8f
Author: lijewski <lijewski>
Date:   Wed Oct 7 18:06:04 2009 +0000

    added some d0's on constants

Src/LinearSolvers/C_TensorMG/MCLO_3D.F

commit 82980c56b811c2dacbca649fb30d3610ca162cbf
Author: lijewski <lijewski>
Date:   Wed Oct 7 17:58:54 2009 +0000

    added some d0's on constants

Src/LinearSolvers/C_TensorMG/DV_3D4.F

commit a54a1233dbdd021e110cbec48cb05cb624eb8ab1
Author: lijewski <lijewski>
Date:   Wed Oct 7 17:58:29 2009 +0000

    little simplification

Src/LinearSolvers/C_CellMG/LO_3D.F

commit c3afbd1cdf9f287fb6b2318a39d055da68df5a6c
Author: lijewski <lijewski>
Date:   Wed Oct 7 17:31:01 2009 +0000

    workaround for PGI OpenMP bug

Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F

commit fb01e4673a3e8275aa8e6ec5cf69a5186e465ef7
Author: lijewski <lijewski>
Date:   Wed Oct 7 17:30:20 2009 +0000

    bug fix -- misspelled couple private() variables for OpenMP

Src/LinearSolvers/C_TensorMG/DV_3D3.F

commit 204cd91eb60fce5b57654d80582152a98433b1bf
Author: gpau <gpau>
Date:   Wed Oct 7 17:03:51 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/PltFileXAve.H
Tools/C_util/Statistics/PltFileXAve.cpp

commit e6b48ef0e4dcd28e0b949ed9182cb3f25dedae4b
Author: gpau <gpau>
Date:   Wed Oct 7 16:35:31 2009 +0000

    added some functionalities

Tools/C_util/Statistics/ComputeAmrDataStat.H
Tools/C_util/Statistics/ComputeAmrDataStat.cpp
Tools/C_util/Statistics/GNUmakefile
Tools/C_util/Statistics/PltFileStat.cpp
Tools/C_util/Statistics/PltFileXAve.H
Tools/C_util/Statistics/PltFileXAve.cpp

commit c526b79ebb13794d92e56822a90264158e78674a
Author: lijewski <lijewski>
Date:   Tue Oct 6 21:40:30 2009 +0000

    removed FORT_SCALADDTO() -- doesn't appear to be used

Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/FLUXREG_F.H

commit 14fe6165b30987e146c2c7232ef7439637611633
Author: lijewski <lijewski>
Date:   Tue Oct 6 21:37:14 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_TensorMG/DV_3D3.F

commit f848933bd030b82fc85bea886b513ed6fbff4716
Author: lijewski <lijewski>
Date:   Tue Oct 6 20:30:16 2009 +0000

    added FORT_FASTONENORM() and FORT_FASTZERONORM()

Src/C_BaseLib/SPECIALIZE_1D.F

commit 30a0ab6509d2aa0efbb12a83c30179c44a52c493
Author: vince <vince>
Date:   Tue Oct 6 20:00:31 2009 +0000

    addend angilas support for mpi.

Tools/C_mk/Make.mpi

commit cab02bc5b42604b077a9b7de41010dd911a9a3f2
Author: lijewski <lijewski>
Date:   Tue Oct 6 16:02:18 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_TensorMG/DV_3D2.F

commit 856313cdb7944a25e459322bc4b2ef0453672e56
Author: lijewski <lijewski>
Date:   Mon Oct 5 22:49:21 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_TensorMG/DV_3D1.F

commit 3de92ff738ace578516063104bcb4b47a389e4b2
Author: almgren <almgren>
Date:   Mon Oct 5 21:51:07 2009 +0000

    Added 1D versions of all the routines.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit f93a35553e888c7bbecd959dab91740369a240d5
Author: lijewski <lijewski>
Date:   Mon Oct 5 21:47:50 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F

commit f523c10bb71eaad8bbfec094b43a231a268abd02
Author: lijewski <lijewski>
Date:   Mon Oct 5 21:13:20 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_TensorMG/MCLO_3D.F

commit 8f843b51fe373c502e16fa35ad32a5de2c8deb33
Author: lijewski <lijewski>
Date:   Mon Oct 5 20:42:30 2009 +0000

    more OpenMP stuff

Src/LinearSolvers/C_NodalMG/hg_multi3d.f
Src/LinearSolvers/C_NodalMG/hg_proj3d.f

commit 23d74f51420c0b7ed2457df440ac60d67799d787
Author: lijewski <lijewski>
Date:   Mon Oct 5 16:41:30 2009 +0000

    OpenMP'd hgints() hgrlxu() & hgresu()

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit 89355c93c455c9ea971a1e1688544e4abaf23e6d
Author: gpau <gpau>
Date:   Fri Oct 2 00:36:14 2009 +0000

    added pdf function.

Tools/C_util/Statistics/ComputeAmrDataStat.H
Tools/C_util/Statistics/ComputeAmrDataStat.cpp
Tools/C_util/Statistics/GNUmakefile
Tools/C_util/Statistics/PltFileStat.cpp
Tools/C_util/Statistics/PltFileXAve.cpp

commit 4af32fa290957e1c7f20d5e9bdcf0dcbf5047efd
Author: lijewski <lijewski>
Date:   Thu Oct 1 21:20:40 2009 +0000

    OpenMP'd node_bilinear_interp

Src/C_AMRLib/INTERP_3D.F

commit a2a1ab6f0d0a0656c0423170731f8c3916bef379
Author: lijewski <lijewski>
Date:   Thu Oct 1 20:51:08 2009 +0000

    *** empty log message ***

Src/C_AMRLib/INTERP_3D.F

commit 9b1df818863c64af8499354c74ccb1a5b81f64d9
Author: lijewski <lijewski>
Date:   Thu Oct 1 19:30:58 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/MG_3D.F

commit 8cda9b7b56d1d8067e4c927550994f123aab2da3
Author: lijewski <lijewski>
Date:   Thu Oct 1 18:18:10 2009 +0000

    Added specialized version of 0 & 1 norms for Real in Fortran

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H

commit 6be3eccc5ae9af20c6b218a67a69de37f691d3c8
Author: lijewski <lijewski>
Date:   Tue Sep 29 20:42:36 2009 +0000

    removed WorkQueue stuff

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp

commit de6ef6dbb5f20e5d624841601e51e2d3ec5727da
Author: lijewski <lijewski>
Date:   Mon Sep 28 21:29:25 2009 +0000

    removed all BL_THREAD junk

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit e5a5d0134f994cb435a46272d7928712797b0bed
Author: lijewski <lijewski>
Date:   Mon Sep 28 21:13:32 2009 +0000

    SELECT instead of IF

Src/LinearSolvers/C_CellMG/LO_3D.F

commit 18b873055090fb42fa6e89e2bcbb2ffa7b52f066
Author: lijewski <lijewski>
Date:   Mon Sep 28 21:13:06 2009 +0000

    removed FORT_CGPRECND()

Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_F.H
Src/LinearSolvers/C_CellMG/LP_2D.F
Src/LinearSolvers/C_CellMG/LP_F.H

commit 6e680886fca4e744f54a528a9cb4f6e6463ef72d
Author: lijewski <lijewski>
Date:   Mon Sep 28 20:29:59 2009 +0000

    use SELECT instead of IF

Src/LinearSolvers/C_CellMG/LO_3D.F

commit 800dfc71c75570ec06618ad13892acbf39e08652
Author: lijewski <lijewski>
Date:   Mon Sep 28 20:14:48 2009 +0000

    some simplification of APPLYBC()

Src/LinearSolvers/C_CellMG/LO_3D.F

commit fe1895451dde40a1010142c1a444e3ca272cedea
Author: lijewski <lijewski>
Date:   Mon Sep 28 19:23:01 2009 +0000

    more OpenMP tweeking

Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/LP_3D.F

commit 92cab89a0c40fc11cc155ad0309f9ddcbe7eb76f
Author: lijewski <lijewski>
Date:   Mon Sep 28 19:13:53 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_CellMG/ABec_3D.F

commit 8304e9cf2f1761a275457ae48493d02edb086418
Author: lijewski <lijewski>
Date:   Mon Sep 28 18:09:11 2009 +0000

    yet more OpenMP tweeking

Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F

commit 48a819b69d5aded6d0a685804bb7ef44d2207999
Author: lijewski <lijewski>
Date:   Mon Sep 28 17:57:54 2009 +0000

    more OpenMP tweeking

Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F

commit ee17182b5900120aad0077833b9687bc982da715
Author: lijewski <lijewski>
Date:   Mon Sep 28 17:51:35 2009 +0000

    OPenMP'd

Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F
Src/LinearSolvers/C_CellMG/MG_3D.F

commit 2c58407b3767c3c3700e6e618b31082458e44ca7
Author: nazgul <nazgul>
Date:   Mon Sep 28 17:06:21 2009 +0000

    Updated compiler options for Atlas.  -mp is deprecated.
    Using -fp-model fast=2 instead.
    
    Louis

Tools/C_mk/Make.Linux

commit 233d5536f3a6329ff3836febd7489ec4373393c6
Author: lijewski <lijewski>
Date:   Mon Sep 28 17:05:50 2009 +0000

    removed OpenMP directives -- slowed down test case

Src/LinearSolvers/C_CellMG/CG_3D.F

commit d3f560a49ba9ea9ac33caeb0bdabad9afa5e3fe7
Author: lijewski <lijewski>
Date:   Mon Sep 28 16:46:16 2009 +0000

    added some OpenMP macros

Src/LinearSolvers/C_CellMG/CG_3D.F
Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/LP_3D.F

commit e2eec3918bb0ba6a06186d3a4c9036800cba2822
Author: lijewski <lijewski>
Date:   Fri Sep 25 23:18:53 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 0dbe06b78006d93746a9376321726387937d3236
Author: lijewski <lijewski>
Date:   Fri Sep 25 21:24:22 2009 +0000

    disable -Ofast for PathScale C++ compiler - causes bug in mglib on franklin

Tools/C_mk/Make.Linux

commit e55cc43b6437f4cd0d773b6b0948ac942e5413e1
Author: lijewski <lijewski>
Date:   Fri Sep 25 18:04:31 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/inputs.3d
Tests/LinearSolvers/C_CellMG/inputs.3d

commit 78ab25819a885c18ce281ded321072e16207b423
Author: lijewski <lijewski>
Date:   Fri Sep 25 03:50:56 2009 +0000

    rearranged some OpenMP stuff

Src/C_AMRLib/INTERP_3D.F

commit e4a3d304e1d6686bf01e22ff39c44841115a4ffc
Author: lijewski <lijewski>
Date:   Thu Sep 24 21:48:47 2009 +0000

    added some OpenMP directives linccinterp

Src/C_AMRLib/INTERP_3D.F

commit ce195cc6e41a8900a7a51b1f6d529b6266a74065
Author: lijewski <lijewski>
Date:   Wed Sep 23 21:59:07 2009 +0000

    some OMP stuff

Tools/C_mk/Make.Linux

commit 3e4c3aff2520d88213f0d3e7f42a2bbd0c0aa5d9
Author: lijewski <lijewski>
Date:   Fri Sep 18 22:10:33 2009 +0000

    some OpenMP stuff

Tools/C_mk/Make.defs

commit 8b9c3b09fb9cbe49c6a45beabd9cf61e79d5383d
Author: ajnonaka <ajnonaka>
Date:   Fri Sep 11 23:26:57 2009 +0000

    OMP=t option for PGI on franklin

Tools/F_mk/GMakedefs.mak

commit 0c9e3e2092be5b6c5450100c9172123a498f9c6e
Author: vince <vince>
Date:   Fri Sep 11 18:20:09 2009 +0000

    more 11.1.

Tools/C_mk/Make.defs

commit a845ca1e1403982321ba0cfd70a2061994deeb77
Author: vince <vince>
Date:   Fri Sep 11 18:13:19 2009 +0000

    intel 11.1.

Tools/C_mk/Make.defs

commit 3146307098c040dd3d40c932df5e98f26f37c3aa
Author: ajnonaka <ajnonaka>
Date:   Thu Sep 10 22:20:02 2009 +0000

    on franklin with pathscale, now you can turn on openmp with OMP=t in your make line

Tools/F_mk/GMakedefs.mak

commit 2f22cc503b5806f30bf8f29a7099c82c30304a12
Author: lijewski <lijewski>
Date:   Wed Sep 2 17:50:59 2009 +0000

    now pass problo and probhi optionally to ml_multifab_write

Src/F_BaseLib/fabio.f90

commit 692cce43310274e14e28e732fa1fdce504513b84
Author: mzingale <mzingale>
Date:   Wed Sep 2 16:27:58 2009 +0000

    no longer abort if a plotfile variable is not found in plotfile_var_index,
    instead just return -1.  The calling program should test on the output.
    This allows you to test for the presence of variables.

Src/F_BaseLib/plotfile.f90

commit ac85f01322d3b255d3d4762cc7cdac7c796d4156
Author: lijewski <lijewski>
Date:   Fri Aug 28 16:55:31 2009 +0000

    default refine_grid_layout to false

Src/C_AMRLib/Amr.cpp

commit d2d3379dd9b5aff3faad56b263ef464120054e6d
Author: ajnonaka <ajnonaka>
Date:   Wed Aug 26 22:24:39 2009 +0000

    got rid of the nx,ny,nz stuff by passing in hi(:) instead

Src/F_BaseLib/tag_boxes.f90

commit afeeeae7396be0ff6d9d4928c2ad596ad14e354b
Author: mzingale <mzingale>
Date:   Sun Aug 23 15:42:59 2009 +0000

    add a routine that calls the C getcwd function to return the output
    directory -- for logging purposes.

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_system.f90
Src/F_BaseLib/system_util_c.c

commit 62a42f9f7ef63102051de5501e029c7ffc761bc8
Author: almgren <almgren>
Date:   Thu Aug 20 20:52:56 2009 +0000

    oops -- left in print statement by accident.

Src/LinearSolvers/F_MG/mg.f90

commit 382d692ba0de1b809948fcc2f6938ca1910fb32e
Author: almgren <almgren>
Date:   Thu Aug 20 20:49:35 2009 +0000

    Redefine "lcross" and call nodal_smoother_1d instead of nodal_line_solve_1d.

Src/LinearSolvers/F_MG/mg.f90

commit 7e07dd5e8ef38df671ba753b25c6d9580772c7d7
Author: almgren <almgren>
Date:   Thu Aug 20 20:48:56 2009 +0000

    1) Add nodal_line_solve_1d.
    2) Modify nodal_smoother_1d to be red-black.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 410aadd0346e47d6fbfc5d9b6c5f42b211ef38ba
Author: almgren <almgren>
Date:   Thu Aug 20 20:48:18 2009 +0000

    Add call to fine_edge_resid_1d instead of aborting.

Src/LinearSolvers/F_MG/ml_util.f90

commit 7c58a40dfe122b7ed606a3eeb2cdf61e4927677e
Author: almgren <almgren>
Date:   Thu Aug 20 20:47:53 2009 +0000

    Fix fine_edge_resid_1d.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit df33e3f00bbbe8ecfd666d5b5b0946dac7ec6c6a
Author: almgren <almgren>
Date:   Tue Aug 18 02:05:31 2009 +0000

    Add 1d version of subtract_divu_from_rhs.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 17cc21e18b3a81b42c271d0756448d1153ce9ff4
Author: almgren <almgren>
Date:   Fri Aug 14 22:28:31 2009 +0000

    Fix indexing in 1d.

Src/LinearSolvers/F_MG/stencil.f90

commit 50a9a8adfcbb31f1549c5840e9765e82c0d1de26
Author: almgren <almgren>
Date:   Fri Aug 14 22:21:48 2009 +0000

    Fix typo.

Src/LinearSolvers/F_MG/stencil.f90

commit 743ceb63f678848868e038223e44dad5b19c417a
Author: almgren <almgren>
Date:   Fri Aug 14 22:21:05 2009 +0000

    Fix stencil_apply_1d.

Src/LinearSolvers/F_MG/stencil.f90

commit 5484d0b623a555fa658713f751cb114ec61f2ba0
Author: almgren <almgren>
Date:   Fri Aug 14 22:20:18 2009 +0000

    1) Fix bug in stencil_1d_apply
    2) Modify stencil_1d_apply and stencil_2d_apply to take lo and hi as
    inputs so we can more easily debug with the actual indices.

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/stencil.f90

commit b2d7afcb713565822499ee4463cd3f64b09959b8
Author: almgren <almgren>
Date:   Fri Aug 14 22:09:47 2009 +0000

    Added 1d capability.

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/interp.f90

commit ab657f19139e0fb8f607a9d8a068e09548ba3f63
Author: almgren <almgren>
Date:   Wed Aug 12 22:38:28 2009 +0000

    Use lo(:),hi(:) instead of nx,ny,nz for easier debugging.

Src/LinearSolvers/F_MG/stencil.f90

commit 43fbacb7d1feb6653522979e48aa2fd77d629ed5
Author: almgren <almgren>
Date:   Tue Aug 11 20:28:28 2009 +0000

    Explicitly add climits.

Src/C_AMRLib/TagBox.cpp

commit 7b4bdd9709fefe549a4ba7945f0566d110cdc5cc
Author: almgren <almgren>
Date:   Tue Aug 11 17:11:19 2009 +0000

    Fixed a bug -- we didn't use to call crse_fine_residual from applyop
    so the coarse grid cell next to a fine grid had the wrong residual.

Src/LinearSolvers/F_MG/ml_cc.f90

commit aef96086fc2d7e2f92b6591c89941f140f0caa2e
Author: ajnonaka <ajnonaka>
Date:   Fri Aug 7 17:16:29 2009 +0000

    added .smp to executable if smp is true

Tools/F_mk/GMakedefs.mak

commit e135151ab74d0dbf4c00104267ac4629b39c6ef4
Author: mzingale <mzingale>
Date:   Fri Aug 7 15:15:04 2009 +0000

    add some error checking to the copying of inputs, probin, and the
    auxfiles

Tools/C_util/regtests/test.py

commit b2936eb471362c05ae43f01281a69cd3766ad03c
Author: almgren <almgren>
Date:   Thu Aug 6 21:51:36 2009 +0000

    Fixed the Minion "full" stencil which is used for variable density.

Src/LinearSolvers/F_MG/stencil.f90

commit 6ce45c515b0921b32ef041cdf6a6f5f7bdebe764
Author: mzingale <mzingale>
Date:   Tue Aug 4 19:17:19 2009 +0000

    update to reflect new directory locatios

Tools/C_util/regtests/Castro-tests.ini

commit 5e3494fc35ecdeacc6781a805fefe95215c91290
Author: mzingale <mzingale>
Date:   Tue Aug 4 18:58:49 2009 +0000

    on second thought, update -d for CASTRO is a bad idea

Tools/C_util/regtests/test.py

commit 63adde2b360c7039c462262c9d8bc20e0d4bbf40
Author: mzingale <mzingale>
Date:   Sun Aug 2 14:37:03 2009 +0000

    do a CVS update -d to capture new directories.
    
    only take the file name (not relative path) for the auxFiles when copying
    to the web directory

Tools/C_util/regtests/test.py

commit 53096042efa0fb8c34e5f5306dbbe5d87ebd6eff
Author: mzingale <mzingale>
Date:   Sun Aug 2 00:59:32 2009 +0000

    update to reflect new directory structures and no more grid files

Tools/C_util/regtests/Maestro-tests.ini

commit c01a45803842890156dff1646925229ee0c74e0c
Author: mzingale <mzingale>
Date:   Thu Jul 30 19:44:28 2009 +0000

    add a check that if there is a floating point constant that it be
    a double precision constant.  At the moment, it catches a bunch, but
    has too many false positives

Tools/F_scripts/fcheck.py

commit dafbbb5faad0c335e3ac53f08b5c66891b361c7b
Author: mzingale <mzingale>
Date:   Thu Jul 30 17:19:13 2009 +0000

    the start of a simple script to check that quantities are allocated
    correctly in our Fortran code.  At the moment, it looks for all the
    'real' variables that aren't 'dp_t'.  Next up is checking all the constants.

Tools/F_scripts/fcheck.py

commit a6dfeb036d5a83c2fe637c1fd92832d2813577e3
Author: ajnonaka <ajnonaka>
Date:   Thu Jul 30 15:58:14 2009 +0000

    on franklin, hpctoolkit will compile in if you add "USE_HPCTOOLKIT=t" when you make

Tools/F_mk/GMakedefs.mak

commit b3c0a0b446985e6f9d690a56ad3a77bfec6b195c
Author: ajnonaka <ajnonaka>
Date:   Thu Jul 30 15:40:58 2009 +0000

    mpi stuff for surveyor at argonne

Tools/F_mk/GMakeMPI.mak

commit de806a853632d6fb456674b93cdf78851e5e1292
Author: almgren <almgren>
Date:   Mon Jul 27 21:50:16 2009 +0000

    Remove unused variable.

Src/LinearSolvers/F_MG/ml_cc.f90

commit c111ed4badf4e9bd74eb2f9c7858076e4bb6f779
Author: almgren <almgren>
Date:   Mon Jul 27 21:48:37 2009 +0000

    Remove extra print statement.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 1dbb1becf35729a1a328862012689fcad614a10f
Author: almgren <almgren>
Date:   Mon Jul 27 20:55:17 2009 +0000

    Shouldn't have had print statement and stop in there.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 733c9df5ab2119bbf1f3201155656092698a982f
Author: almgren <almgren>
Date:   Mon Jul 27 20:28:31 2009 +0000

    Dont need to restrict rh(n) onto rh(n-1) in applyop since rh is
    identically zero.

Src/LinearSolvers/F_MG/ml_cc.f90

commit a799ef17c94f14045aea67d8edce7d2fb7333a91
Author: lijewski <lijewski>
Date:   Fri Jul 24 19:14:09 2009 +0000

    removed cache junk

Src/C_AMRLib/Amr.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 19b4551134682222d5c68bf90462faef08ec7213
Author: lijewski <lijewski>
Date:   Fri Jul 24 17:46:18 2009 +0000

    default copy cache back to on with max size to 10

Src/C_BaseLib/FabArray.cpp

commit cbe8c29fe1a84bb9a21bd20b7fb6b587d1e96745
Author: lijewski <lijewski>
Date:   Thu Jul 23 22:26:01 2009 +0000

    refine_grid_layout only does grids below new_finest

Src/C_AMRLib/Amr.cpp

commit c424c1e4c55db25952c27d7770c5adaa021b0ec1
Author: mzingale <mzingale>
Date:   Thu Jul 23 16:50:07 2009 +0000

    add some useful debugging flags, commented out

Tools/F_mk/GMakedefs.mak

commit 39d0aaaa342dee7183b2dbb40096dadd75c8e7ed
Author: lijewski <lijewski>
Date:   Tue Jul 21 21:19:21 2009 +0000

    fixed bug in grid_places()

Src/C_AMRLib/Amr.cpp

commit df9a4535b6695bb0511b0025e809d509b18a1ae8
Author: lijewski <lijewski>
Date:   Thu Jul 16 18:01:27 2009 +0000

    break up crse domain using maxSize()

Src/LinearSolvers/C_TensorMG/Test/testVI.cpp
Tests/LinearSolvers/C_TensorMG/testVI.cpp

commit 6eee76e2dd65121cc76bd577ee1d446f5178b67e
Author: lijewski <lijewski>
Date:   Thu Jul 16 17:37:20 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/Test/inputs3D
Src/LinearSolvers/C_TensorMG/Test/testVI.cpp
Tests/LinearSolvers/C_TensorMG/inputs3D
Tests/LinearSolvers/C_TensorMG/testVI.cpp

commit e763480dc18879480108714d8c19e8f4a349f239
Author: lijewski <lijewski>
Date:   Thu Jul 16 16:59:51 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/Test/grids/gr.3_2x3x4
Src/LinearSolvers/C_TensorMG/Test/grids/gr16.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr16x8.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr2D
Src/LinearSolvers/C_TensorMG/Test/grids/gr32.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr32x8.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr64.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr8.dog
Src/LinearSolvers/C_TensorMG/Test/inputs3D
Src/LinearSolvers/C_TensorMG/Test/testVI.cpp
Tests/LinearSolvers/C_TensorMG/grids/gr.3_2x3x4
Tests/LinearSolvers/C_TensorMG/grids/gr16.dog
Tests/LinearSolvers/C_TensorMG/grids/gr16x8.dog
Tests/LinearSolvers/C_TensorMG/grids/gr2D
Tests/LinearSolvers/C_TensorMG/grids/gr32.dog
Tests/LinearSolvers/C_TensorMG/grids/gr32x8.dog
Tests/LinearSolvers/C_TensorMG/grids/gr64.dog
Tests/LinearSolvers/C_TensorMG/grids/gr8.dog
Tests/LinearSolvers/C_TensorMG/inputs3D
Tests/LinearSolvers/C_TensorMG/testVI.cpp

commit 974f1ca7a197bc86502d0cb16e3171c50dd934c5
Author: lijewski <lijewski>
Date:   Thu Jul 16 16:32:44 2009 +0000

    first cut at bringing up-to-date

Src/LinearSolvers/C_TensorMG/Test/GNUmakefile
Src/LinearSolvers/C_TensorMG/Test/Make.package
Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp
Src/LinearSolvers/C_TensorMG/Test/main_F.H
Src/LinearSolvers/C_TensorMG/Test/testVI.cpp
Tests/LinearSolvers/C_TensorMG/GNUmakefile
Tests/LinearSolvers/C_TensorMG/Make.package
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp
Tests/LinearSolvers/C_TensorMG/main_F.H
Tests/LinearSolvers/C_TensorMG/testVI.cpp

commit e998bb1459e14eba409f3a30ab0ec13b5469cb70
Author: lijewski <lijewski>
Date:   Mon Jul 13 20:18:28 2009 +0000

    removed simplify() in initialize()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 9f2b21fa47f009e8cc3b4fe49120e51785f1dd7a
Author: lijewski <lijewski>
Date:   Mon Jul 13 20:17:24 2009 +0000

    removed simplify() in GetBndryCells

Src/C_BaseLib/BoxArray.cpp

commit 2da1b61382fe2cc88e19059bad30aff98e6a1977
Author: lijewski <lijewski>
Date:   Sun Jul 12 00:38:32 2009 +0000

    fpb_cache_max_size now defaults to 10.

Src/C_BaseLib/Geometry.cpp

commit 0691b8449fb83b8976819432edb94957d400982c
Author: lijewski <lijewski>
Date:   Sat Jul 11 03:01:19 2009 +0000

    max_live_tasks now defaults to 50.

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit df8da84c11747be6f7b6151a2029a21f93d2cf61
Author: lijewski <lijewski>
Date:   Sat Jul 11 00:49:21 2009 +0000

    use_copy_cache now defaults to false.

Src/C_BoundaryLib/FabSet.cpp

commit 594b59f2e860bf8a655f57d467dacdb18cd548dd
Author: lijewski <lijewski>
Date:   Sat Jul 11 00:45:49 2009 +0000

    use_copy_cache now defaults to false.
    fb_cache_max_size now defaults to 10 instead of being unlimited.

Src/C_BaseLib/FabArray.cpp

commit 9bbb18111bfccfa2ec3db1dc12c5e43538ec3235
Author: ajnonaka <ajnonaka>
Date:   Fri Jul 10 19:27:56 2009 +0000

    allocate arrays at runtime instead of on the stack

Src/F_BaseLib/interp.f90

commit 9da504dbb56ec1a9f94e34f213a3d0bf54e20055
Author: ajnonaka <ajnonaka>
Date:   Fri Jul 10 19:27:45 2009 +0000

    fix a copy statement which was not compatible with intel 9.1.043

Src/F_BaseLib/fillpatch.f90

commit 322c9ce684e52a2c234b1f582ea6af4335d2572f
Author: mzingale <mzingale>
Date:   Mon Jul 6 20:57:53 2009 +0000

    for intel, in debug mode, also set -u, which enforces 'implicit none'
    -- just in case we missed one somewhere

Tools/F_mk/GMakedefs.mak

commit 54fb9bc9ca5e1b7aebf526bc0172fb0f2938a751
Author: ajnonaka <ajnonaka>
Date:   Fri Jun 19 22:45:25 2009 +0000

    got USE_SMP to compile on intrepid

Tools/C_mk/Make.mpi

commit 0aa6f11b17e4fa58a9e987f432171ef2a733558c
Author: ajnonaka <ajnonaka>
Date:   Fri Jun 19 22:32:03 2009 +0000

    compiles now with SMP on intrepid

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 9e2b2d99b946f282226418301e135ef5c8813123
Author: lijewski <lijewski>
Date:   Fri Jun 19 21:07:13 2009 +0000

    SMP -> USE_SMP=TRUE

Tools/C_mk/Make.mpi

commit 256723f4a06c3311e28f8f3bd45beb98ebab66c3
Author: lijewski <lijewski>
Date:   Fri Jun 19 19:20:17 2009 +0000

    added simplify() and maxSize() to GetBndryCells()

Src/C_BaseLib/BoxArray.cpp

commit e564aa84b6950efec91ba94eb6ee3c8ed2d3cad2
Author: lijewski <lijewski>
Date:   Thu Jun 18 17:16:36 2009 +0000

    more work on intrepid

Tools/C_mk/Make.mpi

commit 7741caab76cfd3dd310d930e0d69a97c13d09fd3
Author: lijewski <lijewski>
Date:   Thu Jun 18 16:54:34 2009 +0000

    some work getting HyperCLaw to compileon intrepid

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit 5cd003ef8ed703dd7facc36088c9dcdc1317151d
Author: lijewski <lijewski>
Date:   Wed Jun 17 15:54:28 2009 +0000

    *** empty log message ***

Src/C_AMRLib/AuxBoundaryData.cpp

commit 031bb5a250882a0e41d3c2b3b2da79a4b9313b68
Author: almgren <almgren>
Date:   Tue Jun 16 23:04:38 2009 +0000

    Add Barrier calls at the end of Amr::writePlotFile and Amr::checkPoint.
    Hopefully this fixes the problems we've been having on della.princeton.edu

Src/C_AMRLib/Amr.cpp

commit 0ee8ecdb48b6d9d1dfe4fe6ec5302f206e37210f
Author: mzingale <mzingale>
Date:   Wed Jun 3 21:02:03 2009 +0000

    update to reflect current problem setups

Tools/C_util/regtests/Maestro-tests.ini

commit 90a8d03be924217988205afd707fd248174cf439
Author: ajnonaka <ajnonaka>
Date:   Wed Jun 3 16:34:09 2009 +0000

    added parallel_barrier call to parallel_initialize to give timers better performance

Src/F_BaseLib/parallel.f90

commit d5fe0c040af14a8ed008b5578f6ae3e8a339b815
Author: ajnonaka <ajnonaka>
Date:   Tue Jun 2 21:38:51 2009 +0000

    made timer output much more readable
    added additional timers in put_1d_array_...

Src/F_BaseLib/bl_prof.f90

commit 37d7652d9a7e9734e943cdb8671a6258ccbe80f4
Author: lijewski <lijewski>
Date:   Tue Jun 2 02:51:02 2009 +0000

    Added new version of CrseInit() that takes a single MultiFab.
    This is meant to replace the weird version that takes a FArrayBox and has
    to be followed by a call to CrseInitFinish().  Codes should set themselves
    up to use this version, as the FArrayBox version appears to use too much
    memory in high CPU/high grid count scenarios.

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 85a4df50ca133d76788298447b16527b53f05ff8
Author: lijewski <lijewski>
Date:   Fri May 29 23:38:59 2009 +0000

    default verbose to false for CrseInitFinish()

Src/C_AMRLib/FluxRegister.cpp

commit 8085995aed6539d36845b86070cb05fb7f1635e1
Author: lijewski <lijewski>
Date:   Fri May 29 23:15:57 2009 +0000

    some instrumentation for CrseInitFinish()

Src/C_AMRLib/FluxRegister.cpp

commit 1da5a38714e6e65a5e71e5af6a82d71f62f30391
Author: ajnonaka <ajnonaka>
Date:   Fri May 29 21:57:03 2009 +0000

    #pathscale friendly

Src/C_BaseLib/FabArray.H

commit f6ff4077e58b83ab5516da7d349aadf4f6d619e1
Author: lijewski <lijewski>
Date:   Fri May 29 21:54:15 2009 +0000

    more instrumentation

Src/C_BaseLib/FabArray.H

commit 99d6f761e17842d953ece0b7ff4c742ceb1380ff
Author: lijewski <lijewski>
Date:   Fri May 29 21:13:35 2009 +0000

    added some instrumentation to CollectData()

Src/C_BaseLib/FabArray.H

commit bda7b8118f78d256bc5e8b693dc017ac834b8311
Author: lijewski <lijewski>
Date:   Wed May 27 21:36:59 2009 +0000

    parallel speedup to linComb()

Src/C_BoundaryLib/FabSet.cpp

commit 024a0157d18d2cbb080f061758f35ee75eac1f3e
Author: lijewski <lijewski>
Date:   Wed May 27 21:08:21 2009 +0000

    parallel speedups for Reflux() and CrseInit()

Src/C_AMRLib/FluxRegister.cpp

commit cf7f5cd4274db0df6027a3c4ec08c36553e21aff
Author: lijewski <lijewski>
Date:   Tue May 26 21:02:40 2009 +0000

    added timer to initialize()

Src/C_AMRLib/AuxBoundaryData.cpp

commit f7de295d31c0ead4e4dd32cfe98681d19647d6ed
Author: lijewski <lijewski>
Date:   Tue May 26 20:40:00 2009 +0000

    verbose flag and some timers

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit f8b29412b67cc326f96cadb20b530d742d4fa80b
Author: lijewski <lijewski>
Date:   Tue May 26 20:20:52 2009 +0000

    some timers

Src/C_AMRLib/AmrLevel.cpp

commit 677cd16dfd3567b4340838087b2911604d7aed22
Author: almgren <almgren>
Date:   Tue May 26 17:19:02 2009 +0000

    Remove unused variables bxa_src and bxa_dst.

Src/F_BaseLib/layout.f90

commit 9656d87a05a795f58192bfa552633709e282b2c3
Author: lijewski <lijewski>
Date:   Mon May 18 16:51:25 2009 +0000

    removed unused code in TagBox::coarsen()

Src/C_AMRLib/TagBox.cpp

commit 73dfac0c21a064036be7896d364afac880d9506f
Author: gpau <gpau>
Date:   Fri May 15 16:51:34 2009 +0000

    MultiFab::Initialize() called in BoxLib::Initialize()

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit af4d4cd94756b1f981e9ff93bc6e38638cc6027f
Author: ajnonaka <ajnonaka>
Date:   Mon May 11 20:57:52 2009 +0000

    added
    
    f90sources += mt19937ar.f90

Tests/LinearSolvers/F_MG/GPackage.mak

commit 329a24a91a81157ed85fbe116e4b2d6f89a7ea24
Author: almgren <almgren>
Date:   Sun May 10 05:11:16 2009 +0000

    Added 3d Minion stencil.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/stencil.f90

commit a296ed03e5364afbd69c0cb93c6cdb59dbb18dbb
Author: lijewski <lijewski>
Date:   Fri May 8 18:07:31 2009 +0000

    attempt to deal with empty case

Src/C_AMRLib/AuxBoundaryData.H
Src/C_AMRLib/AuxBoundaryData.cpp

commit 6289cda4dffa74f575c50c88d64b9cd69a743c19
Author: almgren <almgren>
Date:   Wed May 6 23:50:04 2009 +0000

    Put the minus sign back into minion_full_fill_2d.

Src/LinearSolvers/F_MG/stencil.f90

commit 53b7400ce572d00c2fc00d1f50572a38feef0d9f
Author: almgren <almgren>
Date:   Wed May 6 23:40:12 2009 +0000

    Fix up stencil...

Src/LinearSolvers/F_MG/stencil.f90

commit 7a2919f92441d1d81cf919d4b6dca66a2068b439
Author: almgren <almgren>
Date:   Wed May 6 22:50:02 2009 +0000

    Generalize to coeffs having more than one ghost cell.

Src/LinearSolvers/F_MG/stencil.f90

commit 64edf3ab2c0fea76d44a58c39da0d7e552fd84eb
Author: almgren <almgren>
Date:   Wed May 6 21:49:33 2009 +0000

    Uncomment lines.

Src/LinearSolvers/F_MG/stencil.f90

commit 0b000400628a6a00fe920341bf58bcd54a93aa49
Author: almgren <almgren>
Date:   Wed May 6 21:37:40 2009 +0000

    Fix stencil in stencil_minion_full_fill.

Src/LinearSolvers/F_MG/stencil.f90

commit 0317b0185c6e2572b934f700d248f80b37971ee4
Author: almgren <almgren>
Date:   Wed May 6 20:56:00 2009 +0000

    Add stencil for 25-point minion solve.

Src/LinearSolvers/F_MG/stencil.f90

commit bcd0b66f6efb70348cb5554a2b7a576a487c2d76
Author: almgren <almgren>
Date:   Wed May 6 17:27:54 2009 +0000

    Adding stencil_minion_full_fill_2d...

Src/LinearSolvers/F_MG/stencil.f90

commit 07a9571c662d47e972c13d641364089476d38aba
Author: almgren <almgren>
Date:   Wed May 6 16:50:23 2009 +0000

    Added new MINION type -- full vs cross.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/stencil.f90

commit f87c96e2386349f33302db3ee6cec045cd15d7d1
Author: mzingale <mzingale>
Date:   Mon May 4 17:21:21 2009 +0000

    define a new method, plotfile_var_index that returns the index in the
    fab corresponding to a plotfile name.  Rewrite fwdconvect to use this.

Src/F_BaseLib/plotfile.f90

commit d42b178acafc20cccbd26cfec46a8b2b7ea67473
Author: gpau <gpau>
Date:   Sat May 2 00:40:33 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/PltFileXAve.cpp

commit e9f220ef0ca9176d69517d317d1eb357612786fe
Author: almgren <almgren>
Date:   Thu Apr 30 22:04:28 2009 +0000

    Fix print statement for going down in V-cycle.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit efa99c1059bdec0e3cf67fb775035849d36a78a7
Author: lijewski <lijewski>
Date:   Thu Apr 30 17:34:34 2009 +0000

    disallowed copy constructor & assignment operator

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp

commit 3d4f3f39769cc63e9438db3a3f27efbb9cee3711
Author: gpau <gpau>
Date:   Fri Apr 24 19:21:35 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit e57e5ad810d0300c9976e78b2f17b347cf2df8dc
Author: almgren <almgren>
Date:   Tue Apr 21 19:40:00 2009 +0000

    Fixed verbosity again.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 45bcfcb78772aa6e54ade822ea9f937986a8554a
Author: almgren <almgren>
Date:   Tue Apr 21 19:21:16 2009 +0000

    Modified verbosity -- added  extra verbosity to Multigrid when
    verbose > 1.Z

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 622b579bbf4a996677c13893c2dc7a307dac0817
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 21 17:22:08 2009 +0000

    boxassoc deallocate statements weren't being counted properly

Src/F_BaseLib/layout.f90

commit d310552aa9c26e69e853fc2bb10b23477d0ddc37
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 21 17:04:25 2009 +0000

    plugged memory leak

Src/LinearSolvers/F_MG/mg.f90

commit 75ae9a4657d0629e17cfbf4b4946b98001416906
Author: ajnonaka <ajnonaka>
Date:   Mon Apr 20 22:07:06 2009 +0000

    PathScale with MPI works on jaguar

Tools/C_mk/Make.mpi

commit 56c88b2ed1e4b43e256b4e5ad0fcdc52460283f1
Author: almgren <almgren>
Date:   Mon Apr 20 21:44:03 2009 +0000

    We need i3 not i2 to print nboxes in layout_print.

Src/F_BaseLib/layout.f90

commit 54a1353e4cf3e1cc0fd0599787710ce55b4e7ceb
Author: almgren <almgren>
Date:   Mon Apr 20 19:41:19 2009 +0000

    Need to have a ghost cell for rh when nodal.

Src/LinearSolvers/F_MG/mg.f90

commit 66f84d07ba1d41f290b14325709d1e4746f3baf1
Author: almgren <almgren>
Date:   Mon Apr 20 17:38:34 2009 +0000

    Formatting only.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 837f1a9d0db7bbcff2c54075f8d31d74746181a8
Author: almgren <almgren>
Date:   Sat Apr 18 03:21:20 2009 +0000

    Dont think we need to include mlmg.f90 in a make... do we?

Src/LinearSolvers/F_MG/GPackage.mak

commit ea898a3775e37dcbec1ed6c5be6f481f2b8a55d8
Author: almgren <almgren>
Date:   Sat Apr 18 03:20:11 2009 +0000

    Fix case where we set bottom_solver_eps = eps when
    only one mg_level -- we only want this in the case when
    it's not being called as a bottom solver for another mgt,
    so here we test on volume ... this should work well enough for now.

Src/LinearSolvers/F_MG/mg.f90

commit 47c76a0f45c536a1ee72bc8e0d2a5a7599dfe83d
Author: almgren <almgren>
Date:   Fri Apr 17 21:36:12 2009 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg.f90

commit ef063901016ee129a40f49e4a9e65411300b7b9a
Author: almgren <almgren>
Date:   Fri Apr 17 21:20:46 2009 +0000

    IF nodal and using CG or BiCG as bottom solver then build the nodal
    mask at the bottom solver level ahead of time and pass it in to the BiCG
    or CG routine so that they can pass it into the multifab_dot routine
    so we don't build it every time the dot routine is called.

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90

commit 5ce340f53976b6e48fb5bc2285c738a22ecb72cf
Author: almgren <almgren>
Date:   Fri Apr 17 21:19:14 2009 +0000

    Added optional nodal_mask argument to multifab_dot which computes
    a dot product.  Without the nodal_mask argument present the multifab_dot
    function still builds and destroys the nodal mask every time it is called.

Src/F_BaseLib/multifab.f90

commit 2c639c65a9d4b202bca45d0e5855c4d10333901c
Author: ajnonaka <ajnonaka>
Date:   Thu Apr 16 22:20:08 2009 +0000

    plugged memory leak

Src/LinearSolvers/F_MG/mg.f90

commit 6098ec080a21191af0afe9b90e5282b1108298eb
Author: almgren <almgren>
Date:   Thu Apr 16 21:44:46 2009 +0000

    Make sure to allocate bottom_uu and bottom_rh as nodal if need be.

Src/LinearSolvers/F_MG/mg.f90

commit d56a1d4b3acdf720a33817f33cdd5f09826ffd9d
Author: ajnonaka <ajnonaka>
Date:   Thu Apr 16 20:38:46 2009 +0000

    added timer for build_nodal_dot_mask

Src/F_BaseLib/multifab.f90

commit 728504d5409cb9681b6b3be21a2db20a3b39d8f0
Author: almgren <almgren>
Date:   Thu Apr 16 17:30:46 2009 +0000

    Put in the interface for bottom_solver = 4 option with the nodal solver.

Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_solve.f90

commit b95cd5946289566597eab554215d43fff0f95924
Author: almgren <almgren>
Date:   Thu Apr 16 17:24:07 2009 +0000

    New stuff for bottom_solver = 4.

Src/LinearSolvers/F_MG/mg.f90

commit 51ebe9f074d74fd2beb183f1d667f59ba2409fde
Author: almgren <almgren>
Date:   Thu Apr 16 17:22:11 2009 +0000

    Pass bottom_mgt through as an optional argument.

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_solve.f90

commit 0ef7e75c190276c3fda905cb42fb4c73d04e7a6c
Author: lijewski <lijewski>
Date:   Tue Apr 14 17:03:04 2009 +0000

    try to print out something useful when trees unbalanced

Src/F_BaseLib/bl_prof.f90

commit 49febc0bd73770f71600047f2918dc22ce955f2c
Author: lijewski <lijewski>
Date:   Mon Apr 13 23:07:29 2009 +0000

    removed uses of reshape()

Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 37476df877b81013160e141b6377adfd7566959e
Author: lijewski <lijewski>
Date:   Mon Apr 13 17:17:03 2009 +0000

    removed av member of comm_dsc type

Src/F_BaseLib/layout.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 78bd2dbc8c0cd47587c37f47e715d8341449e2d6
Author: vince <vince>
Date:   Tue Apr 7 20:39:54 2009 +0000

    added def for HOST if not set.

Tools/C_mk/Make.mpi

commit 0992475d704b6cbcd10e00c023e5018b6de4d1f7
Author: vince <vince>
Date:   Tue Apr 7 17:37:20 2009 +0000

    updated gojira.

Tools/C_mk/Make.mpi

commit fa539e3d84035468cb64f3eb59044c50d3871af1
Author: gpau <gpau>
Date:   Sun Apr 5 15:28:42 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/PltFileXAve.cpp

commit 482343aae49f83e8a50787e54d82aea0b8e725f4
Author: ajnonaka <ajnonaka>
Date:   Fri Apr 3 20:38:04 2009 +0000

    better job with timer formatting

Src/F_BaseLib/bl_prof.f90

commit 06545e741fa6fdb26859e0dc20922cdbe5a949ed
Author: lijewski <lijewski>
Date:   Fri Apr 3 20:19:05 2009 +0000

    *** empty log message ***

Tests/LinearSolvers/F_MG/inputs

commit c4cafc5eea9df771630b00141a00f0dc8c24114c
Author: lijewski <lijewski>
Date:   Fri Apr 3 20:15:11 2009 +0000

    some simplification

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit c5374325b4f2f16a8ccc1660b4718d9ea52dfb77
Author: ajnonaka <ajnonaka>
Date:   Fri Apr 3 20:02:53 2009 +0000

    changed the bl_timer output width to 40 characters so you can actually see what's being called...

Src/F_BaseLib/bl_prof.f90

commit 860d90b66cc5dfdf7cc926a16c4e5e22da121edd
Author: lijewski <lijewski>
Date:   Thu Apr 2 19:31:52 2009 +0000

    more verbose output

Src/F_BaseLib/layout.f90

commit 79cfe78bbb56aabc67de372fdad0863bb2586e04
Author: lijewski <lijewski>
Date:   Thu Apr 2 17:20:29 2009 +0000

    added simple hash to speed up copyassoc matches

Src/F_BaseLib/layout.f90

commit c417aa575c2a9fed33e4b9d6d605f6d966a97bff
Author: lijewski <lijewski>
Date:   Thu Apr 2 05:10:18 2009 +0000

    back to simpler way of limiting copyassoc cache size

Src/F_BaseLib/layout.f90

commit a9458d126db414e2a90a4d0124114ad2f654451e
Author: lijewski <lijewski>
Date:   Wed Apr 1 20:54:14 2009 +0000

    more sophisticated cache clearing strategy

Src/F_BaseLib/layout.f90

commit 298b5598d7a0835f83badb7c64eacee5486ee6a2
Author: lijewski <lijewski>
Date:   Wed Apr 1 20:24:24 2009 +0000

    smarter about what to delete from copy cache

Src/F_BaseLib/layout.f90

commit 21011b165efceddc99a07bce743cce975d37cc5c
Author: lijewski <lijewski>
Date:   Wed Apr 1 18:23:20 2009 +0000

    print copy cache stats on flush

Src/F_BaseLib/layout.f90

commit 41174bcdbb4c85d4eb430fa44403a14089efd155
Author: lijewski <lijewski>
Date:   Wed Apr 1 18:12:35 2009 +0000

    copyassoc cache refinements

Src/F_BaseLib/layout.f90

commit 29901d43abdf45edc766004bd11348ee6c059850
Author: almgren <almgren>
Date:   Tue Mar 31 17:37:06 2009 +0000

    Don't need to compute residual on the way back up the V-cycle *after*
    the relaxation at that level -- we can compute it later when we need it.
    Left in that we do compute it if do_diagnostics is on.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 5846eb54b2d65b3f2a98a97db301faa43747ad27
Author: ajnonaka <ajnonaka>
Date:   Tue Mar 31 17:24:05 2009 +0000

    fix comment

Src/F_BaseLib/make_new_grids.f90

commit 84397f68e3564417a95126f61579963ff5e8bea5
Author: ajnonaka <ajnonaka>
Date:   Tue Mar 31 17:09:01 2009 +0000

    fixed a comment

Src/F_BaseLib/ml_boxarray.f90

commit 9d365a4aa6c5e4dbff0ed9eb7f308b415dd0dc3c
Author: lijewski <lijewski>
Date:   Mon Mar 30 22:01:29 2009 +0000

    bypass distribution mapping calculation when possible

Src/F_BaseLib/make_new_grids.f90
Src/F_BaseLib/ml_boxarray.f90

commit 43259fc232a14b3187c10618aa9c9a7c4bd96031
Author: lijewski <lijewski>
Date:   Mon Mar 30 21:49:55 2009 +0000

    bypass distribution mapping calculation when possible

Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/ml_solve.f90

commit 29eed1d6a1ebde4b35db9d87f8e91b9ea0d44d45
Author: ajnonaka <ajnonaka>
Date:   Mon Mar 30 21:34:59 2009 +0000

    modified calls to multifab_fill_ghost_cells to not call multifab_fill_boundary for the crse data when the ghost cells have previously been filled.  no change to results.

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit ac370a47825434afa0ad788b0b04e2389238515b
Author: almgren <almgren>
Date:   Mon Mar 30 21:12:12 2009 +0000

    Move call to multifab_fill_boundary out of ml_interp_bcs and into ml_cc
    which is calling ml_interp_bcs 2*BL_SPACEDIM times.  Should reduce the time
    in multifab_fill_boundary by factor of 2*BL_SPACEDIM.

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90

commit d99aa3bc5a351d7a7bceaad6f16b0648b682c03d
Author: ajnonaka <ajnonaka>
Date:   Mon Mar 30 19:31:19 2009 +0000

    sfc_threshold=4 actually is a better idea now that we have turned off the knapsack minimize communication cost optimization

Src/F_BaseLib/layout.f90

commit 353b9bcb694c8c04ae58c2c1f8aa0ea4ebbac5b6
Author: almgren <almgren>
Date:   Mon Mar 30 17:56:57 2009 +0000

    Add new smoother type -- "efficient GSRB" -- doesn't do a fill boundary between
    the red and black sweeps.

Src/LinearSolvers/F_MG/mg.f90

commit 39843b0521ca4caa096a93c647ec4d48c1bfe756
Author: lijewski <lijewski>
Date:   Mon Mar 30 17:51:45 2009 +0000

    set sfc_threshold default to 0

Src/F_BaseLib/layout.f90

commit 559e9acd577f246661c1afd37906a267aae19fba
Author: lijewski <lijewski>
Date:   Mon Mar 30 17:47:33 2009 +0000

    turn off do_mcc by default

Src/F_BaseLib/knapsack.f90

commit 1b6467c106e1a0e8d3466873abd5eeabd17e56fa
Author: lijewski <lijewski>
Date:   Mon Mar 30 16:03:20 2009 +0000

    reverted out the removal of profile timers

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 6a9dbeadd3fc5554716e5ae39f84af820da1ae6f
Author: lijewski <lijewski>
Date:   Sat Mar 28 22:19:10 2009 +0000

    commented out some print statements

Tests/LinearSolvers/F_MG/cc_multi.f90

commit a45e974fb85c0a8c0b21063131704c0e85bb7fa7
Author: ajnonaka <ajnonaka>
Date:   Fri Mar 27 20:26:57 2009 +0000

    make sure to destroy bpt if you return out of a function early

Src/F_BaseLib/cluster.f90

commit 8cd4c3c5525d1a1e0d1bc9771fb6e5bc9ccdcda3
Author: lijewski <lijewski>
Date:   Fri Mar 27 20:06:42 2009 +0000

    remove bl_prof_timers

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 449009227fd617993f81bd4a702e8827692a6c46
Author: lijewski <lijewski>
Date:   Thu Mar 26 21:58:34 2009 +0000

    modest speedup to SSFC stuff

Src/C_BaseLib/DistributionMapping.cpp

commit 1b7dfc1f1aa517bc60f892c7d0e7644634e68565
Author: lijewski <lijewski>
Date:   Thu Mar 26 17:51:53 2009 +0000

    modest optimization to sfc_greater_i()

Src/F_BaseLib/knapsack.f90

commit 295c2be658536a52f6f6977da3d19b6f32f6a97b
Author: lijewski <lijewski>
Date:   Wed Mar 25 19:57:25 2009 +0000

    minor tweeks to previous fix

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 6791710a0caed2313cc02b913f22051308b86cc1
Author: lijewski <lijewski>
Date:   Wed Mar 25 19:04:30 2009 +0000

    added box_get_intersector stuff to ml_interface_c() -- big speedup

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit df006f82f2ceabf31a4148b83957c46eba3ea5ad
Author: ajnonaka <ajnonaka>
Date:   Tue Mar 24 21:45:48 2009 +0000

    make modules go to correct directory on jaguar

Tools/F_mk/GMakedefs.mak

commit 6923e3647b818f3ba25701eb710b8922c44b541b
Author: lijewski <lijewski>
Date:   Tue Mar 24 20:23:35 2009 +0000

    efficiency mods to layout_get_box_intersector

Src/F_BaseLib/layout.f90

commit 0deb53510e2b4a474edc56ad8ae5a3875b06c29f
Author: lijewski <lijewski>
Date:   Mon Mar 23 19:16:59 2009 +0000

    test for out-of-bounds in layout_get_box_intersector()

Src/F_BaseLib/layout.f90

commit f25d5774b569ef5f135daf28ba6ab9c853d74fa2
Author: ajnonaka <ajnonaka>
Date:   Mon Mar 23 18:25:26 2009 +0000

    split up ba_new so the number of intersections per
    box isn't to big. i.e., there is more than one box in ba_new

Src/F_BaseLib/make_new_grids.f90

commit 664c61ed4465aa741531da2990d2c9878c82dbcd
Author: ajnonaka <ajnonaka>
Date:   Sat Mar 21 00:07:10 2009 +0000

    made knapsack verbosity false by default

Src/F_BaseLib/knapsack.f90

commit aeb763ac4000ce75d87ee099f6d907528bda3034
Author: lijewski <lijewski>
Date:   Fri Mar 20 22:20:59 2009 +0000

    plot_nfiles=-1 or checkpoint_nfiles=-1 ==> really use ParallelDescriptor::NProcs().

Src/C_AMRLib/Amr.cpp

commit 2c4c66de5c71dea76daceb7403a51b2c436e2752
Author: almgren <almgren>
Date:   Tue Mar 17 17:03:10 2009 +0000

    This DiffPlot is obsolete -- has been replaced by other Diff... routines.

Tools/C_util/Convergence/DiffPlot.cpp

commit 24879bccac47784ff9507829a1d59bcc8aee68db
Author: vince <vince>
Date:   Fri Mar 13 20:32:58 2009 +0000

    added hyperion.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 66331b045a1f31c81338b48d9191eebdb5cbb050
Author: almgren <almgren>
Date:   Fri Mar 13 18:01:25 2009 +0000

    Add a new routine -- tags_and_untags, which copies both the CLEAR and the SET
    values instead of just the SET values.

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit bb15619cd1492e4082e6f4591cec206619324ce3
Author: vince <vince>
Date:   Thu Mar 12 01:11:37 2009 +0000

    squished denorm mins to zero when writing the header.
    this is for aix.

Src/C_BaseLib/VisMF.cpp

commit d832cc84b3f70cd68c6fc63b068819e94fb5d2a4
Author: lijewski <lijewski>
Date:   Wed Mar 11 16:44:17 2009 +0000

    Removed the grid_loc data member of AmrLevel.
    Also the corresponding accessory function gridLocations().

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StationData.cpp

commit 4656082d044b37294874f8da6b5943667d11cd73
Author: almgren <almgren>
Date:   Tue Mar 10 20:09:21 2009 +0000

    Make the derive functions virtual.

Src/C_AMRLib/AmrLevel.H

commit 4ba409f88ecc3c5f598b3cc37b35a1baf3acd240
Author: lijewski <lijewski>
Date:   Mon Mar 9 16:05:03 2009 +0000

    mods for yana at LLNL from Mike Singer

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit fa14688f483ead2ba060a87bf98f2a1ab0f640a8
Author: lijewski <lijewski>
Date:   Tue Mar 3 20:34:29 2009 +0000

    some cleanup

Src/C_BaseLib/DistributionMapping.cpp

commit 4e2c6d9d029c0a1221e67f0f82752dbfbc1a0fa3
Author: lijewski <lijewski>
Date:   Mon Mar 2 23:23:13 2009 +0000

    more namespace cleanup

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 396c486e400f406c26ce96e97297bb45284d044d
Author: lijewski <lijewski>
Date:   Mon Mar 2 22:38:56 2009 +0000

    some namespace cleanup

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BoundaryLib/FabSet.cpp

commit 590123df905d15284c5b8d0204238774513cae49
Author: lijewski <lijewski>
Date:   Mon Mar 2 21:18:37 2009 +0000

    put FSRec in unnamed namespace

Src/C_BoundaryLib/FabSet.cpp

commit e0617cf2446acfd8f39d3b226c47b5fbb7e5b595
Author: lijewski <lijewski>
Date:   Mon Mar 2 21:17:55 2009 +0000

    use IntVect::Compare instead of IntVectComp

Src/C_AMRLib/TagBox.cpp

commit 44cae48ef7fed462129293b35716c64f9f7507bc
Author: lijewski <lijewski>
Date:   Mon Mar 2 21:17:29 2009 +0000

    put struct in unnamed namespace

Src/C_AMRLib/FluxRegister.cpp

commit 8eafd9119f37373edd4222cdcc2a37661d56b387
Author: lijewski <lijewski>
Date:   Mon Mar 2 21:04:12 2009 +0000

    put BoxCmp in unnamed namespace

Src/C_BaseLib/BoxList.cpp

commit 9448d180e4cd37e9e81c251d900913c60cc85577
Author: lijewski <lijewski>
Date:   Mon Mar 2 21:00:59 2009 +0000

    put SFCToken in unnamed namespace

Src/C_BaseLib/DistributionMapping.cpp

commit e874a951fc1614fa7c0be8651c7921d0bfa863d1
Author: ajnonaka <ajnonaka>
Date:   Fri Feb 27 23:31:54 2009 +0000

    mpi works in 3d now on lawrencium

Tools/C_mk/Make.mpi

commit 4134e75d5df22bd17b123d82a4d204b30590a883
Author: ajnonaka <ajnonaka>
Date:   Fri Feb 27 23:21:11 2009 +0000

    catch mpi for lawrencium

Tools/C_mk/Make.mpi

commit 101751bccf7c77599ca4fd31f5e1f14f49634385
Author: marc <marc>
Date:   Fri Feb 27 00:44:10 2009 +0000

    CYGWIN does support the -f option, move HOSTNAME call

Tools/C_mk/Make.defs

commit 653988e91feb0c349b5f9505afe7aaccc1811e77
Author: ajnonaka <ajnonaka>
Date:   Tue Feb 24 18:49:43 2009 +0000

    Our makefiles for MAESTRO and MAESTRO_paper4 were starting to diverge.  Brought these almost back into sync now - one more possible change coming

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak

commit 7feab5f39725213e54b568b612d6f4dfd8dbe299
Author: mzingale <mzingale>
Date:   Mon Feb 23 18:51:57 2009 +0000

    if making benchmarks + compileTest, nothing to report

Tools/C_util/regtests/test.py

commit 29d5da84b79efba7b636c671640accae3ce08ff7
Author: mzingale <mzingale>
Date:   Fri Feb 20 20:43:53 2009 +0000

    for some reason the BL_AIX flag never made it in for intrepid

Tools/F_mk/GMakeMPI.mak

commit 945a1c75745e7b1486ddf2fb916df88159321993
Author: lijewski <lijewski>
Date:   Fri Feb 20 18:20:15 2009 +0000

    update for pleiades

Tools/C_mk/Make.Linux

commit 66ee1ddc7eb8ad27dae67045b2cab595b90564a7
Author: almgren <almgren>
Date:   Thu Feb 19 18:34:45 2009 +0000

    Fixed settings for pleiades.

Tools/C_mk/Make.mpi

commit 69c73a4c1582098b178253aa9ef9124fec7cfc85
Author: lijewski <lijewski>
Date:   Wed Feb 18 22:03:19 2009 +0000

    can now use space-fill-curves instead of knapsack

Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/layout.f90

commit 445415ec5157e53386dc7d74986f94fd63ed66e5
Author: lijewski <lijewski>
Date:   Tue Feb 17 23:50:36 2009 +0000

    some work on implementing space-filling-curves

Src/F_BaseLib/knapsack.f90

commit 49009d43b3a82a47c2bc96df4cc561128dce104c
Author: lijewski <lijewski>
Date:   Fri Feb 13 18:57:01 2009 +0000

    remove OMP stuff intrepid complained about

Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/sparse_solve.f90

commit c64200c37b4e21609c2e713a5d51ef29dbc232cc
Author: lijewski <lijewski>
Date:   Fri Feb 13 16:39:52 2009 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak

commit 27b0a5ab49979a5ecf249e7336c60632d31838f5
Author: almgren <almgren>
Date:   Thu Feb 12 21:13:02 2009 +0000

    Add BL_USECLOSE for pleiades.

Tools/C_mk/Make.mpi

commit 25b39214dd3e1f0a027211a8efaca282c93b5236
Author: almgren <almgren>
Date:   Thu Feb 12 21:11:32 2009 +0000

    Add special case for pleiades.

Tools/C_mk/Make.Linux

commit 5e388c5f8fb43ab543cda14ee70f73bb94fc46f9
Author: vince <vince>
Date:   Thu Feb 12 20:51:51 2009 +0000

    added option for explicit file closing.

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.cpp

commit a06800b5e0ea6add60be60e68ad0246093c9be6a
Author: mzingale <mzingale>
Date:   Thu Feb 12 19:48:47 2009 +0000

    fix the logic for deciding if a test is successful

Tools/C_util/regtests/test.py

commit e02e8cda218a0b248cb579cd84dfe0630f6d8750
Author: marc <marc>
Date:   Wed Feb 11 23:06:50 2009 +0000

    fix data type

Src/C_BaseLib/ParallelDescriptor.cpp

commit 6d529949d42ff1659640d1bfe1ce60c536347484
Author: mzingale <mzingale>
Date:   Wed Feb 11 22:02:16 2009 +0000

    add support for compile-only tests

Tools/C_util/regtests/test.py

commit a856bcb9b11fbce8315aecc25f6e84c2b043a58f
Author: lijewski <lijewski>
Date:   Wed Feb 11 01:44:06 2009 +0000

    replaced STOP with bl_abort()

Src/C_BaseLib/BLutil_F.f

commit a5748fc73429953000cbf8584ed19bf653c9de5f
Author: lijewski <lijewski>
Date:   Tue Feb 10 21:49:11 2009 +0000

    added some xlC/xlf stuff for intrepid

Tools/C_mk/Make.Linux

commit c244a8896d2d5b31aa74cb91d96c034e683ed825
Author: mzingale <mzingale>
Date:   Mon Feb 9 21:09:30 2009 +0000

    fix a restart comparison bug if the file names are too long

Tools/C_util/regtests/test.py

commit db20140fb3cef55b65bcf36994d60772cefc2d62
Author: gpau <gpau>
Date:   Mon Feb 9 21:09:08 2009 +0000

    Fixes for Lawrencium.

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 4b9c7ec1b51dabe3505d48ed1289ecb87f7b5578
Author: ajnonaka <ajnonaka>
Date:   Mon Feb 9 20:30:54 2009 +0000

    works for Lawrencium mpi

Tools/F_mk/GMakeMPI.mak

commit e4883b382269ab3828a67cb77c353a71d5308f77
Author: mzingale <mzingale>
Date:   Mon Feb 9 15:09:26 2009 +0000

    archive the output
    
    fix a restart issue for Parallel
    
    rename chk files for fParallel jobs using the new commandline setting

Tools/C_util/regtests/test.py

commit 2213d666d9678399b829172e64930f1f38eb8a8f
Author: mzingale <mzingale>
Date:   Fri Feb 6 23:10:50 2009 +0000

    add xlf stuff so we can compile analysis routines on the Intrepid
    frontend

Tools/F_mk/GMakedefs.mak

commit 337bd1b2c567d078fd7db0c1bf083f94dfb32592
Author: vince <vince>
Date:   Fri Feb 6 22:57:03 2009 +0000

    changes for lijewski.

Tools/C_mk/Make.mpi

commit 5581d467ce07251dcc4db84a53414daa4bd518c9
Author: lijewski <lijewski>
Date:   Fri Feb 6 22:14:38 2009 +0000

    Do_AllToAllV is now settable

Src/F_BaseLib/multifab.f90

commit 576fee341d9933c3f5c7ad10f553fb55884a8de4
Author: lijewski <lijewski>
Date:   Fri Feb 6 21:30:57 2009 +0000

    some rearrangement

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit 4b34db192c3ecbb0835086f37b948b0c2212dfdb
Author: mzingale <mzingale>
Date:   Fri Feb 6 20:58:08 2009 +0000

    Chris's Intrepid changes to get Amrvis compiling

Tools/C_mk/Make.defs

commit 408e09a46632797462f82ef5dbee5d2b7ba024ca
Author: almgren <almgren>
Date:   Fri Feb 6 20:46:19 2009 +0000

    Fix previous fix.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 17f147924bcf69c1e5adb34659dbf2f371a7dfe9
Author: lijewski <lijewski>
Date:   Fri Feb 6 19:17:04 2009 +0000

    added allreduce() operations on vectors

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 7e718eaf8e31cfd275b7a2015f6b018f9c5d1e59
Author: mzingale <mzingale>
Date:   Fri Feb 6 16:30:50 2009 +0000

    more clean-ups

Tools/C_util/regtests/test.py

commit c95307df2118b382fd8c918879460c15416a50df
Author: mzingale <mzingale>
Date:   Fri Feb 6 16:02:04 2009 +0000

    -module and -I are now picked up from the PathScale entry in GMakedefs.mak
    so we don't need to repeat them here

Tools/F_mk/GMakeMPI.mak

commit 3f12d4c20c4286a4533a8c3bbe44d85c091fcbac
Author: mzingale <mzingale>
Date:   Fri Feb 6 15:03:50 2009 +0000

    some code clean up + add the ability to override the compiler for
    fParallel.

Tools/C_util/regtests/test.py

commit 080b2abfc1d1d22d4567b29579cf3bb576706e5b
Author: mzingale <mzingale>
Date:   Thu Feb 5 20:22:04 2009 +0000

    neither $HOST nor uname contain "intrepid" on intrepid, so define HOSTNAMEF
    which is the output of hostname -f, which does contain "intrepid".  THis
    is used in GMakeMPI.mak to define the compilers.

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak

commit c9a2cea47a314e96a241206b3f49898fedf8a638
Author: mzingale <mzingale>
Date:   Thu Feb 5 19:49:36 2009 +0000

    for some reason, on jaguar with PathScale, we were explicitly not putting
    in the module path and include path flags for compiling.  This means that
    any .mod files were in the . instead of in t/XXX/m/.  We don't need a
    special case for jaguar here.
    
    Note: this doesn't affect an MPI build, since that uses the jaguar stuff
    setup in GMakeMPI.mak

Tools/F_mk/GMakedefs.mak

commit 8d75fe58818efed0fb57859e21f3e74cf67ef9bb
Author: lijewski <lijewski>
Date:   Tue Feb 3 17:08:10 2009 +0000

    note in comments that if you want Array<bool> use std::vector<bool>

Src/C_BaseLib/Array.H

commit f759e8d1578b6f96d5f1a02894a9c73ebd911bef
Author: vince <vince>
Date:   Mon Feb 2 20:50:44 2009 +0000

    intel 11.

Tools/C_mk/Make.defs

commit aad7090e016c91f6c0ded97acac8fb78ad5ad341
Author: mzingale <mzingale>
Date:   Sat Jan 31 20:04:00 2009 +0000

    add a comment

Tools/F_scripts/make_build_info

commit 21f7fd907319dc13a14a818564cb7f2fd5b2d7ad
Author: mzingale <mzingale>
Date:   Sat Jan 31 19:13:25 2009 +0000

    switching over to uname instead of relying on setting HOST in a makefile
    automagically makes MPI compiling work on nan

Tools/F_mk/GMakeMPI.mak

commit cf0e993ff0ab14034eecbf2dbc5127d94d3b2c46
Author: lijewski <lijewski>
Date:   Thu Jan 29 21:13:24 2009 +0000

    added BL_NOFAST to turn off maximum optimization

Tools/C_mk/Make.Linux

commit 3206c015a0a794e184364063a658852c002018b6
Author: lijewski <lijewski>
Date:   Thu Jan 29 17:47:15 2009 +0000

    removed STRCTLY stuff

Tools/C_mk/Make.defs

commit af6a6c11c26fcc414c04ad0591d088f78bb5e42c
Author: mzingale <mzingale>
Date:   Thu Jan 29 15:02:31 2009 +0000

    make realclean before building the comparison and vis tools

Tools/C_util/regtests/test.py

commit 2bb002043c98fe84a4730e27b5ab42ba92c7eb68
Author: mzingale <mzingale>
Date:   Wed Jan 28 18:00:20 2009 +0000

    make the vis stuff more robust

Tools/C_util/regtests/test.py

commit f64db38b5a45ad923f49f44af66d1dad41e48cdb
Author: almgren <almgren>
Date:   Tue Jan 27 18:21:43 2009 +0000

    We can now set max_level to be smaller than before on restart.

Src/C_AMRLib/Amr.cpp

commit c94e891e0d8e449d6bc70b3907939ee76cbd290f
Author: almgren <almgren>
Date:   Mon Jan 26 21:26:05 2009 +0000

    Added Real Geometry::ProbSize()

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 289b0583534126d5cf3cb3568d70b13c6f6a80fc
Author: almgren <almgren>
Date:   Mon Jan 26 21:06:18 2009 +0000

    Added bool Geometry::isAllPeriodic() to return true only if domain is
    periodic in all directions, otherwise false.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 5ebbc058077986e6cdcd9c319dbc7886cc31b10d
Author: mzingale <mzingale>
Date:   Thu Jan 22 21:21:02 2009 +0000

    f90 -> f95 on intrepid

Tools/F_mk/GMakeMPI.mak

commit 1ecb4cb997de2f7f89b6e30abaf4f7395e862e7b
Author: mzingale <mzingale>
Date:   Fri Jan 16 20:28:01 2009 +0000

    add Chris's ANL Intrepid fixes

Tools/F_mk/GMakeMPI.mak

commit 8456acea47ec4ae609a58689f0267cf2fcd1bb1f
Author: lijewski <lijewski>
Date:   Wed Jan 14 23:13:36 2009 +0000

    made single private definition of ilut_build()

Src/LinearSolvers/F_MG/sparse_solve.f90

commit 00de1c37dcc3a2cabf5583fc14be983f632d5a1c
Author: almgren <almgren>
Date:   Mon Jan 12 22:19:31 2009 +0000

    Removed unused variable.

Src/LinearSolvers/F_MG/ml_cc.f90

commit ed7912f80813225c5277b712f6b3e3d63565aac8
Author: gpau <gpau>
Date:   Sat Jan 10 00:05:56 2009 +0000

    parallelized PltFileXAve.cpp

Tools/C_util/Statistics/GNUmakefile
Tools/C_util/Statistics/PltFileList.cpp
Tools/C_util/Statistics/PltFileStat.cpp
Tools/C_util/Statistics/PltFileXAve.cpp

commit 31a7b5025cc80332bfc3f757d52cff3ed86aa8ec
Author: ajnonaka <ajnonaka>
Date:   Fri Jan 9 23:41:34 2009 +0000

    forgot to declare a variable

Src/F_BaseLib/fabio_c.c

commit 99e9e26ae6c27810fca312d847855ca30e7a641b
Author: vince <vince>
Date:   Mon Jan 5 21:12:15 2009 +0000

    added varan.

Tools/C_mk/Make.mpi

commit 482763e76fa7b685b6d956417d3f3f9ccd0a1b65
Author: mzingale <mzingale>
Date:   Sat Jan 3 19:39:33 2009 +0000

    for nan, if we are doing mpi, use mpif90 and mpicxx

Tools/F_mk/GMakeMPI.mak

commit e3babc9f0819ea3dd32d1eaaa5490cc7b34dd930
Author: lijewski <lijewski>
Date:   Fri Jan 2 18:13:04 2009 +0000

    plugged some memory leaks

Src/LinearSolvers/F_MG/mg_cpp.f90

commit ceeb3807c63643a3756af480e4dc51d02ac59df6
Author: almgren <almgren>
Date:   Sat Dec 27 01:47:51 2008 +0000

    Clean up some memory.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit b179bd9496c3837dd72d0b8cca3bc36cade11d54
Author: lijewski <lijewski>
Date:   Fri Dec 19 22:48:51 2008 +0000

    added contains_nan()

Src/F_BaseLib/fab.f90
Src/F_BaseLib/fabio_c.c

commit b985c054b153a91d6cad9b19d4deff4247aff0bf
Author: vince <vince>
Date:   Wed Dec 17 21:52:22 2008 +0000

    added F90 for franklin.

Tools/C_mk/Make.Linux

commit ab6ad5d3a7ff54c021ebbdfd2ad7bc8c17bdf302
Author: lijewski <lijewski>
Date:   Wed Dec 17 21:00:35 2008 +0000

    *** empty log message ***

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit a1fc7edd70a0f98ec9bc21a56efeeae04af71c00
Author: almgren <almgren>
Date:   Mon Dec 8 21:41:59 2008 +0000

    Let us call CellBilinear if not in 3-d -- it appears to work in 2d anyway.

Src/C_AMRLib/Interpolater.cpp

commit 6d95a087a98adcb17399831bd69874ccd7e91f6c
Author: ajnonaka <ajnonaka>
Date:   Thu Dec 4 18:54:14 2008 +0000

    need to specify which optional argument is going into ml_cc()

Src/LinearSolvers/F_MG/ml_solve.f90

commit 7502ab90aef9a488ec038d1430e0852dc15d2bca
Author: almgren <almgren>
Date:   Thu Dec 4 18:41:11 2008 +0000

    Actually use abs_eps for a change.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 095eb10131bd20fddee669a12c5e035f88768259
Author: almgren <almgren>
Date:   Thu Dec 4 18:40:43 2008 +0000

    Pass abs_tol through into solver.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 43d493374a652d3dbcb3e3b01145b6f59eb97db9
Author: almgren <almgren>
Date:   Tue Dec 2 01:51:59 2008 +0000

    Cleaned up SETAREA.

Src/C_BaseLib/COORDSYS_1D.F

commit 1eab40784a839ea8e15e0e5502d604469e075aef
Author: almgren <almgren>
Date:   Tue Dec 2 01:51:28 2008 +0000

    Cleaned up SETAREA

Src/C_BaseLib/COORDSYS_2D.F

commit 95371d2073ab564885fd4032cabb352be26a723c
Author: almgren <almgren>
Date:   Tue Dec 2 01:49:30 2008 +0000

    Cleaned up SETDLOGA.

Src/C_BaseLib/COORDSYS_2D.F

commit 9925c5fe634d23a9444f62d432b5692d20712284
Author: almgren <almgren>
Date:   Tue Dec 2 00:46:54 2008 +0000

    Fix SETDLOGA and improve the formatting of the others.

Src/C_BaseLib/COORDSYS_1D.F

commit 1eee9a41a5108378f54f250ea52e888238219a79
Author: lijewski <lijewski>
Date:   Mon Nov 17 23:45:55 2008 +0000

    ParmParse do_full_knapsack

Src/C_BaseLib/DistributionMapping.cpp

commit 7b283d7f5a1d93b1d1227792fc1bd2e3807fb435
Author: lijewski <lijewski>
Date:   Mon Nov 17 23:45:39 2008 +0000

    set copy_cache_max_size default to 100

Src/C_BaseLib/FabArray.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 6497378dad890759c21cf69652f122875ff781eb
Author: lijewski <lijewski>
Date:   Thu Nov 13 16:57:52 2008 +0000

    print out reusage rate of various caches

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BoundaryLib/FabSet.cpp

commit ef65bcb5db04b894a8ef4da62843cabd532b1987
Author: lijewski <lijewski>
Date:   Wed Nov 12 21:34:52 2008 +0000

    -1 implies no limit on cache size

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 64dd74de9c95ffa6c1a4ea49ac6f26b3208fefef
Author: lijewski <lijewski>
Date:   Wed Nov 12 04:27:32 2008 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/Geometry.cpp

commit 12f41f92c499a009e60e5b8f291180097b31f5d3
Author: almgren <almgren>
Date:   Tue Nov 11 00:53:56 2008 +0000

    Only define final_resnorm from ni_res if it's been included in the calling sequence.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 442c46bc990277a940a5bd4262a84cc6c7264bd9
Author: almgren <almgren>
Date:   Mon Nov 10 22:56:26 2008 +0000

    Add final_resnorm to calling sequence for mgt_solve and ml_cc. This can
    be used to pass the final resnorm back to the calling routine -- this can
    be used later as a test for correction solves.

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/ml_cc.f90

commit 78e5fb88fac800c16158445cb6539faeb8ec922e
Author: almgren <almgren>
Date:   Mon Nov 10 22:54:38 2008 +0000

    Add final_resnorm to calling sequence for mgt_solve.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 61aff7c72d46a0c51fd93972096bb446360ff21f
Author: almgren <almgren>
Date:   Thu Nov 6 17:26:10 2008 +0000

    Add additional verbosity about which convergence criterion was satisfied.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 094e2a29eed2ed72c9d1e6f5379a3062f58a3176
Author: lijewski <lijewski>
Date:   Thu Nov 6 17:14:49 2008 +0000

    Added do_full_knapsack flag which defaults to false.
    The default implies that we skip the triply nested loop which swaps boxes
    trying to get the efficiency above the threshold.
    We just sort the boxes and pass them out in the most efficient manner we
    can and let that suffice.

Src/C_BaseLib/DistributionMapping.cpp

commit 0c4b0a28a9da805483ce809f4644c17ed08b146d
Author: almgren <almgren>
Date:   Wed Nov 5 18:07:36 2008 +0000

    In gs_rb_smoother_1d, do lexicographical rather than GSRB smoothing --
    GSRB just wasn't working...

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 371653ae860d349b09caf83da8ccc872ee1c3cd6
Author: almgren <almgren>
Date:   Wed Nov 5 18:07:08 2008 +0000

    Don't call line solve for DIM=1 and more than one box -- call gs_rb_smoother_1d
    instead.

Src/LinearSolvers/F_MG/mg.f90

commit d7f74cb600c20f464f801d1a7174cf79d5f20451
Author: lijewski <lijewski>
Date:   Wed Nov 5 00:10:43 2008 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit 80c6c4d26e72b067e717049c4ac1225f0f3f74ea
Author: lijewski <lijewski>
Date:   Mon Nov 3 23:33:30 2008 +0000

    Now count & output # of passes thru core of knapsack() algorithm.
    max_efficienty now defaults to 0.9 and sfc_threshold to 6.

Src/C_BaseLib/DistributionMapping.cpp

commit 56b6721eea39712d3ffe8aa7daca681b568eaec6
Author: lijewski <lijewski>
Date:   Mon Nov 3 20:22:52 2008 +0000

    refine_grid_layout now defaults to true.
    ----------------------------------------------------------------------
    removed automatically CVS: CVS: Committing in .
    ----------------------------------------------------------------------

Src/C_AMRLib/Amr.cpp

commit 48d57db7a4629ba451ba3210e9ee8fcd76b2216c
Author: lijewski <lijewski>
Date:   Fri Oct 31 20:40:02 2008 +0000

    Moved template statics set via ParmParse into FabArraBase & set'm via BoxLib::Initialize().

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit ab8108f51de0387b886f60b49f925d973af7bc46
Author: lijewski <lijewski>
Date:   Thu Oct 30 20:03:31 2008 +0000

    Added refine_grid_layout, but it defaults to false for the time being.

Src/C_AMRLib/Amr.cpp

commit 1ae0f3972219eeb98a5f76403391e1a00d6694cb
Author: sepp <sepp>
Date:   Wed Oct 29 16:50:44 2008 +0000

    1) add MultiFab Divide operation similar to Subtract

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit eb6316693b843f620a08709dd89a46b2570da3ca
Author: sepp <sepp>
Date:   Tue Oct 28 21:51:50 2008 +0000

    1) add a Multiply operation similar to Subtract

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit e6af54e676510c958bbb43b9c4beae10c7707641
Author: lijewski <lijewski>
Date:   Fri Oct 24 21:05:35 2008 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit b127ca9cb4efb1213b55e20eeffb5c6a4ff29ca2
Author: lijewski <lijewski>
Date:   Fri Oct 24 03:47:29 2008 +0000

    skip over orphaned DMs in GetMap()

Src/C_BaseLib/DistributionMapping.cpp

commit 2dd0f7044ed1bd34fb2e30156502dd5e66fbd208
Author: vince <vince>
Date:   Thu Oct 23 19:56:37 2008 +0000

    added gigan.

Tools/C_mk/Make.mpi

commit 3f1a4a9d9e8d9286e6d510ec5e045f02fe0a8c35
Author: ajnonaka <ajnonaka>
Date:   Wed Oct 22 22:45:44 2008 +0000

    fixed bug in index-ing

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 4505f4697aaa993a507a35814450e673d6f5f9b9
Author: lijewski <lijewski>
Date:   Wed Oct 22 19:56:38 2008 +0000

    Fixed bug in build_copy() routines that Candace found.

Src/F_BaseLib/multifab.f90

commit b8d09d253d3bd3470d014ce5acdbad0d0f627b4a
Author: almgren <almgren>
Date:   Tue Oct 21 17:47:58 2008 +0000

    Switched order of lines -- no functional change.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 8202f31ed6461ab672f5c1d18c3555053df44825
Author: almgren <almgren>
Date:   Mon Oct 20 18:24:40 2008 +0000

    Dont need to print the RHS on the way back up the V-cycle ... it hasn't
    changed since the start of the V-cycle...

Src/LinearSolvers/F_MG/mg.f90

commit 1e42451bb0465922254486fa79a3a13b3d16678d
Author: almgren <almgren>
Date:   Mon Oct 20 18:23:10 2008 +0000

    Fixed formatting of print statements for easier reading when debugging.
    (Numbers now line up...)

Src/LinearSolvers/F_MG/mg.f90

commit fe4436e0bb5bf550052f073b8f111cef35d2a0be
Author: lijewski <lijewski>
Date:   Thu Oct 16 18:13:23 2008 +0000

    reverted back out recent GetBndryCells() changes

Src/C_BaseLib/BoxArray.cpp

commit 398d578c060363c8d8215c2191db18108e1f0c66
Author: lijewski <lijewski>
Date:   Thu Oct 16 16:03:01 2008 +0000

    Do a maxSize(64) after simplify() in GetBndryCells().

Src/C_BaseLib/BoxArray.cpp

commit 0fb1ab30496c993f74f29812c7e552765678f2f7
Author: lijewski <lijewski>
Date:   Thu Oct 16 16:02:32 2008 +0000

    Do a maxSize(64) after simplify() in initialize().

Src/C_AMRLib/AuxBoundaryData.cpp

commit 35a6b3e28bb14c901029941d3cf932825646e3e3
Author: lijewski <lijewski>
Date:   Wed Oct 15 22:45:30 2008 +0000

    GetBndryCells() now does a simplify().

Src/C_BaseLib/BoxArray.cpp

commit 8d223e40d3c1e30370139b26ee8d5714b077ccae
Author: lijewski <lijewski>
Date:   Wed Oct 15 22:43:34 2008 +0000

    now do a simplify() in initialize()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 808495d83a2b5880e8ee78a67176a0e1c65ccc4a
Author: marc <marc>
Date:   Sat Oct 11 00:23:53 2008 +0000

    Add default flag to Mikes FPB code interface

Src/C_BaseLib/Geometry.H

commit 2ecad1689d2c207feb420abd313be95d2e8785c3
Author: lijewski <lijewski>
Date:   Fri Oct 10 23:31:57 2008 +0000

    now use Ofast for PathScale optimization

Tools/C_mk/Make.Linux

commit ea6dd82c6d561b14f142a28b3f268878c82c1116
Author: lijewski <lijewski>
Date:   Fri Oct 10 22:35:41 2008 +0000

    FillPeriodicBoundary() is now a template in BoxLib namespace on FabArray<FAB>
    ----------------------------------------------------------------------
    automatically CVS: CVS: Committing in .  CVS: CVS:
    Modified Files: CVS:    Geometry.H Geometry.cpp CVS:
    ----------------------------------------------------------------------

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 375bf5eb505a4303e710de7ebc20bc2744e0b603
Author: lijewski <lijewski>
Date:   Mon Oct 6 20:22:09 2008 +0000

    use 'fast' instead of 'O' for optimization with PGI

Tools/C_mk/Make.Linux

commit 383b33dbd9dacecb01b2f914267db904442b5b69
Author: ajnonaka <ajnonaka>
Date:   Mon Oct 6 17:13:07 2008 +0000

    using -Ofast optimization - seems to give a few more percent speed bonus

Tools/F_mk/GMakedefs.mak

commit 3a843ee02a359118f84a8cd6371d4ca780c189f4
Author: ajnonaka <ajnonaka>
Date:   Mon Oct 6 16:33:38 2008 +0000

    adding -ipa flag back in, so that means you need to
    
    module swap pathscale pathscale/3.2
    
    on franklin before next week, when 3.2 becomes the default.
    
    Testing shows -ipa runs faster

Tools/F_mk/GMakedefs.mak

commit 5398a0d5a8ed5cf89a737e0bd6b0b02c97f70ddc
Author: ajnonaka <ajnonaka>
Date:   Sun Oct 5 00:05:26 2008 +0000

    i've permanently disabled the -ipa flag.
    
    now the default pathscale compilers (3.1) work on jaguar AND franklin.
    
    3.2 should work as well, but I'm going back to the default 3.1

Tools/F_mk/GMakedefs.mak

commit 78fca4e7f488f24275883a6f122f6d61c20afafd
Author: ajnonaka <ajnonaka>
Date:   Sat Oct 4 23:12:47 2008 +0000

    oops; franklin's hostnane is nid*.  works now

Tools/F_mk/GMakedefs.mak

commit ba43b98ee1d58d590dfd2fc3d6a6951dc2dfad1b
Author: ajnonaka <ajnonaka>
Date:   Sat Oct 4 23:05:39 2008 +0000

    if franklin, disable -ipa flags.  after a make realclean, MAESTRO compiles on franklin again

Tools/F_mk/GMakedefs.mak

commit 54794f0ac83cd4339403e1d27df3cea5b5d539dd
Author: almgren <almgren>
Date:   Thu Oct 2 19:10:33 2008 +0000

    Impose a limit on how many times you regrid on initialization.  Previously
    one could go on regridding indefinitely; now there's a limit of 4 times
    through the regridding process.   The integer MaxCnt is locally defined
    and arbitrarily set to 4; we could ParmParse this later if needed.

Src/C_AMRLib/Amr.cpp

commit 20c347c3945b6e058dacde809b9cb6c1d2484e70
Author: almgren <almgren>
Date:   Wed Oct 1 18:20:07 2008 +0000

    Added an option to generate a runlog_terse which prints only the step number,
    time and dt, with no words.   It is set by amr.run_log_terse = filename in the inputs file.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 0d3bce175e3190fdaad32c7a5430a5417c2bd9ff
Author: lijewski <lijewski>
Date:   Tue Sep 30 20:48:29 2008 +0000

    mods for when there are no bndry cells; i.e. triply periodic

Src/C_AMRLib/AuxBoundaryData.cpp

commit 1c37a999bb1410117d38c665c79327cd97bc2a13
Author: lijewski <lijewski>
Date:   Tue Sep 30 17:17:04 2008 +0000

    FillBoundary() is now in FabArray

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit b9dab17ad19cd8789d131cf3aff56039004db413
Author: mzingale <mzingale>
Date:   Tue Sep 30 14:28:49 2008 +0000

    an updated version of the changelog script (taken from
    http://www.red-bean.com/cvs2cl/).
    
    This version seems to work better with recent CVS changes.

Tools/F_scripts/cvs2cl.pl

commit 02f6c735d587407ccc97b2a9a03bbdee46bba23d
Author: almgren <almgren>
Date:   Fri Sep 26 21:01:27 2008 +0000

    For nodal_smoother_3d, Jacobi iteration, only update uu = uu_temp
    if we've actually defined uu_temp.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 667a2d4011430d5419e01e320be187bf8e027a21
Author: vince <vince>
Date:   Thu Sep 25 22:50:21 2008 +0000

    strstream update.

Src/C_AMRLib/DatasetClient.cpp

commit d766fd0b5c20d10f0c123adb7f5d6ce425ecd8ca
Author: sepp <sepp>
Date:   Tue Sep 23 14:45:01 2008 +0000

    1) reverse Ann's change that turns off icc for v 9.0 of compiler

Tools/C_mk/Make.defs

commit 892fa6df3d6eae6d36af04b58264abc2d8f73778
Author: ajnonaka <ajnonaka>
Date:   Mon Sep 22 18:40:03 2008 +0000

    #f90sources += mt19937ar.f90 putting local copy in wdconvect instead since this sompiles so slowly

Src/F_BaseLib/GPackage.mak

commit 9e6d0cd0becb47c3dbdddcec29b48e7e1ba39542
Author: ajnonaka <ajnonaka>
Date:   Mon Sep 22 18:35:33 2008 +0000

    f90sources += mt19937ar.f90

Src/F_BaseLib/GPackage.mak

commit e6f179cea2e41bb385949b2274b547f664acbf60
Author: ajnonaka <ajnonaka>
Date:   Wed Sep 17 20:49:05 2008 +0000

    added mpi capabilities for atragon

Tools/F_mk/GMakeMPI.mak

commit 6f83689e0ad5efd94e18060c747c38bd45327285
Author: vince <vince>
Date:   Wed Sep 17 20:01:52 2008 +0000

    added atragon and gojira.

Tools/C_mk/Make.mpi

commit 23f078aef33bff19a27f27731051bb16a669b75f
Author: ajnonaka <ajnonaka>
Date:   Thu Sep 11 15:19:00 2008 +0000

    aligned the tabs so the logic reads easier

Src/LinearSolvers/F_MG/mg.f90

commit e72c55c8d622fd99794a26677f50207bb54ae671
Author: ajnonaka <ajnonaka>
Date:   Wed Sep 10 21:11:44 2008 +0000

    fixed a line of code that didn't work with intel compiler version 9.1.043

Src/F_BaseLib/fillpatch.f90

commit 6a009601099d8431ec97659e2654f230c2d34690
Author: ajnonaka <ajnonaka>
Date:   Wed Sep 10 21:11:17 2008 +0000

    made the cpy_ functions public

Src/F_BaseLib/multifab.f90

commit f5afb812ab9fe80b1958b00698f89b90d86114db
Author: ajnonaka <ajnonaka>
Date:   Mon Sep 8 19:39:20 2008 +0000

    works for ng = 0

Src/F_BaseLib/fillpatch.f90

commit 2f8768296bd80af36268a2a331e920c2801c39dd
Author: lijewski <lijewski>
Date:   Mon Sep 8 19:26:20 2008 +0000

    fix for case when ng==0

Src/F_BaseLib/fillpatch.f90

commit a5d85147d92ff54e82c03ed9da14198d5a28308b
Author: marc <marc>
Date:   Thu Sep 4 17:14:28 2008 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/inputs.2d
Src/LinearSolvers/C_CellMG/Test/inputs.3d
Tests/LinearSolvers/C_CellMG/inputs.2d
Tests/LinearSolvers/C_CellMG/inputs.3d

commit c948ebac1caf8f10b4541813e5ed225b1e8e6dae
Author: marc <marc>
Date:   Thu Sep 4 17:00:04 2008 +0000

    Added arguments to COEF call to satisfy compiler

Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit a0fc4d1a1fc3f47e3c55c87d19e9a69dfb735f56
Author: ajnonaka <ajnonaka>
Date:   Wed Sep 3 00:16:03 2008 +0000

    including tag_boxes.f90 and make_new_grids.f90 in the boxlib GPackage.mak instead of modifying all of my local directories.

Src/F_BaseLib/GPackage.mak

commit de30a123510a6556602fe0bc869e2ba43fe84bcc
Author: ajnonaka <ajnonaka>
Date:   Tue Sep 2 22:12:23 2008 +0000

    tag_boxes no longer relies on a "ng_cell" from probin.  ng is computed within this function

Src/F_BaseLib/tag_boxes.f90

commit c2bd368700ea98de78599f5936e41621d85bef07
Author: almgren <almgren>
Date:   Mon Sep 1 22:58:40 2008 +0000

    Add scale_residual_1d call so that 1d does the same thing
    as 2d and 3d.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 114c78887bf2495f29013787bd997ee67633dba5
Author: ajnonaka <ajnonaka>
Date:   Thu Aug 28 17:41:48 2008 +0000

    made 2d consistent with 3d

Src/F_BaseLib/tag_boxes.f90

commit 58f2c01ec3937263cfaeb4c86a1939d877467c87
Author: ajnonaka <ajnonaka>
Date:   Wed Aug 27 23:04:11 2008 +0000

    Every instance of tag_boxes.f90 that was not in boxlib was identical.  So I removed them all from the local directories and made the default version in boxlib the same as the removed copies.

Src/F_BaseLib/tag_boxes.f90

commit 6e8d34f178d31634a535a2a50b54d31310feb47a
Author: ajnonaka <ajnonaka>
Date:   Wed Aug 27 22:57:30 2008 +0000

    Fixed a bug where nothing would ever be tagged for level 4 or greater.
    Also, the comments did not match the code.  The code did a nonsensical tagging, so I made the code match the comments, which did make sense.

Src/F_BaseLib/tag_boxes.f90

commit 2e5ae3b3dd7e47ddf2e90b4e1093ce98c014f447
Author: mzingale <mzingale>
Date:   Tue Aug 26 15:18:39 2008 +0000

    add the 2-d gaussian diffusion problem

Tools/C_util/regtests/Castro-tests.ini

commit 159a4ca3f6775509b3db1fc48f3bc7ce9d2bda79
Author: almgren <almgren>
Date:   Mon Aug 25 23:08:04 2008 +0000

    Replace "area" by "coeffs" in set_gravity_coefficients.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 61f3cff25ac1196d7213c347dcb3bf83478f04bc
Author: almgren <almgren>
Date:   Mon Aug 25 23:07:31 2008 +0000

    Replace "area" by "coeffs"

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H

commit 769db6da23636a0f1e373168580554dd39f87512
Author: almgren <almgren>
Date:   Mon Aug 25 23:06:52 2008 +0000

    Remove geom from call to set_gravity_coefficients.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit ed045ff040927194ac938f48b84735b2e3f1a94a
Author: mzingale <mzingale>
Date:   Mon Aug 25 20:56:41 2008 +0000

    fix a crash if the benchmark file was not found

Tools/C_util/regtests/test.py

commit d4538e9a2cb32d3e287ae20326f6b2492d24261b
Author: almgren <almgren>
Date:   Mon Aug 25 20:12:10 2008 +0000

    Add mgt_applyop.

Src/LinearSolvers/F_MG/mg_cpp_f.h

commit be3eff82684339c11f241e691ea94908c0fb00d6
Author: almgren <almgren>
Date:   Mon Aug 25 19:57:32 2008 +0000

    Add mgt_applyop() to be called from MGT_Solver.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit d06a9c57f032ef3f25850e2334aa3e8164897629
Author: almgren <almgren>
Date:   Mon Aug 25 17:38:35 2008 +0000

    Add applyop interface (modeled on compute_residual interface).

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 739774c229edd5405a1684eb672d84a50d6d8218
Author: almgren <almgren>
Date:   Mon Aug 25 17:30:54 2008 +0000

    ml_cc_applyop didn't need fine_mask to be passed in - it was used in defining
    Anorm and bnorm which were unused.

Src/LinearSolvers/F_MG/ml_cc.f90

commit df0356bf2ce39767dcac8a974b56e022fce1377b
Author: ajnonaka <ajnonaka>
Date:   Thu Aug 21 18:19:56 2008 +0000

    fixed a bug in ml_restriction_c where we were filling the boundary on all the components, not lnc.

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 4b11ae02b2a11a00a191b88190dd6a8c1786b04f
Author: mzingale <mzingale>
Date:   Mon Aug 18 19:33:11 2008 +0000

    don't do vis if we are making benchmarks

Tools/C_util/regtests/test.py

commit fe32486c6ab13bb109b75cb14f542ff92c26dca3
Author: mzingale <mzingale>
Date:   Mon Aug 18 14:26:12 2008 +0000

    add the vis image to the report page

Tools/C_util/regtests/test.py

commit 810d5a1b07a5933638b0510dd93964be5779611c
Author: mzingale <mzingale>
Date:   Mon Aug 18 03:10:01 2008 +0000

    start adding the framework for visualization

Tools/C_util/regtests/test.py

commit afd5955cfc561e6a6ac5ce10f170539a82382dc9
Author: mzingale <mzingale>
Date:   Sun Aug 17 23:19:46 2008 +0000

    update to reflect dx = dr changes

Tools/C_util/regtests/Maestro-tests.ini

commit 377b1530dd35527597d57ee2da14ea08088778df
Author: vince <vince>
Date:   Tue Aug 12 00:09:49 2008 +0000

    added battra.

Tools/C_mk/Make.mpi

commit 91a8250ba81a934de2334cac04518260b5b06632
Author: vince <vince>
Date:   Mon Aug 11 19:18:06 2008 +0000

    changes for manda.

Tools/C_mk/Make.mpi

commit d49646397c57d3b80f0bcd6b3b36c4a314352511
Author: almgren <almgren>
Date:   Thu Aug 7 21:30:12 2008 +0000

    Create pmask from la_array(1), not la_array(nlevs)

Src/F_BaseLib/make_new_grids.f90

commit 05a31180cdd311fd68b34be8d40f1f40998ea2e3
Author: almgren <almgren>
Date:   Thu Aug 7 21:18:52 2008 +0000

    1) Fix regridding and proper nesting.
    2) Move min_eff and minwidth to cluster and add functionality to set them through probin.

Src/F_BaseLib/cluster.f90
Src/F_BaseLib/make_new_grids.f90

commit 822ac78a0aea0a83d996a5881b05735afdf7b43d
Author: almgren <almgren>
Date:   Thu Aug 7 21:15:22 2008 +0000

    Don't need cluster_2d.f90 anymore -- we use cluster.f90 for 2d and 3d.

Src/F_BaseLib/cluster_2d.f90

commit 8670e15b3c8748c0ac4cb72b33e2f61c0904941d
Author: almgren <almgren>
Date:   Wed Aug 6 21:58:09 2008 +0000

    Move the test on being close to the domain boundary *after* instead of *before*
    the proper nesting test.

Src/F_BaseLib/make_new_grids.f90

commit 81660235761719f2ec2bfa9acd33806d3c8fc3fa
Author: almgren <almgren>
Date:   Wed Aug 6 21:43:05 2008 +0000

    If a fine grid is within 2 fine cells of a physical non-periodic boundary, then
    make the grid touch the boundary instead of staying 2 cells away.  We don't know
    how to fillpatch the third ghost cell if it's outside the domain but the grid
    doesn't touch the domain boundary.

Src/F_BaseLib/make_new_grids.f90

commit c6098553f14939a723f9e5d184d91e1964e7f864
Author: vince <vince>
Date:   Wed Aug 6 19:38:44 2008 +0000

    changes for naphta.

Tools/C_mk/Make.mpi

commit f54f2a0014bb116c33240f4d5876ddd44378cfea
Author: almgren <almgren>
Date:   Wed Aug 6 19:35:26 2008 +0000

    Only do proper nesting test if there are in fact grids at the finer level.

Src/F_BaseLib/make_new_grids.f90

commit e404ef00456e73c001efb3d797d46a54e3f609e9
Author: almgren <almgren>
Date:   Wed Aug 6 19:29:38 2008 +0000

    Dont call cluster if there are no tagged points.

Src/F_BaseLib/make_new_grids.f90

commit 5d45bf21207d022d3b1ba320eb018a9fa9bb10de
Author: vince <vince>
Date:   Wed Aug 6 18:30:25 2008 +0000

    change for naphta.

Tools/C_mk/Make.mpi

commit bb0431a95517172e20f24485c4bc8e476afc5cbe
Author: lijewski <lijewski>
Date:   Wed Aug 6 16:16:23 2008 +0000

    destroy() tagboxes in enforce_proper_nesting()

Src/F_BaseLib/make_new_grids.f90

commit 7aa52e52149a58b13adef9b78b13f52295c63bc1
Author: almgren <almgren>
Date:   Wed Aug 6 03:09:43 2008 +0000

    1) Removed probin_module from enforce_proper_nesting.
    2) Modified enforce_proper_nesting so it calls the clustering
    algorithm to create the new grids, instead of just adding small grids
    to the existing one.  This allows us to use the minwidth criteria already
    in cluster.

Src/F_BaseLib/make_new_grids.f90

commit c840d16110276d04e11d91030d9da8f6ff2619b7
Author: almgren <almgren>
Date:   Wed Aug 6 00:03:57 2008 +0000

    Modify the call to the proper_nested routine.

Src/F_BaseLib/ml_boxarray.f90

commit 56234e6b739f6b07de50a440f79e17abb0c68cde
Author: almgren <almgren>
Date:   Wed Aug 6 00:03:36 2008 +0000

    Moved enforce_proper_nesting into here.

Src/F_BaseLib/make_new_grids.f90

commit 8b59d08bca5c2485d8673c3e81943593bd5a8835
Author: almgren <almgren>
Date:   Tue Aug 5 23:01:46 2008 +0000

    Set minwidth = 4 instead of 2.

Src/F_BaseLib/make_new_grids.f90

commit 9bbb2b384d03b9ca065a12935ed3495142408aea
Author: almgren <almgren>
Date:   Tue Aug 5 21:10:22 2008 +0000

    Hopefully we fixed the case where multifab_fill_ghost_cells asks fillpatch
    to fill a box which is completely outside the domain.

Src/F_BaseLib/fillpatch.f90

commit 25d8e3b7e5dfe37acd7e4616d2e2e18a26f505d2
Author: gilet <gilet>
Date:   Tue Aug 5 18:08:43 2008 +0000

    mpich now works on gigan

Tools/F_mk/GMakeMPI.mak

commit 5e497bd81a9c95ec8ac0af8d704d86ee9bae3278
Author: almgren <almgren>
Date:   Mon Aug 4 23:19:06 2008 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/stencil.f90

commit ac860ad274039c9ad1e93d43cec75f6fd078eb60
Author: almgren <almgren>
Date:   Mon Aug 4 23:13:02 2008 +0000

    Fix a typo.

Src/LinearSolvers/F_MG/stencil.f90

commit 68e48b55bea10ad578490d7b0cf9f7331d660de5
Author: almgren <almgren>
Date:   Mon Aug 4 23:09:49 2008 +0000

    1) Use the beta's since they carry the viscous coefficients for the viscous/diffusive solves.
    2) Add the alpha -- forgot that last time.

Src/LinearSolvers/F_MG/stencil.f90

commit 6d2fd2989c5a576e01ce8d2f788078c0db917f97
Author: almgren <almgren>
Date:   Mon Aug 4 22:59:43 2008 +0000

    Put full 9-pt cross stencil back in.

Src/LinearSolvers/F_MG/stencil.f90

commit e3d60dd262d80abd7515820b69302c57289f0d8e
Author: almgren <almgren>
Date:   Mon Aug 4 22:45:16 2008 +0000

    I have added the functionality to do Minion's 4th order constant density
    stencil -- the coefficients are independent of beta for now, and the
    1-d stencil would be (i-2,j), (i-1,j), (i,j), (i+1,j) (i+2,j) and analogously
    in 2d.  Only 2d is coded.

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/stencil.f90

commit bd758e0109283441b91b9c3daebe43360adfda58
Author: almgren <almgren>
Date:   Fri Aug 1 23:11:45 2008 +0000

    Remove unused "proc"

Src/F_BaseLib/cluster.f90

commit 93c7fac93048fa5abda08827d25130d9e5c4ed7a
Author: almgren <almgren>
Date:   Fri Aug 1 23:11:02 2008 +0000

    Remove unused ibxs(:)

Src/F_BaseLib/cluster.f90

commit 24bd14f0fe3b452b1bb96b6a47ee025705e636d2
Author: mzingale <mzingale>
Date:   Fri Aug 1 17:49:14 2008 +0000

    the C99 standard moves std::abort into cstdlib and std::strerror into
    cstring, so these header files need to be added in the appropriate places.
    This allows Castro to compile with GCC 4.3

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/ParallelDescriptor.cpp

commit ff69775c3e3e1e26f708d9028ca0666de1dd163a
Author: lijewski <lijewski>
Date:   Thu Jul 31 21:55:48 2008 +0000

    added version of GetVolume() taking a FArrayBox

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit c0250fefe8326f3debd5e0873a2379d9e5303ff7
Author: almgren <almgren>
Date:   Thu Jul 31 20:42:51 2008 +0000

    Replace bl_abort by bl_error.

Src/LinearSolvers/F_MG/mg.f90

commit 333a02938b61f17ee63996c2ae00ee984fddc82a
Author: almgren <almgren>
Date:   Thu Jul 31 19:43:41 2008 +0000

    This changes the default scheme for 1-d cell-centered solves.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_smoother.f90

commit 5e1b9f4afcea7ac044eebae3f460b91625da300a
Author: lijewski <lijewski>
Date:   Thu Jul 31 18:05:48 2008 +0000

    added GetFaceArea() taking FArrayBox & grid index parallel one taking MultiFab and grid

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 68fc28aae036f93ee319e69a7b5a4dd8b6361227
Author: almgren <almgren>
Date:   Thu Jul 31 17:54:27 2008 +0000

    Put new mpi link for manda only.

Tools/C_mk/Make.mpi

commit 5e59022010ff1892e849e84dbf2d39dc01f42447
Author: almgren <almgren>
Date:   Wed Jul 30 20:48:10 2008 +0000

    Don't pass in the default value of omega when defining the solver; instead
    let mg.f90 define an appropriate value.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 0562d68c650fde20db4873de31c1573d14799e40
Author: almgren <almgren>
Date:   Wed Jul 30 20:47:10 2008 +0000

    Add omega default for 1-d : by trial and error, 0.6 seems to work well.

Src/LinearSolvers/F_MG/mg.f90

commit 8af542607bce7030c015f84a0acbaf5aa43fa70e
Author: lijewski <lijewski>
Date:   Wed Jul 30 01:10:47 2008 +0000

    littlea cleanup

Src/C_BaseLib/BaseFab.H

commit b061a04a7f6f724ee897313029a2647383e9f248
Author: lijewski <lijewski>
Date:   Wed Jul 30 00:54:45 2008 +0000

    fixed bug related to calculating FAB byte spread and clear() calls

Src/C_BaseLib/BaseFab.H

commit 87da79b5ccc60497668e79f1518968878820f248
Author: almgren <almgren>
Date:   Tue Jul 29 19:32:04 2008 +0000

    Remove stray line -- no change in functionality (caught by Candace G)

Src/F_BaseLib/multifab.f90

commit a43a2b059f7f7676c2ac1530713ec70ef7df2191
Author: lijewski <lijewski>
Date:   Tue Jul 29 16:28:08 2008 +0000

    modest simplification

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit e5ccb158db0c1dd97ad135704c70ac1cd4facaf1
Author: lijewski <lijewski>
Date:   Wed Jul 23 21:38:57 2008 +0000

    some memory cleanup

Src/C_AMRLib/AmrLevel.cpp

commit 415c0a247654c429fb8a2de125d8a493978ed5dc
Author: lijewski <lijewski>
Date:   Wed Jul 23 17:18:34 2008 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit ce1f87bf8056a78f313a12a8b1113623442b43d9
Author: mzingale <mzingale>
Date:   Mon Jul 21 19:45:46 2008 +0000

    use the new compare tool

Tools/C_util/regtests/Castro-tests.ini

commit f08e4ca050cfae6cde1c15ba26322fcdb32a5c88
Author: mzingale <mzingale>
Date:   Mon Jul 21 19:32:45 2008 +0000

    do the cvs update on fParallel still

Tools/C_util/regtests/test.py

commit 7f7d54ef398bfa33324cb67bbfc1e6cf195afcfd
Author: mzingale <mzingale>
Date:   Mon Jul 21 19:28:27 2008 +0000

    new compare tool

Tools/C_util/regtests/Maestro-tests.ini

commit 91605dbc5aae03889742aef8fae5392db55b5a71
Author: mzingale <mzingale>
Date:   Mon Jul 21 19:27:59 2008 +0000

    switch over to using fParallel/data_processing/fcompare to do the
    comparisons -- this works even if the list of variables changes, so
    a better comparison can be done on those that remain.  It also does
    1-,2-, and 3- all in one executable.

Tools/C_util/regtests/test.py

commit 4cf2c2ae111219aeac2454621310a88ff8c620d4
Author: almgren <almgren>
Date:   Fri Jul 18 23:57:31 2008 +0000

    1) Added gs_rb_smoother_1d as well as line solve -- use gsrb if more than
    one grid at the level, it works better with V-cycle.
    2) Moved defn of mgt%dim to the top because it was getting used before it was defined.

Src/LinearSolvers/F_MG/mg.f90

commit ac96e1bd59a79dad316d9f6a51b1914c551a19c1
Author: almgren <almgren>
Date:   Fri Jul 18 23:45:30 2008 +0000

    Add gs_rb_smoother_1d for 1d gsrb relaxation -- need to use this
    instead of line solve for multiple grids, otherwise mg v-cycles
    seem to have a hard time.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 07b334e82ffe753eba13cc35d323cbf9af337db5
Author: ajnonaka <ajnonaka>
Date:   Thu Jul 17 14:10:14 2008 +0000

    fixed multilevel, 3d, out-of-bounds bug

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit c8de02dfe79396efc00e5e8f484883eaf2a18d06
Author: marc <marc>
Date:   Wed Jul 16 22:48:41 2008 +0000

    marc hacking for gigan

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 85ff82403033e64276542a734800c5394e09328a
Author: almgren <almgren>
Date:   Wed Jul 16 20:57:52 2008 +0000

    Made same changes for 1d as already done for 2d and 3d in setting stencils
    at interior grid boundaries.

Src/LinearSolvers/F_MG/stencil.f90

commit 908cb27c25e4c8e40741da38f5cef36062fc71bd
Author: almgren <almgren>
Date:   Wed Jul 16 17:48:57 2008 +0000

    Introduced new integer member of Amr :  file_name_digits.   This defaults
    to 5, but can be set in parmparse.  This is the number of digits used
    in plotfile names and checkpoint file names.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 91f134043afcd4240e300f4d2348a5a70c2e2db6
Author: lijewski <lijewski>
Date:   Wed Jul 16 17:40:24 2008 +0000

    added mindigits 3rd arg to Concatenate() that defaults to 5

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 868724a66616793573533460b54ae08cf2ef39a5
Author: lijewski <lijewski>
Date:   Tue Jul 15 20:58:20 2008 +0000

    mods for intel -- needs more stuff than xlf95 says it should

Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/layout.f90

commit 53a43144c794630f236998fb5d9c68c2583fa185
Author: lijewski <lijewski>
Date:   Tue Jul 15 20:30:49 2008 +0000

    now compile with no complaints with xlf95 -qlanglev=95std

Src/F_BaseLib/bl_stream.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 9783467307ab19c99b0c88c5aeca2786a059d5d0
Author: lijewski <lijewski>
Date:   Sat Jul 12 18:51:45 2008 +0000

    plugged memory leak found by Candace

Src/LinearSolvers/F_MG/mg.f90

commit 16beda084a441ed3e25597fa1e76f14e10c8ece1
Author: lijewski <lijewski>
Date:   Thu Jul 10 23:24:16 2008 +0000

    removed unneeded module usage

Src/F_BaseLib/make_new_grids.f90

commit cab0f0f101215bd847e44e355140efb87da98a64
Author: lijewski <lijewski>
Date:   Thu Jul 10 20:17:39 2008 +0000

    plugged memory leak & make boxes via copy()

Src/F_BaseLib/make_new_grids.f90

commit df8871418459a084e349d9d65d83755c328799d7
Author: lijewski <lijewski>
Date:   Thu Jul 10 20:08:47 2008 +0000

    added a TODO and a timer

Src/F_BaseLib/cluster.f90

commit ef155deaa46f5c557c7bd4e7cac842962fcf4ee4
Author: almgren <almgren>
Date:   Thu Jul 10 19:29:20 2008 +0000

    Warning on no point flagged is now in make_new_grids instead of in cluster.

Src/F_BaseLib/cluster.f90

commit 47407998c9f4080a020a52b1fdfadae2e3fe76a7
Author: almgren <almgren>
Date:   Thu Jul 10 19:28:49 2008 +0000

    Put warning statement in make_new_grids if no points are tagged for refinement.

Src/F_BaseLib/make_new_grids.f90

commit 467bf9bfcd906ee46e15ba8d9c15fa986b32cc5d
Author: lijewski <lijewski>
Date:   Thu Jul 10 17:42:18 2008 +0000

    *** empty log message ***

Src/F_BaseLib/test/t_knapsack.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/t_knapsack.f90
Tests/F_BaseLib/t_main.f90

commit 39ea09e004ba2a2ec9fb943ac27e15333caff430
Author: lijewski <lijewski>
Date:   Thu Jul 10 17:41:59 2008 +0000

    can now intersect a boxlist with a box or another boxlist

Src/F_BaseLib/list_box.f90

commit d8feffb0482ba61282389c382fef2621bd58fb07
Author: mzingale <mzingale>
Date:   Thu Jul 10 17:12:32 2008 +0000

    get this working for fParallel runs again

Tools/C_util/regtests/test.py

commit 5a791f1e7d5a8ff894eb110b797f1fa405b8ec0d
Author: mzingale <mzingale>
Date:   Thu Jul 10 16:55:57 2008 +0000

    document the MPI stuff

Tools/C_util/regtests/test.py

commit aa5b93db4226a83196e953b0f392dfbc6c4fafe3
Author: lijewski <lijewski>
Date:   Thu Jul 10 16:10:14 2008 +0000

    Moved some list_box routines that were private in boxarray to list_box.
    More could be done but I'm hitting an Intel compiler error.

Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/list_box.f90

commit a085533a78aabcdacf2707081756ef1ad76aa62b
Author: mzingale <mzingale>
Date:   Thu Jul 10 14:21:17 2008 +0000

    add parallel:

Tools/C_util/regtests/Castro-tests.ini

commit f8a7765ffa31c9804c0e1549270072b24047b790
Author: mzingale <mzingale>
Date:   Thu Jul 10 14:20:52 2008 +0000

    get initial MPI stuff in the test suite to do parallel tests

Tools/C_util/regtests/test.py

commit 45025557c951afee098e89e33f46f92d4d3da02d
Author: mzingale <mzingale>
Date:   Thu Jul 10 13:48:18 2008 +0000

    only store ChangeLog.Parallel if we are doing a Parallel/ test

Tools/C_util/regtests/test.py

commit c838ecf9d216b0fbc2b4cf99a7a8303327059ba7
Author: lijewski <lijewski>
Date:   Thu Jul 10 05:57:52 2008 +0000

    removed couple unused & broken routines

Src/F_BaseLib/boxarray.f90

commit 9f35b545023d3da43e670dff3fa0ddb7ebd0f75e
Author: almgren <almgren>
Date:   Thu Jul 10 01:25:37 2008 +0000

    Fixed subroutine buffer.

Src/F_BaseLib/make_new_grids.f90

commit 6d6cbd5a4bb319989fdad8f3b53cda62e34370a1
Author: almgren <almgren>
Date:   Wed Jul 9 22:32:28 2008 +0000

    Set the setval back to true in subroutine buffer.

Src/F_BaseLib/make_new_grids.f90

commit e44c6288363705cd0e1ebbc90d133fe55eacc8b5
Author: almgren <almgren>
Date:   Wed Jul 9 22:30:44 2008 +0000

    Added machine della (Adam Burroughs' machine at Princeton) as an option.

Tools/C_mk/Make.defs

commit 251fb59d4a2e3aa1b4d742e62054f2b666d8319d
Author: almgren <almgren>
Date:   Wed Jul 9 22:28:57 2008 +0000

    Add machines manda and DELLA as new options.

Tools/C_mk/Make.mpi

commit 97e8fb8fc49d0a76b4e6c062e67c225eadea21af
Author: lijewski <lijewski>
Date:   Wed Jul 9 20:16:26 2008 +0000

    some cleanup & memory leak squashing

Src/F_BaseLib/make_new_grids.f90

commit cc4745a6e4545df9a88656300e46097f13d2e6b0
Author: lijewski <lijewski>
Date:   Wed Jul 9 19:48:05 2008 +0000

    changes a setval(.true.) to setval(.false.)

Src/F_BaseLib/make_new_grids.f90

commit 59babc59c3ac13b6308a519b9c2c34e72331570f
Author: almgren <almgren>
Date:   Wed Jul 9 00:04:58 2008 +0000

    Renamed regrid.f90 --> make_new_grids.f90

Src/F_BaseLib/make_new_grids.f90

commit db42c5c3425607e96725b32343f3f8737f831f8f
Author: almgren <almgren>
Date:   Tue Jul 8 23:53:01 2008 +0000

    Separated the tag_boxes functionality out of regrid --
    new files tag_boxes.f90

Src/F_BaseLib/regrid.f90
Src/F_BaseLib/tag_boxes.f90

commit edca25d116ddb9cd6a8fb743eebed5cfca386819
Author: almgren <almgren>
Date:   Tue Jul 8 23:39:52 2008 +0000

    Remove commented line.

Src/F_BaseLib/boxarray.f90

commit ec84735085dd74010bdac40a1a83c12def472e59
Author: lijewski <lijewski>
Date:   Tue Jul 8 23:08:13 2008 +0000

    tiny bit of cleanup

Src/F_BaseLib/multifab.f90

commit 5cafdd09b2f8f64e4ed57058b0d08767b356822e
Author: lijewski <lijewski>
Date:   Tue Jul 8 21:54:12 2008 +0000

    first cut at map_periodic()

Src/F_BaseLib/cluster.f90

commit 954dd032a6335be910cd2f293846d2af2f1bef6c
Author: almgren <almgren>
Date:   Mon Jul 7 18:05:26 2008 +0000

    This takes max_grid_size as an argument to make_new_grids, and some
    other changes..

Src/F_BaseLib/regrid.f90

commit d08eac4d58ad542ae0a48a625bad4f528a7ce97e
Author: almgren <almgren>
Date:   Thu Jul 3 21:32:39 2008 +0000

    Replace set_const_gravity_coefficients by a flagged version of set_gravity_coefficients.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 81e7a26958aa1b0d48f72b067ac446cbdf4ee12f
Author: almgren <almgren>
Date:   Thu Jul 3 00:05:28 2008 +0000

    Add another sanity check for proper nesting.

Src/F_BaseLib/ml_boxarray.f90

commit 7cea7eacf4ce7c5bbf9ea47269e677cc25be98c1
Author: almgren <almgren>
Date:   Thu Jul 3 00:04:30 2008 +0000

    Modify properly nested test to take optional arguments: min_level and max_level,
    so can test just between two levels.

Src/F_BaseLib/ml_boxarray.f90

commit b245b3c170aabfd18feff80addb9b7213b1a513f
Author: almgren <almgren>
Date:   Wed Jul 2 23:15:57 2008 +0000

    Removed commented line.

Src/F_BaseLib/fabio.f90

commit c8d07d382e98d5c15550b4df9d67f702ff2e2bec
Author: almgren <almgren>
Date:   Wed Jul 2 22:52:15 2008 +0000

    Fix ml_layout_restricted_build.

Src/F_BaseLib/ml_layout.f90

commit 400a307668f0007585835f306e0b74c64df98858
Author: almgren <almgren>
Date:   Wed Jul 2 22:18:16 2008 +0000

    Added new "subroutine ml_layout_restricted_build(mla, mba, nlevs, pmask)"
    which builds a ml_layout from the first nlevs levels of the mba.

Src/F_BaseLib/ml_layout.f90

commit 0c309f608deee0b8bd3ddeff308a11f760a48328
Author: ajnonaka <ajnonaka>
Date:   Wed Jul 2 16:13:31 2008 +0000

    plugged a very sneaky memory leak

Src/LinearSolvers/F_MG/mg.f90

commit 7e488348382406a5c9ac679fda3a032298fae1c6
Author: lijewski <lijewski>
Date:   Tue Jul 1 18:00:10 2008 +0000

    now contains GetBndryCells()

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit e9e648abe35f35834f6b512de26a016ac7c7a817
Author: lijewski <lijewski>
Date:   Tue Jul 1 17:59:33 2008 +0000

    moved GetBndryCells() to BoxArray

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit bb98e058a210d16fe9a341f16d6c56b4dc91ba30
Author: lijewski <lijewski>
Date:   Mon Jun 30 22:05:03 2008 +0000

    minimize copy()ing

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit d97ca14aa36a5653fbdf3125f12112d93d63f3b9
Author: lijewski <lijewski>
Date:   Thu Jun 26 23:04:34 2008 +0000

    slight reworking of ml_boxarray_properly_nested()

Src/F_BaseLib/ml_boxarray.f90

commit d71845dc0630a90f1203454121cd12b8ded98a2c
Author: lijewski <lijewski>
Date:   Thu Jun 26 21:02:48 2008 +0000

    more efficient periodic tests in properly_nested()

Src/F_BaseLib/ml_boxarray.f90

commit bffa60a879beb169be02b9d25d5985eed1cee480
Author: lijewski <lijewski>
Date:   Thu Jun 26 20:45:21 2008 +0000

    no need to grow box by ng before passing to box_periodic_shift()

Src/F_BaseLib/fillpatch.f90

commit 09f2e0572bec60f287427a2a193f01c039bfde9f
Author: lijewski <lijewski>
Date:   Thu Jun 26 15:58:19 2008 +0000

    *** empty log message ***

Src/F_BaseLib/boxarray.f90

commit eccb019a5c5872ebcdc8015b293fef095d23ea79
Author: lijewski <lijewski>
Date:   Thu Jun 26 15:57:56 2008 +0000

    added couple uses of boxarray_contains()

Src/F_BaseLib/test/t_knapsack.f90
Tests/F_BaseLib/t_knapsack.f90

commit 8e02e21edcce7b8094cd8e3cc72262ee1168c3a6
Author: almgren <almgren>
Date:   Thu Jun 26 05:38:50 2008 +0000

    I believe we now have a correct implementation of ml_boxarray_properly_nested.
    Only limited testing has been done, but it seems good.

Src/F_BaseLib/ml_boxarray.f90

commit a7a23c5f3f7022b86e0df8bceb8dc7fc48f34b25
Author: ajnonaka <ajnonaka>
Date:   Thu Jun 26 03:51:35 2008 +0000

    added "use_bl_error_module".  Code compiles again.

Src/F_BaseLib/boxarray.f90

commit 277a9424a2fbe46b5e401b7ac68065694348c4b6
Author: almgren <almgren>
Date:   Wed Jun 25 23:31:30 2008 +0000

    New functions added:
    1) function boxarray_boxarray_contains(ba1,ba2)  returns true if ba1 contains ba2
    2) function boxarray_box_contains(ba1,ba2)       returns true if ba  contains bx

Src/F_BaseLib/boxarray.f90

commit 69d154998f165199b830f6c37d415797f0ac89eb
Author: almgren <almgren>
Date:   Wed Jun 25 22:11:05 2008 +0000

    Replace the box_grow_i_m function by box_grow_n_m which actually makes the
    lo lower and the hi higher, unlike the previous box_grow_i_m, which made
    the lo lower and the hi lower (go figure).

Src/F_BaseLib/box.f90

commit 53a1edfb22633414220d71c0348924728f5f8114
Author: almgren <almgren>
Date:   Wed Jun 25 21:19:50 2008 +0000

    Fix ml_boxarray_properly_nested so that it correctly works *except*
    for periodic cases.  It takes an integer, nproper, which is how many
    grow cells are needed at the fine level to be contained by the
    coarser boxarray.

Src/F_BaseLib/ml_boxarray.f90

commit 1d5cdefddfc51f987d73572667838ddcce17f13b
Author: almgren <almgren>
Date:   Wed Jun 25 19:14:47 2008 +0000

    Change ml_boxarray_properly_nested_new -->  ml_boxarray_properly_nested
    and     ml_boxarray_properly_nested    -->  ml_boxarray_properly_nested_old

Src/F_BaseLib/ml_boxarray.f90

commit be42b2561364a1fd65a06cb0108bc9be8b519ec3
Author: almgren <almgren>
Date:   Wed Jun 25 18:04:29 2008 +0000

    Slight change in the test for creating maximum number of multigrid levels.
    One of the criteria for stopping the coarsening is now if the volume
    of the entire boxarray is less than or equal to 2**dim.  This makes the
    single-base-grid XRB initial divu iterations converge.
    
    Hopefully it won't break anything else (?).

Src/LinearSolvers/F_MG/mg.f90

commit 35141da3193b58fea2f66b670aa13a700f2f8459
Author: lijewski <lijewski>
Date:   Wed Jun 25 17:25:51 2008 +0000

    some cleanup

Src/F_BaseLib/cluster.f90

commit 9ffeffda76c2a58ba814c7541eaa1e6eb42b62dd
Author: almgren <almgren>
Date:   Wed Jun 25 15:12:05 2008 +0000

    Should use bchi instead of bclo in test on whether is BC_INT --
    oops!

Src/LinearSolvers/F_MG/stencil.f90

commit 42c006b1e1cc20c7a1286689e2bb87922061325e
Author: almgren <almgren>
Date:   Wed Jun 25 05:25:05 2008 +0000

    Changed the way we define the stencil at interior boundaries
    of grids -- this only changes the stencil values at the level
    of machine precision, but it helps in debugging ... now the stencils
    will be identical whether there is a single grid or multiple grids
    covering the same region.

Src/LinearSolvers/F_MG/stencil.f90

commit ffa8dfc18a95e4633ac510842023f7c52456bcaa
Author: lijewski <lijewski>
Date:   Tue Jun 24 22:29:58 2008 +0000

    fixed another parallel gotcha -- seems OK but more testing required

Src/F_BaseLib/cluster.f90

commit 129c4d783d8633bd549c37175cca5f4279a48d82
Author: almgren <almgren>
Date:   Tue Jun 24 20:09:01 2008 +0000

    Fix ml_edge_restriction to correctly handle the periodic fix.

Src/LinearSolvers/F_MG/ml_restriction.f90

commit f3ff013bc732fe7854ee9d0e6cde8587b369f547
Author: almgren <almgren>
Date:   Tue Jun 24 17:03:08 2008 +0000

    Remove fillpatch and multifab_fill_ghost_cells -- returning to previous approach
    where these are included in the directory where define_bc_tower lives...

Src/F_BaseLib/GPackage.mak

commit 615dab16fd637ddbca34112c7577a87bb4fac0e0
Author: almgren <almgren>
Date:   Tue Jun 24 05:29:58 2008 +0000

    Divide max_grid_size by ref_ratio since we create the new grids at the
    coarser resolution but we want max_grid_size to hold at the fine resolution.

Src/F_BaseLib/regrid.f90

commit 7d7ce5ac9fb186200e8dfdf47e3b13e79c4615b4
Author: almgren <almgren>
Date:   Mon Jun 23 23:29:56 2008 +0000

    Impose boxarray_maxsize on the new boxarray before making
    the new multifabs.

Src/F_BaseLib/regrid.f90

commit 07eeff2438ad0b88071b7ad83cbd63777aa4d0bc
Author: almgren <almgren>
Date:   Mon Jun 23 22:00:19 2008 +0000

    Take max_grid_size as an input into make_new_grids.

Src/F_BaseLib/regrid.f90

commit b398ff8064c6d7f6a9ce953440fcd29b5db2965b
Author: lijewski <lijewski>
Date:   Mon Jun 23 21:54:35 2008 +0000

    removed setval_mask() functions - not apparently used anywhere

Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab.f90

commit 38a194777523f042d5ece4ac18b7eab5f8e6c924
Author: almgren <almgren>
Date:   Mon Jun 23 21:42:34 2008 +0000

    Added fillpatch.f90 and multifab_fill_ghost_cells.f90 to GPackage.mak
    since we took them out of varden/GPackage.mak

Src/F_BaseLib/GPackage.mak

commit 0d55d87bdcbcfa1446213f53dec234cbeaa8e6d3
Author: lijewski <lijewski>
Date:   Mon Jun 23 21:29:27 2008 +0000

    removed potentially troublesome where constructs

Src/F_BaseLib/box.f90

commit 6b61a8e229ffdc7b372b10c58d8868d2140fb3ec
Author: ajnonaka <ajnonaka>
Date:   Mon Jun 23 20:07:52 2008 +0000

    in function box_grow_i_m, loop over dimensions instead of assuming dim=3

Src/F_BaseLib/box.f90

commit b7c9c0d9eefa2095767a7ef81c71412aae7ac716
Author: ajnonaka <ajnonaka>
Date:   Mon Jun 23 19:41:05 2008 +0000

    loop over l(i) instead of using where construct

Src/F_BaseLib/box.f90

commit ef78a96cdde29d8f89e80815bd0db52c2d9bcd8b
Author: lijewski <lijewski>
Date:   Sun Jun 22 18:02:27 2008 +0000

    *** empty log message ***

Src/F_BaseLib/cluster.f90

commit b273b88a0ba217bf71025bff2a3a97a1da427200
Author: lijewski <lijewski>
Date:   Fri Jun 20 16:34:52 2008 +0000

    clustering now works in parallel

Src/F_BaseLib/cluster.f90

commit 06776fcd768d19c05fb035102c292a3f131e67cc
Author: lijewski <lijewski>
Date:   Fri Jun 20 16:33:50 2008 +0000

    changed verbosity defaults

Src/F_BaseLib/knapsack.f90

commit 81e61e36dd914ee29646b2e5a876c727ea98c9ce
Author: lijewski <lijewski>
Date:   Mon Jun 16 20:50:56 2008 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit 128fb7d7c04fe7ae859b6feb53bb7f8cf4554275
Author: lijewski <lijewski>
Date:   Mon Jun 16 17:46:12 2008 +0000

    plugged some memory leaks

Src/LinearSolvers/F_MG/ml_restriction.f90

commit c4a8a4e26eedff2891898b15dcd5eb34dc7ab5a4
Author: almgren <almgren>
Date:   Sat Jun 14 01:56:54 2008 +0000

    Added new routine -- subroutine multifab_copy_on_shift --
    called only by ml_edge_restriction -- this enables copies across
    periodic edges.

Src/F_BaseLib/multifab.f90

commit 240c0d0ede8f67d3f7a7aa1f4cdf56d8b1162160
Author: almgren <almgren>
Date:   Sat Jun 14 01:56:09 2008 +0000

    Enable periodic averaging-down in ml_edge_restriction.

Src/LinearSolvers/F_MG/ml_restriction.f90

commit ba0b725bf865f1ae616d77cfe1b402648a5b19d4
Author: almgren <almgren>
Date:   Wed Jun 11 22:27:53 2008 +0000

    Fix for periodic -- where divu is not zero on the periodic edge.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 2371ebf6bc2fdd5ee302cd4a392c490a25a732f6
Author: lijewski <lijewski>
Date:   Wed Jun 11 17:03:38 2008 +0000

    mods to enable writing plotfiles in single precision

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c

commit be4755e974ae40a5c5c2796412b7916fb329c8b6
Author: mzingale <mzingale>
Date:   Mon Jun 9 23:50:40 2008 +0000

    fix a model file

Tools/C_util/regtests/Maestro-tests.ini

commit e8a90f4eb3d3ab003b75f3cb829247a6fd444ab8
Author: almgren <almgren>
Date:   Mon Jun 9 17:40:02 2008 +0000

    1) Cleaned up the crse/fine resid routine.
    2) We now include fine fluxes on periodic boundaries -- this seems to work for now.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 4f5fe45f32b65758b256e54de8fda704df334ef7
Author: mzingale <mzingale>
Date:   Sun Jun 8 22:30:57 2008 +0000

    update to reflect changes to the spherical problems

Tools/C_util/regtests/Maestro-tests.ini

commit c8193f3659314491d52ce1fb512e7261d77988cb
Author: lijewski <lijewski>
Date:   Tue Jun 3 23:45:09 2008 +0000

    some simplification of VisMF::Write

Src/C_BaseLib/VisMF.cpp

commit e5ce8eae5f68ecaa21b8ee5baee702e4b34bccc7
Author: aaspden <aaspden>
Date:   Tue Jun 3 20:09:14 2008 +0000

    Added a Barrier to prevent running out of PER_PROC message packets (happened on Jagwar)

Src/C_BaseLib/VisMF.cpp

commit 166d4b78845c851d26d0bff18284f15bd6da9efd
Author: almgren <almgren>
Date:   Tue Jun 3 19:44:30 2008 +0000

    Change mla and la from intent "inout" to intent "in"

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_solve.f90

commit 1fa362b7c438d25fad9763df0daa0aea4694f9cc
Author: almgren <almgren>
Date:   Tue Jun 3 19:44:00 2008 +0000

    Change la to "in" from "inout"

Src/F_BaseLib/bndry_reg.f90

commit c20ae4014dfe7b9cc91ace2d77bebc97dc8b53f1
Author: mzingale <mzingale>
Date:   Fri May 30 17:41:58 2008 +0000

    for jaguar, if we are doing PathScale don't include the -module part
    twice

Tools/F_mk/GMakedefs.mak

commit 555c3d7a0e5866c0b522f992eba9b7dd7c78323e
Author: jbb <jbb>
Date:   Wed May 28 17:04:25 2008 +0000

    Fix the print statements for the case where the initial guess solves
    the problem.  Also, in this case, don't even enter the iteration loop.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 5b219d90f0488b51eb082c42f92782b2971431b1
Author: gpau <gpau>
Date:   Sat May 24 14:57:42 2008 +0000

    some files for statistical analysis

Tools/C_util/Statistics/AVGDOWN_2D.F
Tools/C_util/Statistics/AVGDOWN_3D.F
Tools/C_util/Statistics/AVGDOWN_F.H
Tools/C_util/Statistics/ComputeAmrDataStat.H
Tools/C_util/Statistics/ComputeAmrDataStat.cpp
Tools/C_util/Statistics/GNUmakefile
Tools/C_util/Statistics/Make.package
Tools/C_util/Statistics/PltFileList.cpp
Tools/C_util/Statistics/PltFileStat.cpp

commit c464672caa3be9c0ed1983be2b6fd8c09e14dea3
Author: lijewski <lijewski>
Date:   Thu May 15 16:54:02 2008 +0000

    Vince's nOutFile and lUsingNFiles modifications

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c

commit d67bd13ae5320a47e61d3d38a4102185b0734434
Author: lijewski <lijewski>
Date:   Tue May 13 21:52:48 2008 +0000

    Added a couple tests for a mismatch between the size of integer and size
    of off_t in routines writing raw FAB data to disk.  The offset of the
    start of the FAB is an off_t, but is passed back to FORTRAN as an integer.
    If this is ever hit we'll have to redo how I/O is done.  The offset itself
    is stored in the header of the MultiFab on disk so reading proceses know
    where to go on disk to get the data.

Src/F_BaseLib/fabio_c.c

commit e387ee0394f64b5cb10e2ae3091318dbc6330815
Author: mzingale <mzingale>
Date:   Tue May 13 15:22:35 2008 +0000

    Castro now uses 5 digits in the plotfile names

Tools/C_util/regtests/test.py

commit a5e740e9a22f289482269f772040e13cef1bb53e
Author: mzingale <mzingale>
Date:   Tue May 13 15:07:07 2008 +0000

    have homer put the module files into the o/ directory

Tools/C_mk/Make.Linux

commit 26c341a3f73f07a413e5aa9e21738f09b523b8d9
Author: lijewski <lijewski>
Date:   Mon May 12 22:34:16 2008 +0000

    now print out number of CPUs MPI initialized with

Src/F_BaseLib/BoxLib.f90

commit 0d74ac3894b7cded693fc77f93ce6a78952a8aeb
Author: almgren <almgren>
Date:   Fri May 9 17:28:58 2008 +0000

    Remove unneeded variables.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 9b9c8689db47c4d3f30b892d65b8b3bc48ed1556
Author: almgren <almgren>
Date:   Fri May 9 17:26:17 2008 +0000

    Small code cleanup.

Src/LinearSolvers/F_MG/stencil.f90

commit f1f4f8e5432946acde6d743414b90ce522d03561
Author: almgren <almgren>
Date:   Wed May 7 20:20:10 2008 +0000

    Removed unused variables.

Src/C_BaseLib/COORDSYS_1D.F
Src/F_BaseLib/layout.f90

commit fe7af46f827d37f72bdd56d9eb9b06f3d800aee2
Author: almgren <almgren>
Date:   Wed May 7 20:19:34 2008 +0000

    Removed unneeded "lenx".

Src/C_AMRLib/FLUXREG_1D.F

commit 61c49443938c0c88df02c756fb877f595bbcb369
Author: almgren <almgren>
Date:   Fri Apr 25 21:06:54 2008 +0000

    Changed the length in BoxLib::Concatenate from 4 to 5 -- this will
    make pltfiles and chkfiles now use 5 spaces instead of 4 for the step number.

Src/C_BaseLib/Utility.cpp

commit c6a247cabfc2dba4dd9a1dc92562ded1c7977f14
Author: almgren <almgren>
Date:   Fri Apr 25 20:45:49 2008 +0000

    Can't use 0.d0

Src/C_BaseLib/MultiFab.cpp

commit 4152b96c0f99e3087232e479074e1a10abd5f6d2
Author: almgren <almgren>
Date:   Fri Apr 25 19:30:49 2008 +0000

    Added a norm2 function to MultiFab (analogous to norm0).  Doesn't use ghost cells.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 6646fb78e53ff9ad85c3c1f96778077daf349e7d
Author: lijewski <lijewski>
Date:   Mon Apr 21 20:02:00 2008 +0000

    added build_random_boxarray to public interface

Src/F_BaseLib/mt19937ar.f90

commit 44771ad7cba6c2d1862a7d925d5f4fb9b2cea5d2
Author: lijewski <lijewski>
Date:   Fri Apr 18 20:09:07 2008 +0000

    atlas updates from Mike Singer

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit d486f2374cc7ba4f7b6e32e6c163fc37b53ff41e
Author: aaspden <aaspden>
Date:   Thu Apr 17 23:10:54 2008 +0000

    Gimantis update

Tools/C_mk/Make.defs

commit 6876fdcf6c255f047cfa806553708c9439080e78
Author: mzingale <mzingale>
Date:   Tue Apr 15 14:43:23 2008 +0000

    Castro uses a different # of digits in the plotfile name

Tools/C_util/regtests/test.py

commit e50d195dce3c37ad61a4bfa11dd39e32cb827b5f
Author: mzingale <mzingale>
Date:   Mon Apr 14 21:07:09 2008 +0000

    get the Castro test suite back up to date with the latest changes

Tools/C_util/regtests/Castro-tests.ini

commit 0bd96169dce2c59b81dae357c4f6f40217d4ad0d
Author: mzingale <mzingale>
Date:   Mon Apr 14 21:04:33 2008 +0000

    don't generate Parallel Changelog for an fParallel run
    
    remove useFParallel for Parallel builds -- it is always needed now.

Tools/C_util/regtests/test.py

commit 47aab0be0fcebaa46f9f7273cbae597838e1aea4
Author: almgren <almgren>
Date:   Fri Apr 11 20:30:10 2008 +0000

    Another fix of sign error on lo side in stencil_all_flux_3d.

Src/LinearSolvers/F_MG/stencil.f90

commit a4944f01e496977ca41a373b25704494bc43c79e
Author: almgren <almgren>
Date:   Fri Apr 11 20:28:32 2008 +0000

    Fill sign error for lo side in stencil_all_flux_3d.

Src/LinearSolvers/F_MG/stencil.f90

commit 1c5bcdaeb0beac04e01de2258b365fc7111a65e5
Author: lijewski <lijewski>
Date:   Thu Apr 10 21:14:48 2008 +0000

    now print out # CPUs MPI initialized with

Src/C_BaseLib/BoxLib.cpp

commit 1edf91d0a940b5888449962baf51e359f71082db
Author: almgren <almgren>
Date:   Thu Apr 10 20:31:23 2008 +0000

    Moved GetBndryCells to be member function of Geometry.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit ad0f4562cc06702648dee3e7c5f744d173e1db7b
Author: almgren <almgren>
Date:   Wed Apr 9 19:54:35 2008 +0000

    We need this in order to include the right fParallel/boxlib files
    when compiling in the Parallel/Castro subdirectories.

Src/F_BaseLib/FParallelMG.mak

commit 1eebc4cae7d82d491e11dfa79641c64834e264c3
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 8 23:27:17 2008 +0000

    at the end of ml_restriction_c, changed the call to multifab_fill_boundary to multifab_fill_boundary_c

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 9004a2e767b7e11437bc54505587c67265f762e5
Author: lijewski <lijewski>
Date:   Wed Apr 2 20:39:43 2008 +0000

    modest touch-up to norm0()

Src/C_BaseLib/MultiFab.cpp

commit cd5b894e2bbe38bd1a568264d3018b66d217a0ea
Author: almgren <almgren>
Date:   Wed Apr 2 19:21:23 2008 +0000

    Added norm0 function which takes the inf norm of a multifab using no ghost cells.
    Optional comp argument (defaults to zero).

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 7d24b8ed98bd9560dfec49ddd946e3a022b7fba3
Author: almgren <almgren>
Date:   Tue Apr 1 20:02:11 2008 +0000

    1) Move the functions which call the mt19937ar random
    stuff from box_util.f90 into mt19937ar.f90
    2) Remove mt19937ar.f90 from GPackage.mak and NPackage.mak so
    that they are not included in general.  They can still be
    included as needed in the boxlib/test directory (the only
    place I can found where the make_random_box routines are actually called)

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/NPackage.mak
Src/F_BaseLib/box_util.f90
Src/F_BaseLib/mt19937ar.f90

commit 713ff52886631c61abc24215ce77e554eb59f312
Author: almgren <almgren>
Date:   Mon Mar 31 20:39:13 2008 +0000

    Changes by Candace in making varden truly adaptive.

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/regrid.f90

commit 8b175ebd99e098dba9c25f3b45d1bb1856e58454
Author: vince <vince>
Date:   Fri Mar 21 22:24:16 2008 +0000

    i/o float fix.

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.cpp

commit 5e4c883bd37102f5eefa17e16da0fbb9d7e984dd
Author: vince <vince>
Date:   Fri Mar 21 22:07:37 2008 +0000

    i/o fix.

Src/C_BaseLib/RealBox.cpp

commit 1f205d789d9188e09c7b50c1cddaa718db18bdfa
Author: almgren <almgren>
Date:   Tue Mar 18 19:54:58 2008 +0000

    Candace's changes to regrid -- buffer subroutine not complete, but
    this does multiple levels.

Src/F_BaseLib/regrid.f90

commit 06cbf8ac73a337881e450fb72a1f31ea38b94c66
Author: almgren <almgren>
Date:   Tue Mar 18 19:54:35 2008 +0000

    Candace found missing destroy -- fixed here.

Src/F_BaseLib/cluster.f90

commit a68e979cffe464a026c87fdfb415a563a2a6c603
Author: jbb <jbb>
Date:   Sat Mar 8 00:56:53 2008 +0000

    added mpi link for gimantis

Tools/F_mk/GMakeMPI.mak

commit 8551edd439d3b44b9ac9ab0b7c9bc8331ca9f53c
Author: mzingale <mzingale>
Date:   Tue Mar 4 20:03:12 2008 +0000

    fix jaguar compiling -- now it handles modules correctly.

Tools/F_mk/GMakeMPI.mak

commit 64b111a7515387a87fb974cb219fbc3a5f83ee6c
Author: lijewski <lijewski>
Date:   Tue Mar 4 18:41:19 2008 +0000

    removed some profilers

Src/F_BaseLib/multifab.f90

commit 0a3a0114bac9ea8606c194b9907b596f11b1a491
Author: ajnonaka <ajnonaka>
Date:   Mon Mar 3 22:07:23 2008 +0000

    fixed a comment

Src/LinearSolvers/F_MG/ml_nd.f90

commit 24d2d750d8bddec8fb5b2b5c390c777be2403353
Author: mzingale <mzingale>
Date:   Mon Mar 3 20:51:19 2008 +0000

    update homer to use MPICH2

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit a74c631f193822b2fc976c1f99e491cfb8067009
Author: almgren <almgren>
Date:   Mon Mar 3 18:03:07 2008 +0000

    Remove print statement.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit f5c32f101673bcd5719be3ee89a20f17ce699c97
Author: jbb <jbb>
Date:   Mon Mar 3 17:38:15 2008 +0000

    Add case for mothra.

Tools/F_mk/GMakeMPI.mak

commit ac00fff324ec5e7eaa4ac082cd91afc299da8be5
Author: almgren <almgren>
Date:   Mon Mar 3 03:13:43 2008 +0000

    Add subtract_divu_from_rh.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 3de5ba2ad54e6bec80d97a4cb9b46668e39e065a
Author: almgren <almgren>
Date:   Fri Feb 29 22:55:56 2008 +0000

    Oops - forgot to destroy the multifab zero_rh which I'd added.

Src/LinearSolvers/F_MG/ml_nd.f90

commit a2916c53ec854019c35889b896c38200018c10f3
Author: almgren <almgren>
Date:   Fri Feb 29 22:30:02 2008 +0000

    Fix the crse_fine_nodal_residual -- before it was passing in the fine grid rh
    and using that in computing the crse/fine residual -- but in fact the crse/fine
    rhs already sits on the crse grid, so we only want to modify that with the
    crse/fine L(phi), not the full crse/fine (f - Lphi), since the f at the crse/fine
    boundary has been constructed to be the right crse/fine f.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 488e6bf5989568af7cd8baef3aa045b2f9423eb6
Author: lijewski <lijewski>
Date:   Thu Feb 28 17:48:01 2008 +0000

    BL_PGI no longer needed

Src/C_BaseLib/Thread.H
Src/C_BaseLib/Utility.H
Tools/C_mk/Make.Linux

commit fdfa38758e2ab2d618bdae78d53d8ee6764a770b
Author: jbb <jbb>
Date:   Wed Feb 27 20:27:21 2008 +0000

    Make the include c.depends and include f90.depends fail if cant be built.

Tools/F_mk/GMakerules.mak

commit 2643d9b8b7514c5aa6fdc39883738f300046cadb
Author: ajnonaka <ajnonaka>
Date:   Wed Feb 27 05:12:18 2008 +0000

    fixed the format of "Header" so it looks the same regardless of compiler and machine.

Src/F_BaseLib/fabio.f90

commit 8704cdf6fd886f7cef14b47dd00ccae5b6f2351c
Author: ajnonaka <ajnonaka>
Date:   Tue Feb 26 21:08:47 2008 +0000

    Modified the pltXXXX/Header output so it compatible with visIt as well as amrVis.  In particular:
    
    -Any line that begins with an integer cannot have any blank spaces
    before that first integer.
    
    -We had our grid definitions divided up by line, i.e.,
    
    ((0,0) (15,63) (0,0))
    ((0,0) (31,127) (0,0))
    ((0,0) (63,255) (0,0))
    
    where they need to be continuous on one line, i.e.,
    
    ((0,0) (15,63) (0,0)) ((0,0) (31,127) (0,0)) ((0,0) (63,255) (0,0))
    
    There was also a bug in how we computed the physical coordinates of each
    box above the lines "Level_X/Cell".  It was a dx scaling problem which is now fixed.

Src/F_BaseLib/fabio.f90

commit e2179e2fe21e277b528d3ce45594eff0d69a2b6c
Author: ajnonaka <ajnonaka>
Date:   Tue Feb 26 16:55:33 2008 +0000

    remove dx from call to multifab_phybc

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit de918157b46ecf89edfcac553086bd3e1ec62923
Author: ajnonaka <ajnonaka>
Date:   Mon Feb 25 23:28:56 2008 +0000

    some comments about what the inputs to itsol_stencil_apply, mg_defect, and itsol_defect are

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90

commit 130ebd9f7f2376d2d3919384a9dd2aaf85304c28
Author: ajnonaka <ajnonaka>
Date:   Thu Feb 21 21:06:52 2008 +0000

    works for jaguar now

Tools/F_mk/GMakeMPI.mak

commit 6104d6ffd85f75cb0b95c302dffae1d389ebfecd
Author: almgren <almgren>
Date:   Thu Feb 21 18:44:50 2008 +0000

    Add "all = .true." to setval for buf.

Src/F_BaseLib/cluster.f90

commit fa8512110ba0497bbfd922cafb9566692206cdc6
Author: almgren <almgren>
Date:   Thu Feb 21 18:39:37 2008 +0000

    Need to initialize "buf" to false before setting true values in subroutine buffer_nd

Src/F_BaseLib/cluster.f90

commit 1a6f106e110fdfb1f422f8e29a4587f384ec2406
Author: mzingale <mzingale>
Date:   Sun Feb 17 18:33:58 2008 +0000

    work with the new plotfile format (plt00000 instead of plt0000).
    
    Also if we fail in making a benchmark file (the code crashes before output)
    then don't report that we've made a benchmark.

Tools/C_util/regtests/test.py

commit 37b7ad7d96b2f549f4ec37699d352140810bd6d7
Author: vince <vince>
Date:   Wed Feb 13 21:24:57 2008 +0000

    more gimantis additions.

Tools/C_mk/Make.defs

commit d0c5ab64450404ec548a49d97b6297c153a41dcd
Author: vince <vince>
Date:   Mon Feb 11 23:54:22 2008 +0000

    additions for gimantis.

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit c22c35ed8c28abef5797637dc753803eb48e8e50
Author: marc <marc>
Date:   Fri Feb 8 20:56:10 2008 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit ff6fff911d5b71cd145031bede37a6b5d209d874
Author: jbb <jbb>
Date:   Fri Feb 8 20:22:31 2008 +0000

    make mothra work

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 42fc06dbd32dcfd1982979758e2a69d7b72b6c51
Author: lijewski <lijewski>
Date:   Fri Feb 8 18:15:11 2008 +0000

    added some implicit none statements

Src/C_BaseLib/COORDSYS_2D.F
Src/C_BaseLib/COORDSYS_3D.F

commit e67a027c50f47c5a9e524bf3460bc7e60439e312
Author: lijewski <lijewski>
Date:   Fri Feb 8 18:08:01 2008 +0000

    added some implicit none statements

Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/CG_2D.F
Src/LinearSolvers/C_CellMG/CG_3D.F
Src/LinearSolvers/C_CellMG/LO_2D.F
Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/LP_2D.F
Src/LinearSolvers/C_CellMG/LP_3D.F
Src/LinearSolvers/C_CellMG/MG_2D.F
Src/LinearSolvers/C_CellMG/MG_3D.F

commit cebb9da569a5dc924bd76870527d57871561b83b
Author: lijewski <lijewski>
Date:   Fri Feb 8 17:48:46 2008 +0000

    added some implicit none statements

Src/C_AMRLib/FILCC_1D.F
Src/C_AMRLib/FILCC_2D.F
Src/C_AMRLib/FILCC_3D.F
Src/C_AMRLib/FLUXREG_1D.F
Src/C_AMRLib/FLUXREG_2D.F
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/INTERP_1D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/MAKESLICE_3D.F

commit ca1653be47b4cff9baaab796c0d81d900bd15d67
Author: lijewski <lijewski>
Date:   Thu Feb 7 23:48:08 2008 +0000

    some cleanup

Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F

commit ffc2bd2d2a84f05c6bae1dbaae44d74caa714601
Author: lijewski <lijewski>
Date:   Tue Feb 5 21:28:18 2008 +0000

    make explicit that we use O2 not Ofast with PathScale

Tools/F_mk/GMakedefs.mak

commit 1d96e73fa4d933c430fc9744edd2d15521300a52
Author: lijewski <lijewski>
Date:   Tue Feb 5 21:25:50 2008 +0000

    use -O2 -ipa with PathScale to be consistent with stuff in fParallel

Tools/C_mk/Make.Linux

commit 453028a61b629ab0992f054e8a755465671ca00f
Author: lijewski <lijewski>
Date:   Tue Feb 5 20:05:00 2008 +0000

    added -mp for Intel 9/10 optimization

Tools/F_mk/GMakedefs.mak

commit fdc3119bc5e608b321c8b466fde02829e80571fd
Author: ajnonaka <ajnonaka>
Date:   Thu Jan 31 23:26:41 2008 +0000

    commented out code that sets solution to zero.  So far, the multigrid appears to behave better; ie, we've seen convergence for 100 grids and haven't tried anything higher yet.

Src/LinearSolvers/F_MG/itsol.f90

commit 7172a76015fba5e3005c186d0840d346a9b57826
Author: sepp <sepp>
Date:   Thu Jan 31 23:18:18 2008 +0000

    1) removed extraneous blank before comma after _l2 in DIMS for dim 2 and 3

Src/C_BaseLib/ArrayLim.H

commit 6aef11d06b9e1eed86b52101098395e2cd3356ea
Author: almgren <almgren>
Date:   Thu Jan 31 21:51:03 2008 +0000

    Added options to make mpi work on pleiades.

Tools/C_mk/Make.mpi

commit f6fe4d2fc2ac774bf6f5f2294e35af377fb84d1c
Author: marc <marc>
Date:   Thu Jan 31 18:58:36 2008 +0000

    += instead of =

Tools/C_mk/Make.Linux

commit 1924821ff92a8c6bbfff9fe62b58314936666e75
Author: marc <marc>
Date:   Thu Jan 31 18:50:17 2008 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/Make.package

commit 5185180d724b4917d552c65e991d7362b5be0681
Author: lijewski <lijewski>
Date:   Thu Jan 31 18:31:02 2008 +0000

    more IO wraps

Src/F_BaseLib/multifab.f90

commit 006cfbbbd657ed7aa2b1f1b7054ab411464cbf3c
Author: lijewski <lijewski>
Date:   Thu Jan 31 18:25:46 2008 +0000

    parallel_IOProcessor() wraps in print()

Src/F_BaseLib/multifab.f90

commit 7504942b3ff6657929264e6864e223f58074ee86
Author: marc <marc>
Date:   Thu Jan 31 18:20:54 2008 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 7f5c5ae11521aecfcd589c8409b15f3b991181c9
Author: almgren <almgren>
Date:   Tue Jan 29 17:56:49 2008 +0000

    Fix misspelling in command line option.

Tools/C_mk/Make.defs

commit 25663707d9001128fefd0f8d8bf1e588b65df7ec
Author: lijewski <lijewski>
Date:   Mon Jan 28 20:42:10 2008 +0000

    added profiler to ml_nodal_restriction

Src/LinearSolvers/F_MG/ml_restriction.f90

commit db262c1706b47a7bcf62588a27d2c2ffc01e8897
Author: lijewski <lijewski>
Date:   Fri Jan 25 22:17:47 2008 +0000

    some cleanup

Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_solve.f90

commit 0c09dbfc3be7eec1a5b5776e61bbb8dfa337589e
Author: gpau <gpau>
Date:   Thu Jan 24 23:54:18 2008 +0000

    PathScale bug fix

Tools/C_mk/Make.Linux

commit 5583219c1d4d968ebfb3385ef2bacecf265c5043
Author: mzingale <mzingale>
Date:   Thu Jan 24 22:07:34 2008 +0000

    fix the permissions at the end of the suite run so other users can see
    the files

Tools/C_util/regtests/test.py

commit f2063f5b7cba41ec3ca16ba6eebb6aa9c17a6231
Author: mzingale <mzingale>
Date:   Thu Jan 24 19:42:45 2008 +0000

    update the grid file for test_smallscale

Tools/C_util/regtests/Maestro-tests.ini

commit f4de399a5a441f569b4454a7beff791da7e4df65
Author: lijewski <lijewski>
Date:   Thu Jan 24 17:13:30 2008 +0000

    reverting out some changes -- not particularly useful

Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 48c4f0ba9fb80bb110e3ac74bf444403b290db84
Author: lijewski <lijewski>
Date:   Wed Jan 23 23:33:42 2008 +0000

    got rid of gs_rb_smoother_3d_transpose()

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 872c9eab14baa1c3b9e14f361b22ff94fb9a34a3
Author: lijewski <lijewski>
Date:   Wed Jan 23 22:10:49 2008 +0000

    unrolled 3d cross stencil for modest speed improvement

Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit ca0b96a90c58944a0d3b10e2066e9294a92afe3b
Author: lijewski <lijewski>
Date:   Wed Jan 23 20:39:13 2008 +0000

    couple very modest optimizations

Src/LinearSolvers/F_MG/mg_smoother.f90

commit a07a9e0ee7bcf284b5b638af4dc942089f44809a
Author: lijewski <lijewski>
Date:   Tue Jan 22 17:06:31 2008 +0000

    added logical do_mpp to allow turning off minimize comm costs

Src/F_BaseLib/knapsack.f90

commit 9936b1673ecafdee600eb72ca6ec3ada9c71ea83
Author: lijewski <lijewski>
Date:   Tue Jan 22 17:05:40 2008 +0000

    *** empty log message ***

Src/F_BaseLib/test/t_knapsack.f90
Tests/F_BaseLib/t_knapsack.f90

commit ab4117a995087a69bed9146f53c2c331b4f5b557
Author: lijewski <lijewski>
Date:   Mon Jan 21 17:53:52 2008 +0000

    Added the following subroutines:
    
      subroutine setval_fabs_on_init(yes_or_no)
    
      subroutine set_fab_default_init(val)
      subroutine set_zfab_default_init(val)
      subroutine set_ifab_default_init(val)
      subroutine set_lfab_default_init(val)
    
    Previously fabs were always setval()d on being built to a hard-wired value.

Src/F_BaseLib/fab.f90

commit 2712252068148c9af82378b95dad50033164e79b
Author: mzingale <mzingale>
Date:   Sun Jan 20 21:46:03 2008 +0000

    add compilation rules for homer

Tools/F_mk/GMakedefs.mak

commit f348c5639c8d197710735f3a9ff44567553d8f4b
Author: lijewski <lijewski>
Date:   Fri Jan 18 21:18:02 2008 +0000

    now have minimize communication costs ability in knapsack

Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/layout.f90

commit 4141c08ca13a2bf398e26bd54a4fa4df644c2cd9
Author: mzingale <mzingale>
Date:   Wed Jan 16 21:18:47 2008 +0000

    turn on -mp for Intel, and turn on warnings for Intel 10 in debug mode

Tools/F_mk/GMakedefs.mak

commit 62946bf3e1934681ad25cadfe9f6f817bac4915a
Author: mzingale <mzingale>
Date:   Tue Jan 15 22:53:40 2008 +0000

    add support for Intel 10.1

Tools/C_mk/Make.defs

commit 8ee5343b7a77f7dc1b10f96c1a8a1f9d27a5fbaa
Author: ajnonaka <ajnonaka>
Date:   Tue Jan 15 22:01:38 2008 +0000

    changed PathScale compiler options to -O2 -ipa

Tools/F_mk/GMakedefs.mak

commit 0798bb6adc72dd2f88ae6dc948bdbb846c886def
Author: almgren <almgren>
Date:   Tue Jan 15 22:01:27 2008 +0000

    Modify nodal_smoother_2d and nodal_smoother_3d so for the cross stencil:
    if the domain is periodic in x and odd in x (or periodic in y and odd in y for 3d)
    then use Jacobi instead of Gauss-Seidel relaxtion.  Gauss-Seidel red-black is
    bad in this case because the multifab_fill_boundary will overwrite new values
    on the lo side with old values on the hi side, making it not converge.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit f144755153af68c8d92aba4e7ab5709fa2515ef6
Author: almgren <almgren>
Date:   Tue Jan 15 22:00:08 2008 +0000

    1) Modify the number of iterations after a bottom solver failure from 2 to 20.
    2) Define pmask to pass into the nodal smoother to test on whether to do Jacobi (if odd and periodic)
    or Gauss-Seidel (otherwise) for cross stencil.

Src/LinearSolvers/F_MG/mg.f90

commit 15170710a07ce224b19c3079314d7d07c02313a0
Author: almgren <almgren>
Date:   Tue Jan 15 21:58:58 2008 +0000

    Print statement in BiCG if solution is set to zero, also return error stat.

Src/LinearSolvers/F_MG/itsol.f90

commit 79f9823492b5fc2716c649ceeaf44329891700d6
Author: almgren <almgren>
Date:   Tue Jan 15 18:27:12 2008 +0000

    Make it so the CC and the nodal solver call bl_abort if they don't
    converge in max_iter iterations.

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit f0199e022c311498149d6da1cc69c3cc8e77d9d8
Author: lijewski <lijewski>
Date:   Mon Jan 14 21:00:15 2008 +0000

    added back in some stuff I removed -- used by MGT_Solver

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/ml_cc.f90

commit 033266308d990d59ee8a329ccd3773545271b40a
Author: lijewski <lijewski>
Date:   Mon Jan 14 20:54:43 2008 +0000

    added sort_i.f90 needed by fab.f90

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 29e0bfb01849f23aa056d0670290b87189b139df
Author: lijewski <lijewski>
Date:   Mon Jan 14 20:07:31 2008 +0000

    tweaked due to bndry_reg.f90 mods

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_divu.f90

commit de239333eb7212dc85e9c09f48b664b1d02b5fae
Author: lijewski <lijewski>
Date:   Mon Jan 14 20:06:38 2008 +0000

    obmf multifabs are now build optionally

Src/F_BaseLib/bndry_reg.f90

commit d7ff812d25c04b048ec01f934f2d53faca311102
Author: lijewski <lijewski>
Date:   Mon Jan 14 04:37:08 2008 +0000

    bndry_reg_rr_build_1 -> bndry_reg_rr_build

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_divu.f90

commit e9456db356ef7775e55d7d1d49a2e52f0d74f7ef
Author: lijewski <lijewski>
Date:   Mon Jan 14 04:35:31 2008 +0000

    Removed unused function.
    Renamed bndry_reg_rr_build_1 -> bndry_reg_rr_build.
    Some cleanup.

Src/F_BaseLib/bndry_reg.f90

commit 9a0ab5c56ed9220dde08de8766d75cc2cc35b50a
Author: lijewski <lijewski>
Date:   Sat Jan 12 04:44:21 2008 +0000

    fixed parallel bug in bndry_reg_build()

Src/F_BaseLib/bndry_reg.f90

commit 7e72496b2f5f02bedf9490baa5eff876fcdf4d12
Author: lijewski <lijewski>
Date:   Fri Jan 11 22:52:28 2008 +0000

    *** empty log message ***

Src/F_BaseLib/fab.f90

commit 535b4bd3792d3fb9ecaacaca47c45aa74aef0b93
Author: lijewski <lijewski>
Date:   Fri Jan 11 22:30:06 2008 +0000

    use least_used_cpus() when assigning boxes to CPUs

Src/F_BaseLib/layout.f90

commit 162e402c899a4d3f427ed6375d1bba2ba18bc9b4
Author: lijewski <lijewski>
Date:   Fri Jan 11 22:29:36 2008 +0000

    added least_used_cpus()

Src/F_BaseLib/fab.f90

commit 35faa988a44cc3b542ba64ccaf0aa9c94b391e51
Author: lijewski <lijewski>
Date:   Fri Jan 11 18:23:57 2008 +0000

    added MPI_Allgather functionality

Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit d69b56f768819f18e1ec7e0cfcbde60146c518a2
Author: mzingale <mzingale>
Date:   Tue Jan 8 21:45:23 2008 +0000

    make the restart work again (i.e. we need to keep the checkpoint files
    around)

Tools/C_util/regtests/test.py

commit 0fa5e7840843e7ca6715c399f78f51a8d96bea67
Author: mzingale <mzingale>
Date:   Mon Jan 7 21:13:27 2008 +0000

    enable bounds checking for gfortran

Tools/F_mk/GMakedefs.mak

commit 2c01c32be0b39e3316c86c8b530d4fdaa555052f
Author: lijewski <lijewski>
Date:   Thu Jan 3 23:44:21 2008 +0000

    fabs no longer have an ng component

Src/LinearSolvers/F_MG/stencil.f90

commit 0c825dfb0d94b7d24a35eba9ca651c36564e75ad
Author: lijewski <lijewski>
Date:   Thu Jan 3 23:43:59 2008 +0000

    Removed multifab_debug_fill().

Src/F_BaseLib/multifab.f90

commit 3702b6d6dd657721d6002091ea5f1e217daf2bcc
Author: lijewski <lijewski>
Date:   Thu Jan 3 23:43:37 2008 +0000

    Removed the "ng" component of fabs.
    Removed the set_border_val() routines & fab_debug_fill().

Src/F_BaseLib/fab.f90

commit 515d00c8ec639400822416727f8d0e9a8c2c74a1
Author: lijewski <lijewski>
Date:   Thu Jan 3 23:39:22 2008 +0000

    removed multifab_debug_fill() call

Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/t_main.f90

commit a7ccd9bacd8c229d9156b79dc5a7dca851ccd092
Author: lijewski <lijewski>
Date:   Thu Jan 3 06:11:53 2008 +0000

    *** empty log message ***

Src/F_BaseLib/fab.f90

commit 9392c053b68f6eb8b9a51b2989e8924cf4ec9f4b
Author: lijewski <lijewski>
Date:   Thu Jan 3 05:35:29 2008 +0000

    code for calculating & printing fab byte spread

Src/F_BaseLib/fab.f90

commit 92963385d9be62140d8c3809ca8cdb2d65688259
Author: lijewski <lijewski>
Date:   Tue Jan 1 21:04:37 2008 +0000

    fixed more parallel bugs

Src/LinearSolvers/F_MG/itsol.f90

commit 748d852507ec56934fd27d5524684edfdf4a1cdd
Author: lijewski <lijewski>
Date:   Tue Jan 1 17:15:53 2008 +0000

    added aveassoc stuff

Src/F_BaseLib/layout.f90

commit 12d549a6da7b810ffad13bdcc423f4eb163c3829
Author: lijewski <lijewski>
Date:   Tue Jan 1 16:28:45 2008 +0000

    added sort_i.f90

Src/F_BaseLib/GPackage.mak

commit d14db2cea588f993b5fe7cd1a385d561f47ec302
Author: mzingale <mzingale>
Date:   Mon Dec 31 15:44:18 2007 +0000

    switch to realclean instead of clean
    
    don't output checkpoint files (to save space)

Tools/C_util/regtests/test.py

commit f23eca42c7ae22871d8fa1a98e08d194ffc4e450
Author: lijewski <lijewski>
Date:   Sat Dec 29 04:13:52 2007 +0000

    removed the bound member -- not used

Src/F_BaseLib/multifab.f90

commit 45c334e91b6209b693eaf1293621435093fb69b0
Author: lijewski <lijewski>
Date:   Wed Dec 26 20:32:02 2007 +0000

    more mem_stat refinement

Src/F_BaseLib/fab.f90

commit 696f7d40963100b46e5bd332dfc218032b73f7ca
Author: lijewski <lijewski>
Date:   Wed Dec 26 19:49:18 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak

commit 2a87d86c073170780cbcf948c369a9885e463099
Author: lijewski <lijewski>
Date:   Wed Dec 26 19:32:31 2007 +0000

    more work on mem_stats for cached data

Src/F_BaseLib/layout.f90

commit 0b312f77f619e656d669427356a12c7b91ed7103
Author: lijewski <lijewski>
Date:   Wed Dec 26 02:25:05 2007 +0000

    more mem_stats stuff

Src/F_BaseLib/layout.f90

commit 992ba8b51a24677dd6f62d7f6dfc4d6fc7cb402d
Author: lijewski <lijewski>
Date:   Wed Dec 26 01:05:31 2007 +0000

    now calculates min/max cnt & min/max alloc across CPUs

Src/F_BaseLib/bl_mem_stat.f90

commit f59d75a0db475f1552911be757059faa57df295d
Author: almgren <almgren>
Date:   Wed Dec 26 00:50:36 2007 +0000

    Need bl_constants_module now that we're using "ZERO"

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit d245c094e70c9e27ec701a548199e452fc6f0702
Author: lijewski <lijewski>
Date:   Wed Dec 26 00:19:25 2007 +0000

    mem_stats was NOT taking number of components into account

Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab.f90

commit a37e564d8cfdb6d0de71ee9e0ac9a171863512c4
Author: lijewski <lijewski>
Date:   Tue Dec 25 20:40:27 2007 +0000

    added flags to put modules in correct place for PGI

Tools/F_mk/GMakeMPI.mak

commit 65ee2e7e4b9746fdcb7a1e72ad5fc6eaec3083c1
Author: lijewski <lijewski>
Date:   Mon Dec 24 20:36:34 2007 +0000

    run boxarray_maxsize() on boxarray stored in fgassoc

Src/F_BaseLib/layout.f90

commit 8e9281b195d11d4242eabcbd10377ac40cf36a3a
Author: lijewski <lijewski>
Date:   Mon Dec 24 18:09:48 2007 +0000

    removed unimplemented routine

Src/F_BaseLib/list_box.f90

commit 083b73f8837f774bd0d09dc9753ce8a05eee3d28
Author: lijewski <lijewski>
Date:   Mon Dec 24 18:09:23 2007 +0000

    stop -> bl_error() calls

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 10636d87af386c0ffd1b573ed5631cb65f8998e5
Author: lijewski <lijewski>
Date:   Mon Dec 24 06:41:46 2007 +0000

    wrapped some output in parallel_ioprocessor()

Src/LinearSolvers/F_MG/mg.f90

commit ab3cc9bc227fb428771f7b9b5607ab356a09842d
Author: lijewski <lijewski>
Date:   Fri Dec 21 21:46:04 2007 +0000

    fixed box_intersector stuff; needed to make tmp layout w/nodalized boxarray

Src/LinearSolvers/F_MG/ml_solve.f90

commit 2f733a4486be20e0a9c57a8f526bc6a4f7774dc3
Author: lijewski <lijewski>
Date:   Fri Dec 21 21:33:05 2007 +0000

    added check that flux is cell-centered so box_intersector stuff is valid

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 7d62907fe2dcd6e008495cfa82f0b8461f5d272d
Author: lijewski <lijewski>
Date:   Fri Dec 21 21:18:39 2007 +0000

    fixed box_intersector stuff; needed to make tmp layout w/nodalized boxarray

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 1eb7407550580f22dfeb00839cef2316ecb4d9c4
Author: lijewski <lijewski>
Date:   Fri Dec 21 17:26:29 2007 +0000

    moved from varden/MAESTRO directories

Src/LinearSolvers/F_MG/ml_solve.f90

commit 786faa454405bae50d0c1ac10fe3334889ad1957
Author: almgren <almgren>
Date:   Wed Dec 19 22:52:54 2007 +0000

    Need to use ml_util_module in order to call ml_fill_all_fluxes in mgt_compute_flux.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit b3c515fff4a137be15f3f0661c26cf8e039a0123
Author: lijewski <lijewski>
Date:   Wed Dec 19 20:42:10 2007 +0000

    needed bl_constants_module

Src/LinearSolvers/F_MG/nodal_newu.f90

commit 215b6a984e95eb28e47dc69e0ad245c2f21e74a4
Author: lijewski <lijewski>
Date:   Wed Dec 19 20:38:27 2007 +0000

    ml_norm_inf() and ml_norm_l2() are now in ml_util_module

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_util.f90

commit 36cd349fb348e70b24df17442bbe1e4ebccb0196
Author: lijewski <lijewski>
Date:   Wed Dec 19 17:20:51 2007 +0000

    mods to compile with Intel 9.0

Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/layout.f90

commit 6f35f094c44634ab6b5ac9d2afed4a9047402edf
Author: lijewski <lijewski>
Date:   Wed Dec 19 06:11:09 2007 +0000

    some cleanup of use statements

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_nodal_cpp.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_mask.f90
Src/LinearSolvers/F_MG/nodal_newu.f90
Src/LinearSolvers/F_MG/sparse_solve.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 0642ab879c2e947be59a1f4f97bb83e422d1d90d
Author: lijewski <lijewski>
Date:   Wed Dec 19 04:47:27 2007 +0000

    more careful with use statements

Src/F_BaseLib/bl_error.f90
Src/F_BaseLib/bl_mem_stat.f90
Src/F_BaseLib/bl_parmparse.f90
Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/bl_stream.f90
Src/F_BaseLib/bl_string.f90
Src/F_BaseLib/bl_timer.f90
Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/box.f90
Src/F_BaseLib/box_util.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/cluster.f90
Src/F_BaseLib/cluster_2d.f90
Src/F_BaseLib/fab.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/interp.f90
Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/list_box.f90
Src/F_BaseLib/ml_boxarray.f90
Src/F_BaseLib/ml_layout.f90
Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/mt19937ar.f90
Src/F_BaseLib/multifab.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90
Src/F_BaseLib/plotfile.f90
Src/F_BaseLib/ppm_util.f90
Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/t_bx.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/t_bx.f90
Tests/F_BaseLib/t_main.f90

commit 7db50ac9d3d20344843bd4f4cb85324853e07f86
Author: lijewski <lijewski>
Date:   Wed Dec 19 02:54:45 2007 +0000

    some franklin/PathScale mods

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak

commit 19e6fd890791f96cef066ee57e2241219ced244c
Author: lijewski <lijewski>
Date:   Wed Dec 19 02:52:19 2007 +0000

    mods to compile on franklin with PathScale

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/nodal_divu.f90

commit 899584887cd5a1646b53d0b796bcd7f3d8205c4d
Author: lijewski <lijewski>
Date:   Tue Dec 18 17:40:05 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit a33d8138bf3d8d1396a80990d6e34903a72f6d11
Author: lijewski <lijewski>
Date:   Tue Dec 18 17:24:37 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit 592b6074ee8a556c72c78451e2c08807421b50fb
Author: lijewski <lijewski>
Date:   Tue Dec 18 00:22:47 2007 +0000

    fixed test in internal_sync_unique_cover()

Src/F_BaseLib/layout.f90

commit 1d9abe773329d69bd1b81147187ba0b4fbcecf7a
Author: lijewski <lijewski>
Date:   Mon Dec 17 23:10:53 2007 +0000

    fixed bug in boxarray_same_q()

Src/F_BaseLib/boxarray.f90

commit c52edd0e950c959929ca9ed931c44d0d2d6b213e
Author: lijewski <lijewski>
Date:   Mon Dec 17 21:40:00 2007 +0000

    used new fgassoc stuff from layout

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 1f2e4f5eef244707c54cc1c0fe858da1673c0416
Author: lijewski <lijewski>
Date:   Mon Dec 17 21:39:43 2007 +0000

    added fgassoc to cache ghost cell boxarray used by mf_fill_ghost_cells()

Src/F_BaseLib/layout.f90

commit 459b7cbec0b8db4fc9811953bd62b1de27eb1c01
Author: lijewski <lijewski>
Date:   Mon Dec 17 21:39:11 2007 +0000

    more cleanup

Src/F_BaseLib/boxarray.f90

commit 5be48a3c9a2e24752965fda1dba76ca02e86feb6
Author: lijewski <lijewski>
Date:   Mon Dec 17 19:22:07 2007 +0000

    came up with simpler way to remove overlap

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit b660d40be2336ed677f1cc8302772074edd46d3f
Author: lijewski <lijewski>
Date:   Mon Dec 17 19:11:40 2007 +0000

    removed some unused stuff

Src/F_BaseLib/boxarray.f90

commit 425670ec1e2d21a0d835a8b6ea87700696a2eb49
Author: lijewski <lijewski>
Date:   Mon Dec 17 18:24:07 2007 +0000

    cleanup & bug fix in boxarray_add_clean_boxes()

Src/F_BaseLib/boxarray.f90

commit f6f65c3e77ad0de0cf5042fc60446ac5591529c0
Author: lijewski <lijewski>
Date:   Mon Dec 17 18:23:41 2007 +0000

    remove overlap in internal ghost multifab

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 0a7d6fa250f3b04df4f7dd37e229318c943d707d
Author: ajnonaka <ajnonaka>
Date:   Fri Dec 14 21:13:10 2007 +0000

    a couple minor 3d bugs fixed.  cslope_lo and hi need to have 3 components
    a reference to fvcy has been changed to fvcz for a dm=3 case

Src/F_BaseLib/fillpatch.f90

commit 6efeb0c8a945b1d8de521f8e6919dacae61af4b0
Author: ajnonaka <ajnonaka>
Date:   Fri Dec 14 20:55:21 2007 +0000

    inverted the meaning of lim_slope so lim_slope .eq. .true. means use limited slopes.  Change the behavior of the code by leaving the default value as true.
    
    Added lim_slope_input and lin_limit_input as optional input arguments to fillpatch to change the behavior

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/interp.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 50b729ff9c4f678daa661a17d13cb95e1b3beae5
Author: ajnonaka <ajnonaka>
Date:   Fri Dec 14 20:33:46 2007 +0000

    fillpatch now takes icomp_fine and icomp_coarse as inputs instead of just icomp.  The old way, which used just icomp, didn't work if the coarse and fine components didn't have the same index

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 9e3fda958669e79759cc1a1bd817e5e3bd576cd8
Author: lijewski <lijewski>
Date:   Thu Dec 13 18:24:23 2007 +0000

    call bl_error when proc trees are NOT identical

Src/F_BaseLib/bl_prof.f90

commit a549184b2049a93603e047dd7961534a43021e55
Author: lijewski <lijewski>
Date:   Thu Dec 13 18:23:58 2007 +0000

    removed some profilers

Src/F_BaseLib/interp.f90

commit a0e05cdad61f07a0eb8bf1c9e07b3e7567a6d038
Author: lijewski <lijewski>
Date:   Wed Dec 12 20:28:07 2007 +0000

    added TODO note

Src/LinearSolvers/F_MG/nodal_divu.f90

commit fce2aaf7295b81666bcfc83a951fcaa81e1e5a0c
Author: lijewski <lijewski>
Date:   Wed Dec 12 00:12:03 2007 +0000

    use box_intersector stuff in periodic_add_copy()

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 7cda382cc7fe9b202c2f9570b4f73a4e7e1ef534
Author: lijewski <lijewski>
Date:   Tue Dec 11 23:47:19 2007 +0000

    now use box_intersector in ml_crse_divu_contrib()

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 0d58dedde16abfff241f599959c30b467c99492f
Author: lijewski <lijewski>
Date:   Tue Dec 11 22:22:11 2007 +0000

    commented out unused norm_inf() call

Src/LinearSolvers/F_MG/mg.f90

commit 44a1216238b614ff5bfe4edee95dfcde4e6d550f
Author: lijewski <lijewski>
Date:   Tue Dec 11 22:21:30 2007 +0000

    added needed type casts

Src/F_BaseLib/mt19937ar.f90

commit 5354d3d2efbed79856038975e62a4827629b9585
Author: lijewski <lijewski>
Date:   Tue Dec 11 22:21:05 2007 +0000

    some type cleanup

Src/F_BaseLib/ml_boxarray.f90

commit 9f740bc405737d1433cc9fb5b862757a21449c87
Author: lijewski <lijewski>
Date:   Tue Dec 11 22:20:44 2007 +0000

    some cleanup

Src/F_BaseLib/layout.f90

commit 9b3de5759730f5dfe2aea0cd1b688aa9508d9644
Author: lijewski <lijewski>
Date:   Tue Dec 11 22:20:26 2007 +0000

    removed unused declaration

Src/F_BaseLib/fillpatch.f90

commit 18c30b01695423094708c5bf2dbca66acf9f4f4f
Author: lijewski <lijewski>
Date:   Tue Dec 11 22:19:38 2007 +0000

    fixed type issue

Src/F_BaseLib/bl_timer.f90
Src/F_BaseLib/box_util.f90
Src/F_BaseLib/cluster.f90
Src/LinearSolvers/F_MG/mg_smoother.f90

commit 9a4cc8896bff3096e7fc5f1e0335b5eb8a6d65cc
Author: lijewski <lijewski>
Date:   Tue Dec 11 21:19:28 2007 +0000

    check for overflow in box_volume; no longer elemental

Src/F_BaseLib/box.f90

commit 968f02555481ca92e13914520861cf433681c1e4
Author: lijewski <lijewski>
Date:   Tue Dec 11 18:52:48 2007 +0000

    some cleanup

Src/F_BaseLib/box.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/layout.f90

commit 980c11d4f72a9b34b29b7c3d56958ec2322ce2f4
Author: lijewski <lijewski>
Date:   Tue Dec 11 18:52:34 2007 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg.f90

commit 476d904565252882df627c9f640f90cbf54c7442
Author: lijewski <lijewski>
Date:   Tue Dec 11 01:13:28 2007 +0000

    added some bl_prof timers

Src/F_BaseLib/knapsack.f90

commit edbec963bf78eefc1683ca965914f14346a91139
Author: lijewski <lijewski>
Date:   Tue Dec 11 01:01:23 2007 +0000

    added some bl_prof timers

Src/F_BaseLib/interp.f90

commit a2310dd4056dfcb8a33b4c846516a3241614190c
Author: lijewski <lijewski>
Date:   Tue Dec 11 00:42:19 2007 +0000

    added some bl_prof timers

Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 6345a0fc1f8c12eeafe043c43ab55c42a129e583
Author: lijewski <lijewski>
Date:   Mon Dec 10 23:56:18 2007 +0000

    added some profile timers

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_smoother.f90

commit 7d4dca552456582ee93a261d3b0c041524ce1515
Author: lijewski <lijewski>
Date:   Mon Dec 10 20:36:34 2007 +0000

    fixes to bl_prof usage

Src/LinearSolvers/F_MG/ml_cc.f90

commit eaab4c7863777676cb039ae35662917da8e50aea
Author: lijewski <lijewski>
Date:   Mon Dec 10 18:59:56 2007 +0000

    parallelized ml_crse_divu_contrib

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 130ce7f3f6c3165127826841ca7929a0881d4b6d
Author: lijewski <lijewski>
Date:   Sun Dec 9 01:45:20 2007 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit ae3cc91c3e218de8d067e8a0ea77ff0ca5052abf
Author: lijewski <lijewski>
Date:   Sun Dec 9 01:42:25 2007 +0000

    some cleanup

Src/F_BaseLib/box_util.f90
Src/F_BaseLib/fillpatch.f90

commit a90b838e3798f90bb30eb75fee820f26718c4301
Author: lijewski <lijewski>
Date:   Sun Dec 9 00:38:44 2007 +0000

    some cleanup

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit b81aabadcfaa1e6d24926d4fb2cf6af68fc2b0c6
Author: almgren <almgren>
Date:   Sat Dec 8 00:49:01 2007 +0000

    Added multifab_fill_boundary(crse) after restriction.

Src/LinearSolvers/F_MG/ml_restriction.f90

commit ee8e4773d0b597cc154a7136eab7995632a53d7d
Author: almgren <almgren>
Date:   Fri Dec 7 21:28:56 2007 +0000

    Put prototype regridding algorithm here.

Src/F_BaseLib/regrid.f90

commit 0c935e81d6aa2ccf875653f28328c4f321ce043f
Author: lijewski <lijewski>
Date:   Fri Dec 7 21:25:41 2007 +0000

    parallelized ml_interface_c()

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit c8599881da4a6b42d3a31c27446c786ce78c423e
Author: ajnonaka <ajnonaka>
Date:   Fri Dec 7 19:58:14 2007 +0000

    mg test commit

Src/LinearSolvers/F_MG/GPackage.mak

commit a6e68a91f75652bbbbffec1b962306bd95a49c94
Author: lijewski <lijewski>
Date:   Fri Dec 7 18:00:25 2007 +0000

    added parallel check in ml_crse_divu_contrib()

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 3318ee8b68c988fd6adf3b4519fcc0f995d9f912
Author: almgren <almgren>
Date:   Fri Dec 7 17:39:53 2007 +0000

    Need to add multifab_fill_boundary for full_soln after we create it.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 244ce020b197b9cebaeaa46af2b96cb3dde3a7b8
Author: almgren <almgren>
Date:   Thu Dec 6 21:57:47 2007 +0000

    Separated out crse and fine parts of ml_interface_stencil -- only tested in 2d.

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit e959f7070076def3bef521ed09d91d7f5a657016
Author: almgren <almgren>
Date:   Thu Dec 6 21:41:36 2007 +0000

    Needed to add multifab_fill_boundary for multilevel solve to get
    right convergence -- I think it's only needed for periodic but not 100% sure.

Src/LinearSolvers/F_MG/ml_cc.f90

commit e00665ab432fa03ebd28e5fe8897a1d7a2c3d651
Author: almgren <almgren>
Date:   Thu Dec 6 20:39:40 2007 +0000

    formatting cleanup.

Src/LinearSolvers/F_MG/mg.f90

commit 5196769ccb70650389fe51484d181fa172d90f59
Author: almgren <almgren>
Date:   Thu Dec 6 20:39:25 2007 +0000

    Removed commented line.

Src/LinearSolvers/F_MG/ml_cc.f90

commit be0600c0b2fdc778f846072597475bf414b8928e
Author: almgren <almgren>
Date:   Thu Dec 6 20:38:59 2007 +0000

    Fix ml_interface for the periodic case.

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 2eaf7989955b84655901c8972e06cc3f42eec7f6
Author: almgren <almgren>
Date:   Thu Dec 6 20:38:04 2007 +0000

    Fix stuff in ml_prolongation.

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 01b938b88b71035431e1ca19673af85cb0f49bcd
Author: lijewski <lijewski>
Date:   Wed Dec 5 22:35:47 2007 +0000

    bndry_reg_copy now fills in periodic cells outside of domain

Src/F_BaseLib/bndry_reg.f90

commit 0b71860ccf1fef0616f92bf355bd73c11024f78e
Author: lijewski <lijewski>
Date:   Wed Dec 5 19:02:55 2007 +0000

    slight change to calling sequence

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 5b25f4e4eda3af0d7504b50784be142f86fe80d1
Author: almgren <almgren>
Date:   Wed Dec 5 19:00:27 2007 +0000

    Removed commented line.

Src/F_BaseLib/layout.f90

commit b440793f3b2887f14de24a33c4436054ec1ef144
Author: almgren <almgren>
Date:   Wed Dec 5 18:36:21 2007 +0000

    Remove ng from bndry_reg_copy calls.

Src/F_BaseLib/bndry_reg.f90

commit 1598b2fbf05aaebbb5ab4c80a32706785f7aba22
Author: lijewski <lijewski>
Date:   Wed Dec 5 02:23:07 2007 +0000

    more work on parallel-aware more efficient version

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit f2bd5aaeb44133a69cfa29e15c883f065cf3da8f
Author: lijewski <lijewski>
Date:   Wed Dec 5 01:41:59 2007 +0000

    special case when can fill periodic ghost cells from given fine data

Src/F_BaseLib/fillpatch.f90

commit d0808a0c06a60a4f5962d26c552eb801d6ae59f5
Author: lijewski <lijewski>
Date:   Tue Dec 4 23:48:40 2007 +0000

    some cleanup

Src/F_BaseLib/fillpatch.f90

commit 539019c583b9ca9b9009be0a7df920e14c1f6cba
Author: lijewski <lijewski>
Date:   Tue Dec 4 23:39:37 2007 +0000

    plugged some memory leaks

Src/LinearSolvers/F_MG/ml_cc.f90

commit afce25f7d0e69c657347cc1b800c7dfd9c8031de
Author: lijewski <lijewski>
Date:   Tue Dec 4 22:56:18 2007 +0000

    bug fix -- only destroy fla & tmpfine if built

Src/F_BaseLib/fillpatch.f90

commit 74d80f5ba3356255a948fa6ab20ebc8f89f9d930
Author: lijewski <lijewski>
Date:   Tue Dec 4 22:26:35 2007 +0000

    start on making fillpatch periodically-aware

Src/F_BaseLib/fillpatch.f90

commit b5e36656bacd4b92b3dfa3fd118f9eb789a3b08b
Author: lijewski <lijewski>
Date:   Tue Dec 4 00:33:39 2007 +0000

    more error checking

Src/F_BaseLib/fillpatch.f90

commit e5629cdb6954998808e0cbfed8b8cacc5e12be0a
Author: lijewski <lijewski>
Date:   Tue Dec 4 00:29:26 2007 +0000

    start on more efficient parallel version -- more to do ...

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit ed0c816a543f7627df2d90cbb1943a22be0c9e29
Author: lijewski <lijewski>
Date:   Tue Dec 4 00:27:35 2007 +0000

    modest fixes -- still periodic issues

Src/F_BaseLib/fillpatch.f90

commit c6507f25a7a6fae1a2a9652803af0433e4d955d3
Author: mzingale <mzingale>
Date:   Mon Dec 3 22:27:05 2007 +0000

    add a "/" to the end of the paths as required

Tools/C_util/regtests/test.py

commit 2a1b4c4082e3eda4359a6157f0859439000a0b08
Author: lijewski <lijewski>
Date:   Mon Dec 3 22:18:48 2007 +0000

    modest bug fix

Src/F_BaseLib/fillpatch.f90

commit bd9e095d4409546ba8cd993de951343a8d822683
Author: lijewski <lijewski>
Date:   Mon Dec 3 17:37:30 2007 +0000

    mods from Mike Singer

Tools/C_mk/Make.mpi

commit a79ad1edb2ae4f761dba9a42fe3756d00d03bb22
Author: lijewski <lijewski>
Date:   Mon Dec 3 17:28:39 2007 +0000

    mods from Mike Singer

Src/C_BoundaryLib/LO_BCTYPES.H

commit de67799f97c4c9ed1f4d72ba1b712d49e6fe6552
Author: lijewski <lijewski>
Date:   Sun Dec 2 00:49:44 2007 +0000

    layout_get_box_intersector() now call init_box_hash_bin() automagically if needed

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/layout.f90

commit 12cd49796ccbc69f72281bde945a300026381889
Author: lijewski <lijewski>
Date:   Sat Dec 1 00:21:44 2007 +0000

    little cleanup

Src/F_BaseLib/fillpatch.f90

commit 77696298335cce62a221725bfc6a1b46a706b556
Author: almgren <almgren>
Date:   Fri Nov 30 22:52:03 2007 +0000

    Don't include fillpatch and multifab_fill_ghost_cells in the make
    stuff because they depend on stuff in the varden/MAESTRO directories.

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/NPackage.mak

commit cce8b35733e18a6ccd5bbf298f8d356465f8acb3
Author: almgren <almgren>
Date:   Fri Nov 30 22:14:18 2007 +0000

    Add fillpatch and multifab_fill_ghost_cells to GPackage and NPackage.

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/NPackage.mak

commit 545bf251cf65e14a3e8f725af709ab99e427f6df
Author: almgren <almgren>
Date:   Fri Nov 30 22:12:59 2007 +0000

    Move fillpatch and multifab_fill_ghost_cells from varden/MAESTRO into boxlib.

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 7c9dfda8f223345179dcd31580d326b0facfb544
Author: almgren <almgren>
Date:   Fri Nov 30 22:08:59 2007 +0000

    Fixed bug in lin_cc_interp_2d -- was using xok(1) instead of xok(2) for yslope.

Src/F_BaseLib/interp.f90

commit cd2f200d0b5c55cb726c682e43f377539639f560
Author: mzingale <mzingale>
Date:   Sun Nov 25 15:34:32 2007 +0000

    new main webpage -- now it lists each test up front in separate columns

Tools/C_util/regtests/test.py

commit ae6336b7132a1153c0f8f76972dabe1bbc927f8e
Author: mzingale <mzingale>
Date:   Mon Nov 19 03:05:24 2007 +0000

    add a --note option and also fix a crash when making benchmarks and we
    have a restart test

Tools/C_util/regtests/test.py

commit f53cf86a6d8d595cd855b46db33904be7945915b
Author: ajnonaka <ajnonaka>
Date:   Sun Nov 18 06:08:35 2007 +0000

    created ml_edge_restriction_c.  ml_edge_restriction calls ml_edge_restriction_c, which loops over all components in the coarse multifab by default.  I believe the code only restricted the 1st component of coarse before.

Src/LinearSolvers/F_MG/ml_restriction.f90

commit eb40d05df87a94ba788f9484383928d490cc3779
Author: mzingale <mzingale>
Date:   Sun Nov 18 02:57:06 2007 +0000

    add the ability to do restart tests.
    
    Make the script behave gracefully when we fail compiling.

Tools/C_util/regtests/Maestro-tests.ini
Tools/C_util/regtests/test.py

commit a8343dbb23501028d5162764f087d218f0fc0356
Author: ajnonaka <ajnonaka>
Date:   Sat Nov 17 01:53:49 2007 +0000

    cleaned up code for easier reading

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 539e29676e702a503f28fe73341691ee26718caf
Author: lijewski <lijewski>
Date:   Wed Nov 14 22:20:53 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 2e6be8a1d71e8602988cdf5cfdf312cfd1b671ea
Author: lijewski <lijewski>
Date:   Wed Nov 14 21:04:25 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 0057427781e3afcadb6d8662e541a482d920ecc9
Author: lijewski <lijewski>
Date:   Wed Nov 14 20:33:03 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 75b53eb8db211c158ce5fc3b50a6ca29fb3a5e3d
Author: lijewski <lijewski>
Date:   Wed Nov 14 18:42:15 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak

commit 5081a8ad8c58fb8913afd856f3e9db7c509867a1
Author: lijewski <lijewski>
Date:   Wed Nov 14 03:51:45 2007 +0000

    centralized PGI and PathScale stuff

Tools/C_mk/Make.Linux

commit 994d5fb5e61de23d9e474386ea2a6e56b6a5f1ac
Author: ajnonaka <ajnonaka>
Date:   Tue Nov 13 18:43:25 2007 +0000

    plugged a memory leak

Src/LinearSolvers/F_MG/ml_cc.f90

commit bd77285197e6ab7796b0501a255f4594a5707e3c
Author: mzingale <mzingale>
Date:   Tue Nov 13 15:48:56 2007 +0000

    turn off debugging

Tools/C_util/regtests/test.py

commit c935e244d70a17c1e746295bf3087f69e9b21cd8
Author: mzingale <mzingale>
Date:   Tue Nov 13 15:01:34 2007 +0000

    add an entry for nan.astro.sunysb.edu

Tools/F_mk/GMakeMPI.mak

commit 428f1d0f068da69ee35c2710367599207a3a3c87
Author: lijewski <lijewski>
Date:   Fri Nov 9 23:05:40 2007 +0000

    added some commented out options for Franklin

Tools/C_mk/Make.Linux

commit 6a4fde42f42a15aaf19de99a359ff9f6a7764f10
Author: marc <marc>
Date:   Thu Nov 8 02:37:58 2007 +0000

    Near as I can tell, the IFC major and minor version numbers were not
    properly set because ifc doesn't always exist to give the version.
    I tried to unwind the logic to do this right...hope I didn't break anything...

Tools/C_mk/Make.defs

commit 508a653f015b55c2118526464b67000119a78f10
Author: almgren <almgren>
Date:   Thu Nov 8 00:09:29 2007 +0000

    Correct call to set coefficients for 2d and 3d.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 6f0cfb5f2db8c0ebb4230a4d93e3a714d1d2365b
Author: marc <marc>
Date:   Wed Nov 7 00:38:58 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit 853db84068d421614456d6aa5cd087f214e2b2bd
Author: lijewski <lijewski>
Date:   Mon Nov 5 23:00:55 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak

commit 086507bb4211f4bc2a135d936eeaa8196e4adb1e
Author: almgren <almgren>
Date:   Mon Nov 5 19:08:39 2007 +0000

    Stuff to debug Castro 1d.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 9b2d896f2d1d77adc1c5503397baa30210936dc1
Author: almgren <almgren>
Date:   Mon Nov 5 18:54:41 2007 +0000

    New stuff to enable 1d.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit bb318177f9305dfc0ccac40738305a89cde5ba4d
Author: ajnonaka <ajnonaka>
Date:   Thu Nov 1 17:29:54 2007 +0000

    added commented out jacobi option for 7 point 3d nodal smoother

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 4fdf0293bb1ae9910089ecf26e22099fb776957c
Author: ajnonaka <ajnonaka>
Date:   Thu Nov 1 00:45:25 2007 +0000

    added some commented out code to give a jacobi option for gs_rb_smoother_3d

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 02a2e453d78720377be2edf2c1d285a6555794b2
Author: almgren <almgren>
Date:   Wed Oct 31 20:10:15 2007 +0000

    Fix in set_uu_1d.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit c481f59ecff527c0c32d5829de290702074fe54d
Author: almgren <almgren>
Date:   Tue Oct 30 21:04:21 2007 +0000

    Add more 1d functions.

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit c9eb6f21d68f83608e394b033bc035f3cd1560ed
Author: almgren <almgren>
Date:   Tue Oct 30 20:50:27 2007 +0000

    Adding 1d routines.

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit 22ca924b90042d91a90be7347308183cde17c8dd
Author: almgren <almgren>
Date:   Tue Oct 30 20:47:09 2007 +0000

    Making 1d stuff compile.

Src/LinearSolvers/C_CellMG/ABec_1D.F
Src/LinearSolvers/C_CellMG/ABec_F.H
Src/LinearSolvers/C_CellMG/CG_F.H
Src/LinearSolvers/C_CellMG/LO_F.H
Src/LinearSolvers/C_CellMG/LP_1D.F
Src/LinearSolvers/C_CellMG/LP_F.H
Src/LinearSolvers/C_CellMG/MG_F.H

commit d04a867c88e0cc2ea1120c1cfde85ad0c4ca45fb
Author: almgren <almgren>
Date:   Tue Oct 30 20:29:03 2007 +0000

    Need this in 1d.

Src/LinearSolvers/C_CellMG/LP_1D.F
Src/LinearSolvers/C_CellMG/MG_1D.F

commit 8eeb172ad518102df2442aebabacf599dc30fa38
Author: almgren <almgren>
Date:   Tue Oct 30 20:28:18 2007 +0000

    This version actually compiles.

Src/LinearSolvers/C_CellMG/LO_1D.F

commit ab1a1151eab388db7de73fa35608b78eec97faf7
Author: almgren <almgren>
Date:   Tue Oct 30 20:24:39 2007 +0000

    Need one of these in 1d as well.

Src/LinearSolvers/C_CellMG/LO_1D.F

commit 8984c5f1402c72aaed4beed6c479a6f47e9c4e14
Author: almgren <almgren>
Date:   Tue Oct 30 20:10:19 2007 +0000

    Need this in 1d.

Src/C_BoundaryLib/INTERPBNDRYDATA_1D.F

commit 6ae505cf9f01b04d968c8d3ee27ed750eeb9a90e
Author: almgren <almgren>
Date:   Tue Oct 30 19:59:55 2007 +0000

    Need to have one of these in 1d as well.

Src/LinearSolvers/C_CellMG/CG_1D.F

commit 03c18d0b4d2a3bb92767e0333657c88aa51639cb
Author: almgren <almgren>
Date:   Tue Oct 30 19:43:55 2007 +0000

    New 1-d version of ABec*.F

Src/LinearSolvers/C_CellMG/ABec_1D.F

commit 2b46d5aa14d8b49f8c546777b80025a947dd5b53
Author: almgren <almgren>
Date:   Tue Oct 30 19:33:52 2007 +0000

    Add 1-d capability.

Src/LinearSolvers/F_MG/mg_cpp_f.h

commit f1cafc4a8afa8a4e9d9a7b92f272e32589e89778
Author: almgren <almgren>
Date:   Mon Oct 29 04:26:20 2007 +0000

    Necessary modifications to let 1-d work.

Src/C_BoundaryLib/InterpBndryData.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/ABec_F.H
Src/LinearSolvers/C_CellMG/LP_F.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp

commit a2773e048ff9c8083a85111acbfa68ba1c5b92d0
Author: almgren <almgren>
Date:   Mon Oct 29 04:03:02 2007 +0000

    Define GetDLogA for 1d as well as 2d.

Src/C_BaseLib/Geometry.cpp

commit 71df312e2cbd80839e27a8dad0723ed68850b0e1
Author: almgren <almgren>
Date:   Sun Oct 28 19:34:25 2007 +0000

    Added LINCCINTERP for 1-d.

Src/C_AMRLib/INTERP_1D.F
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/Interpolater.cpp

commit d5796256c671c373904ba3f33fcff2ed5987c84a
Author: almgren <almgren>
Date:   Sun Oct 28 14:46:30 2007 +0000

    Need to include ArrayLim.H, not DIMS.

Src/C_BaseLib/COORDSYS_1D.F

commit 1c0c03066ae5eaa206cd0168826fb6432b1ebb39
Author: almgren <almgren>
Date:   Fri Oct 26 04:12:42 2007 +0000

    Change min_width from 1 to 2.

Src/LinearSolvers/F_MG/mg.f90

commit 8afb1b8d64f216edfdc3ce2d24ff12b747b2624d
Author: almgren <almgren>
Date:   Fri Oct 26 00:44:39 2007 +0000

    Put fill boundary outside of need_grad_phi if test.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 4662f735a002d8aacd8274b3ee47cb03c4388ad5
Author: almgren <almgren>
Date:   Tue Oct 23 17:48:35 2007 +0000

    New coefficient arrays for variable coefficient test problems.

Src/LinearSolvers/C_CellMG/Test/COEF_2D.F
Src/LinearSolvers/C_CellMG/Test/COEF_3D.F
Src/LinearSolvers/C_CellMG/Test/COEF_F.H
Tests/LinearSolvers/C_CellMG/COEF_2D.F
Tests/LinearSolvers/C_CellMG/COEF_3D.F
Tests/LinearSolvers/C_CellMG/COEF_F.H

commit ca0d0700d6395f7e9401b9279751c1c0ffd65260
Author: almgren <almgren>
Date:   Tue Oct 23 17:42:21 2007 +0000

    Fix second call to jacobi_smooth.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 27e05c50690adedbaf51f456eac40a4782d8a507
Author: lijewski <lijewski>
Date:   Mon Oct 22 20:29:20 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit bf301e6ddde8f55bd924c19770d28524d4231df7
Author: almgren <almgren>
Date:   Mon Oct 22 20:27:04 2007 +0000

    New version of diagonal (aka Jacobi) preconditioning for solve_bicgstab.

Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/ABec_F.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit b015deba94f8950100b9c135aecff5a5c29f28bd
Author: almgren <almgren>
Date:   Mon Oct 22 03:47:32 2007 +0000

    Put in commented code which actually should work much better.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 1031f8bd2264382d35206fabc62d060e61786698
Author: almgren <almgren>
Date:   Mon Oct 22 02:49:57 2007 +0000

    Added the capability for the BiCG solver in CGSolver.cpp
    to do a Jacobi relaxation as a preconditioner.

Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/ABec_F.H
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit f11c6c50df6f6db49060d16de8390d1ed7cc4c2c
Author: almgren <almgren>
Date:   Fri Oct 19 21:22:05 2007 +0000

    Code was just wrong -- it was computing the diff into a FAB but
    never putting it into the "error" MultiFab.

Tools/C_util/Convergence/DiffUniform.cpp

commit 6610a750a49835df82602dbd4993418c478d56c5
Author: marc <marc>
Date:   Thu Oct 18 00:00:02 2007 +0000

    fix CVS screwup

Tools/C_mk/Make.mpi
Tools/C_mk/Make.rules

commit 2fec3697a779d1fc837434f09d07020995716ad8
Author: marc <marc>
Date:   Wed Oct 17 23:43:53 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.mpi
Tools/C_mk/Make.rules

commit 24a76f8150f25affd9b4a610e0cfeb7b7dd49d24
Author: mzingale <mzingale>
Date:   Tue Oct 16 18:41:40 2007 +0000

    add links to allow for navigation between the test page and individual
    tests
    
    Add ChangeLogs

Tools/C_util/regtests/test.py

commit b6654ed7efb6b93a60c33269797e7aa28c5fd44c
Author: almgren <almgren>
Date:   Mon Oct 15 23:07:47 2007 +0000

    Fix calls to stencil_apply...

Src/LinearSolvers/F_MG/stencil.f90

commit 46892415471a89ceadf68520f1319077219eb1f5
Author: almgren <almgren>
Date:   Mon Oct 15 22:49:06 2007 +0000

    Allow the "dd" (or "rr") to have non-zero ghost cells by passing
    in the ng_d as well as the ng_d.  This is relevant for all stencil_apply
    and stencil_dense_apply calls.

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 19ead2be8c00558d5d61f0612fadb0e13455bc02
Author: lijewski <lijewski>
Date:   Mon Oct 15 21:11:12 2007 +0000

    added -lrt for FRANKLIN

Tools/C_mk/Make.Linux

commit 485fbdab2e178880695057e8c9b7640299b6d730
Author: almgren <almgren>
Date:   Thu Oct 11 20:33:23 2007 +0000

    Commented code which does Jacobi instead of GSRB relaxation for 2d cell-centered
    and 2d nodal.  As is the code does GSRB, but one can uncomment certain lines
    to do Jacobi instead.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 5a8da8db97a8503f5d48f5390e38bdfc113dbb37
Author: lijewski <lijewski>
Date:   Tue Oct 9 21:59:01 2007 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_util.f90

commit 064865e14fd87e46b3b7d90bd74c0ea816bb66f0
Author: lijewski <lijewski>
Date:   Tue Oct 9 21:39:45 2007 +0000

    *** empty log message ***

Src/F_BaseLib/cluster.f90
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_bxasc.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_bxasc.f90
Tests/F_BaseLib/t_main.f90

commit c50ac1b25bed59b7e3c9d8d6b318939eb7a8e58d
Author: ajnonaka <ajnonaka>
Date:   Tue Oct 9 20:22:46 2007 +0000

    Ann's changes in cgsolve.

Src/LinearSolvers/F_MG/itsol.f90

commit 67e900f310437831da3e39f450903e549094ebc2
Author: marc <marc>
Date:   Tue Oct 9 00:30:39 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.CYGWIN_NT

commit 3ab74caf78138bfbd2eddecde536c8e3884f8eea
Author: lijewski <lijewski>
Date:   Fri Oct 5 21:52:52 2007 +0000

    more franklin mods for Castro

Tools/C_mk/Make.Linux

commit 0c11fe67ca037b0228f255ed8d2efcb99aab4311
Author: lijewski <lijewski>
Date:   Fri Oct 5 21:09:37 2007 +0000

    automagically identify franklin in Make.defs/Make.Linux

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit 72b18355c3095c947f83d204a34fcfd5649f1180
Author: lijewski <lijewski>
Date:   Fri Oct 5 21:04:46 2007 +0000

    treat franklin as Linux machine

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 17d8e0079e362759c67e12810de989661e6af37c
Author: almgren <almgren>
Date:   Fri Oct 5 17:07:30 2007 +0000

    Added new mult functions to multifab and ml_multifab.

Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/multifab.f90

commit 9f377005d105bea9887fd685bec2fd018decee4f
Author: lijewski <lijewski>
Date:   Thu Oct 4 22:44:21 2007 +0000

    ansi C++-ified

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 40ee5b728f11654a022447fbb22de0647bd29649
Author: lijewski <lijewski>
Date:   Thu Oct 4 22:41:20 2007 +0000

    commented out pedantic -- conflicts with something in mpi.h

Tools/C_mk/Make.defs

commit e34ce03cb69786b4794eb7782f7b95c7d363eda2
Author: lijewski <lijewski>
Date:   Thu Oct 4 22:31:27 2007 +0000

    some cleanup

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/SlabStat.cpp
Src/C_AMRLib/TagBox.cpp

commit 24f3c047fcc040d1d5de00a3a7e516a830c66686
Author: lijewski <lijewski>
Date:   Thu Oct 4 22:31:17 2007 +0000

    added -pedantic to g++

Tools/C_mk/Make.defs

commit 9b0e2211f74bc7c29c917e8070deab4974c215c4
Author: mzingale <mzingale>
Date:   Mon Oct 1 14:08:04 2007 +0000

    add a comment when the benchmarks are updated so we log the reason for
    the change in the solution

Tools/C_util/regtests/test.py

commit ef4a5f0a13c0f2228bbf5c456dfa809205547807
Author: almgren <almgren>
Date:   Thu Sep 27 18:16:11 2007 +0000

    Fix the copy in ml_multifab to match that in multifab, i.e. you
    can pass number of ghost cells but can no longer pass "all".

Src/F_BaseLib/ml_multifab.f90

commit 9c1d562706e5c82b77a6fd613b76e698070146d0
Author: lijewski <lijewski>
Date:   Tue Sep 25 20:34:13 2007 +0000

    AIX mods

Tools/F_mk/GMakedefs.mak

commit 363d0e81a4a93dcf3840323fdb0cd87e2798ea92
Author: almgren <almgren>
Date:   Tue Sep 25 17:57:39 2007 +0000

    Replace all by ng in bndry_reg copy functions.

Src/F_BaseLib/bndry_reg.f90

commit f3f83ae1a3927a7a37fe2aafa45010b1f21b3467
Author: lijewski <lijewski>
Date:   Mon Sep 24 21:29:35 2007 +0000

    added xt4 block for franklin

Tools/F_mk/GMakedefs.mak

commit cc4c7375829c2fe6cf02d68367ffe03c8c11d6b6
Author: lijewski <lijewski>
Date:   Sun Sep 23 18:39:18 2007 +0000

    nan & inf stuff work with PATHSCALE

Src/C_BaseLib/FArrayBox.cpp

commit 8e43cd94459b7f1052422302072e29f18557523e
Author: lijewski <lijewski>
Date:   Sun Sep 23 16:44:06 2007 +0000

    inf & nan stuff works on AIX

Src/C_BaseLib/FArrayBox.cpp

commit 416f25eb0803904146e99d5a825a7f9bd2402500
Author: lijewski <lijewski>
Date:   Sat Sep 22 15:05:31 2007 +0000

    added nan & inf detection code

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 1ef7026b4e7b736d4474a09f1c863d109d17b63c
Author: lijewski <lijewski>
Date:   Sat Sep 22 15:05:12 2007 +0000

    removed debug stuff from MFIter

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit dff9211c1530a2095122696d7368d0706ea238bc
Author: almgren <almgren>
Date:   Tue Sep 18 20:17:22 2007 +0000

    Didn't mean to commit all the changes in stopping criteria,
    just wanted the change in copy calls.

Src/LinearSolvers/F_MG/itsol.f90

commit 7ecbbef4495aace10b38f404e7a9f52a5ae2663a
Author: lijewski <lijewski>
Date:   Tue Sep 18 20:03:57 2007 +0000

    force Headers to use scientific notation for floating point values

Src/C_BaseLib/VisMF.cpp

commit 37506464605180194ff3e496396ea7e96f376209
Author: lijewski <lijewski>
Date:   Tue Sep 18 19:57:29 2007 +0000

    floating point format change: es30.20 -> es25.15

Src/F_BaseLib/fabio.f90

commit 94249c16d440c152eb51a104700973d27e3e1cc6
Author: almgren <almgren>
Date:   Tue Sep 18 19:42:36 2007 +0000

    Replaced "all" argument by "ng" argument in multifab_copy and multifab_copy_c.

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/sparse_solve.f90

commit fd45cdc7c0d10b6a24d8adc2f7b6937239381171
Author: lijewski <lijewski>
Date:   Mon Sep 17 21:37:27 2007 +0000

    simplified _nfiles stuff previously added

Src/C_AMRLib/Amr.cpp

commit f2c56dbabe7f55cafa2fd8e7a58d925eccff243f
Author: lijewski <lijewski>
Date:   Mon Sep 17 17:47:52 2007 +0000

    changed defaults for *_nfiles to 64

Src/C_AMRLib/Amr.cpp

commit 7cf65215e3f0a696d5c2045e8e059a8806d06ab6
Author: sepp <sepp>
Date:   Wed Sep 12 21:32:26 2007 +0000

    1) add an Add and a Subtract routine like the Copy already there

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 160b5c852d54d60ef1c6689a8662fe45e8aa7445
Author: lijewski <lijewski>
Date:   Fri Sep 7 23:01:43 2007 +0000

    can now regrid single-level calculation

Src/C_AMRLib/Amr.cpp

commit 1861bc1ab6aef8f2ce0118d75b095709ec76998c
Author: almgren <almgren>
Date:   Fri Sep 7 17:09:14 2007 +0000

    These versions of mg.f90 and mg_smoother.f90 actually compile.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_smoother.f90

commit 9100e72267065487814a78cb51c758e7832b6a0f
Author: almgren <almgren>
Date:   Fri Sep 7 17:07:31 2007 +0000

    Modify 2d- and 3d- nodal smoother calls so that when using cross stencil,
    with red-black Gauss-Seidel, we make sure to do a multifab_fill_boundary
    between the red and black sweeps.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_smoother.f90

commit c000fb8f69873d8c2653ede0ebf9208211494ab4
Author: lijewski <lijewski>
Date:   Thu Sep 6 20:27:16 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 9dc0b3a6670bbf3b8edbf32cc0f140633c18edcb
Author: marc <marc>
Date:   Tue Sep 4 21:31:40 2007 +0000

    Do not include wait.h on Columbia...makes Intel compiler unhappy...do we need this elsewhere??

Src/C_BaseLib/Utility.H

commit c70510f7ee7a67f13a13030af385edd5a4c5e512
Author: marc <marc>
Date:   Tue Sep 4 21:25:12 2007 +0000

    Remove wait.h include, already dealt with in Utility.H

Src/C_BaseLib/Utility.cpp

commit e3fa055628ff65319a5ed8887d30a379171b0292
Author: lijewski <lijewski>
Date:   Tue Sep 4 19:50:10 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/in.3_512cubed
Tests/LinearSolvers/C_CellMG/grids/in.3_512cubed

commit 2592824a6ce18ccb29a4f8ddcf650641de3d054b
Author: lijewski <lijewski>
Date:   Tue Aug 28 22:18:55 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared
Tests/LinearSolvers/C_CellMG/grids/in.2_256squared

commit a5f54e97a240915b95f7068b451721d340de71b4
Author: lijewski <lijewski>
Date:   Tue Aug 28 21:38:13 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared
Tests/LinearSolvers/C_CellMG/grids/in.2_256squared

commit fbf42cc6c5ae6f6d57f2a3b49570364660c6fcc3
Author: lijewski <lijewski>
Date:   Tue Aug 28 19:37:45 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 28d5b7429875f44386ab7d2acac76790c4f4c127
Author: almgren <almgren>
Date:   Fri Aug 24 19:27:48 2007 +0000

    Add option to set variable coefficients in solve, flag is use_variable_coef
    which defaults to false.

Src/LinearSolvers/C_CellMG/Test/COEF_2D.F
Src/LinearSolvers/C_CellMG/Test/COEF_3D.F
Src/LinearSolvers/C_CellMG/Test/COEF_F.H
Src/LinearSolvers/C_CellMG/Test/Make.package
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/COEF_2D.F
Tests/LinearSolvers/C_CellMG/COEF_3D.F
Tests/LinearSolvers/C_CellMG/COEF_F.H
Tests/LinearSolvers/C_CellMG/Make.package
Tests/LinearSolvers/C_CellMG/main.cpp

commit 019d72dbf5e22a542f5498692ec52a475c0ae9f5
Author: mzingale <mzingale>
Date:   Fri Aug 24 14:57:43 2007 +0000

    add the ability to do only a single test, if desired

Tools/C_util/regtests/test.py

commit 22080d53d8856f4862cca14a1fa14e8fdf2f6080
Author: mzingale <mzingale>
Date:   Thu Aug 23 14:10:48 2007 +0000

    make it work with python 2.3
    
    switch to inf norm
    
    for fParallel builds, feed in MPI= to disable MPI in the make
    
    add the time and date of the CVS update to the webpage

Tools/C_util/regtests/test.py

commit b9e0b8abb1373cbafde5326166cc96c1fac5c474
Author: lijewski <lijewski>
Date:   Tue Aug 21 21:49:42 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared
Src/LinearSolvers/C_CellMG/Test/grids/in.3_128cubed
Src/LinearSolvers/C_CellMG/Test/grids/in.3_256cubed
Tests/LinearSolvers/C_CellMG/grids/in.2_256squared
Tests/LinearSolvers/C_CellMG/grids/in.3_128cubed
Tests/LinearSolvers/C_CellMG/grids/in.3_256cubed

commit 7fc3aca9ec8414c4fa13e8f4277c8a30695028ac
Author: almgren <almgren>
Date:   Tue Aug 21 21:43:42 2007 +0000

    Two more 3-d grids with a domain just broken up into same-size boxes.

Src/LinearSolvers/C_CellMG/Test/grids/gr.3_256cubed
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_512cubed
Tests/LinearSolvers/C_CellMG/grids/gr.3_256cubed
Tests/LinearSolvers/C_CellMG/grids/gr.3_512cubed

commit 93cf3e8eb56f3ffeda46146cf4f520ce8a16b043
Author: mzingale <mzingale>
Date:   Tue Aug 21 20:36:35 2007 +0000

    echo SUCCESS upon a successful build -- this will be seen by the regression
    test framework (Parallel/util/regtests/) to detect that compilation worked.

Tools/C_mk/Make.rules

commit 26766d0786e0038ba603f0a57ad5d972bbf02c73
Author: almgren <almgren>
Date:   Tue Aug 21 18:21:53 2007 +0000

    Clean this up...

Src/LinearSolvers/C_CellMG/Test/grids/in.3_128cubed
Tests/LinearSolvers/C_CellMG/grids/in.3_128cubed

commit dc99618e28bd52515c29217d01948fc7614c4f65
Author: almgren <almgren>
Date:   Tue Aug 21 18:21:10 2007 +0000

    These are the ones we're testing superlu with.

Src/LinearSolvers/C_CellMG/Test/grids/gr.2_256squared
Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared
Tests/LinearSolvers/C_CellMG/grids/gr.2_256squared
Tests/LinearSolvers/C_CellMG/grids/in.2_256squared

commit a65c79a177cf63761a526af57a3a3697b83065f1
Author: almgren <almgren>
Date:   Tue Aug 21 17:41:11 2007 +0000

    Finished changing mult,div,plus,sub calls take ng instead of "all"
    now.

Src/F_BaseLib/multifab.f90

commit 321612b4309f76353bc14dfcc02707bddd7a82e4
Author: mzingale <mzingale>
Date:   Tue Aug 21 14:48:28 2007 +0000

    add the initial version of the regression testing framework, developed
    initially for Castro.  The Castro-tests.ini file sets up some pure
    hydro tests.  Maestro-tests.ini will setup a single test for Maestro
    (in the fParallel framework).

Tools/C_util/regtests/Castro-tests.ini
Tools/C_util/regtests/Maestro-tests.ini
Tools/C_util/regtests/README
Tools/C_util/regtests/test.py

commit 3a1996eadc511aa4601c97a0330f5e68edfeb5c4
Author: ajnonaka <ajnonaka>
Date:   Mon Aug 20 23:32:11 2007 +0000

    finished Ann's implementation for mandatory ghost cells for plus_plus, div_div, and mult_mult

Src/F_BaseLib/ml_multifab.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit b8e6a8de9b4e142838af46c72c3078a5b4be4484
Author: almgren <almgren>
Date:   Mon Aug 20 23:05:20 2007 +0000

    We are now changing the calling sequence to operations on multifabs
    which used to take "all" as an optional argument -- they now take ng.

Src/F_BaseLib/multifab.f90

commit d0924c9cd4dcc8005a351a288874952dca5452cc
Author: mzingale <mzingale>
Date:   Fri Aug 10 17:59:22 2007 +0000

    add the compressor script from the Parallel tree to help tame our
    plot/chk directories

Tools/F_scripts/compressor

commit 4e6a50d4bfad7c7809a92513bc4f26778c44945a
Author: almgren <almgren>
Date:   Mon Aug 6 22:24:41 2007 +0000

    Shouldn't test on rnorm in cg or bicg solve if stopping
    criterion was reached before any iterations.

Src/LinearSolvers/F_MG/itsol.f90

commit 302f73984da74c9ca118fe0d9e546a4084d5bbe2
Author: mzingale <mzingale>
Date:   Sat Aug 4 23:54:40 2007 +0000

    determine if the files agree by looking at the absolute norms and print
    out a message that the regression suite can detect.

Tools/C_util/Convergence/DiffSameGrid2.cpp

commit 45766b7394be7ed88fc98a05bba685ef79e8407d
Author: mzingale <mzingale>
Date:   Fri Aug 3 17:37:12 2007 +0000

    change the make clean rule from
    
    $(RM) $(EBASE)$(optionsSuffix).ex
    
    to
    
    $(RM) $(executable)
    
    so it works when we invoke make as gmake executable=Castro.exe to rename
    the executable.

Tools/C_mk/Make.rules

commit 0cf740a7294384d3d39ea781fe39f23e6946612d
Author: mzingale <mzingale>
Date:   Thu Aug 2 17:40:00 2007 +0000

    switch over to using a lock file to guarantee that build_info.f90 is
    regenerated and built each time.  This now means that at any make
    invocation, it gets rebuilt (i.e. not only when some other file
    has changed), but it avoids some circular dependencies that I couldn't
    track down.

Tools/F_mk/GMakerules.mak

commit 9f61eaafd894b13b4aab8c04f259469fca3d1543
Author: mzingale <mzingale>
Date:   Wed Aug 1 21:23:42 2007 +0000

    add a new rule for build_info.f90, so that we are sure that it is
    regenerated any time we recompile.  Previously, the script was not
    rerun when a file changed, so the build info could be out of date.
    
    Now there is a new class of files, sf90sources, that do not get
    the dependency check done to them.  Rightnow, build_info.f90 is the
    only such example of this type of file.  This allows it to have as
    dependencies all of the other files, thus guarranting that it
    gets regenerated.

Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak

commit 7f9c7d807b045b752e860ea1c3a44160f5a82143
Author: mzingale <mzingale>
Date:   Wed Aug 1 15:19:55 2007 +0000

    make this compile with compilers that don't allow > 132 columns

Tools/F_scripts/make_build_info

commit 1da95f6d008c78c0bf6d84379b91f11a4fd0972e
Author: almgren <almgren>
Date:   Tue Jul 31 23:56:29 2007 +0000

    Added multifab_print_c and fab_print_c which print
    only a single component of the multifab or fab.

Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab.f90

commit c54300acc0080e1c21a3e38d81ce8e7195f11656
Author: almgren <almgren>
Date:   Mon Jul 30 18:18:10 2007 +0000

    Missed a few places for the BL_ASSERT(num_comp > 0); statement.

Src/C_BaseLib/MultiFab.cpp

commit 6bc3153d5794f132710c4d77ebddc39ba7fc8ab4
Author: almgren <almgren>
Date:   Mon Jul 30 18:10:58 2007 +0000

    Added BL_ASSERT(num_comp > 0); to a number of the plus/minus - type calls...

Src/C_BaseLib/MultiFab.cpp

commit 9bdb42d026febd5e2004a5591657fcd39af00888
Author: almgren <almgren>
Date:   Sat Jul 28 22:24:05 2007 +0000

    Fixed stencil_all_flux_3d to match sign convention of 2d version.

Src/LinearSolvers/F_MG/stencil.f90

commit f6af15d73e79228b45d9db3e8b7b91ad79b734a9
Author: mzingale <mzingale>
Date:   Wed Jul 25 20:34:31 2007 +0000

    make the string length a script parameter

Tools/F_scripts/make_build_info

commit a9e74b0cc62cf1d7ac197fa27472391f7c5b9707
Author: marc <marc>
Date:   Wed Jul 25 01:07:35 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.CYGWIN_NT

commit 977402bb330241f435bb20e75133c938aca6bc3e
Author: almgren <almgren>
Date:   Thu Jul 19 21:04:33 2007 +0000

    Added function ml_resid.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 1782de980752d700a74dda7bb15fabdbd1c5a730
Author: mzingale <mzingale>
Date:   Thu Jul 19 18:49:58 2007 +0000

    add some more comments and documentation

Tools/C_util/Convergence/DiffSameGrid2.cpp

commit 0013045364cf07dc12307860d30032a91b42dde8
Author: ajnonaka <ajnonaka>
Date:   Thu Jul 19 18:04:50 2007 +0000

    fixed bug: in ml_cc_applyop, was computing dm before rh was allocated

Src/LinearSolvers/F_MG/ml_cc.f90

commit 04faf4d539e868eafc0c3873ff8217f8c473b492
Author: ajnonaka <ajnonaka>
Date:   Wed Jul 18 22:52:57 2007 +0000

    residual automatically scales by -1,thus, actually returning (alpha - del dot beta grad)phi in the call to mac_applyop->ml_cc_applyop

Src/LinearSolvers/F_MG/ml_cc.f90

commit 43b9b35c8498620a1022bbf8083290e3f9cffbc8
Author: ajnonaka <ajnonaka>
Date:   Wed Jul 18 22:29:42 2007 +0000

    much more progress in thermal conduction solve; I still need to configure the bc's correctly in thermal_conduct.f90 and actually make the residual and solve calls

Src/LinearSolvers/F_MG/ml_cc.f90

commit 453f3eae7af98650a0f14fc71f4df929483c90a4
Author: mzingale <mzingale>
Date:   Wed Jul 18 20:39:01 2007 +0000

    add a divide method so we can divide the zones in one multifab by
    the value in the corresponding zone of the other.  This is needed for
    the regression testing in util/Convergence/DiffSameGrid2

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 59d6050c5f0b4d8223ff3df6e164a30cd6e89b83
Author: mzingale <mzingale>
Date:   Wed Jul 18 20:37:45 2007 +0000

    new version of DiffSameGrid that does both relative and absolute
    errors -- this will be used as part of the Castro regression suite

Tools/C_util/Convergence/DiffSameGrid2.cpp

commit 5f7695e5e77ba827a47bf4691979d50c628e5bb5
Author: ajnonaka <ajnonaka>
Date:   Wed Jul 18 17:54:03 2007 +0000

    Working on creating a new subroutine, "mac_applyop", which will live in macproject.f90, and simply returns the residual "-(alpha-del dot beta grad)phi".  The subroutine "mac_applyop" is based on subroutine "mac_multigrid", but calls a new subroutine, "ml_cc_applyop" rather than "ml_cc".  Subroutine "ml_cc_applyop" is based on subroutine "ml_cc", but stops after the residual is computed.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 2dc47968a44758805030e6c88d6ecdc195699486
Author: almgren <almgren>
Date:   Tue Jul 17 05:15:37 2007 +0000

    Fix small typos.

Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 22f62ede8bb929afbbd27195e96521c2b6946c75
Author: almgren <almgren>
Date:   Tue Jul 17 05:06:33 2007 +0000

    Needed 3d instead of 2d...

Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 28f77d10a6c05d3b66c7e4313358ab73b2af5101
Author: almgren <almgren>
Date:   Tue Jul 17 04:46:18 2007 +0000

    Remove print statement.

Src/LinearSolvers/F_MG/stencil.f90

commit c88ec9a28639097bda842c7242d914d8f74f8908
Author: almgren <almgren>
Date:   Tue Jul 17 04:42:12 2007 +0000

    Add mgt_compute_residual routine which calls new ml_resid.

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit dd6962e48a65c7e7a5393cd9cb5c06d94c345a85
Author: almgren <almgren>
Date:   Tue Jul 17 04:41:39 2007 +0000

    Added compute_residual routine.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 848a5fa925d8bd0e4e16ad0fcb7b31ca53a1d962
Author: almgren <almgren>
Date:   Tue Jul 17 04:15:31 2007 +0000

    Change name for timing routine.

Src/LinearSolvers/F_MG/mg.f90

commit 9021c05e9b52e440f29153ccc8182f5b4a165b56
Author: almgren <almgren>
Date:   Mon Jul 16 21:34:38 2007 +0000

    Put same minus signs in stencil_all_flux_3d as stencil_all_flux_2d for
    lo-side fluxes.

Src/LinearSolvers/F_MG/stencil.f90

commit 9c1d0bb125c7cde25ea8dc92d58957c4c671ea0e
Author: almgren <almgren>
Date:   Mon Jul 16 17:32:05 2007 +0000

     Make sure all ghost cells of full_soln at fine grid have the correct values before
    computing the initial residual for residual-correction form.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 5357e7041045f6d1f2ed2b865e7e0525463908cd
Author: mzingale <mzingale>
Date:   Mon Jul 16 14:18:39 2007 +0000

    when compiling on jaguar (catamount), put the intermediate module files
    into the m/ directory (as is done on all other platforms), instead of
    sticking them in the top level directory.  This assumes that we are using
    the PGI compilers with catamount (which is the default)

Tools/F_mk/GMakedefs.mak

commit 246196b623e580df0bb07e5bce3a52e849c21cfa
Author: almgren <almgren>
Date:   Sat Jul 14 02:54:12 2007 +0000

    Need to pass in xa, xb since we don't know what AMR level we're actually at.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit ffaf7177b8af5959629ad3a30abb4e5745808484
Author: almgren <almgren>
Date:   Sat Jul 14 00:35:45 2007 +0000

    Remove extra print statements.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit d253f65c655b42f18e3f30f842de32fd642a1868
Author: almgren <almgren>
Date:   Sat Jul 14 00:16:46 2007 +0000

    Remove print statements.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 885e642af3efae70f10c4a7edd5bd3dd4b77eb95
Author: almgren <almgren>
Date:   Fri Jul 13 22:56:49 2007 +0000

    New code to work for gravity in Castro.

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 2fcdcff6745c98e72076f3f39a87a8271f0afaeb
Author: almgren <almgren>
Date:   Fri Jul 13 22:56:17 2007 +0000

    New stuff to work for gravity in Castro.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit c0443de77662c9a8b0baeea014543d40046ce162
Author: mzingale <mzingale>
Date:   Fri Jul 13 16:34:39 2007 +0000

    create a rule to make build_info.f90.  You need to add f90sources +=
    build_info.f90 to your GPackage.mak to get this rule to execute

Tools/F_mk/GMakerules.mak

commit 0cef191bebd9e386faf51dc83bac88d76ebf8eb0
Author: mzingale <mzingale>
Date:   Fri Jul 13 15:15:50 2007 +0000

    a script that automagically generates a Fortran subroutine that returns
    the name of the machine we compiled on, the build date/time, and the
    directory that we built in.

Tools/F_scripts/make_build_info

commit d7c1235e378cd52b8c297047efd2dedf6a3911ff
Author: almgren <almgren>
Date:   Tue Jul 10 21:15:06 2007 +0000

    When need_grad_phi is true, make sure we fill periodic and fine-fine
    ghost cells as well as interpolating from crser grid.

Src/LinearSolvers/F_MG/ml_cc.f90

commit a6f59e675e48614bd3d4ac063d4124185ed63c86
Author: ajnonaka <ajnonaka>
Date:   Mon Jul 9 18:27:27 2007 +0000

    This is a dummy checkin to verify my CVS works.

Tools/F_scripts/coco/coco.pl

commit b9ebe4200572cbd3e979d4c5e0a8199ebfd5b7e8
Author: almgren <almgren>
Date:   Fri Jul 6 01:04:01 2007 +0000

    Fixed bug for multiple grids per level above 0.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 2cce8a444b1156b5ffe2f99bb62f9065e7d51bf7
Author: lijewski <lijewski>
Date:   Thu Jul 5 20:59:05 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit a57e388f4fb4f0628adcaee5190c1093503b5546
Author: almgren <almgren>
Date:   Thu Jul 5 20:51:20 2007 +0000

    Get rid of unused gbox in assertions.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit a6f68e26519dc26d3c782f7e710224fd288a5f5b
Author: almgren <almgren>
Date:   Thu Jul 5 20:50:32 2007 +0000

    Get rid of unused stuff in assertions.

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp

commit fd16e2bfc0e08ab3b16711f10bac8a750071424a
Author: almgren <almgren>
Date:   Thu Jul 5 20:49:18 2007 +0000

    Fix up the MyProc stuff.

Src/C_BoundaryLib/FabSet.cpp

commit d9b64cee142c15dc8c8c3ef2f3177582945e2563
Author: lijewski <lijewski>
Date:   Thu Jul 5 20:43:08 2007 +0000

    *** empty log message ***

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/StationData.cpp

commit 4cb519abcff6c97e16a7e20dfc42a584b0099364
Author: lijewski <lijewski>
Date:   Thu Jul 5 20:02:11 2007 +0000

    *** empty log message ***

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/StateDescriptor.cpp
Src/C_AMRLib/StationData.cpp
Src/C_BoundaryLib/FabSet.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit 2a4d31fd7d1b98f35f9e3b148108b96bb27ce147
Author: lijewski <lijewski>
Date:   Thu Jul 5 17:02:00 2007 +0000

    *** empty log message ***

Src/C_AMRLib/Amr.H
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/LevelBld.H

commit be18f98e38003f9beec2ec036b7b10560bb6f699
Author: lijewski <lijewski>
Date:   Tue Jul 3 21:54:58 2007 +0000

    *** empty log message ***

Src/C_BaseLib/COORDSYS_3D.F
Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F
Src/LinearSolvers/C_CellMG/LO_3D.F

commit ccfe65329715bb903e94339b7ba532d9e6057136
Author: lijewski <lijewski>
Date:   Tue Jul 3 21:22:57 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit 7651597c724546650d8dc42d3d59ad14ae4cdb2a
Author: almgren <almgren>
Date:   Tue Jul 3 21:05:31 2007 +0000

    This main.cpp has a RHS that sums to zero, so it is solvable
    with all-Neumann or all-periodic bc's as well as with Dirichlet.

Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 92c3405ca8c4ab3001f9777fe4a6ce33f976f4a7
Author: almgren <almgren>
Date:   Tue Jul 3 20:41:45 2007 +0000

    New files with 128 cubed divided into 64 patches of 32 cubed.

Src/LinearSolvers/C_CellMG/Test/grids/gr.3_128cubed
Src/LinearSolvers/C_CellMG/Test/grids/in.3_128cubed
Tests/LinearSolvers/C_CellMG/grids/gr.3_128cubed
Tests/LinearSolvers/C_CellMG/grids/in.3_128cubed

commit c1a997247879068977dc9d7738f33b02f3c2b5c5
Author: lijewski <lijewski>
Date:   Tue Jul 3 20:10:56 2007 +0000

    g95 stuff

Tools/C_mk/Make.defs

commit a10cda9d917e1d17558c056e1a3945474cb1b3e4
Author: lijewski <lijewski>
Date:   Tue Jul 3 19:50:33 2007 +0000

    removed extraneous OutOfMemory

Src/C_BaseLib/BoxLib.cpp

commit 2627d126be4ec8f5b3a37a04017699bbbc3411f0
Author: lijewski <lijewski>
Date:   Tue Jul 3 03:37:57 2007 +0000

    removed stencil_flux_fill_st()

Src/LinearSolvers/F_MG/stencil.f90

commit b342af9be7bcfddc168bbaade2c690ef00e5e980
Author: lijewski <lijewski>
Date:   Tue Jul 3 03:13:09 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit 0e933438d3ad6e42b6b10096e8af59a37239fda3
Author: lijewski <lijewski>
Date:   Tue Jul 3 03:10:38 2007 +0000

    some cleanup

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/box.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/fab.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_nodal_cpp.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/sparse_solve.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit c40f3f0a57e1618a66036779cafb169d61a4db5a
Author: lijewski <lijewski>
Date:   Mon Jul 2 23:00:14 2007 +0000

    some cleanup

Src/C_AMRLib/INTERP_2D.F
Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/LO_2D.F
Src/LinearSolvers/C_CellMG/LP_2D.F
Src/LinearSolvers/C_CellMG/LP_F.H

commit ff31d6ec117071fdb51e53c9c8364b9749fcaf21
Author: almgren <almgren>
Date:   Mon Jul 2 17:53:31 2007 +0000

    Comment out the printing of f90 mg settings (for now)

Src/LinearSolvers/F_MG/mg_cpp.f90

commit b79610130191da94efbf12b5b44cbe2d121f7502
Author: almgren <almgren>
Date:   Sun Jul 1 21:49:17 2007 +0000

    Must take multilevel norm of initial residual.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 05b5d4425184298b69c3ffd585c77263a1ab4199
Author: almgren <almgren>
Date:   Sun Jul 1 21:14:54 2007 +0000

    Need to pass ng into mgt_get_uu so that we can pass the ghost
    cells of the fine grid solution back from the f90 to the C++.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 84324bba5aa62487c73dedf0121e4b4085f44a37
Author: almgren <almgren>
Date:   Sun Jul 1 21:14:09 2007 +0000

    Need to pass ng into mgt_get_uu so that we can pass the ghost
    cells of the fine grid solution back to the C++.

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit c99384323994938b993a682fee71b04e89c90b06
Author: almgren <almgren>
Date:   Sat Jun 30 00:30:12 2007 +0000

    Added need_grad_phi argument to mgt_solve

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 39ec68d7d4136884eda40a7a9b136115d0527959
Author: almgren <almgren>
Date:   Sat Jun 30 00:29:58 2007 +0000

    Added need_grad_phi argument to MGT_Solver::solve and mgt_solve

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 808dfa4e5084a744bb3da3b14ef569ff4b2e2be8
Author: almgren <almgren>
Date:   Fri Jun 29 21:34:45 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 577bd82f23595b9128a12901837fe9d23faf8f6d
Author: mzingale <mzingale>
Date:   Fri Jun 29 17:33:16 2007 +0000

    clean up the printing some to now output the variable names

Tools/C_util/Convergence/DiffSameGrid.cpp

commit c8608caa1fb7a4734586eb0d427bfe8866dfa534
Author: sepp <sepp>
Date:   Fri Jun 29 17:06:45 2007 +0000

    1) more adjustment of spaces in comments

Src/C_AMRLib/BC_TYPES.H

commit 49c3490c3e7b9bba5fe0935756af4839bc9d6cb1
Author: sepp <sepp>
Date:   Fri Jun 29 17:01:53 2007 +0000

    1) adjusted spaces in table so columns line up exactly

Src/C_AMRLib/BC_TYPES.H

commit 7e5a63684b8c164228bcb566fa4ba6148988452b
Author: almgren <almgren>
Date:   Thu Jun 28 20:29:56 2007 +0000

    Removed another print statement.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 2446b79a48c0b41a829c7786aed6793aa1ea0a5f
Author: almgren <almgren>
Date:   Thu Jun 28 19:41:20 2007 +0000

    Removed write statement.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit b3832b9ba9558ec7ec5445ce47bb877f9abaa5bb
Author: almgren <almgren>
Date:   Thu Jun 28 19:41:07 2007 +0000

    Removed print statement.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 52cb7dc31547a8f47f3337a7a3a8815c380d7cb1
Author: almgren <almgren>
Date:   Thu Jun 28 18:46:59 2007 +0000

    Get rid of print statements.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 3c981df7599bc574d3ee46ad8027d9614e631a8f
Author: almgren <almgren>
Date:   Thu Jun 28 17:54:43 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg_cpp.f90

commit 2dac7b6e108fffd05b20800571b5c9a3b0ac8e32
Author: almgren <almgren>
Date:   Wed Jun 27 23:20:22 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 491736eed7b8aef9819d9d604d8b1a825149b3e7
Author: almgren <almgren>
Date:   Wed Jun 27 22:17:34 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 836511b36038736d4b83aa53b95ec4ef0ab02798
Author: almgren <almgren>
Date:   Wed Jun 27 17:49:48 2007 +0000

    What's needed for level solve_for_phi in Castro, hopefully.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 31819837e6ff4f2912ae6260b87c25d84f3d5982
Author: almgren <almgren>
Date:   Tue Jun 26 05:22:49 2007 +0000

    Changes in order to more easily set coefficients for a cell-centered gravity solve
    (a = 0, bx = by = bz = 0)

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 175db13aa538533cfa07a774f02ade5d0c031e13
Author: lijewski <lijewski>
Date:   Mon Jun 25 22:54:26 2007 +0000

    only run f90.depends on f90EXE_sources

Tools/C_mk/Make.rules

commit cab0d04040c67c40454a3a86cdd0eb281dd1f934
Author: mzingale <mzingale>
Date:   Fri Jun 22 14:35:56 2007 +0000

    add support for Intel 10.0 compilers.  Note, with Intel 10.0, there is
    no longer an ifc command -- it's all ifort.  Therefore, we need to switch
    the shell test that checks the version of the compiler to use ifort.  This
    will work fine for any Intel compiler since 8.0.  As a result, we drop the
    Intel 7.0 support (those compilers are quite old these days anyway).

Tools/F_mk/GMakedefs.mak

commit 513e18350138ab8c416d7dde2789013dec800029
Author: mzingale <mzingale>
Date:   Tue Jun 12 12:20:21 2007 +0000

    add Intel 10.0 compiler support

Tools/C_mk/Make.defs

commit 5466618172f565f70cb6e5b395c2aafb7e007296
Author: almgren <almgren>
Date:   Thu Jun 7 22:23:07 2007 +0000

    Use -mp flag for all Intel compilers -- doesn't allow optimization to screw
    up the precision.

Tools/F_mk/GMakedefs.mak

commit 02089336b006439110f5b7ebe74529eb9b6fc8b3
Author: almgren <almgren>
Date:   Fri May 11 17:45:04 2007 +0000

    mg_jacobi_smoother now does nu1 relaxations instead of 1.

Src/LinearSolvers/F_MG/mg.f90

commit b071c9b768d385c9010e843e953617030ec7f10f
Author: almgren <almgren>
Date:   Wed May 9 21:30:59 2007 +0000

    Added mg_jacobi_smoother to be called at end of solve...

Src/LinearSolvers/F_MG/mg.f90

commit ccb9519ea793d6de183724239e26b389708d3302
Author: lijewski <lijewski>
Date:   Wed May 9 19:52:05 2007 +0000

    Added reduce_real_sum accessible from Fortran.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 8be0fc5186dc516c5876417375c12899cb87cac7
Author: lijewski <lijewski>
Date:   Wed May 9 19:47:14 2007 +0000

    Added fortran-acessible calls for ::second() and ::ReduceRealMax(IOProc).

Src/C_BaseLib/ParallelDescriptor.cpp

commit 5018d015d919c719645d943dda5661224601a659
Author: lijewski <lijewski>
Date:   Wed May 9 17:55:29 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 85f813e65930583abe8a524f4b6c0d4f80479129
Author: lijewski <lijewski>
Date:   Tue May 8 21:01:15 2007 +0000

    faster sort() in simplify()

Src/C_BaseLib/BoxList.cpp

commit 328f985fce6d8b9b7fd199d89cbda28900d54969
Author: lijewski <lijewski>
Date:   Tue May 8 20:08:21 2007 +0000

    *** empty log message ***

Src/C_AMRLib/Amr.cpp

commit ab99c9d6650172eb87b5071db906610023aab510
Author: lijewski <lijewski>
Date:   Tue May 8 19:28:35 2007 +0000

    Added strategically placed simplify()s
    simplify() scales better than complementIn() in grid_places.
    Basically we're simplify()ing before complementIn().

Src/C_AMRLib/Amr.cpp

commit 7e0d931d74266a1c9a5699557773f6e7d67439b8
Author: lijewski <lijewski>
Date:   Tue May 8 19:26:35 2007 +0000

    now simplify() in batches of 50 not 250

Src/C_BaseLib/BoxList.cpp

commit b4ecdd30ba267c094d673636d8424217b6f2b77a
Author: lijewski <lijewski>
Date:   Tue May 8 19:02:45 2007 +0000

    assert ngrow>=0

Src/C_BaseLib/FabArray.H

commit eb72bf62846368d410bddb855210444da8088acf
Author: jbb <jbb>
Date:   Tue May 8 16:35:31 2007 +0000

    change

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit e1e59bb4d321507c407e0f48e5de638060f5b457
Author: lijewski <lijewski>
Date:   Tue May 8 03:30:43 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit a7cdc3cb5ff3d5f56be9caf7c5c9b6b029a89193
Author: lijewski <lijewski>
Date:   Sat May 5 20:54:12 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/interface.cpp

commit e15165c3ef364319f8bcdb7d62370d5a4ac02f30
Author: lijewski <lijewski>
Date:   Fri May 4 23:21:24 2007 +0000

    *** empty log message ***

Src/C_BaseLib/BoxList.cpp

commit 05dc99fa66d23ae93f9a0901f4aad6e91d050cb8
Author: lijewski <lijewski>
Date:   Fri May 4 23:00:51 2007 +0000

    *** empty log message ***

Src/C_AMRLib/Cluster.cpp
Src/C_BaseLib/BoxArray.cpp

commit 4cf13142a9111f628f4519b7a66d06661018bc51
Author: almgren <almgren>
Date:   Fri May 4 20:29:49 2007 +0000

    This one works on atlas as well as manda (I think).

Tools/F_mk/GMakedefs.mak

commit f71138f21a5512c3342376b2a18a33417a407110
Author: almgren <almgren>
Date:   Fri May 4 20:24:05 2007 +0000

    Include specifics for using mpi on manda.lbl.gov

Tools/F_mk/GMakeMPI.mak

commit 637ac9798c8a4df54e9ea2658716355b77e38182
Author: lijewski <lijewski>
Date:   Fri May 4 19:08:48 2007 +0000

    *** empty log message ***

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.cpp

commit b06684e5ff4e4463fdab6b1e0b845baf071d5740
Author: lijewski <lijewski>
Date:   Thu May 3 23:29:59 2007 +0000

    changed BL_PROFILE() a bit

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.cpp

commit 363b780c01e99d697ce5056fa4a694e79dfba41b
Author: lijewski <lijewski>
Date:   Wed May 2 21:53:15 2007 +0000

    added FastContins()

Src/C_AMRLib/Cluster.cpp

commit 9d13698ed644b363a18325629749592b329d47e3
Author: lijewski <lijewski>
Date:   Wed May 2 21:49:24 2007 +0000

    shortcut for special case of complementIn()

Src/C_BaseLib/BoxList.cpp

commit 5fedf331523e868b38413bd291e5a747cd4eec5a
Author: lijewski <lijewski>
Date:   Wed May 2 21:48:19 2007 +0000

    more profiling

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.cpp

commit 1d943463c1abbd32561d6bef5ab843127acf2465
Author: lijewski <lijewski>
Date:   Wed May 2 16:48:09 2007 +0000

    *** empty log message ***

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit f300d5a203863a50f825963b16459039b1ff2ab2
Author: lijewski <lijewski>
Date:   Wed May 2 16:45:27 2007 +0000

    added intersections() in setVal()

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 63e120f88d16409f235b10cf34bac41637754579
Author: lijewski <lijewski>
Date:   Tue May 1 22:42:34 2007 +0000

    *** empty log message ***

Src/C_BaseLib/BoxList.cpp

commit e76e775c2cfbc77ed5cb1e497cd0b25c118919fc
Author: lijewski <lijewski>
Date:   Tue May 1 22:26:03 2007 +0000

    comment out simplify in grid_places() for now

Src/C_AMRLib/Amr.cpp

commit 5f19fcd3c6e932b35a3a50fd7b40e7a1092181e1
Author: lijewski <lijewski>
Date:   Tue May 1 21:54:43 2007 +0000

    commented out simplify() in removeOverlap() for the time being

Src/C_BaseLib/BoxArray.cpp

commit 2029cc6a789204f39fdd7729fa7639370b78fe50
Author: lijewski <lijewski>
Date:   Tue May 1 20:11:02 2007 +0000

    *** empty log message ***

Src/C_AMRLib/Amr.cpp

commit 20691dac85d1a27c1593cd9eca6fb227f36192a6
Author: lijewski <lijewski>
Date:   Tue May 1 03:12:50 2007 +0000

    ProjPeriodic() now does a simplify()

Src/C_AMRLib/Amr.cpp

commit 19b9f4f6ef476ea00b1caa0da79fed0cdc089676
Author: lijewski <lijewski>
Date:   Tue May 1 02:59:57 2007 +0000

    Initialize() now does full simplify()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 46adc0f35ed766e45792f54b6402ba979642cb4d
Author: lijewski <lijewski>
Date:   Tue May 1 02:59:32 2007 +0000

    complementIn() now does full simplify()

Src/C_BaseLib/BoxList.cpp

commit 4defb19e9ee40e356718e3010875fd10e7c15681
Author: lijewski <lijewski>
Date:   Tue May 1 02:59:20 2007 +0000

    removeOverlap() now does full simplify()

Src/C_BaseLib/BoxArray.cpp

commit d3cbf2afa6c2a96af819f56dc44af5f2b6641e50
Author: lijewski <lijewski>
Date:   Mon Apr 30 21:07:14 2007 +0000

    a really big HCAll grid

Src/C_BaseLib/test/ba.95860.REMOVED.git-id
Tests/C_BaseLib/ba.95860.REMOVED.git-id

commit 15e6d0e1561513643b5ad3e2486acf02303f7db3
Author: lijewski <lijewski>
Date:   Mon Apr 30 20:56:30 2007 +0000

    added back in simplify(); it's now really fast

Src/C_AMRLib/Amr.cpp

commit fb31131f95f4f1a685a3fc29a2b1840510f9d172
Author: lijewski <lijewski>
Date:   Mon Apr 30 20:54:58 2007 +0000

    sped up simplify()

Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit c46027f408f8229918fd1ec28eeabf9211a2a6b2
Author: lijewski <lijewski>
Date:   Wed Apr 25 20:02:34 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit c4a15336165483a6cef4e6c0f93ae4763b2739d2
Author: almgren <almgren>
Date:   Wed Apr 25 19:38:09 2007 +0000

    Change in calling sequence to stencil_fill_nodal (no longer pass h_finest)

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit 8fc1d1233277633bee20c07bf36e410114f63593
Author: lijewski <lijewski>
Date:   Tue Apr 24 21:13:08 2007 +0000

    *** empty log message ***

Src/C_BaseLib/test/ba.15456.REMOVED.git-id
Src/C_BaseLib/test/ba.3865
Src/C_BaseLib/test/ba.mac.294
Src/C_BaseLib/test/tBA.cpp
Src/C_BaseLib/test/tDM.cpp
Tests/C_BaseLib/ba.15456.REMOVED.git-id
Tests/C_BaseLib/ba.3865
Tests/C_BaseLib/ba.mac.294
Tests/C_BaseLib/tBA.cpp
Tests/C_BaseLib/tDM.cpp

commit 7e762a01e0e9f734036fcb3c2cf7c0f8a1ac2a43
Author: lijewski <lijewski>
Date:   Tue Apr 24 21:12:42 2007 +0000

    improved SFC; sfc_threshold now 10

Src/C_BaseLib/DistributionMapping.cpp

commit f0ba0e8c88e0eab253604aae9767e50d72a801b0
Author: lijewski <lijewski>
Date:   Tue Apr 24 21:05:46 2007 +0000

    *** empty log message ***

Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/ba.23925.REMOVED.git-id
Src/C_BaseLib/test/tDM.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/ba.23925.REMOVED.git-id
Tests/C_BaseLib/tDM.cpp

commit c4d4cba76595ec16a73786632cfe07461d82502c
Author: lijewski <lijewski>
Date:   Tue Apr 24 19:43:47 2007 +0000

    uncomment simplify() till further notice

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.cpp

commit 280af56ad7d5ff08b473e7751d3619b6d7c2f140
Author: almgren <almgren>
Date:   Tue Apr 24 17:45:28 2007 +0000

    Fix in function stencil_norm to workaround bug in Intel compiler for large single arrays.

Src/LinearSolvers/F_MG/stencil.f90

commit 6eedd43b787eeb5a44cf38d7555ffdbc7f1a378f
Author: lijewski <lijewski>
Date:   Tue Apr 24 01:13:50 2007 +0000

    commented out simplify() in grid_places()

Src/C_AMRLib/Amr.cpp

commit b7e32f6ae27f0130f975e11f102ba537c265280e
Author: lijewski <lijewski>
Date:   Tue Apr 24 01:13:20 2007 +0000

    commented out complementIn() in removeOverlap()

Src/C_BaseLib/BoxList.cpp

commit 560d9fb605bad393049ba75fcd2bd3c9a2c65406
Author: lijewski <lijewski>
Date:   Tue Apr 24 01:13:06 2007 +0000

    commented out simplify() in removeOverlap()

Src/C_BaseLib/BoxArray.cpp

commit 9c6d6c416902c0a333b22c8a72d7f03c9c4c87f5
Author: nazgul <nazgul>
Date:   Mon Apr 23 20:44:48 2007 +0000

    Commenting out a section of code that appears to be unnecessary and
    makes it impossible to have a Tuple<MultiFab>.  The offending code
    also conflicts with the comments.  If this code really is necessary
    let me know and we can work something else out.
    
    Louis Howell

Src/C_BaseLib/Tuple.H

commit 961403c906364d83a53a4a2dc2706fa60a32796f
Author: nazgul <nazgul>
Date:   Mon Apr 23 16:46:52 2007 +0000

    Minor bug fixes for 1D.  (Doesn't look like 1D gets used very much.)
    
    Louis

Src/C_BaseLib/COORDSYS_1D.F
Src/C_BaseLib/CoordSys.cpp

commit 0a6107ba9bd2468baefc0d2606d3e655ac774c0a
Author: lijewski <lijewski>
Date:   Sat Apr 21 03:32:11 2007 +0000

    yet further refinements to FAB data uniformization

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 6c02d63cd04c806714ea0321e077927b768cbb54
Author: lijewski <lijewski>
Date:   Sat Apr 21 00:51:57 2007 +0000

    further refinements to FAB data uniformization

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 56edbaa75c9539ace339db24085565c859e493eb
Author: lijewski <lijewski>
Date:   Fri Apr 20 21:26:56 2007 +0000

    default for sfc_threshold is now 10

Src/C_BaseLib/DistributionMapping.cpp

commit 348f8edea5c3ee74d3909d3653ff88971fa565cc
Author: lijewski <lijewski>
Date:   Fri Apr 20 20:55:44 2007 +0000

    verbose now defaults to true

Src/C_BaseLib/DistributionMapping.cpp

commit 89f759a8b169ec24e2070ea88858895ace39857f
Author: lijewski <lijewski>
Date:   Fri Apr 20 19:13:58 2007 +0000

    *** empty log message ***

Src/C_AMRLib/Amr.cpp

commit 251939b5f556303e7b6f39940308ed6f2222c063
Author: lijewski <lijewski>
Date:   Fri Apr 20 02:49:08 2007 +0000

    print out FAB byte high-water-mark at end of timestep

Src/C_AMRLib/Amr.cpp

commit bcd58fd988c1725d09a59ec969f40ac743a2dadf
Author: lijewski <lijewski>
Date:   Fri Apr 20 02:48:33 2007 +0000

    now maintain FAB byte high-water-mark

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp

commit 6667dfabf88db1ec6516cf739cb2004b77bd6af4
Author: vince <vince>
Date:   Thu Apr 19 01:23:22 2007 +0000

    added a knob for calling probinit.

Src/C_AMRLib/Amr.cpp

commit 06e5fe920ec9d220246cf149c03b9a56aa8dc8ae
Author: vince <vince>
Date:   Thu Apr 19 00:58:17 2007 +0000

    some defines for serial.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/VisMF.cpp

commit 807ea0b8bb8630feb8663a451d528e4351ff89a8
Author: vince <vince>
Date:   Thu Apr 19 00:19:45 2007 +0000

    more efficient version of the multifab reader.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.cpp

commit d4f4d2a98728d48a2b79772f8bb8b66908d992ae
Author: vince <vince>
Date:   Thu Apr 19 00:17:49 2007 +0000

    added code to limit probin opens.

Src/C_AMRLib/Amr.cpp

commit 81d6fc55bf8b3d48cb95981e6330142a52bb4bf0
Author: lijewski <lijewski>
Date:   Wed Apr 18 17:51:08 2007 +0000

    Must check DistributionMaps, as well as BoxArrays, when deciding on
    caching.

Src/C_BoundaryLib/FabSet.cpp

commit f64cc914382a2c8e0576b0af1dd844a9688666d2
Author: lijewski <lijewski>
Date:   Wed Apr 18 17:37:08 2007 +0000

    Must look at DistributionMapping, not just BoxArray, in FillBoundary().

Src/C_BaseLib/MultiFab.cpp

commit 73bed962ca14091f4aefbb0db0e8f1f26794567f
Author: lijewski <lijewski>
Date:   Wed Apr 18 17:29:15 2007 +0000

    Need to look at DistributionMapping, in addition to BoxArray, when
    caching FPBs.

Src/C_BaseLib/Geometry.cpp

commit 3c39f969094cba927a9f3d6d5205bf700c1fc19f
Author: lijewski <lijewski>
Date:   Wed Apr 18 17:28:03 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.mpi

commit e5e7222f5ea8cc3718268a8e52097efdc5dcc910
Author: lijewski <lijewski>
Date:   Wed Apr 18 17:27:28 2007 +0000

    added -Wno-deprecated for g++

Tools/C_mk/Make.defs

commit 51a0da0c3d8fff1eb0bd6094d7df9a763cc5519e
Author: lijewski <lijewski>
Date:   Wed Apr 18 15:40:23 2007 +0000

    *** empty log message ***

Src/C_BaseLib/test/tBA.cpp
Tests/C_BaseLib/tBA.cpp

commit a994b5c1edf5a9bee3d29cddf9ea4e93696368e3
Author: lijewski <lijewski>
Date:   Tue Apr 17 18:12:14 2007 +0000

    added AuxBoundaryData

Src/C_AMRLib/Make.package

commit 4ece921c4f2ab4cdc05db72f4c0095dad2687b56
Author: lijewski <lijewski>
Date:   Tue Apr 17 16:56:12 2007 +0000

    stripped out of LMC, nova & Castro

Src/C_AMRLib/AuxBoundaryData.H
Src/C_AMRLib/AuxBoundaryData.cpp

commit fcb312b233a5528b224d645ca30a82d7e44a29ea
Author: lijewski <lijewski>
Date:   Tue Apr 10 20:16:27 2007 +0000

    needed <string>

Src/C_BaseLib/ParallelDescriptor.H

commit 35b708e5b091311a5f9b2b61aee58e9fd7900f3e
Author: lijewski <lijewski>
Date:   Mon Apr 9 20:29:45 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit 6c3a0338016ebbdd98bb550177a394b4972a0bd5
Author: vince <vince>
Date:   Fri Apr 6 22:31:42 2007 +0000

    another friendly read.

Src/C_BaseLib/ParmParse.cpp

commit 1f1a1975e4c3cb0a0ee6280290b990589a6318d3
Author: vince <vince>
Date:   Fri Apr 6 19:57:12 2007 +0000

    implemented a mechanism to limit the total number of open
    files when reading a multifab.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 57442ad36f281941c99b262fcb5542f649e11130
Author: lijewski <lijewski>
Date:   Wed Apr 4 05:14:10 2007 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit d333ba9b3644b9ee667ecfb5d7528be4b21f9a4d
Author: lijewski <lijewski>
Date:   Tue Apr 3 23:36:58 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/in.grids.15456
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.25600
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034
Tests/LinearSolvers/C_CellMG/grids/in.grids.15456
Tests/LinearSolvers/C_CellMG/grids/in.grids.213
Tests/LinearSolvers/C_CellMG/grids/in.grids.25600
Tests/LinearSolvers/C_CellMG/grids/in.grids.5034

commit 5a1f23412c65ac96d90816ea7a65320395ec880c
Author: lijewski <lijewski>
Date:   Tue Apr 3 23:34:55 2007 +0000

    add ability to turn off LeastUsedCPUs()

Src/C_BaseLib/DistributionMapping.cpp

commit 322e3351cc0d56637011f4cb776fdf3978003769
Author: lijewski <lijewski>
Date:   Tue Apr 3 22:49:59 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit d79a8afd8981df1221e07c2ad7bc0046880bd06d
Author: lijewski <lijewski>
Date:   Thu Mar 29 19:40:57 2007 +0000

    removed Cray-isms

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FPC.H
Src/C_BaseLib/FPC.cpp
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/REAL.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/winstd.H

commit 32b1af2e7fe702b225a7f79266e3769d4de10fea
Author: lijewski <lijewski>
Date:   Thu Mar 29 18:12:44 2007 +0000

    removed T3E stuff

Src/C_BaseLib/FPC.cpp
Src/C_BaseLib/Utility.cpp

commit 76b0258ce7ad68e39353a3a1d22ebdee00e3e4c9
Author: lijewski <lijewski>
Date:   Thu Mar 29 18:08:50 2007 +0000

    XT3 stuff

Src/C_BaseLib/Utility.cpp

commit 7c9449d724b1a1900b807f0ac658d2e8e921b611
Author: lijewski <lijewski>
Date:   Thu Mar 29 17:57:25 2007 +0000

    XT3 stuff

Src/C_BaseLib/Utility.cpp

commit 224bbd14a2d076284fde1e148a7eeb62a76f98fc
Author: lijewski <lijewski>
Date:   Wed Mar 28 21:33:38 2007 +0000

    added XT3 stuff

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit a1788d95edadeedab700d19a96d655a8add7950b
Author: lijewski <lijewski>
Date:   Mon Mar 26 17:31:37 2007 +0000

    now cognizant of amount of FAB data per CPU

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit e7d48c3bdd90b6964b1574a0f5982fa935ff0849
Author: lijewski <lijewski>
Date:   Thu Mar 22 16:24:40 2007 +0000

    *** empty log message ***

Src/C_BaseLib/BaseFab.H

commit b4d848d8393ec3268be144e530ba84e63a9c0be7
Author: lijewski <lijewski>
Date:   Thu Mar 22 04:21:20 2007 +0000

    add total_bytes_allocated_in_fabs

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp

commit d566a03d76dbba35e81dd66f351ca40ca9b5fe10
Author: almgren <almgren>
Date:   Mon Mar 19 19:15:51 2007 +0000

    Need this to work on Ann and Andy's machines...

Tools/F_mk/GMakedefs.mak

commit 7dbbc8d413e14ea93dcc8999177ea5342c7e1b68
Author: lijewski <lijewski>
Date:   Wed Mar 14 01:17:37 2007 +0000

    Knapsack called beneath SFC when too few grids for SFC, can now do MinimizeCommCosts().

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 0a1f4a5cfeccb547de88a7a896c090a5d9c15c0e
Author: lijewski <lijewski>
Date:   Tue Mar 13 21:35:54 2007 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit 2b475b6a8e44b4473415d1074ad8916b7298902d
Author: lijewski <lijewski>
Date:   Tue Mar 13 17:01:23 2007 +0000

    SFC is now the default

Src/C_BaseLib/DistributionMapping.cpp

commit 0f0eb8db4b91018778c0d432b61e4f3788a2597a
Author: lijewski <lijewski>
Date:   Fri Mar 9 04:40:43 2007 +0000

    removed nProcsCFD() stuff

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 6c645d8db3a063c141e982994fd36c09feb74b06
Author: lijewski <lijewski>
Date:   Fri Mar 9 04:21:05 2007 +0000

    array versions of REDUCE operators

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit f89681e06d363b684acc0502c7ad95814dd96354
Author: lijewski <lijewski>
Date:   Thu Mar 8 22:19:39 2007 +0000

    XT4/PGI

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 8f62dd9dce857fb2e0f5dde24a7c4bc31e709b29
Author: jbb <jbb>
Date:   Wed Mar 7 18:21:02 2007 +0000

    atlas changes

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit a8f5c759603363cbed456ccb52d14bc7ae442e49
Author: lijewski <lijewski>
Date:   Tue Feb 27 22:03:18 2007 +0000

    added hacked up version of writePlotFile()

Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit f5a975f2edb3d5f499516c36e17f667e77a05897
Author: lijewski <lijewski>
Date:   Tue Feb 27 19:01:14 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/grids/in.grids.213
Tests/LinearSolvers/C_CellMG/main.cpp

commit eb3852f48ffd46ece6a237f80ea552935837ad88
Author: lijewski <lijewski>
Date:   Mon Feb 26 23:21:40 2007 +0000

    what we want ANAG to try first

Src/LinearSolvers/C_CellMG/Test/grids/in.grids.15456
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034
Tests/LinearSolvers/C_CellMG/grids/in.grids.15456
Tests/LinearSolvers/C_CellMG/grids/in.grids.5034

commit e8bc4e0d555e7aed9025b5b0405c043c914a8d0a
Author: lijewski <lijewski>
Date:   Sat Feb 24 00:04:59 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/grids.15456.REMOVED.git-id
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.15456
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034
Tests/LinearSolvers/C_CellMG/grids/grids.15456.REMOVED.git-id
Tests/LinearSolvers/C_CellMG/grids/in.grids.15456
Tests/LinearSolvers/C_CellMG/grids/in.grids.213
Tests/LinearSolvers/C_CellMG/grids/in.grids.5034

commit 5cc15983f71b0b1d331342866853d958fb7b1721
Author: lijewski <lijewski>
Date:   Fri Feb 23 23:05:57 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 181583f1eaf519d12306fc9dbc571758219a96b6
Author: lijewski <lijewski>
Date:   Fri Feb 23 22:38:31 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 0f45c6978cfe7a64c3b2b2d54b8a12ec8e63033b
Author: lijewski <lijewski>
Date:   Fri Feb 23 21:42:23 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/grids.15456.REMOVED.git-id
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.15456
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034
Tests/LinearSolvers/C_CellMG/grids/grids.15456.REMOVED.git-id
Tests/LinearSolvers/C_CellMG/grids/in.grids.15456
Tests/LinearSolvers/C_CellMG/grids/in.grids.5034

commit 4d809d5176521115b449c1a2839a6566aa6ff5f0
Author: mzingale <mzingale>
Date:   Thu Feb 22 15:24:37 2007 +0000

    some routines for visualizing Maestro data with IDL

Tools/F_scripts/idlbl/README
Tools/F_scripts/idlbl/batch.pro
Tools/F_scripts/idlbl/color.pro
Tools/F_scripts/idlbl/color_index.pro
Tools/F_scripts/idlbl/colorbar2.pro
Tools/F_scripts/idlbl/dump_surface.pro
Tools/F_scripts/idlbl/flamelength.pro
Tools/F_scripts/idlbl/flash_colors.tbl
Tools/F_scripts/idlbl/get_idlbl_path.pro
Tools/F_scripts/idlbl/nolabel.pro
Tools/F_scripts/idlbl/partvelvec.pro
Tools/F_scripts/idlbl/plotflash.pro
Tools/F_scripts/idlbl/plotraw.pro
Tools/F_scripts/idlbl/rawread.pro
Tools/F_scripts/idlbl/rawread3d.pro
Tools/F_scripts/idlbl/scale_color.pro
Tools/F_scripts/idlbl/start_linux.pro
Tools/F_scripts/idlbl/tvimage.pro
Tools/F_scripts/idlbl/vcolorbar.pro
Tools/F_scripts/idlbl/xaverage.pro

commit 20f30ea751dd64154ae23a3534f2eb4f47542cee
Author: lijewski <lijewski>
Date:   Wed Feb 21 21:36:51 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/grids.25600.REMOVED.git-id
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.25600
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034
Tests/LinearSolvers/C_CellMG/grids/grids.25600.REMOVED.git-id
Tests/LinearSolvers/C_CellMG/grids/in.grids.213
Tests/LinearSolvers/C_CellMG/grids/in.grids.25600
Tests/LinearSolvers/C_CellMG/grids/in.grids.5034

commit 8c12d0a6c30ba7a612bbf167bbfabb2b192523dc
Author: mzingale <mzingale>
Date:   Wed Feb 21 21:28:13 2007 +0000

    fix the sub_fab routines -- they were finding the bounds of a null
    pointer -- not a good thing.

Src/F_BaseLib/filler.f90

commit 2071d52eea95d50e89d3123bccd16385c91ef325
Author: mzingale <mzingale>
Date:   Wed Feb 21 18:15:10 2007 +0000

    add support for my cluster (homer)

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit ed710fbeadd863cf5f6817de886e94c1997c1e36
Author: lijewski <lijewski>
Date:   Wed Feb 21 17:19:34 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit a63d3839d4dd8c0a733af9e3531deb751b98f830
Author: lijewski <lijewski>
Date:   Tue Feb 20 18:30:33 2007 +0000

    print out grid distirbution with boxes

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 454067ab72337115db5c5077128edbc5bd41bc60
Author: lijewski <lijewski>
Date:   Fri Feb 16 21:18:22 2007 +0000

    set eps_rel to 1e12

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 4019bdafbbfc79489bd51afa474342163dbbef9d
Author: lijewski <lijewski>
Date:   Fri Feb 16 00:21:29 2007 +0000

    Added version of FillPeriodic that doesn't do any parallelism to
    support use_jbb_precond in CGSolver.cpp.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit a5e6e494146ca058ca4610b44c8ac05773ff26f5
Author: lijewski <lijewski>
Date:   Fri Feb 16 00:19:19 2007 +0000

    added version of FillBoundary that doesn't do parallel

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit db045847d5bd5f88919bb5e37757ceaea3678c9f
Author: lijewski <lijewski>
Date:   Fri Feb 16 00:15:01 2007 +0000

    Hash the mask calculations.
    Added stuff needed for use_jbb_precond.

Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 28c4d23fe39c12a149c9d9264f54ed07195ca1b0
Author: lijewski <lijewski>
Date:   Fri Feb 16 00:12:58 2007 +0000

    Removed CG_Alt and Automatic stuff.
    Added stuff needed for use_jbb_precond.

Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 51816af90f5be5d3b3113928e19bb4d8a993d3df
Author: lijewski <lijewski>
Date:   Fri Feb 16 00:09:16 2007 +0000

    stuff needed for use_jbb_precond

Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp

commit dd34825a6cafdf99a497723ce08c92a2da2a2656
Author: lijewski <lijewski>
Date:   Fri Feb 16 00:03:14 2007 +0000

    removed CG_Alt stuff

Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 95b9c3a675e3cb8284e146db8f01342a0c07bb4e
Author: lijewski <lijewski>
Date:   Fri Feb 16 00:02:37 2007 +0000

    use hash method for calculating masks

Src/C_BoundaryLib/BndryData.cpp

commit a2dca1278488f1258d37e54843f1511e3c61fdf7
Author: almgren <almgren>
Date:   Mon Feb 12 21:11:14 2007 +0000

    Added new access functions:
      const Geometry& getGeom
      const Real * getDx
      virtual Real get_alpha
      virtual Real get_beta
      virtual const MultiFab& aCoefficients
      virtual const MultiFab& bCoefficients

Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit c753661818d46773d8f446161517513cc93cc649
Author: lijewski <lijewski>
Date:   Fri Jan 26 20:16:45 2007 +0000

    ParmParse'd fpb_cache_max_size

Src/C_BaseLib/Geometry.cpp

commit 3e4c0aa1b736bfc9c2862ebd3dd088ccced626de
Author: lijewski <lijewski>
Date:   Fri Jan 26 19:23:40 2007 +0000

    *** empty log message ***

Src/C_BaseLib/MultiFab.cpp

commit 7c755d4d37c32a8fab77efd6d8f612bb0644b31d
Author: lijewski <lijewski>
Date:   Fri Jan 26 19:17:09 2007 +0000

    ParmParse'd copy_cache_max_size

Src/C_BaseLib/MultiFab.cpp

commit f647b5b467355acf245194749c9889b2abb8f7e1
Author: lijewski <lijewski>
Date:   Fri Jan 26 19:03:14 2007 +0000

    *** empty log message ***

Src/C_BoundaryLib/FabSet.cpp

commit 57c72f4563154e06d8725ac98343edfb8cf516c6
Author: lijewski <lijewski>
Date:   Fri Jan 26 18:47:45 2007 +0000

    ParmParse'd copy_cache_max_size

Src/C_BoundaryLib/FabSet.cpp

commit a0d2dc052dff2cb4e9c8376d8b69182578bb67a9
Author: lijewski <lijewski>
Date:   Fri Jan 26 18:26:04 2007 +0000

    ParmParse'd copy_cache_max_size

Src/C_BaseLib/FabArray.cpp

commit c7fd94b1c2db4bb0c65d3f07f7773004ad9720bc
Author: lijewski <lijewski>
Date:   Wed Jan 24 18:11:28 2007 +0000

    turn on some cache stats

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 252957236e44fecdbccc915b0f730b722beb2468
Author: lijewski <lijewski>
Date:   Thu Jan 18 17:22:19 2007 +0000

    extra assertion in define()

Src/C_BaseLib/FabArray.H

commit d0800687749502e65019f287ae61ffd698d261bf
Author: lijewski <lijewski>
Date:   Thu Jan 18 17:22:04 2007 +0000

    added copy constructor & assignment operator

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 4c8061aa98ce9d3bc00f2428710f1ba80db89015
Author: almgren <almgren>
Date:   Fri Jan 12 20:53:59 2007 +0000

    Changed default nub from 0 to 10 so that after CG or BiCG bottom solver
    the code will do 10 relaxations -- this to deal with case when CG or BiCG
    just doesn't converge (and I don't know why).

Src/LinearSolvers/F_MG/mg.f90

commit 8429abf0eba40ceefcb5e291dba41758b2cf2788
Author: lijewski <lijewski>
Date:   Thu Jan 4 20:43:26 2007 +0000

    oops

Src/C_AMRLib/FluxRegister.cpp

commit e68eb38e08a37da018c2dbcf4e939c25cea5e6f5
Author: lijewski <lijewski>
Date:   Thu Jan 4 20:41:18 2007 +0000

    fixed bug hitting coalescing memory manager

Src/C_AMRLib/FluxRegister.cpp

commit 6a937672449b50bde2a40dee5dbd2a41f90301cc
Author: almgren <almgren>
Date:   Fri Dec 15 00:55:42 2006 +0000

    Bring up to date with new BoxLib stuff.

Tools/C_util/Convergence/DiffUniform.cpp

commit 4b37af90495ff6e03e23ead3a40cc442626d1e66
Author: lijewski <lijewski>
Date:   Fri Dec 8 20:40:29 2006 +0000

    changed some verbose stuff

Src/C_BaseLib/DistributionMapping.cpp

commit c90513619d531acad5bc4b3c8e17245776e313e5
Author: almgren <almgren>
Date:   Mon Dec 4 22:30:08 2006 +0000

    Move multifab_remote after loop thru filenames -- checkpoint reading now
    works in parallel.

Src/F_BaseLib/fabio.f90

commit 7d7a4646737416407cfa094fc990c9f67104aca0
Author: almgren <almgren>
Date:   Mon Dec 4 20:57:53 2006 +0000

    Fix to make ml_multifab_read_d work in parallel...

Src/F_BaseLib/fabio.f90

commit b9b678f567e5c1e3ecf4dc843a45690e4d0a4e07
Author: mzingale <mzingale>
Date:   Fri Dec 1 15:45:33 2006 +0000

    some gfortran fixes

Tools/F_mk/GMakedefs.mak

commit f53a1995968070123bc1f600eb430e0026a09eb9
Author: lijewski <lijewski>
Date:   Wed Nov 22 21:10:58 2006 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/grids/in.2_19boxes
Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3x2
Src/LinearSolvers/C_CellMG/Test/grids/in.2_big
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_d
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_e
Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_d
Src/LinearSolvers/C_CellMG/Test/grids/in.2per_2x2_c
Src/LinearSolvers/C_CellMG/Test/grids/in.3_2boxes_a
Src/LinearSolvers/C_CellMG/Test/grids/in.3_2x3x4
Src/LinearSolvers/C_CellMG/Test/grids/in.3_big
Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_a
Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_b
Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_c
Src/LinearSolvers/C_CellMG/Test/grids/in.3_mac_tst
Src/LinearSolvers/C_CellMG/Test/grids/in.3_shiftedUp
Src/LinearSolvers/C_CellMG/Test/grids/in.3_small_a
Src/LinearSolvers/C_CellMG/Test/grids/in.3_stack_a
Src/LinearSolvers/C_CellMG/Test/grids/in.3per_2x3x4
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/grids/in.2_19boxes
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_a
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_b
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_c
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_a
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_b
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_c
Tests/LinearSolvers/C_CellMG/grids/in.2_3x2
Tests/LinearSolvers/C_CellMG/grids/in.2_big
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_d
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_e
Tests/LinearSolvers/C_CellMG/grids/in.2_small_a
Tests/LinearSolvers/C_CellMG/grids/in.2_small_b
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_a
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_b
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_c
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_d
Tests/LinearSolvers/C_CellMG/grids/in.2per_2x2_c
Tests/LinearSolvers/C_CellMG/grids/in.3_2boxes_a
Tests/LinearSolvers/C_CellMG/grids/in.3_2x3x4
Tests/LinearSolvers/C_CellMG/grids/in.3_big
Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/in.3_mac_tst
Tests/LinearSolvers/C_CellMG/grids/in.3_shiftedUp
Tests/LinearSolvers/C_CellMG/grids/in.3_small_a
Tests/LinearSolvers/C_CellMG/grids/in.3_stack_a
Tests/LinearSolvers/C_CellMG/grids/in.3per_2x3x4
Tests/LinearSolvers/C_CellMG/grids/in.grids.213
Tests/LinearSolvers/C_CellMG/grids/in.grids.5034
Tests/LinearSolvers/C_CellMG/main.cpp

commit 9602cf2058199e99568f3c55da304c6e7f6797ef
Author: lijewski <lijewski>
Date:   Tue Nov 21 23:38:57 2006 +0000

    changed sfc_threshold: 4 ==> 8

Src/C_BaseLib/DistributionMapping.cpp

commit 9e54785b7abe75668500405cb20edb439e24c1db
Author: lijewski <lijewski>
Date:   Tue Nov 21 06:25:50 2006 +0000

    more SFC tweaks

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 152b339b6dcad316ff1f25a5a6aec15d015c66b1
Author: lijewski <lijewski>
Date:   Sun Nov 19 04:09:13 2006 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit 0a60f1c849761547c34d8575918fc19e6e576739
Author: lijewski <lijewski>
Date:   Sat Nov 18 05:07:25 2006 +0000

    removed embedded CVS ID

Src/C_BaseLib/DistributionMapping.H

commit c6a46306cc0688815655a27a3113ed5fc4b03afb
Author: lijewski <lijewski>
Date:   Sat Nov 18 05:05:46 2006 +0000

    initial cut at space filling curve mapping; more work to do ...

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 7c025cc98681928697f20ad85dbace33678c1dc0
Author: almgren <almgren>
Date:   Sat Nov 11 05:57:26 2006 +0000

    Fixed print statement so don't print NaN if res0 = 0.

Src/LinearSolvers/F_MG/ml_cc.f90

commit c68d01c028becf6ca2b38428163ec949cb2cc23b
Author: marc <marc>
Date:   Thu Oct 12 16:45:12 2006 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit e2be34f1e98646abc523d3cb443bab569c1ebd3f
Author: lijewski <lijewski>
Date:   Wed Oct 11 18:15:08 2006 +0000

    added defined()

Src/C_BaseLib/FabArray.H

commit f90d9a944b1e86292b8dcd03ca47e78de2429bdb
Author: sepp <sepp>
Date:   Tue Oct 10 20:52:16 2006 +0000

    1) added stuff for davinci that was checked over my Mike

Tools/C_mk/Make.mpi

commit 30bbe6953c1a1aad1fb4baadb324cab4a7ec0d52
Author: sepp <sepp>
Date:   Fri Oct 6 17:06:30 2006 +0000

    1) correct syntax in comment block

Src/C_BaseLib/ParmParse.H

commit 6bedb4906f29e9ddb7d0df33088522c9a75cb92d
Author: lijewski <lijewski>
Date:   Wed Oct 4 22:27:04 2006 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit cada8d87b97840842747836218d01dc1a82cb847
Author: lijewski <lijewski>
Date:   Sun Sep 24 00:40:19 2006 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit 12c8565d9239845ad8bc1318f4d2548eac9febb1
Author: lijewski <lijewski>
Date:   Sun Sep 24 00:32:57 2006 +0000

    now print out top 5 communicators

Src/C_BaseLib/DistributionMapping.cpp

commit f86e95a775c6e440b0a7bb4f48b3711afb5b73dc
Author: almgren <almgren>
Date:   Sat Sep 16 03:20:59 2006 +0000

    Fixed extra endif.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 9fd3ecc719c991b654d66102be3dc05abaaf4591
Author: almgren <almgren>
Date:   Sat Sep 16 00:52:54 2006 +0000

    Fix weighting of different stencils.

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 7e1b78cb69eee1f9e1f4f62f141ba88e9975bd09
Author: almgren <almgren>
Date:   Sat Sep 16 00:52:35 2006 +0000

    Fix weighting of residual for coarsening operations...

Src/LinearSolvers/F_MG/ml_nd.f90

commit cbb9cecfbdd5e215788684477823b9b668eb3771
Author: almgren <almgren>
Date:   Sat Sep 16 00:52:01 2006 +0000

    Fix calling sequence to stencil_one_sided.

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit 6a4517c4cd8bc31ae68597ddd0ea5656a01809fb
Author: almgren <almgren>
Date:   Sat Sep 16 00:51:35 2006 +0000

    Small cleanup.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 7c2d0a04d34cf726440c652fcad2ea31cb4072d1
Author: almgren <almgren>
Date:   Sat Sep 16 00:50:39 2006 +0000

    Better write statements, also test in gsrb2d on whether any skewed...

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 2ef48f1e6ddd7c0bc825b8cce71c50675d2f3e37
Author: almgren <almgren>
Date:   Fri Sep 15 23:57:51 2006 +0000

    Fix print statement.

Src/LinearSolvers/F_MG/mg.f90

commit 1981dd0d9cc79606f1f92d8c1e021732b8a50cf9
Author: almgren <almgren>
Date:   Thu Sep 14 21:03:49 2006 +0000

    Remove "NXC" print statement.

Src/F_BaseLib/interp.f90

commit 94c9537c216b4c96b38d1970831acd78801a5133
Author: lijewski <lijewski>
Date:   Thu Sep 14 19:57:27 2006 +0000

    *** empty log message ***

Tools/C_util/Convergence/GNUmakefile

commit d853d3e576f4e018689f2741de07209605b3b4b4
Author: lijewski <lijewski>
Date:   Thu Sep 14 19:50:46 2006 +0000

    *** empty log message ***

Tools/C_util/Convergence/ComputeAmrDataNorms.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/GNUmakefile

commit 2ba8192c7a2b18cce7bdefbc685855b1642414e2
Author: lijewski <lijewski>
Date:   Wed Sep 13 20:28:00 2006 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit beacb4488c8354ac838e4295d278cfe012469797
Author: lijewski <lijewski>
Date:   Wed Sep 13 18:03:22 2006 +0000

    cleaned up some compiler warnings

Src/C_BaseLib/BLThread.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 9d874fcaaf49df2de12526a9002705d3d931e7aa
Author: lijewski <lijewski>
Date:   Tue Sep 12 22:51:04 2006 +0000

    refinement to FPB caching

Src/C_BaseLib/Geometry.cpp

commit fdcce1fc01c31f85fc04b2eac5a40b8100e30ae5
Author: lijewski <lijewski>
Date:   Tue Sep 12 21:50:09 2006 +0000

    refinements to caching

Src/C_BoundaryLib/FabSet.cpp

commit 660a25936b363faa3df2fd0fd5bbf4167ff2a3b5
Author: lijewski <lijewski>
Date:   Tue Sep 12 21:38:45 2006 +0000

    *** empty log message ***

Src/C_BaseLib/MultiFab.cpp

commit 1ec56a5db3cfae093505a082e9f402d34a5c2c99
Author: lijewski <lijewski>
Date:   Tue Sep 12 20:46:46 2006 +0000

    refinement to FillBoundary caching

Src/C_BaseLib/MultiFab.cpp

commit 7bf07f28399b3562bc0e26e799c4af18b53d771c
Author: lijewski <lijewski>
Date:   Tue Sep 12 20:01:16 2006 +0000

    refinement to copy caching

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 64d77a4415fab386542c0709dba19ec3b0b618d7
Author: lijewski <lijewski>
Date:   Mon Sep 11 21:43:39 2006 +0000

    flush copy() cache on regrid

Src/C_AMRLib/Amr.cpp

commit 761b230f52d253f812dabf508a64cbec7c09bb89
Author: lijewski <lijewski>
Date:   Mon Sep 11 21:43:20 2006 +0000

    added copy() caching

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit ebe33c55da5e58b2731bd3a0e933c578e116e839
Author: vince <vince>
Date:   Fri Sep 8 23:17:20 2006 +0000

    change for jvn.

Src/C_BaseLib/VisMF.cpp

commit 2d2475f87d6c07a83467286ce8fb3c8a0539baa6
Author: vince <vince>
Date:   Fri Sep 8 20:44:02 2006 +0000

    added support for specifying at run time the number of files
    written for a multifab.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit c23db4067e73ce966ee7c7fd93bf8ad89707b288
Author: almgren <almgren>
Date:   Thu Sep 7 18:30:22 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/GPackage.mak

commit 4ce89afd3d9cb7cc8ab39c3fbf44a65abb891d4c
Author: lijewski <lijewski>
Date:   Wed Sep 6 17:26:53 2006 +0000

    Box::length() -> Box::size()

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/Looping.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit f0d1ec9dcdb4c51dfac95705542215c66164a31c
Author: lijewski <lijewski>
Date:   Fri Sep 1 23:10:36 2006 +0000

    shut up some compiler message

Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp

commit 554b4e21b5823797cde40c823ae59ced16b69014
Author: lijewski <lijewski>
Date:   Fri Sep 1 21:28:06 2006 +0000

    reverted out fillpatch caching

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp

commit e7e96dc6308ea4e867e5e8edba42f6ffad52400b
Author: lijewski <lijewski>
Date:   Fri Sep 1 21:20:51 2006 +0000

    DistributionMappings are now reference counted

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 03664217eea5f6cbd0b40962a45f65c8a827ff31
Author: almgren <almgren>
Date:   Fri Sep 1 18:14:39 2006 +0000

    Added absolute tolerance as optional argument to itsol_converged.

Src/LinearSolvers/F_MG/itsol.f90

commit 958acd65833a83913f9eaa948b8a17becab7603c
Author: almgren <almgren>
Date:   Fri Sep 1 18:13:54 2006 +0000

    Added abs_eps (absolute tolerance) in addition to rel_eps (relative tolerance).
    Also fixed weighting for dense stencil.

Src/LinearSolvers/F_MG/mg.f90

commit ccf6ed0dd5ea4e1456c5dac64ed85a205e8b147a
Author: almgren <almgren>
Date:   Fri Sep 1 18:09:59 2006 +0000

    Hopefully this has correctly weighted stencils for 2d and 3d,
    cross and dense...

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 9e76bc8ff77baf18893eed27aa57dc080a3f552f
Author: lijewski <lijewski>
Date:   Fri Sep 1 16:24:17 2006 +0000

    removed METIS stuff

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit f1e5a2c8c0090274356b502a6f1b8e226791e403
Author: mzingale <mzingale>
Date:   Fri Sep 1 15:09:29 2006 +0000

    a useful script to aggregrate CVS logs into a nice GNU-style ChangeLog
    format

Tools/F_scripts/cvs2cl.pl

commit 97534e0df9881d46b57594de2343e7c6d6aed797
Author: mzingale <mzingale>
Date:   Thu Aug 31 18:57:53 2006 +0000

    add nodal_divu.f90 to the list of packages

Src/LinearSolvers/F_MG/GPackage.mak

commit d1e276910c129f368659e39039c9c4e58043d651
Author: lijewski <lijewski>
Date:   Wed Aug 30 00:39:20 2006 +0000

    some consolidation of caching -v- no caching in CollectData

Src/C_BaseLib/FabArray.H

commit 154069c0708cd45ec5650a90baf83621c24382b0
Author: lijewski <lijewski>
Date:   Tue Aug 29 19:52:49 2006 +0000

    added ParmParse'd variable to disable caching in CollectData

Src/C_BaseLib/FabArray.H

commit e6ba936273f21fd927921178cd52eeded3e9cb23
Author: lijewski <lijewski>
Date:   Mon Aug 28 18:28:42 2006 +0000

    some caching of FillPatch stuff

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 6fa49bc959aa57e957b6f0cec6afd8d3fca1b20d
Author: lijewski <lijewski>
Date:   Sat Aug 26 03:47:42 2006 +0000

    added amr_real[23]d.2.f to help work around columbia bug

Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/amr_real2d.2.f
Src/LinearSolvers/C_NodalMG/amr_real2d.f
Src/LinearSolvers/C_NodalMG/amr_real3d.2.f
Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit d0ed4e00ec1e0069ff399a443bf078fa3e9f0de5
Author: almgren <almgren>
Date:   Fri Aug 25 22:04:03 2006 +0000

    Modified verbosity and removed extraneous argument "solver"

Src/LinearSolvers/F_MG/mg.f90

commit 77b768238ec7699c8ce2992a385bbe38eb0840e1
Author: almgren <almgren>
Date:   Fri Aug 25 22:03:29 2006 +0000

    Modified verbosity in ml_nd...

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 5e9cb4ced68f432f5b52cb7f81fbf9a548a1cb89
Author: almgren <almgren>
Date:   Fri Aug 25 22:02:25 2006 +0000

    Modified the scaling for cross-stencil in 2d and 3d.  Gives same answers
    in 3d as in 2d.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 20b2b422156c05ffc3b81d44fa61de341d5ae824
Author: almgren <almgren>
Date:   Fri Aug 25 22:01:55 2006 +0000

    This nodal_divu is now called from f90 varden codes as well as from mg_nodal_cpp.f90

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 87c5286bd29924d30b1f3951f08536eb35c06d67
Author: almgren <almgren>
Date:   Fri Aug 25 22:01:17 2006 +0000

    Turned off special nodal stopping criterion in CG solve.

Src/LinearSolvers/F_MG/itsol.f90

commit 34880258a58f2874b82ecd08e368e117c9960c99
Author: lijewski <lijewski>
Date:   Thu Aug 24 21:11:50 2006 +0000

    can now choose # of SwapAndTest() calls

Src/C_BaseLib/DistributionMapping.cpp

commit e7a2f04432b6ae8e43b4ec14d4c761eff226e4af
Author: almgren <almgren>
Date:   Thu Aug 24 20:57:24 2006 +0000

    New version - also called from fParallel/varden and fParallel/nova_varden_heating...

Src/LinearSolvers/F_MG/nodal_divu.f90

commit ee27b5c155795bfb25f7d974d44081fd7271acab
Author: lijewski <lijewski>
Date:   Mon Aug 21 00:29:45 2006 +0000

    fixed bug in collectdata with do_alltoallv=1

Src/C_BaseLib/FabArray.H

commit e2d8ca4e16e1f8e98b812f6ac6b833150a04df88
Author: lijewski <lijewski>
Date:   Sat Aug 19 03:47:04 2006 +0000

    didn't have caching quite right

Src/C_BaseLib/FabArray.H

commit 0f586d8225c448a4d98b76f6cd7b67ff40b276cb
Author: lijewski <lijewski>
Date:   Sat Aug 19 03:46:18 2006 +0000

    print out Box when numPts() overflows

Src/C_BaseLib/Box.cpp

commit 62532c6f58de1f2b541dd9f4845f1e19bd6e9d6c
Author: almgren <almgren>
Date:   Fri Aug 18 22:10:47 2006 +0000

    Added the diagonal component to ss(i,j,0) in 2d.  Also set the coefficient to
    zero at a Neumann boundary.

Src/LinearSolvers/F_MG/stencil.f90

commit af57bd45c03a3c67b8a99d4f8835d04aa6da2fc4
Author: almgren <almgren>
Date:   Fri Aug 18 22:05:44 2006 +0000

    Small change in formatting.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 2c015e91318d34b2b07c2ea7d9104db9a5e6aebc
Author: almgren <almgren>
Date:   Fri Aug 18 22:04:38 2006 +0000

    Added "save" to mgts declaration.

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit b27255493ad84b79e99c960f05adfd2a62a37041
Author: almgren <almgren>
Date:   Fri Aug 18 20:29:01 2006 +0000

    New interface for bc's.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit e6a83507078b78310b0e2e795d5de3badc4f68a3
Author: lijewski <lijewski>
Date:   Wed Aug 16 20:41:32 2006 +0000

    can now ParmParse between send/recv & alltoallv in copy & collectdata

Src/C_BaseLib/FabArray.H

commit 4517971111e6a2c1f5c9ce12bb67cc83e5d815a7
Author: almgren <almgren>
Date:   Wed Aug 16 19:53:49 2006 +0000

    Added new functionality to do diffusive solves as well as MAC solves.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit 3c31db4bbcde9516c309b929d2d203bc37720683
Author: almgren <almgren>
Date:   Tue Aug 15 19:17:33 2006 +0000

    Remove extra print statements...

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit 27555f7f4ae903d87149f9563ba177d25122f8c2
Author: almgren <almgren>
Date:   Tue Aug 15 19:16:47 2006 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.f

commit a79b262489e66780423c29b42bec8d183eb03617
Author: almgren <almgren>
Date:   Tue Aug 15 19:14:18 2006 +0000

    Fix definition of nx,ny,nz in grid_divu_3d.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 1276be5b053db0fe46d11a8e45288e1813cbf523
Author: almgren <almgren>
Date:   Tue Aug 15 19:13:52 2006 +0000

    Modify set_vel_2d...

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit c40f94825ef437ae1beb3c59bf0a878fb7b936b6
Author: almgren <almgren>
Date:   Tue Aug 15 19:13:07 2006 +0000

    Dont need those print statements...

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 75aa1439649cbd2e111d964b0ee2fdb0bbc46d52
Author: lijewski <lijewski>
Date:   Tue Aug 15 19:10:30 2006 +0000

    commented out couple prints

Src/LinearSolvers/F_MG/mg_cpp.f90

commit aa7a5b643785bbe56859e875f97eb78e0e5e7042
Author: almgren <almgren>
Date:   Tue Aug 15 05:31:44 2006 +0000

    Fixed diagnostic statements...

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit 46fc9bdac37f1b79487fdfbc6aeeac06259cbe43
Author: almgren <almgren>
Date:   Tue Aug 15 05:06:59 2006 +0000

    Got it right for 3d nodal...

Src/LinearSolvers/F_MG/mg_cpp_f.h

commit ef153582855b51229d20cf88695c158df23ee4fa
Author: almgren <almgren>
Date:   Tue Aug 15 04:40:00 2006 +0000

    Fixed typo.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit ef3acc9fff49b89adfb075f0b2e3bef6a59ff378
Author: lijewski <lijewski>
Date:   Tue Aug 15 02:30:43 2006 +0000

    Can now ParmParse whether or not to use alltoallv in copy().

Src/C_BaseLib/FabArray.H

commit a18e5ce808ba1aa363437f3ed8f72e067ab9bf98
Author: almgren <almgren>
Date:   Tue Aug 15 02:18:18 2006 +0000

    Latest version which calls cc and nodal multigrid solvers.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H

commit 55a86e5a98743c0dd6251d15f4904bcd387184a6
Author: almgren <almgren>
Date:   Tue Aug 15 02:17:52 2006 +0000

    Latest version which calls nodal as well as cc multigrid solvers.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 0fc8339d4009903646073bb091896028cc28d065
Author: almgren <almgren>
Date:   Tue Aug 15 02:15:51 2006 +0000

    Latest stuff to enable cc and nodal multigrid calls from IAMR.

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_nodal_cpp.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit b6d940a4f625b6579fb5da470923174ef2ba1e94
Author: lijewski <lijewski>
Date:   Tue Aug 15 01:19:15 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg.f90

commit e03cc0b2109451c261f45237aafc32ba296f24e6
Author: almgren <almgren>
Date:   Mon Aug 14 21:15:03 2006 +0000

    Remove commented line.

Src/LinearSolvers/F_MG/mg.f90

commit 7b47787c941c383bce9d7feaab543aed0b054aa9
Author: almgren <almgren>
Date:   Mon Aug 14 20:27:02 2006 +0000

    Added new files...

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/GPackage.mak

commit 1ca5a642681ce0bb271e4e9d702d19f6f5a6ad3e
Author: almgren <almgren>
Date:   Mon Aug 14 20:26:44 2006 +0000

    New routines to handle calls from IAMR.

Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_mask.f90
Src/LinearSolvers/F_MG/nodal_newu.f90

commit e208b35e93b48df2c2c148d4ebee3abf29096cec
Author: lijewski <lijewski>
Date:   Mon Aug 14 20:22:12 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 9234b48657e385b433b0147d70a9ece032671648
Author: almgren <almgren>
Date:   Mon Aug 14 20:07:44 2006 +0000

    Make mgt%skewed(nlev,ngrids) a member of mgt instead of calculating every time
    we call the smoother...

Src/LinearSolvers/F_MG/mg.f90

commit 0501215564e27b3ea0e47e7ecdd5f345b4169c18
Author: almgren <almgren>
Date:   Mon Aug 14 20:06:49 2006 +0000

    Tiny modification in function skewed_q.

Src/LinearSolvers/F_MG/stencil.f90

commit 82f3caf54af8b24f6485289e3b0e29048bb39946
Author: almgren <almgren>
Date:   Mon Aug 14 18:43:05 2006 +0000

    Test on skewed-ness at top of gs_rb_smoother_2d and gs_rb_smoother_3d.
    Also put dd calculation inside if test in these routines.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit caecf99d6c6325139efc442f0be5d848dcec315e
Author: lijewski <lijewski>
Date:   Wed Aug 9 18:00:41 2006 +0000

    do NOT do alltoallv() by default

Src/F_BaseLib/multifab.f90

commit b2f9da880fd4dbe10c77b9063b00aa4ce598b17f
Author: lijewski <lijewski>
Date:   Wed Aug 9 04:20:14 2006 +0000

    merged in nocomm=.true. in copy() & fill_boundary()

Src/LinearSolvers/F_MG/sparse_solve.f90

commit 6149f3bf48bd7b8fd58ae9b3a1afb2ef0fae8a55
Author: lijewski <lijewski>
Date:   Wed Aug 9 04:19:38 2006 +0000

    added nocomm flag to fill_boundary & copy

Src/F_BaseLib/multifab.f90

commit 90f927d39ac09e6aad774b6044feb781c1d846ea
Author: almgren <almgren>
Date:   Tue Aug 8 21:21:16 2006 +0000

    Add the necessary stuff to construct the sparse solver as a bottom solver.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 4d930e5aad48d87659b91cdb7578c8107f5691ce
Author: almgren <almgren>
Date:   Tue Aug 8 21:20:48 2006 +0000

    If mg.usecg = 0, then make the default be the sparse solver, not relaxations.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit b989a0c141c13a36424b68215a00a820a42646d2
Author: almgren <almgren>
Date:   Tue Aug 8 18:31:43 2006 +0000

    Modified the verbosity to be more in sync with the multigrid verbosity.

Src/LinearSolvers/F_MG/sparse_solve.f90

commit a9eb36a5abbe77c92e769b110ebd6ab415b2f9d8
Author: lijewski <lijewski>
Date:   Mon Aug 7 18:46:45 2006 +0000

    added mgt_init()

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 47f5617e1207fd05333a5a508f2d6be31b8bf21f
Author: lijewski <lijewski>
Date:   Mon Aug 7 18:39:51 2006 +0000

    added mgt_init() which balls parallel_initialize()

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 649c5d73c655740b168cd5ad656e2099e0b774b4
Author: lijewski <lijewski>
Date:   Mon Aug 7 18:23:00 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg.f90

commit 44c9c838f7d6b46fd3e0fdf1354605d08bff89b5
Author: lijewski <lijewski>
Date:   Mon Aug 7 18:22:45 2006 +0000

    only call MPI_Init() if MPI_Initialized() is false

Src/F_BaseLib/parallel.f90

commit 2019bc4908533169c64d4fbb7c4cea3a6133ec99
Author: lijewski <lijewski>
Date:   Fri Aug 4 22:33:01 2006 +0000

    removed weird embedded comment

Src/F_BaseLib/parallel.f90

commit c2625d83e5bcaac02626726aaea83ae87aa0037e
Author: lijewski <lijewski>
Date:   Fri Aug 4 22:26:57 2006 +0000

    moved mpi.f into parallel.f90

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/parallel.f90

commit bd1cfff5a0ba24a23563315a5740f9e521cc9860
Author: lijewski <lijewski>
Date:   Fri Aug 4 22:26:18 2006 +0000

    *** empty log message ***

Src/F_BaseLib/mpi.f

commit e3e5a55a2ee213bb4727de86e0fde641eb89dc78
Author: lijewski <lijewski>
Date:   Fri Aug 4 22:25:52 2006 +0000

    added save to mgts

Src/LinearSolvers/F_MG/mg_cpp.f90

commit b0959ba84f4c25495257e3fa07eb771164e9e09c
Author: lijewski <lijewski>
Date:   Fri Aug 4 22:25:34 2006 +0000

    removed mpi.f

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 610b301692dbfbde1f7a0a0cc4a086550e298487
Author: lijewski <lijewski>
Date:   Fri Aug 4 22:24:03 2006 +0000

    f90 stuff

Tools/C_mk/Make.AIX
Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 631c92e094c4f8f5f4724b3da94651ab6b3a054d
Author: almgren <almgren>
Date:   Thu Aug 3 20:35:06 2006 +0000

    Improve print statements in itsol...

Src/LinearSolvers/F_MG/itsol.f90

commit f415cea2183477070ac639f5bc86145e5813f7d6
Author: almgren <almgren>
Date:   Thu Aug 3 19:46:42 2006 +0000

    Replaced spacing(Anorm) by epsilon(Anorm)*Anorm to be consistent with itsol_converged.

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit c48d8aa5928c42df2d45581673c55db115b1757d
Author: almgren <almgren>
Date:   Thu Aug 3 18:47:06 2006 +0000

    Fixed bug in FORT_NORMA for 3D computation of matrix norm.

Src/LinearSolvers/C_CellMG/ABec_3D.F

commit feafcc70ed0096444f05b29db39df34caee4e963
Author: almgren <almgren>
Date:   Thu Aug 3 18:29:29 2006 +0000

    Fixed bug in mgt_set_rh_3d.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 8f2a0ac537bcbda0e33f21b9b75411ac51ece926
Author: almgren <almgren>
Date:   Thu Aug 3 18:28:11 2006 +0000

    Latest greatest, works in 2d and 3d with periodic/Neumann/Dirichlet.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 80482b5d4ec50bf25933c4494811275242cff9b4
Author: almgren <almgren>
Date:   Wed Aug 2 21:42:56 2006 +0000

    1) Make consistent with mglib again.
    
    2) Set CG and BiCG bottom solvers so that if (rnorm > bnorm) then return solution = 0.

Src/LinearSolvers/F_MG/itsol.f90

commit 6dcd8f676629f5a94c32fd27f4668a41ea1f7c3f
Author: almgren <almgren>
Date:   Wed Aug 2 21:42:16 2006 +0000

    Need to reset "final" parameter at end of use.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 48054fd77fc3260f51edc41d4682065ef50e2067
Author: almgren <almgren>
Date:   Wed Aug 2 21:41:58 2006 +0000

    Dont print out eps as part of mg_tower since it is set only when solve is called.

Src/LinearSolvers/F_MG/mg.f90

commit e05874657d68c57abcadbe4908b5da4cf135b57e
Author: almgren <almgren>
Date:   Wed Aug 2 21:41:39 2006 +0000

    Formatting only...make it look like Parallel/mglib.

Src/LinearSolvers/F_MG/ml_cc.f90

commit d06335b925c1f1869e176a4035d2df22adb93612
Author: almgren <almgren>
Date:   Wed Aug 2 21:41:00 2006 +0000

    Modify CG bottom solver so that if (rnorm > bnorm) at end then return solution = 0.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit eeb576d919e6e091f6fffaea4dc9c63177db6cd2
Author: almgren <almgren>
Date:   Wed Aug 2 21:37:31 2006 +0000

    1) Make consistent with F90
    
    2) In  BiCG bottom solver, if (rnorm > bnorm) at end then return solution = 0.

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 4073c0f17bc8ca7b5cc115aac7bb068ab3a81dd9
Author: lijewski <lijewski>
Date:   Wed Aug 2 21:14:14 2006 +0000

    *** empty log message ***

Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/ba.25600.REMOVED.git-id
Src/C_BaseLib/test/tMinCommCosts.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/ba.25600.REMOVED.git-id
Tests/C_BaseLib/tMinCommCosts.cpp

commit e307ef1e71fe1d61671415deb0ee5572a056589f
Author: lijewski <lijewski>
Date:   Wed Aug 2 21:13:59 2006 +0000

    speedup of SwapAndTest(); also only call it once.

Src/C_BaseLib/DistributionMapping.cpp

commit c6fa38c64def89d3a9f73b2b7bab8448fbd6118c
Author: almgren <almgren>
Date:   Wed Aug 2 20:13:06 2006 +0000

    1) Make consistent with Parallel/mglib for cell-centered solves.
    
    2) Added nu_b and nu_f...

Src/LinearSolvers/F_MG/mg.f90

commit 1421132a63bf5392ce5c893e638de1cf7ad4dc46
Author: almgren <almgren>
Date:   Wed Aug 2 20:12:20 2006 +0000

    Make the output statements consistent with Parallel/mglib.

Src/LinearSolvers/F_MG/ml_cc.f90

commit f56d306fff5000529f548847e6081e207519a0a4
Author: almgren <almgren>
Date:   Wed Aug 2 20:10:56 2006 +0000

    Allow code to reduce order small grids.

Src/LinearSolvers/F_MG/stencil.f90

commit 0c8228c3e5052a788ed27a7d739c663180c59744
Author: almgren <almgren>
Date:   Wed Aug 2 20:09:53 2006 +0000

    Latest greatest...appears to work.

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit a815ee1b791a0553f431fbda126033b556d3d4ad
Author: almgren <almgren>
Date:   Wed Aug 2 20:09:29 2006 +0000

    1) Make the formatting consistent with the Parallel/mglib (cell-centered) solves.
    2) Add "0" as an argument to mg_precond in the CG and BiCG solves to be consistent
       with Parallel/mglib - this does a copy rather than a relaxation as the preconditioner.

Src/LinearSolvers/F_MG/itsol.f90

commit cb2a2d233b84f4b3cb5ad615506142a021c6b99d
Author: almgren <almgren>
Date:   Wed Aug 2 20:07:45 2006 +0000

    Match the formatting of output statement with the new F90 code.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit d45359860d4dd80f296fb02a8efaafbf66d2475d
Author: almgren <almgren>
Date:   Wed Aug 2 20:07:22 2006 +0000

    Get rid of numiter as a parameter, and always use the update, even
    if it was bad...

Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 8bd7b103b2b427a58a2f0873c499758492f70dc2
Author: almgren <almgren>
Date:   Fri Jul 28 21:29:40 2006 +0000

    Latest in getting interface with iamr correct.

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 510531c0629140a0f72ee440f4b63a4d16b38040
Author: almgren <almgren>
Date:   Fri Jul 28 21:29:09 2006 +0000

    Trying to pass the variables correctly.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 0b371f69311a8e510b806c8a02d7ad25347775a7
Author: almgren <almgren>
Date:   Thu Jul 27 20:57:17 2006 +0000

    Appears to work in conjunction with Parallel/iamrlib and fParallel/mg.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit f40fe74e914a2d7268635f96e42c3323b9f3a175
Author: almgren <almgren>
Date:   Thu Jul 27 20:56:50 2006 +0000

    Appears to work in conjunction with Parallel/iamrlib.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 202db86e1138e5b4a70fbe83512b5e28fbd27332
Author: lijewski <lijewski>
Date:   Fri Jul 21 22:16:39 2006 +0000

    cfe3 -> cfe

Tools/C_mk/Make.defs

commit 9287e506a566d6381397fbf4db2bd1782e0ba696
Author: lijewski <lijewski>
Date:   Thu Jul 20 19:54:39 2006 +0000

    comment out timer stuff

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 92bb8767b95a72e0dc2f1a2ad6413b4748a1a9f2
Author: almgren <almgren>
Date:   Thu Jul 20 19:17:57 2006 +0000

    Replaced cout by std::cout and endl by std::endl

Tools/C_util/Convergence/DiffSameGrid.cpp

commit 80603ba255fe12445d8618510f246cd7a372522c
Author: lijewski <lijewski>
Date:   Tue Jul 18 03:56:30 2006 +0000

    optimization flags for columbia

Tools/C_mk/Make.Linux

commit df6ea7c3d4aee34fa2c11f06e309fb2332210708
Author: lijewski <lijewski>
Date:   Tue Jul 18 03:55:34 2006 +0000

    turn off a bunch of Intel stuff that doesn't always work

Tools/C_mk/Make.defs

commit 1ecb58cea9c7af47e4c576462461766bb2c05b4d
Author: lijewski <lijewski>
Date:   Thu Jul 13 21:08:56 2006 +0000

    ipo -> ip for Columbia

Tools/C_mk/Make.Linux

commit c884648d888e46b3d23a7c9bcccf5cf3ee00fc96
Author: lijewski <lijewski>
Date:   Fri Jul 7 18:23:26 2006 +0000

    some modest simplification to AddBox() routines

Src/C_BaseLib/FabArray.H

commit 9b2b233261dcf3e9514f5ab7fa49e2a69eede14d
Author: almgren <almgren>
Date:   Thu Jul 6 19:01:45 2006 +0000

    Fixed the stencils for stencil_order=3 and Neumann bc's: we can't do higher
    order with Neumann bc's or we will lose solvability.

Src/LinearSolvers/F_MG/stencil.f90

commit 8ee03045dca634876242c290df1529e6281eef9c
Author: almgren <almgren>
Date:   Wed Jul 5 23:33:35 2006 +0000

    Moved ml_norm_inf and ml_norm_l2 into ml_nd.f90 from nodal_multi.f90.
    Also, ml_norm_l2 was just plain wrong for multiple levels.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 950613245d02dfc610e6f0ee80a997855d05092d
Author: almgren <almgren>
Date:   Wed Jul 5 23:29:02 2006 +0000

    Moved ml_norm_inf and ml_norm_l2 into ml_cc and no longer have
    separate copies in cc_multi.  Also made the L2 norm do the right
    thing - it was wrong for multilevel before.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 66c4e384ae4cd3f003fb6478c718089bbd7659e2
Author: almgren <almgren>
Date:   Wed Jul 5 22:43:01 2006 +0000

    bs() around quantities in convergence test *** IN BICGSOLVE ***.
    (PREVIOUSLY ONLY PUT IN CGSOLVE)

Src/LinearSolvers/F_MG/itsol.f90

commit 11d505d6a2e2bbb41816ee67635d0958a1c08c7e
Author: lijewski <lijewski>
Date:   Wed Jun 28 21:07:43 2006 +0000

    finally got bndry_reg_rr_build_1() correct?

Src/F_BaseLib/bndry_reg.f90

commit 5229488a0a8347812a01e1e351a2420da4b65d7f
Author: lijewski <lijewski>
Date:   Wed Jun 28 16:19:13 2006 +0000

    call some fill_boundary()s with cross flag

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 96aa51aba471e3347cbd66eb6ffa90984657c863
Author: lijewski <lijewski>
Date:   Tue Jun 27 20:24:52 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 62ed59d86b1ca8860bdf8940f91cd5246d636590
Author: lijewski <lijewski>
Date:   Tue Jun 27 19:45:04 2006 +0000

    cross stuff now appears to work

Src/F_BaseLib/layout.f90

commit 7fd51afc3fef4a44e17509d2c32eae7d603963f7
Author: almgren <almgren>
Date:   Tue Jun 27 17:30:28 2006 +0000

    Put in 21-point stencil option for case where dense but all the dh the same.

Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 018f2561dc3f8907db6a03d274c664cd8f13010c
Author: almgren <almgren>
Date:   Mon Jun 26 21:00:27 2006 +0000

    Nodal cross (5pt) stencil now works adaptively

Src/LinearSolvers/F_MG/ml_nd.f90

commit ad43a3da305ad5dcd0b2774a05a5bf628bd49d1a
Author: almgren <almgren>
Date:   Mon Jun 26 21:00:05 2006 +0000

    Nodal cross (5pt) stencil now works adaptively...

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 507e44b07976065af1f90303b5262d2d4f49937e
Author: lijewski <lijewski>
Date:   Sat Jun 24 00:00:14 2006 +0000

    Uniform DH optimization for nodal_smoother_3d, stencil_apply_3d_nodal &
    grid_laplace_3d

Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 247fde4fba3385639f92b87b55c00619dbb764ad
Author: car <car>
Date:   Fri Jun 23 20:26:51 2006 +0000

    tweaked interface to c++/fortran solver

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 65420a55bfda3170d9bc1e8b0ae8c616a9b5309a
Author: almgren <almgren>
Date:   Fri Jun 23 18:59:32 2006 +0000

    New code for 5-point nodal stencil in 2d.  5-point doesn't work yet but 9-point
    does still work.

Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit f7aae023a57c3f8ad7a3ec6f5162abbff1624544
Author: lijewski <lijewski>
Date:   Thu Jun 22 22:15:46 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 07a7e3d30b057e8af91d69107b510e57f20837f6
Author: almgren <almgren>
Date:   Thu Jun 22 21:37:01 2006 +0000

    Now has capability for 7-point (3d cross) nodal stencil.

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 8a86094b89000ad3b9eb5507401705dfea53ca98
Author: almgren <almgren>
Date:   Thu Jun 22 21:30:59 2006 +0000

    Now has capability for 7-point (cross stencil in 3d)

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit bfc9691041ee6c9367e0aa788f096a994fb8419a
Author: car <car>
Date:   Thu Jun 22 19:28:13 2006 +0000

    closer

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit afae81b712a8405949753ba7ddf450d8bcc0107f
Author: car <car>
Date:   Thu Jun 22 19:27:37 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 5f75b8c2174323da21a6e95df34a7d9d1d97b42a
Author: car <car>
Date:   Thu Jun 22 19:27:26 2006 +0000

    stop using optional unit

Src/F_BaseLib/layout.f90

commit cd70bc0f04aa2c2579f277b474487fbce766a95f
Author: almgren <almgren>
Date:   Thu Jun 22 02:37:12 2006 +0000

    Fix calling sequence for first subroutine.

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit 88dcdbd4ef431269b9eae2cdf70011116e32d6e6
Author: car <car>
Date:   Wed Jun 21 22:52:15 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 6e6e18af71aef142e4d1ccb576c1533ca604ba16
Author: car <car>
Date:   Wed Jun 21 20:58:25 2006 +0000

    *** empty log message ***

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 10227526f67b4cc4e3f138c628f2232a2b5db247
Author: lijewski <lijewski>
Date:   Wed Jun 21 17:40:12 2006 +0000

    mods for cfe3

Tools/F_mk/GMakeMPI.mak

commit 2650e937eb2a4fb1339a42b963b844d71e69744a
Author: lijewski <lijewski>
Date:   Tue Jun 20 19:36:38 2006 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit 22f203ec842100ce55828a76897463bfa12b9130
Author: car <car>
Date:   Tue Jun 20 16:42:03 2006 +0000

    changes for c++/f90

Src/F_BaseLib/ml_boxarray.f90
Src/F_BaseLib/ml_layout.f90
Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/main.cpp
Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/ml_nd.f90
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/main.cpp
Tools/C_mk/Make.defs

commit 5ba13aade4625b1c87df8630521504d4a1f0838c
Author: almgren <almgren>
Date:   Tue Jun 20 06:50:14 2006 +0000

    Put abs() around quantities in convergence test.

Src/LinearSolvers/F_MG/itsol.f90

commit 467adf7a1a88beabe2ea46154700ee1342f4a9bf
Author: lijewski <lijewski>
Date:   Mon Jun 19 21:06:57 2006 +0000

    removed ml_crse_contrib_easy()

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit b72339bc0abd70d7b4d416a8980fb2e729e0ba94
Author: lijewski <lijewski>
Date:   Fri Jun 16 22:08:13 2006 +0000

    -Ofast => -O2 for PathScale

Tools/F_mk/GMakedefs.mak

commit 6e1ef31ab569f198ff3392eb7d28fcf2ed12ba00
Author: lijewski <lijewski>
Date:   Fri Jun 16 21:24:35 2006 +0000

    *** empty log message ***

Src/F_BaseLib/layout.f90

commit 92e514b1e7995ef2484c25ebbb17da2903bfb577
Author: lijewski <lijewski>
Date:   Fri Jun 16 20:57:52 2006 +0000

    fixed bug in fluxassoc_build

Src/F_BaseLib/layout.f90

commit 7040520c6ca22c21da97ac877f10c749f367080a
Author: lijewski <lijewski>
Date:   Thu Jun 15 21:44:40 2006 +0000

    sped up fluxassoc_build & copyassoc_build

Src/F_BaseLib/layout.f90

commit cb55057a77cfba7053e2a90abcefd64730e18ce5
Author: lijewski <lijewski>
Date:   Thu Jun 15 20:34:10 2006 +0000

    removed all 'easy' functions

Src/F_BaseLib/multifab.f90

commit 1665e410ea6b17fbbbc1d13701922bb215cb4e1b
Author: lijewski <lijewski>
Date:   Thu Jun 15 18:12:09 2006 +0000

    added cpy_? functions taking filter arg

Src/F_BaseLib/multifab.f90

commit a24aa43aaf77b7ab2c0af93123c8eb227103f749
Author: lijewski <lijewski>
Date:   Thu Jun 15 17:35:57 2006 +0000

    Made most communications alltoall.
    Got rid of all reshape() calls.

Src/F_BaseLib/multifab.f90

commit a19a968f87ed80a844ace776369cccfa67f28b2f
Author: lijewski <lijewski>
Date:   Wed Jun 14 22:13:12 2006 +0000

    PGI fixes

Src/F_BaseLib/layout.f90

commit fe14cba43b03e403eb5a024f024ae23ac37e7390
Author: lijewski <lijewski>
Date:   Wed Jun 14 22:06:59 2006 +0000

    fixes for PGI

Src/F_BaseLib/knapsack.f90

commit 31c98ae6ce9a69344e1d6ffb62bfcd40c797a3db
Author: lijewski <lijewski>
Date:   Wed Jun 14 20:55:54 2006 +0000

    PGI mods

Tools/F_mk/GMakedefs.mak

commit 99d552e536a0e2b4108167df8735143cb8b93d36
Author: lijewski <lijewski>
Date:   Tue Jun 13 22:20:29 2006 +0000

    initial cut at XT3 (catamount)

Tools/F_mk/GMakedefs.mak

commit a3ba97505c2f4fe3f381c6d7b3f8f7335803b2de
Author: lijewski <lijewski>
Date:   Tue Jun 13 22:19:31 2006 +0000

    fixes for jaguar (XT3)

Src/F_BaseLib/bl_types.f90
Src/F_BaseLib/sort_box.f90

commit 77c45689c1cdc9f7b41a4aba243e0f31fee68a62
Author: lijewski <lijewski>
Date:   Tue Jun 13 20:45:46 2006 +0000

    sped up boxassoc_build

Src/F_BaseLib/layout.f90

commit eed0c191e2677c0b8c42503a11962e659cb42676
Author: lijewski <lijewski>
Date:   Tue Jun 13 18:23:29 2006 +0000

    speed up of unique_cover

Src/F_BaseLib/layout.f90

commit 3a58b120eb98f1b69103e6d2ed407425a9db58f2
Author: lijewski <lijewski>
Date:   Tue Jun 13 18:00:48 2006 +0000

    added optional sort arg to boxarray_build_l

Src/F_BaseLib/boxarray.f90

commit 67da161ae0932e7a7f6a8363ccfeda9aa539efd3
Author: lijewski <lijewski>
Date:   Tue Jun 13 18:00:10 2006 +0000

    *** empty log message ***

Src/F_BaseLib/bndry_reg.f90

commit 693149c9a64b43a74b533ab444a4974e35649a2e
Author: car <car>
Date:   Tue Jun 13 17:07:10 2006 +0000

    test of knapsack

Src/F_BaseLib/test/ball_def.14656
Tests/F_BaseLib/ball_def.14656

commit 00195651789346dda381e36b779fb53f5e88313e
Author: car <car>
Date:   Tue Jun 13 16:46:20 2006 +0000

    changes for c++/fortran

Src/F_BaseLib/ml_layout.f90
Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 18bfb126aa36a6f25db3bd971078b0cc85710a84
Author: car <car>
Date:   Tue Jun 13 16:46:04 2006 +0000

    changes for fortran/c++

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/ml_cc.f90

commit 646447d0fd21d3b36b40af65c35071904429db79
Author: lijewski <lijewski>
Date:   Tue Jun 13 16:39:56 2006 +0000

    speed up to build_1

Src/F_BaseLib/bndry_reg.f90

commit 32d74b08adf6bb8d16a019a8b23ffb8c3f1709c6
Author: lijewski <lijewski>
Date:   Tue Jun 13 15:41:28 2006 +0000

    bug fix for hash stuff

Src/F_BaseLib/layout.f90

commit 638e6e97f62cccde3b321d6f8efc0e2f1a509869
Author: lijewski <lijewski>
Date:   Tue Jun 13 03:43:51 2006 +0000

    added more timers

Src/F_BaseLib/bndry_reg.f90

commit b079894f444b1b21c46bc4d179102a14ca50d0ed
Author: lijewski <lijewski>
Date:   Mon Jun 12 23:25:48 2006 +0000

    check (a hack) that call trees are the same across CPUs

Src/F_BaseLib/bl_prof.f90

commit f4ef4669b28d7f473f01c28f5ec2be66fa5b5dc2
Author: lijewski <lijewski>
Date:   Mon Jun 12 22:32:03 2006 +0000

    *** empty log message ***

Src/F_BaseLib/bl_timer.f90

commit a93974716d08f5fad7a606753ea762af818630cc
Author: lijewski <lijewski>
Date:   Mon Jun 12 22:31:42 2006 +0000

    removed ba_bndry_periodic timer

Src/F_BaseLib/layout.f90

commit 606c3ca433180060e1826a931847b768f2a11c3a
Author: lijewski <lijewski>
Date:   Mon Jun 12 21:04:10 2006 +0000

    commented out private statement

Src/F_BaseLib/bl_timer.f90

commit 41d2f719dc90db02063d50adced1ed464e62e777
Author: lijewski <lijewski>
Date:   Mon Jun 12 17:14:14 2006 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Utility.cpp

commit 2b15da424cf2dd4386ab95191508262ef5ee15aa
Author: almgren <almgren>
Date:   Fri Jun 9 23:06:00 2006 +0000

    1) added construction of singular flag
    2) added two relaxations at bottom level after the CG solver is called
       (to match results of Parallel/hgproj code)

Src/LinearSolvers/F_MG/mg.f90

commit b9b604ada0f69d0d01457a88fa058d03de84b491
Author: almgren <almgren>
Date:   Fri Jun 9 22:34:19 2006 +0000

    Modify the CG and BiCG solvers to take a flag which says if the
    problem is singular.   If true, then subtract off the average of the
    RHS from each value of the residual to make it solvable.  The flag is optional.

Src/LinearSolvers/F_MG/itsol.f90

commit 8493da246154a8c642780c0b57fbf296eaa8fc56
Author: almgren <almgren>
Date:   Fri Jun 9 22:32:50 2006 +0000

    In the multilevel convergence test, we were incorrectly computing the residual
    on the coarsest level if there were more than two levels, because the
    level 1 residual was averaged down to level 0 before the coarse-fine corrections
    (from the level 1-2 interface) were used to modify the level 1 residual.  This
    is now fixed.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 51efb1261198cfe00bcaac56436677eaee0870ec
Author: almgren <almgren>
Date:   Thu Jun 8 20:53:12 2006 +0000

    This file is a simpler case than gtbig3 of a case that breaks the Parallel/hgproj
    3-d 27-point (dense) solver - the solver will not converge because values of the
    solution on different grids are different.

Src/LinearSolvers/C_NodalMG/gt_breaks_27pt

commit 9d72ebd5705e72dbe9987ca3f08f13589d55f09d
Author: lijewski <lijewski>
Date:   Wed Jun 7 22:15:40 2006 +0000

    added verbose flag

Src/F_BaseLib/layout.f90

commit df8194721c8b6d4fd1c1219833400167b57c52c3
Author: lijewski <lijewski>
Date:   Wed Jun 7 22:15:10 2006 +0000

    removed nocomm stuff

Src/F_BaseLib/multifab.f90

commit 978642b738ea8549c902d5a9271aa1a55e2e48ca
Author: lijewski <lijewski>
Date:   Wed Jun 7 19:33:11 2006 +0000

    cleanup & simplification

Src/F_BaseLib/multifab.f90

commit c1c5d29f54b1b50de219d197e7cd8aba6efb99fe
Author: lijewski <lijewski>
Date:   Tue Jun 6 21:53:33 2006 +0000

    cache stuff for ml_crse_contrib

Src/F_BaseLib/layout.f90

commit 6609cb5778b245807a39270c285c0a06d0736842
Author: lijewski <lijewski>
Date:   Tue Jun 6 21:53:18 2006 +0000

    stubs for alltoall for integer & logicals

Src/F_BaseLib/parallel_stubs.f90

commit 329cec038762ce6c2b304779e62b7d7aef7e480c
Author: lijewski <lijewski>
Date:   Tue Jun 6 21:52:53 2006 +0000

    ml_crse_contrib() now goes fast in parallel

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit f555d9c6b3964728175df11587aec42178cf2bad
Author: lijewski <lijewski>
Date:   Mon Jun 5 21:39:51 2006 +0000

    added alltoall() for integer data

Src/F_BaseLib/parallel.f90

commit 79cad7e57f2f0e6258b79ca564dbacbce6945658
Author: car <car>
Date:   Mon Jun 5 21:25:15 2006 +0000

    pointer, intent conflict

Src/F_BaseLib/layout.f90

commit fa06b6ab4c79ca9ab4883bf1422f0b9414b1d57f
Author: lijewski <lijewski>
Date:   Sat Jun 3 02:27:43 2006 +0000

    tiny bit of cleanup

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 5f44845888628aaad05e79fea4ea1f121d90aad4
Author: lijewski <lijewski>
Date:   Fri Jun 2 16:35:49 2006 +0000

    little cleanup

Src/F_BaseLib/bndry_reg.f90

commit aa409ed8e59db133c328b2b3230a6c4e0d220d20
Author: lijewski <lijewski>
Date:   Thu Jun 1 22:23:37 2006 +0000

    fast parallel internal_sync

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab.f90

commit d609649c3aee9da070c720cf4fc9ea0e8697a500
Author: lijewski <lijewski>
Date:   Thu Jun 1 22:23:20 2006 +0000

    added alltoall()s for MPI_LOGICAL

Src/F_BaseLib/parallel.f90

commit 0f838fdc6b6cc8ac59a86954e4f6facb9d0c4824
Author: lijewski <lijewski>
Date:   Thu Jun 1 20:18:58 2006 +0000

    made a private member public

Src/F_BaseLib/boxarray.f90

commit 2a0a673480bb6d32cd04c6addf0fb19209d72c2a
Author: lijewski <lijewski>
Date:   Wed May 31 20:42:49 2006 +0000

    AIX mods

Tools/F_mk/GMakedefs.mak

commit 7efa4b51436756c4b6eea18e7eb4268fb5d7289b
Author: lijewski <lijewski>
Date:   Wed May 31 20:16:49 2006 +0000

    tad simplification

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 096a90c4f827327c85cc7115e40811d90b6cdff4
Author: lijewski <lijewski>
Date:   Wed May 31 20:14:45 2006 +0000

    some simplification

Src/F_BaseLib/box.f90
Src/F_BaseLib/layout.f90

commit d344d662ccbebdb7862a5331139665bc8c069df5
Author: lijewski <lijewski>
Date:   Tue May 30 23:47:55 2006 +0000

    some cleanup

Src/F_BaseLib/box.f90
Src/F_BaseLib/multifab.f90

commit e54facbafcdd7d896830dc874beeca66b13bb0ce
Author: lijewski <lijewski>
Date:   Tue May 30 20:07:52 2006 +0000

    more speedups to stencil_nodal_fill

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 61895a68b865b73c61150153f060e607441519f8
Author: lijewski <lijewski>
Date:   Tue May 30 20:05:43 2006 +0000

    Added timer to add_clean().
    Also added optional argument to turn off calling simplify().

Src/F_BaseLib/boxarray.f90

commit e3aad032d3c4eab045119b42755eeba443d26863
Author: lijewski <lijewski>
Date:   Tue May 30 17:47:44 2006 +0000

    added timer to boxarray_add_clean

Src/F_BaseLib/boxarray.f90

commit c65b293f816e998e7b8ebd16ff5ed6f34069cd31
Author: lijewski <lijewski>
Date:   Tue May 30 17:47:23 2006 +0000

    sped up stencil_fill_nodal for periodic

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 32f62a487db0aa3cd96757e1362dea11321761e9
Author: lijewski <lijewski>
Date:   Sat May 27 17:59:24 2006 +0000

    memory management cleanup; expanded copy_sum()

Src/LinearSolvers/F_MG/ml_restriction.f90

commit f99fc856b0847599db79145e5ccf125e6193b063
Author: lijewski <lijewski>
Date:   Sat May 27 05:12:00 2006 +0000

    remove dull_copy_d(); use cpy_d(); more remote()s

Src/F_BaseLib/multifab.f90

commit 85808ed052aec393d68b2d8903ab51ce90bf7292
Author: lijewski <lijewski>
Date:   Sat May 27 04:25:05 2006 +0000

    added remote() cycle to internal_sync()

Src/F_BaseLib/multifab.f90

commit 4b02d86e5b8b7881b74ae4b0dbc1a0e5ce1096a6
Author: lijewski <lijewski>
Date:   Sat May 27 03:44:25 2006 +0000

    added timer to internal_sync

Src/F_BaseLib/multifab.f90

commit 03ef6a999a873f273cc9d55c25516d177e732905
Author: lijewski <lijewski>
Date:   Fri May 26 23:39:18 2006 +0000

    added timers

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 3cbee8f52f046e69f7e917215a6fa22fe6c278f4
Author: lijewski <lijewski>
Date:   Fri May 26 23:20:55 2006 +0000

    added a remote() cycle test

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit cfeeb4e9b99fbc29635e7abc79298f20f7aa1341
Author: lijewski <lijewski>
Date:   Fri May 26 23:20:25 2006 +0000

    moved fill_boundary() around

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_util.f90

commit 5bfe34320cf661a6600d909d39c2ff4918d58609
Author: car <car>
Date:   Fri May 26 22:41:37 2006 +0000

    don't grow for obmf

Src/F_BaseLib/bndry_reg.f90

commit 56cc9d5216b715615b23aa580339c91e11a059d0
Author: lijewski <lijewski>
Date:   Fri May 26 20:42:44 2006 +0000

    changed name of timer

Src/F_BaseLib/layout.f90

commit 158015bba2f4c76a63da8a7f271eac7bd004f638
Author: almgren <almgren>
Date:   Fri May 26 19:23:21 2006 +0000

    Fixed bug in indexing in nodal_restriction_3d (ONLY 3D).

Src/LinearSolvers/F_MG/mg_restriction.f90

commit 67aa827a2893d706ca4029fe97ca2fae91e8bb20
Author: lijewski <lijewski>
Date:   Fri May 26 18:23:43 2006 +0000

    removed async stuff & added timers

Src/F_BaseLib/multifab.f90

commit b7764f6d229c0ac5e01b17940173e276bfcd7706
Author: lijewski <lijewski>
Date:   Fri May 26 18:23:16 2006 +0000

    added some timers

Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 0c0dcf9ebca67c73dcc9912968c82425c6881013
Author: car <car>
Date:   Fri May 26 18:11:14 2006 +0000

    unused variable

Src/C_BaseLib/ParmParse.cpp

commit 7cb9a765b3661e69d42d46f330c281f5e99d59f3
Author: lijewski <lijewski>
Date:   Thu May 25 21:50:26 2006 +0000

    merged periodic_add_copy()s

Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_restriction.f90

commit def5e06def4416f6b4de6ed4e39be8f44c4f8ad0
Author: almgren <almgren>
Date:   Thu May 25 20:11:41 2006 +0000

    We need to have two different periodic_add_copy routines, depending
    on whether the multifab src is already synced up at overlapping nodes.

Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_restriction.f90

commit a19ab9f8aea0cb257a5d8c77acb74b062fa8d594
Author: lijewski <lijewski>
Date:   Thu May 25 19:19:51 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_restriction.f90

commit 86d186cb44e03a698b22615f83a76b5fe31a0761
Author: lijewski <lijewski>
Date:   Tue May 23 23:00:33 2006 +0000

    parallelized periodic_add_copy()

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 7961fa5ab1528b4b1454fbd3e24d42edc8a18df7
Author: almgren <almgren>
Date:   Tue May 23 21:36:45 2006 +0000

    Got rid of other call to periodic_add_copy(mf); now both places
    use version in ml_interface_stencil: periodic_add_copy(dest,src)

Src/LinearSolvers/F_MG/ml_nd.f90

commit 548c11873def9439ae1614a8acf49b6e444cbe80
Author: almgren <almgren>
Date:   Tue May 23 21:31:51 2006 +0000

    This is the correct calling sequence for ml_restriction now that a
    periodic_add_copy has been put into ml_nodal_restriction

Src/LinearSolvers/F_MG/ml_nd.f90

commit 444830c4c84a84a66e891875eaeecc13f3283e15
Author: almgren <almgren>
Date:   Tue May 23 21:25:44 2006 +0000

    Replace destroy by bl_prof_destroy...

Src/LinearSolvers/F_MG/mg.f90

commit 12fadcbd91d8ac6332e0136bdcadae7fe99afd44
Author: lijewski <lijewski>
Date:   Tue May 23 18:03:38 2006 +0000

    appears to work in parallel for 2D & no periodic

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 3ad68d16220ca900ae96ccbeb4e71ff8db3a861c
Author: lijewski <lijewski>
Date:   Tue May 23 04:40:22 2006 +0000

    some cleanup

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 6e4fc488095191d2773ce71eae425dd137e8202a
Author: lijewski <lijewski>
Date:   Mon May 22 23:20:52 2006 +0000

    intent(out) -> intent(inout)

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 3e832d67001de52b47640bf972ac42762002816e
Author: lijewski <lijewski>
Date:   Mon May 22 23:20:05 2006 +0000

    wasn't quite right

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 0e8ec7da061630571beead9df3f8dc8078539121
Author: lijewski <lijewski>
Date:   Mon May 22 23:19:20 2006 +0000

     do need to use build_1

Src/LinearSolvers/F_MG/ml_nd.f90

commit fb1196a8bd62b4fcffc700540be8f04dac8499b8
Author: lijewski <lijewski>
Date:   Mon May 22 20:48:03 2006 +0000

    some cleanup

Src/LinearSolvers/F_MG/ml_nd.f90

commit fb352d2ee291e8b45a162dab85f077c4599cb3e0
Author: almgren <almgren>
Date:   Mon May 22 20:42:53 2006 +0000

    Moved periodic_add_copy functionality from ml_nd into ml_restriction for
    first call anyway...will still need to deal with 2nd call to periodic_add_copy...

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 103235da3f822ef267fc9f87902641d55bc1f295
Author: lijewski <lijewski>
Date:   Mon May 22 20:37:42 2006 +0000

    think I got ml_crse_contrib() parallelized

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 1f97df528a68c290383155035552cb2909f416dd
Author: lijewski <lijewski>
Date:   Mon May 22 17:19:21 2006 +0000

    some cleanup; not yet parallel-ready

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit b7752562b5f082896291b805b5648bea2d2c770b
Author: lijewski <lijewski>
Date:   Mon May 22 17:03:22 2006 +0000

    added neede boxarray_destroy()

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit d12b38420a5dffd842acb74c4cbfb67e6e651cee
Author: lijewski <lijewski>
Date:   Sat May 20 00:56:58 2006 +0000

    slight rearrangment of code; not yet parallel-ready

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit b2adf0410a64d75b6f13205a9bdff50c978e60ab
Author: almgren <almgren>
Date:   Fri May 19 21:40:08 2006 +0000

    Need another box_nodalize in the counting part...

Src/F_BaseLib/bndry_reg.f90

commit 478777d0d55339d9ab58f3cc27e72cf84987e1f3
Author: almgren <almgren>
Date:   Fri May 19 18:22:19 2006 +0000

    Make sure to box_nodalize inside bndry_reg_build_1.

Src/F_BaseLib/bndry_reg.f90

commit 54e48643e75fdbab55f7056cf5c8f2a4fe64fe72
Author: vince <vince>
Date:   Fri May 19 00:14:09 2006 +0000

    fixed '>' sign.

Src/C_AMRLib/INTERP_3D.F

commit 9b403570bc3eccf504e0114271a0e22e3c6ec34d
Author: car <car>
Date:   Thu May 18 21:15:24 2006 +0000

    mgt_solver suppt

Src/LinearSolvers/C_CellMG/Make.package
Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/main.cpp

commit 7b4c8a56de9d72b18157f5c38dcb465f34c4a026
Author: car <car>
Date:   Thu May 18 21:14:49 2006 +0000

    *** empty log message ***

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H
Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp
Src/LinearSolvers/C_to_F_MG/Make.package

commit 9552e7f34a1d1fbe0d638e3bfacff157ad18d999
Author: vince <vince>
Date:   Wed May 17 21:34:13 2006 +0000

    gatherv fix for romulus.

Src/C_AMRLib/Amr.cpp

commit b6517ed94adc062100e97060b3b31b2e91dcaacb
Author: almgren <almgren>
Date:   Wed May 17 19:53:40 2006 +0000

    Necessary corrections to handle periodic bcs.
    This has been tested for all combinations of bc's with grids in data/hgproj_grids.

Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 6c9709d2562a987998762a319192cdc8d6b7d1ae
Author: lijewski <lijewski>
Date:   Tue May 16 22:28:37 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_nd.f90

commit b7c5543f4a6ad32871906a957e57f91f16cb1b22
Author: lijewski <lijewski>
Date:   Tue May 16 21:50:21 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_nd.f90

commit 50d7fe66f205915ac1d6893df3dea39ae6c43190
Author: almgren <almgren>
Date:   Tue May 16 21:24:54 2006 +0000

    Cosmetic changes only, I think.

Src/LinearSolvers/F_MG/mg_restriction.f90

commit c3463354fe54d115c7667f09fa72ec705001301e
Author: almgren <almgren>
Date:   Tue May 16 21:21:59 2006 +0000

    Changes necessary for periodic

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 848d994ef3d359d30f3e425212831212edb1674e
Author: lijewski <lijewski>
Date:   Tue May 16 21:17:59 2006 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak

commit cb474db0005c216076eb30bdd4b0969ab69a7398
Author: almgren <almgren>
Date:   Tue May 16 21:04:58 2006 +0000

    Changes needed for periodic algorithm.

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 7f413cc3d0477435af5c2cdf8eb5028513852ab0
Author: almgren <almgren>
Date:   Tue May 16 21:03:14 2006 +0000

    Needed correction for periodic.

Src/LinearSolvers/F_MG/ml_util.f90

commit bffcfbbfa249571c1f729329e4baa8a999bc86d1
Author: car <car>
Date:   Mon May 15 21:10:35 2006 +0000

    a print function

Src/F_BaseLib/ml_layout.f90

commit 10b4116c0d52f129f426ebfebc5c51f8bf17b9c6
Author: car <car>
Date:   Fri May 12 23:01:24 2006 +0000

    needed

Src/F_BaseLib/test/t_bl_prof.f90
Tests/F_BaseLib/t_bl_prof.f90

commit e9645b68277850c0b0f5dfa824d1d63e18377325
Author: car <car>
Date:   Fri May 12 23:01:14 2006 +0000

    some parallel support

Src/F_BaseLib/bndry_reg.f90

commit 9756b8a96aaa2c61f44fbb5d9476b6a5b5546e37
Author: car <car>
Date:   Fri May 12 23:01:05 2006 +0000

    extra printouts

Src/F_BaseLib/layout.f90

commit 72b20b3050f634c5a8d2393477ff0a555b77aba0
Author: car <car>
Date:   Fri May 12 23:00:48 2006 +0000

    should use bnd reg for flux reg

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/flux_reg.f90

commit 1d3b3e5ff356fe35d276172afdf2f43b1f17fe09
Author: car <car>
Date:   Fri May 12 23:00:15 2006 +0000

    nil

Src/F_BaseLib/flux_reg.f90

commit be7e311976f4b75a317bf85cf7dcc9d3035143f0
Author: car <car>
Date:   Fri May 12 22:59:38 2006 +0000

    accomadate  bug in ifort 9.1

Src/F_BaseLib/box.f90

commit 74e4724f90bdc8e627de408ec188d321bfe90b1c
Author: car <car>
Date:   Fri May 12 22:58:46 2006 +0000

    changes for cc ml parallel

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/ml_util.f90

commit 51a1a96ec9c975ec3cb27ef1b1e9c719ef560c9c
Author: lijewski <lijewski>
Date:   Thu May 11 21:22:31 2006 +0000

    yet another bug fix to Gatherv stuff for Hdr

Src/C_BaseLib/VisMF.cpp

commit 48f4d01d4f7921ef36203c51e5a6d77fbc02ef2e
Author: car <car>
Date:   Wed May 10 18:02:35 2006 +0000

    appears that -lguide is not needed in intel link

Tools/C_mk/Make.defs

commit 217c196d92886f6c98ddd7a397a4fe0900abf8bd
Author: car <car>
Date:   Wed May 10 17:47:55 2006 +0000

    maybe a better way to find ifort libraries

Tools/C_mk/Make.defs

commit e26ee509765651b58443812962e9e000c90d5aca
Author: lijewski <lijewski>
Date:   Mon May 8 22:07:45 2006 +0000

    *** empty log message ***

Tools/C_util/dbgTools/GNUmakefile
Tools/C_util/dbgTools/crsGrids.cpp

commit a5f0e572bce12cbde2589cd9b11ec2bd65745589
Author: lijewski <lijewski>
Date:   Mon May 8 21:59:46 2006 +0000

    *** empty log message ***

Tools/C_util/TV_TempWrite.H
Tools/C_util/ViewMF/GNUmakefile
Tools/C_util/ViewMF/MFNorm.cpp
Tools/C_util/ViewMF/viewMFdiff.cpp

commit b2c76362d57d7c236761c22b682272eeca2dd890
Author: lijewski <lijewski>
Date:   Mon May 8 21:41:33 2006 +0000

    *** empty log message ***

Tools/C_util/Convergence/ComputeAmrDataNorms.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/GNUmakefile

commit aef9d43511ec9c07bacb8618ebd6aa13c2a7f5e7
Author: lijewski <lijewski>
Date:   Fri May 5 18:50:42 2006 +0000

    replaced use of std::pow() with D_TERM()

Src/C_AMRLib/Interpolater.cpp

commit 65196d259986dbe2657c1a5b544de7e88bdcdca5
Author: lijewski <lijewski>
Date:   Thu May 4 20:07:51 2006 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/grids.213
Src/LinearSolvers/C_CellMG/Test/grids/grids.5034
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213
Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/grids/grids.213
Tests/LinearSolvers/C_CellMG/grids/grids.5034
Tests/LinearSolvers/C_CellMG/grids/in.grids.213
Tests/LinearSolvers/C_CellMG/grids/in.grids.5034
Tests/LinearSolvers/C_CellMG/main.cpp

commit 0090ac0d89716b58053dea0ef00f60f6ef54d241
Author: sepp <sepp>
Date:   Thu May 4 19:57:30 2006 +0000

    1) to Make.defs, added 2 JFG comments in which CAR explains
    what changes must be done to run on hive
    2) to Make.mpi, added 1 JFG comment pointing out an ifeq block
    that CAR added to run on hive

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 5ba6767cd65545ce1f5c2d60408e4b89fa823a6f
Author: lijewski <lijewski>
Date:   Wed May 3 18:19:29 2006 +0000

    removed length limit on tokens

Src/C_BaseLib/ParmParse.cpp

commit e925b832695aaf6682ab4b86cfdf6c6b013dfe94
Author: lijewski <lijewski>
Date:   Tue May 2 21:25:33 2006 +0000

    *** empty log message ***

Src/C_AMRLib/Amr.cpp

commit 47a648ca88e5287c5828cb3b0905fd6764870f96
Author: car <car>
Date:   Tue May 2 18:41:38 2006 +0000

    *** empty log message ***

Src/C_BaseLib/SPECIALIZE_1D.F

commit e0c0f65c212da0c78c6752b561b552451962bdc1
Author: lijewski <lijewski>
Date:   Tue May 2 18:01:15 2006 +0000

    no <ONE_D.H>

Src/C_AMRLib/INTERP_1D.F

commit 83adf111b5e0cc4305406ede7fee8905c6b8889d
Author: lijewski <lijewski>
Date:   Tue May 2 16:47:05 2006 +0000

    from Greeno

Src/C_AMRLib/ARRAYLIM_1D.F
Src/C_AMRLib/SLABSTAT_1D.F

commit 14eca6e946aab21cf8b8afe9e655d2d9d9ffba02
Author: lijewski <lijewski>
Date:   Tue May 2 16:39:25 2006 +0000

    removed some BL_LANG_CC stuff

Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H
Src/C_BaseLib/Utility.H

commit c253fb635c00d105d734156a2af66b72e85d7277
Author: lijewski <lijewski>
Date:   Mon May 1 20:26:34 2006 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Utility.cpp

commit 88c22c5c4c894920963ee17f2fc281b61775f1bb
Author: lijewski <lijewski>
Date:   Mon May 1 19:19:13 2006 +0000

    up from 200 to 100000 to accomodate long material_input entries in geodyne

Src/C_BaseLib/ParmParse.cpp

commit 58c6ae8b5cdf7dc0ad9a25e67ac604e60566409c
Author: car <car>
Date:   Mon May 1 19:19:12 2006 +0000

    not sure i'll need this

Tests/LinearSolvers/F_MG/bc_interp.f90

commit 5e5a474fce0d48b24f794357e3fb2f3a0e7f30b5
Author: lijewski <lijewski>
Date:   Thu Apr 27 21:22:01 2006 +0000

    bug fix

Src/C_BaseLib/FabArray.H

commit a9463b0b819e0ec0d5f551895a52549a3432c7d0
Author: car <car>
Date:   Thu Apr 27 21:03:08 2006 +0000

    gfortran bug work-around

Src/F_BaseLib/list_box.f90

commit b487b57e73b00e436545aa1061e091eb7a4ea75f
Author: car <car>
Date:   Thu Apr 27 21:02:33 2006 +0000

    discriminate between -pg and BL_PROF

Tools/F_mk/GMakedefs.mak

commit 5322adf7ee816f580b8b5b720e7d123d6c063ff6
Author: car <car>
Date:   Thu Apr 27 21:00:26 2006 +0000

    no overhead when not profiling

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_prof_stubs.f90

commit bac15b74d7cf8abeee3faf306d7fb93fc967f32e
Author: lijewski <lijewski>
Date:   Mon Apr 24 22:36:31 2006 +0000

    more tweaks to CollectData()

Src/C_BaseLib/FabArray.H

commit 165f82c97eafe946f738df9f708f651db2e86bf9
Author: lijewski <lijewski>
Date:   Mon Apr 24 21:11:03 2006 +0000

    added #ifdef BL_MPI ... #endif

Src/C_BaseLib/FabArray.H

commit 02ad77896050bc3bdf1eb4289d9d5dd1d5a11a0c
Author: lijewski <lijewski>
Date:   Mon Apr 24 17:27:49 2006 +0000

    now uses MPI group operations

Src/C_AMRLib/FluxRegister.cpp

commit c774a48255f53bbe7c5760d4bea9f19c6e41508c
Author: car <car>
Date:   Fri Apr 21 20:16:57 2006 +0000

    parallel safe printing

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit dddec892de8aae79b6a0d6b6c762b7b1d9bf84ca
Author: lijewski <lijewski>
Date:   Thu Apr 20 20:15:38 2006 +0000

    slight tweak to CollectData()

Src/C_BaseLib/FabArray.H

commit f9bc6476cc76b90103fb180f0f56d991ed39e18e
Author: lijewski <lijewski>
Date:   Thu Apr 20 18:21:41 2006 +0000

    now use group communication protocols in CollectData()

Src/C_BaseLib/FabArray.H

commit 25ff108ec49fc9cd13b4a2e1379c968b07416a9b
Author: lijewski <lijewski>
Date:   Wed Apr 19 04:30:29 2006 +0000

    substituted alltoallv() for send()/recv() in ::copy()

Src/C_BaseLib/FabArray.H

commit 05a0ae0ddc4b28e8b2ba5323dd5feb2faca9b764
Author: lijewski <lijewski>
Date:   Tue Apr 18 23:19:55 2006 +0000

    wrapped Gatherv()s in BL_MPI_REQUIRE

Src/C_BaseLib/VisMF.cpp

commit d5ec6b704be9db5fdd7a663e7305950eb77cf658
Author: lijewski <lijewski>
Date:   Sat Apr 8 00:01:42 2006 +0000

    use MPI_Gatherv() in VisMF::Write()

Src/C_BaseLib/VisMF.cpp

commit 3c5809db1a26ec899f5d66c64e672824de2417d6
Author: lijewski <lijewski>
Date:   Fri Apr 7 20:51:59 2006 +0000

    use gatherv() instead of send()/recv() for Header build

Src/C_BaseLib/VisMF.cpp

commit 6b298c76e4b31d6077e21c6be3c92796e9664040
Author: car <car>
Date:   Thu Apr 6 13:52:53 2006 +0000

    reformat

Src/F_BaseLib/ml_multifab.f90

commit 9879be386b5f8dcb2b67a8e6bbb4ffb40d7a41e4
Author: car <car>
Date:   Thu Apr 6 13:52:23 2006 +0000

    lall needed to protect all

Src/F_BaseLib/multifab.f90

commit 4520a1cfbc724a910989634f3924e0c6bd3ec50e
Author: almgren <almgren>
Date:   Tue Apr 4 20:15:51 2006 +0000

    Made same fixes for 3d as well.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit aa2ee478fec7e0664bedb4d4d4c15654c3cf260d
Author: almgren <almgren>
Date:   Tue Apr 4 20:11:14 2006 +0000

    Fix to bug in gs_rb_smoother_2d which caused crash at lowest MG level in
    non-square grid.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit b459194a40c440c6beba8163404a002ab4f364a7
Author: marc <marc>
Date:   Fri Mar 31 22:27:35 2006 +0000

    reduce precision

Src/C_AMRLib/Amr.cpp

commit 94612c2450295178e573cda4c1a84f0aabdb38f2
Author: marc <marc>
Date:   Fri Mar 31 21:48:09 2006 +0000

    fix up err in prof statement

Src/C_BaseLib/VisMF.cpp

commit 76c81d69efcdad8ec4dda144f2a15f908539a189
Author: marc <marc>
Date:   Fri Mar 31 21:42:50 2006 +0000

    add a couple of timers

Src/C_BaseLib/VisMF.cpp

commit 90ac727b4fc1b0eaed3d928c85688f044221857c
Author: vince <vince>
Date:   Thu Mar 30 21:52:12 2006 +0000

    test for old style box.

Src/C_BaseLib/Box.cpp

commit 0c997dee62618242a5de9e14cbaab82f79dba644
Author: car <car>
Date:   Tue Mar 28 00:05:30 2006 +0000

    *** empty log message ***

Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_knapsack.f90
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_knapsack.f90

commit 99b23bc47fffe886d541945c8a8e267c4a31cabe
Author: car <car>
Date:   Mon Mar 20 20:06:28 2006 +0000

    test for ann

Src/F_BaseLib/multifab.f90

commit 4f0f921af8c1b7a495778cf25c423d3a7fcf8056
Author: vince <vince>
Date:   Thu Mar 16 19:04:34 2006 +0000

    additions for columbia.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit f375e73d1e72942c92aca21cbc34dfdf9e539a02
Author: lijewski <lijewski>
Date:   Mon Mar 13 21:04:11 2006 +0000

    print out distribution with grid log

Src/C_AMRLib/Amr.cpp

commit 4b98d5bba87a75421a388593578e5baaed450968
Author: car <car>
Date:   Mon Mar 6 22:23:50 2006 +0000

    forward decls needed

Src/C_BaseLib/FabArray.H

commit db5a93020ea818f6728ddd98657ff35c82e935e2
Author: car <car>
Date:   Mon Mar 6 19:24:44 2006 +0000

    missing declarations

Src/C_BaseLib/VisMF.H

commit 00c1cc9f55d6f99a24b5799ba8c1a39c76ad08e1
Author: lijewski <lijewski>
Date:   Wed Feb 15 22:47:12 2006 +0000

    more tweaking of min comm cost code

Src/C_BaseLib/DistributionMapping.cpp

commit 8c2d29b1f954d69f5ec8fc973908fcfd57d21490
Author: lijewski <lijewski>
Date:   Tue Feb 14 18:56:23 2006 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit 46ebda205b0025a998557827b550502c11cc43f1
Author: car <car>
Date:   Fri Feb 10 22:18:40 2006 +0000

    fewer includes when not profiling

Src/C_BaseLib/Profiler.H

commit 64e6a2f693fe5db4497e28ce379f54e8cdda86e2
Author: car <car>
Date:   Fri Feb 10 22:18:17 2006 +0000

    need string include

Src/LinearSolvers/C_NodalMG/RegType.H

commit 95410d51b494d3538cc843d3f0ff31c06866d087
Author: car <car>
Date:   Fri Feb 10 17:22:02 2006 +0000

    some code needing further testing

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 69870bace12f177f3bd7c5febe9f382f76d561be
Author: car <car>
Date:   Fri Feb 10 17:20:22 2006 +0000

    cleaned up makefile

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 27f3189f51f2a24f73d125ab5c089024f32307b2
Author: car <car>
Date:   Fri Feb 10 17:10:31 2006 +0000

    naphta

Tools/C_mk/Make.mpi

commit a3bf4d26816eb0e95af4aebca8cada9286cbea50
Author: car <car>
Date:   Fri Feb 10 17:10:11 2006 +0000

    BROWSE

Tools/C_mk/Make.rules

commit 72553443ce7aa09cf9b78e342fb7bab288fcbf6b
Author: car <car>
Date:   Thu Feb 9 23:00:12 2006 +0000

    need iostream...

Src/C_AMRLib/StateData.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 4cab8d06d2fa5583fbf02bd90693a2034a2afe56
Author: car <car>
Date:   Thu Feb 9 21:40:58 2006 +0000

    can now turn of profiling more completely

Src/C_BaseLib/Make.package
Src/C_BaseLib/Profiler.H

commit 8843742da5c58e3fa5d4775ea6a6dae35c46de88
Author: car <car>
Date:   Thu Feb 9 21:40:02 2006 +0000

    iostream...

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 180ecfdedcca0f98a0b0ec24115267c5e1630872
Author: car <car>
Date:   Thu Feb 9 21:13:58 2006 +0000

    iostream...

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit f9d5083bb29d1752da35b3b17f79f0bd70265328
Author: car <car>
Date:   Thu Feb 9 21:08:25 2006 +0000

    include needed for iostream

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit bbe01d0fad4d3892817f36f6f84a7bad5f1f72a2
Author: car <car>
Date:   Wed Feb 8 21:38:05 2006 +0000

    PGI->BL_PGI

Src/C_BaseLib/Thread.H

commit 08b1bf77e1637bd5e91a0df0aa265d742b9c3a4d
Author: car <car>
Date:   Wed Feb 8 21:37:26 2006 +0000

    wsecond on XT3

Src/C_BaseLib/Utility.cpp

commit 5f3137818f504ed04b5b21fd7fbda83c7d085c0d
Author: car <car>
Date:   Wed Feb 8 21:36:12 2006 +0000

    PGI flag not needed re template specialization

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp

commit 465fbc955a66f821a56deb3fdfc0dfdeb8dc2efa
Author: lijewski <lijewski>
Date:   Mon Jan 30 18:03:18 2006 +0000

    commented out some BL_PROFILE()s

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 47527d8177b1c327188c0f2343a2a61ef4f5daba
Author: lijewski <lijewski>
Date:   Fri Jan 27 23:25:38 2006 +0000

    *** empty log message ***

Src/C_BaseLib/test/tMinCommCosts.cpp
Tests/C_BaseLib/tMinCommCosts.cpp

commit e611f618dc5b2e5e85346b2763c2a6290ecaa1ac
Author: lijewski <lijewski>
Date:   Fri Jan 27 23:24:38 2006 +0000

    speedup of MinimizeCommCosts()

Src/C_BaseLib/DistributionMapping.cpp

commit 3601dc6a670c509ae29b0c06ead4325cf29823b8
Author: car <car>
Date:   Thu Jan 26 23:51:58 2006 +0000

    machinefile not needed

Src/LinearSolvers/C_NodalMG/machinefile.mpi

commit 5fdf19b1a9dc952bac99107f266208c816b63627
Author: lijewski <lijewski>
Date:   Thu Jan 26 00:12:17 2006 +0000

    zeroed out Execute()

Src/C_BaseLib/Utility.cpp

commit 5ea67965fd7dbda544c8d68aaa1642201173ed11
Author: lijewski <lijewski>
Date:   Thu Jan 26 00:09:26 2006 +0000

    *** empty log message ***

Src/C_BaseLib/Make.package

commit da15ae1b31c3f039fdee6850338541ac28ff6c25
Author: lijewski <lijewski>
Date:   Wed Jan 25 23:58:03 2006 +0000

    more profiling

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 589463ff9e3edaea4f2dcdbef6fa04a7e08c7a1f
Author: lijewski <lijewski>
Date:   Mon Jan 23 22:14:00 2006 +0000

    speedup to add()

Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp

commit 371ec232f4d30c7a2759fa98b95a536d4261d4e7
Author: lijewski <lijewski>
Date:   Fri Jan 13 20:26:28 2006 +0000

    use O3 with Fortran & PathScale

Tools/C_mk/Make.Linux

commit 9ef19b43eb474a08db7696ecc8e94dc58aa9f4ab
Author: car <car>
Date:   Tue Jan 10 22:05:28 2006 +0000

    Added another assert.

Src/C_BaseLib/BoxArray.cpp

commit e189c1d565d6f6f68500e3c3fba11b48091eb628
Author: car <car>
Date:   Tue Jan 10 22:05:08 2006 +0000

    Fixed ixType() bug in minimalBox().
    Also added a bunch more asserts.

Src/C_BaseLib/BoxList.cpp

commit 90ecf071b0f17f1bb8e3113b7bca54335eb327fb
Author: lijewski <lijewski>
Date:   Mon Jan 9 19:18:48 2006 +0000

    removed some simplify()s

Src/C_AMRLib/Amr.cpp

commit c9868a3294f6483948eed9d93e6001ef0a5aa187
Author: lijewski <lijewski>
Date:   Mon Jan 9 19:17:24 2006 +0000

    minimize() -> simplify()

Src/C_BaseLib/BoxArray.cpp

commit be963a490fe1b6893e83bbca57b998a485d269b1
Author: lijewski <lijewski>
Date:   Mon Jan 9 19:08:58 2006 +0000

    *** empty log message ***

Src/C_BaseLib/test/ba.15784.REMOVED.git-id
Src/C_BaseLib/test/tBA.cpp
Tests/C_BaseLib/ba.15784.REMOVED.git-id
Tests/C_BaseLib/tBA.cpp

commit 5ee6cb88345bcf7d8a8ce662e50b6d8910d18e10
Author: lijewski <lijewski>
Date:   Mon Jan 9 18:05:16 2006 +0000

    more speedups

Src/C_BaseLib/BoxList.cpp

commit b72119977b3b1c3c2425addbc86285a1259c3fa5
Author: lijewski <lijewski>
Date:   Mon Jan 9 05:00:30 2006 +0000

    use BoxArray to speed up intersects()

Src/C_AMRLib/Cluster.cpp

commit 09e6006641f57ac24966269a700ea0d1fd1d3dc3
Author: lijewski <lijewski>
Date:   Mon Jan 9 04:59:39 2006 +0000

    minimize() -> simplify().
    Use BoxDomain::add(BoxList) instead of BoxDomain::add(Box).

Src/C_AMRLib/Amr.cpp

commit 5cf0e8dc3b2e670ff831cbdd3375c039a2c35c16
Author: lijewski <lijewski>
Date:   Mon Jan 9 04:23:37 2006 +0000

    speedup of add(BoxList)

Src/C_BaseLib/BoxDomain.cpp

commit 381666a58122dd564cf4a2deb7314fe33792379b
Author: lijewski <lijewski>
Date:   Mon Jan 9 02:32:32 2006 +0000

    more profiling

Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxList.cpp

commit fe65cb3e2d6de7b8feb5561ab8b5fdf1c62c9548
Author: lijewski <lijewski>
Date:   Sun Jan 8 18:21:23 2006 +0000

    aded some profiling

Src/C_AMRLib/Cluster.cpp
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxList.cpp

commit 7c9ce6f7e973eefa6896fbc7c2bfd196a080c2eb
Author: lijewski <lijewski>
Date:   Sat Jan 7 20:35:20 2006 +0000

    think it's finally right

Src/C_BaseLib/BoxList.cpp

commit e359a261840b90c6281e01b81b1067850646b435
Author: lijewski <lijewski>
Date:   Sat Jan 7 18:57:30 2006 +0000

    think I fixed complementIn()

Src/C_BaseLib/BoxList.cpp

commit 001a70a7949bc1b261a202a97c2832387638fb82
Author: lijewski <lijewski>
Date:   Sat Jan 7 16:27:05 2006 +0000

    oops, got some weird recursion to work out

Src/C_BaseLib/BoxList.cpp

commit cbe8354253ce16a0d37eef68f08917fcc65e6d93
Author: lijewski <lijewski>
Date:   Sat Jan 7 01:22:09 2006 +0000

    more scalable version of complementIn()

Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit 3e2a1dbca3d886c31999d3240330e241561cf52f
Author: lijewski <lijewski>
Date:   Fri Jan 6 22:58:21 2006 +0000

    one complementIn() now calls other

Src/C_BaseLib/BoxList.cpp

commit a14eb17e8d863d23c29c3337b94c27aa8b320ded
Author: lijewski <lijewski>
Date:   Fri Jan 6 18:47:26 2006 +0000

    efficiency back to .95

Src/C_BaseLib/DistributionMapping.cpp

commit ba7b4f77d4d3ce0a1e8d32dd41a593ba2d7ccc2d
Author: car <car>
Date:   Fri Jan 6 18:46:57 2006 +0000

    newComplementIn

Src/C_BaseLib/test/tBA.cpp
Tests/C_BaseLib/tBA.cpp

commit 687976c44ce22aa9526eee81c0e214bad2e38543
Author: lijewski <lijewski>
Date:   Fri Jan 6 17:59:40 2006 +0000

    mem improvement for knapsack

Src/C_BaseLib/DistributionMapping.cpp

commit 1500fae3e7a5a6f3358631c972829e5a6deb026a
Author: lijewski <lijewski>
Date:   Fri Jan 6 05:34:24 2006 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit b60cdf1799ce57af20cbdb976f6177b044565857
Author: lijewski <lijewski>
Date:   Thu Jan 5 23:53:10 2006 +0000

    added timers to grid_places()

Src/C_AMRLib/Amr.cpp

commit 96e31513ae74c06d4315d522a58d7d2ded8bca46
Author: lijewski <lijewski>
Date:   Thu Jan 5 23:43:26 2006 +0000

    Print out both initial & final knapsack efficiency.

Src/C_BaseLib/DistributionMapping.cpp

commit f7de3734064e16497bae72b6de34e5b37f58cd7f
Author: car <car>
Date:   Thu Dec 22 23:44:06 2005 +0000

    *** empty log message ***

Src/F_BaseLib/test/t_bx.f90
Tests/F_BaseLib/t_bx.f90

commit e823a8f461024326f9625a94125e44cfdfffafa3
Author: car <car>
Date:   Wed Dec 7 17:02:01 2005 +0000

    should, but doesn't fix a problem with gfortran

Src/F_BaseLib/fab.f90

commit d4261c90e3f4580306fa33bfc97416a7a9b3575a
Author: marc <marc>
Date:   Tue Nov 22 22:15:05 2005 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit a2b9808d626a3892ecaae8e13c4514c9ce79641b
Author: marc <marc>
Date:   Tue Nov 22 22:14:47 2005 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 7544dd1519f61bf765bb8716e53b7a2748e0a2d9
Author: car <car>
Date:   Fri Nov 18 22:52:16 2005 +0000

    *** empty log message ***

Src/F_BaseLib/ml_multifab.f90

commit eec73906c67e8283ad8129eae5be384fd3a02ed9
Author: car <car>
Date:   Fri Nov 11 18:47:46 2005 +0000

    *** empty log message ***

Src/F_BaseLib/ml_multifab.f90

commit b89785ddaafe3aac628fa3841edd249ba90762b9
Author: car <car>
Date:   Thu Nov 10 23:42:16 2005 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak

commit 1fdc00587dfa1a639eda3aaccadd0561121d82bd
Author: car <car>
Date:   Thu Nov 10 23:31:33 2005 +0000

    metis is dead

Src/F_BaseLib/test/GNUmakefile
Tests/F_BaseLib/GNUmakefile

commit fb3779c6553deb0d15cb0ed6ca719a099eef9fba
Author: car <car>
Date:   Thu Nov 10 23:24:54 2005 +0000

    PathScale fixes

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak

commit e31f0e2dc50aad9c43a7de31e1b3c27761d2ea4c
Author: car <car>
Date:   Thu Nov 10 23:16:32 2005 +0000

    greenstreet mpi

Tools/F_mk/GMakeMPI.mak

commit 6e30f3cffbb1c479136c243cefcb9b2b62314121
Author: car <car>
Date:   Thu Nov 10 23:11:28 2005 +0000

    farg

Tools/F_mk/GMakeMPI.mak

commit a962239a4f0e4d17665cf64f113dd6a167e39477
Author: car <car>
Date:   Thu Nov 10 23:03:39 2005 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak

commit 7fc25299cbad0d339c488cb6e45b1f1d93a11e14
Author: car <car>
Date:   Thu Nov 10 22:51:18 2005 +0000

    farg in extern

Tools/F_mk/GMakeMPI.mak

commit d308b7f6d82362c5c476b3d8a6594894575132da
Author: car <car>
Date:   Wed Nov 9 17:26:29 2005 +0000

    fix for parallel stats

Src/F_BaseLib/bl_prof.f90

commit 317003ce881bceb1d25c8c28a500eaa63e441d1f
Author: car <car>
Date:   Wed Nov 9 16:53:55 2005 +0000

    new MPI config method

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak

commit 704001f7ac867f5aef88a08495e05479b0682d58
Author: car <car>
Date:   Tue Nov 8 16:23:57 2005 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit d0ddeb5c18a89ef390408a956ebde931681f5422
Author: car <car>
Date:   Tue Nov 8 02:35:19 2005 +0000

    debugging

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/multifab.f90

commit 49219a96c5230b07469f398573afe8ed4c52f78c
Author: car <car>
Date:   Wed Nov 2 23:49:30 2005 +0000

    barrier after mkdir

Src/F_BaseLib/fabio.f90

commit 47f908ceeba518497b7058290223e79317cafc77
Author: marc <marc>
Date:   Wed Nov 2 01:41:00 2005 +0000

    Add stuff to build on Jacquard

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 4788af3de01e08176b50f1062601a6330ce05730
Author: car <car>
Date:   Mon Oct 31 17:19:49 2005 +0000

    more support for dft; and bl_prof for longer running programs

Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/multifab.f90

commit ae1bd6c6e263df98b0e6fe8c78f3915ef3027cf2
Author: lijewski <lijewski>
Date:   Wed Oct 26 18:20:46 2005 +0000

    removed sndcnt/rcvcnt args to startup()

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 4b5635bbb7aae582cacb623bf7cebe2923b57be8
Author: lijewski <lijewski>
Date:   Tue Oct 25 22:13:13 2005 +0000

    some simplification of execute()

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit a6cefa42e7bc7c4b766a7be9a761f85874adbfe9
Author: car <car>
Date:   Mon Oct 24 22:59:40 2005 +0000

    timers

Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/multifab.f90

commit 6ddc25eee92144553e794688527666f06b606c84
Author: lijewski <lijewski>
Date:   Mon Oct 24 21:16:31 2005 +0000

    inlined add_task & depend_on

Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit e91d43164dad996872d93023557d89e08595202c
Author: lijewski <lijewski>
Date:   Sat Oct 22 19:41:09 2005 +0000

    default for verbose is now false

Src/C_BaseLib/DistributionMapping.cpp

commit 3a588b62a2441447bdfb34f03701cbfa92a07943
Author: lijewski <lijewski>
Date:   Fri Oct 21 03:27:42 2005 +0000

    removed timer & freshened code

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit e32d5f6c37362f924dbc5763e9845124b876059c
Author: lijewski <lijewski>
Date:   Thu Oct 20 22:07:38 2005 +0000

    A few more BL_PROFILE calls.

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 1af832ae84c14dcbd677c1615c257bc890092d2e
Author: lijewski <lijewski>
Date:   Tue Oct 18 18:19:57 2005 +0000

    some speedups to alloc()

Src/LinearSolvers/C_NodalMG/interface.cpp

commit 03717febe911155add467a20e367275c8e633b87
Author: lijewski <lijewski>
Date:   Tue Oct 18 15:57:34 2005 +0000

    *** empty log message ***

Src/C_BaseLib/BoxArray.cpp

commit e6dad106801914f29f6b2069257d6d75d3b365f6
Author: lijewski <lijewski>
Date:   Tue Oct 18 15:49:57 2005 +0000

    *** empty log message ***

Src/C_BaseLib/BoxArray.cpp

commit aa3daa82e30d0a7737a0e860e7ca69ccd99a05c0
Author: car <car>
Date:   Mon Oct 17 19:52:48 2005 +0000

    *** empty log message ***

Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_bx.f90
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_bx.f90

commit e2257c1479917efb7affff42e5ef4c8c190dd6c6
Author: lijewski <lijewski>
Date:   Mon Oct 17 18:59:00 2005 +0000

    removed timer from restrict_level()

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 7fb97991739a78b1cd24723b6acef45afc51ed4e
Author: lijewski <lijewski>
Date:   Mon Oct 17 17:50:34 2005 +0000

    merged in intersections()

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 2a5a6d7f63d09e9fca7ee9e9aa7748c891a6f85d
Author: lijewski <lijewski>
Date:   Mon Oct 17 17:50:22 2005 +0000

    added some timers

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 140c7e5b70cfae9d065460825d46d8dfffbf6f9e
Author: lijewski <lijewski>
Date:   Mon Oct 17 03:11:14 2005 +0000

    a working contains(IntVect) using intersections()

Src/C_BaseLib/BoxArray.cpp

commit 30ba588aabc93d5d5ce03491d144df9ae6a1b070
Author: lijewski <lijewski>
Date:   Mon Oct 17 02:21:05 2005 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 3b6086299986eb8787eb539789935c1716e68a51
Author: lijewski <lijewski>
Date:   Fri Oct 14 17:22:40 2005 +0000

    more polishing

Src/C_BaseLib/Box.cpp
Src/C_BaseLib/IntVect.cpp

commit f2754d2c2ee6d37b97bd8e3d03258f756f30d0c3
Author: lijewski <lijewski>
Date:   Thu Oct 13 23:04:50 2005 +0000

    the previous problem was with the contains(IntVect) -- fixed

Src/C_BaseLib/BoxArray.cpp

commit 0a8befe81cd6bfd982c4a69c6ad26130c2751c94
Author: lijewski <lijewski>
Date:   Thu Oct 13 20:14:16 2005 +0000

    reverting out some previous mods

Src/C_BaseLib/BoxArray.cpp

commit 3eae24d944844abdd9d30fb6f7fc761824deb4fe
Author: lijewski <lijewski>
Date:   Thu Oct 13 16:51:04 2005 +0000

    oops

Src/C_BaseLib/BoxArray.cpp

commit 1c5143bc16699a3b9e39a8d73a65601e948c430a
Author: lijewski <lijewski>
Date:   Wed Oct 12 18:01:48 2005 +0000

    merged in BoxMSet

Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp

commit 71e95a02bffcf56924db9d8c4548626a13cebd7e
Author: lijewski <lijewski>
Date:   Wed Oct 12 04:26:31 2005 +0000

    more uses of intersections()

Src/C_BaseLib/BoxArray.cpp

commit 64217e74d3c7080393a33c72c0aed84022abe609
Author: lijewski <lijewski>
Date:   Wed Oct 12 02:54:55 2005 +0000

    slight speed mods

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 142a63b5ad92acfc0cb0079fc156db9c1eed769f
Author: lijewski <lijewski>
Date:   Tue Oct 11 22:23:26 2005 +0000

    use intersections() in restrict_level()

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit a8155c995e160c7c29c328bdf4acd642aecf1465
Author: lijewski <lijewski>
Date:   Tue Oct 11 19:07:23 2005 +0000

    additional constructor

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit a0b975fdb0b591f103caf294f87574edb689dabe
Author: car <car>
Date:   Tue Oct 11 17:12:39 2005 +0000

    ready for mike

Src/LinearSolvers/C_NodalMG/3d_4_level.grids
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/inputs

commit 70f32873bd66d5bf443d0ab8c0ddb150e4e0e5f2
Author: lijewski <lijewski>
Date:   Tue Oct 11 17:01:08 2005 +0000

    use minimize() instead of simplify() in removeOverlap()

Src/C_BaseLib/BoxArray.cpp

commit 831438722958452eda3eb45b8943649251116cfb
Author: lijewski <lijewski>
Date:   Tue Oct 11 16:07:18 2005 +0000

    turned off FillPatch verbosity

Src/C_AMRLib/AmrLevel.cpp

commit 16d8440e205dae0810dad5f10e07e25dc95c1cea
Author: car <car>
Date:   Tue Oct 11 02:32:09 2005 +0000

    added a few timers

Src/LinearSolvers/C_NodalMG/interface.cpp

commit 06fbc33bb54bcf763290ab743635c764a17a19ba
Author: lijewski <lijewski>
Date:   Mon Oct 10 22:28:51 2005 +0000

    *** empty log message ***

Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/tBA.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/tBA.cpp

commit 6cbfff42b0a57feefa3092d0d3af62b63c13f3ae
Author: lijewski <lijewski>
Date:   Mon Oct 10 21:25:33 2005 +0000

    added removeOverlap()

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit 335976f8f7ab4be16a854d34309215e568048315
Author: lijewski <lijewski>
Date:   Mon Oct 10 21:00:23 2005 +0000

    added timer to FillPatch::Initialize()

Src/C_AMRLib/AmrLevel.cpp

commit df2c495755596ee597eaecf0cc895d47f0b6257e
Author: car <car>
Date:   Mon Oct 10 18:20:36 2005 +0000

    remove inclusion of BoxDomain.H where not needed

Src/C_AMRLib/Amr.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/TagBox.H

commit 36958112b25a5e62657b25539cfdbbbd99960d80
Author: car <car>
Date:   Mon Oct 10 18:01:23 2005 +0000

    help find g77 library

Tools/C_mk/Make.defs

commit 71e8458e135e1de3f4643f8f66053477948917e7
Author: lijewski <lijewski>
Date:   Sun Oct 9 03:08:33 2005 +0000

    inlined min()/max()

Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp

commit aa85ebf8048016bdfa298d6629cf67a6abd98615
Author: lijewski <lijewski>
Date:   Sun Oct 9 02:23:00 2005 +0000

    fix to intersections() for empty BoxArrays

Src/C_BaseLib/BoxArray.cpp

commit b78e1d3717f41ea1628d5a8797b3058f0c7e2b11
Author: lijewski <lijewski>
Date:   Sat Oct 8 02:24:48 2005 +0000

    *** empty log message ***

Src/C_BaseLib/test/tBA.cpp
Tests/C_BaseLib/tBA.cpp

commit cc0f19bd82290f06c03be9365efc5348c261e5ed
Author: lijewski <lijewski>
Date:   Sat Oct 8 02:01:05 2005 +0000

    *** empty log message ***

Src/C_BaseLib/test/tBA.cpp
Tests/C_BaseLib/tBA.cpp

commit 0e54be858f9ff3473ea3770850f9e5837779f46a
Author: lijewski <lijewski>
Date:   Sat Oct 8 01:54:46 2005 +0000

    added GetBndryCells()

Src/C_BaseLib/test/tBA.cpp
Tests/C_BaseLib/tBA.cpp

commit eec880d6770d232809c7f430cbc056ac2af83538
Author: lijewski <lijewski>
Date:   Sat Oct 8 01:53:05 2005 +0000

    used by tBA.cpp

Src/C_BaseLib/test/ba.213
Src/C_BaseLib/test/ba.5034
Src/C_BaseLib/test/ba.60
Tests/C_BaseLib/ba.213
Tests/C_BaseLib/ba.5034
Tests/C_BaseLib/ba.60

commit 4e1a11abe4e4cd9b1e0734da49058bcce6fc4366
Author: lijewski <lijewski>
Date:   Fri Oct 7 21:50:29 2005 +0000

    *** empty log message ***

Src/C_BaseLib/BoxArray.cpp

commit 59b8251dbbeb7c67c5bb7ee8c46c444842dbfb6f
Author: car <car>
Date:   Fri Oct 7 17:02:00 2005 +0000

    profiler

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/Geometry.cpp

commit da377106a14aaf99ef88108e9c768e4cbaf7c0f7
Author: lijewski <lijewski>
Date:   Fri Oct 7 17:01:13 2005 +0000

    now use intersections() stuff in one AddBox()

Src/C_BaseLib/FabArray.H

commit c81dd3e50e2cf3a540968bc5c604d183200940ac
Author: lijewski <lijewski>
Date:   Thu Oct 6 17:59:26 2005 +0000

    added/fixed NEEDS_FLUSH_F

Tools/C_mk/Make.AIX
Tools/C_mk/Make.defs

commit ac425c72f696f06c945732ac9047299dd33f4d97
Author: lijewski <lijewski>
Date:   Thu Oct 6 17:26:16 2005 +0000

    now use intersections() in CrseInit(Fab)

Src/C_AMRLib/FluxRegister.cpp

commit 0b9f5a3b977750b3b6b7f800f7b98c0ab82959f3
Author: car <car>
Date:   Wed Oct 5 22:45:56 2005 +0000

    timers

Src/C_AMRLib/FluxRegister.cpp

commit e9f3a4cceea9ecf8042f4af067567eafe949c725
Author: lijewski <lijewski>
Date:   Wed Oct 5 21:44:12 2005 +0000

    use intersections() in FillBoundary

Src/C_BaseLib/MultiFab.cpp

commit 279cd8c63db3d5e1fe690c82313ed57d3bcbc0c6
Author: lijewski <lijewski>
Date:   Wed Oct 5 21:22:14 2005 +0000

    use intersections() in copy()

Src/C_BaseLib/FabArray.H

commit 7ff28aad9ebfbb1cba47cd3e858d68c8f7342a0a
Author: car <car>
Date:   Wed Oct 5 20:28:48 2005 +0000

    pathscale wrong about shared(filter)

Src/F_BaseLib/multifab.f90

commit 2430a52dfd06acdac91c428fa715fed6135fdb95
Author: car <car>
Date:   Wed Oct 5 20:25:05 2005 +0000

    shared fcns?

Src/F_BaseLib/multifab.f90

commit e56a908a190c20dd97c24a87665f8f9b9ee82975
Author: car <car>
Date:   Wed Oct 5 19:53:03 2005 +0000

    *** empty log message ***

Src/F_BaseLib/layout.f90
Src/F_BaseLib/test/t_bx.f90
Tests/F_BaseLib/t_bx.f90

commit e17fc19de6b8fe50d6e119bd8d6e679d506c31c9
Author: lijewski <lijewski>
Date:   Wed Oct 5 19:25:04 2005 +0000

    added intersections()

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 9c2e55d46d2628d5cd0b4b204bec2bbd879e1a01
Author: lijewski <lijewski>
Date:   Wed Oct 5 19:12:59 2005 +0000

    *** empty log message ***

Src/C_BaseLib/test/tBA.cpp
Tests/C_BaseLib/tBA.cpp

commit 750ced4a0c64a3a1af4d69276d09ac81ecf74f7b
Author: car <car>
Date:   Wed Oct 5 17:06:36 2005 +0000

    *** empty log message ***

Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/t_bx.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/t_bx.f90

commit d3fe79fec3d014fdd2136e2321860e631f512c2e
Author: car <car>
Date:   Tue Oct 4 23:01:36 2005 +0000

    *** empty log message ***

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/box.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/test/t_bx.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/stencil.f90
Tests/F_BaseLib/t_bx.f90
Tools/F_mk/GMakedefs.mak

commit c1de8b27e9bcaa4ea62c3f08edc3d05d40a93f3e
Author: lijewski <lijewski>
Date:   Tue Oct 4 17:33:05 2005 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit fa86a37b87475f88e9c8456a8ce06392c6e8cac9
Author: lijewski <lijewski>
Date:   Fri Sep 30 19:26:42 2005 +0000

    *** empty log message ***

Src/C_BaseLib/bl_flush.f

commit 5f7933817e301a4ed439850c10480c6d1c48af1c
Author: lijewski <lijewski>
Date:   Fri Sep 30 17:41:56 2005 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.cpp

commit 1a0e860a9ccceabb97cdd3de2884fe4e30467952
Author: lijewski <lijewski>
Date:   Fri Sep 30 17:41:39 2005 +0000

    add flush(6)

Src/C_BaseLib/BLBoxLib_F.f

commit afd6d42ed49038a490be04a69e1eb86d4e95c400
Author: lijewski <lijewski>
Date:   Fri Sep 30 17:07:58 2005 +0000

    add FORTRAN to bl_ output strings

Src/C_BaseLib/BoxLib.cpp

commit 636871be43b1b921f989478eed99605dabab4e91
Author: car <car>
Date:   Fri Sep 30 16:50:20 2005 +0000

    cerr message on abort

Src/C_AMRLib/StateData.cpp

commit 21c5201cc72007853d8bb194f6de554f0e7398e3
Author: car <car>
Date:   Fri Sep 30 16:47:39 2005 +0000

    cout --> cerr

Src/C_AMRLib/StationData.cpp

commit 6ced8cdca80100d0c691d1bf661801024f4db9f2
Author: car <car>
Date:   Thu Sep 29 15:56:25 2005 +0000

    slight time improvement for boundaries in 3d only at this time

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 307ea48916febf658154ac80ce4e0aed5f44f542
Author: car <car>
Date:   Thu Sep 29 15:55:17 2005 +0000

    timer

Src/LinearSolvers/F_MG/stencil.f90

commit 01dd546c5f3abae1b6249734bfd12e7eaaba6447
Author: car <car>
Date:   Thu Sep 29 15:53:54 2005 +0000

    *** empty log message ***

Src/F_BaseLib/box.f90
Src/F_BaseLib/test/t_bx.f90
Src/LinearSolvers/F_MG/mg.f90
Tests/F_BaseLib/t_bx.f90

commit e4fb6e891c92c9784b1ed120eed9494d2facd3b6
Author: car <car>
Date:   Wed Sep 28 20:59:07 2005 +0000

    *** empty log message ***

Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/box_util.f90
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_bx.f90
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_bx.f90

commit 0b4bf38f9b96346e189dd0ec625ccd9a7001ba60
Author: car <car>
Date:   Wed Sep 28 17:48:08 2005 +0000

    speed up of boxarray_boxarray_diff; for 5000 box case stencil_fill_cc is 3 x faster

Src/F_BaseLib/box.f90
Src/F_BaseLib/boxarray.f90

commit a903947b84e30eedc31f941a82ba850aeec8d320
Author: car <car>
Date:   Tue Sep 27 18:12:04 2005 +0000

    ba_coarsen

Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 851de70edb8c9ea514333b59fb17f903be422bf7
Author: car <car>
Date:   Tue Sep 27 16:42:11 2005 +0000

    gcc 4.0 support

Tools/C_mk/Make.defs

commit 76dd5a9968f3870d6877172f27fa6626010ac35c
Author: car <car>
Date:   Tue Sep 27 16:40:09 2005 +0000

    *** empty log message ***

Src/C_BaseLib/.cvsignore

commit 1be86432b097c9ad52757382f90fb99220585033
Author: lijewski <lijewski>
Date:   Fri Sep 23 22:46:07 2005 +0000

    added do_alltoallv stuff to copy()

Src/F_BaseLib/multifab.f90

commit 1bf0f3e246fcb2a4ed07e5f4cd4bb6d37a4ac752
Author: car <car>
Date:   Fri Sep 23 15:40:07 2005 +0000

    max min and count

Src/F_BaseLib/bl_prof.f90

commit cc72d11ab4983aff74f971ab81151d38d6ab05eb
Author: car <car>
Date:   Thu Sep 22 22:39:43 2005 +0000

    remove testing smoothers

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 09d5e0dfe2e2e0ae00e5b676955fcd3b2886b968
Author: lijewski <lijewski>
Date:   Thu Sep 22 22:23:40 2005 +0000

    optimized copyassoc_build()

Src/F_BaseLib/layout.f90

commit 2136c2a9ca7fb91667ba646334375bb59eb56fb4
Author: car <car>
Date:   Thu Sep 22 22:00:23 2005 +0000

    back off the fancy stuff

Src/LinearSolvers/F_MG/mg_smoother.f90

commit d02345a0a7c2dde3f6930ebb890c96fad1dcc621
Author: car <car>
Date:   Thu Sep 22 20:00:01 2005 +0000

    in serial, use cpu time

Src/F_BaseLib/bl_prof.f90

commit 5009ad68f6532e500cedbc2d24f121a582cb262d
Author: car <car>
Date:   Thu Sep 22 19:59:05 2005 +0000

    new smoother, doesn't seem faster

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 1384d2882f3206c1e89986587dd6a8233deccd0f
Author: car <car>
Date:   Wed Sep 21 23:01:13 2005 +0000

    if not parallel dont reprise numbers

Src/F_BaseLib/bl_prof.f90

commit a58216b88c48ff2b1266ddd17f7cef0238cb51f1
Author: car <car>
Date:   Wed Sep 21 20:11:28 2005 +0000

    *** empty log message ***

Src/F_BaseLib/bl_prof.f90

commit 3967e95c78e785772dc1365dd045c51909fdacbb
Author: car <car>
Date:   Wed Sep 21 19:52:13 2005 +0000

    finally fixed

Src/F_BaseLib/bl_prof.f90

commit f0950875138e98b2ab1cf0963932bbfa8ca188ce
Author: lijewski <lijewski>
Date:   Wed Sep 21 19:34:53 2005 +0000

    hueristic for chunksize

Src/F_BaseLib/layout.f90

commit 7ccaf9ae05cc9933d3735a9eea2aa7a5e63f2ee3
Author: car <car>
Date:   Wed Sep 21 19:25:54 2005 +0000

    better bl_prof

Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/test/t_bl_prof.f90
Tests/F_BaseLib/t_bl_prof.f90

commit 02aa4c03911162aed4a5d58b732264569903ecd5
Author: car <car>
Date:   Wed Sep 21 18:59:20 2005 +0000

    *** empty log message ***

Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_bl_prof.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_bl_prof.f90

commit d15f4eaf090d4ae1725ac6bf43d4e6886d4538c5
Author: lijewski <lijewski>
Date:   Wed Sep 21 17:47:50 2005 +0000

    merge two nested loops into one in boxassoc_build()

Src/F_BaseLib/layout.f90

commit d086141acb79ec1909a708bc89d541722b4c7d34
Author: car <car>
Date:   Wed Sep 21 16:22:13 2005 +0000

    no more do_atav

Src/F_BaseLib/multifab.f90

commit fc9aa3e1087600632d96e2b837949ba8ef340a16
Author: car <car>
Date:   Wed Sep 21 01:01:21 2005 +0000

    *** empty log message ***

Src/F_BaseLib/bl_prof.f90

commit 8cdceaf91abda411e2c7d77ab75b0f9fbe596801
Author: car <car>
Date:   Wed Sep 21 00:27:01 2005 +0000

    fix for reduction

Src/F_BaseLib/bl_prof.f90

commit c6b3fcc18fec0c51452baddbd37f1873809bf6f8
Author: lijewski <lijewski>
Date:   Tue Sep 20 22:42:34 2005 +0000

    got do_atav working

Src/F_BaseLib/multifab.f90
Src/F_BaseLib/parallel.f90

commit 6b94d16b16f7cb3364a87098d6cf68535ab7252c
Author: car <car>
Date:   Tue Sep 20 20:12:15 2005 +0000

    parallel_alltoall

Src/F_BaseLib/multifab.f90
Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit 8318ae5aa8cfe06c31934e475358b9d62c1d78a2
Author: car <car>
Date:   Tue Sep 20 17:22:56 2005 +0000

    *** empty log message ***

Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_bxasc.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_bxasc.f90
Tests/F_BaseLib/t_main.f90
Tools/F_mk/GMakedefs.mak

commit 166fa06b983a4fd84f95a75341a89a39abcd0560
Author: lijewski <lijewski>
Date:   Tue Sep 20 16:40:30 2005 +0000

    added timer around boxassoc_build

Src/F_BaseLib/layout.f90

commit 7a223e21b6cc1b15f47250e343a8ae1c051ccd10
Author: car <car>
Date:   Tue Sep 20 00:09:29 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 852b4fc3b949ac1a863f3cac1d2d794ad0f731c7
Author: car <car>
Date:   Tue Sep 20 00:09:04 2005 +0000

    cpy_d improves things

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/multifab.f90

commit 31b9ddd81492c0a55a704012647e01883950f93d
Author: almgren <almgren>
Date:   Mon Sep 19 20:51:01 2005 +0000

    Bug fix in ml_interface_stencil_3d.

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit d6440b62b4ee7776c182527270893ca41280948f
Author: car <car>
Date:   Mon Sep 19 20:46:33 2005 +0000

    norm profiling

Src/F_BaseLib/multifab.f90

commit e9ed9fc29b3be4fcc890f70063a0ec6a4b3a48cf
Author: car <car>
Date:   Mon Sep 19 19:50:24 2005 +0000

    summary stats

Src/F_BaseLib/bl_prof.f90

commit db444b8995f677d195d0436e61cf6f95aa06e376
Author: car <car>
Date:   Sun Sep 18 23:54:13 2005 +0000

    more profiling

Src/F_BaseLib/cluster.f90
Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 3c38238610c8dcec01c096b7cf9a44a7b32e056d
Author: car <car>
Date:   Sun Sep 18 21:53:11 2005 +0000

    profiling

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 2661700bc3def5c650fe399e2530124617c5d0dd
Author: car <car>
Date:   Sun Sep 18 21:52:59 2005 +0000

    profiler

Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/multifab.f90

commit 7f723798352e4112d10fa772bdea3c74f91b4ea5
Author: car <car>
Date:   Sun Sep 18 17:54:00 2005 +0000

    good first cut of bl_prof

Src/F_BaseLib/bl_prof.f90

commit 38a92ed6d5647edaed9fbadeb978806906064e1d
Author: car <car>
Date:   Sun Sep 18 00:21:14 2005 +0000

    *** empty log message ***

Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/test/GNUmakefile
Tests/F_BaseLib/GNUmakefile

commit 940c0d76dc7e593199b5749d24b795160c9260cb
Author: car <car>
Date:   Sat Sep 17 18:35:35 2005 +0000

    profiling being added

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/main.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/main.f90

commit 64d844faffba9f82669b871333fb9ad837dc3ca4
Author: car <car>
Date:   Sat Sep 17 13:58:41 2005 +0000

    tweak for reduce

Src/F_BaseLib/bl_timer.f90

commit ad65bb9dc4bf383dc5548c0b9072465f7239ba4e
Author: car <car>
Date:   Sat Sep 17 13:57:58 2005 +0000

    mg_tower_print

Src/LinearSolvers/F_MG/mg.f90

commit 602575526c1f2f90b624495aa8daa773637900fc
Author: almgren <almgren>
Date:   Fri Sep 16 19:26:41 2005 +0000

    Cleaner implementation that looks more like ml_interface_3d_divu in varden/hgproject.f90

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 327d1796ca3d8c85a6fe741ce79676841a0485f2
Author: lijewski <lijewski>
Date:   Mon Sep 12 16:14:05 2005 +0000

    turn off minimize comm costs stuff

Src/C_BaseLib/DistributionMapping.cpp

commit f7e08f6e3c22a5692552ed0c65ebdd5e088b7989
Author: car <car>
Date:   Mon Sep 12 14:12:19 2005 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit d015a5915fb97a2e3c36fc5369f22d6a31667db6
Author: car <car>
Date:   Fri Sep 9 20:35:16 2005 +0000

    tweaks for f90 and Intel 9

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit b2971a180b316bcca8c0201f74116f728ed0f9b4
Author: almgren <almgren>
Date:   Thu Sep 8 21:55:46 2005 +0000

    An attempt to make CG_solve and BiCG_solve not create huge answers
    when the problem is almost completely solved.

Src/LinearSolvers/F_MG/itsol.f90

commit c71de3937ce8a7b10db44f630020298205c62018
Author: car <car>
Date:   Thu Sep 8 19:35:22 2005 +0000

    pure is a stumbling block for PathScale, save for later

Src/F_BaseLib/ml_multifab.f90

commit 14d0dc9870af8d7c83ab55ad1c2ba34a2273025f
Author: jbb <jbb>
Date:   Wed Sep 7 21:13:00 2005 +0000

    Oops - typo in previous INTERP_2D.F

Src/C_AMRLib/INTERP_2D.F

commit 4fecdc3248f073462b304e2de42d79150381652c
Author: jbb <jbb>
Date:   Wed Sep 7 21:11:47 2005 +0000

    Fix in LINCC_INTERP (and set-up for it) so that the routine which sets alpha
    loops over all of the fine cells in each coarse grid cell, not just the
    ones to be interpolated.  This was needed because of a umac_periodic_bust
    because regions of different size were setting alpha differently.

Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/Interpolater.cpp

commit 6ea58b46d29cff83e8c7a051b723885c5c5f693e
Author: car <car>
Date:   Wed Sep 7 19:22:31 2005 +0000

    added marc's dsp generating code

Tools/C_mk/Make.rules

commit 5f34dcff25e9694419f5c3cda14c39f4269a3294
Author: car <car>
Date:   Wed Sep 7 19:01:45 2005 +0000

    Got Rid of Lib's added f90 dependencies

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 6e757187e953d7c74a3a25b8dd7d8a06643cda87
Author: car <car>
Date:   Wed Sep 7 17:27:36 2005 +0000

    we don't buid libraries anymore

Src/C_AMRLib/GNUmakefile
Src/C_BaseLib/GNUmakefile
Src/C_BoundaryLib/GNUmakefile
Src/LinearSolvers/C_TensorMG/GNUmakefile

commit 1f767380abc8bd387fd0c45c6b7f14d97db21c24
Author: car <car>
Date:   Wed Sep 7 17:02:14 2005 +0000

    *** empty log message ***

Tools/C_scripts/moddep.pl

commit cdc15096801e4ab26f2aa482bbf7514b6ebed656
Author: car <car>
Date:   Tue Sep 6 22:52:23 2005 +0000

    Intel9 support

Tools/F_mk/GMakedefs.mak

commit 4caade34e3a5748d9b7a0b3ab414b7d2641d20bc
Author: car <car>
Date:   Tue Sep 6 22:51:54 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 0f6ecb8b7553f78967e7ffc4d7d9dd5ea6d8d9b1
Author: car <car>
Date:   Tue Sep 6 22:06:27 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/FParallelMG.mak
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 63b214527df84716dbc094dce2523d8d0d05c141
Author: car <car>
Date:   Tue Sep 6 21:06:25 2005 +0000

    mg_cpp changes

Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_cpp_f.h
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 8bb5cf4660d2543c2eb2f653ef5aea848c232966
Author: almgren <almgren>
Date:   Thu Sep 1 21:35:00 2005 +0000

    Needed to make same index fixed in lin_cc_interp_3d as in lin_cc_interp_2d.

Src/F_BaseLib/interp.f90

commit 663283536d904a8a7e44e1962cf28a370fc27db4
Author: almgren <almgren>
Date:   Thu Sep 1 19:18:24 2005 +0000

    I believe this is the correct scaling for 3-d nodal.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 562960e255d9e279da20e02c96e0da0b1b8ba99e
Author: almgren <almgren>
Date:   Thu Sep 1 17:57:38 2005 +0000

    The ml_layout_build from a ml_boxarray was not correctly passing
    the problem domain to the layout...instead the problem domain was
    being defined as the bounding box at that level.  Now the problem
    domain from the ml_boxarray is passed through the layout_build call.

Src/F_BaseLib/ml_layout.f90

commit 4f902f1af638a4cd0dbdb9b40f3fcc8e0819039d
Author: car <car>
Date:   Tue Aug 30 20:34:07 2005 +0000

    dead code elimination

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/boxarray.f90

commit 674e3c4077f8be3132aee8ae6c7d4dcb25ae810d
Author: lijewski <lijewski>
Date:   Mon Aug 29 16:27:16 2005 +0000

    amr.restart=init -> call initialInit() not restart()

Src/C_AMRLib/Amr.cpp

commit 2297f164e0d163b99b765563fa9213b661725ef6
Author: car <car>
Date:   Mon Aug 29 15:07:11 2005 +0000

    more generics

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/box.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/fab.f90
Src/F_BaseLib/flux_reg.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/ml_boxarray.f90
Src/F_BaseLib/ml_layout.f90
Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/stencil.f90

commit 4a143096ea66a2c4b664e90b97eef230ea307317
Author: car <car>
Date:   Wed Aug 24 20:22:46 2005 +0000

    added cluster_2d.f90, temporarily

Src/F_BaseLib/GPackage.mak

commit d3fc959c01f50aff2187b996b8a93c2c15321813
Author: car <car>
Date:   Wed Aug 24 16:41:02 2005 +0000

    one more check for underflow

Src/LinearSolvers/F_MG/itsol.f90

commit 3c20ed3b7d93430aa92f5043c1e895941632f0bb
Author: car <car>
Date:   Tue Aug 23 19:02:29 2005 +0000

    better error control

Src/LinearSolvers/F_MG/itsol.f90

commit 21671775d9fbb51dc083961dcbd182f874af4b96
Author: car <car>
Date:   Tue Aug 23 18:18:32 2005 +0000

    hack to fix cg/bicg when r.a.r is zero

Src/LinearSolvers/F_MG/itsol.f90

commit 51ac7a25c9c3f549425ac899e8eb5481df0c2cce
Author: car <car>
Date:   Mon Aug 22 19:19:46 2005 +0000

    remove c++ wrapper from compilation

Src/LinearSolvers/F_MG/GPackage.mak

commit 675f36bd4c6f2c16a6ad0d364a129b34f7dac495
Author: car <car>
Date:   Mon Aug 22 19:19:16 2005 +0000

    some clean up of I/O

Src/F_BaseLib/box.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/flux_reg.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/ml_boxarray.f90
Src/F_BaseLib/multifab.f90

commit 6f1675893d93e794443ff7264ebb57e3593fddbe
Author: car <car>
Date:   Sun Aug 21 17:13:55 2005 +0000

    fleshing out more of the operations on types

Src/F_BaseLib/bl_error.f90
Src/F_BaseLib/bl_string.f90
Src/F_BaseLib/fab.f90
Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/multifab.f90

commit be004338be75ccdc689f5cc2004ee5bc8518c4e8
Author: car <car>
Date:   Sat Aug 20 19:40:27 2005 +0000

    more setvals

Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab.f90
Src/F_BaseLib/test/t_cls.f90
Tests/F_BaseLib/t_cls.f90

commit b991d22391ddf3ca2e150cab99228303069bc11f
Author: car <car>
Date:   Sat Aug 20 19:35:26 2005 +0000

    b1 and b2 might be shrunk in recursive call

Src/F_BaseLib/cluster.f90

commit 3fa4c88575e63ba68c294970ae0b5c236692cd24
Author: car <car>
Date:   Sat Aug 20 16:39:57 2005 +0000

    cluster should be debugged

Src/F_BaseLib/cluster.f90

commit aed40153c00235107f28e812bae7f0fa71679f3c
Author: almgren <almgren>
Date:   Sat Aug 20 05:27:28 2005 +0000

    2D version of cluster.f90 used by Ann until cluster.f90 is debugged.

Src/F_BaseLib/cluster_2d.f90

commit 80ead52287c1fd5c6fe42bd3180e1b5d798253bb
Author: car <car>
Date:   Fri Aug 19 23:08:32 2005 +0000

    tweaks for mpi

Tools/F_mk/GMakedefs.mak

commit da9293f3f48ef1b12b6fd81d3f75130343cb6817
Author: car <car>
Date:   Fri Aug 19 23:08:08 2005 +0000

    get_boxarray

Src/LinearSolvers/F_MG/mg.f90

commit 441b37079806a801f029cbde13d2f590f51cd08b
Author: car <car>
Date:   Fri Aug 19 23:07:49 2005 +0000

    *** empty log message ***

Src/F_BaseLib/box.f90
Src/F_BaseLib/cluster.f90
Src/F_BaseLib/test/t_cls.f90
Tests/F_BaseLib/t_cls.f90

commit 727dd9f170dc113f7d7709b69901fe1d3c32fe6a
Author: car <car>
Date:   Wed Aug 17 13:29:56 2005 +0000

    *** empty log message ***

Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab.f90

commit ded8071d68edeb14824d4c82271dd1c8be998d9c
Author: car <car>
Date:   Sat Aug 13 15:47:54 2005 +0000

    missed some

Src/F_BaseLib/parallel.f90

commit e2525278ec281f9bb771237673083ba64da05b54
Author: car <car>
Date:   Fri Aug 12 17:28:32 2005 +0000

    intel is too permissive...

Src/F_BaseLib/multifab.f90
Src/F_BaseLib/parallel_stubs.f90

commit f7744131e9c6776f9e6d9812197c58f3f98e301e
Author: car <car>
Date:   Fri Aug 12 17:21:57 2005 +0000

    oops

Src/F_BaseLib/parallel_stubs.f90

commit 5bca3b1595c678e4399687c86264b81c37f33e7e
Author: car <car>
Date:   Fri Aug 12 16:50:19 2005 +0000

    more complex support

Src/F_BaseLib/multifab.f90
Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit c842ae1e030ae90965db2c28009a58a6555525a7
Author: car <car>
Date:   Thu Aug 11 23:43:10 2005 +0000

    fab, multifab complex for fmm

Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab.f90

commit 294d926eb04915a9776689383273bfd0921b4f1d
Author: car <car>
Date:   Wed Aug 3 20:25:32 2005 +0000

    oops

Src/F_BaseLib/ml_layout.f90

commit 19b4cdb37426d09388c412d27fbc5bd767f444c0
Author: car <car>
Date:   Wed Aug 3 14:43:43 2005 +0000

    extra vars

Src/F_BaseLib/multifab.f90
Src/F_BaseLib/test/t_cls.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/t_cls.f90
Tests/F_BaseLib/t_main.f90

commit fd5d9ed68aa63c644a7490855234dd1ebf6470a1
Author: car <car>
Date:   Wed Aug 3 14:43:09 2005 +0000

    ml_layout

Src/F_BaseLib/layout.f90
Src/F_BaseLib/ml_layout.f90

commit 6886dc402bef9c6a494accab28ca37e9e13a224d
Author: car <car>
Date:   Fri Jul 29 21:34:27 2005 +0000

    fix for 3d

Src/F_BaseLib/cluster.f90
Src/F_BaseLib/test/t_cls.f90
Tests/F_BaseLib/t_cls.f90

commit 35e65ce7b3db302effe6007e8de3ac89c4811162
Author: almgren <almgren>
Date:   Fri Jul 29 20:53:13 2005 +0000

    Make sure to set the boxarray%dim = 2 in the 2d case...

Src/F_BaseLib/cluster.f90

commit d350889ec96f75c9cb60515ea117a668f2ba4582
Author: car <car>
Date:   Fri Jul 29 19:13:19 2005 +0000

    mask out  ghostcells, more debugging

Src/F_BaseLib/cluster.f90
Src/F_BaseLib/test/t_cls.f90
Tests/F_BaseLib/t_cls.f90

commit e9d1aad29f8666fac989dd810708f1ee1a6613b5
Author: car <car>
Date:   Fri Jul 29 17:10:05 2005 +0000

    i think a fixed cluster

Src/F_BaseLib/cluster.f90
Src/F_BaseLib/multifab.f90
Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_cls.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_cls.f90
Tests/F_BaseLib/t_main.f90

commit d336db416c3477d91188881fb10d7b830b211b5f
Author: almgren <almgren>
Date:   Thu Jul 28 19:34:04 2005 +0000

    Dont need to test on (n>1) on the way back up because
    that code is only called for n = 2,...nlevs.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 446171e65a3329fd8de97dc981ef6c0b7e0881e6
Author: almgren <almgren>
Date:   Thu Jul 28 19:33:19 2005 +0000

    Make sure to use "mini_cycle" instead of mg_tower_cycle when
    relaxing at a fine AMR level so that the smoother and not the
    bottom solver will be called.

Src/LinearSolvers/F_MG/ml_cc.f90

commit cb2785ebf6550f5f66df0365d02f41ce11d494c4
Author: almgren <almgren>
Date:   Wed Jul 27 20:26:09 2005 +0000

    Index bug...

Src/F_BaseLib/cluster.f90

commit a99e323d08989f0565505a2ee03abbdd1837bf8d
Author: car <car>
Date:   Wed Jul 27 17:12:58 2005 +0000

    some fixes

Src/F_BaseLib/cluster.f90
Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit 6d993dd729aa513ae9df52c3d3edabf20badd799
Author: car <car>
Date:   Tue Jul 26 16:48:37 2005 +0000

    lets build boxarrays out of list_boxes

Src/F_BaseLib/boxarray.f90

commit 591a8a85854e9bddc38643022b86f929cad7bafe
Author: car <car>
Date:   Thu Jul 21 18:13:13 2005 +0000

    complex fabs

Src/F_BaseLib/fab.f90

commit afebb410edfaa9cbdd328aceeeab37d660e86ce9
Author: lijewski <lijewski>
Date:   Wed Jul 13 19:56:31 2005 +0000

    Some mods for Portland Group C++ compiler.
    I'm using PGI as a placeholder for the "appropriate" predefined compiler symbol.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/Thread.H

commit 78b2ffb892fdb054312f7d2f4a54c9ab358bace1
Author: car <car>
Date:   Mon Jul 4 23:12:22 2005 +0000

    *** empty log message ***

Src/F_BaseLib/bl_types.f90

commit 594dc949113d9db39dcec412471af0550ff7b4fa
Author: car <car>
Date:   Mon Jul 4 22:52:01 2005 +0000

    endian test

Src/F_BaseLib/bl_types.f90

commit da12b8212456b0ebc3794cd875959ccb03e487bc
Author: car <car>
Date:   Thu Jun 23 16:50:22 2005 +0000

    some multicomponent adjustments

Src/F_BaseLib/fab.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/multifab.f90

commit a38e65d09e62c5ac72cbfc74f782d4280beba5b2
Author: lijewski <lijewski>
Date:   Tue Jun 21 21:42:03 2005 +0000

    added Plot_Files_Output()

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit e2edc891584b9d72762f6492f4774562177936d8
Author: lijewski <lijewski>
Date:   Tue Jun 21 20:09:47 2005 +0000

    fixed the bug in the speed upgrades

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit a55347dbfdc89a37902d547a2043890cb5bc7f16
Author: car <car>
Date:   Sat Jun 18 19:04:36 2005 +0000

    *** empty log message ***

Src/F_BaseLib/test/t_boxlib.dsp
Src/F_BaseLib/test/t_boxlib.dsw
Tests/F_BaseLib/t_boxlib.dsp
Tests/F_BaseLib/t_boxlib.dsw

commit 61f6d42cf91247584884089a76de5cc0b20dd063
Author: car <car>
Date:   Fri Jun 17 17:08:31 2005 +0000

    OMP fix

Src/LinearSolvers/F_MG/stencil.f90

commit 55214aac725effa2ab4fe1a5df16e4e8e8abc623
Author: car <car>
Date:   Fri Jun 17 02:03:28 2005 +0000

    new mech for intrisics

Tools/F_mk/GMakedefs.mak

commit 246f57fdac26bcdfc8a877f46d112a39ce6a4875
Author: car <car>
Date:   Thu Jun 16 22:53:14 2005 +0000

    box_projectable

Src/F_BaseLib/box.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/ppm_util.f90

commit bb5ed4a3c51abed6647fba9c9105de1ecb44a3bb
Author: car <car>
Date:   Tue Jun 14 20:00:24 2005 +0000

    support for Intel 9

Tools/F_mk/GMakedefs.mak

commit 6434c20fdd3cb909e396c0640e32a1948590515c
Author: car <car>
Date:   Tue Jun 14 16:30:11 2005 +0000

    not need external on iagc

Src/F_BaseLib/f2kcli.f90

commit 7575538fb78aebe918ebfce661d41f8d6d4eb29f
Author: car <car>
Date:   Tue Jun 14 16:23:08 2005 +0000

    Lahey checking

Tools/C_mk/Make.Linux

commit 4b37269a3e4754a13f34773e1b394078a1bfdf68
Author: car <car>
Date:   Tue Jun 14 16:22:54 2005 +0000

    icpc/ifort version 9

Tools/C_mk/Make.defs

commit b19aeb4c36a85be853817571cc91f6725e8c7ef1
Author: car <car>
Date:   Fri Jun 10 16:56:28 2005 +0000

    reversion to April 1, 2005

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real2d.f
Src/LinearSolvers/C_NodalMG/amr_real3d.f
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 49dfd40399b7241b5200a2914e5b567137ff2dd6
Author: lijewski <lijewski>
Date:   Thu Jun 9 17:27:56 2005 +0000

    some simplification

Src/F_BaseLib/cluster.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/sparse_solve.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 0379f0a83e467e90e52fd3f3095dbd3771bc3bd9
Author: almgren <almgren>
Date:   Thu Jun 9 00:08:58 2005 +0000

    Fix to the problem of one-cell thick domains getting the boundary
    nodes incorrectly set to nodal.   Fix is in combination to fix
    to box_contains function...

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 14971bcda06e2384bd039183e0e1cdd6b144c933
Author: almgren <almgren>
Date:   Thu Jun 9 00:08:04 2005 +0000

    "Contains" now checks lo against lo and hi, and hi against lo and hi.

Src/F_BaseLib/box.f90

commit f25d2ad4d593ba8cbcce7aa65cb4e79d6b409985
Author: lijewski <lijewski>
Date:   Wed Jun 8 21:50:04 2005 +0000

    ml_nodal_restriction is now parallelized

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 7610d6792d8b173985afdbf6d2ce03bdd9dab927
Author: lijewski <lijewski>
Date:   Wed Jun 8 17:26:00 2005 +0000

    added filtering ability to copy routines

Src/F_BaseLib/multifab.f90

commit f619cf01a3166f11029c8db53abecd6bc91d0b36
Author: almgren <almgren>
Date:   Tue Jun 7 18:23:10 2005 +0000

    Change so that we only do interface updates if it is truly
    a crse-fine point, not a fine-fine point.

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 6bc7525af61a9a68bf0e5853bd40c8477bf714f3
Author: lijewski <lijewski>
Date:   Tue Jun 7 18:09:53 2005 +0000

    added nodal zero routines

Src/LinearSolvers/F_MG/mg_restriction.f90

commit 8ff13e753dffaa7adfd0c4a82cb1045fc72e7a89
Author: almgren <almgren>
Date:   Tue Jun 7 18:03:31 2005 +0000

    Formatting...

Src/LinearSolvers/F_MG/ml_nd.f90

commit f44ac78390dace21f28c62ddd80196230690c297
Author: almgren <almgren>
Date:   Tue Jun 7 16:33:03 2005 +0000

    Fix to how we zero the crse array before restriction.

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 159c4b7dfa432c74363bac3d2d8ab0d887102288
Author: car <car>
Date:   Mon Jun 6 18:17:43 2005 +0000

    lnc

Src/F_BaseLib/multifab.f90

commit 6499825a90708e5a117d291da1fdf15cb766ca3d
Author: almgren <almgren>
Date:   Mon Jun 6 16:37:06 2005 +0000

    Put the same changes in lin_cc_interp_3d as in lin_cc_interp_2d to
    get indexing thru crse and fine correct.

Src/F_BaseLib/interp.f90

commit b5d1d90f5f3049556ec21c983182445461357ee9
Author: almgren <almgren>
Date:   Sun Jun 5 21:06:58 2005 +0000

    Fixed lin_cc_interp_2d...NOTE: 3d needs to be fixed as well!!!

Src/F_BaseLib/interp.f90

commit 96bd11c1c44e6950c3620436a5b1eded2b6094d9
Author: lijewski <lijewski>
Date:   Fri Jun 3 22:49:05 2005 +0000

    added error checks in dataptr routines

Src/F_BaseLib/fab.f90

commit a4a386a264dcf098c9938d638dca27f39ede0f64
Author: lijewski <lijewski>
Date:   Fri Jun 3 21:35:02 2005 +0000

    Got rid of bunch of redundant code by calling more general routines when possible.
    All the norms now use "mask" consistently.
    The "mask" is now always considered to be a 1 compolent multifab; i.e. it
    represents a geometric mask even in the case when we're interested in the
    norm of multiple components of a multifab at one time.

Src/F_BaseLib/multifab.f90

commit b9630ae3b7e205c3b64bb25f8452a781bdd5cb6e
Author: lijewski <lijewski>
Date:   Fri Jun 3 19:39:49 2005 +0000

    parallelized ml_edge_restriction

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 7fb5e29716bd2dd554fe6bd5ad9a2293e035bd73
Author: lijewski <lijewski>
Date:   Fri Jun 3 19:16:51 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 172423f185724b88b0c7546304d297e38ce71164
Author: lijewski <lijewski>
Date:   Fri Jun 3 17:45:16 2005 +0000

    moved destroy code to after final uses

Src/LinearSolvers/F_MG/ml_cc.f90

commit b13c65472416f9062965df2bfedf04c8e1a174c6
Author: almgren <almgren>
Date:   Fri Jun 3 05:16:26 2005 +0000

    Pass "n" thru calling sequence instead of looping
    over.   Note that multifabs coming in are now edge-based.

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 0c5bbe17525aa6905bd758059d8c1050dba61e15
Author: lijewski <lijewski>
Date:   Thu Jun 2 20:35:36 2005 +0000

    a little cleanup

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 3da5758eb31967e6068331e03d28e415d1253422
Author: lijewski <lijewski>
Date:   Thu Jun 2 16:38:39 2005 +0000

    out -> inout in a couple places

Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_restriction.f90

commit 6a7a2ca8064a3a78a7677c7d840ba8cdc9a69fb7
Author: vince <vince>
Date:   Thu Jun 2 00:28:08 2005 +0000

    added support for jvn.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 5d811c4153f48c78f8fdc252c14ee91ef71705c6
Author: lijewski <lijewski>
Date:   Wed Jun 1 22:28:52 2005 +0000

    some cleanup

Src/LinearSolvers/F_MG/mg_restriction.f90

commit e5a63febfed9a878aee398c97ed841ecde034db9
Author: car <car>
Date:   Wed Jun 1 21:40:35 2005 +0000

    should read ml_boxarray with != rr properly

Src/F_BaseLib/box_util.f90

commit 7185005aa5a40db46516c990006614c6ff81c480
Author: almgren <almgren>
Date:   Wed Jun 1 21:08:56 2005 +0000

    Fix problem in defn of jbot vs jtop.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 7c23a3aebc366ea719d62566c956f463d1d17806
Author: lijewski <lijewski>
Date:   Wed Jun 1 20:14:38 2005 +0000

    parallelized ml_prolongation

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 8fa1f54aa452a1d63567056313c0ea749b0caeeb
Author: lijewski <lijewski>
Date:   Wed Jun 1 16:44:16 2005 +0000

    messed up something in ml_nodal_restricton

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 1c57233314a403be954765693538c3c1a2413385
Author: lijewski <lijewski>
Date:   Tue May 31 21:38:19 2005 +0000

    some cleanup

Src/LinearSolvers/F_MG/mg_restriction.f90

commit cc6242d557558efe269ccd2b83ca9acb0a398081
Author: lijewski <lijewski>
Date:   Tue May 31 21:38:04 2005 +0000

    parallelized cell-centered restriction

Src/LinearSolvers/F_MG/ml_restriction.f90

commit fea37d04355998fcfd1329156bb1de3c4c90cbc5
Author: marc <marc>
Date:   Tue May 31 18:11:22 2005 +0000

    make sure filpatches called using amrlevels in hierarchy--required subtle change to regrid function

Src/C_AMRLib/Amr.cpp

commit 38ab5f4d72b380739efd31acef710eccfad0a90e
Author: car <car>
Date:   Tue May 31 17:21:44 2005 +0000

    more ignorance

Tests/LinearSolvers/F_MG/.cvsignore

commit 7b985ab9c65bc946ca97607fc2c8d343d315ea0f
Author: car <car>
Date:   Fri May 27 21:59:23 2005 +0000

    strengthen optimization on non amd systems

Tools/F_mk/GMakedefs.mak

commit 907f11ae1aceb42e69b17bb9db82dfc392acbd11
Author: car <car>
Date:   Fri May 27 21:58:11 2005 +0000

    BC_UNDEF

Src/F_BaseLib/bc.f90

commit 344b56f08bfdfecf2497332b3178480e53fc2a90
Author: car <car>
Date:   Fri May 27 21:57:21 2005 +0000

    memory leak fix; pointer->allocatable

Src/LinearSolvers/F_MG/ml_nd.f90

commit edd7aef60785ee0910652db73de73f42d95234fa
Author: lijewski <lijewski>
Date:   Thu May 26 20:48:13 2005 +0000

    Added WhereToStart().
    Now do "fairer" job laying out multifabs across CPUs.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit a864af5f042006ac575bb7b7bee4855f43715d82
Author: car <car>
Date:   Thu May 26 16:42:02 2005 +0000

    memory leak

Src/LinearSolvers/F_MG/ml_cc.f90

commit ddc90495568afb6beacb2e09bb4add9b1b7f97fa
Author: almgren <almgren>
Date:   Wed May 25 21:10:38 2005 +0000

    Was bug in how we were computing ML residual within the iteration loop.
    Now appears to work on 2-level and 3-level problems.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 67a291c665e8c452a305d2f64803ad34ae9ad83e
Author: colella <colella>
Date:   Wed May 25 18:29:23 2005 +0000

    Comment out pretty_print.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit ae72f554f59ed39bd35c66958b761e614b7d67d4
Author: lijewski <lijewski>
Date:   Tue May 24 22:31:22 2005 +0000

    added the_copyassoc_head

Src/F_BaseLib/layout.f90

commit 13af223ac8e49c57348c1eaae1447864ddebb787
Author: lijewski <lijewski>
Date:   Mon May 23 21:21:44 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_restriction.f90

commit a079cf144404e0f743ebdfa2743f7ee8ac949d19
Author: lijewski <lijewski>
Date:   Mon May 23 20:08:28 2005 +0000

    ml_interp_bcs now calls ml_interp_bcs_c

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 263391b2da05d7ef7a6396cd64608f8a2922ff40
Author: lijewski <lijewski>
Date:   Mon May 23 19:43:11 2005 +0000

    ml_cc_restriction now call ml_cc_restriction_c

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 0eae8af7d0f9f925360f043f9231c0ff91dd3d47
Author: lijewski <lijewski>
Date:   Fri May 20 21:30:11 2005 +0000

    removed local_boxes stuff

Src/F_BaseLib/layout.f90

commit 5f9faac679482c5d8176e85161d2f449c74756a0
Author: lijewski <lijewski>
Date:   Fri May 20 20:42:29 2005 +0000

    added multifab_internal_sync_c

Src/F_BaseLib/multifab.f90

commit 4146c3ef64f3455fc4cb48979c22e586f75f7295
Author: lijewski <lijewski>
Date:   Fri May 20 18:22:09 2005 +0000

    more copyassoc stuff

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab.f90

commit 141259c6fa88d9614a90517023e4667ed6c9a552
Author: lijewski <lijewski>
Date:   Wed May 18 21:57:16 2005 +0000

    some work toward a fancy parallel copy

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab.f90

commit a12746270ae70bbe18602b9afeb64d5021d9711e
Author: car <car>
Date:   Wed May 18 21:16:28 2005 +0000

    try to get the alpha term right

Src/LinearSolvers/F_MG/stencil.f90

commit 3302494e1ef3a7b972f9d1de97ab4805ebf96bd7
Author: lijewski <lijewski>
Date:   Tue May 17 22:03:17 2005 +0000

    copy fixes

Src/F_BaseLib/multifab.f90

commit 9ab1a0b838157be8023a767d7e6b35e9bd1d62ab
Author: lijewski <lijewski>
Date:   Tue May 17 22:02:53 2005 +0000

    added component to debug output

Src/F_BaseLib/fab.f90

commit 1c6fd110369ee3c5b66e1b11acb0a5ca5a2f30da
Author: car <car>
Date:   Tue May 17 20:46:41 2005 +0000

    false alarm

Src/F_BaseLib/fab.f90

commit 8edc145fbfd0412863422a5920ab888db81e12ec
Author: car <car>
Date:   Tue May 17 20:19:05 2005 +0000

    make sure multicomponet fabs print correctly in 1 and 2 dimensions

Src/F_BaseLib/fab.f90

commit 286cd32dc7853d1323fd28f0d4cd7535131bf0c6
Author: car <car>
Date:   Sun May 15 21:11:52 2005 +0000

    more multicomponent fixes

Src/F_BaseLib/bl_constants.f90
Src/F_BaseLib/multifab.f90

commit 5ad874f5cc5662ba176e7063ce2d7ea623528be6
Author: car <car>
Date:   Tue May 10 22:11:41 2005 +0000

    print generic for ml_multifab

Src/F_BaseLib/ml_multifab.f90

commit fa7a599cf235f2bb15d48af05ded472bc89d219a
Author: car <car>
Date:   Tue May 10 22:11:11 2005 +0000

    simple abec code

Src/LinearSolvers/F_MG/stencil.f90

commit f621c287e2a5017435e8cbfabaf9b7f628e961b9
Author: car <car>
Date:   Tue May 10 13:51:28 2005 +0000

    single component applicators

Src/LinearSolvers/F_MG/stencil.f90

commit c0724c04583a8da35f4b443781b8589abdbb591b
Author: car <car>
Date:   Fri May 6 19:59:11 2005 +0000

    select bottom level

Src/LinearSolvers/F_MG/mg.f90

commit 795823b6f32d23d5d4be46fcf9323c9c5513e2d6
Author: car <car>
Date:   Thu May 5 22:32:58 2005 +0000

    more suger

Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/multifab.f90

commit ba899d7a27f361cf8e7983f97e8d7027c0557ca4
Author: car <car>
Date:   Thu May 5 22:32:47 2005 +0000

    more options to output plotfiles

Src/F_BaseLib/fabio.f90

commit fbd00787623906a173a813218675ad31b3b2fc35
Author: car <car>
Date:   Thu May 5 22:32:14 2005 +0000

    not needed modules

Src/LinearSolvers/F_MG/ml_cc.f90

commit c3d3b2a725310e74461e8b765e94491e69ee30e4
Author: car <car>
Date:   Thu May 5 20:29:11 2005 +0000

    PROF only uses BLMpi.cpp

Src/C_BaseLib/Make.package

commit 69f311ac336d7314bce09a69676bbc2bd64f03d6
Author: car <car>
Date:   Thu May 5 04:35:01 2005 +0000

    more suger

Src/F_BaseLib/ml_multifab.f90

commit b57e5463de579788e12cc0ba2eb377889cd6c848
Author: car <car>
Date:   Wed May 4 21:06:15 2005 +0000

    more helper fcns

Src/F_BaseLib/bl_constants.f90
Src/F_BaseLib/ml_layout.f90
Src/F_BaseLib/ml_multifab.f90

commit 3d3c9432b252047b9f3657567d6633bd389e6247
Author: lijewski <lijewski>
Date:   Tue May 3 17:46:01 2005 +0000

    oops

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 4ed8ed56dea30987586d112372d3f94891cb7a14
Author: car <car>
Date:   Fri Apr 29 20:34:15 2005 +0000

    layout lev 1 owns finer level layouts

Src/F_BaseLib/ml_layout.f90

commit 08181a5a72175e1d78c4317090c37ecddcb9b139
Author: lijewski <lijewski>
Date:   Thu Apr 28 23:09:13 2005 +0000

    memory cleanup

Src/F_BaseLib/ml_layout.f90

commit 68c10b047da7d09ddb48976a65ca0e2521c495d5
Author: lijewski <lijewski>
Date:   Thu Apr 28 22:15:41 2005 +0000

    memory cleanup

Src/LinearSolvers/F_MG/ml_nd.f90

commit 0afaf239298b7884f52bd9c46cb1dc859c898c0f
Author: lijewski <lijewski>
Date:   Thu Apr 28 18:29:49 2005 +0000

    memory cleanup

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/ml_layout.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 4fa42c1336d1a296f0d781a10c765dfe0c35ac02
Author: almgren <almgren>
Date:   Thu Apr 28 16:54:25 2005 +0000

    ml_layout_build can now take periodic flag pmask...(passes flag through into
    layout_build)

Src/F_BaseLib/ml_layout.f90

commit d4867a5a0d53cd222c8cc696b571d47dc0295a69
Author: almgren <almgren>
Date:   Thu Apr 28 16:54:04 2005 +0000

    Need this change to make nodal work.

Src/F_BaseLib/fabio.f90

commit 28f292c8e0cf7f55603c341ce292b961c1014efd
Author: lijewski <lijewski>
Date:   Thu Apr 28 16:31:12 2005 +0000

    simplification of buildFPB()

Src/C_BaseLib/Geometry.cpp

commit 0fcc79b5b99e7a973fd5fb9aba5f31dae4730115
Author: lijewski <lijewski>
Date:   Mon Apr 25 18:25:56 2005 +0000

    nodal fix to set_bc_nodal

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 0f18844645e749193efdc40a8d2e0583afacd30c
Author: car <car>
Date:   Sat Apr 23 19:49:49 2005 +0000

    sparse data distribution speed up

Src/C_BaseLib/FabArray.H

commit ddb0250e90a70570f07eec01d58d3917de1c9ff2
Author: lijewski <lijewski>
Date:   Fri Apr 22 20:59:22 2005 +0000

    mods to speedup interface_residual

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.H

commit f0fcce6d1f0596d7d6952b14b236ef3d62c47b82
Author: car <car>
Date:   Fri Apr 22 17:24:16 2005 +0000

    added profiler

Src/C_AMRLib/AmrLevel.cpp

commit 405e170886c9bb1e3b56e862376f761c09452626
Author: lijewski <lijewski>
Date:   Fri Apr 22 02:35:30 2005 +0000

    Array<int> -> Array<char> for did_work storage

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 178211150aa8b4e8a9ad299bd821e4d7699c6c69
Author: lijewski <lijewski>
Date:   Fri Apr 22 02:01:10 2005 +0000

    speedup for fill_internal_borders

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp

commit f6a058926d3d8e0b93f1c1996217f3f34defaf3c
Author: lijewski <lijewski>
Date:   Thu Apr 21 19:53:49 2005 +0000

    speedups to fill_interface()

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 0e9bfeff592e2e0ecdab0f5d4dc2c09c8d9be0e7
Author: almgren <almgren>
Date:   Thu Apr 21 17:08:48 2005 +0000

    Use ml_layout mla instead of array of layouts la_tower(:)

Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 7a0ba01a53f5dbad00148f6da21b73c5247a878d
Author: almgren <almgren>
Date:   Thu Apr 21 16:22:21 2005 +0000

    Add option to fix boundary conditions on solution so we can correctly
    compute the gradient afterwards.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 93225d4a6fb20a9e2b8c8af4808d808c8f3f7b12
Author: almgren <almgren>
Date:   Thu Apr 21 15:12:44 2005 +0000

    New ml_cc routine (called by cc_multi), and modifications to ml_cc and ml_nd
    so that we don't test on the full multilevel residual unless the fine residual
    is already converged.

Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90

commit 16b0fbcd77109775f5e59938550a32450a7d2f1e
Author: almgren <almgren>
Date:   Thu Apr 21 14:45:57 2005 +0000

    Add restriction of rh in beginning, and better convergence criteria.

Src/LinearSolvers/F_MG/ml_nd.f90

commit b55a9127deb7ff8a53687e44c3dd0f44bbbaa439
Author: almgren <almgren>
Date:   Wed Apr 20 18:04:41 2005 +0000

    Fixed bug in stencil_flux_2d for lo-j sides.

Src/LinearSolvers/F_MG/stencil.f90

commit e7175a3f20b83e28cd175c9cb47a4c9643928a4c
Author: car <car>
Date:   Tue Apr 19 21:04:20 2005 +0000

    can no turn of all i/o;
    improves grid_places for large numbers of grids

Src/C_AMRLib/Amr.cpp

commit c8a336bfde9484d42f57b5366563b457083a7aa0
Author: car <car>
Date:   Tue Apr 19 20:42:24 2005 +0000

    fill_patch::restrict_level: seems to speed up cases with > 1000 grids

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real2d.f
Src/LinearSolvers/C_NodalMG/amr_real3d.f
Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 1adaf20986559744078121fcd9d267ea53743074
Author: car <car>
Date:   Tue Apr 19 03:32:37 2005 +0000

    hate assert

Src/F_BaseLib/bl_error.f90
Src/F_BaseLib/boxarray.f90

commit 49e954308372a4363b53f2aa13aaabb3bb438a00
Author: lijewski <lijewski>
Date:   Mon Apr 18 19:21:21 2005 +0000

    fix to box_periodic_shift when nodal.
    ----------------------------------------------------------------------
    removed automatically CVS: CVS: Committing in .
    ----------------------------------------------------------------------

Src/F_BaseLib/box.f90

commit 015caad98ec7596658daa483013f097b9d59fae2
Author: lijewski <lijewski>
Date:   Mon Apr 18 18:26:39 2005 +0000

    Checked in some mask code for dealing with periodicity; not fully working.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 635b6487f4cafe262c8106c6d140791395dd08d4
Author: car <car>
Date:   Mon Apr 18 16:25:57 2005 +0000

    ml_nd

Src/LinearSolvers/F_MG/GPackage.mak

commit a6569b66e35c9e8c9c9474d5a451e7a9caa8ce6f
Author: almgren <almgren>
Date:   Mon Apr 18 00:51:20 2005 +0000

    Use bl_constants_module instead of redefining constants.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 6ba07d0b1e01b912095c8600bca51fd3ecb93d7e
Author: almgren <almgren>
Date:   Fri Apr 15 21:05:54 2005 +0000

    This contains the multilevel loop that does nodal multilevel multigrid solves.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 7588056419eba4ec7d841043c4cc18e58b4e80df
Author: almgren <almgren>
Date:   Fri Apr 15 17:06:14 2005 +0000

    Intersect box with the problem domain in stencil_set_bc so that
    Neumann boundary conditions are not over-written by coarse-fine loop.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit bbddb66edc84f049fd7de2c848f129f35391070b
Author: lijewski <lijewski>
Date:   Thu Apr 14 23:22:36 2005 +0000

    fixed typo

Src/F_BaseLib/multifab.f90

commit 28199bb57d864622093fc7f2c0ba7f6914a24599
Author: lijewski <lijewski>
Date:   Thu Apr 14 21:50:11 2005 +0000

    Now pretty print nodal masks.

Src/LinearSolvers/F_MG/stencil.f90

commit 48366dce8b6fb056600e6a8b91248bdf57b40f90
Author: lijewski <lijewski>
Date:   Thu Apr 14 18:22:17 2005 +0000

    Just a little rearrangement; no substantive changes.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 8107e89514a9965accbce6b0daa63cce76aedcd2
Author: almgren <almgren>
Date:   Thu Apr 14 17:49:27 2005 +0000

    Make the same change for 1-d and 3-d.

Src/LinearSolvers/F_MG/sparse_solve.f90

commit de06ac8d6c7799a1e2172b11a8ec4be4c74d78a1
Author: almgren <almgren>
Date:   Thu Apr 14 17:41:38 2005 +0000

    Changed order of operations in filling/copying index array for sparse solver
    on more than one grid.

Src/LinearSolvers/F_MG/sparse_solve.f90

commit 80dce12eeee75a76966359a78c1dd77bbb79fa85
Author: almgren <almgren>
Date:   Wed Apr 13 20:12:05 2005 +0000

    Fixed a bug in the s_simple_2d_nodal (and probably the 1d and 3d as well)
    routine - the part which assigned BC_DIR to coarse-fine boundary nodes.
    New code is the same for all dimensions and more like the cc code.
    Tested on gr.2_19grids.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 35b1e4d39a831c0c8ff0bdf33681a7a7f4f33ee6
Author: lijewski <lijewski>
Date:   Wed Apr 13 15:59:26 2005 +0000

    fixed some typos

Src/F_BaseLib/parallel.f90

commit 46550e99b9bfbb9a7a8fb8cee8fe6050828b472e
Author: car <car>
Date:   Tue Apr 12 23:25:27 2005 +0000

    fix for vector bcast

Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit 57881f5c121f214f906dc57bd4d55512cc3bc047
Author: car <car>
Date:   Tue Apr 12 23:21:01 2005 +0000

    bcast error condition

Src/LinearSolvers/F_MG/mg.f90

commit cbb3b8292015f02497737e2882e64725f5ee7e50
Author: car <car>
Date:   Tue Apr 12 23:20:23 2005 +0000

    broadcast of scalars

Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90

commit b905169db92eda6f6864871dcd3e8088136243c8
Author: lijewski <lijewski>
Date:   Tue Apr 12 20:30:15 2005 +0000

    Added call destroy(mm_grown)

Src/LinearSolvers/F_MG/sparse_solve.f90

commit e95f6cc7f727a11e54ea157573a087e51930304d
Author: lijewski <lijewski>
Date:   Tue Apr 12 18:22:29 2005 +0000

    Some modest name changes due to adding support for single-level nodal solves.

Tests/LinearSolvers/F_MG/makefile

commit b8a69bd3c3fd9eb60d89931680b6f6867ae2b8dd
Author: almgren <almgren>
Date:   Tue Apr 12 17:00:45 2005 +0000

    New interface routines which take fine mask as well as coarse.

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 1e5185fe85856914fc84759624b5e8f997775a78
Author: lijewski <lijewski>
Date:   Mon Apr 11 17:57:26 2005 +0000

    Fixed bug in copy() routines.

Src/F_BaseLib/multifab.f90

commit e23597c07613182d77e47a4742edb05b081e6029
Author: car <car>
Date:   Mon Apr 11 17:33:07 2005 +0000

    parallel

Src/LinearSolvers/F_MG/sparse_solve.f90

commit 1f88724f37d2a029a27f04428820f44b0d9f65ea
Author: car <car>
Date:   Mon Apr 11 16:31:47 2005 +0000

    reclaim memory

Src/LinearSolvers/F_MG/mg.f90

commit f8bd6f262e875b429eebc1c6edd965ede7f86853
Author: car <car>
Date:   Sun Apr 10 00:50:14 2005 +0000

    fix up that bottom solver...

Src/LinearSolvers/F_MG/mg.f90

commit 56dca9e33d2de480fb7a8ff19bc7987be33983f0
Author: lijewski <lijewski>
Date:   Thu Apr 7 22:51:31 2005 +0000

    -O4 buggy on AIX

Tools/F_mk/GMakedefs.mak

commit c9a7859b4c03ce22d12f20dc79e4e380665eafb4
Author: lijewski <lijewski>
Date:   Wed Apr 6 16:58:42 2005 +0000

    Always do fill_boundary()s using asynchronous recv's.

Src/F_BaseLib/multifab.f90

commit f666bd184c96230be05c500a531f8b53724ac769
Author: car <car>
Date:   Tue Apr 5 16:54:47 2005 +0000

    change of calling sequence to stencil_fill_cc; pxa and pxb are the locations of the 'physical boundary' relative to the celll geometry edge; normally, these are set to ZERO

Src/LinearSolvers/F_MG/stencil.f90

commit d192027929f986b7d21555b9610cfcd37d39e99a
Author: lijewski <lijewski>
Date:   Mon Apr 4 21:43:12 2005 +0000

    Call fab_destroy() unconditionally to fix mem_stats bug.

Src/F_BaseLib/multifab.f90

commit e8e39fd92b2342c6f2f0578dd868fc2b780c1a65
Author: almgren <almgren>
Date:   Mon Apr 4 17:28:32 2005 +0000

    Don't use mg_bc.f90 any more.

Src/LinearSolvers/F_MG/GPackage.mak

commit 565a8457fbcabb442903743123728b4e0443a8ad
Author: car <car>
Date:   Fri Apr 1 22:15:17 2005 +0000

    seem to have 2nd order adaptive 'working'

Src/F_BaseLib/bl_error.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/ml_boxarray.f90
Src/F_BaseLib/ml_layout.f90
Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/test/t_main.f90
Src/LinearSolvers/F_MG/mg.f90
Tests/F_BaseLib/t_main.f90

commit e970741e7e175654c2ffa389c0d0802aad5a36b3
Author: car <car>
Date:   Thu Mar 31 18:44:14 2005 +0000

    ml operations added

Src/LinearSolvers/F_MG/stencil.f90
Tools/F_mk/GMakedefs.mak

commit f4e81cb22015789a11b82856491a5477089a49a3
Author: car <car>
Date:   Thu Mar 31 18:43:57 2005 +0000

    *** empty log message ***

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_constants.f90
Src/F_BaseLib/box_util.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/ml_boxarray.f90
Src/F_BaseLib/ml_layout.f90
Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/t_main.f90

commit 2294fdc72b8e0511b534566a6e87229d810252ca
Author: welcome <welcome>
Date:   Wed Mar 30 01:49:01 2005 +0000

    Added "probStartTime" data member to Amr class to record the system time
    just before init/restart was called.
    Needed for "Time since start(restart)" value printed when dumping plotfile.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 365e125c177dab67b6aee00e8e9e532c9b4ad032
Author: lijewski <lijewski>
Date:   Thu Mar 24 21:39:23 2005 +0000

    Got working on Jacquard with PathScale compiler.

Src/F_BaseLib/mboxarray.f90
Tools/F_mk/GMakedefs.mak

commit c54d80e9fdff354f0cc259142e0f838daa076002
Author: lijewski <lijewski>
Date:   Thu Mar 24 17:49:51 2005 +0000

    Added pretty printing for mask arrays.
    Fixed a bug in the Z-direction stuff in *_aaa().

Src/LinearSolvers/F_MG/stencil.f90

commit 57d90871c0e0c7ec89b083b6afb0da034f2f146f
Author: car <car>
Date:   Tue Mar 22 22:59:07 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg.f90

commit 967818457ff13cf3ff0d3709874e0dc7e5025ab0
Author: lijewski <lijewski>
Date:   Tue Mar 22 21:40:32 2005 +0000

    Just more goo from periodic testing.

Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/t_main.f90

commit 615d5ef108d4aad7e21a7434172e1e5e08980a26
Author: lijewski <lijewski>
Date:   Tue Mar 22 21:38:04 2005 +0000

    Modified arguments to stencil_fill_bc_st()

Tests/LinearSolvers/F_MG/t_stencil.f90

commit 7b1406aaa67bf6e670ea4afe2c60a3de903a0185
Author: lijewski <lijewski>
Date:   Tue Mar 22 21:23:18 2005 +0000

    Set mg.v=2 & added ability to set periodicity.

Src/LinearSolvers/C_CellMG/Test/grids/in.2_19boxes
Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3x2
Src/LinearSolvers/C_CellMG/Test/grids/in.2_big
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_d
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_e
Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_d
Tests/LinearSolvers/C_CellMG/grids/in.2_19boxes
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_a
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_b
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_c
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_a
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_b
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_c
Tests/LinearSolvers/C_CellMG/grids/in.2_3x2
Tests/LinearSolvers/C_CellMG/grids/in.2_big
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_d
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_e
Tests/LinearSolvers/C_CellMG/grids/in.2_small_a
Tests/LinearSolvers/C_CellMG/grids/in.2_small_b
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_a
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_b
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_c
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_d

commit 536c2f7720a7758145b17e17694a3f476d107522
Author: lijewski <lijewski>
Date:   Tue Mar 22 21:22:53 2005 +0000

    Changed the default tol & made dump_VisMF default to true.

Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 8bbdd5db8e9797367ceae6e6ef715f266447359f
Author: lijewski <lijewski>
Date:   Tue Mar 22 19:23:08 2005 +0000

    Progress merging in periodic stuff.

Src/LinearSolvers/F_MG/stencil.f90

commit 47b8626dbb199ef640b94e852cd2e79949e9854d
Author: car <car>
Date:   Thu Mar 17 23:34:52 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/stencil.f90

commit 1ca69aacd95fe3204045f296f54d922239da5ddc
Author: lijewski <lijewski>
Date:   Thu Mar 17 22:05:51 2005 +0000

    Work needed to add "cross" argument to fill_boundary.

Src/F_BaseLib/layout.f90

commit d4c52506612aaff6e0fda66460ba1ae10c5a92fa
Author: lijewski <lijewski>
Date:   Thu Mar 17 21:57:25 2005 +0000

    slight code rearrangment

Src/F_BaseLib/boxarray.f90

commit 25ac3448396e62d6bbc9abefb497ac89d59edb7b
Author: lijewski <lijewski>
Date:   Thu Mar 17 21:56:54 2005 +0000

    Added optional cross argument to fill_boundary.

Src/F_BaseLib/multifab.f90

commit dad342d0dce6cbd64e8c6ba92197de7358268e2e
Author: car <car>
Date:   Wed Mar 16 23:33:59 2005 +0000

    corner/edge extrap

Src/LinearSolvers/F_MG/stencil.f90

commit 7086b012b37363ed90c8be91b6702df607df1539
Author: lijewski <lijewski>
Date:   Wed Mar 16 21:56:00 2005 +0000

    Added boxarray_box_corners()

Src/F_BaseLib/boxarray.f90

commit 75b6304831786fec04e952c7cf8688b8a341a02c
Author: car <car>
Date:   Wed Mar 16 19:00:42 2005 +0000

    OMP syntax fixes

Src/F_BaseLib/multifab.f90

commit e2901289288454680b12d3d5ce59586043b96580
Author: car <car>
Date:   Wed Mar 16 17:30:23 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/stencil.f90

commit 19b76eaef7fab5cd81408b8fb28b11ab769e4778
Author: lijewski <lijewski>
Date:   Tue Mar 15 21:43:34 2005 +0000

    Better test for early return from multifab_internal_sync_shift

Src/F_BaseLib/multifab.f90

commit 7fd0ddf8cc0a3dcca3469976570fcf6e6faabeb0
Author: lijewski <lijewski>
Date:   Tue Mar 15 21:00:30 2005 +0000

    internal_sync's now appear to work for periodic.

Src/F_BaseLib/multifab.f90

commit d133f62ddf99eae8f4e87a4710d446cc738eac98
Author: lijewski <lijewski>
Date:   Tue Mar 15 20:59:38 2005 +0000

    slight change in notation

Src/F_BaseLib/box.f90

commit 20fa607f3e76a96cdf0a292f0dcdd2de68e796cd
Author: car <car>
Date:   Tue Mar 15 19:14:00 2005 +0000

    think i've fixed ann's checkpoints

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_main.f90

commit 8c88a056f3384b4353c2010687c06e62bb61976e
Author: car <car>
Date:   Mon Mar 14 22:56:37 2005 +0000

    denodalize

Src/F_BaseLib/box.f90

commit 80ace0b4e8224972c655888ef596a346cbcbc43d
Author: almgren <almgren>
Date:   Mon Mar 14 20:58:35 2005 +0000

    Remove nodal from the writing of the bounding box in fabio_ml_multifab_write_d.

Src/F_BaseLib/fabio.f90

commit ec031d2891aedf48504fbc0f42fdb55de9cdeb6a
Author: car <car>
Date:   Mon Mar 14 20:45:11 2005 +0000

    add flux_reg.f90

Src/F_BaseLib/GPackage.mak

commit 894be3f9ef0ab001436d9466217136184ca1789f
Author: car <car>
Date:   Mon Mar 14 20:44:50 2005 +0000

    read nodal mf

Src/F_BaseLib/box.f90
Src/F_BaseLib/fabio.f90

commit 410e40101dcf938ef7aa6b6886ad9dffc93a51f8
Author: almgren <almgren>
Date:   Mon Mar 14 20:29:12 2005 +0000

    New flux register code - this differs from boundary registers
    in that these are defined in fine index space at the boundaries
    of fine grids.

Src/F_BaseLib/flux_reg.f90

commit 00df4da58c3bd47790eb3ca5cb78c0bda49d1a8d
Author: car <car>
Date:   Sat Mar 12 19:43:51 2005 +0000

    cvs strings

Src/F_BaseLib/ppm_util_c.c
Src/F_BaseLib/timer_c.c

commit a08d707a316ef4ea23bb129cc9630720531ee74f
Author: car <car>
Date:   Sat Mar 12 14:39:49 2005 +0000

    mac i/o is like aix

Src/F_BaseLib/fabio_c.c

commit 9088e54c87e5b065b489eb8279428450e031062f
Author: lijewski <lijewski>
Date:   Sat Mar 12 00:24:34 2005 +0000

    Some work to make internal_sync periodic-aware.  Needs to be tested.

Src/F_BaseLib/multifab.f90

commit cfcb6534aeca1b4c535515d5a494ecc4b7d45cad
Author: lijewski <lijewski>
Date:   Sat Mar 12 00:23:34 2005 +0000

    A little simplification.

Src/F_BaseLib/layout.f90

commit bc017ede278139672349222431c08199ea9c0bb9
Author: lijewski <lijewski>
Date:   Sat Mar 12 00:22:31 2005 +0000

    periodic_shift() -> box_periodic_shift()

Src/F_BaseLib/box.f90

commit a5fa5e09beeed3c28243ba40a682cb86e17e53c7
Author: lijewski <lijewski>
Date:   Fri Mar 11 22:28:16 2005 +0000

    Added box_contains_strict()

Src/F_BaseLib/box.f90

commit da87eb547544dda4c2cb6b4ab63ef075d136ad29
Author: lijewski <lijewski>
Date:   Fri Mar 11 19:20:37 2005 +0000

    Didn't have easy() functions quite correct for nodal MultiFabs.

Src/F_BaseLib/multifab.f90

commit 20b24e3e10d6ee940441f350786a41892a558107
Author: lijewski <lijewski>
Date:   Thu Mar 10 23:00:05 2005 +0000

    Made the easy() functions in multifab fill_boundary periodic-aware.

Src/F_BaseLib/multifab.f90

commit 0130c53384ae25331c815827ac753e20195ac416
Author: lijewski <lijewski>
Date:   Tue Mar 8 21:50:44 2005 +0000

    Some progress on making fill_boundary periodic-aware.

Src/F_BaseLib/layout.f90

commit 054e598ccab0dcaa32ea2e891071457aacead2cb
Author: almgren <almgren>
Date:   Tue Mar 8 17:29:13 2005 +0000

    Fix for 3d so now works correctly with Neumann bcs.

Src/LinearSolvers/F_MG/sparse_solve.f90

commit 198eb064268ae2e7dd28c0dca0e2cc141e1b4519
Author: lijewski <lijewski>
Date:   Mon Mar 7 23:11:41 2005 +0000

    Looking good.

Src/F_BaseLib/box.f90

commit 568bc33ecc980852fe33a8d30ae2ae8f45ecfffb
Author: almgren <almgren>
Date:   Mon Mar 7 22:16:01 2005 +0000

    Works now in 3-d for Dirichlet bc's, still broken for 3-d Neumann.

Src/LinearSolvers/F_MG/sparse_solve.f90

commit e62866d728a316f2152bc500ddae1be937809fb3
Author: lijewski <lijewski>
Date:   Mon Mar 7 21:52:39 2005 +0000

    Rewrote a few things slightly differently.

Src/F_BaseLib/box.f90

commit 5373c1de5bbd84edb5457ace26da53700ce22eb4
Author: almgren <almgren>
Date:   Mon Mar 7 21:52:19 2005 +0000

    Fix bug in setting coarse-fine interfaces to Dirichlet.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 543eff91b78db77f1e6b527bacfab177d27ad913
Author: almgren <almgren>
Date:   Mon Mar 7 20:28:56 2005 +0000

    Fixed Neumann bug in 2-d.

Src/LinearSolvers/F_MG/sparse_solve.f90

commit a210f723b5fb73e264ce0f64be936e8daf1f8a11
Author: almgren <almgren>
Date:   Mon Mar 7 19:57:04 2005 +0000

    Now works with Neumann bc's in 2d.  Still need to fix 3d.

Src/LinearSolvers/F_MG/sparse_solve.f90

commit 1e2ca940323da3601271cb63b51360750c7efe8c
Author: car <car>
Date:   Fri Mar 4 20:27:10 2005 +0000

    efactor is used in case doing a residual or an operator application

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 32497989040300afff9edb6a54cb204f3f427e24
Author: car <car>
Date:   Fri Mar 4 20:25:48 2005 +0000

    remove extraneous print statments

Src/LinearSolvers/F_MG/stencil.f90

commit 96b3f58d706e3120da1effc44d3219787db1422f
Author: lijewski <lijewski>
Date:   Thu Mar 3 23:35:38 2005 +0000

    Added periodic_shift.
    Still got to test it a tad more.

Src/F_BaseLib/box.f90

commit e6b3d3bbcc1044ceaaff1d40bf7c6fa371377efc
Author: almgren <almgren>
Date:   Thu Mar 3 19:18:31 2005 +0000

    Fixed some bugs in order to run on more than one grid.  Runs
    on multiple grids with Dirichlet bc's but not yet working for Neumann.

Src/LinearSolvers/F_MG/sparse_solve.f90

commit a188430c467e8ea216979379839f5f51f91c23f9
Author: car <car>
Date:   Thu Mar 3 02:25:05 2005 +0000

    -C converts cvmgt to MERGE; as per f90

Tools/C_scripts/strip72

commit 77260d80c95d5a419ac6a9f07a50558094828338
Author: almgren <almgren>
Date:   Wed Mar 2 22:35:36 2005 +0000

    Cleaned up so it doesn't use the neighbors stuff, that was only
    used to generate an approximate size.

Src/LinearSolvers/F_MG/sparse_solve.f90

commit d1c692eff764809bbfd89f850ab62c7aba7b26cb
Author: almgren <almgren>
Date:   Wed Mar 2 22:21:03 2005 +0000

    Added sparse solver for nodal system.  Tested on single grid as
    top-level solver and bottom solver for MG, works in both cases.

Src/LinearSolvers/F_MG/sparse_solve.f90

commit 9c9d0edfdf3d1bdfea2562279c403b8a29ebb85b
Author: almgren <almgren>
Date:   Wed Mar 2 22:20:09 2005 +0000

    Now allows for call of nodal sparse solver as bottom solver.

Src/LinearSolvers/F_MG/mg.f90

commit 5082aa474e3201d6b7d06d59198c5695c271e1b7
Author: almgren <almgren>
Date:   Wed Mar 2 21:35:08 2005 +0000

    Bug in ml_interface_2d : should test on face +/- 1, instead
    was testing on +1 vs -2.

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit e68a52893978775bd4c3691bb92f67347721ba73
Author: car <car>
Date:   Wed Mar 2 17:42:56 2005 +0000

    newest intel 8.1 fixes check shape pointer

Tools/F_mk/GMakedefs.mak

commit c346419fa7920319f8e5cabf969ceea95b8bb829
Author: almgren <almgren>
Date:   Tue Mar 1 20:10:54 2005 +0000

    Fixed the stencil for nx or ny = 2 (shouldn't be skewed).
    Added some new code for fluxes...

Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit f6e940cdf231df8fea916a7b23d3da637faedd48
Author: almgren <almgren>
Date:   Tue Mar 1 20:09:57 2005 +0000

    Changes the way the mini-cycle is handled.

Src/LinearSolvers/F_MG/mg.f90

commit e2c1ecb842189b27f22cb2346652fbf3094ba7c5
Author: almgren <almgren>
Date:   Tue Mar 1 20:03:25 2005 +0000

    Clean-up...

Src/LinearSolvers/F_MG/sparse_solve.f90

commit c7071b7f95be2436e068ba3fa866f3a717600332
Author: car <car>
Date:   Fri Feb 25 16:27:24 2005 +0000

    somedebugging

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Tools/F_mk/GMakedefs.mak

commit 0954314d324d0674b7fe6dcf1ea01736a539e0fc
Author: car <car>
Date:   Sun Feb 20 16:51:34 2005 +0000

    fixes for dft

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/fab.f90
Src/F_BaseLib/interp.f90
Src/F_BaseLib/multifab.f90
Src/F_BaseLib/test/t_bx.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/t_bx.f90
Tests/F_BaseLib/t_main.f90

commit 883230ef9220bc19dfe8c24797ed653cf9098b35
Author: car <car>
Date:   Sun Feb 20 16:50:57 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/stencil.f90

commit 9e47ef623bb548418cefd8764ce2244f8caea125
Author: car <car>
Date:   Fri Feb 18 14:25:53 2005 +0000

    *** empty log message ***

Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_bx.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_bx.f90

commit 1e35231daf5e154a2ee008291580565751454bbf
Author: car <car>
Date:   Thu Feb 17 23:21:09 2005 +0000

    debug and opt flags for IBM on Mac

Tools/F_mk/GMakedefs.mak

commit e51763f3379d6d6400ab41070cdd2a73a51e2d84
Author: car <car>
Date:   Thu Feb 17 22:03:31 2005 +0000

    no stinking mutex's

Src/C_AMRLib/AmrLevel.cpp

commit 483438ce9fc979f0ace5801eb6b9b0d9b7b33d0e
Author: car <car>
Date:   Wed Feb 16 23:10:40 2005 +0000

    more arithmetic in multifab

Src/F_BaseLib/multifab.f90

commit a392809b0c92b49e386ccd34d31323aef991dfc1
Author: car <car>
Date:   Tue Feb 15 21:54:19 2005 +0000

    more dft debug changes

Src/F_BaseLib/multifab.f90

commit 723a8e79e6c7bdce36a5c2bae225b72e09e54b51
Author: car <car>
Date:   Sat Feb 12 20:15:43 2005 +0000

    MPI_recv takes a status argument

Src/F_BaseLib/pingpong.f90

commit 411d010e616d3447dd4c75a441a94ba3ff313625
Author: car <car>
Date:   Thu Feb 10 23:37:21 2005 +0000

    more fixes for dft

Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_util.f90

commit ff480a09feeab6887d102abf2156a5619c0c7ab4
Author: car <car>
Date:   Wed Feb 9 23:35:33 2005 +0000

    more progress

Src/F_BaseLib/box_util.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Tools/F_mk/GMakedefs.mak

commit fdedd0f5978587e7514857fa683606c8c214ba15
Author: car <car>
Date:   Tue Feb 8 23:54:13 2005 +0000

    fixes for eigensolvers

Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/stencil.f90
Tools/F_mk/GMakedefs.mak

commit dc0a913a33f6b40988919421d3f578b4d3b62c9b
Author: lijewski <lijewski>
Date:   Wed Jan 26 23:20:51 2005 +0000

    Got rid of std::pow() call.

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 010c0ef8da0fd0646c207649d2a8a25819b9c16d
Author: lijewski <lijewski>
Date:   Wed Jan 26 23:20:30 2005 +0000

    Got rid of std::pow().

Src/C_BoundaryLib/InterpBndryData.cpp

commit 3bfb976d9f7109c3143ce75259c2d24ab83eb42a
Author: lijewski <lijewski>
Date:   Wed Jan 26 22:52:54 2005 +0000

    Fix for Jacquard.

Src/C_BoundaryLib/InterpBndryData.cpp

commit 6db487679515969366e1a44323dbbe1bec961943
Author: car <car>
Date:   Wed Jan 26 16:33:15 2005 +0000

    fancy gfortran

Tools/C_mk/Make.defs

commit 7233048b02e2b9876f95f80899c787092f3353b4
Author: car <car>
Date:   Wed Jan 26 16:31:27 2005 +0000

    fancy gfortran

Tools/C_mk/Make.defs

commit a5d45a5df5da028cd370146d1f7a3937fb5d630a
Author: car <car>
Date:   Wed Jan 26 00:20:31 2005 +0000

    crafty way of getting path to libf95.a

Tools/C_mk/Make.defs

commit 6b1a36024fbc44b46141de901abfcffbf243b882
Author: lijewski <lijewski>
Date:   Tue Jan 25 21:27:19 2005 +0000

    Mod for PathScale when USE_MPI=TRUE on jacquard.

Tools/C_mk/Make.Linux

commit a4ffedea1d8d792d3a66cf320e8661a437ac5328
Author: lijewski <lijewski>
Date:   Tue Jan 25 18:45:00 2005 +0000

    Mods to PathScale to compile on NERSC's jacquard system.

Tools/C_mk/Make.Linux

commit 3ab6bf71e740f13179a0430ea6af10a5833c0b71
Author: car <car>
Date:   Mon Jan 24 23:54:32 2005 +0000

    *** empty log message ***

Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/pingpong.f90
Src/F_BaseLib/ppm_util_c.c
Src/F_BaseLib/test/main.f90
Tests/F_BaseLib/main.f90

commit 3d3d4288db34b01face3c2488856b293992a6819
Author: almgren <almgren>
Date:   Tue Jan 11 21:48:30 2005 +0000

    Put trim(names(i)) instead of names(i) so that amrvis can
    read the names of the variables without the extra white spaces...

Src/F_BaseLib/fabio.f90

commit 40b02322bd161b124e92abd92c61c44194425045
Author: car <car>
Date:   Mon Jan 10 22:04:45 2005 +0000

    White Space Fix dos->unix

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit c294768193af601af1dec03d6acdc0e5d120a6f5
Author: lijewski <lijewski>
Date:   Fri Jan 7 17:38:55 2005 +0000

    fix to operator=

Src/C_BoundaryLib/BndryRegister.cpp

commit 9072c2000ea574e7c746a9aad56a254494d0801b
Author: lijewski <lijewski>
Date:   Thu Jan 6 22:18:50 2005 +0000

    extra gunk for LAM

Tools/C_mk/Make.mpi

commit 71b10e49e2fa7ddc8e2cfa6ca43ff74457bd0832
Author: lijewski <lijewski>
Date:   Wed Jan 5 22:19:46 2005 +0000

    fix to operator=

Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.cpp

commit aedce090a628e6e5cbb1129ee98b4a53693a8338
Author: lijewski <lijewski>
Date:   Wed Jan 5 21:53:21 2005 +0000

    fix to operator=

Src/C_BaseLib/Tuple.H

commit 7bef65ebbbabea43475bec11647869377a4674b8
Author: car <car>
Date:   Tue Jan 4 23:33:22 2005 +0000

    JEFF_TEST turns on mpi_waitall

Src/C_BaseLib/ParallelDescriptor.cpp

commit f68c181d66cf679eadfd5b673a20e1ddd38ac4dd
Author: car <car>
Date:   Tue Jan 4 22:36:15 2005 +0000

    name map

Tools/C_mk/Make.frank

commit 72dae790503862f551bd104b0a1f42f07adf5fd3
Author: car <car>
Date:   Tue Jan 4 22:10:41 2005 +0000

    frank archive file

Tools/C_mk/Make.frank

commit 96297ec7da57b970c79b612774f61938b03af1b0
Author: car <car>
Date:   Tue Dec 21 17:10:59 2004 +0000

    g95 tweaks

Src/F_BaseLib/filler.f90
Tools/F_mk/GMakedefs.mak

commit e25d77ebfa822af5358e6d36f09d65e36e516f38
Author: car <car>
Date:   Tue Dec 21 15:32:03 2004 +0000

    darwin

Src/F_BaseLib/GPackage.mak

commit 1122e9d5f2d454b09b663ba333c45d0a2b93fbc0
Author: car <car>
Date:   Tue Dec 21 15:22:58 2004 +0000

    some minor fixes to silence warnings

Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/fabio.f90
Tools/F_mk/GNUmakefile
Tools/F_mk/makefile

commit 4437415232ae7ff0dd1a560ae194c4229353d395
Author: car <car>
Date:   Fri Dec 17 21:53:05 2004 +0000

    *** empty log message ***

Src/F_BaseLib/bl_constants.f90
Src/F_BaseLib/bl_string.f90
Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/interp.f90
Src/F_BaseLib/mboxarray.f90
Src/F_BaseLib/parallel_stubs.f90

commit e53eb44c2b647b267343430b865b6f76a6e76ee8
Author: car <car>
Date:   Fri Dec 17 17:33:53 2004 +0000

    MF_DEBUG_FILL: untested

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real2d.f
Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit 6c5f766b16e6af69793e9ef61bdf680a37d2603d
Author: vince <vince>
Date:   Thu Dec 16 20:36:54 2004 +0000

    this version works for me using CC.

Tools/C_mk/Make.IRIX64

commit 397e49f0a045aefb7bafd3df84410c4aed15eed2
Author: car <car>
Date:   Wed Dec 15 18:40:42 2004 +0000

    can now read denfile to setup test case

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 41829590fc4761ad8a893fb9d5607cda7a3b83d6
Author: car <car>
Date:   Wed Dec 15 18:39:56 2004 +0000

    changes:
    1) now bottom toleranced decreased by a factor of 10
    2) Expert mode is default and gone
    3) failure to converge is not a BoxLib::Error; it sets
       the return code to 8

Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit 3c62e472bee7b78059fd18b5bcab8cdf8d669ccb
Author: car <car>
Date:   Wed Dec 15 18:06:54 2004 +0000

    stupid warning wrap w/ IOProcessor()

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 2e16292ac758e41f9d4feb4c50aeba49e98469a7
Author: lijewski <lijewski>
Date:   Tue Dec 14 22:39:07 2004 +0000

    *** empty log message ***

Src/C_BaseLib/test/tVisMF2.cpp
Tests/C_BaseLib/tVisMF2.cpp

commit 26e336ae547114b252b04742fc5d8c2b9162e782
Author: car <car>
Date:   Fri Dec 3 18:54:52 2004 +0000

    clean/realclean not as painful

Tools/C_mk/Make.rules

commit e13be4fbda9c630013644c7be4a6065f1d485de6
Author: car <car>
Date:   Fri Dec 3 17:44:04 2004 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak

commit 349932412a9d6fa20eebdf4bca86ae32f150d399
Author: almgren <almgren>
Date:   Wed Dec 1 18:37:17 2004 +0000

    Need change in setting up mba%rr in order to be consistent
    with new mboxarray_build_rr routine.

Src/F_BaseLib/box_util.f90

commit c568d1421572876a79161421c50abde612d85826
Author: lijewski <lijewski>
Date:   Tue Nov 30 19:21:09 2004 +0000

    added Compare class

Src/C_BaseLib/IntVect.H

commit 2b7b6a9c6206e717ed7e64055f4b6e5cbc370cb4
Author: almgren <almgren>
Date:   Mon Nov 29 22:42:16 2004 +0000

    Use bc_module as opposed to mg_bc_module.

Src/LinearSolvers/F_MG/stencil.f90

commit 33ea3d8d1d2f858f05a97780fd6347ce639dacaf
Author: almgren <almgren>
Date:   Mon Nov 29 22:40:55 2004 +0000

    Added edge restriction.

Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/ml_restriction.f90

commit 0f16050c23c64a2917b0964d114a0df1c6b29fe4
Author: almgren <almgren>
Date:   Mon Nov 29 22:40:30 2004 +0000

    Removed print statements.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit bd9f69f63de6b5171330c0bcb9efe54e92e5ba43
Author: car <car>
Date:   Mon Nov 29 20:53:24 2004 +0000

    bc interp renewed

Src/F_BaseLib/GPackage.mak

commit 01c966c67de45165ca373caed8137b11dc401766
Author: almgren <almgren>
Date:   Mon Nov 29 20:14:32 2004 +0000

    bc.f90 holds the definitions of the bc type parameters.
    lincc_interp2d in interp.f90 has a bug fix.

Src/F_BaseLib/bc.f90
Src/F_BaseLib/interp.f90

commit 007562a944b6a8727331db61a20b1e87af1e7a79
Author: car <car>
Date:   Sat Nov 27 20:28:09 2004 +0000

    fix for totalview

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/interp.f90
Src/F_BaseLib/mboxarray.f90

commit 5bf8b178ae798dce16c77ad7e85a9b7cfd0bd9ec
Author: almgren <almgren>
Date:   Fri Nov 19 20:28:22 2004 +0000

    Bug in index loop for defining voffx.

Src/F_BaseLib/interp.f90

commit e4a08abdc6ac9ecbb7a1abf49460583cb9afacaa
Author: car <car>
Date:   Thu Nov 18 17:55:46 2004 +0000

    bipolar disorder

Src/F_BaseLib/multifab.f90
Src/F_BaseLib/test/GNUmakefile
Tests/F_BaseLib/GNUmakefile

commit fcb99dde695b2a39c7728e254488d80d0ef9769e
Author: car <car>
Date:   Thu Nov 18 17:42:01 2004 +0000

    XLC fixes

Src/F_BaseLib/multifab.f90
Tools/F_mk/GMakedefs.mak

commit 349020cee3cb868f5ffc1297a77b54c69a9e1be5
Author: almgren <almgren>
Date:   Thu Nov 18 17:36:36 2004 +0000

    Modified calling sequence of lin_cc_interp_3d so it matches that of 2d.

Src/F_BaseLib/interp.f90

commit 08641960137e41430550b7a06cd084b5b182719a
Author: car <car>
Date:   Wed Nov 17 20:08:25 2004 +0000

    using lbound,ubound should work

Src/F_BaseLib/multifab.f90

commit e3c0b22e9310e4bd60e1e57387422acd96caa373
Author: car <car>
Date:   Wed Nov 17 19:09:22 2004 +0000

    multifab_fab_copy

Src/F_BaseLib/multifab.f90

commit b86bd3eff421a50f85b72033d8e731cd5dd9e8a1
Author: car <car>
Date:   Wed Nov 17 16:29:36 2004 +0000

    FreeBSD

Tools/F_mk/GMakedefs.mak

commit 6e2f6720bf6999a3810e7f92363877ff4ba8d029
Author: car <car>
Date:   Tue Nov 16 23:56:24 2004 +0000

    order of include Darwin?

Src/F_BaseLib/timer_c.c

commit a910d0b28debaf706d61d75b726df8c59005232d
Author: car <car>
Date:   Tue Nov 16 23:21:19 2004 +0000

    MacOS X

Src/C_BaseLib/FPC.cpp
Tools/C_mk/Make.Darwin

commit f4710f69ca7e8dfce6541db7e62dff84da0fb8dc
Author: car <car>
Date:   Sun Nov 14 01:21:32 2004 +0000

    *** empty log message ***

Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/stencil.f90
Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak

commit dd6968be77626a24457df0284d99f31ac8254789
Author: car <car>
Date:   Fri Nov 12 20:55:33 2004 +0000

    gotta go home

Src/LinearSolvers/F_MG/stencil.f90

commit 9ea8a4fdd12e740228aa89d734bc60101a579f26
Author: car <car>
Date:   Thu Nov 11 22:31:29 2004 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_util.f90

commit 44d75da840402026d8fcc03867a0c4f31b2c1fe0
Author: car <car>
Date:   Thu Nov 11 22:24:34 2004 +0000

    *** empty log message ***

Src/F_BaseLib/box.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/fab.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/mboxarray.f90
Tools/F_mk/GMakedefs.mak

commit d4c8d32c7e5b4a48e2c274b693ed900eb2c70b13
Author: car <car>
Date:   Wed Nov 10 22:39:14 2004 +0000

    minor tweaks

Src/F_BaseLib/bl_constants.f90
Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 702f94fcebd51c1cde0a54228a13234a1f4767ba
Author: car <car>
Date:   Mon Nov 8 22:33:33 2004 +0000

    minor tweaks for F

Src/F_BaseLib/bl_mem_stat.f90
Src/F_BaseLib/bl_stream.f90
Src/F_BaseLib/bl_string.f90
Src/F_BaseLib/bl_timer.f90
Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/box.f90
Src/F_BaseLib/box_util.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/cluster.f90
Src/F_BaseLib/fab.f90
Src/F_BaseLib/interp.f90
Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/mt19937ar.f90
Src/F_BaseLib/multifab.f90
Src/F_BaseLib/pingpong.f90
Src/F_BaseLib/plotfile.f90
Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit acbc89095a3076284eca0fd3ebdd40b181f5a111
Author: car <car>
Date:   Fri Nov 5 19:11:16 2004 +0000

    MLW: barrier in glean prevents buffer overrrun

Src/C_BaseLib/BLProfiler.cpp

commit 761c53a4fcfce77cb0e9002382e4adbaa75df593
Author: car <car>
Date:   Thu Oct 28 19:17:15 2004 +0000

    tweak

Tools/F_mk/GMakedefs.mak

commit 2a7645fd7d1a296c31b1d58cb2d58f3111326dfa
Author: car <car>
Date:   Thu Oct 28 17:27:37 2004 +0000

    *** empty log message ***

Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/t_main.f90

commit edec0da57c5934032707ea88bc95dab5ae0cb10f
Author: car <car>
Date:   Fri Oct 15 21:36:35 2004 +0000

    *** empty log message ***

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/t_main.f90

commit 6c48adeae0300a4659d5ac8a19aa14fcd1e69fb0
Author: car <car>
Date:   Fri Oct 15 20:34:51 2004 +0000

    more changes for eigenproblem

Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/ml_util.f90
Tools/F_mk/GMakerules.mak

commit 900b521804dc65d3f2fb4f876a9bce0f4116a1f2
Author: car <car>
Date:   Fri Oct 15 20:31:58 2004 +0000

    first cut at ml_multifab_read

Src/F_BaseLib/bl_stream.f90
Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/list_box.f90
Src/F_BaseLib/multifab.f90
Src/F_BaseLib/plotfile.f90
Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_main.f90

commit 211a22360b6b3c0d9060180a18b9982dd66a182d
Author: lijewski <lijewski>
Date:   Wed Oct 13 21:52:22 2004 +0000

    Set default for "verbose" to true for the time being.
    Added "only_heaviest_cpu".

Src/C_BaseLib/DistributionMapping.cpp

commit be82e93bc00952c6cf5a63856ea5a9cd15b76b82
Author: lijewski <lijewski>
Date:   Wed Oct 13 20:57:03 2004 +0000

    output a bit more stuff

Src/C_BaseLib/DistributionMapping.cpp

commit 5a895ca5af5ce1cb137aef524c08792773be5385
Author: car <car>
Date:   Tue Oct 12 15:44:07 2004 +0000

    If the number of processors is <= 8 then use the 'better' metis
    partitioner.

Src/C_BaseLib/DistributionMapping.cpp

commit 38dcdcc7606c4aefb89632ccd9d15d5d5b03f7fd
Author: car <car>
Date:   Mon Oct 11 23:26:35 2004 +0000

    If metis_opt is != 0 then use edgeweights in addition to vertex weights.
    The edgeweights are equal to the volume of the intersection of the target
    box grown by one and the source boxs.

Src/C_BaseLib/DistributionMapping.cpp

commit 63fda6d1988e4d5535253a34a0e3be2e6827438e
Author: lijewski <lijewski>
Date:   Mon Oct 11 22:45:37 2004 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit 157f832a24b2d866c6c36a0b6cc4a23ec45ad1e5
Author: lijewski <lijewski>
Date:   Mon Oct 11 22:00:12 2004 +0000

    Fixed Chuck's bug

Src/C_BaseLib/DistributionMapping.cpp

commit b6bc72726b3bb43fa21f32d2184c15677204c14e
Author: lijewski <lijewski>
Date:   Mon Oct 11 21:57:09 2004 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit d586aaaa2059d7124709b3e7d28d895a166e4c17
Author: lijewski <lijewski>
Date:   Mon Oct 11 21:47:03 2004 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit 327aeccdf4c7c6569e29889d6959e0db31142cc9
Author: car <car>
Date:   Mon Oct 11 21:17:13 2004 +0000

    for metis

Tools/C_mk/Make.defs

commit ed87788876392e69f7e10e351e04bc6f4828e8e3
Author: car <car>
Date:   Mon Oct 11 20:33:17 2004 +0000

    ops

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/test/GNUmakefile
Tests/C_BaseLib/GNUmakefile

commit b297203b266f906b52ecc758894ae66a57daf4dc
Author: car <car>
Date:   Mon Oct 11 20:20:47 2004 +0000

    added metis

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 53ab355a2489dd434a8aacbd4417d355f12627eb
Author: vince <vince>
Date:   Wed Oct 6 23:54:50 2004 +0000

    zero pointer after delete so clear can be called
    on uninitialized fabs.

Src/C_BaseLib/VisMF.cpp

commit f2e9190bbe7f1a0d01ba22412a0b112998cb1b93
Author: car <car>
Date:   Tue Oct 5 01:41:46 2004 +0000

    minor fixes

Src/F_BaseLib/fabio_c.c

commit e82f3bc4d4e07b3ec4891ecac3bf3bb37a04f155
Author: car <car>
Date:   Tue Oct 5 01:40:56 2004 +0000

    windows fixes

Src/F_BaseLib/plotfile.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/stencil.f90

commit a7c1d24e824bbf5810e21b1f84f9432085cd1ee2
Author: car <car>
Date:   Mon Oct 4 19:41:54 2004 +0000

    ml changes

Src/F_BaseLib/multifab.f90

commit 76fbff6c43747ebacd29c0f9d39ed0124ebfc3e0
Author: car <car>
Date:   Sat Oct 2 22:49:41 2004 +0000

    *** empty log message ***

Src/F_BaseLib/filler.f90
Src/F_BaseLib/mt19937ar.f90
Src/F_BaseLib/multifab.f90
Src/F_BaseLib/plotfile.f90
Src/F_BaseLib/test/main.f90
Src/LinearSolvers/F_MG/stencil.f90
Tests/F_BaseLib/main.f90
Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak

commit 36a075224a260f71c3276661eeae83d758ef3cd9
Author: car <car>
Date:   Thu Sep 30 19:02:41 2004 +0000

    corrected fab dimensions

Src/F_BaseLib/fabio.f90

commit 52b21666a78d0b774f48aebc82b2f69352a3729a
Author: car <car>
Date:   Tue Sep 28 17:56:35 2004 +0000

    formatted io for plotfiles

Src/F_BaseLib/fabio.f90

commit 94a89bf35c886af089170c85c5317cbd70c9440f
Author: car <car>
Date:   Wed Sep 22 17:53:41 2004 +0000

    more constants

Src/F_BaseLib/bl_constants.f90

commit b594a1f3cd2b78e498209957df555c51a40c9753
Author: car <car>
Date:   Tue Sep 21 17:38:17 2004 +0000

    fixes for ia64

Src/F_BaseLib/mt19937ar.f90

commit 01095cc2a388eb99ab20e1d25074502157b16119
Author: car <car>
Date:   Mon Sep 20 21:49:34 2004 +0000

    make extrap bc eat boundary value

Src/LinearSolvers/F_MG/stencil.f90

commit c9487e3a5a96b99df307c0cbf71c0f3a3380c64c
Author: car <car>
Date:   Fri Sep 17 22:45:39 2004 +0000

    minor thrashing

Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/fabio.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/ml_util.f90
Tools/F_mk/GMakedefs.mak

commit 6196a2b4ef881422608fccd10b8e497ccbf8a8b7
Author: car <car>
Date:   Fri Sep 17 20:30:36 2004 +0000

    Make.IRIX64

Tools/C_mk/Make.IRIX64

commit 3914f4b1da7b469dd526e71ae4b1a38697fe81af
Author: car <car>
Date:   Thu Sep 16 16:12:45 2004 +0000

    intel8 bug fixes

Src/F_BaseLib/bl_constants.f90
Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/box.f90
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_main.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_util.f90
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_main.f90
Tools/F_mk/GMakedefs.mak
Tools/F_mk/GNUmakefile

commit 71082b1b66b5ca445881163de236f406d204eac4
Author: car <car>
Date:   Wed Sep 15 22:22:18 2004 +0000

    windows fixes

Src/F_BaseLib/NPackage.mak
Tools/F_mk/NMakedefs.mak
Tools/F_mk/NMakerules.mak

commit 4e9324af3363f4a5732fe4fdfd2c8fe92e58d9a1
Author: car <car>
Date:   Mon Sep 13 19:55:34 2004 +0000

    *** empty log message ***

Src/F_BaseLib/f2kcli_crayx1.f90

commit 22edc03421c877e7662a4b9cb497e981633d5542
Author: vince <vince>
Date:   Mon Sep 13 19:02:23 2004 +0000

    flags for cxx.

Tools/C_mk/Make.OSF1

commit 5eb9e944c881b19365bd58ffe58b802189ae599d
Author: car <car>
Date:   Thu Sep 9 16:35:08 2004 +0000

    more spinning

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90
Tools/F_mk/GMakedefs.mak

commit fad650ffe77d0a924784a805b7d34080bc0e08aa
Author: car <car>
Date:   Tue Sep 7 16:22:00 2004 +0000

    minor changes

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab.f90
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_main.f90
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/stencil.f90
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_main.f90
Tools/F_mk/GMakedefs.mak

commit dfaa7e17b876648adba0af9f51a7f8aee123cf9d
Author: vince <vince>
Date:   Fri Sep 3 23:59:19 2004 +0000

    added check for capfinestlevel.

Src/C_AMRLib/StationData.cpp

commit 7186242283d9f921860bcb402eeb975e5238ec19
Author: welcome <welcome>
Date:   Fri Aug 27 17:47:57 2004 +0000

    Changed options for CRAYX1
    removed -O in C++, does nothing
    Default C++ optimization is -O2
    Added options for loopmark listings to see where vectorization happens.

Tools/C_mk/Make.CRAYX1

commit 0721b1a6e9c54c08ce58884e36b2c39d3afa9cca
Author: car <car>
Date:   Wed Aug 25 19:32:27 2004 +0000

    FCOMP=g77

Tools/C_mk/Make.defs

commit 78227cec8f992cb727bd78f957002d229087993c
Author: car <car>
Date:   Tue Aug 24 22:33:16 2004 +0000

    Intel/Lahey fix

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit b6b3876ce21d3c85c1fefa364086f3438c6ebf07
Author: marc <marc>
Date:   Mon Aug 16 22:40:50 2004 +0000

    Add test for max ref ratio in PROTECT_INTERP

Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F

commit 42213ab3e7f8f0f99dfd38007cee05fed2fa55f1
Author: car <car>
Date:   Thu Aug 5 22:21:54 2004 +0000

    slight changes

Src/F_BaseLib/knapsack.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_util.f90
Src/LinearSolvers/F_MG/stencil.f90

commit d7c55d06cb4d582ba4080feb17071333b9283539
Author: car <car>
Date:   Thu Aug 5 16:45:18 2004 +0000

    windows fixes

Src/F_BaseLib/bl_IO.f90
Src/F_BaseLib/cluster.f90
Src/LinearSolvers/F_MG/stencil.f90

commit a5e885339f38f1c37c64f826e6ce56a41bbfcf82
Author: car <car>
Date:   Wed Aug 4 22:46:08 2004 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/ml_restriction.f90

commit f2cb29f722b89a083fe64e11b6c8496dac94f42f
Author: car <car>
Date:   Wed Aug 4 19:53:26 2004 +0000

    more mboxarray stuff

Src/F_BaseLib/mboxarray.f90

commit 756e43d7e5989346222168c84f4eece12fb89440
Author: car <car>
Date:   Wed Aug 4 00:52:04 2004 +0000

    windows update

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 9a5a2a140c7a1647969c29ac447d2299ffb0a486
Author: car <car>
Date:   Tue Aug 3 22:47:17 2004 +0000

    *** empty log message ***

Src/F_BaseLib/bndry_reg.f90
Src/LinearSolvers/F_MG/stencil.f90

commit e15eba5661180ed9a116cf62c40e0aa123e736e3
Author: car <car>
Date:   Mon Aug 2 22:11:38 2004 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/stencil.f90

commit 8fdbc1627b54ab4cd4c36e0035cf2e729a599e33
Author: car <car>
Date:   Fri Jul 30 18:01:29 2004 +0000

    minor tweaks

Src/LinearSolvers/F_MG/mg_smoother.f90
Tools/F_mk/GMakedefs.mak

commit 3ff88aa9cf8c8b1fa856825bfb7be2b36c97696f
Author: car <car>
Date:   Fri Jul 30 17:46:49 2004 +0000

    smaller files

Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_prolongation.f90
Src/LinearSolvers/F_MG/mg_restriction.f90
Src/LinearSolvers/F_MG/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/ml_prolongation.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/ml_util.f90

commit c624c543ec9448bd9be99313e97208d3531acc55
Author: car <car>
Date:   Thu Jul 29 20:32:23 2004 +0000

    altrix

Tools/C_mk/Make.defs

commit a6abde51ce08d701a3f978f065ae43f4859e7a31
Author: car <car>
Date:   Thu Jul 29 18:53:12 2004 +0000

    altix

Src/C_BaseLib/FPC.cpp

commit 66444630a78fd470bff7a33d591cb367e610fe26
Author: car <car>
Date:   Thu Jul 29 15:35:03 2004 +0000

    crayx1

Tools/C_mk/Make.CRAYX1

commit 0a3ea4370183b38a1d24a15661279aa7fb37f961
Author: welcome <welcome>
Date:   Wed Jul 28 20:48:30 2004 +0000

    Modification for NEC SX6.
    Needed to explicitly strip-mine the main loops in
    hgrlxu.  Brain-dead Sx6 compiler partially vectorizes
    the loop but needs to allocate temporary array.  Makes an
    assumption about the max length of the loop and generates a
    run-time error if the actual length is larger than the assumption.
    Can request larger array with pragma, but only up to about 15000.
    New function only called on SX6, since not very well tested.

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit bcd9aa399274b832d785a63881f741262d593d71
Author: welcome <welcome>
Date:   Wed Jul 28 20:20:24 2004 +0000

    try again to update makefiles for NEC SX6

Tools/C_mk/Make.SUPERUX
Tools/C_mk/Make.defs

commit d55a7cd6eee2e8085271a117702a1c5aa085beee
Author: welcome <welcome>
Date:   Wed Jul 28 19:52:18 2004 +0000

    Minor updates for NEC SX6

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/FPC.cpp

commit 9b50bfe4844a7ff665dc40968bcc03780edc832a
Author: car <car>
Date:   Wed Jul 28 18:06:05 2004 +0000

    fixes for X1

Tools/C_mk/Make.CRAYX1

commit 3109abab5c734ebbfda7e6ff83d6e87e952efa60
Author: vince <vince>
Date:   Tue Jul 27 22:51:25 2004 +0000

    added std::

Src/C_AMRLib/DatasetClient.cpp

commit 0a08b7a9e78466a69fa82e0e6d38ee53d3dc526d
Author: vince <vince>
Date:   Mon Jul 26 22:24:29 2004 +0000

    call fix for arrayview.

Src/C_AMRLib/DatasetClient.cpp

commit b6470af68cfe86d4d9767e556579a6d79f36a22a
Author: car <car>
Date:   Mon Jul 26 20:49:39 2004 +0000

    *** empty log message ***

Src/F_BaseLib/bl_types.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/t_main.f90

commit 72eb71b04bab1b3469925fe0943ecbefed88c197
Author: car <car>
Date:   Mon Jul 26 20:49:09 2004 +0000

    gfortran trial

Tools/F_mk/GMakedefs.mak

commit d8f0312c52423a26e21cb2d66f4c0c0c7fd1e453
Author: car <car>
Date:   Mon Jul 26 20:48:18 2004 +0000

    cray x1 fixes

Src/F_BaseLib/f2kcli_crayx1.f90
Tools/F_mk/GMakedefs.mak

commit 308db54d460fdb8dbad5403af95938440698fa97
Author: car <car>
Date:   Mon Jul 26 19:37:21 2004 +0000

    ihi->ilo

Src/F_BaseLib/interp.f90

commit 20fedb2cbf8671afe781adf8651a3a5ab68f986a
Author: car <car>
Date:   Mon Jul 26 19:36:59 2004 +0000

    pointer association, not

Src/F_BaseLib/cluster.f90

commit f3bf137f66b946ad676032f6678fb56810ffb456
Author: car <car>
Date:   Mon Jul 26 19:25:57 2004 +0000

    broken unitialized variables on IRIX

Tools/F_mk/GMakedefs.mak

commit 97953be18556308271ff62f4a8f1951b4edde0ca
Author: car <car>
Date:   Fri Jul 23 23:37:28 2004 +0000

    cray bug work around

Src/F_BaseLib/boxarray.f90

commit 1888a52fa5ede2af987007a8e5c7ccd94cbf6ba3
Author: car <car>
Date:   Fri Jul 23 22:04:22 2004 +0000

    crayx1

Src/F_BaseLib/f2kcli_crayx1.f90
Tools/F_mk/GMakedefs.mak

commit 46459cb7b8f6284cf822bf8af741d526d25e68b5
Author: car <car>
Date:   Thu Jul 22 17:33:12 2004 +0000

    CRAY X1 port

Src/C_BaseLib/CoordSys.cpp
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Tools/C_mk/Make.CRAYX1
Tools/C_mk/Make.defs

commit d5281354df394c07d44db1b9c9b0f3071d26cca5
Author: car <car>
Date:   Thu Jul 22 17:31:33 2004 +0000

    fix for CRAY X1

Src/C_BaseLib/FPC.cpp
Src/C_BaseLib/winstd.H

commit 348b0bf434400904cf7278c2011c85ec0e2088fa
Author: car <car>
Date:   Wed Jul 21 23:50:01 2004 +0000

    Makes CRAY X1 a little happier

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Pointers.H

commit 1362c09f91d617c59fa7e1e510a9fd18d83df8f5
Author: marc <marc>
Date:   Thu Jul 15 17:16:50 2004 +0000

    Add BL_NOLINEVALUES to list of defines

Tools/C_scripts/dsp.mak

commit 133ce1eed5dd67ef9739913841fed502bc118ec6
Author: car <car>
Date:   Fri Jul 2 19:59:25 2004 +0000

    new types definitions

Src/F_BaseLib/bl_types.f90

commit 78f388b9cd6870a2f51a89b84c82498d3eb0268d
Author: car <car>
Date:   Wed Jun 30 22:10:48 2004 +0000

    testing purposes

Src/F_BaseLib/bl_types.f90
Src/F_BaseLib/multifab.f90

commit 0662eb229b121158dbe08197d2be39e53fdb97be
Author: almgren <almgren>
Date:   Tue Jun 29 20:19:45 2004 +0000

    Removed some print statements.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 17c27aeec444f0e5418724f6fad9c0210c55ac12
Author: almgren <almgren>
Date:   Tue Jun 29 19:58:48 2004 +0000

    Removed print statements.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit bc5ce3c98e8c2ffa54cc56546866e1fe1f9e6452
Author: car <car>
Date:   Mon Jun 28 16:00:30 2004 +0000

    minor fixes

Src/F_BaseLib/BoxLib.f90
Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/test/fornberg_weights.f90
Tests/F_BaseLib/fornberg_weights.f90
Tools/F_mk/GMakedefs.mak

commit 2c963801d3556c895be08460ad0c907dd467801e
Author: car <car>
Date:   Mon Jun 28 15:57:33 2004 +0000

    *** empty log message ***

Src/F_BaseLib/bl_IO.f90
Tools/F_scripts/coco/coco.pl
Tools/F_scripts/coco/e1.FF
Tools/F_scripts/coco/e1.II

commit c4eff2651ec9e8ba6f9d224ba72bdb058ed807e6
Author: almgren <almgren>
Date:   Fri Jun 25 22:38:30 2004 +0000

    Typo: had ny instead of nx.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 3173d662efb5c335c65bc9f546e6c6f875af41e1
Author: almgren <almgren>
Date:   Fri Jun 25 20:01:32 2004 +0000

    Changes to accomodate Neumann bcs in the case of factor 4 refinement.
    Change also relevant for factor 2 but that already worked.
    This uses values inside the domain instead of those reflected
    outside by Neumann condition (which didn't exist for factor 4).

Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 72277441416649dbd9ed2223111ae43f1ac21687
Author: almgren <almgren>
Date:   Thu Jun 24 22:06:30 2004 +0000

    Fix in nodal_restriction_2d which gives same (working) result for factor 2
    refinement but fixes the (broken) factor 4 refinement.  Only fixed in 2d for now.

Src/LinearSolvers/F_MG/mg.f90

commit d9dcffe58a5fcca0ad26947c16ea89081614fc27
Author: almgren <almgren>
Date:   Thu Jun 24 20:23:14 2004 +0000

    Fixed code for Neumann boundary conditions in 2d and 3d.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit e5a97a70dd0385d345a25b2c3a5440bbc266343e
Author: almgren <almgren>
Date:   Thu Jun 24 20:22:32 2004 +0000

    Typo mis-spelling corrected.

Src/LinearSolvers/F_MG/stencil.f90

commit a8f52092276b16830a15c83e87106e59c875d2d7
Author: car <car>
Date:   Wed Jun 23 17:23:42 2004 +0000

    bl_kiss not needed

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/NPackage.mak
Src/F_BaseLib/bl_kiss.f90
Src/F_BaseLib/test/.cvsignore
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/.cvsignore
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_main.f90

commit 1debffcf8d56b68a72406d9f981e10ce1e0fd979
Author: car <car>
Date:   Tue Jun 22 16:42:05 2004 +0000

    *** empty log message ***

Tools/F_scripts/coco/coco_e.FF
Tools/F_scripts/coco/e1.FF
Tools/F_scripts/coco/e1.II

commit 002a20494cfd2fffaa1d87a1d37ac59c5689caa5
Author: car <car>
Date:   Tue Jun 22 16:42:05 2004 +0000

    *** empty log message ***

Tools/F_scripts/coco/coco_e.II

commit 05598a4b5e3ddf378d2818d3ba31b4c1849ac841
Author: car <car>
Date:   Tue Jun 22 16:42:05 2004 +0000

    *** empty log message ***

Tools/F_scripts/coco/coco.pl

commit cd47cacf990f681764392dd640f63c72e2097d59
Author: car <car>
Date:   Tue Jun 22 15:11:43 2004 +0000

    initial

Tools/F_scripts/coco/coco.pl

commit 08daff055e395e9b6396e385688b0109d0aa60ab
Author: almgren <almgren>
Date:   Fri Jun 18 17:18:18 2004 +0000

    Need to check _comp instead of COMP

Tools/F_mk/GMakedefs.mak

commit 7c2c9a3724804c65febd18ba5c1d70c8d7e80626
Author: lijewski <lijewski>
Date:   Tue Jun 15 19:24:16 2004 +0000

    Added -mp flag

Tools/C_mk/Make.defs

commit 67e8ca16a59070abfc328003c5e76a4fb9c70df7
Author: car <car>
Date:   Fri Jun 11 21:42:21 2004 +0000

    *** empty log message ***

Src/F_BaseLib/bl_timer.f90

commit d441d2ad5827c0cc10c433b8c8422a907c4ab0cf
Author: car <car>
Date:   Fri Jun 11 03:50:41 2004 +0000

    timer

Src/F_BaseLib/bl_timer.f90
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_main.f90
Src/F_BaseLib/timer_c.c
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_main.f90

commit 550399b831fe42849beee923bc8198964ebca937
Author: car <car>
Date:   Tue Jun 8 18:14:34 2004 +0000

    *** empty log message ***

Tools/F_mk/GMakerules.mak

commit f5e8ec7ad959a77bccb8d2e4b10b21da4f4a7b9f
Author: car <car>
Date:   Tue Jun 8 01:01:16 2004 +0000

    *** empty log message ***

Src/F_BaseLib/list_box.f90
Src/F_BaseLib/test/makefile
Tests/F_BaseLib/makefile

commit f3b08ec15b3d863aa0b82cc9eed8cc0f0c2c0ccf
Author: car <car>
Date:   Mon Jun 7 16:05:55 2004 +0000

    *** empty log message ***

Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/test/.cvsignore
Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/def_knapsack.out
Src/F_BaseLib/test/t_knapsack.f90
Tests/F_BaseLib/.cvsignore
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/def_knapsack.out
Tests/F_BaseLib/t_knapsack.f90

commit 9deaadcc0d7dff926602a2f16d4d16a67e1a4216
Author: car <car>
Date:   Mon Jun 7 15:56:59 2004 +0000

    formatted output

Src/F_BaseLib/test/knapsack.out
Tests/F_BaseLib/knapsack.out

commit b38c28277d814911d49d6b41e6be4394e44dfba4
Author: car <car>
Date:   Sat Jun 5 16:23:08 2004 +0000

    *** empty log message ***

Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/test/knapsack.out
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/knapsack.out
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_main.f90
Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak
Tools/F_scripts/f90doc/stmts.pl

commit 30def42a45e9e77a5879014f3e37e4cafefd06f9
Author: car <car>
Date:   Sat Jun 5 15:29:01 2004 +0000

    conn_defs no longer uses processor defs

Src/F_BaseLib/test/conn_defs
Tests/F_BaseLib/conn_defs

commit 544ae6e27c4192943b1d48cdf965be58db9bc928
Author: car <car>
Date:   Sat Jun 5 15:07:18 2004 +0000

    *** empty log message ***

Src/F_BaseLib/GPackage.mak
Tools/F_mk/GMakedefs.mak

commit 32923c8d61b0594d4f7500f0c79625774c5429ba
Author: car <car>
Date:   Sat Jun 5 00:16:42 2004 +0000

    Fixes for Intel8

Src/F_BaseLib/cluster.f90
Src/F_BaseLib/test/inputs.domain
Src/F_BaseLib/test/main.f90
Tests/F_BaseLib/inputs.domain
Tests/F_BaseLib/main.f90
Tools/F_mk/GMakedefs.mak

commit b86e8be454c12b06ab9730c6a4aa128db758b2fe
Author: car <car>
Date:   Fri Jun 4 17:03:19 2004 +0000

    OMP typos

Src/F_BaseLib/multifab.f90
Src/LinearSolvers/F_MG/mg_smoother.f90

commit 7dda15991a1e9f703b74ed9e05c6b84498f06303
Author: car <car>
Date:   Fri Jun 4 16:48:42 2004 +0000

    OMP typos

Src/F_BaseLib/multifab.f90
Src/F_BaseLib/test/GNUmakefile
Tests/F_BaseLib/GNUmakefile

commit 8ce4a8da7388c1c84b6641684befe8fc23c8861e
Author: car <car>
Date:   Thu Jun 3 21:10:20 2004 +0000

    86 ieee

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_ieee.f90
Src/F_BaseLib/bl_ieee_c.c
Src/F_BaseLib/bl_ieee_c.h
Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/t_ieee.f90
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/stencil.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/t_ieee.f90
Tools/F_mk/GMakedefs.mak

commit a569d2c0255f18bb0529aa526ff416438280f8c8
Author: car <car>
Date:   Tue Jun 1 04:46:59 2004 +0000

    more refinements on windows makefiles

Src/F_BaseLib/NPackage.mak
Src/F_BaseLib/test/makefile
Tests/F_BaseLib/makefile
Tools/F_mk/NMakedefs.mak
Tools/F_mk/NMakerules.mak
Tools/F_scripts/mkdep.pl

commit d93a11da628024d44d1c94a1eee2fda0a537a1d0
Author: car <car>
Date:   Mon May 31 19:29:17 2004 +0000

    *** empty log message ***

Src/F_BaseLib/NPackage.mak
Src/F_BaseLib/f2kgetcl.c
Src/F_BaseLib/test/makefile
Tests/F_BaseLib/makefile
Tools/F_mk/NMakedefs.mak
Tools/F_mk/NMakerules.mak

commit 8365d270a128ceee7c4391dfba2254120d2d0127
Author: car <car>
Date:   Sun May 30 04:09:53 2004 +0000

    *** empty log message ***

Src/F_BaseLib/bl_ieee_c.c
Src/F_BaseLib/bl_ieee_c.h
Tools/F_mk/GMakedefs.mak
Tools/F_scripts/mkdep.pl

commit 9fe5839da5e4608cd5c083a6dee5c8c2f480bd43
Author: car <car>
Date:   Sat May 29 22:07:59 2004 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak
Tools/F_scripts/mkdep.pl

commit 58bc4962376b68e9cfcf6683417d74e92f4a2431
Author: car <car>
Date:   Sat May 29 19:02:46 2004 +0000

    *** empty log message ***

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_ieee.f90
Src/F_BaseLib/bl_ieee_c.c
Src/F_BaseLib/bl_ieee_c.h
Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_ieee.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_ieee.f90
Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak
Tools/F_scripts/mkdep.pl

commit 098db076c129dc9f0bb60e5157721550b029d93e
Author: car <car>
Date:   Sat May 29 16:05:34 2004 +0000

    *** empty log message ***

Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/test/inputs.domain
Src/F_BaseLib/test/main.f90
Tests/F_BaseLib/inputs.domain
Tests/F_BaseLib/main.f90

commit 4782accff44a0f4cf304d29607c92d907c0f5c7f
Author: car <car>
Date:   Fri May 28 22:48:01 2004 +0000

    john wants comments

Src/F_BaseLib/bl_IO.f90
Src/F_BaseLib/bl_constants.f90
Src/F_BaseLib/bl_error.f90
Src/F_BaseLib/bl_kiss.f90
Src/F_BaseLib/bl_mem_stat.f90
Src/F_BaseLib/bl_parmparse.f90
Src/F_BaseLib/bl_types.f90
Src/F_BaseLib/fab.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/test/GNUmakefile
Tests/F_BaseLib/GNUmakefile

commit e06a3f12cbd66f0dd32cc7ba77402322593dbde0
Author: car <car>
Date:   Thu May 27 22:32:25 2004 +0000

    more makefile fixes

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/plotfile.f90
Src/F_BaseLib/test/GNUmakefile
Tests/F_BaseLib/GNUmakefile
Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak

commit 27a86f6ad538b56412f29743adbc2c1a64616204
Author: car <car>
Date:   Wed May 26 21:48:51 2004 +0000

    *** empty log message ***

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_main.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_main.f90

commit fc12903af2d0e16c470bf031403f679c4af7b2ec
Author: car <car>
Date:   Wed May 26 13:05:51 2004 +0000

    *** empty log message ***

Src/F_BaseLib/test/.cvsignore

commit ef34454c74163d63f407ba9fc2fe3f65a90c9972
Author: car <car>
Date:   Wed May 26 13:01:39 2004 +0000

    *** empty log message ***

Src/F_BaseLib/test/.cvsignore
Tests/F_BaseLib/.cvsignore

commit f875d0d5f67eca98a3d252d279e909c6210469db
Author: car <car>
Date:   Wed May 26 13:01:39 2004 +0000

    *** empty log message ***

Tests/F_BaseLib/.cvsignore

commit 8be21aae9c6b61a34deaf56f6827a4c080e76c7e
Author: car <car>
Date:   Tue May 25 22:39:51 2004 +0000

    *** empty log message ***

Src/F_BaseLib/multifab.f90
Src/F_BaseLib/test/main.f90
Src/LinearSolvers/F_MG/mg.f90
Tests/F_BaseLib/main.f90
Tools/F_mk/GMakedefs.mak

commit 8fbb967b3079c98b174edb55bc20f68904c8324e
Author: car <car>
Date:   Tue May 25 04:27:55 2004 +0000

    module name mismatch

Src/F_BaseLib/bl_parmparse.f90

commit 89ebce2878defb9d7d2b9677d14f5efc101da032
Author: car <car>
Date:   Tue May 25 04:12:59 2004 +0000

    *** empty log message ***

Src/F_BaseLib/test/t_boxlib.dsp
Src/F_BaseLib/test/t_boxlib.dsw
Tests/F_BaseLib/t_boxlib.dsp
Tests/F_BaseLib/t_boxlib.dsw

commit 98fa928ae008e1595afaf0cff3998d43f8067c13
Author: car <car>
Date:   Tue May 25 04:03:19 2004 +0000

    missed bl_parmparse.f90

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/NPackage.mak

commit 8314d7c60db83fa52e727066c60fd4c5f525fc3a
Author: car <car>
Date:   Tue May 25 02:00:45 2004 +0000

    aux-->extern

Src/LinearSolvers/F_MG/GPackage.mak

commit 020c950d64118a90ba0abbd0f55b20f2fadc4b3a
Author: car <car>
Date:   Mon May 24 22:58:04 2004 +0000

    f90doc; mostly ignore for now

Src/F_BaseLib/test/main.f90
Tests/F_BaseLib/main.f90
Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak
Tools/F_scripts/f90doc/expr_parse.pl

commit fa3ef910b4ae91c7057b95f1872fd83f407c89f7
Author: car <car>
Date:   Mon May 24 22:40:52 2004 +0000

    add f90doc; you never know

Tools/F_scripts/f90doc/README
Tools/F_scripts/f90doc/expr_parse.y
Tools/F_scripts/f90doc/f90doc
Tools/F_scripts/f90doc/htmling.pl
Tools/F_scripts/f90doc/stmts.pl
Tools/F_scripts/f90doc/typing.pl
Tools/F_scripts/f90doc/utils.pl

commit 0ee73d45fb8afae08d784dc9e5c0457ee64fce1c
Author: car <car>
Date:   Mon May 24 22:32:37 2004 +0000

    *** empty log message ***

Src/F_BaseLib/NPackage.mak

commit 263cd08a67aaca75c893dab9194a2f32c7ff8004
Author: car <car>
Date:   Mon May 24 22:25:41 2004 +0000

    *** empty log message ***

Tools/F_mk/NMakedefs.mak
Tools/F_mk/NMakerules.mak

commit 0faefcccb4ad935852813de2c3aad01a0e7260e5
Author: car <car>
Date:   Mon May 24 22:11:02 2004 +0000

    *** empty log message ***

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_mem_stat.f90
Src/F_BaseLib/filler.f90
Src/F_BaseLib/plotfile.f90
Src/F_BaseLib/test/t_main.f90
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/stencil.f90
Tests/F_BaseLib/t_main.f90

commit f3745eef3e58d5c07adb3db5f8be101bf731e03c
Author: car <car>
Date:   Mon May 24 22:10:10 2004 +0000

    split files

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_IO.f90
Src/F_BaseLib/bl_kiss.f90
Src/F_BaseLib/bl_mem_stat.f90
Src/F_BaseLib/bl_parmparse.f90
Src/F_BaseLib/bl_stream.f90
Src/F_BaseLib/bl_string.f90
Src/F_BaseLib/bl_timer.f90
Src/F_BaseLib/bl_utility.f90

commit da197d87ad085003077387284a2bbb3f38e7a8f7
Author: car <car>
Date:   Mon May 24 21:59:14 2004 +0000

    *** empty log message ***

Tools/F_scripts/ibm_sp_batch.poe

commit 1aaf5c7151e8875fab661929d609700835dd26bb
Author: car <car>
Date:   Mon May 24 21:50:06 2004 +0000

    Initial revision

Src/F_BaseLib/BoxLib.f90
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_constants.f90
Src/F_BaseLib/bl_error.f90
Src/F_BaseLib/bl_space.f90
Src/F_BaseLib/bl_types.f90
Src/F_BaseLib/bl_utility.f90
Src/F_BaseLib/bndry_reg.f90
Src/F_BaseLib/box.f90
Src/F_BaseLib/box_util.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/cluster.f90
Src/F_BaseLib/f2kcli.f90
Src/F_BaseLib/f2kcli_nag.f90
Src/F_BaseLib/f2kcli_win32.f90
Src/F_BaseLib/f2kgetcl.c
Src/F_BaseLib/fab.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/interp.f90
Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/list_box.f90
Src/F_BaseLib/mboxarray.f90
Src/F_BaseLib/mpi.f
Src/F_BaseLib/mt19937ar.f90
Src/F_BaseLib/multifab.f90
Src/F_BaseLib/omp.f90
Src/F_BaseLib/omp_stubs.f90
Src/F_BaseLib/parallel.f90
Src/F_BaseLib/parallel_stubs.f90
Src/F_BaseLib/pingpong.f90
Src/F_BaseLib/plotfile.f90
Src/F_BaseLib/ppm_util.f90
Src/F_BaseLib/ppm_util_c.c
Src/F_BaseLib/sort_box.f90
Src/F_BaseLib/sort_d.f90
Src/F_BaseLib/sort_i.f90
Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/conn_defs
Src/F_BaseLib/test/inputs.domain
Src/F_BaseLib/test/knapsack.out
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_main.f90
Src/F_BaseLib/timer_c.c
Src/F_BaseLib/vector_i.f90
Src/LinearSolvers/F_MG/GPackage.mak
Src/LinearSolvers/F_MG/itsol.f90
Src/LinearSolvers/F_MG/mg.f90
Src/LinearSolvers/F_MG/mg_cpp.f90
Src/LinearSolvers/F_MG/mg_smoother.f90
Src/LinearSolvers/F_MG/sparse_solve.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/conn_defs
Tests/F_BaseLib/inputs.domain
Tests/F_BaseLib/knapsack.out
Tests/F_BaseLib/main.f90
Tests/F_BaseLib/t_main.f90
Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak
Tools/F_mk/GNUmakefile
Tools/F_mk/NMakedefs.mak
Tools/F_mk/makefile
Tools/F_scripts/moddep.pl
Tools/F_scripts/tcsort.pl

commit f5619a2794aafe4b14a61214c30e674bb7d060a6
Author: car <car>
Date:   Mon May 24 21:50:06 2004 +0000

    Initial revision

Tests/LinearSolvers/F_MG/regression
Tests/LinearSolvers/F_MG/t_smoother.f90

commit 1c8619f3d541fbe7029babca8e11ffa44bff5f8f
Author: vince <vince>
Date:   Fri Apr 30 21:11:23 2004 +0000

    index type fix.

Src/C_BaseLib/BoxList.cpp

commit 5908d8e24e300eb83d50efcf2383787efe67a632
Author: car <car>
Date:   Tue Apr 27 17:04:05 2004 +0000

    no longer builds by default

Src/C_BaseLib/GNUmakefile

commit b5b10e660c2dd68a205c9810be6600f272641623
Author: car <car>
Date:   Tue Apr 27 17:00:44 2004 +0000

    cout -->> std::cout needed by gcc 3.4.0

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/test/GNUmakefile
Tests/C_BaseLib/GNUmakefile

commit bfb44ed8c6eff8483d150bc1e28f61a367feb140
Author: car <car>
Date:   Wed Mar 31 23:18:22 2004 +0000

    some checks for vismf file correctnes

Src/C_BaseLib/VisMF.cpp

commit 48121aad6be2757996c87616fa0042340d824fcd
Author: almgren <almgren>
Date:   Tue Mar 16 20:50:52 2004 +0000

    OOPS last time - should have deleted this line from every case,
    not added it for the i-face.   Test that this is correct is that
    coarse residual sums to zero - only true for this line missing.

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit df3071e0c190d2c0ce8d53ad5b0928f4b25a73d9
Author: almgren <almgren>
Date:   Tue Mar 16 20:00:49 2004 +0000

    Missing line "fac0 = fac0 / (...)" in the case of faces in the i-direction
    only; this scaling was there for faces in the j- and k-direction.  Would
    only affect multilevel solves in 3-d.

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit 61c0dbd4e43129b6207a89de65667d5bc9d671a0
Author: car <car>
Date:   Tue Mar 9 18:35:37 2004 +0000

    PathScale support

Tools/C_mk/Make.Linux

commit 4526d09dda96c071aa9a356c8c1076b3f94b0a3f
Author: car <car>
Date:   Tue Mar 9 18:28:51 2004 +0000

    cpp seems to the right way to invoke pre-processor

Tools/C_mk/Make.Linux

commit 9d0f54d13f5e3f0ff8597786e1180daa06a6314a
Author: car <car>
Date:   Mon Mar 8 23:06:36 2004 +0000

    swap is never defined, but declared

Src/C_BaseLib/Array.H

commit b382a5a1f71010f2e2c7d9b8d8500230caab7e36
Author: car <car>
Date:   Fri Mar 5 17:53:30 2004 +0000

    obsolete

Src/C_BaseLib/test/tThread.cpp
Tests/C_BaseLib/tThread.cpp

commit c457d0225eecaad35f3448288e859c0aa992e979
Author: car <car>
Date:   Fri Mar 5 17:49:38 2004 +0000

    make tests compile

Src/C_BaseLib/test/t8BIT.cpp
Src/C_BaseLib/test/tCArena.cpp
Src/C_BaseLib/test/tFAC.cpp
Src/C_BaseLib/test/tFB.cpp
Src/C_BaseLib/test/tMF.cpp
Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/t8BIT.cpp
Tests/C_BaseLib/tCArena.cpp
Tests/C_BaseLib/tFAC.cpp
Tests/C_BaseLib/tFB.cpp
Tests/C_BaseLib/tMF.cpp
Tests/C_BaseLib/tVisMF.cpp

commit 105a26bc47c76a4a87498eccee926a84714e15c4
Author: car <car>
Date:   Thu Mar 4 18:09:40 2004 +0000

    PathScale

Src/C_BaseLib/FPC.cpp

commit 6a1ca0c41878d45dfe2f386fe23b52787d44ca57
Author: car <car>
Date:   Thu Mar 4 18:09:01 2004 +0000

    *** empty log message ***

Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/tFB.cpp
Src/C_BaseLib/test/tMF.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/tFB.cpp
Tests/C_BaseLib/tMF.cpp

commit fdf90cb12a75a199755b2b1a5ee858792fa1da92
Author: car <car>
Date:   Fri Feb 27 21:20:32 2004 +0000

    We should care if the bottom solve fails, print a warning and break;
    what really should matter is that the composite solve itself converge.

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 91da88c2dc81ab9332f5705e516b70f30d2a979e
Author: car <car>
Date:   Thu Feb 19 18:17:54 2004 +0000

    valgrind: tuples constructors have default values

Src/C_BaseLib/Tuple.H

commit f68c9820572b559c5d0069571833db77c1f7860d
Author: car <car>
Date:   Thu Feb 19 17:52:40 2004 +0000

    valgrind says that dx is uninitialized, 0 is a reasonable bad value for dx

Src/C_BaseLib/CoordSys.cpp

commit e8bfcde9e87fd02585ddd506440f612f0119176c
Author: car <car>
Date:   Wed Feb 11 20:26:28 2004 +0000

    SUPERUX is the sx-6

Src/C_BaseLib/Thread.H
Src/C_BaseLib/winstd.H

commit f8c8dea0dd284ffa6da9551b492b918bff4bae31
Author: car <car>
Date:   Thu Feb 5 23:23:51 2004 +0000

    SX-6 specific stuff, note that SUPER-UX ==> SUPERUX

Tools/C_mk/Make.SUPERUX
Tools/C_mk/Make.defs

commit 8854279f81d19c994bac32fb4500ebfbc9440083
Author: lijewski <lijewski>
Date:   Wed Jan 21 21:04:13 2004 +0000

    First version.

Src/C_BaseLib/test/tParmParse.cpp
Tests/C_BaseLib/tParmParse.cpp

commit f4811db0cbaf970c658b7ab699e6c874b44d1956
Author: lijewski <lijewski>
Date:   Tue Jan 20 21:54:10 2004 +0000

    Added tParmParse

Src/C_BaseLib/test/GNUmakefile
Tests/C_BaseLib/GNUmakefile

commit f04fd6367f7ad54753abf6c4fae26d14509d6a11
Author: lijewski <lijewski>
Date:   Tue Jan 20 21:53:31 2004 +0000

    fixed bug

Src/C_BaseLib/ParmParse.cpp

commit 0fe0fedd7925651f0264b6fdacdae52655faa144
Author: car <car>
Date:   Wed Jan 7 21:45:03 2004 +0000

    tweak for std::size_t

Src/C_BaseLib/winstd.H

commit 450004ef4fdb0a791fa84d5c414e3f250d0618dd
Author: car <car>
Date:   Wed Jan 7 21:44:20 2004 +0000

    windows tweaks for std::size_t

Src/C_BaseLib/Arena.H
Src/C_BaseLib/winstd.H

commit eb8e6571d31562f5b7c5d6750d6c9b702d45655d
Author: car <car>
Date:   Wed Jan 7 21:18:19 2004 +0000

    for some compilers size_t, pow, sqrt, etc, need to be in the std namespace

Src/C_AMRLib/Interpolater.cpp
Src/C_BaseLib/Arena.H
Src/C_BaseLib/Arena.cpp
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BArena.cpp
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/Utility.cpp
Src/C_BoundaryLib/InterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit e27febbc6acbd4508934d10c9afc08274fe28a90
Author: car <car>
Date:   Wed Dec 10 18:09:43 2003 +0000

    support for BGL and Intel 8.0

Tools/C_mk/Make.bgl
Tools/C_mk/Make.defs

commit 68c00965c66b9bb924e47795f05323f411a23850
Author: car <car>
Date:   Mon Dec 8 23:13:46 2003 +0000

    powerpc for BGL

Src/C_BaseLib/FPC.cpp

commit 9813060a6c43b7a9ff1bebee66b0c64f801e66d0
Author: marc <marc>
Date:   Wed Oct 15 18:01:33 2003 +0000

    Add quarter time levels into which_time

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit ec5c20fcf529fc9cddc5c67e3ba9cd56bdf4d487
Author: lijewski <lijewski>
Date:   Thu Sep 18 19:21:00 2003 +0000

    Got rid of cdir$ ivdep stuff

Src/LinearSolvers/C_CellMG/MG_2D.F
Src/LinearSolvers/C_CellMG/MG_3D.F
Src/LinearSolvers/C_NodalMG/amr_real2d.f
Src/LinearSolvers/C_NodalMG/amr_real3d.f
Src/LinearSolvers/C_NodalMG/hg_multi2d.f
Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f
Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.f
Src/LinearSolvers/C_NodalMG/hg_multi3d.f
Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f

commit 169470300821c1ad281336e35fb388d650f65713
Author: almgren <almgren>
Date:   Tue Sep 16 18:39:45 2003 +0000

    Changes in FORT_LINCCINTERP so that in the case of being next
    to a HOEXTRAP or EXT_DIR boundary, but with xok or yok (or zok)
    not true, we now use a correct stencil to incorporate a wall-based value
    instead of defaulting to the centered stencil as before.

Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F

commit 94c8ff0a7b3b97865478053197ee1dba5abd8514
Author: lijewski <lijewski>
Date:   Mon Sep 15 21:17:03 2003 +0000

    removed CellConservative

Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp

commit 952666bc8a067ba6345dcd87be6269d12cbadcec
Author: lijewski <lijewski>
Date:   Mon Sep 8 22:22:38 2003 +0000

    some bringing up-to-date

Tools/C_util/TV_TempWrite.H
Tools/C_util/ViewMF/GNUmakefile
Tools/C_util/ViewMF/MFNorm.cpp
Tools/C_util/ViewMF/viewMF.cpp
Tools/C_util/ViewMF/viewMFdiff.cpp

commit 1c7a99cc003251e1495e37760b72632d0ae8251d
Author: lijewski <lijewski>
Date:   Mon Sep 8 21:07:45 2003 +0000

    Make tags declaration & call of buffer() consistent.

Src/C_AMRLib/Amr.cpp

commit 1e1d43b7334b37d20d99253692dd1951a243eb16
Author: car <car>
Date:   Thu Aug 28 17:17:27 2003 +0000

    __amd64__

Src/C_BaseLib/FPC.cpp

commit 612841a382e8b490e580aec7a28a9db25767edb9
Author: car <car>
Date:   Tue Aug 19 15:19:42 2003 +0000

    strip72 doesn't work with f90

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit f319bf324f6470179bd5495ee7fd0a1462cb0c5f
Author: lijewski <lijewski>
Date:   Thu Aug 14 22:26:57 2003 +0000

    some cleanup

Src/C_AMRLib/TagBox.cpp

commit af6b09665cba93e5642c47ed05e170f5046561f9
Author: lijewski <lijewski>
Date:   Thu Aug 14 19:18:14 2003 +0000

    minimized comm costs in collate()

Src/C_AMRLib/TagBox.cpp

commit 89eb2fdcddd2955e69ef8ad326cefcbd02f12c04
Author: lijewski <lijewski>
Date:   Wed Aug 6 21:04:01 2003 +0000

    added -cm to Intel Fortran

Tools/C_mk/Make.defs

commit 725503ff2357d7bfb877887e8d52efea02c9c1d1
Author: car <car>
Date:   Wed Jul 30 15:07:34 2003 +0000

    debugging changes

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/main.cpp

commit 53f9fdf292774dcd2b502ed49bf443ae6ac3b6b9
Author: lijewski <lijewski>
Date:   Mon Jul 21 21:22:26 2003 +0000

    First cut -- can parse chemkin & therm files.

Tools/C_scripts/ckread.pl

commit 321d756216dd73561f7dc9f0e49994ff0e0cc58c
Author: lijewski <lijewski>
Date:   Fri Jul 18 04:57:11 2003 +0000

    Gather -> Alltoall

Src/C_AMRLib/FluxRegister.cpp

commit 5793060ba6707e44c4c1485f65bffa63f7a9d8b9
Author: lijewski <lijewski>
Date:   Fri Jul 18 04:51:46 2003 +0000

    Gather -> Alltoall

Src/C_BaseLib/FabArray.H

commit 8df5e30497bb73be236b1e1239f8ca2ed30c4edb
Author: car <car>
Date:   Tue Jul 8 20:48:23 2003 +0000

    cleanup

Src/LinearSolvers/C_TensorMG/visc2d.m

commit 338447b317701ee12a4f7064fa3fe9eeea7d0d8d
Author: car <car>
Date:   Tue Jul 8 20:19:30 2003 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/visc2d.m
Src/LinearSolvers/C_TensorMG/visc3d.m

commit e37180e343a793357618e8880811d089fdd42ca2
Author: car <car>
Date:   Tue Jul 8 20:04:02 2003 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/visc3d.m

commit bd20fd54deb9561905603611bf4c8d77cee9167e
Author: car <car>
Date:   Tue Jul 8 19:42:33 2003 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/visc3d.m

commit c653260b3034564b2c8c933b086d48d4beb2ba33
Author: car <car>
Date:   Tue Jul 8 19:10:52 2003 +0000

    stripped out mathematica code for tensor
    solve generation

Src/LinearSolvers/C_TensorMG/visc2d.m
Src/LinearSolvers/C_TensorMG/visc3d.m

commit 761f5559554cbf9328ae5f4e3ce2f87fab99f578
Author: car <car>
Date:   Sat Jul 5 15:22:30 2003 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/Format.m

commit 11fa162b784f7f4d045d850c0e9ab30c3d6b9f42
Author: car <car>
Date:   Fri Jul 4 21:58:36 2003 +0000

    Mathematica 5.0 fixes

Src/LinearSolvers/C_TensorMG/Format.m

commit d91b090bd1da8b2063466da4815723dd1fdd5491
Author: car <car>
Date:   Fri Jul 4 17:24:27 2003 +0000

    Mathematica packages need by the notebooks

Src/LinearSolvers/C_TensorMG/Format.m
Src/LinearSolvers/C_TensorMG/Optimize.m

commit 589383930debbda375cfe936fd5986835e4e7369
Author: lijewski <lijewski>
Date:   Tue Jun 24 17:18:21 2003 +0000

    merged in d_numPts()

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Cluster.cpp
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 33eec024160aa21341a80d672739022ba893a35f
Author: car <car>
Date:   Fri Jun 20 19:37:11 2003 +0000

    *** empty log message ***

Tools/C_mk/Make.IRIX64

commit 0e99f69af33816b1be198e9e5cfd37f01172c7a1
Author: car <car>
Date:   Fri Jun 13 22:03:23 2003 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.H

commit f921be8f91d44648345fdb2d8c529ad3484d8286
Author: car <car>
Date:   Fri Jun 13 19:50:47 2003 +0000

    inline out of order

Src/LinearSolvers/C_NodalMG/interface.H

commit 13b07d06cff803b6737df0fc097c5af84e596fb2
Author: car <car>
Date:   Wed Jun 4 21:41:56 2003 +0000

    redhat 7.1 fortran

Tools/C_mk/Make.defs

commit 734045541b9f06d521a81f7a39d1d6cab23e9c73
Author: vince <vince>
Date:   Wed May 21 22:47:52 2003 +0000

    fix for escher

Tools/C_mk/Make.defs

commit 3c0e9051a96249d241467be1ec21d7f135968139
Author: vince <vince>
Date:   Wed May 21 22:47:13 2003 +0000

    fix for escher.

Tools/C_mk/Make.IRIX64

commit d5bbf378c33d37710b33c69d2f9cb90603e7b1d3
Author: lijewski <lijewski>
Date:   Thu May 15 22:01:01 2003 +0000

    Removed the BL_PROFILE() line.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp

commit 2b8b11cd0c0a09e8c82474ad72eb0b449380d552
Author: car <car>
Date:   Fri Apr 11 17:16:06 2003 +0000

    redhat 7.1

Tools/C_mk/Make.defs

commit 0d69768010566ab9650d1f8104367be68e1a50be
Author: marc <marc>
Date:   Wed Apr 9 22:35:24 2003 +0000

    change constant to a long

Src/C_BaseLib/DistributionMapping.cpp

commit b0b3ee7e639c67048b289fbad24b3bc91abb6bad
Author: car <car>
Date:   Thu Apr 3 18:44:31 2003 +0000

    flush at end of grid log entry

Src/C_AMRLib/Amr.cpp

commit 715c0c9983f41a19129448c3cd8fafb97f5b7d38
Author: marc <marc>
Date:   Fri Mar 14 23:44:57 2003 +0000

    fixes to be compatible with g++ 3.x in cygwin

Tools/C_mk/Make.CYGWIN_NT
Tools/C_mk/Make.defs

commit 01d26baee407a99f8d9530091d720f41abaed912
Author: lijewski <lijewski>
Date:   Wed Mar 12 21:03:32 2003 +0000

    fixed divide by zero in verbose output

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 3a37037c3b89cdf5e282e73073f926032aea8adc
Author: lijewski <lijewski>
Date:   Wed Mar 12 20:54:59 2003 +0000

    fixed divide by zero in verbose output

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit c588d28f1f27ee3569b66c8175693f688e5a2fd5
Author: lijewski <lijewski>
Date:   Fri Mar 7 17:39:39 2003 +0000

    set_preferred_boundary_values() now takes a MultiFab

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 17934d081fd7d522d1766ea973bf2edbff08c6e4
Author: lijewski <lijewski>
Date:   Fri Mar 7 16:59:25 2003 +0000

    ParmParse'd in max_efficiency

Src/C_BaseLib/DistributionMapping.cpp

commit 91f89ba86a00d3aaeb0480fc76e09390419b2a9d
Author: lijewski <lijewski>
Date:   Thu Mar 6 23:57:38 2003 +0000

    wrapped knapsack times in verbose

Src/C_BaseLib/DistributionMapping.cpp

commit 5d896e2d8930bc0746523723bf2741576f466418
Author: lijewski <lijewski>
Date:   Thu Mar 6 22:34:56 2003 +0000

    print out some knapsack() timings

Src/C_BaseLib/DistributionMapping.cpp

commit cbbb293a5d960946077aaef80d7eff48d71137c6
Author: lijewski <lijewski>
Date:   Fri Feb 28 22:42:15 2003 +0000

    removed the static collate space in TagBox

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit a4bd2b3b9c8b9498a32280d2e809db4140902f16
Author: lijewski <lijewski>
Date:   Wed Feb 26 18:07:08 2003 +0000

    added verbose option

Src/C_BaseLib/DistributionMapping.cpp

commit 6ec44fc73e90b675e74635e08cf4868e224d42d7
Author: car <car>
Date:   Fri Feb 21 22:49:10 2003 +0000

    compiles, probably doesn't work in parallel

Tools/C_mk/Make.defs

commit 57ad6e6cdc0a616220dbbdcce393180a7eeeaf77
Author: almgren <almgren>
Date:   Wed Feb 19 18:34:19 2003 +0000

    New routine, pressure_project, to be used for initializing calculations
    with hydrostatic (from gravity) background.

Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 62296b694eac8cfd44c13794a64e58aa1ec6718e
Author: almgren <almgren>
Date:   Tue Feb 18 21:13:18 2003 +0000

    Removed all calls to writeMF.

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit d56befc9e41f49ab9a0ef8ca5838e6daf45819a6
Author: car <car>
Date:   Tue Feb 18 20:55:00 2003 +0000

    strstream -> sstream

Src/C_AMRLib/AmrLevel.cpp

commit d83b75735f561defddedeebd75d49938523b726b
Author: car <car>
Date:   Tue Feb 18 20:54:40 2003 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/ABec_UTIL.F

commit ce6e0af8b5dbdf02eaee192e23bbc3a08f334674
Author: car <car>
Date:   Wed Feb 12 22:31:53 2003 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit 4c72b831d8b00afb33666f897ffae5349e78ae44
Author: car <car>
Date:   Wed Feb 12 22:31:12 2003 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit f1637be2c6f96281767bf30868cbc7a261c1f41a
Author: car <car>
Date:   Fri Feb 7 17:42:26 2003 +0000

    minor problem, periodic fillpatch

Src/C_AMRLib/AmrLevel.cpp

commit 161db21b36badb73074def18226a5a4cd6f9fb49
Author: car <car>
Date:   Fri Feb 7 16:34:12 2003 +0000

    some additional diagnostics; now don't solve the CGSolve if norm is initially zero.

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 03715082ffcd77c6cc7e21fbc530642446e0e3ac
Author: lijewski <lijewski>
Date:   Thu Feb 6 18:14:29 2003 +0000

    more work on bunching fill operations

Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp

commit a679c7618e6747df72479af6bd726652a8a93784
Author: car <car>
Date:   Wed Feb 5 16:33:24 2003 +0000

    fixes, I think, for Intel compilers

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit fad563c0eeef71f93b763084a64c04482dd62ddc
Author: marc <marc>
Date:   Tue Jan 28 20:55:35 2003 +0000

    Modernize lib builder

Tools/C_scripts/dsp.lib.mak

commit 82b0803bb5bbe06388e88faa262602cacb7b625a
Author: car <car>
Date:   Mon Jan 27 17:10:36 2003 +0000

    bl_pd_is_ioproc

Src/C_BaseLib/ParallelDescriptor.cpp

commit adad6f8e742b0a41d4d35bf4731ea82206a912ae
Author: car <car>
Date:   Thu Jan 23 20:10:01 2003 +0000

    win32 hates templates

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp

commit 500ece7296685f2b84d19deadf9f62de43499d19
Author: lijewski <lijewski>
Date:   Wed Jan 22 22:39:44 2003 +0000

    Mods to Fill_Boundary() multiple comps at once

Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp

commit 2a3543ed41de014f1372678be3ad2a58fd63fa60
Author: car <car>
Date:   Wed Jan 22 19:19:27 2003 +0000

    optimization for Intel compilers

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit a5053aed5f5717b6b8a2ed38402ac5aa495d13e3
Author: car <car>
Date:   Fri Jan 3 19:25:11 2003 +0000

    foolish mistakes

Src/C_BaseLib/BLParmParse_F.f
Src/C_BaseLib/ParmParse.cpp

commit 30dadbe53189ff65b62b403be9f658f93d42cbbc
Author: car <car>
Date:   Thu Jan 2 22:30:26 2003 +0000

    libpthread

Tools/C_mk/Make.Linux

commit acd76cf215c915b954a166f04af5d232bba44cc9
Author: car <car>
Date:   Thu Jan 2 14:59:30 2003 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 7865f7e58332280a1dadcc65ea37bd5da8c3229b
Author: almgren <almgren>
Date:   Mon Dec 30 22:09:45 2002 +0000

    Making area(i,j) = abs(a) instead of area(i,j) = a in FORT_SETAREA
    for the r-z case.   NOte that FORT_SETVOL and all other cases
    of FORT_SETAREA already return guaranteed-positive values.

Src/C_BaseLib/COORDSYS_2D.F

commit 26a212be6b475b0f2d0c32264acf3bcc31ca3e3e
Author: car <car>
Date:   Fri Dec 20 23:05:39 2002 +0000

    fix for FluxRegister::ADD

Src/C_AMRLib/FluxRegister.cpp

commit fd11da5ca05136380eb4db57b50231f378647b75
Author: lijewski <lijewski>
Date:   Wed Dec 18 18:44:23 2002 +0000

    fixed comment

Src/C_BaseLib/FabArray.H

commit 2674c6524d33b6a6b1740743cb6fe730f37f0ead
Author: almgren <almgren>
Date:   Tue Dec 17 22:19:56 2002 +0000

    Fix for inflow on hi-side boundaries...was screwing up before,
    all better now.

Src/LinearSolvers/C_NodalMG/boundary.cpp

commit 5a07382eef110431ae4aea1a7d0d7f1b43f4e0d6
Author: almgren <almgren>
Date:   Wed Dec 11 20:43:22 2002 +0000

    In the case where the fine cells didn't cover all of the coarse cell
    being interpolated from, there was an index bust.  It has been fixed
    so that the fine correction is only modified on cells where it actually
    exists.

Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F

commit 2152679bba5b03276479a979f683970aca9ce2b9
Author: almgren <almgren>
Date:   Wed Dec 11 18:33:45 2002 +0000

    Should have used cvol instead of ratiox*ratioy for denominator in icase=1.

Src/C_AMRLib/INTERP_2D.F

commit d9fdc4b91ab6904f3880bcde5d402a0e385609fd
Author: lijewski <lijewski>
Date:   Wed Dec 11 17:02:16 2002 +0000

    removed an assertion that isn't correct in serial

Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/FabSet.cpp

commit a1fd088bf66c550635412b84b9ac65a9a30a5e54
Author: lijewski <lijewski>
Date:   Tue Dec 10 20:31:14 2002 +0000

    Commented out HeaviestCPU() stuff used by MinimizeCommCosts().

Src/C_BaseLib/DistributionMapping.cpp

commit e6ecdbf163d9743b5be30f2698d12052cc7d165a
Author: lijewski <lijewski>
Date:   Sat Dec 7 16:25:26 2002 +0000

    fixed syntax error

Src/C_AMRLib/INTERP_3D.F

commit 38d05ddbe20c614e4bf49e02f32390b936b8fc1e
Author: lijewski <lijewski>
Date:   Sat Dec 7 16:09:16 2002 +0000

    increased the cache hit rate

Src/C_BoundaryLib/FabSet.cpp

commit 3361b505a057f66ec163a6b015c4c694423780e3
Author: almgren <almgren>
Date:   Sat Dec 7 05:59:35 2002 +0000

    Do the right thing for icase=1 when fine_state is zero to
    start with.  Same as the recent fixes in 3d.

Src/C_AMRLib/INTERP_2D.F

commit c1eb130b1c8baba1282201b0b55b845701c7102f
Author: almgren <almgren>
Date:   Sat Dec 7 05:57:09 2002 +0000

    Same problem as before for icase=1; the correction wasn't being
    zeroed out first for states which were 0 at first.

Src/C_AMRLib/INTERP_3D.F

commit caa3d5539d4a1ed310d2fb6ba5161f446304db48
Author: lijewski <lijewski>
Date:   Wed Dec 4 23:06:53 2002 +0000

    same error in plus() as in copy() in CrseInit

Src/C_AMRLib/FluxRegister.cpp

commit 756ac6a78d2c01c820b6c220bd268506ee22f10e
Author: lijewski <lijewski>
Date:   Tue Dec 3 18:35:38 2002 +0000

    improved FillPeriodic cache hit ratio

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit be231ae5b2c5c69d9f6853e46baa37f4404a1827
Author: lijewski <lijewski>
Date:   Tue Dec 3 18:03:27 2002 +0000

    improved FillBoundary cache hit ratio

Src/C_BaseLib/MultiFab.cpp

commit 2b16013bf7c7a9f506c8cd766001596d3028303d
Author: lijewski <lijewski>
Date:   Tue Dec 3 00:02:42 2002 +0000

    added new accessor functions

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/ParallelDescriptor.H

commit 69746209bd0f94cdcf56f1c4625030a32561c497
Author: jbb <jbb>
Date:   Mon Dec 2 20:45:01 2002 +0000

    Need to restrict the copy in FluxRegister::CrseInit to be only
    on the region that was just filled from the coarse grid, NOT from
    the whole fab, some of which is still unfilled.  This was causing
    errors and core dumps.

Src/C_AMRLib/FluxRegister.cpp

commit 8b7ad15d4a2a5c72df75493e79a739e077e50894
Author: car <car>
Date:   Fri Nov 29 22:12:18 2002 +0000

    no trailing semicolons

Src/C_BaseLib/SPECIALIZE_F.H

commit 01657d478e04e6736165273f03c5faba75eb554b
Author: car <car>
Date:   Wed Nov 27 21:54:19 2002 +0000

    replace a stop

Src/C_AMRLib/SLABSTAT_2D.F
Src/C_AMRLib/SLABSTAT_3D.F
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/LO_2D.F
Src/LinearSolvers/C_CellMG/LO_3D.F

commit 2e4b7ba23737dfc13a1d2987ab9e0a0a458cd36b
Author: lijewski <lijewski>
Date:   Tue Nov 26 22:47:22 2002 +0000

    modest performance improvement

Src/C_BoundaryLib/BndryData.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 97cb4a4633e4e46627e2abc43aa8f55dbc2f3352
Author: lijewski <lijewski>
Date:   Tue Nov 26 22:37:40 2002 +0000

    modest performance improvement

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 49dc138c33d022d8176e1fd4907123783dc6d2eb
Author: lijewski <lijewski>
Date:   Wed Nov 20 16:55:55 2002 +0000

    additional arg to compFlux()

Src/LinearSolvers/C_CellMG/ABecLaplacian.H

commit cc80d6936585ba1a8d61adc7fbe08d234f81a890
Author: lijewski <lijewski>
Date:   Wed Nov 20 16:52:07 2002 +0000

    Added addition signature for compFlux() that avoids applyBC() call.

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp

commit 8eb4eaee414420b7bc28d6b49622201955e0f753
Author: lijewski <lijewski>
Date:   Thu Nov 14 23:04:56 2002 +0000

    using bl_abort() in place of stop

Src/C_AMRLib/FLUXREG_1D.F
Src/C_AMRLib/FLUXREG_2D.F
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_BaseLib/COORDSYS_1D.F
Src/C_BaseLib/COORDSYS_2D.F
Src/C_BaseLib/COORDSYS_3D.F

commit f85903cd850607675118e37d0cbce3fcf818bc43
Author: lijewski <lijewski>
Date:   Thu Nov 14 21:13:08 2002 +0000

    removed statics from template functions

Src/C_BaseLib/FabArray.H

commit 4be714ff3257d058f54acae86af32c4f8be68c45
Author: car <car>
Date:   Thu Nov 14 18:43:29 2002 +0000

    *** empty log message ***

Src/C_BaseLib/BLBoxLib_F.f
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/ParallelDescriptor.cpp

commit 7193e1d202abd89e4876800059de5c5ac2ea3d9f
Author: marc <marc>
Date:   Thu Nov 14 07:08:32 2002 +0000

    Add option to add instead of copy on CrseInit operations

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 08de9f413e94f40128b6cc4c70d3979ccdcf2cef
Author: marc <marc>
Date:   Thu Nov 14 00:13:23 2002 +0000

    fix Mikes extra arg fix

Src/C_AMRLib/AmrLevel.cpp

commit 480e6fe980f95598113389e298afa55a3fec6988
Author: lijewski <lijewski>
Date:   Wed Nov 13 17:15:20 2002 +0000

    quiet valgrind

Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp

commit 53d6cbcea42557e63ce3a00377dce9aacd0223ed
Author: lijewski <lijewski>
Date:   Wed Nov 13 05:04:58 2002 +0000

    tad rearrangment

Src/C_AMRLib/AmrLevel.cpp

commit 36d8c65a5a033c010e1941622da3de95e5b02159
Author: lijewski <lijewski>
Date:   Tue Nov 12 20:49:35 2002 +0000

    to shut up valgrind

Src/C_BaseLib/PArray.H

commit 505c846edac761e2ae386fb5ddb80e1811b7dec8
Author: lijewski <lijewski>
Date:   Tue Nov 12 17:08:48 2002 +0000

    fixed mismatched deltes

Src/C_BoundaryLib/InterpBndryData.cpp

commit 254736d9c60ceec0f69583f0fb3e7b0832992b30
Author: lijewski <lijewski>
Date:   Mon Nov 11 17:49:53 2002 +0000

    can now do some semblance of tracing

Src/C_BaseLib/BLProfiler.cpp

commit ff96744ce6912a7306142a91196ec4dd5d8188f1
Author: almgren <almgren>
Date:   Sun Nov 10 14:57:54 2002 +0000

    Modified icase=1 in PROTECT_INTERP to fix a problem
    with case 1, which wasn't setting the correction to zero
    for states that were zero, it was leaving the previous
    value in there.  Now the correction is set to zero there.

Src/C_AMRLib/INTERP_3D.F

commit 31f98fee1409d5f0a09608026e42d3c7216b3281
Author: lijewski <lijewski>
Date:   Sat Nov 9 02:15:52 2002 +0000

    more BL_PROFILE()s

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/StateData.cpp

commit 18019d63ac055e084bc890ae5c813017fa6e8ccf
Author: lijewski <lijewski>
Date:   Fri Nov 8 22:00:51 2002 +0000

    added some BL_PROFILE()s

Src/C_AMRLib/Interpolater.cpp

commit b7bd003484aca82bf97ee5dbb22cd7e36417a523
Author: car <car>
Date:   Fri Nov 8 18:34:42 2002 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/lo_bctypes.fi

commit 4012fb309c2b49d6f7773d381f1d4f4f2c8fbae0
Author: lijewski <lijewski>
Date:   Thu Nov 7 19:04:01 2002 +0000

    specialized performCopy() for Reals

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H

commit f91b2f0b39b94c85e20ebbd1e528b637df571060
Author: lijewski <lijewski>
Date:   Wed Nov 6 20:51:41 2002 +0000

    tad bit o cleanup

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp

commit 3d7a8aa0c950c1223c3db89646dd3356d47e9045
Author: almgren <almgren>
Date:   Tue Nov 5 21:21:58 2002 +0000

    Restored cmax and cmin seeing the corner data (we believe it should be there).
    Put a test for alpha > 1.
    Protected against divide by zero in computation of alpha.

Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F

commit b40fc4bfda877c01e2cb246501490e04b059ea43
Author: lijewski <lijewski>
Date:   Tue Nov 5 21:06:17 2002 +0000

    +K2 -> +K1

Tools/C_mk/Make.AIX

commit aa9585bcd7f92a98a327ea3bbd94310c8404c8c1
Author: lijewski <lijewski>
Date:   Tue Nov 5 05:34:21 2002 +0000

    removed extraneous end do

Src/C_AMRLib/INTERP_3D.F

commit 4cbc9c55ff3f7d923ed19a6f415fde1366f6e48e
Author: almgren <almgren>
Date:   Mon Nov 4 18:43:06 2002 +0000

    Modified calculation of cmax/cmin in CCINTERP so that it doesn't
    see corner values, which may not be filled since they aren't used
    in the actual slope calculation.

Src/C_AMRLib/INTERP_2D.F

commit 9e609e50c1ae1b3c9e072335a0eb56ca584dd3f0
Author: almgren <almgren>
Date:   Mon Nov 4 18:39:50 2002 +0000

    Modified the calculation of cmax/cmin in CCINTERP so that it
    doesn't see corner values (since they may not be filled, they
    aren't used in the slope calculations.)

Src/C_AMRLib/INTERP_3D.F

commit e17587188be2c1708ec9b9e169e9e6fa5a747a66
Author: lijewski <lijewski>
Date:   Thu Oct 31 21:59:21 2002 +0000

    Added -qrtti=all when debugging.

Tools/C_mk/Make.AIX

commit 484e5fbc9f7d6c0de13e80b7e58dcacee6dbb14a
Author: lijewski <lijewski>
Date:   Thu Oct 31 21:56:33 2002 +0000

    removed excess profiling gunk

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/FabArray.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 346cf29ced1c7b6ad64a48c83574bcefddc34a4c
Author: lijewski <lijewski>
Date:   Thu Oct 31 21:01:30 2002 +0000

    removed excess profiling gunk

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 1a01907925bcea1b0edaded06326db47523f4ac5
Author: car <car>
Date:   Thu Oct 31 18:44:00 2002 +0000

    fixes for microsoft

Src/C_BaseLib/ParallelDescriptor.H

commit aeea97f88c55acf1792879eedc951fcd5f7a8cac
Author: car <car>
Date:   Thu Oct 31 18:09:00 2002 +0000

    some inlineing

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit fae73cc1d989ae2102e1b33a0aaabb8d3dc1e565
Author: lijewski <lijewski>
Date:   Thu Oct 31 17:01:50 2002 +0000

    more profiling stuff

Src/C_BaseLib/BaseFab.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 5ba370a33ce47756edf8b54202b95a2ae9a5597b
Author: lijewski <lijewski>
Date:   Wed Oct 30 21:33:13 2002 +0000

    added some profiling calls

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit d45db96ffb9d19a087a8066f32daf960c2346c54
Author: lijewski <lijewski>
Date:   Fri Oct 25 22:21:44 2002 +0000

    speed improvements

Src/C_BaseLib/Utility.cpp

commit 95e0a7e42a1dc4feb7861f6f97e620cf88a2ceac
Author: lijewski <lijewski>
Date:   Thu Oct 24 21:56:00 2002 +0000

    added InvNormDist stuff

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit ae1e9ee145564c4bd377cbad07b5bc9a48d9fe8c
Author: car <car>
Date:   Sat Oct 19 18:33:28 2002 +0000

    silence warnings

Src/C_AMRLib/INTERP_1D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F
Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F
Src/C_BoundaryLib/LO_UTIL.F

commit ba0d87804b39ccba24e503052bed9510617709da
Author: almgren <almgren>
Date:   Fri Oct 11 18:23:00 2002 +0000

    Missed a subcase in the first logic case.

Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F

commit 0e8cd2ad4039e70c27ce33732b9d0833c989045f
Author: car <car>
Date:   Fri Oct 11 18:20:44 2002 +0000

    improved error message

Src/C_BaseLib/BLProfiler.cpp

commit 9fdbf9c3bcf98fbbe7792b7fcd5b8ed6c0f7a20c
Author: car <car>
Date:   Fri Oct 11 18:20:29 2002 +0000

    profiling fix

Src/C_AMRLib/TagBox.cpp

commit a502f5fb4a927bf78e35d6caab01a76b891341ba
Author: car <car>
Date:   Fri Oct 11 13:28:27 2002 +0000

    more profiling

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.cpp

commit 66be8b254fbeb8cea6247c11a4158ebb50ab268e
Author: car <car>
Date:   Wed Oct 9 21:43:20 2002 +0000

    *** empty log message ***

Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/StateData.cpp

commit c6fa60fa81389130aa69826919ed2f242bd93aca
Author: car <car>
Date:   Wed Oct 9 13:59:04 2002 +0000

    more timers

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/TagBox.cpp

commit 5203e34cd5a4f28080a30fc14e2bd7ddb0fef229
Author: vince <vince>
Date:   Tue Oct 8 21:33:28 2002 +0000

    added ,n to a few crse reference.

Src/C_AMRLib/INTERP_3D.F

commit cca8c37fb9813fdd3497641bf619d59d5a59531c
Author: almgren <almgren>
Date:   Mon Oct 7 20:44:37 2002 +0000

    Fixes to CCINTERP which require that the new fine-grid values
    interpolated conservatively from the coarse grid not exceed any
    max's or min's of the local coarse grid values.  Does this by
    modifying the slopes which are used in the cell if a max/min
    would be violated by the slopes as first calculated.

Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/Interpolater.cpp

commit 8c69b84cb072ea0e7f114fdb27f1f57387c771aa
Author: lijewski <lijewski>
Date:   Mon Oct 7 20:28:10 2002 +0000

    remove MISMATCH stuff ...

Src/C_AMRLib/INTERP_2D.F

commit 531d19cd170b46a317dc9deb7e9f1327ab6db1b7
Author: car <car>
Date:   Sun Oct 6 18:02:43 2002 +0000

    more profiling

Src/C_BaseLib/DistributionMapping.cpp

commit f7504138cd96c300c9f302846dbdababd7cc21fe
Author: car <car>
Date:   Wed Oct 2 22:26:12 2002 +0000

    silence some warnings

Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f

commit 3dd2ce3a374ef9d005daa055f5c82c5e116a19d6
Author: marc <marc>
Date:   Tue Oct 1 23:56:07 2002 +0000

    Allow ratio up to 4 in protected interp func

Src/C_AMRLib/INTERP_3D.F

commit 32a6116cfa48df5044e6d3b94223bf58504431f1
Author: lijewski <lijewski>
Date:   Tue Oct 1 22:38:42 2002 +0000

    ensure sprintf() buffer big enough

Src/C_BaseLib/Utility.cpp

commit ca36981fded0c3b7e18e4e278394e4c3e8ed7aa2
Author: lijewski <lijewski>
Date:   Sat Sep 28 19:03:35 2002 +0000

    silenced compiler warnings

Src/C_AMRLib/Interpolater.cpp

commit 3d485d29b5ac39401f2a3ea10683e0ec9c2a87e6
Author: lijewski <lijewski>
Date:   Sat Sep 28 19:03:07 2002 +0000

    bug fix for AIX

Src/C_AMRLib/INTERP_F.H

commit ecf4f98604ca827c01d5df3d390ea594486a40f3
Author: almgren <almgren>
Date:   Fri Sep 27 19:20:00 2002 +0000

    New interpolation code which allows one to modify the interpolated corrections
    to a field in order to keep that field non-negative as much as possible.

Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp

commit d5999ba19e7245fb9e21b1318dd95d824b84df53
Author: lijewski <lijewski>
Date:   Mon Sep 23 19:06:21 2002 +0000

    *** empty log message ***

Tools/C_scripts/compressor

commit 5bb7f3784a3351a69c47c26f76003096fc6b4319
Author: car <car>
Date:   Mon Sep 23 17:02:45 2002 +0000

    compressor has a lock file

Tools/C_scripts/compressor

commit 086a9ed12c1dc17afc6d52add8d21f5ef77d9e32
Author: car <car>
Date:   Mon Sep 23 16:57:36 2002 +0000

    testing new compressor

Tools/C_scripts/compressor

commit 1cb7030bd95b4d6f2729a59b8630101feb0fc319
Author: car <car>
Date:   Thu Sep 19 21:02:14 2002 +0000

    do'h

Src/C_BaseLib/Utility.cpp

commit 80bc721221b65ae9880de59b7927475da313de08
Author: car <car>
Date:   Thu Sep 19 19:26:22 2002 +0000

    fort call to initrand

Src/C_BaseLib/Utility.cpp

commit ec727fe1794be20fc6d9bebc983cc78662c5e0e2
Author: lijewski <lijewski>
Date:   Fri Sep 13 19:19:41 2002 +0000

    Added MinimizeCommCosts()

Src/C_BaseLib/DistributionMapping.cpp

commit f20e5d2404fe54f82a41aaade32decf6cace5d09
Author: car <car>
Date:   Fri Sep 13 14:00:47 2002 +0000

    say GPROF=TRUE to got F/C/C++ -pg

Tools/C_mk/Make.defs

commit c6dbc5074154088b5363e7a0be4e53f3d08ce310
Author: car <car>
Date:   Tue Sep 10 19:41:59 2002 +0000

    3d corrected

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/inputs

commit fda9d4e22853bad18d7e98676d76a93d394ab1f1
Author: car <car>
Date:   Tue Sep 10 18:25:27 2002 +0000

    oops

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 0d14836dddbbd156d01f2d26f26a270ae0664393
Author: car <car>
Date:   Tue Sep 10 18:19:57 2002 +0000

    more debugging output

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit a87adc8fbfce9e8364ca121f575b2afc5e3cf28d
Author: car <car>
Date:   Tue Sep 10 16:03:05 2002 +0000

    3d re-rolled, un-rolled

Src/LinearSolvers/C_NodalMG/hg_multi3d.f
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f

commit 437e526cd7704d9961fc514adec9a1a826073cd5
Author: car <car>
Date:   Tue Sep 10 14:07:14 2002 +0000

    re-rolled, unrolled routines

Src/LinearSolvers/C_NodalMG/hg_multi2d.f
Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit 3518e7520b27a1639f3373c60b81d3fa31c7541e
Author: marc <marc>
Date:   Mon Sep 9 22:30:33 2002 +0000

    remove __kcc... define-it breaks compiles on brainerd

Tools/C_mk/Make.defs

commit 1130991912e375e12edb34a06fd8c05a96a41c9b
Author: car <car>
Date:   Mon Sep 9 22:00:57 2002 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.f
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 95abb36d22ce1895e05da54bb3b94e153e384740
Author: car <car>
Date:   Mon Sep 9 20:52:24 2002 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.f
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 87cf8b49d59d3759f3ad7d13ffdb1caa03b5dcea
Author: car <car>
Date:   Thu Sep 5 20:59:10 2002 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.f

commit 8aa42d2f46d65d00d3112b67e49194e5501d1aa0
Author: car <car>
Date:   Thu Sep 5 16:34:41 2002 +0000

    e200 might have been to fierce, changed 'infinity' to e50 (should still be ok for sne

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 131984a6d0c1cf9e834102ba4591d852c61c5ba3
Author: car <car>
Date:   Wed Sep 4 15:29:53 2002 +0000

    use .f not .F

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit daa43ff468f2048cd1a2cb0c6133ac24a431928e
Author: car <car>
Date:   Tue Sep 3 19:07:05 2002 +0000

    left in some debugging cruft

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 45b519044aaeb29a39df57191caedaf7647acf09
Author: car <car>
Date:   Tue Sep 3 18:10:30 2002 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_avg2d.f
Src/LinearSolvers/C_NodalMG/hg_multi2d.f
Src/LinearSolvers/C_NodalMG/hg_proj2d.f
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 892780a36164a4bab07f60a6564dee6e37db8fcf
Author: car <car>
Date:   Tue Sep 3 16:42:40 2002 +0000

    let fortran be fortran

Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/amr_real2d.f
Src/LinearSolvers/C_NodalMG/amr_real3d.f
Src/LinearSolvers/C_NodalMG/hg_avg2d.f
Src/LinearSolvers/C_NodalMG/hg_avg3d.f
Src/LinearSolvers/C_NodalMG/hg_multi2d.f
Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f
Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.f
Src/LinearSolvers/C_NodalMG/hg_multi3d.f
Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f
Src/LinearSolvers/C_NodalMG/hg_proj2d.f
Src/LinearSolvers/C_NodalMG/hg_proj3d.f

commit b50c054236c09a15d7d97b6b5068497ba25d1a01
Author: car <car>
Date:   Tue Sep 3 16:34:54 2002 +0000

    useless

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hgdebug.F
Src/LinearSolvers/C_NodalMG/hgdebug_F.H
Src/LinearSolvers/C_NodalMG/proj.cpp

commit f448aaad728b09ae23d8285d4a0cb781c2261946
Author: lijewski <lijewski>
Date:   Fri Aug 30 22:10:34 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.AIX

commit 6e9698914e0dbf3f5d14ca0f7b00236455571964
Author: car <car>
Date:   Thu Aug 29 22:17:09 2002 +0000

    silence a warning on int<>bool

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 1cfc1524c40272f7248febdb84d3cf44f15d0ed9
Author: car <car>
Date:   Thu Aug 29 22:14:34 2002 +0000

    single precision constants in fortran

Src/C_AMRLib/INTERP_1D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_BoundaryLib/LO_UTIL.F
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/CG_2D.F
Src/LinearSolvers/C_CellMG/CG_3D.F
Src/LinearSolvers/C_CellMG/LO_2D.F
Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/LP_2D.F
Src/LinearSolvers/C_CellMG/LP_3D.F

commit 75e851aea6c5803ab879246ac644e3beb6c10297
Author: car <car>
Date:   Thu Aug 29 18:03:15 2002 +0000

    some single precision constants

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 5fb0f316ff16b4cf62bea9902b19f9b7163ad892
Author: car <car>
Date:   Wed Aug 21 20:12:40 2002 +0000

    more e20/e30-->e200 changes

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.cpp
Src/C_BoundaryLib/BndryRegister.cpp

commit a25fd324826516cdca86733c95c2ff59c4ba74fa
Author: lijewski <lijewski>
Date:   Tue Aug 20 21:00:55 2002 +0000

    Increased data size ...

Tools/C_mk/Make.AIX

commit 2b2d5666aa603fbddee25430162a693b56e63e2d
Author: car <car>
Date:   Fri Aug 16 23:15:27 2002 +0000

    change infinity from e20 to e200

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit e2c51d309533bfa2f0f548b0af324e53904ecc8f
Author: car <car>
Date:   Fri Aug 16 22:07:07 2002 +0000

    Intel 7.0 support

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 3a7515b0f9c8d68bca3189f40d0bbc5598179ced
Author: car <car>
Date:   Wed Aug 7 17:23:56 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit d8f2bdc455d31edf768d12dd27951cd2ac63db79
Author: car <car>
Date:   Tue Aug 6 18:09:06 2002 +0000

    *** empty log message ***

Src/C_AMRLib/AmrLevel.cpp

commit d870ef0a36f6dcb19b93beaf2f927a2ec5e657f0
Author: car <car>
Date:   Mon Aug 5 15:41:22 2002 +0000

    remove intel temp files

Tools/C_mk/Make.rules

commit 7427a4a7866eebcfe980cb7e84b5288f6eefc087
Author: lijewski <lijewski>
Date:   Wed Jul 31 22:32:02 2002 +0000

    got formulas consistent

Src/C_AMRLib/FILCC_2D.F
Src/C_AMRLib/FILCC_3D.F

commit 9fa61cd28ad07414990b1d8986b34302a84f2694
Author: car <car>
Date:   Wed Jul 24 23:42:57 2002 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 6782ca0fe1b7c19a1bb2857ce210a1bdfb063b9c
Author: car <car>
Date:   Wed Jul 24 21:18:16 2002 +0000

    changed bicg so that if the solution criteria is met before the iteration begins, we return

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 2368bb7149d361939260ae5f8bb1a908585501d5
Author: lijewski <lijewski>
Date:   Thu Jul 18 21:28:15 2002 +0000

    *** empty log message ***

Src/C_AMRLib/FILCC_2D.F
Src/C_AMRLib/FILCC_3D.F

commit b48618e7202859294e216e9fcaa10f06deaebcbf
Author: lijewski <lijewski>
Date:   Fri Jul 12 23:07:38 2002 +0000

    was NOT right

Src/C_BaseLib/DistributionMapping.cpp

commit 4d5a8e5d0cd18780d68c0b1337e785d827098efd
Author: marc <marc>
Date:   Wed Jun 26 18:06:44 2002 +0000

    Add lf to result file

Tools/C_scripts/dsp.mak

commit 98379250a4fdb114636d94cc8bba4baca924f07d
Author: marc <marc>
Date:   Wed Jun 26 00:02:01 2002 +0000

    Fix up dsp generation to allow config changes, ie independent/concurrent Release and Debug builds

Tools/C_scripts/dsp.mak

commit ca798c2bc5a2048b5ac256645935c51a3d1cbe96
Author: car <car>
Date:   Thu Jun 20 18:28:00 2002 +0000

    another fortran header file

Src/C_AMRLib/bc_types.fi

commit 6b219edf149a7e7f0a9869544a2de1b83c3d7ab3
Author: car <car>
Date:   Thu Jun 20 15:59:36 2002 +0000

    allow upper/lower case in fortran INCLUDE

Tools/C_scripts/mkdep

commit c5ef9fbed828d9d5dfbfaf589d354083f580c7d6
Author: car <car>
Date:   Wed Jun 19 22:21:38 2002 +0000

    *** empty log message ***

Src/C_BaseLib/BLParmParse_F.f
Src/C_BaseLib/ParmParse.cpp

commit 4c58c90be78480141c334b3b47004f0a719c6ea6
Author: car <car>
Date:   Wed Jun 19 20:49:44 2002 +0000

    *** empty log message ***

Src/C_BaseLib/BLutil_F.f
Src/C_BaseLib/ParmParse.cpp

commit 06922d8e36d12d16952b98ab83cdedd511746ca0
Author: car <car>
Date:   Tue Jun 18 16:28:28 2002 +0000

    cvs strings

Src/C_BaseLib/BLParmParse_F.f
Src/C_BaseLib/BLutil_F.f

commit 870972d45e985d3e259c261235ff73f843dbf62e
Author: car <car>
Date:   Tue Jun 18 14:26:24 2002 +0000

    better support for \.f files

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 7f4aa43a363242269f7a4b0fe721dfa3b25c9874
Author: car <car>
Date:   Mon Jun 17 22:00:17 2002 +0000

    added arrays

Src/C_BaseLib/BLParmParse_F.f
Src/C_BaseLib/BLutil_F.f
Src/C_BaseLib/ParmParse.cpp

commit b474e39c9d1b750c2fa2d7a06b184ff439f77a7f
Author: car <car>
Date:   Mon Jun 17 19:40:42 2002 +0000

    Fortran includes with -fortran flag

Tools/C_mk/Make.Linux
Tools/C_mk/Make.rules

commit 3410838317d865b756d8175b3e7f9fd8ae97fc76
Author: car <car>
Date:   Mon Jun 17 19:40:27 2002 +0000

    mkdep now parsers fortran includes when the -fortran flag is thrown

Tools/C_scripts/mkdep

commit a0fd7606d21641f8eceadc4886d75acb9b3838d9
Author: lijewski <lijewski>
Date:   Mon Jun 17 19:36:46 2002 +0000

    *** empty log message ***

Src/C_BaseLib/BLParmParse_F.f

commit 13ae96f51edc13c50ded158c5ab718d2f678005c
Author: car <car>
Date:   Mon Jun 17 19:34:49 2002 +0000

    *** empty log message ***

Src/C_BaseLib/BLParmParse_F.f
Src/C_BaseLib/Make.package

commit cc816f44390244e5c1bd98c9b22aeb7949ae4296
Author: car <car>
Date:   Mon Jun 17 17:01:27 2002 +0000

    isStateVariable, is a bool

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 9f3af684759e38a1e41dd82d120a7ee009815876
Author: car <car>
Date:   Mon Jun 17 17:00:40 2002 +0000

    *** empty log message ***

Src/C_BaseLib/BLParmParse_F.f
Src/C_BaseLib/BLutil_F.f
Src/C_BaseLib/Make.package
Src/C_BaseLib/ParmParse.cpp

commit 62487cd895f2cf4451e5a98f8bb414410f8f9ced
Author: car <car>
Date:   Tue Jun 4 17:42:37 2002 +0000

    Some support for GCC 3.1

Tools/C_mk/Make.defs

commit e52f1864c6678726d8a9f68348849a17fd6b3f52
Author: car <car>
Date:   Tue Jun 4 16:48:48 2002 +0000

    add DIMARG;
    Use BL_USE_FORT_STAR_PRECISION to get real*8 and real*4 instead of DOUBLE PRECISION and REAL

Src/C_BaseLib/ArrayLim.H
Src/C_BaseLib/BLFort.H
Src/C_BaseLib/REAL.H

commit 85f8184c54e8e692c2a2c988806fd5dd92daefe7
Author: car <car>
Date:   Wed May 29 22:37:47 2002 +0000

    gcc 3.1 needs to include <iterator>

Src/C_BaseLib/BLProfiler.cpp

commit 3c5ff8414379af709c801bf0a0225a7356925de6
Author: marc <marc>
Date:   Tue May 28 23:21:12 2002 +0000

    Add a routine to hoextrap to cc

Src/C_AMRLib/FILCC_2D.F

commit 60d35a70847e39cdfa239074de9099a2b50c003c
Author: car <car>
Date:   Thu May 23 22:22:49 2002 +0000

    set BL_FORT_STRICT_REAL_T if you want
    REAL_T to be DOUBLE PRECISION or REAL depending on BL_USE_FLOAT setting

Src/C_BaseLib/REAL.H

commit 856e6b2015d110bf03e88c8204a885ff0b512a5a
Author: car <car>
Date:   Thu May 23 19:10:38 2002 +0000

    BoxLib\BLFort.H

Src/C_BaseLib/BLFort.H

commit 9a9c90382cfb5664fbdd0e96b0fc8c3a0f896618
Author: car <car>
Date:   Thu May 23 18:22:13 2002 +0000

    *** empty log message ***

Src/C_BaseLib/Make.package

commit 8f0b24e39552727029ee606c3d0d09c9a9ea37bf
Author: car <car>
Date:   Thu May 23 18:21:48 2002 +0000

    BLFort macros useful for FORTRAN calls

Src/C_BaseLib/BLFort.H

commit 940fa27cf58e1e99db878aa4faae4b52dbe26756
Author: vince <vince>
Date:   Thu May 23 18:21:10 2002 +0000

    some changes for opal.

Tools/C_mk/Make.OSF1
Tools/C_mk/Make.mpi

commit 12035cc561613134cf8fdb30535f37176f39b287
Author: lijewski <lijewski>
Date:   Mon May 20 22:14:20 2002 +0000

    -O3 -> -O2 due to xlF bug in tranfit_d.f

Tools/C_mk/Make.AIX

commit 040acc7ddd42fcc9a548b94e8324b4bd31de235e
Author: car <car>
Date:   Wed May 1 03:37:32 2002 +0000

    The *.dsp files were not maintained

Src/C_AMRLib/amrlib.dsp
Src/C_BaseLib/BoxLib.dsp
Src/C_BoundaryLib/bndrylib.dsp
Src/LinearSolvers/C_CellMG/mglib.dsp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 8b695acb730f697a2562acfce08438fc50499b4e
Author: marc <marc>
Date:   Sat Apr 27 07:10:24 2002 +0000

    generalize a bit

Tools/C_util/WritePlotFile.H
Tools/C_util/WritePlotFile.cpp

commit f1cad0030afae6d6d8c33daa35f9f910520aa5e7
Author: marc <marc>
Date:   Sat Apr 27 07:07:41 2002 +0000

    Allow making a geom without needing a ParmParse file

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 5e821ad28503e7c5d09c38b76c33deb981f168e2
Author: car <car>
Date:   Fri Apr 26 22:40:00 2002 +0000

    BL_USE_SETBUF removed from command line;
    set in BoxLib/winstd.H, if needed

Src/C_BaseLib/winstd.H
Tools/C_mk/Make.defs
Tools/C_util/WritePlotFile.cpp
Tools/C_util/dbgTools/crsGrids.cpp
Tools/C_util/dbgTools/intersectGrids.cpp

commit 6af280487e478bd9528929dd624b6b92766a3fa3
Author: car <car>
Date:   Fri Apr 26 22:24:43 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux
Tools/C_mk/Make.rules

commit 2db9f68924721cbd7fd41c7dbdd98a39660e8e78
Author: lijewski <lijewski>
Date:   Fri Apr 26 22:10:01 2002 +0000

    defaulted BL_LANG_CC

Src/C_AMRLib/BC_TYPES.H
Src/C_AMRLib/FLUXREG_F.H
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/MAKESLICE_F.H
Src/C_AMRLib/PROB_AMR_F.H
Src/C_AMRLib/SLABSTAT_F.H
Src/C_BaseLib/COORDSYS_F.H
Src/C_BaseLib/SPACE.H
Src/C_BoundaryLib/INTERPBNDRYDATA_F.H
Src/LinearSolvers/C_CellMG/ABec_F.H
Src/LinearSolvers/C_CellMG/CG_F.H
Src/LinearSolvers/C_CellMG/LO_F.H
Src/LinearSolvers/C_CellMG/LP_F.H
Src/LinearSolvers/C_CellMG/MG_F.H
Src/LinearSolvers/C_TensorMG/DivVis_F.H
Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_F.H
Src/LinearSolvers/C_TensorMG/MCLO_F.H
Src/LinearSolvers/C_TensorMG/Test/main_F.H
Tests/LinearSolvers/C_TensorMG/main_F.H
Tools/C_util/Convergence/AVGDOWN_F.H

commit 72a1d03386fae19231022abd12ea0779d778c05e
Author: car <car>
Date:   Wed Apr 24 22:25:20 2002 +0000

    another fix for ICC

Src/C_BaseLib/winstd.H

commit 574ef73b4a28fcfdbca7ba053edd12dbcb1fea5e
Author: car <car>
Date:   Wed Apr 24 17:55:30 2002 +0000

    support for 6.0 Intel compilers

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit f8ce7a3781f013ec24040b7beadafc917d94c884
Author: vince <vince>
Date:   Wed Apr 17 22:22:19 2002 +0000

    added flag for null KCC version parse.

Src/C_BaseLib/VisMF.cpp
Tools/C_mk/Make.defs

commit 077213ebc1d162afde9b9123616d9eed2d3a26da
Author: vince <vince>
Date:   Tue Apr 16 18:06:28 2002 +0000

    added synchronization of random tables in parallel.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/PROB_AMR_F.H

commit fd04f5708d0d9d0d1af9471074494d80d804a3a3
Author: lijewski <lijewski>
Date:   Tue Apr 16 15:20:28 2002 +0000

    forgot to update LDFLAGS earlier

Tools/C_mk/Make.AIX

commit 1b64dbd23147c7fc0f1ae0e0debdec575df98a4d
Author: car <car>
Date:   Mon Apr 15 20:12:26 2002 +0000

    oops

Src/C_BaseLib/BLThread.cpp

commit 20080f70db77a30681a8ffa25b7f888f9b10a37c
Author: car <car>
Date:   Fri Apr 12 17:24:52 2002 +0000

    tweak for f77/g77;
    if you compile COMP=Intel then FCOMP=Intel seems necessary for now.
    This is not enforced

Tools/C_mk/Make.Linux

commit 5c7a2c0773e02c3a28bb62feac1ebef7924098bb
Author: car <car>
Date:   Fri Apr 12 17:09:17 2002 +0000

    better support for icc

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 927d79f73ae31265e184fad78757ac48e3562620
Author: car <car>
Date:   Thu Apr 11 19:40:29 2002 +0000

    icc support

Src/C_BaseLib/Thread.H
Src/C_BaseLib/winstd.H
Tools/C_mk/Make.Linux

commit 03fb68a4c4694d283440640e67e9805521a8f31c
Author: car <car>
Date:   Mon Apr 8 20:51:36 2002 +0000

    *** empty log message ***

Src/C_BaseLib/Thread.H

commit abe496899780e8f5ae9b05ca854feb51b9524c3a
Author: car <car>
Date:   Mon Apr 8 20:46:46 2002 +0000

    max_threads is now unsigned long

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/Thread.H

commit ad5823674063b7226307993933b3738b7d29db5e
Author: car <car>
Date:   Mon Apr 8 17:25:05 2002 +0000

    f90 and f no longer preprocess, F90 and F do

Tools/C_mk/Make.rules

commit 9a8a1b911f93d255f5a447b6841a5332ee54226b
Author: car <car>
Date:   Sun Apr 7 17:00:44 2002 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp
Tools/C_mk/Make.FreeBSD

commit 7149fc2b9e8c8ac5799f322c687cc6f9c74405fb
Author: lijewski <lijewski>
Date:   Thu Mar 28 21:00:12 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.OSF1

commit 3164f52618fcd60f386c41419f895ef982f4dfd1
Author: car <car>
Date:   Wed Mar 27 23:58:50 2002 +0000

    std::abs on BL_OSF1

Src/C_BaseLib/winstd.H

commit e27cf9367d12fd77093e94a7ad7d2feac8994d18
Author: lijewski <lijewski>
Date:   Wed Mar 27 23:49:07 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.OSF1

commit 7333878ad4b08164f9b9482c928f01657bfe3ebf
Author: car <car>
Date:   Wed Mar 27 21:35:59 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.OSF1
Tools/C_mk/Make.mpi

commit f2721443b77418f19aeb312d70d1afe8bccfe20b
Author: lijewski <lijewski>
Date:   Wed Mar 27 19:21:54 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.AIX

commit aa3f0c2f3f32939b775485482478b146415b98f9
Author: lijewski <lijewski>
Date:   Wed Mar 27 17:54:34 2002 +0000

    mods to quiet xlC

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 87c77ee0ceb96093f54748c90cb80f1f0946211b
Author: lijewski <lijewski>
Date:   Wed Mar 27 17:10:20 2002 +0000

    *** empty log message ***

Src/C_AMRLib/AmrLevel.H

commit 24365ae040453080244bd4778051eed292bb64dd
Author: lijewski <lijewski>
Date:   Tue Mar 26 23:59:29 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.AIX

commit 3b8ed4dc17b8888ebe53ab6018f9fb9b41a946ae
Author: lijewski <lijewski>
Date:   Tue Mar 26 22:23:58 2002 +0000

    *** empty log message ***

Src/C_BaseLib/Utility.cpp

commit cf175d9315d0bcf95c1a2bb4d92c3caa1fcd9c6e
Author: car <car>
Date:   Tue Mar 26 22:15:43 2002 +0000

    different support for f90/f/F/F90

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit a7fc7b553a9c663f1bfb486b873d88de50c2221b
Author: car <car>
Date:   Tue Mar 26 22:14:33 2002 +0000

    only sleep

Src/C_BaseLib/BLThread.cpp

commit e2c3315aad6ba866765ce5d44d22c0d0b59013e9
Author: lijewski <lijewski>
Date:   Tue Mar 26 21:50:49 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.AIX
Tools/C_mk/Make.defs

commit 27820ad64fc914af3c60a5a28b59d09b43ba5f06
Author: lijewski <lijewski>
Date:   Tue Mar 26 20:47:02 2002 +0000

    changes to work with xlC

Src/C_BaseLib/ParmParse.cpp

commit 591aac8ab77eec16da762a4197127acec5447cf3
Author: lijewski <lijewski>
Date:   Tue Mar 26 20:04:06 2002 +0000

    changes to work with xlC

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 6e33ce42d26632a009bff83ef841a941372410b9
Author: car <car>
Date:   Fri Mar 22 23:29:24 2002 +0000

    Small change: Only print unused ParmParse variables if there are any unused
    ParmParse variables.

Src/C_BaseLib/ParmParse.cpp

commit 4ac41070023867262f02359288533f11e67c8e91
Author: vince <vince>
Date:   Thu Mar 21 00:41:08 2002 +0000

    added -ieee flag for opal.

Tools/C_mk/Make.OSF1

commit 1c99f4700776d8fd2fb36f6ad09013b5939f84f7
Author: almgren <almgren>
Date:   Mon Mar 18 22:31:54 2002 +0000

    Modifications needed to correct for the fact that the scalings of
    Du, S and DGphi are different between the v5 and v9 versions.

Src/LinearSolvers/C_NodalMG/hg_avg2d.F

commit 371fb5fcf915e402c611cf1147bfb617630b5bbf
Author: almgren <almgren>
Date:   Fri Mar 15 20:47:52 2002 +0000

    Modified the weighting of the source term in hgavg, hgfavg, hgcavg
    for use with the 9-pt instead of 5-pt stencil.

Src/LinearSolvers/C_NodalMG/hg_avg2d.F

commit f1a3087cf7e8179f3903f6d800fdd1153b20106f
Author: marc <marc>
Date:   Fri Mar 15 20:20:32 2002 +0000

    Rework frac calc to avoid using domain.numPts

Src/C_AMRLib/Amr.cpp

commit 159a754e6c3950ec0e05cbab6ae20e639ac39744
Author: marc <marc>
Date:   Fri Mar 15 19:01:47 2002 +0000

    dsp maker for libs

Tools/C_scripts/dsp.lib.mak

commit aeb78d0fa91c09a26738658c6d8fcb54cb2fa227
Author: car <car>
Date:   Thu Mar 14 23:56:07 2002 +0000

    fix for gcc3 and KCC

Tools/C_mk/Make.defs

commit bf27a7bdf755fa1001528656c824d999bcae062a
Author: car <car>
Date:   Thu Mar 14 23:05:16 2002 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 6f6956a84f0220fd334eede179441ee21bd54c4f
Author: vince <vince>
Date:   Thu Mar 14 01:48:58 2002 +0000

    changes for kcc 3.9

Tools/C_mk/Make.defs

commit f333f2ca4ca3ee5fc1da96df89133dcc6b94657c
Author: vince <vince>
Date:   Thu Mar 14 00:27:03 2002 +0000

    changes for brainerd.

Src/C_BaseLib/VisMF.cpp

commit 35b44a3dd1dedb52f5ebf1906a5b1ef57ec5b466
Author: almgren <almgren>
Date:   Wed Mar 13 22:07:49 2002 +0000

    Updated version of test results with 2-d test cases.

Src/LinearSolvers/C_NodalMG/files.2d

commit 6a881c0fbf5525170fef671094f809e5703bc7f4
Author: almgren <almgren>
Date:   Wed Mar 13 21:54:59 2002 +0000

    Improved version of the test code.  Fixed some bugs even.

Src/LinearSolvers/C_NodalMG/proj.cpp

commit c3fd2b5eeb434ecacad645994c44135704c61162
Author: almgren <almgren>
Date:   Wed Mar 13 21:54:24 2002 +0000

    We dont do factor of 8 refinement.

Src/LinearSolvers/C_NodalMG/tests/gr.19s8
Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s8

commit 8f3977005c22bcbcd14aec0562f50ede7242ba66
Author: almgren <almgren>
Date:   Wed Mar 13 21:52:54 2002 +0000

    This test case fails because it needs an absolute tolerance in the CG solver.
    Not worth worrying about here.

Src/LinearSolvers/C_NodalMG/tests/gr1rick
Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick

commit ed17fe6adf38cfb09b8f02d0d57ebc8f08e77cd2
Author: almgren <almgren>
Date:   Wed Mar 13 21:49:16 2002 +0000

    A grid 201 long does not coarsen!  Try making this 0-199 instead of 0-200...

Src/LinearSolvers/C_NodalMG/tests/gr1rick2
Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick2

commit 0065503662bca6788bbc5100e4482368a7a6899b
Author: vince <vince>
Date:   Wed Mar 13 21:43:58 2002 +0000

    Added FabArray shift for hchem support.

Src/C_BaseLib/FabArray.H

commit 536c4207daf1c8604fafb010a1915d4abad3b958
Author: almgren <almgren>
Date:   Wed Mar 13 21:39:03 2002 +0000

    This grids file assumes a factor of 8 refinement - get rid of it!

Src/LinearSolvers/C_NodalMG/tests/gr2a8
Tests/LinearSolvers/C_NodalMG/test_grids/gr2a8

commit 718142363728c68eb446843edc21b53ac7c799ec
Author: almgren <almgren>
Date:   Wed Mar 13 21:32:34 2002 +0000

    Make this a 3-level instead of 1-level test case, with
    same grids at finest level.

Src/LinearSolvers/C_NodalMG/tests/gtclearsmall
Tests/LinearSolvers/C_NodalMG/test_grids/gtclearsmall

commit 83d30e01fddac9cac5fd48a2aebce37d975cc872
Author: almgren <almgren>
Date:   Wed Mar 13 21:31:41 2002 +0000

    Previous grids file had files not contained in domain.

Src/LinearSolvers/C_NodalMG/tests/gt12.2
Tests/LinearSolvers/C_NodalMG/test_grids/gt12.2

commit 6f14f6fff4598ef26acd388be78e8a6e350e3fc6
Author: almgren <almgren>
Date:   Wed Mar 13 21:30:37 2002 +0000

    Latest update on what works of the 3-d test cases.

Src/LinearSolvers/C_NodalMG/files.3d

commit 3042d947a7b10a26735721a710af10f4547b46e9
Author: almgren <almgren>
Date:   Wed Mar 13 21:17:25 2002 +0000

    Too small to be interesting.

Src/LinearSolvers/C_NodalMG/tests/gt2t2
Tests/LinearSolvers/C_NodalMG/test_grids/gt2t2

commit 13b9720a56865176f6cd6f8531447a2371def5da
Author: lijewski <lijewski>
Date:   Wed Mar 13 19:07:00 2002 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/files.2d

commit d52f759cd2949216375e99d52141bec569532f16
Author: lijewski <lijewski>
Date:   Wed Mar 13 18:31:42 2002 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/files.2d

commit 65a475d43dfce70923c06d18a95b9bcfff2b86ad
Author: almgren <almgren>
Date:   Wed Mar 13 18:29:38 2002 +0000

    Fixes for 2d only: length --> size, etc...

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 4ef872bcd816669d49ca315921b4f31370f0a1b9
Author: almgren <almgren>
Date:   Wed Mar 13 00:57:35 2002 +0000

    New test problem which failed with previous code but now works.  A
    smaller version of the critical grids of this problem are in gtclearsmall.

Src/LinearSolvers/C_NodalMG/tests/gtclearlarge
Tests/LinearSolvers/C_NodalMG/test_grids/gtclearlarge

commit d026a97c59c48a4f5b97827459a59ba6dba917a6
Author: almgren <almgren>
Date:   Wed Mar 13 00:56:56 2002 +0000

    New test problem which failed with the previous version of the code.
    This is extracted from gtclearlarge.

Src/LinearSolvers/C_NodalMG/tests/gtclearsmall
Tests/LinearSolvers/C_NodalMG/test_grids/gtclearsmall

commit de15f205daf94846ac0e1f7b164d24d2b37b9ade
Author: almgren <almgren>
Date:   Wed Mar 13 00:56:02 2002 +0000

    Updated list of which of the tests/gt* files are 3-d problems, and
    whether they work with the current version of the code.

Src/LinearSolvers/C_NodalMG/files.3d

commit 1ac4aa00e3e26bba19492fba58a49b60c4349bff
Author: almgren <almgren>
Date:   Wed Mar 13 00:55:33 2002 +0000

    Fixed a bug in the construction of the level interface objects - code
    used to fail on test code gtclearsmall and now works.   Replaced
    "contains" by a box by "contains" by a BoxArray.

Src/LinearSolvers/C_NodalMG/interface.cpp

commit 22cb2a162e9d3ab0ad191dda67755e2ebc29b43d
Author: lijewski <lijewski>
Date:   Mon Mar 11 23:05:53 2002 +0000

    added <cstdio>

Src/LinearSolvers/C_NodalMG/proj.cpp

commit e78669da0c4ce41c58698ed4506601ad31281ebf
Author: car <car>
Date:   Mon Mar 11 21:53:57 2002 +0000

    Now an empty BoxList is constructed from an empty BoxArray.

Src/C_BaseLib/BoxArray.cpp

commit 920f4c3ac07f46bf3c467e2fd4cf4b87bf93bbfd
Author: lijewski <lijewski>
Date:   Mon Mar 11 19:24:08 2002 +0000

    got rid of unsigned on aux() -- it's an int

Src/LinearSolvers/C_NodalMG/interface.H

commit 6b47b8cca0eb2ecbac281f9b26d46711653bad23
Author: car <car>
Date:   Tue Feb 26 23:41:45 2002 +0000

    gcc 3

Tools/C_mk/Make.defs

commit 1f7c145e18913074a71367b6d05a792d2dde8bbe
Author: car <car>
Date:   Tue Feb 26 23:41:31 2002 +0000

    some systems require explicit include of pthread

Src/C_BaseLib/BLThread.cpp

commit bf9d3afd1b24fe7037708991b9c3049b5a58a939
Author: car <car>
Date:   Mon Feb 25 20:59:43 2002 +0000

    UnitBox was implemented as a 2x2x2 box.

Src/C_BaseLib/Box.cpp

commit 4b74e6143fe04257dd7cb4d9abebe0980e989cce
Author: lijewski <lijewski>
Date:   Fri Feb 22 20:53:54 2002 +0000

    Fixed FixUpPyhsCorners() bug

Src/C_AMRLib/AmrLevel.cpp

commit 942781915ec62e5e1950717a7df366b895a6bdfe
Author: car <car>
Date:   Tue Feb 19 23:36:06 2002 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit df06e6982db379987476cd6ae951536e062aba12
Author: car <car>
Date:   Wed Feb 6 18:14:46 2002 +0000

    Fixed random number seeding.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit a3680ce81de37fd1c18ae8872194b24541708765
Author: car <car>
Date:   Tue Jan 8 16:30:24 2002 +0000

    no message

Src/C_BaseLib/BLProfiler.cpp

commit cba564c6e21582eeb0d94249d049f8052f85d44c
Author: car <car>
Date:   Fri Jan 4 00:17:23 2002 +0000

    no message

Src/C_BaseLib/BoxLib.dsp

commit fe97f51e9993427ecfc6c9ac6e65b4b30d176a20
Author: car <car>
Date:   Thu Dec 13 23:46:08 2001 +0000

    properly initialize m_used

Src/C_BaseLib/CArena.cpp

commit 614bae79406e6958960389c78b38511f54b7fb45
Author: car <car>
Date:   Thu Dec 13 18:24:59 2001 +0000

    makefile system knows fortran

Tools/C_mk/Make.defs

commit c5aa18122aefb54b890d8fb0ec1249faeb824f8e
Author: car <car>
Date:   Tue Dec 4 21:28:17 2001 +0000

    OSF1 now discriminates between V3 and all others

Tools/C_mk/Make.OSF1
Tools/C_mk/Make.defs

commit bacab6a12cb31b6566bc2e743540fffb891ba460
Author: lijewski <lijewski>
Date:   Mon Dec 3 22:35:54 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp

commit 0cc079ff0e59d78175f57040cd7e30bb80598ec5
Author: lijewski <lijewski>
Date:   Mon Dec 3 22:24:54 2001 +0000

    removed mpi_data_type() stuff

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/ccse-mpi.H
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp

commit cbccf3a46f5d71d4be324e1e332cccf6ae988667
Author: car <car>
Date:   Mon Nov 26 18:17:58 2001 +0000

    fix for max_threads

Src/C_BaseLib/BLThread.cpp

commit aa45c741ae3d028c098c669fb502841b77bef51c
Author: car <car>
Date:   Mon Nov 26 18:14:26 2001 +0000

    refinement of BLThread.cpp for WINNT

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/Utility.cpp

commit b2aab7ac284e4ad60874d64999f16b116731150f
Author: car <car>
Date:   Wed Nov 21 19:50:44 2001 +0000

    CriticalSections seem to work better for mutex's

Src/C_BaseLib/BLThread.cpp

commit 8c08667ffba905dd0e42311d98608f4e61d2a733
Author: car <car>
Date:   Mon Nov 19 19:10:49 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BoxLib.dsp

commit 4079c9cd80d7ebfedd0cd8e35354cca78bb71c2c
Author: car <car>
Date:   Fri Nov 16 18:19:33 2001 +0000

    cv needs to be mutable

Src/C_BaseLib/WorkQueue.H

commit 0280ec49a92b18536b822258f938a37744502aee
Author: car <car>
Date:   Fri Nov 16 18:05:16 2001 +0000

    numthreads needs a lock

Src/C_BaseLib/BLWorkQueue.cpp

commit 214d02d44a7f9576ac0b91d10399086c46d375bf
Author: car <car>
Date:   Tue Nov 13 00:08:29 2001 +0000

    KCC doesn't always like PTHREAD_STACK_MIN?

Src/C_BaseLib/BLThread.cpp

commit b7adaf6e3a63ebbc19c81101c862f4272749f991
Author: car <car>
Date:   Mon Nov 12 23:28:03 2001 +0000

    Windows fixes

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/Utility.cpp

commit 43c985a15582bb48320594e8314ee27664733bdd
Author: lijewski <lijewski>
Date:   Mon Nov 12 21:38:21 2001 +0000

    *** empty log message ***

Tools/C_mk/Make.AIX

commit ccf5488c49da10a6f294c107fbc4feb794a7504a
Author: car <car>
Date:   Fri Nov 9 14:33:10 2001 +0000

    fix for unix threads

Src/C_BaseLib/BLThread.cpp

commit ee80a04348de98aba8f4b1ddf89caf1cf07fbe6d
Author: car <car>
Date:   Wed Nov 7 22:00:57 2001 +0000

    More WIN32 support

Src/C_BaseLib/BLThread.cpp

commit a4a35f4d821e2db7f7332f2ecf02a448946564f5
Author: lijewski <lijewski>
Date:   Wed Nov 7 19:05:01 2001 +0000

    *** empty log message ***

Tools/C_mk/Make.AIX

commit 859a479709e7aed287e87e349f02263ca90b5c7b
Author: car <car>
Date:   Thu Nov 1 23:52:50 2001 +0000

    restored a user-specified TSD destructor

Src/C_BaseLib/Thread.H
Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/tWorkQueue.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/tWorkQueue.cpp

commit b7817598a6e9d912ff867a12444d1d216f04eb1c
Author: lijewski <lijewski>
Date:   Thu Nov 1 23:21:34 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp

commit ebce6425de3beca53ef11912330dabdfe6c6501e
Author: car <car>
Date:   Thu Nov 1 18:53:15 2001 +0000

    baseThread

Src/C_BaseLib/BLThread.cpp

commit 468a31f35ddd97823af4714943f42149fa08fc89
Author: car <car>
Date:   Thu Nov 1 18:46:37 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp

commit 30627b1b8177f978707f85b92d5662676c5e16c6
Author: lijewski <lijewski>
Date:   Thu Nov 1 17:57:30 2001 +0000

    re-added BLMpi.cpp

Src/C_BaseLib/FabArray.H

commit 461389f6c773904d2045cd36d047d8c31085f75b
Author: car <car>
Date:   Thu Nov 1 17:08:41 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp

commit 7f907f1e10b2964816e30648887dedf51999a0aa
Author: lijewski <lijewski>
Date:   Thu Nov 1 16:50:38 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLMpi.cpp

commit 8ef6ee3851b343d90bc9d50c4a8db4ddbeba7e3f
Author: lijewski <lijewski>
Date:   Wed Oct 31 22:42:01 2001 +0000

    re-added BLMpi.cpp

Src/C_BaseLib/Make.package

commit a10fc2dbfbbb8729a47467c520309fb99d527493
Author: lijewski <lijewski>
Date:   Tue Oct 30 22:03:42 2001 +0000

    more threading work

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit a13824bcc5e09a3bf974ce7a5659c8d5f6477d1b
Author: lijewski <lijewski>
Date:   Tue Oct 30 20:26:29 2001 +0000

    removed no-threadsafe constructs

Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp

commit 70090192584334f12af5d94d6fff31a349e322e5
Author: car <car>
Date:   Wed Oct 24 19:48:44 2001 +0000

    PGI C++, which doesn't work

Tools/C_mk/Make.Linux

commit ff8b20d4ed0164dfc1d0e73076fae3d3f347c0fb
Author: lijewski <lijewski>
Date:   Tue Oct 23 17:31:02 2001 +0000

    *** empty log message ***

Src/C_AMRLib/FluxRegister.cpp

commit 16813e44d01096e385aed62a4052662111b1bd1d
Author: lijewski <lijewski>
Date:   Tue Oct 23 17:01:02 2001 +0000

    added BoxLib::ResetArena()

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/Arena.H
Src/C_BaseLib/BaseFab.cpp

commit 3fd8f79a9a35676cd3111da5ba3632f7631628f4
Author: car <car>
Date:   Mon Oct 22 22:49:53 2001 +0000

    Fix for windows

Src/C_BaseLib/BLThread.cpp

commit e405a8bc77c5bb6420747740cbd41883b9f3015c
Author: lijewski <lijewski>
Date:   Mon Oct 22 21:12:45 2001 +0000

    thread stacksize stuff

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BLWorkQueue.cpp
Src/C_BaseLib/Thread.H
Tools/C_mk/Make.OSF1

commit 4c93567682ac951c6d29282bd84096bffcfe0f97
Author: car <car>
Date:   Sat Oct 20 22:45:32 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BLWorkQueue.cpp
Src/C_BaseLib/Thread.H

commit c36187ce4827f48113addec285ba9f4d6d0924a6
Author: car <car>
Date:   Thu Oct 18 21:54:13 2001 +0000

    Added BaseFab.cpp

Src/C_BaseLib/BoxLib.dsp

commit b37f4962c6a3de9a7a5a570f93eebe3d05e0bfd0
Author: lijewski <lijewski>
Date:   Thu Oct 18 17:55:31 2001 +0000

    some thread fixes

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/Thread.H

commit eade3ab0d2c60df5f707b435947731a18c4293a5
Author: lijewski <lijewski>
Date:   Wed Oct 17 17:53:33 2001 +0000

    removed unneeded BL_USE_SETBUF and BL_USE_NEW_HFILES

Src/C_BaseLib/test/tCArena.cpp
Src/C_BaseLib/test/tFB.cpp
Src/LinearSolvers/C_TensorMG/Test/testVI.cpp
Tests/C_BaseLib/tCArena.cpp
Tests/C_BaseLib/tFB.cpp
Tests/LinearSolvers/C_TensorMG/testVI.cpp
Tools/C_mk/Make.CRAY
Tools/C_mk/Make.CYGWIN_NT
Tools/C_mk/Make.IRIX64
Tools/C_mk/Make.Linux
Tools/C_mk/Make.T3E
Tools/C_util/Convergence/Add.cpp
Tools/C_util/Convergence/DiffFab.cpp
Tools/C_util/Convergence/DiffPlot.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileNormB.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp
Tools/C_util/ViewMF/MFNorm.cpp
Tools/C_util/ViewMF/checkMFghostcells.cpp
Tools/C_util/ViewMF/main.cpp
Tools/C_util/ViewMF/viewMF.cpp
Tools/C_util/ViewMF/viewMFdiff.cpp
Tools/C_util/ViewMF/viewMFdiffHardWire.cpp
Tools/C_util/WritePlotFile.cpp
Tools/C_util/dbgTools/crsGrids.cpp
Tools/C_util/dbgTools/intersectGrids.cpp

commit a903c0e29dcce2007a34c37347a5eefa57764a42
Author: lijewski <lijewski>
Date:   Wed Oct 17 16:49:27 2001 +0000

    Need BL_USE_SETBUF for g++

Tools/C_mk/Make.defs

commit 1e455959ef9aee95373ade78ebb4111171754319
Author: lijewski <lijewski>
Date:   Wed Oct 17 16:43:22 2001 +0000

    always use pubsetbuf()

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/VisMF.cpp

commit 75fc152526b42d710802400726b1471d1f2ce06c
Author: lijewski <lijewski>
Date:   Tue Oct 16 22:45:34 2001 +0000

    got rid of libmiranda.a

Tools/C_mk/Make.AIX

commit 71ba288b4c5619ebc3b7cdda1c29ab85d76192cc
Author: lijewski <lijewski>
Date:   Tue Oct 16 19:59:51 2001 +0000

    Integrated in BoxLib::The_Arena()

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/Arena.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/FabArray.H
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 3f6a2a5193636707e846fd1f1889e8becfaa3dd3
Author: car <car>
Date:   Mon Oct 15 23:01:27 2001 +0000

    debugging flags for PGI

Tools/C_mk/Make.Linux

commit b91f04de32b27321fd556cc0c941d43b8e2b8dfd
Author: lijewski <lijewski>
Date:   Mon Oct 15 21:01:50 2001 +0000

    Set up PGI to use pgf90.

Tools/C_mk/Make.Linux

commit fdf18a0c6cd69c46732b54b20881891db342c527
Author: car <car>
Date:   Mon Oct 15 18:37:35 2001 +0000

    Don't need the timespec declaration anymore.

Src/C_BaseLib/winstd.H

commit b7183a8eed30bb1891d7dd1e493a90ca5785b722
Author: car <car>
Date:   Mon Oct 15 18:17:51 2001 +0000

    just replicate the data members of timespec in our Timer

Src/C_BaseLib/Utility.H

commit 13eba0c7d0bad0de0647a78a1d1edbee49e4ca31
Author: lijewski <lijewski>
Date:   Mon Oct 15 18:15:22 2001 +0000

    Removed COALESCE_FABS stuff and NEW_HFILES stuff.

Tools/C_mk/Make.AIX

commit b8c06326b62459f6c3c104b8f7fb8a5722004aa2
Author: lijewski <lijewski>
Date:   Fri Oct 12 17:44:25 2001 +0000

    added Mutex

Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp

commit 688f396d5c8c8f6e08e4722f3ac9bb20ff8973de
Author: lijewski <lijewski>
Date:   Thu Oct 11 16:33:38 2001 +0000

    add tread.cpp

Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/tread.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/tread.cpp

commit 559ea361fa609b3e0a6395fc88f94b25d2fb10aa
Author: car <car>
Date:   Wed Oct 10 20:12:44 2001 +0000

    mpi typemaps for some BoxLib types

Src/C_BaseLib/Box.H
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ccse-mpi.H

commit b2512af21f8ed04ab0dd289749b12deb3394d1e2
Author: car <car>
Date:   Wed Oct 10 15:44:41 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLProfiler.cpp

commit 61f1ebe1090c9d34ce41184d0fe346cc7dd494c4
Author: car <car>
Date:   Tue Oct 9 22:37:46 2001 +0000

    MINGW32, a minimal gnu under win32

Src/C_BaseLib/winstd.H

commit 7ce56e29638eba89e732593f73196d38aa0289dc
Author: lijewski <lijewski>
Date:   Fri Oct 5 19:47:55 2001 +0000

    Up'd -bmaxdata size ...

Tools/C_mk/Make.AIX

commit 2afe53654513189bdfc71f906841249edf49f6ec
Author: marc <marc>
Date:   Fri Oct 5 07:19:55 2001 +0000

    iAdd check for instability (due typically to case where initial
    residual is very small).  this code was basically copied from the
    scalar solver stuff, except that the expert setting to turn it
    on was put into the cg parm parse stuff.

Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp

commit 103188b07bea3ccf6e8723d43dd23906c3036861
Author: lijewski <lijewski>
Date:   Wed Oct 3 19:53:51 2001 +0000

    output maxthreads only if verbose

Src/C_BaseLib/BLWorkQueue.cpp

commit 5da536222afb59c9459107d8ffb86a9158a505bd
Author: lijewski <lijewski>
Date:   Tue Oct 2 16:30:41 2001 +0000

    mods to get working with KCC

Src/C_BaseLib/ParallelDescriptor.H

commit 34f09082fb182d45885dd48fe6f9fb7f667340c8
Author: lijewski <lijewski>
Date:   Thu Sep 27 21:54:13 2001 +0000

    removed the default arguments

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 951888185f71268a7add80ae65d388f3dc454ec5
Author: lijewski <lijewski>
Date:   Thu Sep 27 21:05:15 2001 +0000

    got it right (I think) ...

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit a5e1e556fc63c40d1e1ee54fe8967c42cf1657bf
Author: lijewski <lijewski>
Date:   Thu Sep 27 19:52:14 2001 +0000

    oops -- had a parallel bug in there somewhere

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 33419539c950928cb0acda0275bed4eb24633256
Author: lijewski <lijewski>
Date:   Thu Sep 27 18:03:26 2001 +0000

    some std stuff

Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 1a6dfb1c0d23d66f25d651e470f93672360c2745
Author: lijewski <lijewski>
Date:   Thu Sep 27 17:57:21 2001 +0000

    removed more BL_USE_MPI stuff

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ccse-mpi.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 3ba787581441db36d983b02a55e197bb3ffa6ea9
Author: car <car>
Date:   Thu Sep 27 16:11:49 2001 +0000

    -DBL_KCC_VERSION added

Tools/C_mk/Make.defs

commit bb5e8e2e119f1c0b9f5543ba9500172d454bd8a4
Author: lijewski <lijewski>
Date:   Wed Sep 26 16:59:53 2001 +0000

    removed unused variable

Src/C_AMRLib/FluxRegister.cpp

commit fff524dd362d28cd15dd0298a87f50e733af9613
Author: lijewski <lijewski>
Date:   Wed Sep 26 15:47:54 2001 +0000

     for clarity ...

Src/C_BaseLib/FabArray.cpp

commit 80817573ffa5a82cd360175e9d150fa26deaadd7
Author: car <car>
Date:   Wed Sep 26 15:43:31 2001 +0000

    debugging of MFIters taken from HG
    
    removed 2 static array decls in Collect Data that broke MSVC.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit da09a91423e9d8771213d282ef33fabd0e4f1fd0
Author: car <car>
Date:   Wed Sep 26 02:16:58 2001 +0000

    HG_is_debugging is only defined in IAMR
    
    CollectData not in macros triggers a bug in VC++

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit a56ca1ee9ffa5c55ac519a809ffaf6c0c015a73d
Author: lijewski <lijewski>
Date:   Tue Sep 25 22:45:40 2001 +0000

    more hiding of MPI-specifics

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ccse-mpi.H

commit 2c8f75e97db7fb85d09f7322c266ef61ad879925
Author: car <car>
Date:   Tue Sep 25 21:02:54 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 5ba9149aea3f46f7b580d91ccda79cd27a830494
Author: lijewski <lijewski>
Date:   Mon Sep 24 20:31:35 2001 +0000

    output wallclock time since start(restart)

Src/C_AMRLib/Amr.cpp

commit a70f10677c599e1905d99f597c99eb2d1d6581bb
Author: lijewski <lijewski>
Date:   Mon Sep 24 19:10:03 2001 +0000

    *** empty log message ***

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.cpp

commit b64429b28f91db6c8528cf70e11573799e254af5
Author: lijewski <lijewski>
Date:   Fri Sep 21 21:38:21 2001 +0000

    removed some BL_USE_MPI blocks

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/VisMF.cpp

commit 54d3f11c6cf1be5dbed521c57aad38bc7b45466f
Author: car <car>
Date:   Wed Sep 19 17:04:43 2001 +0000

    no dependencies in real fortran

Tools/C_mk/Make.rules

commit 6c48d5bcd05331279341ab3b3a44f3b071776f5d
Author: car <car>
Date:   Wed Sep 19 17:03:58 2001 +0000

    in serial ParallelDescriptor::second now returns wall clock time

Src/C_BaseLib/ParallelDescriptor.cpp

commit 02a8bc93775d340dbeb6cbe1ad3205239fa63a2f
Author: lijewski <lijewski>
Date:   Wed Sep 19 16:54:05 2001 +0000

    Added stuff to get threading to work.

Tools/C_mk/Make.AIX

commit 2f9b4a7152a17cebe4036b3440b99ba31a609952
Author: car <car>
Date:   Wed Sep 19 02:39:53 2001 +0000

    -CB loses mostly

Tools/C_mk/Make.Linux

commit 187dd78339c2bfb7ee68166400a73971f26c83d8
Author: car <car>
Date:   Wed Sep 19 02:37:20 2001 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit daa9c28e32db761d311088ae49028d1fb2d9cc0d
Author: car <car>
Date:   Wed Sep 19 02:36:47 2001 +0000

    need header

Src/C_BaseLib/BLWorkQueue.cpp

commit 54f0aba6a9aff378da116131ee289f62f43a7d92
Author: lijewski <lijewski>
Date:   Tue Sep 18 20:40:27 2001 +0000

    Wrapped an I/O statement appropriately.

Src/C_BaseLib/BLWorkQueue.cpp

commit 241971920e8d0878774e9d5975c63329c50968f2
Author: marc <marc>
Date:   Tue Sep 18 18:15:03 2001 +0000

    Split out tests for defined junk.

Src/C_BaseLib/std/limits

commit 203a3d5d4dea875acf2c7fc67fd31433b66d07ac
Author: car <car>
Date:   Tue Sep 18 03:34:49 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit ea590d2ea3b8b0e5120da18ab45bae1fdb211edc
Author: lijewski <lijewski>
Date:   Mon Sep 17 22:03:03 2001 +0000

    add thread_safe for mpKCC

Tools/C_mk/Make.defs

commit 095d92dd0c0120fa8f2b09441e6a1f4ab889b56b
Author: car <car>
Date:   Sun Sep 16 16:44:24 2001 +0000

    more support for Intel, must upgrade set gigan:/var/tmp/RPMS/extra

Tools/C_mk/Make.Linux

commit 9aeb80a366953faa9b052afceeeb79656c7597cd
Author: marc <marc>
Date:   Sat Sep 15 05:29:29 2001 +0000

    Fix for little-f files

Tools/C_mk/Make.Linux

commit 44f094c67a9cc04782ba921df79a7e657d43c375
Author: lijewski <lijewski>
Date:   Fri Sep 14 21:03:06 2001 +0000

    Now always print out workqueue.maxthreads at startup ...

Src/C_BaseLib/BLWorkQueue.cpp

commit 303ee73a16d38cd5bf948c2390204c083d19dfae
Author: car <car>
Date:   Fri Sep 14 04:03:39 2001 +0000

    fixes for KCC

Src/C_BaseLib/Thread.H

commit 9742d8c8ba60bdfd4ce867bb071c6ca426ae253f
Author: lijewski <lijewski>
Date:   Thu Sep 13 23:09:16 2001 +0000

    Now print out # of cells advanced at each level as we go ...

Src/C_AMRLib/Amr.cpp

commit 921ace7223dc53eb18cb76354acd1fc44f343062
Author: lijewski <lijewski>
Date:   Fri Sep 7 23:06:44 2001 +0000

    *** empty log message ***

Src/C_AMRLib/FluxRegister.cpp

commit 807c18d7623407f9d8af19b8175f4fbb8cfe3d01
Author: car <car>
Date:   Fri Sep 7 22:03:21 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp

commit 32de1352383526bd89ec871e91ef65723b4b4ee4
Author: car <car>
Date:   Fri Sep 7 00:35:02 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 4d8e0bbd247eb9aa7143b71dc083a02ab2d5e8fe
Author: lijewski <lijewski>
Date:   Thu Sep 6 22:49:19 2001 +0000

    added a default getID() for USE_THREADS=TRUE.

Src/C_BaseLib/BLThread.cpp

commit 6b3e88b9ed15bc169b1fa25f1892fb3f70a75739
Author: car <car>
Date:   Wed Sep 5 19:29:59 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 92371bcfeb8a7148e464490dc75dca3d011439f1
Author: car <car>
Date:   Tue Sep 4 16:59:41 2001 +0000

    Threading Fixes

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BLWorkQueue.cpp
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Thread.H

commit 6ba19a0dda3bddcfed07b30f56b2d1b57fd402a5
Author: car <car>
Date:   Thu Aug 23 21:58:04 2001 +0000

    simplify thread

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/Thread.H

commit 9faef0875e130afd8a6a32c9b8aa5293809ed897
Author: car <car>
Date:   Thu Aug 23 21:44:32 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxLib.dsp
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Thread.H

commit 04c1effe3ef4aa4ccbf01bc0173edae4ace82982
Author: lijewski <lijewski>
Date:   Thu Aug 23 20:07:43 2001 +0000

    *** empty log message ***

Src/C_AMRLib/FluxRegister.cpp

commit eeed082d0f9f47063d57fc0f5637d474c9c3de68
Author: lijewski <lijewski>
Date:   Wed Aug 22 21:35:25 2001 +0000

    removed an assert()

Src/C_AMRLib/AmrLevel.cpp

commit 8b0b392947b22ce54b07bec8a2704e5bb6c4222c
Author: lijewski <lijewski>
Date:   Wed Aug 22 20:18:14 2001 +0000

    made probin_file default to probin

Src/C_AMRLib/Amr.cpp

commit ecc5eb267d2f63085747112264695200bbfe8100
Author: lijewski <lijewski>
Date:   Wed Aug 22 19:21:00 2001 +0000

    reverted to older style copy constructor

Src/C_BaseLib/Geometry.cpp

commit 4502658b9100a4a8bf0629be3168aeff38ff1d47
Author: car <car>
Date:   Tue Aug 21 22:15:37 2001 +0000

    revitalized threads

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BLWorkQueue.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/WorkQueue.H
Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/tWorkQueue.cpp
Src/C_BoundaryLib/InterpBndryData.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/macprojTest.cpp
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/tWorkQueue.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/macprojTest.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 922025d0b7524dd1359cb8ff097cac255e536458
Author: car <car>
Date:   Tue Aug 21 20:30:02 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/Thread.H

commit 8f913f72c868e5c7c74f25906efcd7ce10cf90ea
Author: lijewski <lijewski>
Date:   Tue Aug 21 19:01:51 2001 +0000

    simplification

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 0db707ac0e68f5002b6a705f44242671c762d0ff
Author: lijewski <lijewski>
Date:   Tue Aug 21 18:08:46 2001 +0000

    simplification

Src/C_BaseLib/FArrayBox.cpp

commit 4eeb606df24f0501b8c9cff3187f34e47ca2eb97
Author: car <car>
Date:   Tue Aug 21 17:10:31 2001 +0000

    minor leak

Src/C_BaseLib/BoxLib.cpp

commit 7b10c4391585fa26dd4a5b7764d6a6d6e2224261
Author: car <car>
Date:   Mon Aug 20 02:48:50 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 01d19ee174dae26d5f40f9897bafb019d0f1006e
Author: car <car>
Date:   Sat Aug 18 23:39:10 2001 +0000

    added souce numega filters.

Src/C_BaseLib/.cvsignore

commit 833ff7fce0f90515b2a792d4161d9c5cce603e7d
Author: lijewski <lijewski>
Date:   Fri Aug 17 15:41:33 2001 +0000

    Reverted out the greeno stuff; shouldn't have been checked in :-(

Src/C_AMRLib/Amr.cpp

commit df78fd8d0ef5e48f74292ee83ecb7b1d073ed894
Author: lijewski <lijewski>
Date:   Thu Aug 16 23:06:47 2001 +0000

    Modifications as per greeno.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/FILCC_1D.F
Src/C_AMRLib/FLUXREG_1D.F
Src/C_AMRLib/INTERP_1D.F
Src/C_AMRLib/Interpolater.cpp

commit 0694402c6eb4351b225eaab7f7601876ae1a79d7
Author: lijewski <lijewski>
Date:   Thu Aug 16 20:11:38 2001 +0000

    Refined the way we call ParmParse::Initialize().

Src/C_BaseLib/BoxLib.cpp

commit f0f99427b9805afb406ff5277ff56fd55403feda
Author: lijewski <lijewski>
Date:   Thu Aug 16 17:57:43 2001 +0000

    some simplification ...

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/REAL.H

commit a0719c9333e650d46dc5febfd4d916be19ec5186
Author: almgren <almgren>
Date:   Wed Aug 15 21:51:55 2001 +0000

    Dont define spherical_origin_fix with 0.0 (double) but with 0 (int).

Src/C_BaseLib/Geometry.cpp

commit 37190422efe52e9137860b78f7e83a0c834bbf96
Author: lijewski <lijewski>
Date:   Wed Aug 15 19:23:55 2001 +0000

    stuff needed by greeno

Src/C_BaseLib/COORDSYS_1D.F
Src/C_BaseLib/COORDSYS_2D.F
Src/C_BaseLib/COORDSYS_3D.F
Src/C_BaseLib/COORDSYS_F.H
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 6e3a077753a84845b508a5474fa5dadaa949bb02
Author: lijewski <lijewski>
Date:   Wed Aug 15 16:25:21 2001 +0000

    Removed some _GNUC_ stuff.

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BaseFab.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 51e58097e0ba4d0609df5cf66c173edcc33b9798
Author: lijewski <lijewski>
Date:   Tue Aug 14 22:21:08 2001 +0000

    Can now turn off profiling via ParmParse with "profiler.profiling=0"

Src/C_BaseLib/BLProfiler.cpp

commit d2b572ff3919e296faf36f9e6dfd0e92f31ac4c3
Author: car <car>
Date:   Tue Aug 14 22:14:00 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 9ab69eac956799ef451257ce772981d8e9d57560
Author: car <car>
Date:   Tue Aug 14 16:07:31 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 641bcc3cea102cb2f027b2cb40625238d8a82ab0
Author: car <car>
Date:   Mon Aug 13 22:34:45 2001 +0000

    MSVC fixes

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxLib.dsp
Src/C_BaseLib/FArrayBox.cpp

commit ee8888269112f92c7afab76b74783886a00c8f41
Author: car <car>
Date:   Mon Aug 13 01:54:26 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit f0b50192cab0981403c429151e3d7d957f0c6461
Author: car <car>
Date:   Sat Aug 11 21:19:04 2001 +0000

    MSVC fix

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 7c12f23ebef1bd4920ffe559bbb5e5f29f46e069
Author: car <car>
Date:   Sat Aug 11 21:14:20 2001 +0000

    Fix for WIN32

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit d7b601a7a989c333c9d197fc08742a335913a17d
Author: car <car>
Date:   Sat Aug 11 20:50:14 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 5b4c7b9b277cd43dcd7e504445aa8aa0c2042f0f
Author: car <car>
Date:   Sat Aug 11 20:45:55 2001 +0000

    Added ParmParse 'Record' types

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit c3d96db94e8c77bef1cbb5e0833307fc8c6fc991
Author: almgren <almgren>
Date:   Fri Aug 10 19:57:53 2001 +0000

    Changed the way we input periodic.

Src/LinearSolvers/C_NodalMG/inputs
Src/LinearSolvers/C_TensorMG/Test/inputs2D
Tests/LinearSolvers/C_TensorMG/inputs2D

commit 510203f3b86658f7f75313de2bb3fe588386aa0a
Author: almgren <almgren>
Date:   Fri Aug 10 19:52:21 2001 +0000

    Changed the way we input periodic.

Src/C_BaseLib/Geometry.cpp

commit 1e9e3c0ffe16b85528ee66a34101e2bf373a91df
Author: marc <marc>
Date:   Thu Aug 9 22:50:20 2001 +0000

    change fwd declare from class to struct

Src/C_BaseLib/Geometry.H

commit f15617af995c9766097ff3552027ff7926a2d085
Author: marc <marc>
Date:   Thu Aug 9 22:41:59 2001 +0000

    added winstd for MSVC debug builds

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/SlabStat.cpp
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StationData.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/SPACE.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.cpp
Src/C_BoundaryLib/InterpBndryData.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp
Tools/C_scripts/dsp.mak

commit f46244821e146a930a0387824ae0e3f7e49fff4c
Author: marc <marc>
Date:   Thu Aug 9 16:21:26 2001 +0000

    Change concat function to satisfy DVF compiler

Src/C_BaseLib/REAL.H

commit f13db4d2d431d33df1715d0bba8a60b78139bc34
Author: marc <marc>
Date:   Thu Aug 9 16:20:37 2001 +0000

    Minor fixes to satisfy MSVC compiler

Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/SlabStat.cpp
Src/C_AMRLib/StateDescriptor.cpp

commit 32a5c830f884c24cc09be0023538e8e86598506c
Author: car <car>
Date:   Mon Aug 6 19:40:27 2001 +0000

    Box constructor/user defined conversion

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit b5fa0066ace065562a35b323611c8e544fd5cdf5
Author: car <car>
Date:   Mon Aug 6 19:39:59 2001 +0000

    ParmParse hacks

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 9f66ae669f1a780a5f9edccaa6583418b7da398c
Author: car <car>
Date:   Mon Aug 6 19:39:25 2001 +0000

    windows

Src/C_BaseLib/VisMF.cpp

commit 27000a1ce9d27b694061b2d0ebebfdc50d1eabd8
Author: car <car>
Date:   Thu Aug 2 16:37:49 2001 +0000

    Typo

Src/C_BaseLib/CONSTANTS.H

commit 80f58685eac367875da2caeacb5c0946e4b6c848
Author: car <car>
Date:   Thu Aug 2 16:18:15 2001 +0000

    CONSTANTS change, use BL_REAL

Src/C_BaseLib/CONSTANTS.H

commit 2b88faef7d8f2811348ca61c57e73ed0dae5d4b0
Author: car <car>
Date:   Thu Aug 2 16:04:11 2001 +0000

    append->push_back

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/SlabStat.cpp
Src/C_BaseLib/RealBox.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp

commit 67bb16c6d219abafd7823ac9deb1cfa8e0251f44
Author: car <car>
Date:   Thu Aug 2 16:01:43 2001 +0000

    append->push_back, prepend->push_front, Fab[] stubs, Fab=, MultiFab=

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 23cfe8ffef90ca6bab57ca8a8e5b23cd8907f4e6
Author: car <car>
Date:   Thu Aug 2 01:23:44 2001 +0000

    BL_REAL macro to make constants

Src/C_BaseLib/REAL.H

commit 256bf8109271d43d1dbebbe060e880eddf92bc8d
Author: car <car>
Date:   Thu Aug 2 01:22:48 2001 +0000

    removed fwd decl of ConstFabArrayIterator

Src/C_BaseLib/FabArray.H

commit b2f85c9b2732d08c562211c6f0d5dbf722307a42
Author: car <car>
Date:   Thu Aug 2 01:11:36 2001 +0000

    MSVC fixes

Src/C_BaseLib/Array.H
Src/C_BaseLib/FabArray.H

commit 56a303c681ed86cc8bb6765ee692ab38555c20d6
Author: car <car>
Date:   Wed Aug 1 22:32:23 2001 +0000

    make fixes for g++

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit cde8b520e11627317e95acfd1c4adb8781100832
Author: lijewski <lijewski>
Date:   Wed Aug 1 21:50:44 2001 +0000

    now using BoxLib

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/BCRec.H
Src/C_AMRLib/BCRec.cpp
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/DatasetClient.cpp
Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/ErrorList.cpp
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/SlabStat.H
Src/C_AMRLib/SlabStat.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp
Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/COORDSYS_F.H
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/RealBox.H
Src/C_BaseLib/RealBox.cpp
Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp
Src/C_BoundaryLib/InterpBndryData.cpp
Src/C_BoundaryLib/Mask.H
Src/C_BoundaryLib/Mask.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/LP_F.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_19boxes
Src/LinearSolvers/C_CellMG/Test/main.cpp
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/RegType.H
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp
Src/LinearSolvers/C_TensorMG/DivVis.H
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/grids/gr.2_19boxes
Tests/LinearSolvers/C_CellMG/main.cpp
Tools/C_mk/Make.OSF1
Tools/C_mk/Make.defs
Tools/C_util/WritePlotFile.H
Tools/C_util/WritePlotFile.cpp

commit 137e3e506d093440489565eaac8419bead99eef6
Author: lijewski <lijewski>
Date:   Wed Aug 1 20:24:21 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/VisMF.cpp

commit 908cb19809d92e8d6405575f67e3f817e0c6afeb
Author: lijewski <lijewski>
Date:   Wed Aug 1 18:14:13 2001 +0000

    now include <cmath> where needed for std::abs()

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Utility.H

commit 955d70fc0788aef8ea807c91fd2fa869610f991d
Author: lijewski <lijewski>
Date:   Tue Jul 31 22:43:16 2001 +0000

    Inlined trivial functions.
    Without inlining I was 20% slower than old code on my example.

Src/C_BaseLib/Array.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/Orientation.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/UseCount.cpp

commit 8050d4ed2ce12de3cbdb5ae13f898c35b423c0e5
Author: lijewski <lijewski>
Date:   Tue Jul 31 19:24:10 2001 +0000

    No more RunStats.

Src/C_BaseLib/Make.package
Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp

commit a1a940f520174eef366403090bb5f51c15837e4d
Author: lijewski <lijewski>
Date:   Tue Jul 31 17:56:24 2001 +0000

    Some cleanup

Src/C_BaseLib/Arena.H
Src/C_BaseLib/Array.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BArena.cpp
Src/C_BaseLib/BLMpi.cpp
Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 3107dd516e9a903da30c83a87cb01a24b210a43b
Author: lijewski <lijewski>
Date:   Tue Jul 31 15:03:42 2001 +0000

    Got rid or old Iterator stuff

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.H

commit 2fa0036583b2388714cb40844631cc0ddcd29ce2
Author: car <car>
Date:   Thu Jul 26 20:50:05 2001 +0000

    more winstd.H uses

Src/C_BaseLib/CArena.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/ccse-mpi.H
Src/C_BaseLib/winstd.H

commit a2e8afc08f647d2a3f8b25e6aa580bccfcdc0ae7
Author: car <car>
Date:   Thu Jul 26 20:31:38 2001 +0000

    include file tweaks; Utility.H need iostream defns

Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/Utility.H

commit 9f1077891eb46e66f031242e2b3bdde7fdd32669
Author: car <car>
Date:   Thu Jul 26 20:27:27 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLWorkQueue.cpp

commit 8491ef3da2e8db7c77766af56910439f04e83bf6
Author: lijewski <lijewski>
Date:   Thu Jul 26 20:08:43 2001 +0000

    More forward declaration including <iosfwd>

Src/C_BaseLib/Array.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/Orientation.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/RunStats.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.H

commit 63d7ad859f8c18cf0b6fc266ee6d46b832162a29
Author: lijewski <lijewski>
Date:   Thu Jul 26 14:55:25 2001 +0000

    *** empty log message ***

Src/C_BaseLib/FabArray.cpp

commit 1c95994de2f4c09ba88e7c321dc6816789b33379
Author: car <car>
Date:   Thu Jul 26 13:51:54 2001 +0000

    Removed redundant member

Src/C_BaseLib/FabArray.H

commit 98f542eccff2276d5a015cfc2d0930f0059428fc
Author: lijewski <lijewski>
Date:   Wed Jul 25 23:42:02 2001 +0000

    *** empty log message ***

Src/C_BaseLib/FabArray.H

commit cecd2fa2a5264e0326f2104fecb8eb6236c39fbd
Author: lijewski <lijewski>
Date:   Wed Jul 25 23:39:18 2001 +0000

    oops

Src/C_BaseLib/FabArray.H

commit 36ac9c9caa33616cd1e650ce33ebb9b0cc279366
Author: lijewski <lijewski>
Date:   Wed Jul 25 23:36:15 2001 +0000

    *** empty log message ***

Src/C_BaseLib/Array.H
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 14357803bd1c77b55a7d5400914990e431eb3b0b
Author: car <car>
Date:   Wed Jul 25 05:22:56 2001 +0000

    BL_NO_LEGACY_ITERATORS

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/VisMF.cpp

commit a7173323431a168b9ffe894018273cc8ade071a5
Author: car <car>
Date:   Wed Jul 25 04:45:55 2001 +0000

    MFIter

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp

commit 0b86f20a476fee7df1ed82947403120a1082aa71
Author: car <car>
Date:   Wed Jul 25 01:15:13 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.cpp

commit 0f6c5e637daea01565b1cef3da344f26b214cb01
Author: car <car>
Date:   Tue Jul 24 22:42:12 2001 +0000

    MFIter...

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit a5c844d943f2dc4307e977e978273969c5610e4b
Author: lijewski <lijewski>
Date:   Tue Jul 24 22:04:47 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit 75f1cda463aed16ca7bceaca14a07e8c83fec011
Author: lijewski <lijewski>
Date:   Tue Jul 24 20:15:38 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.cpp

commit 44b3c392387dbe230f9d61b0577fd9f2a7a413f0
Author: car <car>
Date:   Tue Jul 24 19:47:17 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 9203a74a0b57bf946aeb2254f67a31ca07415427
Author: lijewski <lijewski>
Date:   Tue Jul 24 18:16:51 2001 +0000

    Now use size() instead of length()

Src/C_BaseLib/Array.H
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/List.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/RunStats.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 191e9dc98b43056199b5a15e8cd7ea577ade3bcb
Author: car <car>
Date:   Tue Jul 24 18:16:26 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BaseFab.H

commit 62286bc3732ebcf195fe980e407e49afef5212ea
Author: car <car>
Date:   Tue Jul 24 18:12:34 2001 +0000

    Fab Copy constructor

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 4374dfec2d25539b40793cf93261de540cb496a8
Author: car <car>
Date:   Tue Jul 24 14:38:21 2001 +0000

    removed 'options'

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit a8d59f5611bbdc8e6f1cbac2ba333c0da47abde1
Author: car <car>
Date:   Tue Jul 24 05:12:47 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 8949f4f4f2d0b0d69fa7429f388191f056006498
Author: lijewski <lijewski>
Date:   Mon Jul 23 23:07:36 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp

commit ba547e81817cd175d9cf1ff462cb3d8cfd0f44af
Author: car <car>
Date:   Mon Jul 23 22:30:23 2001 +0000

    minor changes

Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FabArray.H

commit 71c3373282a772ddd3b9f12bcee21e42af72f6fb
Author: car <car>
Date:   Mon Jul 23 21:32:38 2001 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp

commit ba437c4a83eab55cc0d9bee897c8ddc841e6d7be
Author: car <car>
Date:   Mon Jul 23 21:15:16 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit 52c59cabee7d644263f16f92d4d6988b37f9e00c
Author: lijewski <lijewski>
Date:   Mon Jul 23 20:07:14 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit 7c3e80cd2c273e08b7d39f7515db936993942806
Author: vince <vince>
Date:   Mon Jul 23 20:06:06 2001 +0000

    Added derived quantities.

Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp

commit f69355a70ebbe4beff590074ceb4bb8f5f677bb0
Author: lijewski <lijewski>
Date:   Mon Jul 23 19:34:23 2001 +0000

    *** empty log message ***

Src/C_BaseLib/WorkQueue.H

commit d333f2664e8575be6a1d898a7695410cfe8e0cac
Author: car <car>
Date:   Mon Jul 23 19:33:36 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 69ea9cdec781223e39b27007246b2e9c76ba803e
Author: lijewski <lijewski>
Date:   Mon Jul 23 18:15:21 2001 +0000

    aString is gone for good

Src/C_BaseLib/ParmParse.cpp

commit 410b354dd297fbd563f3d08a5b976b8b753219c7
Author: lijewski <lijewski>
Date:   Mon Jul 23 17:55:32 2001 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp

commit 70b94ecede13d4f41b84e26f05b4d7a8cef3ed3a
Author: lijewski <lijewski>
Date:   Mon Jul 23 17:39:00 2001 +0000

    asdfdfasdfkasdf asdf

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Utility.H

commit db68d076df99d485f657545ae2efc64523216443
Author: car <car>
Date:   Mon Jul 23 04:31:03 2001 +0000

    *** empty log message ***

Src/C_BaseLib/.cvsignore
Src/C_BaseLib/BoxLib.dsp
Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/GNUmakefile.tCArena
Src/C_BaseLib/test/tCArena.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/GNUmakefile.tCArena
Tests/C_BaseLib/tCArena.cpp

commit 0a43f9e1c815b703c6039c43f53db3994ddf8bb3
Author: car <car>
Date:   Mon Jul 23 04:25:47 2001 +0000

    *** empty log message ***

Src/C_BaseLib/test/.cvsignore
Tests/C_BaseLib/.cvsignore

commit b5b5179d0b162049c94b1af286462f0cd0b06062
Author: car <car>
Date:   Mon Jul 23 04:16:52 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/ParallelDescriptor.H

commit fdf4d4ada8f77237c4e4ef311b2dc63ca5ba8251
Author: car <car>
Date:   Sun Jul 22 23:46:40 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.cpp

commit cbd5c543e1a6658937860ea287ecfebaf08fec4b
Author: car <car>
Date:   Sun Jul 22 23:41:27 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 3af39cdf1a53bf588b834b27ada84f6753a631f2
Author: car <car>
Date:   Sun Jul 22 23:25:24 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Profiler.H

commit 7556cfb3a2469154b6804227b25528ab12941a62
Author: car <car>
Date:   Sun Jul 22 22:12:22 2001 +0000

    WIN32 Fixes

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/test/tProfiler.cpp
Tests/C_BaseLib/tProfiler.cpp

commit 2f2534d6ae580134652d01a2e52b543509b9a011
Author: car <car>
Date:   Sun Jul 22 22:12:10 2001 +0000

    Hides Profiling stuff in Initialize

Src/C_BaseLib/BoxLib.cpp

commit 68eb7780ae14ca0094419a39bb0516640f800f5e
Author: car <car>
Date:   Sun Jul 22 22:11:43 2001 +0000

    parm parses into std::string instead of aStrings

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 4b9015ae6a5bf2c3666b41d4c0c2af87853970ca
Author: car <car>
Date:   Sun Jul 22 20:44:30 2001 +0000

    *** empty log message ***

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Utility.cpp

commit 5a927ceaf541211f91db06d4b528d7057dc10585
Author: car <car>
Date:   Sun Jul 22 20:21:16 2001 +0000

    *** empty log message ***

Src/C_BaseLib/test/tRan.cpp
Tests/C_BaseLib/tRan.cpp

commit 0b72a64ac5dcd8965e795e5db54bf3c1edc748f7
Author: car <car>
Date:   Sun Jul 22 19:38:15 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/Thread.H

commit fa244b61362767249add884bdef02ed75be8e0f7
Author: car <car>
Date:   Sun Jul 22 18:52:16 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/ParallelDescriptor.H

commit 684ea5b2df1b5fec1e160288aa3eea074d0dfc33
Author: car <car>
Date:   Sun Jul 22 18:25:48 2001 +0000

    upto BoxLib spec

Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/tDir.cpp
Src/C_BaseLib/test/tFAC.cpp
Src/C_BaseLib/test/tFB.cpp
Src/C_BaseLib/test/tProfiler.cpp
Src/C_BaseLib/test/tThread.cpp
Src/C_BaseLib/test/tVisMF.cpp
Src/C_BaseLib/test/tWorkQueue.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/tDir.cpp
Tests/C_BaseLib/tFAC.cpp
Tests/C_BaseLib/tFB.cpp
Tests/C_BaseLib/tProfiler.cpp
Tests/C_BaseLib/tThread.cpp
Tests/C_BaseLib/tVisMF.cpp
Tests/C_BaseLib/tWorkQueue.cpp

commit 80c46df23ca54b8c96f20cbbf5105f7c187a7f04
Author: car <car>
Date:   Sun Jul 22 18:11:02 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/test/GNUmakefile
Tests/C_BaseLib/GNUmakefile

commit 09a55d0a23d9474287fd35f19c032ce8dee82473
Author: car <car>
Date:   Sun Jul 22 18:10:45 2001 +0000

    Random number validation file

Src/C_BaseLib/test/mt19937int.out
Tests/C_BaseLib/mt19937int.out

commit 4579913949ab03f8b0c3d7b870eb88c48681b685
Author: car <car>
Date:   Sat Jul 21 17:37:09 2001 +0000

    *** empty log message ***

Src/C_BaseLib/Array.H
Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/RunStats.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/aString.cpp
Src/C_BaseLib/winstd.H

commit 90c4b072801eb6ae25a01fe3c160ca2ae30bea56
Author: car <car>
Date:   Sat Jul 21 17:37:09 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLProfiler.cpp

commit 20de776b38c869f375563ad7ecfd8937cc35860c
Author: car <car>
Date:   Sat Jul 21 01:17:25 2001 +0000

    *** empty log message ***

Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 34e0fd6d29b66e9f3a17ef1489886ad1afb56bd4
Author: car <car>
Date:   Sat Jul 21 00:53:50 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/Thread.H
Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/tProfiler.cpp
Src/C_BaseLib/test/tThread.cpp
Src/C_BaseLib/test/tWorkQueue.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/tProfiler.cpp
Tests/C_BaseLib/tThread.cpp
Tests/C_BaseLib/tWorkQueue.cpp

commit cbeecaa3966b3c27c386cccf0f5f077ad34879e6
Author: car <car>
Date:   Sat Jul 21 00:33:15 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLWorkQueue.cpp

commit 8b076f91240b0bef56b2587dc54057b996e90f53
Author: car <car>
Date:   Sat Jul 21 00:32:37 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLWorkQueue.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/WorkQueue.H

commit 9f41823161690d7b27713caa04ef7aa1cc97744e
Author: car <car>
Date:   Sat Jul 21 00:32:37 2001 +0000

    *** empty log message ***

Src/C_BaseLib/WorkQueue.H

commit 0964e060bf456c0c474dabd1b756d6a6b2de186d
Author: lijewski <lijewski>
Date:   Fri Jul 20 23:06:17 2001 +0000

    *** empty log message ***

Src/C_BaseLib/Array.H
Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/RunStats.cpp
Src/C_BaseLib/Thread.H
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp

commit f2b4670f94fa5bc0166906bbc41b6aba4825f5fe
Author: car <car>
Date:   Fri Jul 20 19:52:54 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp

commit a591e253890f0b136bf976b1b6799b7e32983ac6
Author: car <car>
Date:   Fri Jul 20 19:44:24 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Thread.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/tProfiler.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/tProfiler.cpp

commit 960659929b14cfe5657d5f95f90e1a2f05198709
Author: car <car>
Date:   Fri Jul 20 19:37:36 2001 +0000

    *** empty log message ***

Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/tProfiler.cpp
Src/C_BaseLib/test/tThread.cpp
Src/C_BaseLib/test/tWorkQueue.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/tProfiler.cpp
Tests/C_BaseLib/tThread.cpp
Tests/C_BaseLib/tWorkQueue.cpp

commit 0341fc65b804dcf538b93eb2e00e21e217971fd3
Author: car <car>
Date:   Fri Jul 20 19:31:06 2001 +0000

    Parallel Fixes

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.cpp

commit cfb67175f0662ed73b39e02ffc061df95232253c
Author: car <car>
Date:   Fri Jul 20 18:18:42 2001 +0000

    *** empty log message ***

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.cpp

commit b82e95e66822450c785b93d077381e5ebc7bebef
Author: car <car>
Date:   Fri Jul 20 17:57:27 2001 +0000

    Fixes for Parallel

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 33f2abe03cb1fda11725885c431b5850612f863c
Author: lijewski <lijewski>
Date:   Fri Jul 20 17:28:16 2001 +0000

    Removed index>=0 checks ...

Src/C_BaseLib/aString.cpp

commit 9fc149a9c5d940e5d128cee6c679d9b1cd398b27
Author: car <car>
Date:   Fri Jul 20 17:24:30 2001 +0000

    windows normalization

Src/C_BaseLib/winstd.H

commit 578c057a618d30ac7a6c04d7ce372079713cc769
Author: car <car>
Date:   Fri Jul 20 17:20:48 2001 +0000

    FabArray takes only one template arg

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 09a7778333455c3f80f6f786cad07031b14ef92a
Author: car <car>
Date:   Fri Jul 20 17:01:44 2001 +0000

    *** empty log message ***

Src/C_BaseLib/Array.H
Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BLTimer.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/SPACE.H
Src/C_BaseLib/Thread.H
Src/C_BaseLib/Timer.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp
Src/C_BaseLib/ccse-mpi.H

commit e1d65f30503f2a7c18ea0c97d69b75f3865a7570
Author: lijewski <lijewski>
Date:   Fri Jul 20 16:54:07 2001 +0000

    Merged BaseFab among other tweaks.

Src/C_BaseLib/ArithFab.H
Src/C_BaseLib/Array.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/NormedFab.H
Src/C_BaseLib/OrderedFab.H

commit 6b3e02fd2176f805fcf35fce7b355bc77c76ec98
Author: car <car>
Date:   Fri Jul 20 04:46:21 2001 +0000

    profiling works in serial

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BLTimer.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Thread.H
Src/C_BaseLib/Timer.H
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp

commit d1dc9f1e2c2507c5d240583983ce8c4f8166feec
Author: car <car>
Date:   Fri Jul 20 01:45:48 2001 +0000

    *** empty log message ***

Src/C_BaseLib/Array.H
Src/C_BaseLib/PArray.H

commit 025f52d8040a31eaafb1aad75084eb281c1d1021
Author: lijewski <lijewski>
Date:   Thu Jul 19 21:31:09 2001 +0000

    Fixed a small bug we introduced.

Src/C_BaseLib/IntVect.cpp

commit 85dc53c3222cc684a2bdbe8ffc6ea4039b07ed42
Author: lijewski <lijewski>
Date:   Thu Jul 19 21:11:50 2001 +0000

    *** empty log message ***

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/RunStats.cpp
Src/C_BaseLib/VisMF.cpp

commit 7e6f6699614d04710573c4077973769c0ad104cb
Author: lijewski <lijewski>
Date:   Thu Jul 19 20:02:43 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ArithFab.H
Src/C_BaseLib/Array.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/List.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/NormedFab.H
Src/C_BaseLib/OrderedFab.H
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/Orientation.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/UseCount.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp

commit 5b16bd096eb25cb4812c4bef71c42854977667e8
Author: lijewski <lijewski>
Date:   Thu Jul 19 19:02:42 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/MultiFab.cpp

commit b46652ee1209765713186022e5aee6ff50711b77
Author: lijewski <lijewski>
Date:   Thu Jul 19 17:51:48 2001 +0000

    Mods due to BoxLib:: namespace

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/FabArray.H

commit 3131f06b1e991d0386d3fca31eea9d8e72065216
Author: car <car>
Date:   Thu Jul 19 17:19:33 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxList.cpp

commit 15e45842e56f40ab7c03b05d608ca8ed0f1f2023
Author: car <car>
Date:   Thu Jul 19 17:19:32 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Thread.H

commit 263f6398443b2fe2f80694b3befccb9b860187b1
Author: lijewski <lijewski>
Date:   Thu Jul 19 16:57:30 2001 +0000

    Got rid of namespace.

Src/C_BaseLib/Arena.H
Src/C_BaseLib/Arena.cpp
Src/C_BaseLib/ArithFab.H
Src/C_BaseLib/Array.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BArena.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FPC.H
Src/C_BaseLib/FPC.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/List.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/NormedFab.H
Src/C_BaseLib/OrderedFab.H
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/Orientation.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/REAL.H
Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp
Src/C_BaseLib/SPACE.H
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp
Src/C_BaseLib/ccse-mpi.H

commit 1c5d3b6a195234d4477880b368d43a1f81d82b04
Author: car <car>
Date:   Thu Jul 19 16:51:22 2001 +0000

    *** empty log message ***

Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp

commit 117d6849f5e917583a2a483aa7a1016a6391bce3
Author: lijewski <lijewski>
Date:   Thu Jul 19 15:26:47 2001 +0000

    We've now got an Arena.cpp.

Src/C_BaseLib/Arena.H
Src/C_BaseLib/Arena.cpp
Src/C_BaseLib/Make.package

commit 1bb6d252d4935ad16c6ebc1c1c737ac6ba67ff2e
Author: lijewski <lijewski>
Date:   Wed Jul 18 23:07:06 2001 +0000

    More work toward the one true BoxLib ...

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.cpp

commit ab3e5275f8626d22f558fc6176bea1b2f0eb0cf2
Author: car <car>
Date:   Wed Jul 18 22:21:15 2001 +0000

    Profiling stuff

Src/C_BaseLib/BLMpi.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/Make.package
Src/C_BaseLib/MultiFab.cpp

commit bfb513574868b478185973e0528ff14e51b17e66
Author: car <car>
Date:   Wed Jul 18 22:20:29 2001 +0000

    Initial loads, don't work

Src/C_BaseLib/BLMpi.cpp
Src/C_BaseLib/BLMpi.w
Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Thread.H

commit 43315a02bd97e0f8875a129bbf39770c5188b071
Author: car <car>
Date:   Wed Jul 18 20:41:04 2001 +0000

    Max->std::max

Src/C_BaseLib/MultiFab.cpp

commit dbf9f2dcf11e3598c1548f3c64db9128beedbc30
Author: car <car>
Date:   Wed Jul 18 20:40:29 2001 +0000

    Abs->std::abs

Src/C_BaseLib/NormedFab.H

commit 529033c6124606a1b20941e2b105faf3a1710e8d
Author: lijewski <lijewski>
Date:   Wed Jul 18 19:37:19 2001 +0000

    A few more tweaks ...

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 3a827d1ba3a45ae646fa65c1cc9bb0caea08044c
Author: car <car>
Date:   Wed Jul 18 17:33:04 2001 +0000

    another Max

Src/C_BaseLib/RunStats.cpp

commit 0f2140dc731783bb1538cc72a62dc57ab5ecb25e
Author: lijewski <lijewski>
Date:   Wed Jul 18 17:31:06 2001 +0000

    2-D bug

Src/C_BaseLib/FArrayBox.H

commit b899136954c04b12fbf4f91b16807dc91c0f8988
Author: car <car>
Date:   Wed Jul 18 16:46:09 2001 +0000

    fix for KCC 4.0f

Tools/C_mk/Make.defs

commit 9a39f08ba20feb6ff5e2cef76c6143ff9eddf2d7
Author: car <car>
Date:   Tue Jul 17 23:40:08 2001 +0000

    Fortran process // comments

Src/C_BaseLib/CONSTANTS.H

commit 8745cb3484ca919486144e2742c081680a61a6ed
Author: car <car>
Date:   Tue Jul 17 23:14:38 2001 +0000

    Fortran can't process // comments

Src/C_BaseLib/REAL.H

commit ddf319374930edff9cb1ac65339049c2709fa0d5
Author: car <car>
Date:   Tue Jul 17 23:14:13 2001 +0000

    inline changes

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp

commit 494b32562c2cfcd035d6d5821324cfd5215ca5b1
Author: lijewski <lijewski>
Date:   Tue Jul 17 23:02:17 2001 +0000

    numerous changes

Src/C_BaseLib/Arena.H
Src/C_BaseLib/ArithFab.H
Src/C_BaseLib/Array.H
Src/C_BaseLib/ArrayLim.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BArena.cpp
Src/C_BaseLib/BLVERSION.H
Src/C_BaseLib/BLassert.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/CONSTANTS.H
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FPC.H
Src/C_BaseLib/FPC.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/List.H
Src/C_BaseLib/Looping.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/Misc.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/NormedFab.H
Src/C_BaseLib/OrderedFab.H
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/Orientation.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/REAL.H
Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp
Src/C_BaseLib/SPACE.H
Src/C_BaseLib/SPACE_F.H
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp
Src/C_BaseLib/ccse-mpi.H

commit f7104d8b032b8ab4f99f26a7ce6bcb05fc44628b
Author: marc <marc>
Date:   Tue Jul 17 21:21:12 2001 +0000

    Remove Wimplicit for little-f files, as they are generally written
    by 'someone else', and we don't want to rewrite everything...

Tools/C_mk/Make.Linux

commit 2d518f0351e88bd7129f1d09a9f9eeae61ecedf7
Author: lijewski <lijewski>
Date:   Tue Jul 17 16:58:05 2001 +0000

    Added for GNU

Src/C_BaseLib/std/limits

commit 41f3ac2599bf462a839a39e5f54bc4a620549249
Author: lijewski <lijewski>
Date:   Tue Jul 17 16:47:35 2001 +0000

    Getting rid of some stuff.

Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H
Src/C_BaseLib/Specialize.cpp
Src/C_BaseLib/Tracer.H
Src/C_BaseLib/Tracer.cpp

commit dbe000a5a3d3513f9f6659ccd727d46751130244
Author: car <car>
Date:   Fri May 18 16:49:24 2001 +0000

    ampersand is a better continuation character, RE:
    Fortran standard

Tools/C_scripts/strip72

commit b8e376401f6b38daa495a5cea09d389ec8f60ba1
Author: car <car>
Date:   Thu May 17 21:52:13 2001 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 196cf06d299b221868ec826cfa415bce08a002eb
Author: car <car>
Date:   Tue May 15 16:31:23 2001 +0000

    changes in flags

Tools/C_mk/Make.Linux

commit aeadde2a9cac3431fb3c7efd397896151112c6b1
Author: lijewski <lijewski>
Date:   Mon May 14 17:48:12 2001 +0000

    Removed tar_and_rm_files stuff.
    The compressor utility seems to work fine.

Src/C_AMRLib/Amr.cpp

commit 7d543992601b1cd57c1024cc9266ef7ff905bbea
Author: wyc <wyc>
Date:   Fri May 11 19:44:24 2001 +0000

    added small change to handle PGI compiler

Tools/C_mk/Make.Linux

commit 501733762dc0b3e3510ccc0339cea7d13574292e
Author: lijewski <lijewski>
Date:   Thu May 10 17:16:40 2001 +0000

    No longer compile in Tracer.[H,cpp]

Src/C_BaseLib/Make.package

commit 542ce34e712bcd440513e68c49eceda4dd0e6303
Author: lijewski <lijewski>
Date:   Wed May 9 22:42:22 2001 +0000

    Simplified report().

Src/C_BaseLib/RunStats.cpp

commit b9db89229893876b5408f2018bc34eca944a5dd9
Author: lijewski <lijewski>
Date:   Wed May 9 22:41:45 2001 +0000

    Removed more RunStats stuff.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit c35feab8a16c6b2a1bd805bf8a77c377e4cbf98f
Author: lijewski <lijewski>
Date:   Wed May 9 22:30:59 2001 +0000

    Simplified how RunStats is used in code.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/SlabStat.cpp
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/TagBox.cpp

commit 313fbd308caadbbed752ffdb221cc75ade6a0ad9
Author: lijewski <lijewski>
Date:   Wed May 2 20:20:40 2001 +0000

    New -L option for mpi on OSF1

Tools/C_mk/Make.mpi

commit 8160d45db5a5859dd9a2c8e500e2fa46e25ad62d
Author: car <car>
Date:   Fri Apr 27 20:07:11 2001 +0000

    Added support for Intel compiler

Tools/C_mk/Make.Linux

commit 41b7d20f27251ac5ad65f8bafe3533ef6ead031b
Author: car <car>
Date:   Wed Apr 25 22:54:09 2001 +0000

    minor bugs

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 73a9e0d1078e8197bb67b43660ed784f5e64f84d
Author: car <car>
Date:   Wed Apr 25 04:16:20 2001 +0000

    isDouble should return bool

Src/C_BaseLib/ParmParse.H

commit bff785c93ece49ba4795ab27ff3dc2ab8ab84176
Author: car <car>
Date:   Tue Apr 24 19:42:19 2001 +0000

    quiet warnings

Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/aString.cpp

commit c6b075ca39f4eea4807194adb11d92f40f69e9e3
Author: car <car>
Date:   Mon Apr 23 20:08:20 2001 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit 9eac80e95fe459241bdac9d7e26bfb428e45064e
Author: car <car>
Date:   Mon Apr 23 19:33:30 2001 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/main.cpp

commit c13320f5ff9f1b5ee8f144f88a76a2a57c669de9
Author: car <car>
Date:   Fri Apr 20 14:25:30 2001 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit 91c4ea8d3f8068ac58659643767f8dba610e78d2
Author: lijewski <lijewski>
Date:   Thu Apr 19 22:24:19 2001 +0000

    Removed some RunStats.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/VisMF.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 7d954501c735a4724e842566ab361897e93abb99
Author: car <car>
Date:   Mon Apr 16 22:38:17 2001 +0000

    *** empty log message ***

Tools/C_util/wrappergen/Makefile
Tools/C_util/wrappergen/wrappergen.c

commit af4166b6529eb71ce145eda2ce90506beeda326c
Author: car <car>
Date:   Mon Apr 16 22:20:49 2001 +0000

    *** empty log message ***

Tools/C_util/wrappergen/Makefile
Tools/C_util/wrappergen/args.c
Tools/C_util/wrappergen/readproto.c
Tools/C_util/wrappergen/wrappergen.c
Tools/C_util/wrappergen/wrappergen.h

commit 7f567212cf6d3fb2823f8d60b336b500eef61bcc
Author: car <car>
Date:   Mon Apr 16 21:32:55 2001 +0000

    *** empty log message ***

Tools/C_util/wrappergen/wrappergen.c

commit e88d8d4da2f7a36001d875d725f2a2548e5b1a1d
Author: car <car>
Date:   Fri Apr 13 17:18:54 2001 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit b7456cc3a8fd9966eadc8a3c5e66ec4afe17cb9e
Author: lijewski <lijewski>
Date:   Wed Apr 11 18:11:04 2001 +0000

    Further simplification to copy().

Src/C_BaseLib/FabArray.H

commit a4ba6c4c6970b689d76a74ff55354e91b5085cd7
Author: car <car>
Date:   Fri Apr 6 20:27:52 2001 +0000

    *** empty log message ***

Tools/C_util/wrappergen/Makefile
Tools/C_util/wrappergen/PROTO
Tools/C_util/wrappergen/README

commit d7fcf120d314f5abf03cb214a745f4673001b696
Author: car <car>
Date:   Fri Apr 6 20:17:03 2001 +0000

    minor changes

Tools/C_util/wrappergen/.cvsignore
Tools/C_util/wrappergen/Makefile
Tools/C_util/wrappergen/PROTO

commit 3a3d84e372f5544a91d683dd41219c2b3898d3e4
Author: car <car>
Date:   Fri Apr 6 20:12:14 2001 +0000

    Initial revision

Tools/C_util/wrappergen/Makefile
Tools/C_util/wrappergen/PROTO
Tools/C_util/wrappergen/README
Tools/C_util/wrappergen/args.c
Tools/C_util/wrappergen/args.h
Tools/C_util/wrappergen/doc.c
Tools/C_util/wrappergen/doc.h
Tools/C_util/wrappergen/driver.c
Tools/C_util/wrappergen/expandingList.h
Tools/C_util/wrappergen/mpifn
Tools/C_util/wrappergen/petsccfg.h
Tools/C_util/wrappergen/prof.c
Tools/C_util/wrappergen/prof_wrapper.c
Tools/C_util/wrappergen/readproto.c
Tools/C_util/wrappergen/sample.c
Tools/C_util/wrappergen/sample.w
Tools/C_util/wrappergen/system.c
Tools/C_util/wrappergen/system.h
Tools/C_util/wrappergen/tools.h
Tools/C_util/wrappergen/wrappergen.c
Tools/C_util/wrappergen/wrappergen.h
Tools/C_util/wrappergen/write_proto.c

commit 7191f0a5ea9e05f47293e9cb4722c8b9f12d5e08
Author: car <car>
Date:   Fri Apr 6 20:04:52 2001 +0000

    MPI off fix

Src/C_BaseLib/VisMF.cpp

commit c03b1479ce6402cf0f3a4be346ff39bd6ca92d0c
Author: lijewski <lijewski>
Date:   Mon Apr 2 17:58:59 2001 +0000

    Now use MPI_Waitsome() instead of MPI_Wait() ...

Src/C_AMRLib/FluxRegister.cpp

commit c74e9c3c57bf04136aa1dc116d2311bd16328dc7
Author: lijewski <lijewski>
Date:   Mon Apr 2 16:48:31 2001 +0000

    Simplified and improved the MPI stuff ...

Src/C_BaseLib/VisMF.cpp

commit dea06748ad81966ce21ee62aff4709ad2a16e5c4
Author: lijewski <lijewski>
Date:   Fri Mar 30 23:25:31 2001 +0000

    Now use MPI_Waitsome() instead of busy-waiting with MPI_Test().

Src/C_BaseLib/FabArray.H

commit dbfa17a899f0d47fe8e36f96c33ac1fbc823666e
Author: car <car>
Date:   Wed Mar 28 21:22:20 2001 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 674c5e649f8235ca860e58dc911ed08eb6ddfa35
Author: car <car>
Date:   Wed Mar 28 21:08:51 2001 +0000

    Removed FPU code, wasn't useful

Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Tools/C_mk/Make.CYGWIN_NT
Tools/C_mk/Make.Linux

commit 6322e52d1d5da20ee6b04263089f7a4518bb229a
Author: car <car>
Date:   Wed Mar 28 20:25:53 2001 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit fe718320981a1d0b6604e81f4006ad0b9c89b922
Author: car <car>
Date:   Wed Mar 28 19:36:44 2001 +0000

    Makefile tweaks

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_NodalMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit 7e5d160b118e4b3806803635a293c930c0de5bd2
Author: lijewski <lijewski>
Date:   Fri Mar 23 21:10:21 2001 +0000

    More asynchronicity in fab_copy.
    Now use MPI_Send() instead of MPI_Ssend() as well.

Src/C_BaseLib/FabArray.H

commit cf7f7f01269ea358e600e0b0bb059d6ebf7b7860
Author: lijewski <lijewski>
Date:   Fri Mar 23 18:23:20 2001 +0000

    Some additional asynchronous computation in CollectData().
    Definite improvement when running 2-D iamr on many CPUs.

Src/C_BaseLib/FabArray.H

commit 09301a90ca439075a3cd61eedca8297611785ae7
Author: lijewski <lijewski>
Date:   Thu Mar 22 22:58:40 2001 +0000

    Adde SeqNum() for use by CollectData().

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 019046932671708913fcb8e5d8c0452861638447
Author: car <car>
Date:   Wed Mar 21 14:58:59 2001 +0000

    makefile tweaks; CPP-->FORT_CPP

Tools/C_mk/Make.AIX
Tools/C_mk/Make.CRAY
Tools/C_mk/Make.CYGWIN_NT
Tools/C_mk/Make.IRIX64
Tools/C_mk/Make.Linux
Tools/C_mk/Make.OSF1
Tools/C_mk/Make.T3E
Tools/C_mk/Make.rules

commit cc6d436c141bdd48b55e611a058a399ba954bec6
Author: car <car>
Date:   Tue Mar 20 19:42:02 2001 +0000

    maxorder flag

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit e5a8716c56af13c262dfcf237b8ece12ba11bbd0
Author: car <car>
Date:   Tue Mar 20 19:41:42 2001 +0000

    verbose flags

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 2a740254626e6b1ebb10f0e7ec694ac155631725
Author: car <car>
Date:   Tue Mar 20 19:40:43 2001 +0000

    namespace correction

Src/C_BaseLib/ParallelDescriptor.cpp

commit e02d57b123630225f5f2eafa65fd16ab2cb1abfe
Author: lijewski <lijewski>
Date:   Wed Mar 14 22:02:29 2001 +0000

    Removed some virtual calls and other simplifications.

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit dddacbb297e64d041a41881e049a9f2e8af92414
Author: wyc <wyc>
Date:   Thu Mar 1 21:17:34 2001 +0000

    added preprocessor foobah to protect squirrelly namespace stuff

Src/C_BaseLib/ParallelDescriptor.cpp

commit 354753c2df0f51e59bf528ccc9c15140abcebe47
Author: lijewski <lijewski>
Date:   Wed Feb 28 18:07:31 2001 +0000

    Removed FORT_FLUSH stuff ...

Src/LinearSolvers/C_NodalMG/hgdebug.F

commit 031a96bad2e9b25aa1c83af5d0ed64da69ab3fcb
Author: lijewski <lijewski>
Date:   Tue Feb 27 18:49:14 2001 +0000

    Rearranged some HG_DEBUG stuff.

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit b7fa8451ae1ba45a1e882abdf97904fd96ce698c
Author: marc <marc>
Date:   Sat Feb 17 01:17:36 2001 +0000

    A little more fixup for Athlon compile of stuff.

Tools/C_scripts/dsp.mak

commit 827042311f109d6cd90ccb83f7d5ecb082cbe149
Author: almgren <almgren>
Date:   Fri Feb 16 22:59:51 2001 +0000

    Don't need this declaration.

Src/C_BaseLib/COORDSYS_2D.F

commit 73e0ff6fe7939a9063aec7bef90a708a74a3106f
Author: lijewski <lijewski>
Date:   Wed Feb 14 19:05:44 2001 +0000

    Deprecated BL_USE_ARLIM junk

Src/C_BaseLib/ArrayLim.H

commit 60bd10ee5700606ddd06f6cb54877d0b168242c1
Author: lijewski <lijewski>
Date:   Wed Feb 14 17:57:57 2001 +0000

    Deprecated BL_USE_ARLIM ...

Src/C_BaseLib/ArrayLim.H

commit 0d2faeaa0d3ff54377bf467fcbfb4463de819f38
Author: lijewski <lijewski>
Date:   Thu Feb 1 23:39:35 2001 +0000

    Removed AlternateApplyBC junk.

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 65bf0193a85def70207df7aeb1b2706a446a732f
Author: lijewski <lijewski>
Date:   Thu Feb 1 23:17:57 2001 +0000

    BiCG is now default CG solver.

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 8b012e3614bcc8e08e0b7978fdbeaa502bfe0cbf
Author: vince <vince>
Date:   Thu Feb 1 21:28:27 2001 +0000

    Added support for cygwin under nt.

Tools/C_mk/Make.CYGWIN_NT

commit b1dc57a913d5cda718e50346507e859640a48c6c
Author: vince <vince>
Date:   Thu Feb 1 00:49:02 2001 +0000

    Added support for cygwin.

Tools/C_mk/Make.defs

commit 33173521f94bae0684c181eb4ad7f3c92c2b25a3
Author: lijewski <lijewski>
Date:   Fri Jan 26 18:08:14 2001 +0000

    Forgot the non-MPI section

Src/C_BaseLib/ParallelDescriptor.cpp

commit 57ad6f0be0267a3d05d041b2a71091dad3ccdfb7
Author: lijewski <lijewski>
Date:   Thu Jan 25 23:53:23 2001 +0000

    Removed a BL_ASSERT() ...

Src/C_BoundaryLib/FabSet.cpp

commit 00592b4f5c4f4f6eb50194cf9e6c31c3dc979129
Author: lijewski <lijewski>
Date:   Thu Jan 25 23:52:36 2001 +0000

    Added NProcsCFD() to ParallelDescriptor.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit ea2b90f65e1f18fc34cbce9bb7300a881ea740a5
Author: lijewski <lijewski>
Date:   Wed Jan 24 22:50:47 2001 +0000

    Now compiles.

Src/C_BaseLib/test/tCArena.cpp
Tests/C_BaseLib/tCArena.cpp

commit caaf0e2e2d4d34246cf62fc6314416c91ab3a2b0
Author: marc <marc>
Date:   Fri Jan 19 22:57:48 2001 +0000

    Incorporate larger stencil in tang interp at c-f

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F
Src/C_BoundaryLib/InterpBndryData.cpp

commit b12571515b3ab4cd345f7d4cabd655257660084b
Merge: 7a69181e3 24e3d0b53
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Jan 4 06:52:45 2001 -0800

    Merge branch 'master' of gamera.lbl.gov:/home/CCSE/gitroot/BoxLib

commit 7a69181e354761fd68906024d6139fda1b626571
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Jan 4 06:51:17 2001 -0800

    PyBoxLib: Fix int size bug.

Src/Python/F90/fboxlib/boxarray.py

commit 30bff5876cc34e213e1302a304e9f2193e127f9a
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Fri Nov 14 03:54:34 2014 +0300

    PyBoxLib: Flesh out a few more things.

Src/Python/F90/fboxlib/__init__.py
Src/Python/F90/fboxlib/layout.py
Src/Python/F90/fboxlib/multifab.py
Src/Python/F90/src/fboxlib_c.c

commit b78150934753d56b662d28b879aae35aa67dc4e4
Author: marc <marc>
Date:   Thu Jan 4 00:49:52 2001 +0000

    Fix up script a little more...

Tools/C_scripts/dsp.mak

commit 711bef5d80f53d096ce90efcf7b24372171427d6
Author: car <car>
Date:   Mon Dec 11 18:45:53 2000 +0000

    main.cpp

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/main.cpp

commit ed60313c3db7ae82747a2e5e71be2b19ce909a18
Author: marc <marc>
Date:   Thu Dec 7 17:39:05 2000 +0000

    Small mod to script for opt

Tools/C_scripts/dsp.mak

commit 4ee38a2aebf2347489ed235068bda3c238106137
Author: marc <marc>
Date:   Wed Dec 6 23:44:28 2000 +0000

    Set maxmem stuff to be unlimited

Tools/C_mk/Make.AIX

commit dc2b57a8614778113a32991329b0a2445bb36a5e
Author: almgren <almgren>
Date:   Wed Dec 6 23:13:58 2000 +0000

    Modified AddFPB to allow the Geometry::FillPeriodicBoundary call to
    handle edge-centered as well as cell- and node-centered data.

Src/C_BaseLib/Geometry.cpp

commit 84bbec8bf1eecf948d64895c084d5111445f2426
Author: marc <marc>
Date:   Tue Dec 5 01:05:29 2000 +0000

    Fix up to build on Athlon with W2K + MSVC 6

Tools/C_scripts/dsp.mak

commit 3ee17ff6c345e4a5bdc5aa556a5b5ce3952eb353
Author: marc <marc>
Date:   Fri Dec 1 23:35:19 2000 +0000

    Move stop tests to avoid relax/print if incoming problem already solved.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit ba7d284f4c46e29a876a39e6de65f21ede3d8d51
Author: lijewski <lijewski>
Date:   Fri Nov 17 18:01:09 2000 +0000

    Consolidated some duplicated code.

Src/C_AMRLib/StateData.cpp

commit b9ec7dfb8d3f1f02a0c8cad489ced54859d28320
Author: lijewski <lijewski>
Date:   Fri Nov 17 18:00:55 2000 +0000

    Little simplification ...

Src/C_AMRLib/Interpolater.cpp

commit cbf36fd7621c4ad9d8c3ca3e5359bcd7d6799f53
Author: car <car>
Date:   Wed Nov 15 20:12:02 2000 +0000

    D_PICK expands to 1st, 2nd, or 3rd argument
    dependinging on BL_SPACEDIM; Happy Compiling

Src/C_BaseLib/SPACE.H

commit 3bafa86d56fe5595708f65c1affa29455934db8f
Author: car <car>
Date:   Sun Nov 12 17:26:12 2000 +0000

    added a NumPts to BoxArray

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 8ae3ea420ec6979b1194c171f614591d23dfb7a9
Author: car <car>
Date:   Wed Nov 8 22:01:50 2000 +0000

    book != bool

Src/C_BaseLib/BaseFab.H

commit 7473a058fb82b34bac68b550f0439b267d15000b
Author: lijewski <lijewski>
Date:   Wed Nov 8 21:48:21 2000 +0000

    Added bool isAllocated () ...

Src/C_BaseLib/BaseFab.H

commit 4b68a52a723d59cf91e54d818e4e8151650b3ca7
Author: lijewski <lijewski>
Date:   Thu Nov 2 23:07:27 2000 +0000

    A tad simplification ...

Src/LinearSolvers/C_TensorMG/DivVis.cpp

commit f56f3aadea4b9ae9c5bf131af4cc3d03bdc5e759
Author: lijewski <lijewski>
Date:   Wed Nov 1 18:29:37 2000 +0000

    A little simplification ...

Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/RealBox.cpp

commit c399cc572fe52df454d6731de8a375297805cfc1
Author: lijewski <lijewski>
Date:   Wed Nov 1 18:06:14 2000 +0000

    A little simplification ...

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp

commit 4ad8bad8e3951ccd140511e1a2cf97ca9849d0cd
Author: lijewski <lijewski>
Date:   Tue Oct 31 21:11:21 2000 +0000

    Minimized memory overhead in MF -> FAB copy().

Src/C_BaseLib/FabArray.H

commit bf024155c2114ec5938913b5a00e115d8c54f756
Author: vince <vince>
Date:   Fri Oct 27 00:50:18 2000 +0000

    Added setbuf ifdefs.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/VisMF.cpp

commit 23e08015c22f1b30878c0410da72634a20ed0dbb
Author: lijewski <lijewski>
Date:   Thu Oct 19 18:04:17 2000 +0000

    Removed "nproc" stuff from DistributionMapping interface.
    Added specialized DistributionMapping constructor.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H

commit cb140d92bd123e84e5a641f1317bc665c770f813
Author: lijewski <lijewski>
Date:   Tue Oct 3 20:26:49 2000 +0000

    Small change for BL_AIX

Src/C_BaseLib/Utility.cpp

commit fd1d53df7b936948085152c99f83f57291d6e7b7
Author: lijewski <lijewski>
Date:   Tue Oct 3 18:17:27 2000 +0000

    Added an explicit type

Src/LinearSolvers/C_CellMG/LP_2D.F

commit 07c7708e31ba6104946e9bc83eea82c1fe75cbcc
Author: lijewski <lijewski>
Date:   Mon Oct 2 21:08:52 2000 +0000

    Removed copyright macro.

Tools/C_util/Convergence/Add.cpp
Tools/C_util/Convergence/DiffFab.cpp
Tools/C_util/Convergence/DiffPlot.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileNormB.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp
Tools/C_util/dbgTools/crsGrids.cpp
Tools/C_util/dbgTools/intersectGrids.cpp

commit 3592610112e3a0b14e24a1d89402695ed30f5756
Author: lijewski <lijewski>
Date:   Mon Oct 2 20:48:40 2000 +0000

    Removed copyright macro.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/BCRec.H
Src/C_AMRLib/BCRec.cpp
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/DatasetClient.H
Src/C_AMRLib/DatasetClient.cpp
Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/ErrorList.cpp
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/LevelBld.H
Src/C_AMRLib/SlabStat.H
Src/C_AMRLib/SlabStat.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp
Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/Arena.H
Src/C_BaseLib/ArithFab.H
Src/C_BaseLib/Array.H
Src/C_BaseLib/ArrayLim.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BArena.cpp
Src/C_BaseLib/BLVERSION.H
Src/C_BaseLib/BLassert.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/CONSTANTS.H
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FPC.H
Src/C_BaseLib/FPC.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/List.H
Src/C_BaseLib/Looping.H
Src/C_BaseLib/Misc.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/NormedFab.H
Src/C_BaseLib/OrderedFab.H
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/Orientation.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/REAL.H
Src/C_BaseLib/RealBox.H
Src/C_BaseLib/RealBox.cpp
Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp
Src/C_BaseLib/SPACE.H
Src/C_BaseLib/SPACE_F.H
Src/C_BaseLib/Tracer.H
Src/C_BaseLib/Tracer.cpp
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp
Src/C_BaseLib/ccse-mpi.H
Src/C_BaseLib/test/t8BIT.cpp
Src/C_BaseLib/test/tCArena.cpp
Src/C_BaseLib/test/tDir.cpp
Src/C_BaseLib/test/tFAC.cpp
Src/C_BaseLib/test/tFB.cpp
Src/C_BaseLib/test/tVisMF.cpp
Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/BoundCond.H
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp
Src/C_BoundaryLib/Mask.H
Src/C_BoundaryLib/Mask.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_NodalMG/RegType.H
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.H
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp
Src/LinearSolvers/C_TensorMG/DivVis.H
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp
Tests/C_BaseLib/t8BIT.cpp
Tests/C_BaseLib/tCArena.cpp
Tests/C_BaseLib/tDir.cpp
Tests/C_BaseLib/tFAC.cpp
Tests/C_BaseLib/tFB.cpp
Tests/C_BaseLib/tVisMF.cpp

commit 48d075f85212df62d1f7c1fc3908119f09fc7b8a
Author: car <car>
Date:   Mon Oct 2 18:13:08 2000 +0000

    Lab Sanctions Source License

Src/C_AMRLib/OpenSource.txt
Src/C_BaseLib/OpenSource.txt
Src/C_BoundaryLib/OpenSource.txt
Src/LinearSolvers/C_CellMG/OpenSource.txt
Src/LinearSolvers/C_NodalMG/OpenSource.txt
Src/LinearSolvers/C_TensorMG/OpenSource.txt

commit 6f8d126016270098bccfa68e039069491163eab6
Author: car <car>
Date:   Tue Sep 26 18:19:25 2000 +0000

    helper macro for FORTRAN calls

Src/C_BaseLib/ArrayLim.H

commit cae0639e68fcdc971217177bca90628851e2911b
Author: car <car>
Date:   Tue Sep 26 18:18:57 2000 +0000

    fix for min max

Src/C_BaseLib/MultiFab.cpp

commit 118a1ed36f71dc39dcbc167f2fe575f14a7a9907
Author: almgren <almgren>
Date:   Thu Sep 14 19:44:06 2000 +0000

    Changes to allow for multiple datalog files if more than one file
    name is specified in the inputs file.  It's up to the user to not
    try to access more files than names are given.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 955d586719336163f41861ba8086d828f6af319f
Author: lijewski <lijewski>
Date:   Thu Sep 14 15:25:26 2000 +0000

    Cut down on sleep time.

Tools/C_scripts/compressor

commit 5c199a6a9c35feef5b1048ceb1809f22076f6e1d
Author: lijewski <lijewski>
Date:   Wed Sep 13 20:09:12 2000 +0000

    BiCG is now the default ...

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit ff26cfa8f53b2bfdd11a0ae26985cb50fbe4560a
Author: almgren <almgren>
Date:   Mon Sep 11 22:03:57 2000 +0000

    Fix to propp's re-write of build_sigma...we need to copy the zeros
    in ghost cells when for_sync_reg != 0.

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 588f412f902f3dd3ac70620c69f0bd40dc3e6ee9
Author: car <car>
Date:   Tue Sep 5 17:40:54 2000 +0000

    filter profiling files

Src/LinearSolvers/C_CellMG/Test/.cvsignore
Tests/LinearSolvers/C_CellMG/.cvsignore

commit d4ac45668618b23c755b955b056504ed19e53444
Author: car <car>
Date:   Wed Aug 30 19:19:13 2000 +0000

    New convergence criteria:
    relative tolerances may need to be reduced by a factor of 5 or 10.
    Absolute tolerances may not be needed at all.

Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit b63dbf4bd185c3a2957b6ea0fbadcaba3cb8d09b
Author: car <car>
Date:   Mon Aug 28 15:54:01 2000 +0000

    Use new convergence criteria by default; must still select BiCGStab in ParmParse

Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit c10ea96b199cf0f8b29945a06baab7e2575e01c6
Author: car <car>
Date:   Sat Aug 26 19:41:00 2000 +0000

    3D Norm

Src/LinearSolvers/C_CellMG/ABec_3D.F

commit 515ac65331fd8d6ce6fc898936ef79ff6792748b
Author: car <car>
Date:   Fri Aug 25 19:23:28 2000 +0000

    fix for bicg with initial zero residual

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit cad579b09909ed449e464d949643fc530e6477df
Author: car <car>
Date:   Fri Aug 25 17:50:25 2000 +0000

    annotation tweak

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit eec21b74546a041493a2cd89044c808291696be9
Author: car <car>
Date:   Thu Aug 24 22:45:46 2000 +0000

    profiling fix

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 2c766543e9ae4dac9d8e3f4acb3eb22869c232f5
Author: car <car>
Date:   Thu Aug 24 22:39:02 2000 +0000

    solver selection, timing

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 5916df9f1c67cd544cf2e9d8e008f4ad31ec8f35
Author: car <car>
Date:   Thu Aug 24 20:28:28 2000 +0000

    fix initialize, add norm

Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_F.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/LP_2D.F
Src/LinearSolvers/C_CellMG/LP_F.H
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit d0c9b7eb949c6f9bfe9dde87155945ed0df7c7f2
Author: car <car>
Date:   Thu Aug 24 16:02:46 2000 +0000

    Added BiCGStab

Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/CG_2D.F
Src/LinearSolvers/C_CellMG/CG_3D.F
Src/LinearSolvers/C_CellMG/CG_F.H
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 0e52c05fb01a457116c45cb72b30751ec9e8e579
Author: lijewski <lijewski>
Date:   Wed Aug 23 20:16:29 2000 +0000

    Fixed some PlotVar stuff ...

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp

commit c120731e880d3062eedf8be1ab5fa6c72da05437
Author: marc <marc>
Date:   Thu Aug 17 17:31:00 2000 +0000

    Enable array of blocking factors.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 5b4150a2454052ed39b52aefd85c64e7ad9b1059
Author: car <car>
Date:   Tue Aug 15 19:37:31 2000 +0000

    Make.mpi

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit c45957611a526efc02469edfcb6b44cde3dfe92d
Author: car <car>
Date:   Tue Aug 15 19:24:29 2000 +0000

    a new way of making MultiFabs: pass in a
    Distribution Mapping;  changes to Distribution mapping to aid
    access to knapsack

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H

commit 04e613e552499c6acad6221efc9e2b1a095b057f
Author: lijewski <lijewski>
Date:   Wed Aug 9 20:23:04 2000 +0000

    Removed an unnecessary parallel reduction.

Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit dd207f25c2473fe55a7f41abe704b232b2d2b145
Author: lijewski <lijewski>
Date:   Wed Aug 9 15:38:50 2000 +0000

    Removed unnecessary paralllel reduction.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit e10b3969f9de6d1352e1d4cf292dfdbdaeb2a68a
Author: car <car>
Date:   Fri Aug 4 18:06:22 2000 +0000

    another Profile

Src/C_BaseLib/FabArray.H

commit db2b930e3f7db971d18db297be097cd3e1d09aa7
Author: lijewski <lijewski>
Date:   Fri Aug 4 18:00:58 2000 +0000

    Removed need for MPI_Gather() in copy().

Src/C_BaseLib/FabArray.H

commit 1708d99978ee8a0c7b444c10f8cc6583cadfb755
Author: car <car>
Date:   Thu Aug 3 18:27:51 2000 +0000

    c++ comments in fortran

Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F

commit a5c907246bc286d520969b38cce832ca731ee322
Author: almgren <almgren>
Date:   Wed Aug 2 21:03:50 2000 +0000

    Modified LinOp::applyBC to take src_comp and num_comp arguments.

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 20f1b7c9c1c2db6dfc522ddcf3e02da5124af016
Author: car <car>
Date:   Wed Aug 2 16:11:53 2000 +0000

    BoxLib3 Profiling code and threading

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/main.cpp

commit ad87a29e2f431e0cd282fbe18657eb8b556bbf50
Author: car <car>
Date:   Wed Aug 2 16:09:45 2000 +0000

    MPICH 1.2.0 Support

Tools/C_mk/Make.mpi

commit a6fd7a57338fec0ac44abe27479f9b17430ccbce
Author: car <car>
Date:   Wed Aug 2 16:08:35 2000 +0000

    Thread Safety Support

Tools/C_mk/Make.defs

commit 6363b8688b4f538e4523ae0eac1f95c5ed4890da
Author: car <car>
Date:   Wed Aug 2 16:08:10 2000 +0000

    profiling support

Tools/C_mk/Make.Linux

commit 1088a1cc4ce321135d342051044d6bc4a0b70a68
Author: car <car>
Date:   Wed Aug 2 16:06:32 2000 +0000

    BoxLib3 Profiling code; commented out

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 60a0f20762b431ba53fe10c8c537d7f70caba90e
Author: car <car>
Date:   Wed Aug 2 16:00:53 2000 +0000

    Added Profiling Code;
    ParallelDescriptor::StartParallel fixed to allow multiple calls with no error

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.cpp

commit 58f54c0cf16bd6cef44142e26298a0593cb04fb6
Author: lijewski <lijewski>
Date:   Tue Jul 25 19:10:38 2000 +0000

    which_time() now asserts that time is in (oldtime,newtime) interval

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 8c26eead709d86ca4e964ee6dc05b5fff55c8de2
Author: almgren <almgren>
Date:   Fri Jul 21 22:45:04 2000 +0000

    Added code to take a velocity field and return the stream function.
    This is done by computing the vorticity and solving Laplacian(phi ) = vort.
    Called from Projection::getStreamFunction in iamrlib.  The computation
    of vorticity and inversion of the Laplacian are full multilevel operations.

Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit ab1cea3ad27b3df75cf30c545f6a6947f5502d84
Author: lijewski <lijewski>
Date:   Fri Jul 21 20:45:21 2000 +0000

    Added AmrHalfTime to support rho_half in NS.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit a1e056bd4c58bb9902c9a21919cb01663847f68d
Author: lijewski <lijewski>
Date:   Wed Jul 19 19:53:36 2000 +0000

    Removed some unused foo ...

Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F

commit 2fb89c322ba1e99f81de6fc20e0457c574cace38
Author: sstanley <sstanley>
Date:   Mon Jul 17 16:58:03 2000 +0000

    Mudified the logic in MultiGrid::coarsestSmooth() so that when the CG solver
    fails (presumably due to the stability criterion), that the standard
    bottom end smoother is called instead.  This has the potential to make the
    MG solves more robust.  Also, it will allow the CG solver to be used on
    the bottom end of the diffusion solve while allowing the regular smoother
    to help the solution of the mac projection.

Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 9610bf28c8bb1e6a7f11be40d10f3f4c1dcd7014
Author: sstanley <sstanley>
Date:   Mon Jul 17 16:26:19 2000 +0000

    Minor changes to the mac projection input and grid files.

Src/LinearSolvers/C_CellMG/Test/grids/gr.3_mac_tst
Src/LinearSolvers/C_CellMG/Test/grids/in.3_mac_tst
Tests/LinearSolvers/C_CellMG/grids/gr.3_mac_tst
Tests/LinearSolvers/C_CellMG/grids/in.3_mac_tst

commit 6c2f61fee06e140e3b1040d5487262c26be06e34
Author: sstanley <sstanley>
Date:   Sat Jul 15 00:13:42 2000 +0000

    Added the input and grid files for the mac projection test code.

Src/LinearSolvers/C_CellMG/Test/grids/gr.3_mac_tst
Src/LinearSolvers/C_CellMG/Test/grids/in.3_mac_tst
Tests/LinearSolvers/C_CellMG/grids/gr.3_mac_tst
Tests/LinearSolvers/C_CellMG/grids/in.3_mac_tst

commit f23315df232116a81295cb14fded21e836401d92
Author: sstanley <sstanley>
Date:   Sat Jul 15 00:12:23 2000 +0000

    Added a test routine to read the information for a specific mac projection
    and set up and solve this problem.

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/Make.package
Src/LinearSolvers/C_CellMG/Test/macprojTest.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/Make.package
Tests/LinearSolvers/C_CellMG/macprojTest.cpp

commit 13ada30311fda85cdbb10b8c5944a8dfd752c9c5
Author: sstanley <sstanley>
Date:   Sat Jul 15 00:11:01 2000 +0000

    Added writeOn and readFrom routines to dump and read boundary data objects.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp

commit 80094a8248857a9c5a3aa746a2d16248f3532eec
Author: almgren <almgren>
Date:   Fri Jul 14 23:37:06 2000 +0000

    Added the code for line solvers in each direction in FORT_GSRB.
    The default is still set to do Gauss-Seidel red-black, but the
    code is now in place to do line solves if wanted.

Src/LinearSolvers/C_CellMG/ABec_3D.F

commit 5bd49aabf35284ed264202429b8bc0c56b9ce6d8
Author: almgren <almgren>
Date:   Thu Jul 13 23:26:55 2000 +0000

    Handle the case differently where t < t1-teps...require that
    the flag extrap be set in order to allow this, then extrap backwards,
    instead of just setting to the "old" value.

Src/C_BaseLib/MultiFab.cpp

commit 87c58e23156e4cd66f8a985bdacc882721ae900d
Author: sstanley <sstanley>
Date:   Thu Jul 13 23:10:03 2000 +0000

    Added this new routine which checks all interior ghostcells in a multifab
    to insure that they are consistent with the cells in the valid region.  This
    utility only works with disjoint multifabs.

Tools/C_util/ViewMF/checkMFghostcells.cpp

commit 3daf32fdac35dcf696601bb18f6cb3361ef1641a
Author: sstanley <sstanley>
Date:   Tue Jul 11 21:03:55 2000 +0000

    Modified the interface to SlabStats::checkPoint so that the AmrLevels
    are passed in.  This allows the problem domain and the grid spacing to be
    output in the header files for the SlabStats.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/SlabStat.H
Src/C_AMRLib/SlabStat.cpp

commit 4113ee63cd44dbaaf9abbcd1c415fbfde23e05af
Author: lijewski <lijewski>
Date:   Tue Jul 11 20:47:48 2000 +0000

    Move which_time() from HeatTransfer to here.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 76c4eff5b15e6bb08193d1f3f91043ca46546025
Author: lijewski <lijewski>
Date:   Thu Jul 6 17:03:57 2000 +0000

    Protected a couple cout's with IOProcessor() checks.

Src/C_BaseLib/ParmParse.cpp

commit d2520949f6f98c9f1a1fe0804eb7cc2b4006de0b
Author: lijewski <lijewski>
Date:   Mon Jul 3 23:40:02 2000 +0000

    Tad more simplification ...

Tools/C_scripts/compressor

commit af08316afdea887242d3b10fbac64262c39a893e
Author: lijewski <lijewski>
Date:   Mon Jul 3 22:02:50 2000 +0000

    Removed couple declarations that were never defined.

Src/C_AMRLib/FluxRegister.H

commit 74828a19968debb80987a6dfd1cef8b592f0218d
Author: sstanley <sstanley>
Date:   Thu Jun 29 21:14:42 2000 +0000

    Shifted the maxdata option over to LDFLAGS since it is a load time option.

Tools/C_mk/Make.AIX

commit 211e88440549142a097ea90ff9abc98e11cde2f5
Author: lijewski <lijewski>
Date:   Tue Jun 27 20:54:50 2000 +0000

    Removed "inline" from isBoolean() definition.

Src/C_BaseLib/ParmParse.cpp

commit 25b4eacb16a20304150f9e2d54dffef5ec091600
Author: lijewski <lijewski>
Date:   Fri Jun 23 16:48:00 2000 +0000

    Uped maxmem for optimization a tad more.

Tools/C_mk/Make.AIX

commit d3ad8f5cf70e5965489587953cdd8380aa88cced
Author: car <car>
Date:   Thu Jun 22 22:52:28 2000 +0000

    decrease size of temporarys in ABEC's GSRB

Src/LinearSolvers/C_CellMG/ABec_2D.F

commit 24a3ad81817c2a47f59046396a491b00fa580901
Author: car <car>
Date:   Thu Jun 22 20:56:22 2000 +0000

    ABecLaplacian.cpp

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp

commit aa5492fea12e45af8cdafd576c283887562889a9
Author: car <car>
Date:   Thu Jun 22 20:00:15 2000 +0000

    Threading...

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit 3058772b0ed78d0b5e87d6694d93d0e7b9f82682
Author: car <car>
Date:   Thu Jun 22 18:34:50 2000 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 8a632bef35c50d59556d8d0ad13adbefb38d0599
Author: car <car>
Date:   Thu Jun 22 18:33:45 2000 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/main.cpp

commit 01dcf85674a46af6c51bb3059a195e9cde4a7d8d
Author: lijewski <lijewski>
Date:   Thu Jun 22 16:07:32 2000 +0000

    ::intersect() of two BoxLists wasn't right.

Src/C_BaseLib/BoxList.cpp

commit 529e3ef777d9bc41ba9d83377a6bda07b76a6e26
Author: sstanley <sstanley>
Date:   Wed Jun 21 22:07:34 2000 +0000

    Added a global include file defining the fortran flush() function.  Changed
    a few routines to use this global function, FORT_FLUSH.  This was done
    because the flush fucntion call is different on different machines.

Src/C_AMRLib/FLUSH_F.H
Src/LinearSolvers/C_NodalMG/hgdebug.F

commit f37b81d218b4245abdc983cfb1f148a1412dd4a5
Author: sstanley <sstanley>
Date:   Wed Jun 21 18:27:45 2000 +0000

    Added the options to use up to 1Gb of memory per node.

Tools/C_mk/Make.AIX

commit 19a58e2a196e7b1cc31db34adb53048b882fe04f
Author: sstanley <sstanley>
Date:   Tue Jun 20 23:43:22 2000 +0000

    Changed the compile options for lower and upper case fortran files.  Lower
    case .f files compile with 80 columns and uppercase compiel with 72 columns.

Tools/C_mk/Make.T3E

commit 2421967db59848b52f1b942e6743142c1ce8fd09
Author: marc <marc>
Date:   Tue Jun 20 23:28:59 2000 +0000

    Allow separate options for f and F files.

Tools/C_mk/Make.AIX
Tools/C_mk/Make.CRAY
Tools/C_mk/Make.IRIX64
Tools/C_mk/Make.Linux
Tools/C_mk/Make.OSF1
Tools/C_mk/Make.T3E
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 7203478afe2f3543d7e2f23d172a559c79ccd955
Author: lijewski <lijewski>
Date:   Tue Jun 20 21:44:11 2000 +0000

    A little more finagling with sleeps.

Tools/C_scripts/compressor

commit 3bcb28b594e480c0154b47bd404bb76e463e912d
Author: lijewski <lijewski>
Date:   Tue Jun 20 20:45:51 2000 +0000

    Changed sleep interval.

Tools/C_scripts/compressor

commit 8333abeb675ad1ac1357733dabcc3f9e8e3e77cf
Author: lijewski <lijewski>
Date:   Fri Jun 16 17:39:49 2000 +0000

    Fixed bug in grid_places().  Probably needs more testing, but ...

Src/C_AMRLib/Amr.cpp

commit fcd694569afd9e4382f050c63ee395b1c65a84bd
Author: lijewski <lijewski>
Date:   Thu Jun 15 17:29:01 2000 +0000

    Got rid of CXXFLAGS; moved stuff to CXXOPTS & CXXDBG.

Tools/C_mk/Make.AIX

commit 31206d21724bdc6c10ba9f4753311556a581ff16
Author: lijewski <lijewski>
Date:   Thu Jun 15 16:57:41 2000 +0000

    Now print grid info to cout as well as gridlogout.

Src/C_AMRLib/Amr.cpp

commit 9c6526776d2334f8525891dd3d3e68e392e2184e
Author: lijewski <lijewski>
Date:   Tue Jun 13 16:52:28 2000 +0000

    Don't tar up last plotfile.  Wait till next one is written.

Tools/C_scripts/compressor

commit b8ba728d5a2d426f6148a7da00928dbc4fcca2f9
Author: almgren <almgren>
Date:   Mon Jun 12 23:43:03 2000 +0000

    Now pass iteration into post_timestep so it will eventually get passed
    into the sync project in IAMR.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H

commit a2bdaf19aafe3f159b55ed258d39585b48f15688
Author: sstanley <sstanley>
Date:   Fri Jun 9 21:25:51 2000 +0000

    Changed errorEstimate to work properly on all levels, not just level 0.
    Midfied the logic slightly when dumping residuals in the bottom smoother.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit b6ee7e90669d8244eedf3aa80e97cdb03adf195e
Author: lijewski <lijewski>
Date:   Fri Jun 9 21:10:31 2000 +0000

    Use CXXFLAGS instead of XTRADEFS in one case.

Tools/C_mk/Make.AIX

commit 74b7efbe2ccdc885d55584108fd88d743805f22f
Author: sstanley <sstanley>
Date:   Thu Jun 8 20:26:33 2000 +0000

    Added a few constants that I needed.

Src/C_BaseLib/CONSTANTS.H

commit 6a8bc584fda84cf70e34b172d16a0ff73ff37ac2
Author: lijewski <lijewski>
Date:   Thu Jun 8 17:38:02 2000 +0000

    Increased maxmem a tad more.

Tools/C_mk/Make.AIX

commit 3f21ad65aa9873bd77994c8c3363a891c48e50e8
Author: marc <marc>
Date:   Wed Jun 7 23:18:11 2000 +0000

    Reverse order of define and namespace close

Src/C_BaseLib/Specialize.cpp

commit e7fc2dd919d8dac341f2d34e31ea0444f621b6be
Author: lijewski <lijewski>
Date:   Wed Jun 7 20:59:16 2000 +0000

    Turn on coalescing memory manager.
    Bump memory used by C compiler for optimization.

Tools/C_mk/Make.AIX

commit a7384b4a3d3358379a34d84456996995ef158d52
Author: sstanley <sstanley>
Date:   Wed Jun 7 00:33:23 2000 +0000

    Added writing of the residuals when using the simple smoother on the
    bottom end of the multigrid.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit e8d3b282ab4585fd4671c7da9f135462c5cdcd62
Author: lijewski <lijewski>
Date:   Mon Jun 5 22:37:37 2000 +0000

    Removed no_overlap arg from FillPeriodicBoundary().

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit f6026456d7e63defa8f09408f2cd1b7e34f48ef4
Author: car <car>
Date:   Mon Jun 5 19:11:16 2000 +0000

    namespace fix

Src/C_BaseLib/ParallelDescriptor.cpp

commit fdf923bc84fb1df967ba4dda655a806d177dc355
Author: car <car>
Date:   Mon Jun 5 18:56:08 2000 +0000

    another bc buster

Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_3
Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_3

commit 58e6f0e68137486b29a65912b86bb303778cd203
Author: car <car>
Date:   Mon Jun 5 18:39:31 2000 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit f316413e577735a6c49ffc09b1bb4727a49dd67c
Author: marc <marc>
Date:   Fri Jun 2 22:58:53 2000 +0000

    extern c chuck you moron

Src/C_BaseLib/ParallelDescriptor.cpp

commit 75d98742aa9a6df5f9ae49e52f06887735342117
Author: lijewski <lijewski>
Date:   Fri Jun 2 22:37:40 2000 +0000

    Added new intersect() functions.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit 35732d7921c118a83e1a21681c9e5a1ac3dbd043
Author: almgren <almgren>
Date:   Fri Jun 2 17:59:53 2000 +0000

    Chnage the time interpolation so it allows t >= t1-teps instead of just
    t > t1-teps.  This matters in the case where t1=t2 so teps = 0.

Src/C_BaseLib/MultiFab.cpp

commit 6e81a72e84923d05f9c4ea2fa846ac3152eb35dd
Author: lijewski <lijewski>
Date:   Fri Jun 2 17:09:16 2000 +0000

    Cleaned up a bit.

Src/C_AMRLib/FLUXREG_2D.F
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F

commit 62e6d4674853db8e66e7c617018c0bb9d5bef44b
Author: car <car>
Date:   Fri Jun 2 01:04:12 2000 +0000

    Bad BL_PD_ABORT defn

Src/C_BaseLib/ParallelDescriptor.cpp

commit 0d117db551eac58f15d9115ab7c494a6e6a6a25a
Author: car <car>
Date:   Thu Jun 1 23:10:36 2000 +0000

    Support for KCC 3.4, Thread, and Strict compilation

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 37513f0f9c1e1408a196ef0f9869d210028ecc66
Author: car <car>
Date:   Thu Jun 1 23:09:28 2000 +0000

    use ksh in Make

Tools/C_mk/Make.OSF1

commit 99afd6379661a166e071e17568573df7ccea61dc
Author: car <car>
Date:   Thu Jun 1 22:59:47 2000 +0000

    g++ fixes

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/inputs

commit 6405a8810dd04aa65f915dd828b02fc72b897e3f
Author: car <car>
Date:   Thu Jun 1 21:39:54 2000 +0000

    using ParallelDescriptor::Communicator()

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit a615409c5c64a930458f6ad796acd8516cf71c12
Author: lijewski <lijewski>
Date:   Thu Jun 1 21:28:57 2000 +0000

    Added extrap() member to StateDescriptor & integrated into code.
    Really only used in FillPatch().

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp

commit c0b66371ba7f1b9c3342d0e65fc0caffda1bf74c
Author: car <car>
Date:   Thu Jun 1 21:22:31 2000 +0000

    using ParallelDescriptor::Communicator()

Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/PltFileNormB.cpp

commit 7316a9200cb77307d4beb76899ac048384a15e0a
Author: car <car>
Date:   Thu Jun 1 21:07:51 2000 +0000

    Two Parallel Changes:
    1) ParallelDescriptor::Communicator() should be used instead of
       MPI_COMM_WORLD.  This will allow us to mix other libraries that
       use MPI without message passing tag collisions.
    2) Added a few FORTRAN bindings to ParallelDescriptor calls:
       BL_PD_ABORT
       BL_PD_COMMUNICATOR
       BL_PD_NPROCS
       BL_PD_IOPROC
       BL_PD_MYPROC
       BL_PD_BARRIER
       Its probably not worthwhile to add any others.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/RunStats.cpp
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/ccse-mpi.H

commit cf5b97ec92b0538ae19f8b8bee55320e8b39a581
Author: car <car>
Date:   Thu Jun 1 20:59:38 2000 +0000

    not needed here: --one_instantiation_per_object

Src/LinearSolvers/C_CellMG/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/main.cpp

commit 7a6a7b8dde7996820d87dc640c5a4b21f40ee873
Author: sstanley <sstanley>
Date:   Thu Jun 1 16:41:14 2000 +0000

    Fixed a problem with how quoted strings were broken up.  This caused file
    name problems on the SP machines.

Tools/C_scripts/strip72

commit 0dc4369ec3ea34aec46b26228cf3426a5952446c
Author: car <car>
Date:   Thu Jun 1 15:39:16 2000 +0000

    boolean values are now parsed
    'true', non-zero numerics ---> true
    'false',    zero numerics ---> false

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit e68fd92c5225f1eb6e940126f8625b8de0aa3153
Author: car <car>
Date:   Wed May 31 20:35:25 2000 +0000

    const-ness issue

Src/C_BaseLib/Geometry.H

commit c04ae6ec75c77061ca35576225a79213ad369ea6
Author: car <car>
Date:   Wed May 31 20:33:40 2000 +0000

    Silence a warning

Tools/C_util/WritePlotFile.cpp

commit 88f9a8d5be2d6696f3c2e66ebbb5c24b33a43fc1
Author: car <car>
Date:   Wed May 31 20:33:14 2000 +0000

    KCC 4.0 support

Src/C_BaseLib/Utility.H
Src/C_BaseLib/VisMF.H

commit 072fc09a3bdf7feb66bc1ea9f9a30df2107219c4
Author: lijewski <lijewski>
Date:   Wed May 31 17:44:24 2000 +0000

    Removed FillCoarsePress() -- figured out how to reuse FillCoarsePatch().

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 2b26a51ff9f179a487274bf597b84fa850522873
Author: almgren <almgren>
Date:   Tue May 30 21:10:47 2000 +0000

    Added SetNewTimeLevel and SetOldTimeLevel calls in StateData.

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit 8d9e6e139f138bc30ea270753f2e0389e6068189
Author: almgren <almgren>
Date:   Tue May 30 20:24:54 2000 +0000

    Added AmrLevel::FillCoarsePress routine which is willing and able
    to fill ghost cells as well as valid region of NODAL data only.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit ce819493c933fa34e7497ce63c2a4eeee2a73d8e
Author: car <car>
Date:   Thu May 25 15:49:25 2000 +0000

    .cvsignore

Src/LinearSolvers/C_CellMG/Test/.cvsignore
Tests/LinearSolvers/C_CellMG/.cvsignore

commit 5d996ce17a1c6c4d7d61d34a8cf1779debda2e6e
Author: car <car>
Date:   Thu May 25 15:40:03 2000 +0000

    Removed unused variables

Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/Looping.H
Src/C_BaseLib/VisMF.cpp

commit 873edddc223cc35dcdb5dec7ecbd4338aa18f038
Author: car <car>
Date:   Thu May 25 15:39:28 2000 +0000

    RealDescriptor needs virtual destructor

Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp

commit 580e4b26bf4205bb17f1038e3e998c3d98d5e2de
Author: lijewski <lijewski>
Date:   Wed May 24 17:19:53 2000 +0000

    Added some more of scott's test cases.

Src/LinearSolvers/C_NodalMG/files.3d

commit 222d55e97901b9a35852b43c4f8cc6db9bcba010
Author: car <car>
Date:   Mon May 22 23:19:24 2000 +0000

    support for hypre

Tools/C_util/Make.package
Tools/C_util/WritePlotFile.cpp

commit 680c76358c79078bc8529c673db8ace8afec6f52
Author: car <car>
Date:   Mon May 22 23:18:51 2000 +0000

    revamped to test hypre

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/Make.package
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/Make.package
Tests/LinearSolvers/C_CellMG/main.cpp

commit 42e27523608c7dfd98f25f908c6ad0d04327eb48
Author: lijewski <lijewski>
Date:   Mon May 22 20:14:25 2000 +0000

    Added gt.sas.

Src/LinearSolvers/C_NodalMG/files.3d

commit d46e2c6910203a38e70a257495733b31f34b78c3
Author: lijewski <lijewski>
Date:   Mon May 22 20:13:45 2000 +0000

    Tests some doubly-periodic stuff.

Src/LinearSolvers/C_NodalMG/tests/gt.sas
Tests/LinearSolvers/C_NodalMG/test_grids/gt.sas

commit 213a8f547360e8c8825d604d50dadd97621b11ad
Author: sstanley <sstanley>
Date:   Mon May 22 19:54:00 2000 +0000

    Minor changes to the slabstat files.  Added $Id: $ fields to the fortran
    and changed the #define variable to force only single inclusion of the
    header file.

Src/C_AMRLib/SLABSTAT_2D.F
Src/C_AMRLib/SLABSTAT_3D.F
Src/C_AMRLib/SLABSTAT_F.H

commit 8e19ce7c7eae53a8063da94c42b12f410b0d70f5
Author: lijewski <lijewski>
Date:   Thu May 18 20:13:42 2000 +0000

    More periodic fixes.

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 074e91290acfd191c46b4cd1046293f65df62f1f
Author: lijewski <lijewski>
Date:   Thu May 18 20:02:16 2000 +0000

    Added some comments on how to set boundary conditions.

Src/LinearSolvers/C_NodalMG/inputs

commit 7c7d1a2f58cf0ee9be86e7440e606d02d1471968
Author: lijewski <lijewski>
Date:   Thu May 18 19:55:44 2000 +0000

    Made the stencil default to cross.

Src/LinearSolvers/C_NodalMG/inputs

commit 9c06593c48723267cbd146a9d0453022c83c0d45
Author: car <car>
Date:   Mon May 15 19:45:17 2000 +0000

    trying to fix fill_border

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 13af3eda2241cfa7efb423cd3eec99b42ffb27af
Author: lijewski <lijewski>
Date:   Mon May 15 16:47:50 2000 +0000

    Fixed a bug in task_bdy_fill::ready().

Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 36d26d3c746f163b1fa719a4517de79abd7e123e
Author: lijewski <lijewski>
Date:   Fri May 12 18:08:45 2000 +0000

    Added task_local_base().

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 0062a35de7ef0c645679d1818d95256fa2b247de
Author: lijewski <lijewski>
Date:   Fri May 12 16:36:30 2000 +0000

    Strenghens the depens_on_q() test in task_copy_local().

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 840a9f39e9bc42519f955e9fc3c33b3448752b5b
Author: car <car>
Date:   Thu May 11 16:38:18 2000 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 2ceefb21deda4f1757876dfc31517005c1ba5dda
Author: sstanley <sstanley>
Date:   Mon May 8 22:17:52 2000 +0000

    Initial commit of the utility intersectGrids.  This one reads a fixed_grids
    file and checks to see which grids intersect a specified box.  All of the
    grids intersecting the box are written out in a fixed_grids format.
    
    Care should be taken when using this for more than 2-level cases since it
    doesn't insure proper nesting.

Tools/C_util/dbgTools/intersectGrids.cpp

commit fac3126bf2329258cd25da613c78623282948f4a
Author: propp <propp>
Date:   Thu May 4 23:43:49 2000 +0000

    reordered build_sigma a little bit

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit e84220d55baa78d51aa7c469fc0fa9d2a0175234
Author: car <car>
Date:   Thu May 4 20:16:44 2000 +0000

    integer promotion?

Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F

commit 38c68b9a583280ee78888e3824120ae94067c2a2
Author: sstanley <sstanley>
Date:   Wed May 3 22:32:45 2000 +0000

    Corrected a mistake I committed yesterday where zero was used instead of 0.0d0.

Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F

commit 774d4a0ce2eb2a62589c75c6ae3228998697e692
Author: almgren <almgren>
Date:   Wed May 3 21:08:47 2000 +0000

    Fill_borders call should have been boundary.terrain_sigma() call
    to start with, before fill_borders became fill_sync_reg_borders.

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 37646207c6caca32fa474a0ac3aaf09907a1403c
Author: almgren <almgren>
Date:   Wed May 3 18:27:16 2000 +0000

    Changes in order to handle periodic boundaries correctly when defining
    the coarse contribuation to the sync registers, i.e. Sync_resid_crse.
    We used to fill ghost cells at periodic boundaries; now we don't
    fill them at all (i.e. we use fill_sync_reg_borders calls instead
    of fill_borders calls), and the periodic stuff is taken care of
    in SyncRegister::CrseInit instead.

Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 52e25159ad000d24ff2e222636a86eb43fa5c453
Author: propp <propp>
Date:   Wed May 3 17:12:11 2000 +0000

    changed default for NAMESPACE to be FALSE

Src/C_BaseLib/GNUmakefile

commit d5119e7fb4f1af0297f838214408db2c6a11c926
Author: propp <propp>
Date:   Wed May 3 03:36:40 2000 +0000

    fixed bug so libraries would be built correctly

Src/C_AMRLib/Make.package

commit 7305ac0d6b64408ef25753088c8e4f1baf61edcc
Author: sstanley <sstanley>
Date:   Tue May 2 22:13:59 2000 +0000

    Further fix to how the values in the cen array are calculated and dealt with.
    Added logic in thew hgcen_full and hgcen_terrain to set cen=0 when the sigmas
    sum to zero.  Changed logic in hgres_terrain and hgres_full to deal
    properly with the zero values in the cen array.

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F
Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F

commit 12cb88100c871e9ba95a5b8165e66af273ec499b
Author: car <car>
Date:   Tue May 2 17:17:41 2000 +0000

    add fp exceptions for Linux

Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Tools/C_mk/Make.Linux

commit bf8b824a247e42668561fe3d763be71673cfe49f
Author: car <car>
Date:   Tue May 2 15:55:33 2000 +0000

    modified hgcen to give cen=0 when sigma's are zero

Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit 72b673e5fc29dfc61d8c45b1f82a1c80f6c01700
Author: sstanley <sstanley>
Date:   Mon May 1 22:06:38 2000 +0000

    Fixed a problem in build_sigma when for_fill_sync_reg==1.  Turns out you don;t
    need to calculate cen for this case since it never gets used.  Also, it can not
    be calculated since the sigma_node is set up so it is zero on all covered
    cells and we divide by sigma_node when calculating cen.

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 63ee35b277ed03fa5345efca94e226b6af47eca5
Author: car <car>
Date:   Mon May 1 17:53:24 2000 +0000

    Remove Assert.H from Make.package

Src/C_BaseLib/Make.package

commit 68f3ca4db893f9d195db7cc33e9ffd2d0b9f0088
Author: car <car>
Date:   Tue Apr 25 18:03:39 2000 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 223f2b457a74ff12c638530bc6a1f6c44ae09975
Author: car <car>
Date:   Tue Apr 25 16:29:56 2000 +0000

    more namespace fluff

Src/C_BaseLib/FabArray.H

commit 7eb68527ecf32de33166b3420e4ed8f9294f2b8f
Author: car <car>
Date:   Mon Apr 24 18:00:52 2000 +0000

    missed one

Src/C_BaseLib/SPACE.H

commit 6c9471bc26bcd83858fba4281366e7e2c9ee246e
Author: car <car>
Date:   Mon Apr 24 17:52:32 2000 +0000

    Minimal namespace support.  The changes here should have no impact
    on user code.  Two c-preprocesor symbols are used to control the
    changes:
    
    1) BL_NAMESPACE: if defined, BoxLib code is wrapped within a
       namespace whose name is given by the BL_NAMESPACE macro.
    2) BL_NO_USING_DIRECTIVE: if defined, no 'using namespace BL_NAMESPACE;'
       is implicitly given in for each module.
    
    The Makefile system was made namespace aware about a month ago.  If you
    say 'NAMESPACE = TRUE' you will get the effect of saying:
    BL_NAMESPACE=BoxLib2.  The default is 'NAMESPACE=FALSE'
    
    The intent is that two versions of BoxLib can be used within the same program.
    I don't expect that apart from a forced recompile that there will be
    any changes required to user code.

Src/C_BaseLib/.cvsignore
Src/C_BaseLib/Arena.H
Src/C_BaseLib/ArithFab.H
Src/C_BaseLib/Array.H
Src/C_BaseLib/Assert.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BArena.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FPC.H
Src/C_BaseLib/FPC.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/List.H
Src/C_BaseLib/Looping.H
Src/C_BaseLib/Misc.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/NormedFab.H
Src/C_BaseLib/OrderedFab.H
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/Orientation.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/REAL.H
Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp
Src/C_BaseLib/SPECIALIZE_F.H
Src/C_BaseLib/Specialize.cpp
Src/C_BaseLib/Tracer.H
Src/C_BaseLib/Tracer.cpp
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp
Src/C_BaseLib/ccse-mpi.H

commit 26cc56728ca50ecfee528b8d2d1423867ac79711
Author: sstanley <sstanley>
Date:   Sat Apr 22 00:34:14 2000 +0000

    Moved the storage of the statistics data from being in the checkpoint
    files to being in their own directory, 'slabstats'.  The data for each
    level 0 timestep where it is saved is stored under subdirectories,
    'slabstats/stats0000', etc.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/SlabStat.H
Src/C_AMRLib/SlabStat.cpp

commit e388160e98462a9251e7e5a46db1fb54a21efa1c
Author: sstanley <sstanley>
Date:   Sat Apr 22 00:16:26 2000 +0000

    Modified the constructors for SlabStatList and SlabStatRec so that
    if the boxes are read form the file, then the level is read from the
    file as well.  If the boxes are included in the constructor, then
    the level is included in the constructor.  Makes sense since the boxes
    are defined on a specific level and are generally not valid except on this
    level.

Src/C_AMRLib/SlabStat.H
Src/C_AMRLib/SlabStat.cpp

commit 2dc1da1b77b2d392135afc9493ce1805f7eeef91
Author: sstanley <sstanley>
Date:   Fri Apr 21 22:31:04 2000 +0000

    Corrected a couple of problems with the derive function which takes a
    multifab to be filled.  There were a few things still in place which
    assumed you were working with the level multifabs.

Src/C_AMRLib/AmrLevel.cpp

commit 3e075be8fcfa4297d38715beeeb4f131ee254fb3
Author: sstanley <sstanley>
Date:   Fri Apr 21 22:29:39 2000 +0000

    Corrected a problem with the ordering of the variables passed into the
    running statistics fortan routines.

Src/C_AMRLib/SLABSTAT_2D.F
Src/C_AMRLib/SLABSTAT_3D.F

commit e34ded7b35b43767689d25f78c6ba422f129ca43
Author: sstanley <sstanley>
Date:   Fri Apr 21 22:28:16 2000 +0000

    Elaborated on the documentation for SlabStatRec.

Src/C_AMRLib/SlabStat.H

commit cb803de49e63ca3342ca0660f5888476c650b6a0
Author: car <car>
Date:   Fri Apr 21 18:46:06 2000 +0000

    fix for g++

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp

commit 5d3f8018ad97044d35a0784b9410adb3404c987d
Author: sstanley <sstanley>
Date:   Fri Apr 21 16:26:15 2000 +0000

    Added a couple of general SlabStat statistics routines that save the
    values required to calculate the first four moments of whatever state
    components are passed in.  Routines were added to do this using Reynolds
    averages and Favre averages.  These are likely to be used in NS, HT as well as
    HCAll, so they were added here.

Src/C_AMRLib/Make.package
Src/C_AMRLib/SLABSTAT_2D.F
Src/C_AMRLib/SLABSTAT_3D.F
Src/C_AMRLib/SLABSTAT_F.H

commit 8b48ec51af9df3d9d1e6ed20f48e7822e0cbd216
Author: sstanley <sstanley>
Date:   Fri Apr 21 16:24:02 2000 +0000

    Corrected a typo in an error message about the format if the ParmParse
    inputs.

Src/C_AMRLib/SlabStat.cpp

commit b4819bc9f630f424a3cc884b62d23bc62214e95f
Author: car <car>
Date:   Fri Apr 21 16:23:32 2000 +0000

    *** empty log message ***

Src/C_BaseLib/CoordSys.H

commit 1a80d848da57621a306894819f23cdf7be825479
Author: sstanley <sstanley>
Date:   Fri Apr 21 16:20:21 2000 +0000

    Added ARRAYLIM_2D.F and ARRAYLIM_3D.F to amrlib.  These contain a couple of
    helper fortran routines that convert back and forth from the DIMDEC type
    cpp defined array dimensions to dimensions stored in arrays, lo(SDIM) and
    hi(SDIM).

Src/C_AMRLib/ARRAYLIM_2D.F
Src/C_AMRLib/ARRAYLIM_3D.F

commit eeb075118c78c04fa34b38d01c93ff4473fa9e91
Author: car <car>
Date:   Fri Apr 21 14:22:24 2000 +0000

    fixes for fill_sync_reg memory allocation problems

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/RegType.H
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F
Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgdebug.F
Src/LinearSolvers/C_NodalMG/hgdebug_F.H
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.H
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 66440d3036b98d8d77dfd6e24605b4afe09c004f
Author: car <car>
Date:   Thu Apr 20 17:46:47 2000 +0000

    noquotes in fortran

Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F

commit 049b3c8828d3ff1fc207b9de595166687f299d25
Author: car <car>
Date:   Mon Apr 17 21:16:10 2000 +0000

    partial backout fix for fill_sync_reg

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 670237f751deec3b55e2ed23b33b3a979262ce51
Author: car <car>
Date:   Mon Apr 17 20:53:29 2000 +0000

    partial backout fix for fill_sync_reg

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit e82962200eddeb930c2c125e7187ad3ec38d7d09
Author: car <car>
Date:   Mon Apr 17 17:58:37 2000 +0000

    I think a fix for fill_sync_reg allocation

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/inputs

commit bb8aa30d316591a8368da55c772e1844e6701b52
Author: propp <propp>
Date:   Fri Apr 14 20:56:12 2000 +0000

    deleted extra arguments

Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F
Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F

commit 6c23f9321fa2a911d1b5281c0d6f36411a8bbc5a
Author: lijewski <lijewski>
Date:   Fri Apr 14 20:45:48 2000 +0000

    Fixed some bugs.

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 89e5ea0e9eca411800a878bae79c67d7ec22b0d2
Author: sstanley <sstanley>
Date:   Wed Apr 12 16:14:23 2000 +0000

    Added a newline at the end to eliminate a warning message on mothra.

Src/C_BaseLib/Utility.cpp

commit 13954427cdd7b6144ddd9486a58234c5e11ace89
Author: sstanley <sstanley>
Date:   Thu Apr 6 17:05:39 2000 +0000

    Changed some comments from // to /* */ since cpp on cobalt isn't stripping the
    // comments.

Src/C_BaseLib/SPACE.H

commit 54158faa00e4cfa7f642fd6965f6d6750bc5560f
Author: sstanley <sstanley>
Date:   Wed Apr 5 18:22:02 2000 +0000

    Rewrote the nodal interpolation routines in 2-d and 3-d.    This was done
    in order to make them give the same results for nodes which are periodically
    duplicated.  The new interpolation does not give identical results to the old
    however the changes are extremely small (<1.0e-14).

Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/Interpolater.cpp

commit 75dda74e0883980334ea42485077f15afa2719d7
Author: sstanley <sstanley>
Date:   Tue Apr 4 18:28:59 2000 +0000

    Changed the box definitions.

Tools/C_util/ViewMF/viewMFdiffHardWire.cpp

commit 5952d06fc098630c64b70864434ee76ee054293b
Author: vince <vince>
Date:   Tue Apr 4 00:20:13 2000 +0000

    Added a denormal fix option.

Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp

commit c8257f87e742b32f4ef2d8119a03c2614cdf4bdb
Author: marc <marc>
Date:   Mon Apr 3 23:13:03 2000 +0000

    ifdef out os stuff...see Utility.[H,cpp]

Src/C_AMRLib/Amr.cpp

commit 92fd212b98bd1834a5f7d0a298842d9bbd74b371
Author: marc <marc>
Date:   Mon Apr 3 23:11:40 2000 +0000

    ifdef out pid stuff for WIN32...there's probably a way to implement
    this, but it's low priority.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit ecf14e5d305381dd0f366a67e17d018c94a4725e
Author: sstanley <sstanley>
Date:   Wed Mar 29 23:05:54 2000 +0000

    Added the ability to build in place.

Tools/C_util/ViewMF/GNUmakefile

commit f490e05240c7950be0cb26ac868616ba673b59ea
Author: sstanley <sstanley>
Date:   Wed Mar 29 23:05:30 2000 +0000

    This is a variation on the viewMFdiff routine.  THis allows boxes to be
    specified for the two multifabs to be compared.  THis allows the same
    multifab to be passed in twice and to be compared periodically.

Tools/C_util/ViewMF/viewMFdiffHardWire.cpp

commit eeca8b87a3fd2380b45beed2cc359ac129ee17f1
Author: lijewski <lijewski>
Date:   Wed Mar 29 21:42:38 2000 +0000

    Now can specify boxes via ParmParse.

Src/C_AMRLib/SlabStat.H
Src/C_AMRLib/SlabStat.cpp

commit ff26049e830ad6d2a54d40c48629c7987c401bff
Author: marc <marc>
Date:   Mon Mar 27 20:23:18 2000 +0000

    Changes to port to mahler.ca.sandia.gov

Tools/C_mk/Make.IRIX64
Tools/C_mk/Make.defs

commit 5a15738f9fd4f8b24c16d13ca3e8081520c55638
Author: car <car>
Date:   Mon Mar 27 20:06:07 2000 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgdebug.F

commit 0b2742982ed9c802db4aa8b6663d75089f0a75b2
Author: lijewski <lijewski>
Date:   Mon Mar 27 16:26:13 2000 +0000

    Added some copy constructors and copy assignment operators.

Src/C_BoundaryLib/BoundCond.H
Src/C_BoundaryLib/InterpBndryData.H

commit 051c96748877c67e5a021fc616f8947a312aa8ef
Author: lijewski <lijewski>
Date:   Fri Mar 24 22:10:01 2000 +0000

    Some mods for AuxBoundayrData ...

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 64388a33b24f8d3da8c8f5cd5e885d58aaf2e5ce
Author: car <car>
Date:   Fri Mar 24 18:13:19 2000 +0000

    Removed path dependence of tarch, tdevice.

Tools/C_mk/Make.mpi

commit 181dd17654ca6cc42523ef388a58853eb76b50c8
Author: car <car>
Date:   Fri Mar 24 18:12:36 2000 +0000

    uses tarch, tdevice in mpich:  must be on path.

Tools/C_mk/Make.mpi

commit ef7965b436e9ae8cf1419b00f2e13d1a819861d2
Author: sstanley <sstanley>
Date:   Thu Mar 23 22:09:44 2000 +0000

    Added a new tool to the utils directory which will read a fixed_grids
    type grid format and coarsen.

Tools/C_util/dbgTools/GNUmakefile
Tools/C_util/dbgTools/Make.package
Tools/C_util/dbgTools/crsGrids.cpp

commit 36bdabd0166d3f8ecdd24cd2cb22b33e8e3e56c0
Author: lijewski <lijewski>
Date:   Thu Mar 23 21:39:06 2000 +0000

    Turned off a couple things.

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 10afa9880c51e364726b0c1bfb7584ada634a69f
Author: lijewski <lijewski>
Date:   Thu Mar 23 21:38:27 2000 +0000

    These are 3d test cases that are known to work with periodic bcs.

Src/LinearSolvers/C_NodalMG/files.3d

commit 1a29774ee886ff868b8fabf22ea7568073ba0cd4
Author: car <car>
Date:   Thu Mar 23 21:16:59 2000 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/RegType.H
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit eab12d8334af8063364971e9e7ebb3760308fabb
Author: car <car>
Date:   Wed Mar 22 21:10:11 2000 +0000

    inflow bug fix: grow the srcbox

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit b842f9f34a707879629e3ccd3c7489f2f196c849
Author: lijewski <lijewski>
Date:   Wed Mar 22 15:51:45 2000 +0000

    Some mods for g++ and cxx.  Don't use -lm_sqrt with V4 OSF1

Tools/C_mk/Make.OSF1

commit 4c2997f5479a337ab14147e97ed9092c64237062
Author: lijewski <lijewski>
Date:   Tue Mar 21 19:24:04 2000 +0000

    Added INCLUDE_LOCATIONS stuff for OSF1

Tools/C_mk/Make.mpi

commit 00248f5efb2bec44481e4b4904d90478116bacaf
Author: marc <marc>
Date:   Fri Mar 17 22:01:01 2000 +0000

    Add slashes around saved common block name

Src/LinearSolvers/C_NodalMG/hgdebug_F.H

commit 18a1e3dc4212bdc0bfe9e507893d04cd9346ab1d
Author: car <car>
Date:   Fri Mar 17 21:58:59 2000 +0000

    k

Src/LinearSolvers/C_NodalMG/hgdebug.F

commit 00063bcc15cb2401c858c23062d67141b075eebc
Author: car <car>
Date:   Thu Mar 16 23:15:07 2000 +0000

    Added BL_NAMESPACE support

Tools/C_mk/Make.defs

commit f7dccaafc216512d298d5106ecda1f429a3a4f11
Author: car <car>
Date:   Thu Mar 16 23:13:40 2000 +0000

    clean is now a double colon rule

Tools/C_mk/Make.rules

commit 74e5cfd9c883a4803a1b72c3f45e74a18ff0c846
Author: car <car>
Date:   Thu Mar 16 23:11:32 2000 +0000

    fixes an inflow bug, might not break the periodic code

Src/LinearSolvers/C_NodalMG/.cvsignore
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgdebug.F
Src/LinearSolvers/C_NodalMG/hgdebug_F.H
Src/LinearSolvers/C_NodalMG/inputs
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 075c1167471dd7d7d1d72f937035c9a41b907b91
Author: car <car>
Date:   Thu Mar 16 16:43:34 2000 +0000

    Linux fixes for mpich/lam and Vince's WHICHLINUX

Tools/C_mk/Make.mpi

commit a92ec23120cee45d77be71bd8382a68139d5ef70
Author: lijewski <lijewski>
Date:   Wed Mar 15 16:51:23 2000 +0000

    Some changes to MPI environment on mothra due to mpich1.1.2 install.

Tools/C_mk/Make.mpi

commit c4f28d9ad9f9ebe6be226fbdc8df9348b372292c
Author: sstanley <sstanley>
Date:   Wed Mar 15 00:03:06 2000 +0000

    Fixed a bug with how data was filled from the AmrData object.  The wrong
    level was used.

Tools/C_util/Convergence/DiffPlot.cpp

commit 046ecb4d410dd90039dff0433c8ce83b276bafa6
Author: car <car>
Date:   Mon Mar 13 18:25:20 2000 +0000

    trivially different from sstanley_2.32

Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_3.32
Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_3.32

commit 656403f3eb4987f09b6df74cb97391794e21aab9
Author: car <car>
Date:   Mon Mar 13 17:19:17 2000 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_2.32
Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_2.64
Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_3.32
Src/LinearSolvers/C_NodalMG/tests/gt2t4
Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_2.32
Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_2.64
Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_3.32
Tests/LinearSolvers/C_NodalMG/test_grids/gt2t4

commit 33a0df4e16587824b057df3993e4afd7e80952e1
Author: lijewski <lijewski>
Date:   Wed Mar 1 21:58:51 2000 +0000

    Upped the precision in checkPoint().

Src/C_AMRLib/SlabStat.cpp

commit 5c36e7ed0dfe22b902df232cf0ca9a1318eb54cd
Author: lijewski <lijewski>
Date:   Wed Mar 1 20:19:02 2000 +0000

    More work getting SlabStats going.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/SlabStat.cpp

commit 43f3191577a8a3de3bcc5b41d81dd629ce277a96
Author: lijewski <lijewski>
Date:   Wed Mar 1 15:43:34 2000 +0000

    Stuff for checkPoint()ing SlabStat stuff

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/SlabStat.H
Src/C_AMRLib/SlabStat.cpp

commit 6593ff78eddee49eea0638d6e5c08e37c9188016
Author: lijewski <lijewski>
Date:   Wed Mar 1 15:43:03 2000 +0000

    Defaulted another argument.

Src/C_BaseLib/VisMF.H

commit a31b4e7eed16cbedeb2c5981bce77fb2effce68f
Author: lijewski <lijewski>
Date:   Mon Feb 28 23:27:00 2000 +0000

    Some mods for the statistics stuff ...

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 78278d020db26012cbcabb5d2e825b11c46c1ec0
Author: lijewski <lijewski>
Date:   Mon Feb 28 23:26:36 2000 +0000

    Mods for some statistics stuff ...

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Make.package
Src/C_AMRLib/SlabStat.H
Src/C_AMRLib/SlabStat.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit 00d87edc8cfed0528cec888f7a0eb1455c918826
Author: sstanley <sstanley>
Date:   Fri Jan 28 01:14:05 2000 +0000

    Modification to the doc++ stuff to make it work properly.

Src/C_AMRLib/StateDescriptor.H

commit 28db038b55dbb9da26d8e858ca4ad717bf3942eb
Author: vince <vince>
Date:   Mon Jan 10 23:55:15 2000 +0000

    Added support for yukon (ARSC).

Tools/C_mk/Make.defs

commit 248a7d8b86d1d252685e045c77459f9bbe45a253
Author: lijewski <lijewski>
Date:   Thu Jan 6 19:03:27 2000 +0000

    Fixed docxx comments to compile with latex.

Src/C_AMRLib/AmrLevel.H

commit 053c755e04a956f0d919f17ed12aab25805a743b
Author: lijewski <lijewski>
Date:   Thu Jan 6 18:26:40 2000 +0000

    Updated docxx documentation so it can be latex'd.
    Had to add a '\' to some BL_ASSERT()s and BL_SPACEDIMs.

Src/C_BaseLib/BLassert.H
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/Looping.H
Src/C_BaseLib/Orientation.H

commit 35201aebda195e8f14d1ffe1be1546abd7b45480
Author: lijewski <lijewski>
Date:   Thu Jan 6 18:14:36 2000 +0000

    The docxx style file we use for latex.

Src/C_BaseLib/docxx_squish.sty

commit 52f6a58475d9f47d48a191c2d1db65c2e4858e10
Author: dailey <dailey>
Date:   Mon Jan 3 14:02:56 2000 +0000

    Make.IRIX64 modified for use with SGIs at the Univ. of Wisconsin
    
    01-03-00    Sara Bauman

Tools/C_mk/Make.IRIX64

commit fbb861952eb5989b5bffd2d39380d3f9586ddefc
Author: lijewski <lijewski>
Date:   Thu Dec 9 22:06:08 1999 +0000

    Now use Mersenne Twister random number generator.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit e2b10fe46c5ade3c93742366228f2c1879b80d0e
Author: sstanley <sstanley>
Date:   Thu Dec 2 07:43:05 1999 +0000

    Modified the logic in HT::manual_tags_placement() to fix the problem
    with to many cells left uncovered near the outflow.  This, unfortunately
    required a change in the interface to this routine, and thus a change in
    the header which fed all the way back to AmrLevel.H.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit a9ecef303a79116c9aa57b15d9db00a4d377471f
Author: lijewski <lijewski>
Date:   Wed Dec 1 16:37:24 1999 +0000

    Shut up a warning on SGI ...

Src/C_BoundaryLib/BoundCond.H

commit d512bb98258a673429c22c64a7ee244f79dcd8a2
Author: lijewski <lijewski>
Date:   Wed Dec 1 16:17:10 1999 +0000

    Shut up a warning ...

Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.H

commit e184b43e43fb3c293cd34ed40aa9701d025976e4
Author: lijewski <lijewski>
Date:   Wed Dec 1 16:16:45 1999 +0000

    Shut up warnings ...

Src/C_BaseLib/BoxList.H
Src/C_BaseLib/MultiFab.cpp

commit fc2a3fa18344a39c826d4da0883ca6774235b045
Author: lijewski <lijewski>
Date:   Sun Nov 28 19:48:51 1999 +0000

    Don't try to read .profile

Tools/C_scripts/compressor

commit 82416729ec829d3341a0c56c7138fcbf62b03fa1
Author: lijewski <lijewski>
Date:   Sun Nov 28 19:48:22 1999 +0000

    Mod to fix bug on T3E

Tools/C_scripts/compressor

commit 8aaee9d05d0c35292b8885b5d31e8e78e7822e21
Author: lijewski <lijewski>
Date:   Fri Nov 26 20:02:41 1999 +0000

    Strip out any possible tar files.

Tools/C_scripts/compressor

commit c61f8af88e1edfd9307390253fb76abe86851221
Author: lijewski <lijewski>
Date:   Sat Nov 20 19:41:38 1999 +0000

    Direct error output of `ls' commands to /dev/null.

Tools/C_scripts/compressor

commit 6d4bc5c7eba894ff86d63274bd0340984a0f8608
Author: lijewski <lijewski>
Date:   Sat Nov 20 00:09:12 1999 +0000

    Beefed it up a bit so job chaining will work.

Tools/C_scripts/compressor

commit b553d176f50dce1cd8ebc01f5ac6c1450c7afe78
Author: car <car>
Date:   Thu Nov 18 22:19:43 1999 +0000

    We think we fixed inflow on the high side of an idim.

Src/LinearSolvers/C_NodalMG/boundary.cpp

commit 2706753f5e18072191fa9754871a2385a4449233
Author: sstanley <sstanley>
Date:   Thu Nov 18 21:29:57 1999 +0000

    Minor change to fix a documentation problem.

Src/C_BoundaryLib/FabSet.H

commit 55053973ad6330f5b2ba864d5306ea156637b68e
Author: car <car>
Date:   Thu Nov 18 00:27:51 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 6aa2df8970d3bef121acbf4668ab14e468e2b0b6
Author: car <car>
Date:   Thu Nov 18 00:09:07 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/tests/gr.ann.1
Src/LinearSolvers/C_NodalMG/tests/gr.sstanley.1
Tests/LinearSolvers/C_NodalMG/test_grids/gr.ann.1
Tests/LinearSolvers/C_NodalMG/test_grids/gr.sstanley.1

commit 80fdf472afe8cdbe99af1d69765e872986da5296
Author: lijewski <lijewski>
Date:   Fri Nov 12 21:37:54 1999 +0000

    A ksh script to tar up and rm chk and plt directories.
    Mostly useful in batch scripts :-)

Tools/C_scripts/compressor

commit accd3b0b982fcca08f1a85f8e7ee6f1add58200e
Author: lijewski <lijewski>
Date:   Thu Nov 11 21:26:08 1999 +0000

    Make the default for tar_and_rm_files to false, even on T3E ...

Src/C_AMRLib/Amr.cpp

commit ade581fc599964f11d880e9736e08711512850a6
Author: propp <propp>
Date:   Wed Nov 3 16:33:25 1999 +0000

    eliminated inlined function to make totalview happy

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit eb90c821cd904eac1590c662363a9b9aefdd76e0
Author: propp <propp>
Date:   Sat Oct 30 00:01:36 1999 +0000

    moved static function to appease totalview

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 9e3e5dd223fe3648ab76e4a58699601d024b9af6
Author: sstanley <sstanley>
Date:   Fri Oct 29 17:31:48 1999 +0000

    Fixed a problem with the level used from the exact data.  The old code
    is still intact.

Tools/C_util/Convergence/DiffUniform.cpp

commit 084127e37bfcf2cf2e1065f216514807d5763669
Author: sstanley <sstanley>
Date:   Fri Oct 29 16:36:03 1999 +0000

    Small modifications to DiffSameGrid.cpp (all documentation) and added
    the routine DiffSameGridRefined.cpp which does the same thing as
    DiffSameGrid.cpp but allows the two plotfiles to have different
    levels of refinement, as long as they have the same physical region
    refined.

Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffSameGridRefined.cpp
Tools/C_util/Convergence/GNUmakefile

commit 883704896b63daa6390be56a77626e788ae776e9
Author: lijewski <lijewski>
Date:   Thu Oct 28 21:49:52 1999 +0000

    When amr.tar_and_rm_files is true ...
    
    We now stagger deleting the ckfiles to support restart() and job chaining.

Src/C_AMRLib/Amr.cpp

commit f725a9b56aaa2c8dac02935a6e79a0c063b9722f
Author: vince <vince>
Date:   Wed Oct 27 21:24:40 1999 +0000

    Moved a flag.

Tools/C_mk/Make.T3E

commit 4a2cd8feb361a0b86b1d0665236f1af0451ff195
Author: marc <marc>
Date:   Mon Oct 25 18:31:33 1999 +0000

    Do explicit C-style caststo shut gcc up on my Linux box

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 6007231e5c6502bf291135698471fa98dfee9d06
Author: marc <marc>
Date:   Mon Oct 25 18:29:54 1999 +0000

    Add optimization to FFlags for opt.

Tools/C_mk/Make.Linux

commit e14b601aa3c2a335958292b6d0bd23b339b1b7c3
Author: lijewski <lijewski>
Date:   Thu Oct 21 17:27:21 1999 +0000

    Now remember pid for chk and plt tar_and_rm commands so can grok them.

Src/C_AMRLib/Amr.cpp

commit 94057b43d3d8567be6e8861943154a89223a84f1
Author: sstanley <sstanley>
Date:   Wed Oct 20 22:35:37 1999 +0000

    Added volume factor to the norms in DiffSameGrid.cpp.  Added the routine
    PltFileNormB.cpp which just does the norms of the values in a plotfile.

Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/PltFileNormB.cpp

commit 3d8a1bcc3e45209a2811a422b67ca3d58839c713
Author: sstanley <sstanley>
Date:   Wed Oct 20 20:08:35 1999 +0000

    Marc's changes to the DiffUniform.cpp routine (along with minor documentation
    of my own).  Similar documentation in PltFileNorm.cpp

Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/PltFileNorm.cpp

commit 2bbdecf32c72338e4d2c8c2d06a8011afa0a12b2
Author: lijewski <lijewski>
Date:   Wed Oct 20 18:25:13 1999 +0000

    Added Execute().

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 8fb12379ba7cabb362905037d3dc429011bbd9a4
Author: lijewski <lijewski>
Date:   Wed Oct 20 18:24:58 1999 +0000

    Added amr.tar_and_rm_files ability.

Src/C_AMRLib/Amr.cpp

commit 78795f93137186c5db52b9b17a52eba17fc29f65
Author: vince <vince>
Date:   Fri Oct 15 23:44:29 1999 +0000

    Additions for the LBNL Alpha cluster.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 611d895ca174907959d536805358a46820ab8a9c
Author: propp <propp>
Date:   Fri Oct 8 20:54:50 1999 +0000

    added plotfile_on_restart option

Src/C_AMRLib/Amr.cpp

commit e1b2a38844a329c50bf8255890b33d067a3d52a4
Author: sstanley <sstanley>
Date:   Thu Sep 30 15:55:12 1999 +0000

    Minor change to doc++ stuff, but it seemed like a good time...

Src/C_BaseLib/BoxArray.H

commit a653e49cac0224a61d38a70a118517a21f40ee07
Author: lijewski <lijewski>
Date:   Thu Sep 30 14:56:19 1999 +0000

    Removed cached MultiFabCopyDescriptor stuff ...

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 9a9c8cdfa347027d4720f26c491d1b081e58ac32
Author: lijewski <lijewski>
Date:   Thu Sep 30 14:55:53 1999 +0000

    Removed cached MultiFabCopyDescriptor junk from MultiFab.

Src/C_BaseLib/Geometry.cpp

commit 955b3b13cf88873baa4310d4b346675cb59e2276
Author: sstanley <sstanley>
Date:   Wed Sep 29 21:46:08 1999 +0000

    Modification to fix compiling on the T3E

Tools/C_util/ViewMF/GNUmakefile

commit c99e646157f4a1780db9d5373c4349c66b98b76e
Author: sstanley <sstanley>
Date:   Fri Sep 24 21:26:34 1999 +0000

    Fixed a problem with doing the max norm.

Tools/C_util/Convergence/DiffSameGrid.cpp

commit e4f116ff32331c1cc48fb136af98d93b8e6eb7d4
Author: marc <marc>
Date:   Thu Sep 23 21:06:56 1999 +0000

    Surround output func by ifdef HG_DEBUG to satisfy compiler

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit fde0e1f1afffbf0c171deaa40b24d41fd1ad3530
Author: vince <vince>
Date:   Sat Sep 18 00:50:34 1999 +0000

    Added changes for the vis server (escher, an sgi) and
      n2001 (the pc linux cluster).

Tools/C_mk/Make.IRIX64
Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit b01845fe869124ccd77d8ccf8bf2359fcbb2e76d
Author: lijewski <lijewski>
Date:   Fri Sep 17 23:32:45 1999 +0000

    Fix to make level 0 regridding work with fixed grids.

Src/C_AMRLib/Amr.cpp

commit 858a7e0f25969b57c35dbfcf1f3b8005bee2e33b
Author: lijewski <lijewski>
Date:   Fri Sep 17 21:45:06 1999 +0000

    amr.regrid_on_restart=1 will force regrid() on 1st timestep on restart.

Src/C_AMRLib/Amr.cpp

commit ed75327bc9dc63fcf957b2b1a37ee3a4dbab496d
Author: car <car>
Date:   Fri Sep 17 17:22:47 1999 +0000

    tweak

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 1bfca1886f13e45f9e4d1b99a2c68002b049aa8d
Author: lijewski <lijewski>
Date:   Thu Sep 16 23:12:41 1999 +0000

    Some mods to allow regridding at level 0 if max_grid_size changes.

Src/C_AMRLib/Amr.cpp

commit ecd836abc0eda24b0afe3378817644b42fbccb44
Author: car <car>
Date:   Wed Sep 15 16:58:32 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 90972fdb4aa4c95b6edb84af2be3571ef0803521
Author: car <car>
Date:   Tue Sep 14 18:26:56 1999 +0000

    support for dense stencils is added

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F
Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.H
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 2628e3af5b882904ff97ea351875ae423c595ca8
Author: lijewski <lijewski>
Date:   Fri Sep 10 21:07:30 1999 +0000

    Added -qdpc to promote FP constants to double precision ...

Tools/C_mk/Make.AIX

commit 95f64c92a2d14031fdf5b1a406e0bedc77f2f9f7
Author: lijewski <lijewski>
Date:   Fri Sep 10 20:53:01 1999 +0000

    Added -fpconstant to FOPTF and FDEBF

Tools/C_mk/Make.OSF1

commit bcb82edfb22f96845ccc7fbe7e1c38de16225168
Author: almgren <almgren>
Date:   Thu Sep 2 22:00:27 1999 +0000

    Removed the is_sync flag.

Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit e8666ebb35efb458479c676635dd8871c6de1e70
Author: sstanley <sstanley>
Date:   Thu Sep 2 00:12:38 1999 +0000

    Corrected the definition of the grids for this case.  They were improperly
    defined, although it doesn't show up for this test case.

Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_a

commit 6531cf9525df7b348a7c8fe2e217df6b3475bfb5
Author: sstanley <sstanley>
Date:   Sat Aug 28 00:43:57 1999 +0000

    A couple of small changes to allow it to compile.

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/Make.package
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/Make.package

commit 4bcfbb85e3951dced1e48981a0a77f1913701322
Author: sstanley <sstanley>
Date:   Fri Aug 27 15:10:53 1999 +0000

    Removed the nprocs from the StartParallel call.

Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 1bde6bd72097f909f8eaa1acb335305e267b733e
Author: lijewski <lijewski>
Date:   Thu Aug 26 18:10:47 1999 +0000

    Now recognizing leading ! character as a comment.
    Don't currently allow any preceding space before the ! ...

Tools/C_scripts/strip72

commit 7986ee17bd089acb747b34810c9d3624040da1d2
Author: lijewski <lijewski>
Date:   Thu Aug 26 17:19:58 1999 +0000

    Changed test for KCC to also recognize mpKCC and newKCC ...

Tools/C_mk/Make.defs

commit bf46a75523ca15b5ce1882185e43e7b035ccc455
Author: propp <propp>
Date:   Wed Aug 25 18:03:58 1999 +0000

    added BL_FORT_USE_LOWERCASE option

Src/C_BaseLib/SPECIALIZE_F.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BoundaryLib/INTERPBNDRYDATA_F.H
Src/LinearSolvers/C_CellMG/ABec_F.H
Src/LinearSolvers/C_CellMG/CG_F.H
Src/LinearSolvers/C_CellMG/LO_F.H
Src/LinearSolvers/C_CellMG/LP_F.H
Src/LinearSolvers/C_CellMG/MG_F.H
Src/LinearSolvers/C_TensorMG/DivVis_F.H
Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_F.H
Src/LinearSolvers/C_TensorMG/MCLO_F.H

commit 638bc20e8078dd5c7d320c47aae7cda6efaecd27
Author: lijewski <lijewski>
Date:   Wed Aug 25 17:52:33 1999 +0000

    Fixed bug regarding usage of ConstFabSetIterator.

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 899267ead6cab5f902ed1c9f2d88e2356b71a83a
Author: lijewski <lijewski>
Date:   Tue Aug 24 21:02:22 1999 +0000

    Use new hfiles with KCC ...

Tools/C_mk/Make.AIX

commit 4bc0d7f462212d65e9dac2a54f2c7d186ec622f3
Author: lijewski <lijewski>
Date:   Tue Aug 24 20:08:46 1999 +0000

    Simplified some settings.

Tools/C_mk/Make.AIX

commit d64996046cbb9c654611dfb8f71944050a6eb2d1
Author: lijewski <lijewski>
Date:   Tue Aug 24 16:28:29 1999 +0000

    Cleaned up the FillPatch stuff a tad more.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 7f6f1a5fafdf435c7522e5b77bcc6a3355cefc40
Author: lijewski <lijewski>
Date:   Mon Aug 23 21:19:58 1999 +0000

    Added tokenize() ...

Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp

commit d82600e2c5561c5361b19d96a95e7381c102346a
Author: car <car>
Date:   Mon Aug 23 21:16:49 1999 +0000

    support for Geometry

Src/LinearSolvers/C_NodalMG/inputs

commit 3b1c9e8e3553c23212a697d255bd787c17ea8804
Author: lijewski <lijewski>
Date:   Fri Aug 20 21:54:22 1999 +0000

    Oops -- needed to define FillPatch::operator++() ...

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 576b85e752adb18047bdb1e491e45ef2794791b2
Author: lijewski <lijewski>
Date:   Fri Aug 20 17:52:55 1999 +0000

    Removed --no_restrict; Crays header files use it :-(

Tools/C_mk/Make.T3E

commit 1e028f327af6182e42ed48c78e83e3595b0febc0
Author: lijewski <lijewski>
Date:   Fri Aug 20 17:38:02 1999 +0000

    Added --no_restrict

Tools/C_mk/Make.T3E

commit 5b100cfe47edd987820a94e56507c100ac4b70b9
Author: lijewski <lijewski>
Date:   Thu Aug 19 20:16:32 1999 +0000

    Fixed yet more memory leaks ...

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 527b7e2fe7b7c2bc63d9139433ea7d899c254736
Author: lijewski <lijewski>
Date:   Wed Aug 18 21:53:01 1999 +0000

    FillPatchIterator now uses the appropriate Iterator for each of the
    components at a specified StateDescriptor index.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp

commit ef4b189092dc9ddfd154a25bca0fbda6473cd0ba
Author: propp <propp>
Date:   Mon Aug 16 18:21:53 1999 +0000

    *added ability to derive multicomponent data with separate names for each
    component
    *added ability in heat transfer to derive mole fracs

Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp

commit 649441d3c4868e6ca18b93c3604ca72885a4654e
Author: propp <propp>
Date:   Fri Aug 13 16:28:57 1999 +0000

    fixed up writePlotFile routines
    added setPlotVariables routine

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 13da5ce51c55a91b4bde4d22ea41dddde085288a
Author: lijewski <lijewski>
Date:   Wed Aug 11 19:52:05 1999 +0000

    Added FOPTF+=-O for default case

Tools/C_mk/Make.Linux

commit c70246a83e9e900aafb8feb6feafc58c0d426103
Author: marc <marc>
Date:   Tue Aug 10 00:12:42 1999 +0000

    Generalize for prversion/parallel junk

Tools/C_scripts/dsp.mak

commit 3db1051a4e2ac26d89a816b2f6b470a7cdeb1229
Author: car <car>
Date:   Mon Aug 9 16:44:41 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 0c9ae1133e391435d6b455f637ffd074daeeb76d
Author: car <car>
Date:   Fri Aug 6 23:10:05 1999 +0000

    bndrylib is now needed

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit ca56a92d5bea4b5ed200f47022f0a363871540aa
Author: sstanley <sstanley>
Date:   Fri Aug 6 22:45:28 1999 +0000

    Fix to BoxArray::contains(BoxArray ).

Src/C_BaseLib/BoxArray.cpp

commit a8617ab87ba92adc36655d3af99021ed9a94282c
Author: propp <propp>
Date:   Fri Aug 6 21:48:35 1999 +0000

    deleted parmparse variable verbose, now must use parmparse variable v

Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit 322b73f941caafcc9889a7fbe2928447b0e65184
Author: propp <propp>
Date:   Fri Aug 6 18:20:16 1999 +0000

    eliminated verbose ParmParse argument; it was being overwritten by v ParmParse
    argument

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 6ce859c8a51b8687e1e713f4d21e0251390ef18b
Author: almgren <almgren>
Date:   Tue Aug 3 07:03:37 1999 +0000

    Need to include bndrylib now because we're using a Geometry object.

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit e741a0420ba5c99d4ec478eca4cb367993f2cae9
Author: almgren <almgren>
Date:   Tue Aug 3 07:02:35 1999 +0000

    A different paradigm for doing Sync_resid_fine - the previous way just
    wouldnt work for periodic in 3d.

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit e4d3f616295db94cf29d9f5b3328bdcfa44fe358
Author: propp <propp>
Date:   Tue Aug 3 00:37:24 1999 +0000

    Fixed bug in FORT_APPLYBC where 1st component of bc array was used to determine
    bc type instead of the dir-th component of bc array.
    This change has already been made in the 2D version of the code.

Src/LinearSolvers/C_TensorMG/DV_3D4.F
Src/LinearSolvers/C_TensorMG/DV_3D4.mF

commit 336dd86c0775724213a57ae60e1421a459a81571
Author: almgren <almgren>
Date:   Mon Aug 2 20:24:16 1999 +0000

    Need to fill rhs_local periodically as well in fill_sync_reg.

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 915d575ab54b9a728040cf34b864d38a5b8e865d
Author: sstanley <sstanley>
Date:   Mon Aug 2 19:22:16 1999 +0000

    Minor changes in the location of the doc++ information.  Put it after the
    forward declarations instead of before.

Src/C_BaseLib/Box.H
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/MultiFab.H

commit 623060614c2bf705f1cddb787915127e94ff6e99
Author: almgren <almgren>
Date:   Sun Aug 1 15:11:44 1999 +0000

    Changes in order to get periodic right.

Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit d9d818fb08aa8722b4cb9cd9c0ee248f6e543584
Author: almgren <almgren>
Date:   Fri Jul 30 23:46:06 1999 +0000

    Warning message in hgfres.

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit b149f468fc3f4e4ad6955d079187be2a974f32b4
Author: marc <marc>
Date:   Thu Jul 29 01:07:06 1999 +0000

    Add options for specifying serial hgproj and prversion....note that this
    is all still a little flimsy...

Tools/C_scripts/dsp.mak

commit 14f31e18ed501200aaa52b016a81a9978349ed3c
Author: almgren <almgren>
Date:   Wed Jul 28 17:19:24 1999 +0000

    Should only do the special r-z stuff if i+m=0, not just i=0.

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 04acd2f8e3f48e4fdd77b80b2746ae7d2bd370c0
Author: marc <marc>
Date:   Tue Jul 27 17:35:51 1999 +0000

    Remove manual_grid_placement in favor of tagbox processing

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H

commit 7f3c3131962957e104d18c54d47afe1f2ab2e7eb
Author: marc <marc>
Date:   Tue Jul 27 17:34:59 1999 +0000

    Make const args const in signature

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 29ee23c01b926a5e0fa2dfdfcf6e3d8cb7ee11bf
Author: marc <marc>
Date:   Tue Jul 27 17:34:06 1999 +0000

    Make physicalBndryTrpes available to Fortran

Src/C_AMRLib/BC_TYPES.H

commit aa7cf471c93ac8513f657de1fec1cea7dbda0505
Author: lijewski <lijewski>
Date:   Mon Jul 26 16:59:42 1999 +0000

    Updated a comment :-(

Src/C_BaseLib/ParallelDescriptor.H

commit 7463973514f1824bf87e69a702666a18f75e9f19
Author: almgren <almgren>
Date:   Fri Jul 23 23:56:13 1999 +0000

    Made a bunch of changes having to do with how the sync register stuff
    is computed.  In this new version, the contributions to the sync registers
    are computed in hgproj, not in SyncRegister...

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit c12f46ed39e620e3225a49725193613b0c7796d4
Author: car <car>
Date:   Fri Jul 23 21:29:13 1999 +0000

    test case for inflow bust

Src/LinearSolvers/C_NodalMG/tests/gr2.inf
Tests/LinearSolvers/C_NodalMG/test_grids/gr2.inf

commit b41b1e70dfe617f349b48c9a25600746bf08d5c6
Author: car <car>
Date:   Fri Jul 23 21:28:31 1999 +0000

    saves work in serial

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit c200fd1124b651939512d1f356fb4a5646ef6e6a
Author: car <car>
Date:   Fri Jul 23 21:28:00 1999 +0000

    fix for array bounds bust

Src/LinearSolvers/C_NodalMG/boundary.cpp

commit 4c470e17126830a544d2e73d8f5d6e3e47eb8a8d
Author: car <car>
Date:   Fri Jul 23 17:56:40 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit e906ce17eb869fef4b1195a62038f358c3312a0d
Author: sstanley <sstanley>
Date:   Wed Jul 21 21:09:20 1999 +0000

    Modified the location of the call to manual_tags_placement().

Src/C_AMRLib/Amr.cpp

commit a53ac631a79fdedb1be5ac3fa59a3ec1664c2d74
Author: lijewski <lijewski>
Date:   Wed Jul 21 21:07:38 1999 +0000

    Output CArena stats ...

Src/LinearSolvers/C_NodalMG/proj.cpp

commit a6ee7c2f903360d900c37043d443b1cfbafc9e0b
Author: lijewski <lijewski>
Date:   Wed Jul 21 21:06:08 1999 +0000

    Oops -- forgot to remove a commented out #if

Src/C_BaseLib/CArena.cpp

commit d9b9cb5fecc5dd548bdc0a4d841e28e0722378b5
Author: lijewski <lijewski>
Date:   Wed Jul 21 21:02:49 1999 +0000

    Added heap_space_used().

Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp

commit d77bc85c9ace4869a1b5cb0a936682161ade435a
Author: lijewski <lijewski>
Date:   Wed Jul 21 21:02:40 1999 +0000

    Added extra newline to an output message for additional separation ...

Src/C_BaseLib/RunStats.cpp

commit fb1977fa968669df499dcd9880a9eca5403c1fa9
Author: lijewski <lijewski>
Date:   Wed Jul 21 17:26:08 1999 +0000

    Removed commented out line ...

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 182ad4ba8abff1284d89602c3f43a4cbf79d6426
Author: lijewski <lijewski>
Date:   Wed Jul 21 17:20:34 1999 +0000

    Got memory mods working with periodic.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit cbc4d4187ec5e48d34f9ffa375d991a8bd0e1f6c
Author: lijewski <lijewski>
Date:   Wed Jul 21 15:28:00 1999 +0000

    Some mods to minimize communication when in parallel.

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit d9aaf9b152c07a41d36f2099367e1ebeb7947ffb
Author: lijewski <lijewski>
Date:   Tue Jul 20 23:45:02 1999 +0000

    The restrict_level stuff wan't quite right ...

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 22776294825c0933889c8d4393903771eefbfc59
Author: almgren <almgren>
Date:   Tue Jul 20 20:42:13 1999 +0000

    Added manual_tags_placement which will replace manual_grid_placement.  It
    is only virtual here, to be defined in applications.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H

commit 26d12136bc66e833a4ae5bb4a5645c57b7ebb1cf
Author: lijewski <lijewski>
Date:   Tue Jul 20 17:13:59 1999 +0000

    Slight mod of what I checked in yesterday.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 50ea5699d6ad04b14bde8a5fe2db3685fd287a3f
Author: lijewski <lijewski>
Date:   Tue Jul 20 15:45:04 1999 +0000

    Made restrict_level() more memory efficient in parallel.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 639fb6b7b9c8400861b7ead8df33d70c8e6fe9b1
Author: lijewski <lijewski>
Date:   Mon Jul 19 23:05:06 1999 +0000

    Added some statistics to track parallel data transfer.
    FillPatch routines now transfer less data in parallel.

Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit a63e8b9b6002941a4e697c6b4b0e7dcfb8aa45a7
Author: almgren <almgren>
Date:   Mon Jul 19 19:54:24 1999 +0000

    Fixed code for r-z with 5-point stencil, also removed some routines which
    weren't being used.

Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 2394d192f585fb5902f0171cc69ebf1186238961
Author: propp <propp>
Date:   Mon Jul 19 17:40:48 1999 +0000

    added 3d fortran routines...

Tools/C_util/Convergence/AVGDOWN_3D.F
Tools/C_util/Convergence/Make.package

commit dff87ccfc229cb9b3045829ea124b525504e4d3f
Author: sstanley <sstanley>
Date:   Fri Jul 16 18:23:49 1999 +0000

    Increased the precision at which the Header in  plotfiles and checkpoint
    files gets written.  We were losing precision in the timestep.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/StationData.cpp
Tools/C_util/WritePlotFile.cpp

commit 7ba8d555ed89718372bdc11d7a233dddf4a71678
Author: almgren <almgren>
Date:   Fri Jul 16 17:14:46 1999 +0000

    Fix in hgcdiv to correctly do 5-point stencil at r=0 (for r-z only!).

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 10b4c950c8edd3a22ede041aa30c60f33970c6ed
Author: lijewski <lijewski>
Date:   Thu Jul 15 17:07:04 1999 +0000

    Got rid of all those computeBoxLen() calls.
    Now only call it when length() is called.

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp

commit b5f30e424dd86b111dc02a3d0d898e18e94b1a7b
Author: sstanley <sstanley>
Date:   Thu Jul 15 01:37:02 1999 +0000

    Corrected a couple of the Docs.

Src/C_AMRLib/StateData.H

commit 22d11c8156a5de1ebd86c7f2caf3f49e51f52689
Author: lijewski <lijewski>
Date:   Wed Jul 14 23:06:15 1999 +0000

    Did copy constructor correctly.

Src/C_BaseLib/Geometry.cpp

commit 31daf4b127624887bafd1d727ab423d477b581fd
Author: lijewski <lijewski>
Date:   Wed Jul 14 19:20:44 1999 +0000

    Added malloc_stats(0) call for BL_T3E in OutOfMemory().

Src/C_BaseLib/Utility.cpp

commit a6e62aca5dce9fc1ee09ea7dc0f94a6b5653d03e
Author: marc <marc>
Date:   Tue Jul 13 01:30:48 1999 +0000

    Fix a few little problems...still work-in-progress

Tools/C_scripts/dsp.mak

commit 5b99a235ba824f5247d498cffa697c0e5d369d97
Author: lijewski <lijewski>
Date:   Mon Jul 12 16:42:11 1999 +0000

    Fix for periodic-nonperiodic boundary cells.
    Also moved more heap-based stuff into FillPatchIterator data member area.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 42721987c552042544e968efa8d900414234123e
Author: car <car>
Date:   Wed Jul 7 22:48:33 1999 +0000

    MPI type safety

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ccse-mpi.H

commit 00f832f2aaf9b75ec54d78f135e96482537054a5
Author: almgren <almgren>
Date:   Wed Jul 7 21:45:12 1999 +0000

    IsRZ() only exists if BL_SPACEDIM == 2.

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit a91891178cc0292b1a5af791f8cdcd13628deeee
Author: almgren <almgren>
Date:   Wed Jul 7 18:30:43 1999 +0000

    IsRZ() is only defined in 2-d

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 04c03acd88da01bb807faa189c4e2a617f093b8c
Author: almgren <almgren>
Date:   Thu Jul 1 23:18:31 1999 +0000

    Modifications to correct the 5-point stencil in r-z at r=0.

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit 241413d1079cbc11aa4906772e158e1efe01f651
Author: lijewski <lijewski>
Date:   Thu Jul 1 20:12:24 1999 +0000

    Changed how RunStats stuff was done ...

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 06561a4541f7fc07da67929188e401194f6ea9af
Author: lijewski <lijewski>
Date:   Thu Jul 1 19:44:49 1999 +0000

    Added ReduceIt() to fix bug with how the List<RunStatsData> is reduce()d.

Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp

commit a7b36ea5ab45c52e7e88143feb6dc17a451a0316
Author: lijewski <lijewski>
Date:   Thu Jul 1 19:44:04 1999 +0000

    Got rid of old-style cast.

Src/C_BaseLib/VisMF.cpp

commit 3bb8f8713b44b2c4d3d1567776c6b8a7d53f0166
Author: lijewski <lijewski>
Date:   Thu Jul 1 16:36:00 1999 +0000

    Fixed bug in readStats().

Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp

commit 9efd4eec1fc333a4f0f65ee1286bd650f55d73a6
Author: marc <marc>
Date:   Wed Jun 30 23:46:38 1999 +0000

    Fix a few random (and mysteriously uncovered) bugs in the averaging routines/calls

Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit bccc7132e9a507de4983858e626a280438dc6c60
Author: almgren <almgren>
Date:   Wed Jun 30 21:46:14 1999 +0000

    Corrected the averaging of cell-centered source terms onto nodes at r=0.

Src/LinearSolvers/C_NodalMG/hg_avg2d.F

commit 63343a1279647ff3f3dc5faead17f3a3d9c2e161
Author: almgren <almgren>
Date:   Wed Jun 30 21:43:29 1999 +0000

    Removed already-commented-out code.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit e2aa51919f0d3dc93936491dda0e7ccf49d6a49a
Author: marc <marc>
Date:   Tue Jun 29 18:09:53 1999 +0000

    Externified typedef fixed up for 2D by Chuck.

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 95af0492c21fc5a49b2a5db477cd53da412c7961
Author: car <car>
Date:   Mon Jun 28 20:37:00 1999 +0000

    changes for KCC version 3.4, should be innocuous for 3.3

Src/C_AMRLib/StateDescriptor.H
Src/C_BaseLib/Arena.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/MultiFab.H
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp
Src/LinearSolvers/C_TensorMG/DivVis_F.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp

commit 8b7b6eeda6532431016d9a2747b5920e9799b50a
Author: car <car>
Date:   Thu Jun 24 22:09:47 1999 +0000

    Bone headed IntVect usage

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit fdcdf4a7b7a03592e2ce2a450374af5ab8910986
Author: marc <marc>
Date:   Thu Jun 24 21:21:55 1999 +0000

    Oops!  src was written as rc...

Src/LinearSolvers/C_NodalMG/hg_avg2d.F

commit 0bca89193a4eed732bff4fdcf31f50ed4b7a896c
Author: car <car>
Date:   Wed Jun 23 17:59:40 1999 +0000

    changes to support KCC 3.4

Src/C_BaseLib/VisMF.H
Tools/C_mk/Make.defs

commit b4020cfbaf9a3bc3ee6388510c7129d186816a37
Author: lijewski <lijewski>
Date:   Tue Jun 22 20:06:43 1999 +0000

    Redid how HG RunStats are setup to work around RunStats bug.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit b99ac16b153c33458f0dd02ced45200a2e0265cc
Author: car <car>
Date:   Sat Jun 19 03:57:55 1999 +0000

    added hg_{irecv,isend,test} to runstats

Src/LinearSolvers/C_NodalMG/inputs

commit 1c6c9d2e93c01fe6058e5ca473d087f069d84d9d
Author: lijewski <lijewski>
Date:   Fri Jun 18 19:16:28 1999 +0000

    Added RunStats for MPI_IRecv() MPI_ISend() and MPI_Test()

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 80f8663a7f6a8fb897db6371abd1a714248f9f35
Author: lijewski <lijewski>
Date:   Fri Jun 18 16:01:57 1999 +0000

    Some cleanup.

Src/C_BaseLib/Geometry.cpp

commit f282940d221960bc04698721527da94f02e00f83
Author: almgren <almgren>
Date:   Wed Jun 16 22:51:16 1999 +0000

    The extra terms for r-z should only be used with the 9-point stencil.

Src/LinearSolvers/C_NodalMG/hg_avg2d.F

commit 4661577f2b382fe060f1421fee0450dc9ebc1866
Author: lijewski <lijewski>
Date:   Wed Jun 16 22:13:03 1999 +0000

    Removed some dead code.

Src/C_BaseLib/RunStats.cpp

commit abd7c9f36289741412dedf1fef600d8334ee1173
Author: car <car>
Date:   Mon Jun 14 17:07:26 1999 +0000

    defused loop

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 706a7f7450def2cc2bb9452121cbe564f24a7ccb
Author: marc <marc>
Date:   Sat Jun 12 00:10:14 1999 +0000

    First cut at a script to make MSVC project input file.

Tools/C_scripts/dsp.mak

commit 0374a8c479c07766f29a729847d2fa2dc4319c40
Author: almgren <almgren>
Date:   Wed Jun 9 18:25:35 1999 +0000

    We don't want to use the additional rz terms for the five-point stencil.
    These terms *should* be included for the nine-point stencil only.

Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit fb24ff9b4d30dd3eb65fc87840202eb0f41619b7
Author: car <car>
Date:   Tue Jun 8 14:39:54 1999 +0000

    *** empty log message ***

Tools/C_mk/Make.mpi

commit 7af1da817b6becc24652c469f4b786d244d536c1
Author: marc <marc>
Date:   Tue Jun 8 00:57:37 1999 +0000

    Hack a little more on the derive_plot_vars junk.

Src/C_AMRLib/Amr.cpp

commit 7aecfd4739c6baaf1f167ce643cf032d859c45b3
Author: marc <marc>
Date:   Mon Jun 7 20:57:38 1999 +0000

    Remove rz assertion

Src/LinearSolvers/C_NodalMG/amr_multi.H

commit d66e2e3282655675fc9066fefdb211995ba22cba
Author: car <car>
Date:   Sun Jun 6 19:07:42 1999 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 86f95c3bab7ac56d919675f8d84e5205815cddd9
Author: sstanley <sstanley>
Date:   Fri Jun 4 17:03:52 1999 +0000

    Changes to make it work properly in parallel.

Tools/C_util/Convergence/DiffSameGrid.cpp

commit 6f8a074f32efce5dc68b5170b6c942b9069f0519
Author: sstanley <sstanley>
Date:   Fri Jun 4 01:03:25 1999 +0000

    Modification to make it work on the T3E.

Tools/C_util/Convergence/GNUmakefile

commit 7f9d3a1644d76ca536c5e34c5fa0b2b78d2450fe
Author: sstanley <sstanley>
Date:   Thu Jun 3 23:38:43 1999 +0000

    Converted to allow building in place.  Also removed nProc from
    ParallelDescriptor::StartParallel() call.

Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp

commit 3438b0e35456a2febd751fb37879bb04207d8740
Author: lijewski <lijewski>
Date:   Thu Jun 3 22:57:14 1999 +0000

    Changed way MPI message tags are calculated.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit d95d67c05aba6fbb7f0f9907666ac2d727817ef4
Author: lijewski <lijewski>
Date:   Wed Jun 2 20:09:00 1999 +0000

    Don't add MPI_HOME/include to INCLUDE_LOCATIONS if MPI_HOME is null

Tools/C_mk/Make.mpi

commit 5b4f18ba2152ee22b7c9c6f9538e0bb9e625d854
Author: lijewski <lijewski>
Date:   Wed Jun 2 19:20:53 1999 +0000

    Tightened up some assert()s

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 6eef4cf3df0f3df0aeb9f17366f13deab91d5481
Author: sstanley <sstanley>
Date:   Thu May 27 20:55:59 1999 +0000

    Added the bit of logic to allow derive_plot_vars[0]="ALL" force inclusion
    of all derived fields in the plot files.

Src/C_AMRLib/Amr.cpp

commit 7cbc22bf3ef19153f2a0cda483347054e2bb1eb4
Author: sstanley <sstanley>
Date:   Thu May 27 19:15:54 1999 +0000

    Added the logic to allow the inclusion of derived quantities in plotfiles.
    Added a new Array, derive_plot_vars, which controls which derived
    fields are included in plotfiles.  Also made the lists static and added
    hooks addPlotVar and addDerivePlotVar to allow variables to be added
    to the lists from within the code.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 48e9c1382d888bdf9a2bc994fe1fb317e5cc5033
Author: marc <marc>
Date:   Wed May 26 19:33:33 1999 +0000

    Remove implicit cast to shut up the MSVC compiler

Src/C_BaseLib/FArrayBox.cpp

commit 9ace929a2871b87a36f1de61dd4fbf3f1b9db71d
Author: marc <marc>
Date:   Tue May 25 23:09:02 1999 +0000

    Fix include for WIN32

Src/C_BaseLib/CoordSys.cpp

commit 4ed2a853ae1e2518906016879949243e072ba7fd
Author: lijewski <lijewski>
Date:   Tue May 25 22:02:20 1999 +0000

    small bug fix ...

Src/C_BaseLib/FArrayBox.cpp

commit 76df1cbc5583b10b5f2a1adce3d32f54f8337b17
Author: car <car>
Date:   Mon May 24 18:11:44 1999 +0000

    Makefile system now MPI aware

Src/C_AMRLib/GNUmakefile
Src/C_BaseLib/GNUmakefile
Src/C_BoundaryLib/GNUmakefile
Src/LinearSolvers/C_CellMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_TensorMG/GNUmakefile
Tools/C_mk/Make.defs
Tools/C_util/Convergence/GNUmakefile
Tools/C_util/ViewMF/GNUmakefile

commit 7c71fe7bf417e457b657e250720eb47c9e149fb9
Author: car <car>
Date:   Mon May 24 17:51:57 1999 +0000

    mpi support

Tools/C_mk/Make.Linux
Tools/C_mk/Make.OSF1
Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 9ae8b698eb3253ce8d25b286e7a2654928bb6440
Author: lijewski <lijewski>
Date:   Tue May 11 17:42:59 1999 +0000

    Got rid of remove(int) and clear(int) -- they're weren't parallel safe.

Src/C_BaseLib/FabArray.H

commit 0f58b8f480aace0742b0f7a96a7b17e3d3a9f9f6
Author: car <car>
Date:   Mon May 10 21:32:52 1999 +0000

    tune for absoft, g77

Tools/C_mk/Make.Linux

commit 27b513c4aa5703ddd572feb70fca0e988ccd27d2
Author: car <car>
Date:   Mon May 10 21:26:31 1999 +0000

    tune for absoft, g77

Tools/C_mk/Make.Linux

commit 6ce554832ccb10a663f14e80e0b5574ed2d05be0
Author: car <car>
Date:   Mon May 10 21:25:32 1999 +0000

    Added LOWERCASE Fortran Types

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 92b32d8ec37983f141c4e9ce1d99d804a010b0a4
Author: lijewski <lijewski>
Date:   Mon May 10 20:44:50 1999 +0000

    DBL_MIN -> -DBL_MAX and likewise for FLT_???

Src/C_BaseLib/MultiFab.cpp

commit ce868a5930e2480b690e13a34f5d76fa7d5b99be
Author: marc <marc>
Date:   Mon May 10 20:31:14 1999 +0000

    Move logical reset inside loop to behave correctly.

Src/C_AMRLib/Amr.cpp

commit 72f4ff12abb769940f991d0ef47f430de87527d7
Author: car <car>
Date:   Mon May 10 18:54:07 1999 +0000

    BLassert -->> BL_ASSERT.
    
    Good luck typing it.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/BCRec.cpp
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/DatasetClient.cpp
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/ErrorList.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp
Src/C_AMRLib/StationData.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/Array.H
Src/C_BaseLib/BLassert.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/List.H
Src/C_BaseLib/Looping.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/NormedFab.H
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/RealBox.H
Src/C_BaseLib/RunStats.cpp
Src/C_BaseLib/Specialize.cpp
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp
Src/C_BaseLib/test/tCArena.cpp
Src/C_BaseLib/test/tFAC.cpp
Src/C_BaseLib/test/tFB.cpp
Src/C_BaseLib/test/tVisMF.cpp
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/BoundCond.H
Src/C_BoundaryLib/FabSet.cpp
Src/C_BoundaryLib/InterpBndryData.cpp
Src/C_BoundaryLib/Mask.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp
Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp
Tests/C_BaseLib/tCArena.cpp
Tests/C_BaseLib/tFAC.cpp
Tests/C_BaseLib/tFB.cpp
Tests/C_BaseLib/tVisMF.cpp
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp
Tools/C_util/Convergence/DiffFab.cpp
Tools/C_util/Convergence/DiffPlot.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp
Tools/C_util/ViewMF/MFNorm.cpp
Tools/C_util/ViewMF/viewMFdiff.cpp

commit 3e48456e3452678a0faa598a4389673e95654b1f
Author: car <car>
Date:   Mon May 10 17:18:27 1999 +0000

    Replace all asserts with BLassert.
    Replace all #include Assert.H with #include BLassert.H
    This avoids incompatiblities on systems which insist on using the
    system assert in their library header files.
    
    Assert.H will be removed soon.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/BCRec.cpp
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/DatasetClient.cpp
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/ErrorList.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp
Src/C_AMRLib/StationData.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/Array.H
Src/C_BaseLib/Assert.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/List.H
Src/C_BaseLib/Looping.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/NormedFab.H
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/RealBox.H
Src/C_BaseLib/RunStats.cpp
Src/C_BaseLib/Specialize.cpp
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp
Src/C_BaseLib/test/tCArena.cpp
Src/C_BaseLib/test/tFAC.cpp
Src/C_BaseLib/test/tFB.cpp
Src/C_BaseLib/test/tVisMF.cpp
Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/BoundCond.H
Src/C_BoundaryLib/FabSet.cpp
Src/C_BoundaryLib/InterpBndryData.cpp
Src/C_BoundaryLib/Mask.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp
Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp
Tests/C_BaseLib/tCArena.cpp
Tests/C_BaseLib/tFAC.cpp
Tests/C_BaseLib/tFB.cpp
Tests/C_BaseLib/tVisMF.cpp
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp
Tools/C_mk/Make.Linux
Tools/C_util/Convergence/DiffFab.cpp
Tools/C_util/Convergence/DiffPlot.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp
Tools/C_util/ViewMF/MFNorm.cpp
Tools/C_util/ViewMF/viewMFdiff.cpp

commit 06fcc22b6d996c1dfdd3669291f1ac481649db5f
Author: marc <marc>
Date:   Fri May 7 20:39:40 1999 +0000

    Add manual grid placement function in grid_places routine for
    hacking with grid distributions during regrid operation.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H

commit c1e4af58b959e032ea46f0890117461b42e3be1b
Author: lijewski <lijewski>
Date:   Fri May 7 15:36:56 1999 +0000

    We now output list of unused variables on final destructor call.

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit f36a2575ca18c7a99f800e9f9079775fe0870953
Author: car <car>
Date:   Thu May 6 16:57:28 1999 +0000

    Allows quiet_nans even when running ndebug

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp

commit 4688abe7847ff0f1cea3c650ad3a64ebe9e5b7e4
Author: lijewski <lijewski>
Date:   Thu May 6 16:31:41 1999 +0000

    Hack to work around array bounds error ...

Src/LinearSolvers/C_NodalMG/boundary.cpp

commit 00b3069252d7ecf7f465d3ccba80beed83f093b4
Author: car <car>
Date:   Tue May 4 17:59:06 1999 +0000

    assertion for intersection of src,dest boxes

Src/LinearSolvers/C_NodalMG/boundary.cpp

commit 5c5031c41e3865fabf5d9320d1dd40f21a0b8081
Author: car <car>
Date:   Tue May 4 17:58:59 1999 +0000

    ofstream truncate???

Src/LinearSolvers/C_NodalMG/proj.cpp

commit cb99647384c552276f8165d38f87758b357bf4f5
Author: lijewski <lijewski>
Date:   Tue May 4 17:54:22 1999 +0000

    periodic in x & z and refWall in y

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 5d1674c1dd8c85b68e045353b92bf9cfb46f7a7c
Author: car <car>
Date:   Mon May 3 21:32:00 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/tests/gt.jbb.1
Tests/LinearSolvers/C_NodalMG/test_grids/gt.jbb.1

commit 3de42cba2ef3b99ecc6bba972518a17d5e3ead74
Author: lijewski <lijewski>
Date:   Thu Apr 29 20:41:45 1999 +0000

    Now properly call constructor and destructor of T.

Src/C_BaseLib/BaseFab.H

commit ec5844fd3fbcbb3b6c58bdf16a80c20a9bd72d59
Author: car <car>
Date:   Wed Apr 28 15:41:52 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit ecb8d76db051a27719175d42b4eb75cf85ca693b
Author: car <car>
Date:   Wed Apr 28 00:01:26 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/tests/gt.scott.1
Tests/LinearSolvers/C_NodalMG/test_grids/gt.scott.1

commit edaf9633ab645cf1925a4a23e62d9418c9da90f1
Author: lijewski <lijewski>
Date:   Tue Apr 27 21:38:04 1999 +0000

    Removed BoxAssoc ...

Src/C_BaseLib/BoxAssoc.H
Src/C_BaseLib/BoxAssoc.cpp
Src/C_BaseLib/Make.package

commit 079fdf215fea12bc0a761edab3735ad84502811e
Author: lijewski <lijewski>
Date:   Tue Apr 27 18:24:45 1999 +0000

    Made proj_project() a static member function.
    Added hack to add back in level 0 procmap after regrid at level 0.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 5e8e17ed6b8ae07a56a7f2fce7fd61b0f3ed0a93
Author: lijewski <lijewski>
Date:   Mon Apr 26 20:09:56 1999 +0000

    Removed MaxSizeBox() -- it's now BoxList::maxSize(const IntVect&).

Src/C_AMRLib/Amr.cpp

commit 43f9d7d00312a8eb90626a8052c250f6bc779e32
Author: lijewski <lijewski>
Date:   Mon Apr 26 20:09:22 1999 +0000

    SpaceDim -> BL_SPACEDIM.

Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/Looping.H
Src/C_BaseLib/Orientation.H

commit a26186aa33080f94a8899572588a50820fe5de75
Author: lijewski <lijewski>
Date:   Mon Apr 26 20:09:11 1999 +0000

    Added maxSize(const IntVect&); maxSize(int) calls it.

Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit ba799c21ab78131594f32d878e3ad3d297a53228
Author: lijewski <lijewski>
Date:   Fri Apr 23 18:42:26 1999 +0000

    Removed the BoxList data member from FillBoxId -- wasn't used.

Src/C_BaseLib/FabArray.H

commit 2d0b11b58e271eec338d06e6a6194cb6092a4903
Author: lijewski <lijewski>
Date:   Fri Apr 23 18:06:48 1999 +0000

    Set CPP=KCC -E if have KCC

Tools/C_mk/Make.IRIX64

commit 74f27e491a5436faa36531b62da286dd4888b1c7
Author: sstanley <sstanley>
Date:   Fri Apr 23 17:47:07 1999 +0000

    Modified so that the fabs in the boundary registers are assigned values
    of BL_SAFE_BOGUS after they are generated.  This is done to be safe since
    FORT_APPLYBC in the tensor operator uses these values before checking
    the masks to see if they are needed.  So, they are used before being assigned.

Src/C_BoundaryLib/BndryRegister.cpp

commit bd93103d86fd173e44013497f7cb067b0b9be7b1
Author: marc <marc>
Date:   Thu Apr 22 17:13:19 1999 +0000

    YAAF: yet another access function.

Src/C_AMRLib/Amr.H

commit 0de72076f9137b4ab8fa20a1ead3490a6357f833
Author: sstanley <sstanley>
Date:   Tue Apr 20 23:54:55 1999 +0000

    Fixed a 3-d bug in compFlux.  yflux was passed into the fortran instead
    of zflux.

Src/LinearSolvers/C_TensorMG/DivVis.cpp

commit 8992df0435df6f1e6178f740087d92b269ba0d7a
Author: car <car>
Date:   Tue Apr 20 01:26:16 1999 +0000

    added BLassert.H, will remove Assert.H later

Src/C_BaseLib/BLassert.H
Src/C_BaseLib/Make.package

commit 20325c7d4022e75d9415521624c025f2f21783cc
Author: lijewski <lijewski>
Date:   Mon Apr 19 23:17:03 1999 +0000

    Some mods to CollectData() ...

Src/C_BaseLib/FabArray.H

commit 1d42dbf9d40c7e9625ab95b0e856df7dd2d4648a
Author: car <car>
Date:   Mon Apr 19 00:42:12 1999 +0000

    CRAY --> BL_FORT_USE_UPPERCASE, and tweaks

Src/C_BaseLib/Make.package

commit d9d68e665bd3d0240f5aa499f628321cf39c2da0
Author: lijewski <lijewski>
Date:   Fri Apr 16 19:19:48 1999 +0000

    tune ev5 -> tune host

Tools/C_mk/Make.OSF1

commit 4ff1eeda46cf7e7a7dd41f0d991cfd61786c81b4
Author: propp <propp>
Date:   Fri Apr 16 18:17:55 1999 +0000

    added -C and -u flags for debugging on mothra.
    Note that -u only produces a warning for undeclared variables

Tools/C_mk/Make.OSF1

commit 85ca26d22f03cc8b57978d88be306e0406a787a5
Author: lijewski <lijewski>
Date:   Fri Apr 16 17:38:06 1999 +0000

    Reverting out random_shuffle() stuff -- not a big win.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/DistributionMapping.cpp

commit b01f8d004df56e50ae1de10ab6cc3c727c16c5e0
Author: lijewski <lijewski>
Date:   Fri Apr 16 00:19:05 1999 +0000

    Didn't get the optimization options quite right.

Tools/C_mk/Make.T3E

commit 1e025e4371e2be1415b0eafe63fe18c9db351940
Author: lijewski <lijewski>
Date:   Fri Apr 16 00:09:23 1999 +0000

    More CXXOPTF options for backend C compiler with KCC.

Tools/C_mk/Make.T3E

commit e090803579600f003e2a664fe5d76ef765b86fa2
Author: lijewski <lijewski>
Date:   Thu Apr 15 23:29:12 1999 +0000

    Updated to make random_shuffle() stuff in knapsack work.

Src/C_AMRLib/Amr.cpp

commit 95d5d81be69a9226bc0276821a05e098543bc47e
Author: lijewski <lijewski>
Date:   Thu Apr 15 23:28:37 1999 +0000

    Added random_shuffle() stuff to knapsack.

Src/C_BaseLib/DistributionMapping.cpp

commit 92b9c89c81985a08a594d5ad7d7d81bc97a2e1ee
Author: lijewski <lijewski>
Date:   Thu Apr 15 23:27:58 1999 +0000

    Removed all virtual functions.
    Inlined some more stuff.

Src/C_BaseLib/ArithFab.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/NormedFab.H
Src/C_BaseLib/OrderedFab.H

commit 0eafc29bab97f3f11a821ad5da07edf066845be8
Author: sstanley <sstanley>
Date:   Tue Apr 13 21:37:36 1999 +0000

    Modified so that the norm of the residual get calculated over all
    components instead of just the first one.

Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp

commit e484f5347ffff410e070a7d90305ec567c003376
Author: sstanley <sstanley>
Date:   Tue Apr 13 21:36:11 1999 +0000

    Modified CGXDOTY to calculate the multicomponent dot product in 3-d the
    same as in 2-d.  Ie. sum the dot product over components.

Src/LinearSolvers/C_CellMG/CG_3D.F

commit a05253a16b584b7dbfeb3b140f30b06ce22a71ba
Author: lijewski <lijewski>
Date:   Tue Apr 13 15:28:19 1999 +0000

    Removed GNUG hack junk.

Src/C_AMRLib/BCRec.H
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/RealBox.H

commit f26b14af0bd577215f0de33be30a6bc8d321f2e1
Author: lijewski <lijewski>
Date:   Tue Apr 13 00:09:14 1999 +0000

    Modest simplification of FabArray -> FabArray copy().

Src/C_BaseLib/FabArray.H

commit 7a5280a87f917114b24516e828bbbd47f4e8325e
Author: marc <marc>
Date:   Tue Apr 13 00:09:11 1999 +0000

    Remove ProxyGeometry class, in favor of "explicit" modifier to
    Geometry ctr preventing auto-type-conversion

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp

commit 38393ab30a7e6c338df611803723c3064317c29b
Author: marc <marc>
Date:   Tue Apr 13 00:08:05 1999 +0000

    Prohibit auto-type-conversion from box to Geometry, enable removal of
    ProxyGeometry class.

Src/C_BaseLib/Geometry.H

commit bf9eaa611971b278b02a2789695b60dbf84ae54a
Author: lijewski <lijewski>
Date:   Mon Apr 12 20:31:47 1999 +0000

    Added additional assert() in ::Copy().

Src/C_BaseLib/MultiFab.cpp

commit af5ce3607e48fb58cd34024eee18b986bd990786
Author: lijewski <lijewski>
Date:   Sun Apr 11 23:31:22 1999 +0000

    Added truesize data member to make resize() really work as expected.
    Also inlined some more stuff.

Src/C_BaseLib/BaseFab.H

commit f1a0a0a6b062d1a9c9239abb3d536f3afbf7cf73
Author: lijewski <lijewski>
Date:   Sun Apr 11 23:30:47 1999 +0000

    Simplified FabArray -> FArrayBox copy().

Src/C_BaseLib/FabArray.H

commit 644073afa02f1fec0a16a4057020060b75635c59
Author: lijewski <lijewski>
Date:   Sun Apr 11 23:30:26 1999 +0000

    Inlined some more stuff.
    Removed unnecessary new of length 1 in default constructor.

Src/C_BaseLib/Array.H

commit bf699b69c917cf0db71dd286b27736d62c4a17c9
Author: lijewski <lijewski>
Date:   Sun Apr 11 23:29:58 1999 +0000

    Inlined some more stuff.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/FabSet.cpp

commit db288b8306703d3b3fbc416f634020840f188564
Author: car <car>
Date:   Thu Apr 8 21:00:56 1999 +0000

    rename hgparallel.h --> hgparallel.H

Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/hgparallel.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 527780e8bca5c89ec474605efcf42b018f47fce3
Author: lijewski <lijewski>
Date:   Thu Apr 8 20:52:11 1999 +0000

    Fixed problem with INFINITY macro being redefined on Suns.

Src/C_BaseLib/MultiFab.cpp

commit 6ca65e786c9c51d6869b6baf2e26502db7e1aff9
Author: lijewski <lijewski>
Date:   Thu Apr 8 20:22:43 1999 +0000

    Also now cache FasSet/MultiFab BoxArray intersection junk.

Src/C_BoundaryLib/FabSet.cpp

commit eff09b56dbb09fd8b0cd1fc63047a74aefda16a7
Author: marc <marc>
Date:   Thu Apr 8 17:49:12 1999 +0000

    Remove unnecessary copy-on-intersect when loading boundary data objects

Src/C_BoundaryLib/InterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp

commit 12b413887b84cbe8aa2edf4b0986388425923c93
Author: lijewski <lijewski>
Date:   Thu Apr 8 17:01:45 1999 +0000

    Fixed latent bug in plusFrom()

Src/C_BoundaryLib/FabSet.cpp

commit 22b36b2aacbf78a9d003aa52c58eea8df3aa2c61
Author: lijewski <lijewski>
Date:   Wed Apr 7 17:11:45 1999 +0000

    Devirtualized task_fab::fab() and inlined it as well.

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 6bb4a4f5cbcecb16923d3fb347220dc9beb60223
Author: lijewski <lijewski>
Date:   Tue Apr 6 18:15:59 1999 +0000

    Some cleanup.

Src/C_BaseLib/Array.H

commit 1f98466c9ae8ba32b9aff223192e41cd962117c0
Author: lijewski <lijewski>
Date:   Tue Apr 6 16:53:37 1999 +0000

    Added -M 1110 to FC

Tools/C_mk/Make.T3E

commit 9cb6cd547f00a77279f2b89a8a573f2d66b7b385
Author: lijewski <lijewski>
Date:   Tue Apr 6 16:41:18 1999 +0000

    Ignore additional warning 7212

Tools/C_mk/Make.T3E

commit b8f897719a633e2c3d7556901fa245ba1ef7ccb3
Author: car <car>
Date:   Mon Apr 5 17:39:20 1999 +0000

    BL_AIX --> BL_FORT_USE_LOWERCASE, where appropriate.
    Makefile tweaks in pAmrvis and DataServices.

Src/C_AMRLib/FLUXREG_F.H
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/MAKESLICE_F.H
Src/C_AMRLib/PROB_AMR_F.H
Src/C_BaseLib/COORDSYS_F.H
Src/LinearSolvers/C_NodalMG/GNUmakefile
Tools/C_mk/Make.AIX

commit 0c8dab8d914958b768c43cb0406cb66be51d9b9a
Author: car <car>
Date:   Mon Apr 5 16:49:25 1999 +0000

    fix non-inplace compile

Src/LinearSolvers/C_TensorMG/Make.package

commit 10e767836e9ad9b154c2589266252229a2117d5e
Author: sstanley <sstanley>
Date:   Fri Apr 2 20:47:23 1999 +0000

    Added a -r in one of the $(RM) lines under clean: to allow
    removing a directory.  Thsi didn't work properly on the T3E.

Tools/C_mk/Make.rules

commit bba81c1978d70368410995e2523548579377389f
Author: lijewski <lijewski>
Date:   Thu Apr 1 23:52:55 1999 +0000

    A special FORTPREP for T3E ...

Tools/C_mk/Make.T3E

commit f0eee2d211fa6c2e95401863b01c2842530489cc
Author: lijewski <lijewski>
Date:   Thu Apr 1 22:31:01 1999 +0000

    Fixed bug in FabArray::copy(FabArray).
    I had a improperly nested parallel loop :-(

Src/C_BaseLib/FabArray.H

commit 71baf54fef82c8fe1af30e7659f66ea276ec41c5
Author: car <car>
Date:   Thu Apr 1 21:43:10 1999 +0000

    harmless, I think, makefile thrashing

Src/C_AMRLib/Make.package
Src/LinearSolvers/C_CellMG/Make.package
Src/LinearSolvers/C_TensorMG/Make.package

commit a3d7d7de5a31be320086930352b2aa29d206d382
Author: car <car>
Date:   Thu Apr 1 21:42:49 1999 +0000

    FORT_FLUX added

Src/LinearSolvers/C_CellMG/LP_F.H

commit 501af9c686f2c173567d565b56d48183f57e4597
Author: car <car>
Date:   Thu Apr 1 16:57:48 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit f777586315e842ab6676bb11416fb03a7d72d884
Author: car <car>
Date:   Wed Mar 31 22:52:27 1999 +0000

    Linux updates

Src/C_AMRLib/GNUmakefile
Src/C_BaseLib/GNUmakefile
Src/C_BoundaryLib/GNUmakefile
Src/LinearSolvers/C_CellMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_TensorMG/GNUmakefile

commit 0d23d065c1377ed9cdb405834df89151dc2666ae
Author: car <car>
Date:   Wed Mar 31 18:19:37 1999 +0000

    linux changes

Src/C_AMRLib/GNUmakefile
Src/C_BaseLib/GNUmakefile
Src/C_BoundaryLib/GNUmakefile
Src/LinearSolvers/C_CellMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_TensorMG/GNUmakefile
Tools/C_mk/Make.Linux

commit cb2ac2e025bfbf2a52674de8c0c75aa21eba2bbf
Author: lijewski <lijewski>
Date:   Wed Mar 31 18:19:03 1999 +0000

    Turn off message warning 1135

Tools/C_mk/Make.T3E

commit 0237ef895d3fbe6d4cf55e9e150dd44087aabd3d
Author: lijewski <lijewski>
Date:   Wed Mar 31 17:04:48 1999 +0000

    Now also call FabSet::FlushCache() to clear some cached CollectData() stuff.

Src/C_AMRLib/Amr.cpp

commit 3bc61b18687238f500eaee7fc77beafcb66d4b57
Author: lijewski <lijewski>
Date:   Wed Mar 31 17:04:17 1999 +0000

    FabSets now cache some CollectData() stuff.
    Now use CommDataCache for the cache in question.

Src/C_BaseLib/Geometry.H
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 46d5a48aa7c8fe87f32f9e69046c92748ee1f579
Author: lijewski <lijewski>
Date:   Wed Mar 31 17:03:47 1999 +0000

    Fixed deadlock I introduced in CollectData().

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp

commit a8ba1bb8882b7ad1dde8f41abc4b327e4382a6c2
Author: car <car>
Date:   Tue Mar 30 00:54:06 1999 +0000

    New defines for linux

Src/C_BaseLib/FPC.cpp

commit 486c722df8d14eaee3058c16e2dfcb34a9fd78bd
Author: car <car>
Date:   Tue Mar 30 00:49:50 1999 +0000

    A first approximation to a Make.Linux

Tools/C_mk/Make.Linux

commit 6f0568c5d0d85a5588d8a5ff766c8c038346ee5e
Author: lijewski <lijewski>
Date:   Mon Mar 29 23:26:46 1999 +0000

    Removed OneFilePerFab option.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 14a505e1260fa1cbdddba0ea343d23ed32dacf0e
Author: lijewski <lijewski>
Date:   Mon Mar 29 22:27:57 1999 +0000

    Turn off message 191 when using KCC on T3E.

Tools/C_mk/Make.T3E

commit a2550c164b7aea90a79f502e6910fb065b4a9e34
Author: lijewski <lijewski>
Date:   Mon Mar 29 19:27:52 1999 +0000

    Yet another bug fix to CollectNumPts().

Src/C_BaseLib/RunStats.cpp

commit 60a005eb61e0dfe001a8a3421c6d5de18369eb01
Author: lijewski <lijewski>
Date:   Sat Mar 27 01:00:58 1999 +0000

    Mods to cache some CommData stuff in CollectData().

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit c7e242c3e2779f604deb117df3504b0f997149f0
Author: lijewski <lijewski>
Date:   Sat Mar 27 01:00:23 1999 +0000

    Added operator<<() for CommData.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 13b3f55ba8259c66f953c9a13b1aa521058c3f97
Author: lijewski <lijewski>
Date:   Fri Mar 26 19:19:34 1999 +0000

    Added operator==() and operator!=() for CommData.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit a4112e7e0d04c5fc21a74e32ca48be20e0f3530f
Author: marc <marc>
Date:   Mon Mar 22 21:31:27 1999 +0000

    Minor fixups to support ngrow option.

Tools/C_util/ViewMF/viewMF.cpp

commit 35666fd20c85fee89cdad04d62c3eda4bf45d51a
Author: marc <marc>
Date:   Mon Mar 22 21:19:02 1999 +0000

    Add a couple options, and make mfab ins manditory

Tools/C_util/ViewMF/viewMF.cpp
Tools/C_util/ViewMF/viewMFdiff.cpp

commit 8326bac86e8cf3a0b6d4312d81e7a4f78ae6a7c8
Author: lijewski <lijewski>
Date:   Mon Mar 22 15:57:48 1999 +0000

    Arguments to clear(int,int) in declaration & definition were messed up.

Src/C_BaseLib/VisMF.H

commit 76b4140025bd786c0fcc806a64d5590d02a60d52
Author: marc <marc>
Date:   Fri Mar 19 23:08:46 1999 +0000

    Add support for diffing MultiFabs having different box arrays

Tools/C_util/ViewMF/MFNorm.H
Tools/C_util/ViewMF/MFNorm.cpp
Tools/C_util/ViewMF/viewMFdiff.cpp

commit 79a72542d9d649728af3f25f85cc2e995e8c8a2d
Author: lijewski <lijewski>
Date:   Fri Mar 19 17:57:35 1999 +0000

    The per-processor allocation of FABs wasn't being output.

Src/C_BaseLib/RunStats.cpp

commit e6a44ef88640e5420494c82bdc32a142c5c52094
Author: lijewski <lijewski>
Date:   Thu Mar 18 22:12:01 1999 +0000

    Restored clear(int) and remove(int) for Vince.

Src/C_BaseLib/FabArray.H

commit 1af6289f6e60adc313578e7877fb883bd6c83a67
Author: lijewski <lijewski>
Date:   Thu Mar 18 17:05:35 1999 +0000

    Added dt_min to checkpoint files, maintaining upward compatibility.

Src/C_AMRLib/Amr.cpp

commit 59c804e8c811b051c4d5a7c09b115cbf401b0e1f
Author: lijewski <lijewski>
Date:   Thu Mar 18 00:13:01 1999 +0000

    Spiffed up message coming from coarsestSmooth().

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 473f1b528ffb424b358fdfecc0d81d73407043f2
Author: lijewski <lijewski>
Date:   Wed Mar 17 21:58:46 1999 +0000

    Added init() to consolidate copy ctor and assignment operator.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp

commit eef7d07ce1799b88524fc642a1db6958b4e773f6
Author: lijewski <lijewski>
Date:   Wed Mar 17 21:58:13 1999 +0000

    Added init() function to consolidate copy constructor and assignment operator.

Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit db41d569bed49454540c21eed51423ca0af235dd
Author: lijewski <lijewski>
Date:   Wed Mar 17 21:57:45 1999 +0000

    Removed a couple dangerous member functions:
    
      clear(int)
      removeFab(int)
      clearUnmanaged()

Src/C_BaseLib/FabArray.H

commit 3eef76804438f839b148de4dbd20eaff5aed6250
Author: lijewski <lijewski>
Date:   Wed Mar 17 21:49:13 1999 +0000

    Fixed bug in dumpReport() regarding wall clock time.

Src/C_BaseLib/RunStats.cpp

commit 5d4675d6a3eac1013de15d206b00ec7f8e76845b
Author: lijewski <lijewski>
Date:   Fri Mar 12 21:17:12 1999 +0000

    Removed limits on cache size.

Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit 1e1b3f0e5bbf93e546ca01fe1263399e6d304462
Author: sstanley <sstanley>
Date:   Fri Mar 12 20:09:07 1999 +0000

    The makefiles now point to the versions of these files which are
    stored elsewhere.  DataSetClient is gotten from pAmrvis/.

Tools/C_util/ArrayView.H
Tools/C_util/Convergence/Add.cpp
Tools/C_util/Convergence/ComputeAmrDataNorms.cpp
Tools/C_util/Convergence/DiffFab.cpp
Tools/C_util/Convergence/DiffPlot.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp
Tools/C_util/DatasetClient.H
Tools/C_util/DatasetClient.cpp

commit 13395408a55bff603b19a1d4b580394cefa40f16
Author: sstanley <sstanley>
Date:   Fri Mar 12 18:55:48 1999 +0000

    Modified so that the compile is done against the libraries.
    Added the seperate routines viewMF.cpp viewMFdiff.cpp which have
    been extracted from main.cpp and view and diff multifab files.
    viewMFdiff.cpp has the option for the validbox only or defaults to the
    fabbox for comparisons.

Tools/C_util/ViewMF/GNUmakefile
Tools/C_util/ViewMF/MFNorm.H
Tools/C_util/ViewMF/MFNorm.cpp
Tools/C_util/ViewMF/Make.package
Tools/C_util/ViewMF/main.cpp
Tools/C_util/ViewMF/viewMF.cpp
Tools/C_util/ViewMF/viewMFdiff.cpp

commit ff4e5a927a0da1666bb2d119b3abdf8367120ab3
Author: lijewski <lijewski>
Date:   Fri Mar 12 03:27:07 1999 +0000

    Tab cleanup.

Src/C_BaseLib/test/tFB.cpp
Tests/C_BaseLib/tFB.cpp

commit b7627e94ead81e6f642b19fa8c9a1bdf22cbe194
Author: lijewski <lijewski>
Date:   Fri Mar 12 02:55:43 1999 +0000

    Beefed up the test case a bit.

Src/C_BaseLib/test/tFB.cpp
Tests/C_BaseLib/tFB.cpp

commit 55eb0633c192c00c85d38ffd71bf75556b579208
Author: lijewski <lijewski>
Date:   Fri Mar 12 02:55:26 1999 +0000

    Some cleanup and simplification.

Src/C_BaseLib/MultiFab.cpp

commit 7a0cd5ccb6e28930fc722253a78ee3fe9b83ce15
Author: lijewski <lijewski>
Date:   Fri Mar 12 01:09:24 1999 +0000

    Mod for T3E.

Src/C_BaseLib/Utility.cpp

commit 37d5a9d4448e9934c5b783f523079451a062817c
Author: lijewski <lijewski>
Date:   Thu Mar 11 17:56:58 1999 +0000

    Added Concatenate().

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit c7aa4bbb4e00c0ece0f7ddfa0b56d374e599be19
Author: lijewski <lijewski>
Date:   Thu Mar 11 17:56:44 1999 +0000

    Merged in Utility::Concatenate() and some cleanup.

Src/C_AMRLib/Amr.cpp

commit 4b02a6f9d071effb0df01ea125737c0e07750028
Author: marc <marc>
Date:   Thu Mar 11 17:48:39 1999 +0000

    Make initial dt something so that old and new time are always different

Src/C_AMRLib/Amr.cpp

commit f2f771be47b5054a21ca8e1398b4eba738f10591
Author: marc <marc>
Date:   Thu Mar 11 17:48:07 1999 +0000

    Add def for virtual function used by FillPatch

Src/C_AMRLib/AmrLevel.H

commit 7e6195bd6f074c3c5f9ce7ebdd9e99826720daad
Author: marc <marc>
Date:   Wed Mar 10 16:54:15 1999 +0000

    Add a virtual called to intercept FillPatch allowing for application-
    specific overwrite of FillPatched boundary data.  Defaults to no-op.

Src/C_AMRLib/AmrLevel.cpp

commit c1bbb1c62801664a9cbfd8fb8f8a6fe51f47eecc
Author: lijewski <lijewski>
Date:   Wed Mar 10 16:33:31 1999 +0000

    Added flag to ignore double precision constants on T3E.

Src/LinearSolvers/C_TensorMG/GNUmakefile

commit 0f798fdb80af752ca9d2172cfa41f463d68a9d91
Author: almgren <almgren>
Date:   Fri Mar 5 23:18:37 1999 +0000

    Add AmrLevel::okToRegrid() flag which asks whether this level should
    go ahead and allow the regridding tests.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit fafad54941a2e46c52f0834a5e1a49dc1808106b
Author: lijewski <lijewski>
Date:   Thu Mar 4 22:18:37 1999 +0000

    Added static void Copy().

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit d91015f4c7c8dc327b3e1b2e762b1f1a43e39078
Author: car <car>
Date:   Thu Feb 25 17:35:35 1999 +0000

    re-name again, BOX->Box REAL->Real

Src/C_BaseLib/CoordSys.cpp

commit f446015dd715356d483da0b6f1e6427c90193ac3
Author: sstanley <sstanley>
Date:   Wed Feb 24 23:31:20 1999 +0000

    Added utilities for convergence studies.

Tools/C_util/Convergence/AVGDOWN_2D.F
Tools/C_util/Convergence/AVGDOWN_F.H
Tools/C_util/Convergence/Add.cpp
Tools/C_util/Convergence/ComputeAmrDataNorms.H
Tools/C_util/Convergence/ComputeAmrDataNorms.cpp
Tools/C_util/Convergence/DiffFab.cpp
Tools/C_util/Convergence/DiffPlot.cpp
Tools/C_util/Convergence/DiffSameGrid.cpp
Tools/C_util/Convergence/DiffUniform.cpp
Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Convergence/GNUmakefile.temp
Tools/C_util/Convergence/Make.package
Tools/C_util/Convergence/Make.package.SAVE
Tools/C_util/Convergence/Make.package.temp
Tools/C_util/Convergence/PltFileNorm.cpp
Tools/C_util/Convergence/PltFileScalConvRate.cpp

commit 0ac0c4402a28ba3c912146be02ffa2fa40443873
Author: car <car>
Date:   Wed Feb 24 18:36:24 1999 +0000

    Changed the way holy_grail_amr_multigrid constructor is invoked.
    Previously, three bool's were used to select either full, cross, or
    terrain stencils.  Now an enum is used: holy_grail_amr_multigrid::stencil,
    which has three values (terrain, cross, full).
    There still is no full stencil support.

Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 434c219a956bbeed0f5bcd504bbccc2956bff50a
Author: lijewski <lijewski>
Date:   Wed Feb 24 16:50:31 1999 +0000

    Simplified the FabSet interface.

Src/C_AMRLib/FluxRegister.cpp
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit f92167986ffec3642d2bb6835e3796dc02fa43f8
Author: propp <propp>
Date:   Wed Feb 24 01:56:04 1999 +0000

    fixed some 2D to 3D bugs in BndryData
    added bcComponentsNeeded function to MCLinOp

Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 6378d7d0bb8fa741b3b0e0fe78d33fbf771b3805
Author: lijewski <lijewski>
Date:   Wed Feb 24 01:03:47 1999 +0000

    Fixed some bugs and added FabSet::copyFrom(FabSet).

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit cb2c2d6b08f61e55a6c76ae20537975f0b3c57a9
Author: sstanley <sstanley>
Date:   Tue Feb 23 00:34:46 1999 +0000

    Changed sign on the fluxes calculated in DV_2D.F and DV_3D2.F to be
    consistent with this in the scalar viscous terms.  Added the new notebook
    files for mathematica.  Should use the new, but I left the old ones for
    safety sake.

Src/LinearSolvers/C_TensorMG/DV_2D.F
Src/LinearSolvers/C_TensorMG/DV_2D.mF
Src/LinearSolvers/C_TensorMG/DV_3D1.F
Src/LinearSolvers/C_TensorMG/DV_3D2.F
Src/LinearSolvers/C_TensorMG/DV_3D2.mF
Src/LinearSolvers/C_TensorMG/DV_3D3.F
Src/LinearSolvers/C_TensorMG/DV_3D4.F
Src/LinearSolvers/C_TensorMG/visc2d.nb
Src/LinearSolvers/C_TensorMG/visc3d.nb

commit df12a443c2db434d76737e4ca26a39574dc96181
Author: lijewski <lijewski>
Date:   Wed Feb 17 21:44:17 1999 +0000

    Added Lp.alternateApplyBC flag.

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit a2db8d81c8c700326ce149ac39311912f60cd801
Author: lijewski <lijewski>
Date:   Wed Feb 17 00:10:35 1999 +0000

    Explicitly turn off exceptions.

Tools/C_mk/Make.T3E

commit d521c406843ce5df6278c0fab3499c4936ebe177
Author: lijewski <lijewski>
Date:   Fri Feb 12 00:07:05 1999 +0000

    +K2 -> +K3 when COMP=KCC

Tools/C_mk/Make.T3E

commit 004e7adf51d487a435f2be8e1d6466701a70058f
Author: marc <marc>
Date:   Thu Feb 11 18:07:23 1999 +0000

    Modernize driver

Src/LinearSolvers/C_TensorMG/Test/GNUmakefile
Src/LinearSolvers/C_TensorMG/Test/testVI.cpp
Tests/LinearSolvers/C_TensorMG/GNUmakefile
Tests/LinearSolvers/C_TensorMG/testVI.cpp

commit 740410da8592ee4d90be260d7e56b7c3cde17f3b
Author: marc <marc>
Date:   Thu Feb 11 18:06:59 1999 +0000

    Remove area multiplies in compFlux fortran.  Extensive fluxes obtained
    by setting transport coefficient to include local areas. Fix up Mma
    and fortran manually.

Src/LinearSolvers/C_TensorMG/DV_2D.F
Src/LinearSolvers/C_TensorMG/DV_2D.mF
Src/LinearSolvers/C_TensorMG/DV_3D2.F
Src/LinearSolvers/C_TensorMG/DV_3D2.mF

commit d451a6af58902b0625c5fcb2f98122a8a85ea95c
Author: car <car>
Date:   Thu Feb 11 17:07:01 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 8b995402949699319c803bd159999a73d9c10889
Author: lijewski <lijewski>
Date:   Wed Feb 10 21:09:44 1999 +0000

    Boolean.H has been removed from Parallel BoxLib.

Src/C_BaseLib/Array.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Boolean.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxAssoc.H
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/CArena.H
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/List.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/Utility.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_TensorMG/DivVis.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H

commit 50e17cf12afb342f9b1423d693a8ab815058787b
Author: lijewski <lijewski>
Date:   Tue Feb 9 21:21:45 1999 +0000

    Little cleanup suggested by Bill.

Src/C_BaseLib/Boolean.H

commit 916f33fb4a8febcc4ad315ad872bb1e812fa2f7b
Author: lijewski <lijewski>
Date:   Mon Feb 8 17:49:37 1999 +0000

    From Matt Bettencourt.

Tools/C_mk/Make.IRIX64

commit 972434d151f8add9b8fa09a904ccea11c4467a06
Author: lijewski <lijewski>
Date:   Fri Feb 5 18:56:06 1999 +0000

    Some cleanup.
    Elided some do-while loops in Iterators when !BL_USE_MPI.

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H

commit 1a7029a1a742fe884ec675b01886c5041a178b14
Author: lijewski <lijewski>
Date:   Fri Feb 5 18:54:29 1999 +0000

    Forgot to comment out 3rd stuff.

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 084636948fc33b0de97b6c16e4fef5c5cd784cd8
Author: car <car>
Date:   Wed Feb 3 23:31:36 1999 +0000

    backed out CONSTANT REAL_T

Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit 5a8b703e80f9ee18a2ab171e9af9860c7132f117
Author: lijewski <lijewski>
Date:   Wed Feb 3 22:50:28 1999 +0000

    Added -M 1110 to f90 options on T3E to quiet warnings re: double precision.

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 0e1f3076f831cdfe887072425b555a9dd932aa2d
Author: lijewski <lijewski>
Date:   Wed Feb 3 21:56:58 1999 +0000

    Fixed typo.

Src/C_BaseLib/RunStats.cpp

commit 7d080100a5c841430f0fb60e3f7501d0e18d9128
Author: lijewski <lijewski>
Date:   Wed Feb 3 21:55:32 1999 +0000

    Made some RunStats objects static.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp

commit 30cabfd8aeedfecd59326de6259215e71fd2060b
Author: lijewski <lijewski>
Date:   Wed Feb 3 21:55:15 1999 +0000

    *** empty log message ***

Src/C_BaseLib/RunStats.cpp

commit ce66b928f7f69b3e81630280ac60cff4a743c34d
Author: lijewski <lijewski>
Date:   Wed Feb 3 21:48:51 1999 +0000

    Removed RunStats junk.

Src/C_BaseLib/CArena.cpp

commit 4183be4bfe3836ab27eae062e5d836d1f47bdf50
Author: lijewski <lijewski>
Date:   Wed Feb 3 19:29:57 1999 +0000

    Fixed bug in CollectNumPts().

Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp

commit f24c20db3b263358f997bc84c3e369783dfb16b6
Author: lijewski <lijewski>
Date:   Wed Feb 3 19:29:26 1999 +0000

    Cleaned up checkPoint() a bit.

Src/C_AMRLib/Amr.cpp

commit e7fcda0c6743e0c09cf85f049cf6c39a87a40be1
Author: lijewski <lijewski>
Date:   Wed Feb 3 00:39:25 1999 +0000

    Needed to include <CONSTANTS.H>

Src/LinearSolvers/C_CellMG/LO_2D.F
Src/LinearSolvers/C_CellMG/MG_2D.F

commit a96b009f12c4cdb1807a3ac25309bd31feeadbb9
Author: lijewski <lijewski>
Date:   Wed Feb 3 00:16:31 1999 +0000

    Replaced some fp constants with macros.

Src/C_BaseLib/COORDSYS_2D.F
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/LO_2D.F
Src/LinearSolvers/C_CellMG/MG_2D.F

commit b2464e778ca239dd423cf85d51d77e81ff4b7fa0
Author: lijewski <lijewski>
Date:   Tue Feb 2 23:36:05 1999 +0000

    Removed FORT_SCALADDTO

Src/C_AMRLib/FLUXREG_2D.F

commit e69122613b0e5c3d73e92e29ddd3f3eaa3b1c634
Author: car <car>
Date:   Tue Feb 2 23:24:41 1999 +0000

    d comment line!

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 581078fe1325a52995f257fcb61d18f0658d30a9
Author: car <car>
Date:   Tue Feb 2 17:14:57 1999 +0000

    no 2d rz

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/interface.H

commit fcfa49321742f32c6cbb83989b89b6620e67101e
Author: lijewski <lijewski>
Date:   Tue Feb 2 00:24:03 1999 +0000

    Substituted BL_SPACEDIM for some numbers.

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit b2aeb40f498049cef2ed03adb74bef60a45e1b24
Author: car <car>
Date:   Mon Feb 1 18:17:35 1999 +0000

    Make task_proxy a friend of task so that it can access protected members.
    Is this a bug in MSVC5?

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 3e34b3a6d19c2c88db708a9730ff2be6674b860c
Author: lijewski <lijewski>
Date:   Sat Jan 30 17:57:00 1999 +0000

    Simplified task_proxy.  Cuts way down on heap allocations.

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 7077a495d5a0656a47f492078238513f48879f69
Author: lijewski <lijewski>
Date:   Fri Jan 29 23:20:25 1999 +0000

    Removed CVS ID string.

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 026ef02ce4733529e150e4d2f8d41279e38151c5
Author: lijewski <lijewski>
Date:   Fri Jan 29 23:19:50 1999 +0000

    Yet more performance enhancements.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit e0704bcd5874dbbffdf115dbf2fe9950962feaf7
Author: car <car>
Date:   Fri Jan 29 20:13:52 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 3a34e8c12f28ed0337ebda55d71a2ca2b8b62e4f
Author: lijewski <lijewski>
Date:   Fri Jan 29 19:23:57 1999 +0000

    Some cleanup and copyright macro insertion.

Src/LinearSolvers/C_NodalMG/RegType.H
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.H
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit ab39e610317b72b9aeed83a052f63a6535ccbd9a
Author: car <car>
Date:   Fri Jan 29 19:09:56 1999 +0000

    minor changes to quit warnings

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit ef0b6774b63733dd06b1c671352b4f8e7bef506e
Author: car <car>
Date:   Fri Jan 29 18:33:46 1999 +0000

    fixes for 2D

Src/C_BaseLib/pBoxLib_2.dsp
Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit a9da2412907cfe24ee7096ba7bc52ab54377d3d1
Author: car <car>
Date:   Fri Jan 29 17:50:10 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit d1f37dda3bd7e88d0240036ad3370052bc2908be
Author: car <car>
Date:   Fri Jan 29 00:20:27 1999 +0000

    more 2d

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 2a869db5b8fc7ac629a0a32384e93f0a6f6979b9
Author: car <car>
Date:   Thu Jan 28 23:36:13 1999 +0000

    changes for 2D

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit a92eb85e02f1bbcdcff293accb3baf7d27023264
Author: lijewski <lijewski>
Date:   Thu Jan 28 21:00:49 1999 +0000

    More performance enhancements.

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 35b6114e0e7403d287c7641a5e751f051ab683f3
Author: lijewski <lijewski>
Date:   Thu Jan 28 18:50:38 1999 +0000

    More performance enhancements.

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 0a80acacd0b15a09ddf5ad15f74b256aedba1bcc
Author: lijewski <lijewski>
Date:   Thu Jan 28 16:58:28 1999 +0000

    More performance enhancements.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit a2caca1104c77e584d63468711ebd9912e6317bb
Author: lijewski <lijewski>
Date:   Wed Jan 27 17:35:51 1999 +0000

    Some performance enhancements.

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit cac50d225dab90e11a84b083d0456d0041167bc9
Author: marc <marc>
Date:   Fri Jan 22 21:34:16 1999 +0000

    Prettier still...

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 59fd9eb94d1b91b4ce4d0e6fe6441a2fa57f856f
Author: marc <marc>
Date:   Fri Jan 22 21:24:41 1999 +0000

    Make verbose out a little prettier...nothing significant here...

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 45c8fb4e8cc354d58bf6982eaaeddfb6cfe03b2f
Author: vince <vince>
Date:   Fri Jan 22 21:05:07 1999 +0000

    Deleted an assertion in copy(...).  It was causing problems in parallel.
    The assertion is checked later, so it was also redundant.

Src/C_BaseLib/FabArray.H

commit 6d03c1acf63a73e56524fab60d93185c500960f1
Author: lijewski <lijewski>
Date:   Thu Jan 21 22:03:14 1999 +0000

    FillCoarsePatch() was still doing some ghost cells when didn't need to.

Src/C_AMRLib/AmrLevel.cpp

commit 84dbec77527199db3971e8714c4314a6444ffc0a
Author: lijewski <lijewski>
Date:   Thu Jan 21 20:27:05 1999 +0000

    Fixed bug in and added argument to FillCoarsePatch().

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 2a92076e5afd769f02171c3cb1bdcdb574108cc9
Author: lijewski <lijewski>
Date:   Wed Jan 20 19:24:00 1999 +0000

    Must do physical bndry conditions after periodic junk in isValid().

Src/C_AMRLib/AmrLevel.cpp

commit 9785d598ea532c6d58092d9d46d177865213ab33
Author: lijewski <lijewski>
Date:   Wed Jan 20 04:41:36 1999 +0000

    Fixed bug in FillPeriodicBoundary().

Src/C_BaseLib/Geometry.cpp

commit cee40cba249c2a71d5b2d9c324c1deb5b03b9cd2
Author: lijewski <lijewski>
Date:   Fri Jan 15 21:44:22 1999 +0000

    Dealt with periodic nodal quantities in FillPatchIterator::Initialize().

Src/C_AMRLib/AmrLevel.cpp

commit 3a48c6de77ca4de91d3f68dbc589ea1d18000105
Author: car <car>
Date:   Thu Jan 14 22:48:47 1999 +0000

    Really old comments

Src/LinearSolvers/C_NodalMG/README
Src/LinearSolvers/C_NodalMG/Rewrite

commit 61e5972d15c270b70b80db0b7a86b455265b1a28
Author: lijewski <lijewski>
Date:   Wed Jan 13 04:14:19 1999 +0000

    Removed the hash junk.  Simplified things a bit.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 1d7f977d956650b1192452425f3b8e28a4850055
Author: lijewski <lijewski>
Date:   Tue Jan 12 19:00:18 1999 +0000

    Added carena RunStats for CArena::alloc() and CArena::free()

Src/C_BaseLib/CArena.cpp

commit 83a84b6a60d7371aeda7dde9dc76d44f8062e391
Author: lijewski <lijewski>
Date:   Tue Jan 12 17:56:46 1999 +0000

    Added RunStats for regrid.

Src/C_AMRLib/Amr.cpp

commit c9d4d68c2f7951b81a92c99845cf5d20d530944c
Author: lijewski <lijewski>
Date:   Wed Jan 6 21:27:58 1999 +0000

    Changing how the DatasetClient stuff is wired into the code.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/DatasetClient.H
Src/C_AMRLib/GNUmakefile
Src/C_AMRLib/Make.package

commit dee30e43182f75f22bd93d45a9821c06133ebf28
Author: lijewski <lijewski>
Date:   Wed Jan 6 20:06:56 1999 +0000

    Some cleanup.  Always compile in TagBox stuff.

Src/C_AMRLib/DatasetClient.cpp

commit 4b9c0fc420af4ba0e7079cd023b2b7eca6956226
Author: marc <marc>
Date:   Wed Jan 6 00:32:37 1999 +0000

    Update makefile stuff, and member args for IBD, also make test
    runnable in 2D.

Src/LinearSolvers/C_TensorMG/Test/GNUmakefile
Src/LinearSolvers/C_TensorMG/Test/Make.package
Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.H
Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp
Src/LinearSolvers/C_TensorMG/Test/main_3D.F
Src/LinearSolvers/C_TensorMG/Test/testVI.cpp
Tests/LinearSolvers/C_TensorMG/GNUmakefile
Tests/LinearSolvers/C_TensorMG/Make.package
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp
Tests/LinearSolvers/C_TensorMG/main_3D.F
Tests/LinearSolvers/C_TensorMG/testVI.cpp

commit 3009caf1c31ab3ca3ca8dbb902f5ee85611f9ca2
Author: marc <marc>
Date:   Wed Jan 6 00:31:42 1999 +0000

    Make this stuff look more like the mglib stuff...nothing really new here...

Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp

commit 210192197f86ca539cc55852dfb600344e7b5727
Author: marc <marc>
Date:   Wed Jan 6 00:30:52 1999 +0000

    Fix bug to shift back mask box after periodic crud.

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 93e3b4cd20a53d18952a1f25375bb2312d4bdae8
Author: lijewski <lijewski>
Date:   Wed Jan 6 00:15:06 1999 +0000

    Had to move header file so FArrayBox was properly declared.

Src/C_AMRLib/DatasetClient.cpp

commit 78c05aeae0471fa192049ada450d1aa3ba1a9e32
Author: lijewski <lijewski>
Date:   Mon Jan 4 21:31:48 1999 +0000

    Just some cleanup -- must have been bored over holidays.

Src/LinearSolvers/C_TensorMG/DivVis.H
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit 632b34039889991598c67c19922335bb7589c443
Author: marc <marc>
Date:   Mon Jan 4 19:01:07 1999 +0000

    Add include for constants.

Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F

commit 3accef59ea611754a4f2c3944788f9a85df0c185
Author: marc <marc>
Date:   Mon Jan 4 18:28:45 1999 +0000

    Add code for pure fort files (.f)

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit c19c8d16294636e90b4175cd0d3a867eff895f30
Author: marc <marc>
Date:   Mon Jan 4 18:27:14 1999 +0000

    Add target

Src/C_AMRLib/GNUmakefile

commit 0b1dc3e9377b540866f192310e9684190c03df6a
Author: marc <marc>
Date:   Mon Jan 4 18:26:32 1999 +0000

    Add arg for lib make

Src/LinearSolvers/C_TensorMG/GNUmakefile

commit 7e79e820de634cb70a3c87af4a54012e2d43cba6
Author: marc <marc>
Date:   Mon Jan 4 18:12:08 1999 +0000

    Make it better

Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 3124202b504746b1d3dc84a45caa76b757627386
Author: marc <marc>
Date:   Mon Jan 4 18:11:45 1999 +0000

    Add code for flux compute member, similar to that in tensor stuff.

Src/LinearSolvers/C_CellMG/LP_2D.F
Src/LinearSolvers/C_CellMG/LP_3D.F
Src/LinearSolvers/C_CellMG/LP_F.H
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H

commit 6f469852056b84fd9f044ba86b9f84cf45c459fe
Author: marc <marc>
Date:   Mon Jan 4 18:11:14 1999 +0000

    Add multicomponent stuff.  Make first stab at output function for ||.

Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp

commit ff8114f5d4e1351e643b128e538996b2dfe7bd55
Author: marc <marc>
Date:   Mon Jan 4 18:10:22 1999 +0000

    Increase verbose output, for mg add code for mg.v>2 to dump mg levels

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 0b9d62de22573c6c97fe08f3b4d82344bdba5c9c
Author: marc <marc>
Date:   Mon Jan 4 18:09:36 1999 +0000

    Add multi-component stuff.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp

commit 51808d173ea770febf25e584e26a57a2e984f6ea
Author: marc <marc>
Date:   Mon Jan 4 18:09:00 1999 +0000

    Add flux compute member function, similar to that in the tensor stuff.

Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/ABec_F.H

commit d971f96dba5c8dea3272b83481440602f315bf42
Author: lijewski <lijewski>
Date:   Fri Dec 25 18:58:09 1998 +0000

    Minimized more heap allocations in FillPatchIterator.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit eb5c068ea916fdf4859d6e37359b5f9702fd9e09
Author: lijewski <lijewski>
Date:   Wed Dec 23 23:14:07 1998 +0000

    FillPatch now does periodic correctly.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 11815f426348a68ca4aba76a48ae586d73ab30f4
Author: almgren <almgren>
Date:   Tue Dec 22 22:42:56 1998 +0000

    OOPS - pc_domain was a coarsened domain, what I really wanted was geom[levf].Domain()

Src/C_AMRLib/Amr.cpp

commit a8e9818bf2cbc5091a217dcc924310c1c1f4580f
Author: lijewski <lijewski>
Date:   Fri Dec 18 16:47:52 1998 +0000

    Added catenate().

Src/C_BaseLib/BoxList.H

commit 0f64e6b7d2ad491a54bb4e3b729b29be1d422e07
Author: wyc <wyc>
Date:   Fri Dec 18 00:40:41 1998 +0000

    Its miraculous that this bug never was noticed before.  ncx and ncy were
    declared as logicals, despinte being used as integers......

Src/C_AMRLib/INTERP_2D.F

commit a1127c24bf3824da5fdef07b4fc3c2be9f7ad184
Author: lijewski <lijewski>
Date:   Wed Dec 16 22:27:39 1998 +0000

    Fixed memory leak.

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit ee7bcfadef03ca09aa5d9b16853fd4b9cf3e144e
Author: car <car>
Date:   Wed Dec 16 20:51:00 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/machinefile.mpi

commit 2369ae8e9ab66d2127cd12b8521ee0c8ee0ed3c3
Author: car <car>
Date:   Wed Dec 16 18:54:14 1998 +0000

    a new bad grid set

Src/LinearSolvers/C_NodalMG/tests/gt.inputs.3d.spin.grids
Tests/LinearSolvers/C_NodalMG/test_grids/gt.inputs.3d.spin.grids

commit 8f7ea7db942e0f155fe0630b3a54b959b15f9022
Author: car <car>
Date:   Wed Dec 16 18:42:53 1998 +0000

    test infrastructure

Src/LinearSolvers/C_NodalMG/inputs
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 38977095bcbf3493bd3e08cca116bd023f4ca16a
Author: car <car>
Date:   Wed Dec 16 17:51:17 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit e0374a8b0987208f6b700d92d9c76daf801374fd
Author: car <car>
Date:   Wed Dec 16 17:33:42 1998 +0000

    fix for task_copy::depends_on_q

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 148facd45956bd4a9d276205fcc9615659b48737
Author: car <car>
Date:   Tue Dec 15 23:34:56 1998 +0000

    more checking options

Src/LinearSolvers/C_NodalMG/proj.cpp

commit f19d728a18bc0191735cca9b2cd006e16e18f2f2
Author: lijewski <lijewski>
Date:   Tue Dec 15 18:51:27 1998 +0000

    Attempt to speed up processing of local tasks.

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit cb3f1798954309c57ff840c122f19f559f560692
Author: lijewski <lijewski>
Date:   Tue Dec 15 18:13:24 1998 +0000

    Had a bug in task_list::execute().

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit d023deac1615242ad57b9fff9512bf15cb55ff43
Author: lijewski <lijewski>
Date:   Tue Dec 15 17:32:32 1998 +0000

    Prepended cout's with "HG:"

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit ae2a4ce955a74c654d28c8daca0da9759286ca0e
Author: lijewski <lijewski>
Date:   Tue Dec 15 17:22:47 1998 +0000

    An improvement to task_list::execute() loop.

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 744046ce9bea4b970cb20ade2fe664bcd466c1f0
Author: car <car>
Date:   Tue Dec 15 17:01:30 1998 +0000

    better execute loop

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit d6677935513e9fb9861560a47a1e49337cbd485c
Author: car <car>
Date:   Tue Dec 15 04:01:33 1998 +0000

    Fix for explosion in number of tasks.  The ParmParse parameter
    HG.max_live_tasks, limits the number of tasks that can be pending in a task
    loop.  The default limit is 50.  Since tasks always are issued in pairs,
    and the tasks are asynchronous sends/recvs this should not deadlock.
    
    The fortran change is to get the line length of a few lines back down to
    72 or smaller.

Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit ecd84eaa4e55399ea9e27e8da060f753a6b1c06d
Author: lijewski <lijewski>
Date:   Mon Dec 14 22:43:11 1998 +0000

    Integrated in <REAL.H> and <CONSTANTS.H>.

Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit 5b3bfbaecdc99519d3ada4774259f6137c6ecc6e
Author: lijewski <lijewski>
Date:   Mon Dec 14 20:23:47 1998 +0000

    Got rid of hard-wired double-precision constants to snuff T3E warnings.

Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/LP_3D.F
Src/LinearSolvers/C_CellMG/MG_3D.F

commit 6c8428f5dc823729c0e5af725a45faa9209b7759
Author: car <car>
Date:   Sun Dec 13 01:21:38 1998 +0000

    sleep flag

Src/LinearSolvers/C_NodalMG/proj.cpp

commit f8f6cea88b05c878f66c2fc7222f867e69286560
Author: car <car>
Date:   Fri Dec 11 21:55:40 1998 +0000

    T3E KCC change

Src/C_BaseLib/Utility.cpp
Tools/C_mk/Make.T3E

commit 3109fab39676b61e5b5414fc24e10c2191d5e602
Author: car <car>
Date:   Fri Dec 11 21:54:25 1998 +0000

    T3E change in prototype for _rtc

Src/C_BaseLib/Utility.cpp

commit 29f9715bf6c03c85dac0787a18c3c66f8d95f99a
Author: car <car>
Date:   Fri Dec 11 19:21:26 1998 +0000

    fix for rwtime == 0

Src/C_BaseLib/RunStats.cpp

commit b5e7339e44a2faec21b4d16157ad3b3e9cc0143c
Author: car <car>
Date:   Fri Dec 11 18:55:32 1998 +0000

    added inputs file

Src/LinearSolvers/C_NodalMG/inputs

commit 6bb89d44eed4c0d43628ca7cc3db5f33a5818b9f
Author: car <car>
Date:   Fri Dec 11 18:54:57 1998 +0000

    Additional ParmParse support

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 46097abc203e14b37a09c2452adeaf402c109830
Author: car <car>
Date:   Fri Dec 11 18:37:46 1998 +0000

    ParmParse and RunStats support

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 15ebcf27453a9b081bfef9d9a939bab13302d330
Author: lijewski <lijewski>
Date:   Fri Dec 11 02:47:14 1998 +0000

    Removed IncrementPeriodicBoundary().
    Shouldn't have been checked in.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 48f54f611d3323d3d25750a1a42ff0f939d9de4d
Author: lijewski <lijewski>
Date:   Fri Dec 11 02:46:18 1998 +0000

    Removed the FillFabPlus() stuff.  Shouldn't have been checked in.

Src/C_BaseLib/FabArray.H

commit 47ce67b42ed048df638d432bd02abed4f735c0d8
Author: car <car>
Date:   Fri Dec 11 00:26:57 1998 +0000

    *** empty log message ***

Src/C_BaseLib/pBoxLib_2.dsp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit e21b11c90090a3d7f68cab7d3eca485c2b1d2752
Author: car <car>
Date:   Fri Dec 11 00:01:22 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit c60621052e25c6eacfae586ca486ebf9e3ebe977
Author: lijewski <lijewski>
Date:   Thu Dec 10 23:34:58 1998 +0000

    Added FillFabPlus().

Src/C_BaseLib/FabArray.H

commit 215baf4dc64fc2bc361dee28c56d2b56f92d9cf0
Author: lijewski <lijewski>
Date:   Thu Dec 10 23:31:58 1998 +0000

    The node centered stuff in buildPIRMMap() wasn't quite right.

Src/C_BaseLib/Geometry.cpp

commit ebd146f918f3c74e8f69bcd9bda9a06165e2904d
Author: lijewski <lijewski>
Date:   Thu Dec 10 23:24:14 1998 +0000

    Fixed a bad assert().

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 9c0e817e6768625b40921d75c5678cbdb079330c
Author: car <car>
Date:   Thu Dec 10 23:16:01 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 3a49a6d1cb4d31d2b4cc8f7f2ddf3b8f69d7b7d9
Author: car <car>
Date:   Thu Dec 10 23:10:41 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit ca151403edcbf85ebd9a5819044a3538d0c7a44d
Author: car <car>
Date:   Thu Dec 10 22:54:32 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/.cvsignore
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 675ccfe039f99027a441c91634fc8c8813332193
Author: lijewski <lijewski>
Date:   Thu Dec 10 22:16:07 1998 +0000

    Changes to buildPIRMMap() for nodal MultiFabs.

Src/C_BaseLib/Geometry.cpp

commit 652b41bb651c16999887ccde22b1019d14908149
Author: car <car>
Date:   Thu Dec 10 20:57:39 1998 +0000

    non MPI projection

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/pBoxLib_2.dsp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 214bfa9b2e236bd28e526296d790f5aa9a0f5650
Author: car <car>
Date:   Thu Dec 10 18:41:21 1998 +0000

    remove extraneous dependency check

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 407893736ef7357fbde6bf31f77b965c7efb0008
Author: car <car>
Date:   Thu Dec 10 01:02:38 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 7352e2b085b96080eb3566d61491ab4af7c9fb9b
Author: car <car>
Date:   Thu Dec 10 01:00:32 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 554ee2c892142019edc04ea8b7bed5d769a1e403
Author: car <car>
Date:   Wed Dec 9 23:13:31 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/tests/gt.bill1
Tests/LinearSolvers/C_NodalMG/test_grids/gt.bill1

commit 8b846f69fed2fe768c36c5e74ea6b15a91711e68
Author: wyc <wyc>
Date:   Wed Dec 9 21:56:28 1998 +0000

    Mike put some T3E defines where he meant BL_T3E.

Src/C_BaseLib/Utility.cpp

commit f0d8674cda46bf500da12b0d729aee74acbc3b1a
Author: lijewski <lijewski>
Date:   Wed Dec 9 20:21:30 1998 +0000

    In buildPIRMap(), restrict src box to be in Domain().

Src/C_BaseLib/Geometry.cpp

commit da3594b74983b20a53d198f42be874b5b295d47d
Author: wyc <wyc>
Date:   Tue Dec 8 18:25:44 1998 +0000

    These changes allow CGSolver to recognise a loss-of-accuracy event and
    deal with it gracefully.  By default, CGSolver will act in the old-die-
    horribly mode.  However, you can activate expert mode which will allow
    CGSolver::solve() to return an integer indicating status.  MultiGrid.cpp
    has been modified to use expert mode.

Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 7216b4df5520a35c561099894c97570551ad082d
Author: lijewski <lijewski>
Date:   Tue Dec 8 18:13:20 1998 +0000

    A fix to task_copy::depends_on_q().

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit f2fcfa6cc98531f791cc723bf1f0c3877d8c91d1
Author: lijewski <lijewski>
Date:   Mon Dec 7 18:39:21 1998 +0000

    Mods to compile on T3E.

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 35cb695ef97068a27cf267a1d56cae27a51a7e55
Author: almgren <almgren>
Date:   Sat Dec 5 00:39:44 1998 +0000

    This contains the fix to the previous regridding "fix" submitted by Almgren -
    the grow by n_proper had been neglected in the earlier "fix".

Src/C_AMRLib/Amr.cpp

commit 2985ee7acfc29fb11156ebe90cb3d81f3ad4617c
Author: car <car>
Date:   Fri Dec 4 21:32:48 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit a66bade541a23229cd6672d50b4a4eb115e71b33
Author: car <car>
Date:   Fri Dec 4 21:19:31 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 3f1a7b913d48aa8fad04231e2810c7305bd8c48e
Author: lijewski <lijewski>
Date:   Fri Dec 4 17:33:24 1998 +0000

    time -> time+dt_level[level] in station.report() call.

Src/C_AMRLib/Amr.cpp

commit ed8122d464be1cd3046e221e0eb14be57de1b4be
Author: lijewski <lijewski>
Date:   Wed Dec 2 18:36:45 1998 +0000

    Removed bad assert().

Src/C_AMRLib/AmrLevel.cpp

commit 800a79387b3a165f3733428d25df7797b9689805
Author: lijewski <lijewski>
Date:   Wed Dec 2 17:52:55 1998 +0000

    Fixed another periodic bug in FillPatchIterator.

Src/C_AMRLib/AmrLevel.cpp

commit 0c30d99f7178b829644533f22c92e4922ac4307f
Author: car <car>
Date:   Wed Dec 2 05:58:57 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit fda145647f8512827b3ca35ddd2769db43554978
Author: lijewski <lijewski>
Date:   Wed Dec 2 00:04:37 1998 +0000

    Added poe junk ...

Src/C_AMRLib/GNUmakefile
Src/C_BoundaryLib/GNUmakefile
Src/LinearSolvers/C_CellMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_TensorMG/GNUmakefile

commit 14761830d8f30b27a1ec9e48f44e750902942f1f
Author: lijewski <lijewski>
Date:   Wed Dec 2 00:04:06 1998 +0000

    A tad cleanup.

Src/C_BaseLib/GNUmakefile

commit 5320f6f09e6982e578c68a0719326b2a79c35781
Author: lijewski <lijewski>
Date:   Tue Dec 1 21:56:39 1998 +0000

    Reverted out the cache stuff.  Not a significant win.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit bc0ef05de8d897c7232fe03713a8431e8de5a863
Author: lijewski <lijewski>
Date:   Tue Dec 1 21:56:23 1998 +0000

    Reverted out the cache junk.  Not a significant win.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp

commit 137ed14f2e1b3e1bd74d5632bcd8a9eb2fbe5994
Author: lijewski <lijewski>
Date:   Mon Nov 30 21:30:09 1998 +0000

    Added more assert()s in operator() per Dan Graves.

Src/C_BaseLib/BaseFab.H

commit 47ea150f8e0047f322cd076726ce0ca1d5cbe90c
Author: lijewski <lijewski>
Date:   Mon Nov 30 21:13:38 1998 +0000

    Mod to get to run on T3E.

Src/C_AMRLib/StationData.cpp

commit f58051a1e30a381daea397a126db4c588d289442
Author: lijewski <lijewski>
Date:   Mon Nov 30 18:52:05 1998 +0000

    Now use getType() of StateDescriptor to get appropriate IntVect into FAB.

Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp

commit 5d5c7d4af158fdcc9341aac1b35ff52a012506c1
Author: lijewski <lijewski>
Date:   Mon Nov 30 02:12:35 1998 +0000

    Some cleanup.  Almost done ...

Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp

commit 77bd244bfd391b5f26b97992f4c31f3ebeb737fe
Author: lijewski <lijewski>
Date:   Sun Nov 29 01:33:53 1998 +0000

    Now support putting station files in sub-directory.

Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp

commit 0e9f7b3e4dbd87c3c42df89a9ab6edd76a5368db
Author: lijewski <lijewski>
Date:   Sun Nov 29 00:22:36 1998 +0000

    Merged in DataStation junk.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Make.package

commit f6446d518e1e87b372c5520b37a8ee81bdba3cfa
Author: lijewski <lijewski>
Date:   Sun Nov 29 00:22:09 1998 +0000

    Added some const versions of member functions.

Src/C_AMRLib/AmrLevel.H

commit 673ea017871e511dbcdd28307588d3f6c23e3b8a
Author: lijewski <lijewski>
Date:   Sun Nov 29 00:21:41 1998 +0000

    Looking pretty good ...

Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp

commit 2371e215d251dba7897c75e6f1eb444ad67fb0c8
Author: lijewski <lijewski>
Date:   Sat Nov 28 21:58:43 1998 +0000

    More work bring up-to-date with amrlib structures.

Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp

commit 634fe9676c4914fa27ee6554462e863f39d8be64
Author: car <car>
Date:   Thu Nov 26 20:30:13 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 9a419ce039efb70c68434c1943323567e470901d
Author: lijewski <lijewski>
Date:   Wed Nov 25 23:58:22 1998 +0000

    Progress moving from AmrSS to current amrlib ...
    Still a work in progress though.

Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp

commit ed97a42f642a776dbf8939ae7113de23c20e0875
Author: car <car>
Date:   Wed Nov 25 23:52:34 1998 +0000

    Fixes for HGPROJ MultiLevel

Src/LinearSolvers/C_NodalMG/.cvsignore
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 81a960034e4d89d556bdcbbe970f09a050df91b3
Author: lijewski <lijewski>
Date:   Wed Nov 25 19:14:16 1998 +0000

    From very old amrSS code ...

Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp

commit 04484597bc05be0afca914a597249313b3895d74
Author: wyc <wyc>
Date:   Tue Nov 24 23:17:52 1998 +0000

    added chuck's patch for a problem which was causeing hg not to converge

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit cc9f455bb7d273aec9e60c54c98b320333764f55
Author: lijewski <lijewski>
Date:   Tue Nov 24 19:22:57 1998 +0000

    Now caching Snds stuff for CollectData().

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit d72f57972860fc2b47ea757a0bca1d98ab31a52d
Author: lijewski <lijewski>
Date:   Tue Nov 24 19:22:38 1998 +0000

    Now cacheing Snds stuff in CollectData().

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp

commit f149eb1ca35cd9b2e45895e12757917e9bf6c1e0
Author: lijewski <lijewski>
Date:   Tue Nov 24 01:01:14 1998 +0000

    Merged in new Reduce() functions.

Src/C_AMRLib/Amr.cpp

commit a476cee54cbd94a01b2eb5943e7c9a0027e924b5
Author: lijewski <lijewski>
Date:   Tue Nov 24 01:00:54 1998 +0000

    Merged in new Reduce() functions taking cpu to reduce to.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/RunStats.cpp

commit 69f93808df85ca2aa3fd25910920ba8862346360
Author: lijewski <lijewski>
Date:   Mon Nov 23 22:39:26 1998 +0000

    Added const versions of newData() and oldData().

Src/C_AMRLib/StateData.H

commit 4f7c5424927c98a5427ebcb4bdad90621c322db6
Author: lijewski <lijewski>
Date:   Mon Nov 23 18:27:01 1998 +0000

    Removed canned procedure.  Was proving too much trouble.

Tools/C_mk/Make.rules

commit d4402fb05b72889d6731a7a0e156bf95f72c14d8
Author: lijewski <lijewski>
Date:   Mon Nov 23 17:56:42 1998 +0000

    Fix for busted gmake on T3E.

Tools/C_mk/Make.rules

commit 9cea9858941b4d255513367be9285c2c98c6ce18
Author: car <car>
Date:   Mon Nov 23 17:31:36 1998 +0000

    *** empty log message ***

Src/C_BaseLib/pBoxLib_2.dsp

commit 5d99e5686c60b6c33caf66d448b13b2dd724d56a
Author: car <car>
Date:   Mon Nov 23 00:50:23 1998 +0000

    *** empty log message ***

Src/C_BaseLib/pBoxLib_2.dsp

commit 1840e58b09c5cbb451aca513b513cd5811532c7e
Author: lijewski <lijewski>
Date:   Sun Nov 22 17:42:54 1998 +0000

    Wrapped the closelib junk into a canned procedure.

Tools/C_mk/Make.rules

commit aca54123ad14184bfa4e8b00abd9bb3b9f78081e
Author: lijewski <lijewski>
Date:   Sat Nov 21 19:34:19 1998 +0000

    Added ti_files directory for cleaning.

Tools/C_mk/Make.rules

commit 1b879d1d798aaac8c6b2fe96ebbd87623e06d0a4
Author: lijewski <lijewski>
Date:   Sat Nov 21 19:02:54 1998 +0000

    Reverting out the simplification of *OUTPUT_OPTION junk.

Tools/C_mk/Make.AIX
Tools/C_mk/Make.CRAY
Tools/C_mk/Make.T3E
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit fe7a068e01c43b878aaf5d0a1bd5318c4568a3b7
Author: lijewski <lijewski>
Date:   Sat Nov 21 03:12:10 1998 +0000

    Some simplification.

Tools/C_mk/Make.AIX
Tools/C_mk/Make.CRAY
Tools/C_mk/Make.T3E
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 9c36ad7bc13a49d4da47aa2733cc65d899259cef
Author: lijewski <lijewski>
Date:   Sat Nov 21 02:49:39 1998 +0000

    Simplified the library closure junk.

Tools/C_mk/Make.rules

commit 12e47901f995acdd3db39b60d6242e7d8f82ccd4
Author: lijewski <lijewski>
Date:   Sat Nov 21 00:27:43 1998 +0000

    Yet more OUTPUT_OPTION mods.

Tools/C_mk/Make.defs

commit 3dede12c2847f54fcf111203975d77b2c81abdd1
Author: lijewski <lijewski>
Date:   Sat Nov 21 00:24:14 1998 +0000

    Bug fix to form of *LIB_OUTPUT_OPTION.

Tools/C_mk/Make.defs

commit f7712f479806974297203ca0400135a5f908b8de
Author: lijewski <lijewski>
Date:   Sat Nov 21 00:15:40 1998 +0000

    Now have four *_OUTPUT_OPTION variables.

Tools/C_mk/Make.AIX
Tools/C_mk/Make.CRAY
Tools/C_mk/Make.T3E
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit ba1426892584a371d5297fbd0990f37a4ab2c3d7
Author: lijewski <lijewski>
Date:   Fri Nov 20 23:18:02 1998 +0000

    Some fixes relating to OUTPUT_OPTION & FORT_OUTPUT_OPTION

Tools/C_mk/Make.OSF1
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit dd7980708b23b2150a417a37ecd5a7fae9017d70
Author: lijewski <lijewski>
Date:   Fri Nov 20 21:58:24 1998 +0000

    Added real time clock routines for second()  & wsecond() on T3E.

Src/C_BaseLib/Utility.cpp

commit b3e9db76635425680ba004baca4f4f37d7c7c5bf
Author: car <car>
Date:   Fri Nov 20 21:42:41 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit ce086bafcc58dffc33d833e626e8dbe1d29971e6
Author: lijewski <lijewski>
Date:   Fri Nov 20 21:23:36 1998 +0000

    ld -> d on an sprintf() call

Src/C_BaseLib/VisMF.cpp

commit 8fdc243e6b20d4ebbe7812511e319ff5c34828b8
Author: car <car>
Date:   Fri Nov 20 20:34:10 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 2545e19028236c2c51c8eb4f3256eb9cc1463dd3
Author: car <car>
Date:   Fri Nov 20 20:29:45 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 7209bceffdc49e305c0d9da531f42cad5b7c9784
Author: car <car>
Date:   Fri Nov 20 19:09:48 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 9e11b0e72c623ab58b57496e69a12022589a210c
Author: car <car>
Date:   Fri Nov 20 05:01:10 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 686c3f8e9edb61de99c8a9447056039557dcc381
Author: car <car>
Date:   Fri Nov 20 00:01:03 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 92718d63278d50dfa6760967849828a3430cf953
Author: car <car>
Date:   Thu Nov 19 22:32:45 1998 +0000

    fixed task_fecdiv_2

Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit cb308943e034691d9f2a775ac1b8d52bb9782d30
Author: car <car>
Date:   Thu Nov 19 22:10:17 1998 +0000

    parallel hgproj changes

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/pBoxLib_2.dsp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 95aeaeb56a5fb5b46b4356f0d4308050983d5724
Author: car <car>
Date:   Thu Nov 19 18:09:53 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/bl_abort.cpp
Src/LinearSolvers/C_NodalMG/matherr.f90

commit d48cbe6634be9b4737c7c814c0953c36787cf4e0
Author: car <car>
Date:   Thu Nov 19 16:48:23 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/bl_abort.cpp
Src/LinearSolvers/C_NodalMG/matherr.f90

commit 9a8face422e16d09d69b0ac5e3b51dfd584efd53
Author: car <car>
Date:   Thu Nov 19 02:20:46 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit fd7cbf1a209f47fb25310224b7fca717b92811d2
Author: car <car>
Date:   Wed Nov 18 23:01:23 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp

commit d9c4419aced54b1831f2b75ad5ccf129b9b4cec4
Author: car <car>
Date:   Wed Nov 18 21:46:44 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 9eac975ce10ce3718b270bb2254081aeb88dc5e5
Author: car <car>
Date:   Wed Nov 18 21:08:15 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit cd64c24f0d0be4d676b065175e3c2ff12caa9ca5
Author: lijewski <lijewski>
Date:   Wed Nov 18 20:47:05 1998 +0000

    Updated to reflect new Make.defs.

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit d95ac2f79d755983112bd80a08de6017bed9e596
Author: car <car>
Date:   Wed Nov 18 20:40:28 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 190eea1c4b35224f8fe32d720486bf2f76a31393
Author: lijewski <lijewski>
Date:   Wed Nov 18 20:34:50 1998 +0000

    Updated to reflect MPI in machineSuffix.

Src/LinearSolvers/C_TensorMG/GNUmakefile

commit f7f0d21379d1bc88363e829e337f2a9931262040
Author: lijewski <lijewski>
Date:   Wed Nov 18 20:33:02 1998 +0000

    Updated to reflect MPI in library names.

Src/C_AMRLib/GNUmakefile
Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/test/GNUmakefile.test
Src/C_BoundaryLib/GNUmakefile
Src/LinearSolvers/C_CellMG/GNUmakefile
Tests/C_BaseLib/GNUmakefile.test

commit 4d9159f93dd4827fd15684d6d2345ad75a3702fa
Author: lijewski <lijewski>
Date:   Wed Nov 18 20:32:40 1998 +0000

    Now distinguish between libraries built w/ or w/o MPI.

Tools/C_mk/Make.defs

commit c7277c2565e9b0de682c6552d21977d16160e10d
Author: lijewski <lijewski>
Date:   Wed Nov 18 20:31:56 1998 +0000

    Removed the unneeded first argument to StartParallel().

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit c51ed2d4d40f30cddadf81baa60c3a8d4648641b
Author: car <car>
Date:   Wed Nov 18 19:19:30 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit b538c4a016b3e3c7cbda18d7c1ab85548c5a38d6
Author: car <car>
Date:   Wed Nov 18 17:59:07 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 6f8879cfa745425a3e1465e329771304e6edabba
Author: car <car>
Date:   Wed Nov 18 17:57:45 1998 +0000

    fixed up for LIB AND EXE support in same directories and Makefiles.

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 4e2f9a9cd9ee5088d9ca8cd8132e0292dca8ada2
Author: car <car>
Date:   Wed Nov 18 01:30:51 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp

commit 28c0e238bf1d8e8f7d5b08ab6b6318b79f25edad
Author: car <car>
Date:   Wed Nov 18 01:00:24 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit e8a8f5ee7c9e581e36c4062273bd982c4656ed32
Author: car <car>
Date:   Tue Nov 17 20:07:53 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interpolator.H
Src/LinearSolvers/C_NodalMG/restrictor.H

commit 0549ef2184c451d68d1b2fa9bb0943dfbcc7dcb3
Author: lijewski <lijewski>
Date:   Tue Nov 17 19:15:39 1998 +0000

    Small touchup.

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 9801a3865fe1c57711956c09f0c7cd74bc2b605f
Author: lijewski <lijewski>
Date:   Tue Nov 17 19:11:09 1998 +0000

    Brought up-to-date with latest Parallel stuff.

Src/LinearSolvers/C_TensorMG/GNUmakefile
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCLO_2D.F
Src/LinearSolvers/C_TensorMG/MCLO_F.H
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/Make.package

commit a987979f41f7028cd36fb80df6a7eb62981a90db
Author: car <car>
Date:   Tue Nov 17 18:00:49 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 6e3d5c2a02dafeee26340965f09d1ded86116700
Author: car <car>
Date:   Tue Nov 17 17:48:36 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit bda064809210ef07a0912ab8226e6dca7b4a94cc
Author: car <car>
Date:   Tue Nov 17 00:51:16 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 6bcee24182428f7e127da031576a7da3ac4c7f53
Author: car <car>
Date:   Tue Nov 17 00:48:50 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 5d1e371d034bb857802962d6801f92a4b894f4c9
Author: car <car>
Date:   Tue Nov 17 00:38:05 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 7a25a20a4a2c96cd655ecf6c3cabdb6a2c844c45
Author: car <car>
Date:   Tue Nov 17 00:18:14 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit e866f5934bed57dbb8b033ae0c164737af13ac43
Author: car <car>
Date:   Mon Nov 16 23:52:36 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit bc78f849927692fdcfa34badb33148277b4781b5
Author: car <car>
Date:   Mon Nov 16 22:54:15 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit dd8e601e6a394fdd46aefc16f67bdd22d207046b
Author: car <car>
Date:   Mon Nov 16 21:57:23 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 8660b414355ca4267539462760ce432abfef51b2
Author: car <car>
Date:   Mon Nov 16 21:44:10 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 150f8d9ab68d126728e837c3d711fab0fbb96acf
Author: car <car>
Date:   Mon Nov 16 18:11:49 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit ffe557787fdfd669a361e1ca6e51d32a063a5d11
Author: car <car>
Date:   Mon Nov 16 17:47:58 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 88dcf21ef42d9beefb871823a2e7044442e6823c
Author: car <car>
Date:   Mon Nov 16 17:31:01 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit c2f9eaaaadfffea0c382ce477b19c46b499ae1b4
Author: car <car>
Date:   Mon Nov 16 15:53:17 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp

commit 1f9c06522f7540c5995db64ed8e91b4e00d5b4fd
Author: car <car>
Date:   Mon Nov 16 03:52:11 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 756f5b26f5a418331f2bd6097b33daed7ee8221b
Author: car <car>
Date:   Mon Nov 16 00:47:47 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 59e5863bbe7a3d73a083a3099e1456fac84c031f
Author: car <car>
Date:   Sun Nov 15 23:40:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 90759a068cbfcbf932bd44e48adb1a649734afb0
Author: car <car>
Date:   Sun Nov 15 00:01:27 1998 +0000

    win32 support

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit e26c775b52b693ace9b7fd54720481ea9d2e3a98
Author: car <car>
Date:   Sat Nov 14 19:38:21 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 7f8c59df1a1b973d819540114f0254547c0f30a9
Author: car <car>
Date:   Sat Nov 14 00:34:13 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit d70d1d2ddcce8380f20a57d1dda5cc01c0e71609
Author: car <car>
Date:   Sat Nov 14 00:34:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.cpp

commit c9d14f4aa2c588a4335e281b68562fd691a83a13
Author: car <car>
Date:   Fri Nov 13 22:14:39 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit ce53dcef7361791f2814becacdc0797fbfe0c7f1
Author: car <car>
Date:   Fri Nov 13 20:09:28 1998 +0000

    Temp file name.

Src/LinearSolvers/C_NodalMG/.cvsignore

commit 204c320c37707b42d4c3261121685d13d5f4e442
Author: car <car>
Date:   Fri Nov 13 20:08:45 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 79887a9f0ff5b487ac07cd44c4870a4bf314b5ae
Author: car <car>
Date:   Fri Nov 13 17:25:52 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 8cf6188c40514a2be04df50651d4741fba504f30
Author: car <car>
Date:   Fri Nov 13 16:03:51 1998 +0000

    EBASE should be null

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 63fffad6de2c1ceb8c47c40c5d8eac68f9b2ea92
Author: car <car>
Date:   Fri Nov 13 16:03:07 1998 +0000

    quiet some warnings

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 3dec428241494354a5e476b29a52a84620eb7429
Author: car <car>
Date:   Fri Nov 13 00:25:01 1998 +0000

    fixes for parallel, throws find bugs

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit dd8acc29bddb258c2311d05dd4014e9682ebf337
Author: marc <marc>
Date:   Fri Nov 13 00:16:14 1998 +0000

    Fix up a couple of 1D-specific bugs.

Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/Looping.H

commit 8dfac2f530f32b5288853284e4cacefb0fb1384c
Author: car <car>
Date:   Tue Nov 10 02:21:59 1998 +0000

    libs target

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 597132aca6d68dab7a89265745cf274886ddee0f
Author: car <car>
Date:   Mon Nov 9 23:13:14 1998 +0000

    Makefile tweaks: no type make COMP=... EBASE=proj to buildlocally

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/Make.package

commit 8e290e6ac51cc2ed7425c48ba99d76a5255ac0db
Author: car <car>
Date:   Sat Nov 7 21:42:14 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 6395377f863b78c04eabeca8eda600364390d590
Author: car <car>
Date:   Sat Nov 7 21:34:16 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit f4cb1fc354a1293c2207ee5847e9f88ee0c4e94f
Author: car <car>
Date:   Sat Nov 7 21:19:56 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 9369bb81ed060ae3c888e2be3e79b012fc8a9358
Author: lijewski <lijewski>
Date:   Sat Nov 7 02:51:08 1998 +0000

    Updated to reflect FillPeriodicBoundary() mod.

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 1442b1c951daf09dfbde165ad2ae459dc36fd78c
Author: marc <marc>
Date:   Sat Nov 7 01:45:11 1998 +0000

    Remove indenting whitespace.  Uglier f77 generated, but guaranteed correct

Tools/C_scripts/strip72

commit b54fa72ac384ad1f924d6449c40d79b08ed241f0
Author: marc <marc>
Date:   Sat Nov 7 01:14:42 1998 +0000

    Remove whitespace that was inserted on a continuation line, since that
    is space that may be inserted into a character string.

Tools/C_scripts/strip72

commit b70719b72912842e07cc9e8b97db5aa5f02ea27d
Author: lijewski <lijewski>
Date:   Sat Nov 7 00:35:19 1998 +0000

    Added do_corners boolean to FillPeriodicBoundary().

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 9f2486cad8b853f3080b1ecd4792c52b067c0695
Author: lijewski <lijewski>
Date:   Sat Nov 7 00:30:43 1998 +0000

    Mods for FillPeriodicBoundary().

Src/C_BaseLib/MultiFab.H

commit 6d9693da92a3947b8a29bd1f73d8232da0c88477
Author: car <car>
Date:   Fri Nov 6 21:35:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/RegType.H

commit e0ba793e94e2976687a3f91687171da47e29f001
Author: car <car>
Date:   Fri Nov 6 21:31:53 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/RegType.H
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 890f2e145a16012f73cb0fb127df45474434ff89
Author: car <car>
Date:   Fri Nov 6 04:22:35 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 187c2b6e41ca15a444aa09eef201ab2ae8c5814a
Author: car <car>
Date:   Fri Nov 6 04:03:28 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit b2022bb37bdd364ee1585782e82d127847e3d6c6
Author: almgren <almgren>
Date:   Thu Nov 5 06:42:59 1998 +0000

    Fixed a bug in the recent fix to not buffer the buffer cells - we can't assume
    that grid cells next to a domain boundary were buffer, not tagged, cells...

Src/C_AMRLib/Amr.cpp

commit c4fc5e93ccdd9c6fd93371df70a5618b501ffb88
Author: almgren <almgren>
Date:   Wed Nov 4 20:30:22 1998 +0000

    Removed the following snippet of code:
        if (!sub_cycle) {
              // must adjust regridding trigger
            int factor = 1;
            for (k = max_level-1; k >= 0; k--) {
                factor *= MaxRefRatio(k);
                regrid_int[k] = ri*factor;
            }
        }
    which for no subcycling did funny things to regrid_int.  Now regrid_int
    at each level is just what is set in the inputs file, which means effectively
    you will now regrid every regrid_int time steps with lbase = 0.

Src/C_AMRLib/Amr.cpp

commit 58e30546bf8aa08ce5940f643891034034b4b2a1
Author: lijewski <lijewski>
Date:   Wed Nov 4 00:45:16 1998 +0000

    Added DataLog() ...

Src/C_AMRLib/Amr.H

commit 2d43c22b3e4b31bf9af87bd04f8721894d631d10
Author: marc <marc>
Date:   Tue Nov 3 21:56:08 1998 +0000

    Add write for AmrData object as well.

Tools/C_util/WritePlotFile.H
Tools/C_util/WritePlotFile.cpp

commit 14e4ba8752a5a6a053f1470d5f965584458972c9
Author: almgren <almgren>
Date:   Tue Nov 3 21:53:05 1998 +0000

    Two changes are made in regridding: first, an "intersect with domain"
    is added to a loop which tests whether fine grids are properly nested
    within coarser grids.  Second, the way that fine grids affect coarse
    grids is modified in that only the boxes around fine *tagged* cells
    are coarsened to re-tag at the coarser levels, not the boxes around
    tagged *and* buffered fine cells.

Src/C_AMRLib/Amr.cpp

commit 0cbc23859d84dbacb8b803a15334b5278ba023de
Author: lijewski <lijewski>
Date:   Tue Nov 3 18:16:36 1998 +0000

    Sync'd with serial _amr.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/MAKESLICE_3D.F
Src/C_AMRLib/MAKESLICE_F.H
Src/C_AMRLib/PROB_AMR_F.H
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp

commit ef4301f4c03c23f6ba0756abcaa6bca752228dd4
Author: lijewski <lijewski>
Date:   Mon Nov 2 18:35:55 1998 +0000

    HG_DEBUG is defined only when building executable.

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 8760d4e059791eb89af78847bb9fe6f39ddee4a5
Author: lijewski <lijewski>
Date:   Mon Nov 2 18:19:48 1998 +0000

    Added PROB_AMR_F.H

Src/C_AMRLib/Make.package

commit e413163c6b2f0d86c4a716b2cfae36bf1cc73de9
Author: lijewski <lijewski>
Date:   Mon Nov 2 18:16:13 1998 +0000

    Forgot about amr_defs.H

Src/LinearSolvers/C_NodalMG/Make.package

commit 39922cbee5e0e922b435789ab2c516e1347f40e0
Author: lijewski <lijewski>
Date:   Mon Nov 2 17:13:25 1998 +0000

    Added LevelBld.H.

Src/C_AMRLib/Make.package

commit 2cbcc552d47bef2575b682d797623b2aa960a563
Author: lijewski <lijewski>
Date:   Fri Oct 30 19:02:44 1998 +0000

    Mods to get doc++ to build proper TeX.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/TagBox.H

commit 72c80ea3e29b3a3c5e5dd676bcc7ab44603529e8
Author: lijewski <lijewski>
Date:   Thu Oct 29 21:56:56 1998 +0000

    Fixup for doc++ DVI generation.

Src/C_BaseLib/VisMF.H

commit 4c37ddbcef3a2e020079df79a840bdec5886ec33
Author: car <car>
Date:   Thu Oct 29 21:56:26 1998 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit 0dcb6499259183f9702bec05b516c58bc10d03c5
Author: lijewski <lijewski>
Date:   Thu Oct 29 17:33:53 1998 +0000

    More work on Parallel GNUmakefile consistency.

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/Make.package

commit 6ccc46f7d47d17eb6b5f9d450416e6de5857c481
Author: lijewski <lijewski>
Date:   Thu Oct 29 16:54:03 1998 +0000

    More work on Parallel GNUmakefile consistency.

Src/C_AMRLib/GNUmakefile
Src/C_BaseLib/GNUmakefile
Src/C_BoundaryLib/GNUmakefile
Src/LinearSolvers/C_CellMG/GNUmakefile

commit 37b12d3af4ec2b12930d24d761e3cdbc8b8421d2
Author: lijewski <lijewski>
Date:   Thu Oct 29 16:33:39 1998 +0000

    Simplified decision regarding how to set QNAN.

Src/C_BaseLib/FArrayBox.cpp

commit 368cfec05948214aa6a72e57b1c1d0a3ec3baee2
Author: lijewski <lijewski>
Date:   Wed Oct 28 22:47:55 1998 +0000

    More readily build standalone library.

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 26874b5e907546934d32a9b4047d41e266407499
Author: lijewski <lijewski>
Date:   Wed Oct 28 22:03:45 1998 +0000

    Now can build the library standalone.

Src/LinearSolvers/C_CellMG/GNUmakefile
Src/LinearSolvers/C_CellMG/Make.package

commit d559ba83eff0b4d7111e6c8531dc6347b846e618
Author: lijewski <lijewski>
Date:   Wed Oct 28 22:01:15 1998 +0000

    Forgot BC_TYPES.H

Src/C_AMRLib/Make.package

commit 83c6589a270d82fed5635a7d3756c5cd5171eda0
Author: car <car>
Date:   Wed Oct 28 18:43:04 1998 +0000

    __GNUC__

Src/C_BaseLib/FArrayBox.cpp

commit b7eca13f4c64f5498cdd8390da6fb58211733832
Author: lijewski <lijewski>
Date:   Wed Oct 28 18:15:13 1998 +0000

    More work on getting standalone library to build.

Src/C_AMRLib/GNUmakefile
Src/C_AMRLib/Make.package

commit 9927643059493bc21547276bc8c5f4f7645125d9
Author: lijewski <lijewski>
Date:   Wed Oct 28 17:49:32 1998 +0000

    More work on building standalone libraries.

Src/C_BoundaryLib/GNUmakefile
Src/C_BoundaryLib/Make.package

commit 1eeb056c5f0d3d8ff4e216ec6b97fc05556049fb
Author: lijewski <lijewski>
Date:   Wed Oct 28 17:42:16 1998 +0000

    More work on building and installing library.

Src/C_BaseLib/GNUmakefile

commit 26416c5ec92f0b02cb9b536ad42804e02b667d4c
Author: marc <marc>
Date:   Wed Oct 28 02:01:56 1998 +0000

    Change the name of the function Utility::CreateDirectory to Utility::
    UtilCreateDirectory.

Tools/C_util/TV_TempWrite.H
Tools/C_util/WritePlotFile.cpp

commit cb86bf203eb932cf69632fe39ebfd9bcbdabe854
Author: lijewski <lijewski>
Date:   Tue Oct 27 22:07:10 1998 +0000

    Redid previous fix in a slightly clearer way.

Src/C_BaseLib/FabArray.H

commit a57311e7e247857f9403321f75c6b9a5391e2010
Author: lijewski <lijewski>
Date:   Tue Oct 27 21:58:25 1998 +0000

    Forgot to set dataAvailable = true on early return in CollectData().

Src/C_BaseLib/FabArray.H

commit 8861008c91b65122688ade95a2fb1f289caa0258
Author: almgren <almgren>
Date:   Tue Oct 27 19:22:09 1998 +0000

    Put if (sub_cycle) around loop Vince added for multifluid, and set parameters
    correctly for no subcycling.

Src/C_AMRLib/Amr.cpp

commit aae5628e8e06075b22196e0c91eb095bef017547
Author: lijewski <lijewski>
Date:   Tue Oct 27 17:33:05 1998 +0000

    Simplified reflux() slightly & worked around g++ 2.8.1 bug.

Src/C_AMRLib/FluxRegister.cpp

commit 8418a4cc861b16dbeea68802bd23f613b5d22853
Author: lijewski <lijewski>
Date:   Mon Oct 26 23:58:50 1998 +0000

    __GNUC -> __GNUC__

Src/C_BaseLib/FArrayBox.cpp

commit 70ddcc88ea63f4ef232a50991b85cca99b8d1b98
Author: lijewski <lijewski>
Date:   Mon Oct 26 20:51:38 1998 +0000

    mpi_waitall -> mpi_wait for RunStats.

Src/C_AMRLib/FluxRegister.cpp

commit 154d59e0a02af0c1c8aaa6384b4678d993ace934
Author: lijewski <lijewski>
Date:   Mon Oct 26 20:51:15 1998 +0000

    Optimized MPI communication in copy().

Src/C_BaseLib/FabArray.H

commit 0e8f7bddd429ce584722a0a7c3a598a09cc04d03
Author: lijewski <lijewski>
Date:   Mon Oct 26 20:50:53 1998 +0000

    Added tFAC.cpp

Src/C_BaseLib/test/GNUmakefile.test
Src/C_BaseLib/test/tFAC.cpp
Tests/C_BaseLib/GNUmakefile.test
Tests/C_BaseLib/tFAC.cpp

commit 9bc15016e0704a622b230cbfd78a7e617cce5bd7
Author: lijewski <lijewski>
Date:   Sat Oct 24 22:26:42 1998 +0000

    Figured out the bug in 1.49 -- Yes!

Src/C_AMRLib/FluxRegister.cpp

commit 41a8c1d43283a508d6735fc3385fe427f7664214
Author: lijewski <lijewski>
Date:   Sat Oct 24 20:24:49 1998 +0000

    Reverting to previous version; something's not quite right :-(

Src/C_AMRLib/FluxRegister.cpp

commit f83a60e5f86b82b6f15cf2cb003ffa341df74620
Author: lijewski <lijewski>
Date:   Sat Oct 24 16:49:25 1998 +0000

    Optimized communication in CrseInitFinish().

Src/C_AMRLib/FluxRegister.cpp

commit 97be32ddce0a379ccff062a3e55cfb48d0c9471c
Author: car <car>
Date:   Fri Oct 23 23:46:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 797dc4a69cbf1be0158fa737eabc9985457f0e46
Author: lijewski <lijewski>
Date:   Fri Oct 23 16:54:00 1998 +0000

    A little cleanup.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/VisMF.cpp

commit fec5a6d1cc7564e11076c3cf1497f49088c22aa3
Author: lijewski <lijewski>
Date:   Fri Oct 23 01:59:35 1998 +0000

    Added immediate return in CollectData() if NProcs() == 1.

Src/C_BaseLib/FabArray.H

commit 6cec58a510b105378c5e7c4ffe6049943825527f
Author: lijewski <lijewski>
Date:   Thu Oct 22 17:27:56 1998 +0000

    Added a few strategically placed ios::binary in open() calls.

Src/C_BaseLib/VisMF.cpp

commit db24e6b2ed64af6736d829bf5230d0170013e947
Author: lijewski <lijewski>
Date:   Sun Oct 18 03:48:16 1998 +0000

    Now use coalescing FAB heap for FAB data in CollectData().

Src/C_BaseLib/FabArray.H

commit 0ef28cda87996de992f48ef893684e953f13be57
Author: lijewski <lijewski>
Date:   Sun Oct 18 01:44:17 1998 +0000

    Added new cut at CollectData() minimizing # of communications.

Src/C_BaseLib/FabArray.H

commit 5e10cd5941729faf0b93cbe9876019b7035dcb8f
Author: lijewski <lijewski>
Date:   Sun Oct 18 01:43:50 1998 +0000

    Added copy constructor and assignment operator for CommData.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 682d013f01be9044775f2b61dbbc5c618763eb4b
Author: lijewski <lijewski>
Date:   Thu Oct 15 21:53:02 1998 +0000

    Now cache the AddBox() info in the CopyDescriptor.

Src/C_BaseLib/Geometry.cpp

commit d5faa92d5b5913b5f548817e491f37f87acc149f
Author: lijewski <lijewski>
Date:   Thu Oct 15 21:52:40 1998 +0000

    Now cache the AddBox() gunk in the CopyDescriptor.

Src/C_BaseLib/MultiFab.cpp

commit fea6f72d48cc15ef5146432d45363af21dadf594
Author: lijewski <lijewski>
Date:   Thu Oct 15 21:52:15 1998 +0000

    No longer clear fabComTagList() in CollectData().
    This allows caching of CopyDescriptors between calls to CollectData().

Src/C_BaseLib/FabArray.H

commit ef6864568fff909f40a68a9f918736913b20c7c0
Author: lijewski <lijewski>
Date:   Thu Oct 15 17:14:32 1998 +0000

    Added instrumentation code.

Src/C_BaseLib/FabArray.H

commit a8de30a57c775abab46fea62e01f603b3eadcd03
Author: car <car>
Date:   Tue Oct 13 18:20:32 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 1ea9dd65da922838d55e72817124062070bc70b5
Author: car <car>
Date:   Tue Oct 13 18:19:34 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 24eed233ff7d9e9c39f10a4a8015f154b215bb82
Author: sstanley <sstanley>
Date:   Mon Oct 12 23:22:54 1998 +0000

    Replacement of EXTRAP with FOEXTRAP to be consistent with change in
    amrlib/BC_TYPES.H from v.1.3 to v.1.4.

Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp

commit 055e020c9d6fb033c3718dfa7d20c4db10af6298
Author: car <car>
Date:   Thu Oct 8 20:23:57 1998 +0000

    minor refinement of message

Src/C_BaseLib/BoxLib.cpp

commit b4c1daa14e2009baa874dce58d7fc8fe34ce5e47
Author: car <car>
Date:   Thu Oct 8 18:19:42 1998 +0000

    oops

Src/C_BaseLib/BoxLib.cpp

commit f1a225648adcabc17759a33c58e21f222d142191
Author: car <car>
Date:   Thu Oct 8 18:05:45 1998 +0000

    id string for abort/error

Src/C_BaseLib/BoxLib.cpp

commit 3f4d614d4ea79f084800c571f4632cbc32ef3d13
Author: vince <vince>
Date:   Wed Oct 7 21:18:18 1998 +0000

    Added modifications for Multifluid and a few changes for the pc.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/BC_TYPES.H
Src/C_AMRLib/FILCC_2D.F
Src/C_AMRLib/FILCC_3D.F
Src/C_AMRLib/FLUXREG_2D.F
Src/C_AMRLib/FLUXREG_F.H
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/MAKESLICE_F.H
Src/C_AMRLib/PROB_AMR_F.H
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_BaseLib/COORDSYS_2D.F
Src/C_BaseLib/COORDSYS_F.H
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/SPECIALIZE_F.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/test/tDir.cpp
Tests/C_BaseLib/tDir.cpp

commit acf9a6105dd719c9382c214272c7f7a33bcf15da
Author: vince <vince>
Date:   Wed Oct 7 20:51:59 1998 +0000

    Added Make.AIX for blue.

Tools/C_mk/Make.AIX

commit 6f580f6637f117c44d2403213e781fec2683be44
Author: lijewski <lijewski>
Date:   Tue Oct 6 23:00:10 1998 +0000

    Don't need -DBL_SETBUF_SIGNED_CHAR with KCC

Tools/C_mk/Make.T3E

commit 6c4938bdae79fb5a10653e0e26403dee4d03e09f
Author: lijewski <lijewski>
Date:   Tue Oct 6 22:56:47 1998 +0000

    Removed -e I option to FC.
    hgproj needs more cleanup before it'll pass this.

Tools/C_mk/Make.T3E

commit f8424bca35680f1d70c1c1d77edddb0e73a84b1b
Author: lijewski <lijewski>
Date:   Tue Oct 6 22:54:08 1998 +0000

    Removed a unary plus that killed T3E compiler.

Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F

commit a0172ff961339f4d919932410be67a650761f58c
Author: car <car>
Date:   Tue Oct 6 20:11:01 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit d536964040d0080f45c5747da2ec4009cf25bd0e
Author: lijewski <lijewski>
Date:   Fri Oct 2 19:36:48 1998 +0000

    Relaxed a couple assert()s in copy()

Src/C_BaseLib/BaseFab.H

commit 4f0a47600552556b41da5f010d031303a4a24cf8
Author: car <car>
Date:   Fri Oct 2 18:42:13 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 2a180ce12e7623463b5901d2f4f72c619f19c3e5
Author: car <car>
Date:   Thu Oct 1 17:17:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 20d6e043848a784f697a62c29f61fb565e8139f8
Author: lijewski <lijewski>
Date:   Wed Sep 30 20:07:18 1998 +0000

    Added tad more useful error output for bldTable().

Src/C_BaseLib/ParmParse.cpp

commit 2d1842d76141ecd1f4ed97d191391e8746649581
Author: lijewski <lijewski>
Date:   Wed Sep 30 19:28:56 1998 +0000

    Fixed bug in & simplified FillPeriodicBoundary().

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.H

commit 422f2f2ced6d2a3832a6bf5fc608d6be64d8bcd9
Author: lijewski <lijewski>
Date:   Wed Sep 30 17:07:39 1998 +0000

    Added tFB.cpp.

Src/C_BaseLib/test/GNUmakefile.test
Src/C_BaseLib/test/tFB.cpp
Tests/C_BaseLib/GNUmakefile.test
Tests/C_BaseLib/tFB.cpp

commit 4d9367c8dd3277520ba2d9dd03cd89d612cbe7ff
Author: lijewski <lijewski>
Date:   Wed Sep 30 17:05:55 1998 +0000

    Fixed bug in FillBoundary() in parallel.  Simplified it as well.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 52c01626b4bb2adf1391842bbc24fb297c78afca
Author: lijewski <lijewski>
Date:   Tue Sep 29 20:08:27 1998 +0000

    Added copyright macro.

Src/C_AMRLib/DatasetClient.cpp

commit 835b56f9a7ced1211f57414c9ceb1f4b17b7dd65
Author: car <car>
Date:   Tue Sep 29 18:05:20 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit ad2346a5d88aded12c346f385109a352706f5b8f
Author: car <car>
Date:   Fri Sep 25 23:00:22 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit d778c8264d80860b16c45a92b5ca435acef5aaae
Author: lijewski <lijewski>
Date:   Fri Sep 25 17:57:13 1998 +0000

    Added t8BIT.cpp

Src/C_BaseLib/test/GNUmakefile.test
Src/C_BaseLib/test/t8BIT.cpp
Tests/C_BaseLib/GNUmakefile.test
Tests/C_BaseLib/t8BIT.cpp

commit 29b662953d300251bb07baaeb2b1971d5fa221bc
Author: car <car>
Date:   Wed Sep 23 22:46:17 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 54f1564b8e446c3645085978c5ef111226a0e0fd
Author: lijewski <lijewski>
Date:   Wed Sep 23 22:00:10 1998 +0000

    Needed to use finest_level instead of max_level in bldFinestLevels().

Src/C_AMRLib/Amr.cpp

commit 67a17ed4329ca690059f4e32f7bb7b007f2c7207
Author: lijewski <lijewski>
Date:   Wed Sep 23 20:19:38 1998 +0000

    bldFineLevels() now iterates through regrid() till grids don't change.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 5d4a46984efffd845cd920c2179f2ddfb6a2d3e4
Author: lijewski <lijewski>
Date:   Tue Sep 22 23:42:59 1998 +0000

    Removed Amr_Auxil.H

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Amr_auxil.H

commit 85e6ca293f9ab425d6a93d7b9d83aa372038a067
Author: car <car>
Date:   Tue Sep 22 20:29:00 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit acbdd5c0c1d38ba91da2a11c4ecf4244c6e9aa9f
Author: car <car>
Date:   Tue Sep 22 18:06:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit a68590e7b43a3ce4a343559fbd43fc030715b1dd
Author: car <car>
Date:   Fri Sep 18 20:26:12 1998 +0000

    proj.cpp

Src/LinearSolvers/C_NodalMG/proj.cpp

commit c7e8c0d1de6d488ef2b0c096b80d5dc6cf9e6a95
Author: car <car>
Date:   Fri Sep 18 18:03:46 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 83e5edbd908679fd230b35df8120a795d1277d7f
Author: car <car>
Date:   Fri Sep 18 00:09:28 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 0cf16f9f713937ab65b59667ed1d86fd696a60d9
Author: car <car>
Date:   Thu Sep 17 17:05:35 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 35c60ff37010fc06a0b0a9ac55f1037d4d4c39e8
Author: car <car>
Date:   Thu Sep 17 16:46:06 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 0c1390c58ea8ae1c5d3e58c055c46e9dfd091827
Author: car <car>
Date:   Wed Sep 16 18:18:37 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit bfdee9deb76faf9bdd162f526d92fcc244bb7e0b
Author: car <car>
Date:   Wed Sep 16 03:36:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit e118923bab13acb3b58af8ef4262a721e6c30a73
Author: lijewski <lijewski>
Date:   Tue Sep 15 22:31:40 1998 +0000

    Added amr.plot_vars ParmParse variable and a couple supporting functions.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit a6be4fd5be0fef81741db00d3f211954bf771dab
Author: lijewski <lijewski>
Date:   Tue Sep 15 00:11:06 1998 +0000

    Undid 1.20.

Src/C_AMRLib/StateData.cpp

commit e7b5e5ef62a9ad1234f1ec562a893d75d1e3d4c3
Author: lijewski <lijewski>
Date:   Mon Sep 14 23:28:56 1998 +0000

    Ability to set ghost cells to average of min/max in Write()

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 302812ca9c915b49b2955adcca1862e41bb49b74
Author: lijewski <lijewski>
Date:   Mon Sep 14 23:28:13 1998 +0000

    Set ghost cells to average of min/max on VisMF::Write() in checkPoint().

Src/C_AMRLib/StateData.cpp

commit d0b844f051748e7c9868065c36981b65b42da557
Author: lijewski <lijewski>
Date:   Mon Sep 14 21:50:34 1998 +0000

    format and fabio weren't in sync after an init() or setFormat().

Src/C_BaseLib/FArrayBox.cpp

commit af6d02f2301daee7cde747271ecc72f238c9563f
Author: lijewski <lijewski>
Date:   Mon Sep 14 21:49:56 1998 +0000

    checkPoint() always used fab.format=NATIVE

Src/C_AMRLib/Amr.cpp

commit 2d3a211dc6b93e676d214e3221e1ea038bce10bd
Author: car <car>
Date:   Fri Sep 11 21:15:42 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit c2bc44d6f4ae18358eec8569c8debc49f602ccfb
Author: lijewski <lijewski>
Date:   Fri Sep 11 20:04:17 1998 +0000

    Added some stat output stuff in #if 0 ... #endif block.

Src/C_BaseLib/DistributionMapping.cpp

commit e25dd8cf18b4e4c9ff49cb478270f907650f0c22
Author: lijewski <lijewski>
Date:   Fri Sep 11 19:58:15 1998 +0000

    Minor cleanup to linInterp stuff.

Src/C_AMRLib/StateData.cpp

commit fa7cc9cc9b2c1df62de041b8303f69371c4ac410
Author: lijewski <lijewski>
Date:   Thu Sep 10 17:59:13 1998 +0000

    StartParallel() now does a MPI_Barrier() as a last step.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 985322b6979b312a11e3e9e592689b955094451c
Author: car <car>
Date:   Wed Sep 9 23:49:28 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit eb8b67681682234dcc4e4d5fa8817779880576f4
Author: car <car>
Date:   Wed Sep 9 19:57:26 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 4af929bddfbaee3c288e24472952603563bc120e
Author: car <car>
Date:   Wed Sep 9 17:17:45 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 62e6edac25cf23b391b12b640cc31b3a7ab99bf7
Author: car <car>
Date:   Tue Sep 8 23:12:15 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hglib.dsp

commit 257d3ab6d6deed0462924c8c6cb63cf4d1ba1ce1
Author: car <car>
Date:   Tue Sep 8 23:06:26 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 650523ad16728d91a41c3a69f486af2d1c8fb6f7
Author: car <car>
Date:   Tue Sep 8 23:00:04 1998 +0000

    *** empty log message ***

Src/C_BaseLib/pBoxLib_2.dsp

commit 7f1494300d4f88d94eaeff9ddba54f2cb38f96d5
Author: car <car>
Date:   Tue Sep 8 22:59:40 1998 +0000

    cleanup

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 3bf7e93acfe4b05a803f2c2bf6a0ff8fd8578922
Author: car <car>
Date:   Tue Sep 8 22:35:55 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 5996557a649deafd8fad29bcb65a94ccee635fd5
Author: car <car>
Date:   Tue Sep 8 21:07:32 1998 +0000

    counted pointer

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 824bcf47faaf417e94bd9bc1bd6fa4e224309de1
Author: car <car>
Date:   Fri Sep 4 22:31:12 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/interface.H

commit 7095a143e5d8bcec7ab98da64a11bb5aaebf78b8
Author: car <car>
Date:   Fri Sep 4 19:30:28 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 55762bf78fa33fbd006df781476d63330fe94542
Author: car <car>
Date:   Thu Sep 3 18:30:15 1998 +0000

    Really No changes.

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 607e8fc5575bbdd9a3b27743516859f99f12d05f
Author: car <car>
Date:   Wed Aug 26 17:48:15 1998 +0000

    added back graph stuff

Src/LinearSolvers/C_NodalMG/interface.cpp

commit 3191a1c839dfb5212152049c00c1dcf1a57c7229
Author: car <car>
Date:   Tue Aug 25 23:44:25 1998 +0000

    added some more temporary files to .cvsignore

Src/LinearSolvers/C_NodalMG/.cvsignore

commit 4709c5015dca56fae449aa28a65df694dc7f02d2
Author: car <car>
Date:   Tue Aug 25 23:43:04 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 06327110839ebbf3185ba828f415ab762eddf51b
Author: car <car>
Date:   Fri Aug 21 23:19:14 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit c19075340e0079120848835c53068f63a545edd3
Author: car <car>
Date:   Fri Aug 21 22:20:19 1998 +0000

    ErrorString

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 45d05ed57c8098fc3cdc896b5a2cadd51e71283d
Author: car <car>
Date:   Fri Aug 21 18:06:08 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/test/GNUmakefile.tCArena
Tests/C_BaseLib/GNUmakefile.tCArena

commit 8d61a344aa51fd913b0a489c2f7ac18299ecd0b8
Author: car <car>
Date:   Fri Aug 21 17:58:28 1998 +0000

    More Abort changes

Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/test/GNUmakefile.test
Src/C_BoundaryLib/BndryData.cpp
Src/LinearSolvers/C_NodalMG/GNUmakefile
Tests/C_BaseLib/GNUmakefile.test

commit d66922bcbaad2fb941e83280a41fb6b2cb27dba3
Author: car <car>
Date:   Thu Aug 20 23:53:47 1998 +0000

    Abort switch

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 726e54da09e9f7e183dd5b4e8440a2d9d419dc46
Author: car <car>
Date:   Thu Aug 20 17:53:59 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit d19e7d7b33acef67215a4e157a8df39e7ee5e706
Author: car <car>
Date:   Thu Aug 20 17:40:09 1998 +0000

    Support for KCC_VERSION

Src/C_BaseLib/GNUmakefile
Src/LinearSolvers/C_NodalMG/GNUmakefile
Tools/C_mk/Make.defs

commit ccd97c33c15ba9ccaaa30fd16e2fd17bb46126f3
Author: car <car>
Date:   Wed Aug 19 17:52:20 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit a02ac89b0f454c2abe83d406e6fda108b0bdb822
Author: car <car>
Date:   Wed Aug 19 17:35:20 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/amr_defs.H

commit dc50a5c868fd8a9f0b3b0c1bc0ab2d14fe51c99a
Author: car <car>
Date:   Wed Aug 19 17:22:00 1998 +0000

    Minor changes.

Src/LinearSolvers/C_NodalMG/amr_defs.H

commit bc7d03bd4c54a0d247780ac260e3228da8a7f5a2
Author: car <car>
Date:   Fri Aug 14 22:51:08 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 1ed79ac89cce0ac1524d3d04ff4d66020ef32a1c
Author: car <car>
Date:   Fri Aug 14 17:26:39 1998 +0000

    Fix for g++, no limits header file

Src/C_BaseLib/FArrayBox.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit e6a26f2c37074ef67fd4339ed21044dfa66bc28a
Author: car <car>
Date:   Fri Aug 14 16:37:34 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 79b91b27c1055ad58c4f827c72e3f16a14c03900
Author: car <car>
Date:   Fri Aug 14 16:36:19 1998 +0000

    Fixes for WIN32

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp

commit 06c750c9d41ce73655ba57e98051f88cc2f382ff
Author: car <car>
Date:   Fri Aug 14 16:28:19 1998 +0000

    added portable support for quiet_NaN

Src/C_BaseLib/FArrayBox.cpp

commit fff2d0a47e52bccd965ddf7c02a9f7f95be13a8e
Author: car <car>
Date:   Fri Aug 14 14:31:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 53133428a9ad67a1e157999ec82828d1eab8bff7
Author: car <car>
Date:   Fri Aug 14 00:22:09 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 6fb62a945f0ee51337b1f55947d068ae868ccbe5
Author: car <car>
Date:   Thu Aug 13 22:54:40 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 2fd5c5fad63bfe55dacb96c4d9a9cf7ee0bc35a1
Author: car <car>
Date:   Thu Aug 13 22:48:56 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit c0dff225aa2d87d00fb02f8c3f10ebd520d8497a
Author: lijewski <lijewski>
Date:   Wed Aug 12 18:00:53 1998 +0000

    Added more MPI RunStats.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.cpp

commit dc2af11173335094a73afd58229064e23e000e42
Author: lijewski <lijewski>
Date:   Tue Aug 11 20:33:38 1998 +0000

    Added mpi RunStats

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.cpp

commit 6145a17da30e1f3064ea3493b25ca1a933f5ec20
Author: lijewski <lijewski>
Date:   Tue Aug 11 20:33:20 1998 +0000

    Added mpi RunStats.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit f5d2ab0ffc2e5018fa3b010947441ae29b0efb68
Author: lijewski <lijewski>
Date:   Mon Aug 10 17:03:57 1998 +0000

    Didn't get BL_T3E & BL_CRAY stuff quite right.

Src/C_BaseLib/CONSTANTS.H

commit cdc81e29d3180f9269b37d6288a88087c0d913c8
Author: lijewski <lijewski>
Date:   Sat Aug 8 17:25:23 1998 +0000

    Merged in BL_OLD_STL

Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/CONSTANTS.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/tVisMF.cpp
Tools/C_mk/Make.CRAY
Tools/C_mk/Make.OSF1
Tools/C_mk/Make.T3E
Tools/C_mk/Make.defs

commit e2b5ceb880f51fb002c99a11c8d4e0a89571d43e
Author: car <car>
Date:   Fri Aug 7 17:46:59 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 6252cf4b10923a9fdc1f70a46648b40b5bb6c3f3
Author: car <car>
Date:   Thu Aug 6 23:12:04 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit e1655d8e7f2eb2617e2c89cccd9d3610e01c1d0c
Author: car <car>
Date:   Thu Aug 6 20:56:37 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H

commit 24f124b44efbf90c7dfdaaeba74eb74206eb43d5
Author: car <car>
Date:   Thu Aug 6 20:31:09 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H

commit 782b4485715d3f101764f39a64115164ab325457
Author: car <car>
Date:   Thu Aug 6 20:30:04 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 8d098dc8a691205a3481257e1f82dacffd630f40
Author: car <car>
Date:   Thu Aug 6 03:46:58 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit e064629091a034ef081578db5eaff3ab09158dd6
Author: car <car>
Date:   Wed Aug 5 21:42:15 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 8ae87928b523a8f9b55021e25c6aa51d0ac7311a
Author: car <car>
Date:   Wed Aug 5 21:24:42 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp

commit e6f8a740c9430cec2d5ecfb435156ece44214fa5
Author: car <car>
Date:   Wed Aug 5 20:57:59 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 055d94fea9b6ae37df597d8e0feda81120166086
Author: car <car>
Date:   Wed Aug 5 19:21:34 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/.cvsignore
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 314cba5060e343e2fc7e351e4a7d4c5c8b14c6dc
Author: car <car>
Date:   Wed Aug 5 17:49:25 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 35096a6fe2509ecdaf21a8d61899e83aa47ef5e1
Author: car <car>
Date:   Wed Aug 5 17:38:20 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 6f2e25b736f15cb538e13debc93f9996b45e3667
Author: car <car>
Date:   Tue Aug 4 22:57:33 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/hgproj.pg

commit f04343d72d21afe2369b0ac432cde0eb88227bff
Author: car <car>
Date:   Tue Aug 4 21:48:58 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 9880d1c1619ee3e18b467df34e2863abd92b415f
Author: car <car>
Date:   Tue Aug 4 18:25:22 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit aa711f5b1f6302c9c7ad68088b3904b4a1db1116
Author: lijewski <lijewski>
Date:   Tue Aug 4 16:41:55 1998 +0000

    Removed verbose output referring to flushing various caches.
    Open gridlog, datalog and runlog in append mode.

Src/C_AMRLib/Amr.cpp

commit 9d1a221f3ec1eac0adb1c6d63e09c1b911d33aea
Author: car <car>
Date:   Mon Aug 3 20:35:00 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 7a865d336a17fa2c6e4b0daebaee5b3b7b74504c
Author: car <car>
Date:   Mon Aug 3 20:02:39 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit ad27d2c1702d98e30fafb8e64f4cf1c7f82da3d8
Author: car <car>
Date:   Mon Aug 3 19:26:26 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit caf87eb1a45bab6ccf73ffcaf6fcb043eb4d888e
Author: car <car>
Date:   Mon Aug 3 18:01:56 1998 +0000

    Some parallel fixes for single level.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 2d64b23f1c1bf932972940ac67ad49a6b169200f
Author: car <car>
Date:   Fri Jul 31 17:23:04 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 7eafaa7d5c0e2a8f8b80c5e3628b8e9c24939320
Author: car <car>
Date:   Thu Jul 30 23:14:14 1998 +0000

    Removing BSP

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/Make.package
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/Make.package
Tests/LinearSolvers/C_CellMG/main.cpp

commit 32978dd30013a48b5ba02b7f6df8a5835f33cbaf
Author: car <car>
Date:   Thu Jul 30 23:13:45 1998 +0000

    more preload removal mods

Tools/C_util/README

commit 3aa8d5a9499020e7f9a9013652cb1537c2bd6676
Author: car <car>
Date:   Thu Jul 30 23:06:43 1998 +0000

    Rid ourselves of BSP files...

Tools/C_util/preload.cpp

commit 5a0a4653370ebe8d60ddd1d09ca7e602f75079e1
Author: car <car>
Date:   Thu Jul 30 21:01:06 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 4f8c64e3585136790ce0b832d1dbd30c0f1c4cd1
Author: lijewski <lijewski>
Date:   Wed Jul 29 20:44:12 1998 +0000

    Use Barrier() instead of Synchronize() to sync across processors.

Tools/C_util/WritePlotFile.cpp

commit 54f73a5ab9351ea864396b5c1ac0020e8a3227a8
Author: lijewski <lijewski>
Date:   Wed Jul 29 20:25:55 1998 +0000

    Brought up-to-date with latest ParallelDescriptor mods.

Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp
Src/LinearSolvers/C_TensorMG/Test/testVI.cpp
Tests/LinearSolvers/C_TensorMG/testVI.cpp

commit b587af721b78200a3d1c15bf19181e4813133153
Author: lijewski <lijewski>
Date:   Wed Jul 29 20:04:35 1998 +0000

    Added back in Broadcast() -- needed by some vis code.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit b05b5b4acd261cc3c64c643e4189020a9bfedcd5
Author: lijewski <lijewski>
Date:   Wed Jul 29 19:26:39 1998 +0000

    Only use cache if BL_USE_MPI && !BL_NO_PROCMAP_CACHE

Src/C_BaseLib/DistributionMapping.cpp

commit 6023333a3d42059ea569d5ff4c8c2e6527472fdf
Author: lijewski <lijewski>
Date:   Wed Jul 29 19:09:30 1998 +0000

    Brought up-to-date with new ParallelDescriptor and FabArray.H.

Src/C_BoundaryLib/FabSet.cpp

commit 91333ecfc6805411105ad30ca446d1f5a20ba566
Author: lijewski <lijewski>
Date:   Wed Jul 29 19:09:05 1998 +0000

    Brought up-to-date with new ParallelDescriptor and FabArray.H

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.cpp
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/InterpBndryData.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 78483c3c480b79a757c93f72367937b03c010f69
Author: car <car>
Date:   Wed Jul 29 17:21:30 1998 +0000

    Added comment for Windows.

Src/C_BaseLib/Utility.H

commit 546589ac41e0a59ebbc3cef467fc839165843702
Author: car <car>
Date:   Wed Jul 29 00:06:04 1998 +0000

    Dosify.

Src/C_BaseLib/Utility.cpp

commit e8a485fc0adb43b654d4f6c61c5037fd718fd499
Author: lijewski <lijewski>
Date:   Tue Jul 28 17:47:49 1998 +0000

    Undid the static RunStat -- T3E had a bug.

Src/C_BaseLib/DistributionMapping.cpp

commit f77e226b5eeb656262b548de2e75116e849982d0
Author: car <car>
Date:   Tue Jul 28 17:16:06 1998 +0000

    Added ccse-mpi.H as a T_source.

Src/C_BaseLib/Make.package

commit caa642b152f12f2982ba021302729ced586acce3
Author: car <car>
Date:   Tue Jul 28 03:21:17 1998 +0000

    windows fixes

Src/C_BaseLib/ccse-mpi.H
Src/C_BaseLib/pBoxLib_2.dsp

commit c4ff8ac29c2f9b25ac8ed98ecfd80c9b4bb69cce
Author: lijewski <lijewski>
Date:   Mon Jul 27 21:33:36 1998 +0000

    Now using <ccse-mpi.H> instead of <mpi.h>

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit 8186fe09c17d8b69589c55c667ee541cc50b2dee
Author: lijewski <lijewski>
Date:   Mon Jul 27 21:33:06 1998 +0000

    Now using <ccse-mpi.H>

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/VisMF.cpp

commit 3c5cdb66510427444320d0231f403ad8d2178090
Author: lijewski <lijewski>
Date:   Mon Jul 27 21:32:46 1998 +0000

    Encapsulates <mpi.h> making it slightly easier to change from
    using BL_USE_MPI or not.

Src/C_BaseLib/ccse-mpi.H

commit 1f558f6a85761f365401b3276d0c035fb18ab1a3
Author: lijewski <lijewski>
Date:   Mon Jul 27 21:14:16 1998 +0000

    Made RunStats(fabarray_copy) a static object.

Src/C_BaseLib/FabArray.H

commit 599aa935f3277f4fe54e8d5a4485c31e8a2f1c73
Author: lijewski <lijewski>
Date:   Mon Jul 27 20:43:37 1998 +0000

    Added BL_NO_PROCMAP_CACHE to enable the turning off of caching.

Src/C_BaseLib/DistributionMapping.cpp

commit 4200f76071b449f32ff63e288ce4af5d48f07230
Author: lijewski <lijewski>
Date:   Fri Jul 24 22:40:46 1998 +0000

    RunStats object is now static.

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 957e1b0d135bcdde93e0e78f0b132000316ce910
Author: lijewski <lijewski>
Date:   Fri Jul 24 01:25:37 1998 +0000

    Constructor now takes aString instead of char*.

Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp

commit dfde8ef42eccc07c6d310f0c0f63bf30fe86d7e7
Author: lijewski <lijewski>
Date:   Fri Jul 24 01:24:51 1998 +0000

    Brought up-to-date with latest RunStats mods.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BoundaryLib/FabSet.cpp

commit e6baf45ee0a4758feda3ea245af5898b5d7217bb
Author: lijewski <lijewski>
Date:   Thu Jul 23 20:53:10 1998 +0000

    Some code rearrangment to fix g++ 2.8.1 bug on Solaris.

Src/C_BaseLib/DistributionMapping.cpp

commit 2c77613f47bfba5dcba24d31f2837bbe0beca17a
Author: car <car>
Date:   Thu Jul 23 16:34:00 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit e9fa9a876377e1d431cd1aaf730945af2423ebaa
Author: car <car>
Date:   Thu Jul 23 02:49:27 1998 +0000

    Not needed

Src/LinearSolvers/C_NodalMG/Notes.doc

commit 6d3cbd65c3e82e3cf03f6ba49ba8b4acc96c4491
Author: car <car>
Date:   Wed Jul 22 21:23:33 1998 +0000

    *** empty log message ***

Src/C_AMRLib/amrlib.dsp
Src/C_BoundaryLib/bndrylib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit edfd0b923ce8e64ef6f3772be5f12e7e80a32681
Author: car <car>
Date:   Wed Jul 22 19:45:25 1998 +0000

    *** empty log message ***

Src/C_AMRLib/amrlib.dsp
Src/C_BaseLib/pBoxLib_2.dsp
Src/C_BoundaryLib/bndrylib.dsp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 1945b59ab07f0ea61169f8f6512609abd604e2ae
Author: car <car>
Date:   Tue Jul 21 17:44:45 1998 +0000

    MSVC change

Src/C_AMRLib/TagBox.cpp

commit 9b192d4aa4059a202d4fea38ce1cbff83463b503
Author: lijewski <lijewski>
Date:   Tue Jul 21 15:23:40 1998 +0000

    Now can use this stuff in serial w/o calling Start & Stop routines.

Src/C_BaseLib/ParallelDescriptor.cpp

commit e820238b3f1959e2fb6403021954c2cb7b02d428
Author: car <car>
Date:   Fri Jul 17 17:59:07 1998 +0000

    Testing.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit c83cc4c53616704f8295bb5a781316f48df5f2ca
Author: car <car>
Date:   Fri Jul 17 17:32:59 1998 +0000

    Minor changes.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit f1e6548f2967355eabebe683734b2f66646a9969
Author: lijewski <lijewski>
Date:   Thu Jul 16 18:19:18 1998 +0000

    Make sure CoarseBox() for NodeBilinear doesn't produce degenerate boxes.

Src/C_AMRLib/Interpolater.cpp

commit af7c64b42c4ca1711f62378e7f447f89c5b1f3dc
Author: car <car>
Date:   Thu Jul 16 17:34:59 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/Notes.doc
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 589fed441fdf27bdd663a56d10fd118db4cb4fb2
Author: lijewski <lijewski>
Date:   Wed Jul 15 22:42:09 1998 +0000

    Removed TagBoxArray::mergeUnique().
    TagBoxArray::collate() now removes the duplicate IntVects.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit fb196b286b5e7e11493fc2799aff8e060d512432
Author: car <car>
Date:   Tue Jul 14 20:47:26 1998 +0000

    test

Src/LinearSolvers/C_NodalMG/Notes.doc

commit 861afdafbd14142f23bbd7e15eb39bd6d007dd8e
Author: car <car>
Date:   Tue Jul 14 20:23:41 1998 +0000

    Anal changes

Src/LinearSolvers/C_CellMG/ABec_UTIL.F
Src/LinearSolvers/C_CellMG/CG_2D.F
Src/LinearSolvers/C_CellMG/CG_3D.F

commit 6108eca8693b0beb5389a4bb93547319ee3e23a5
Author: car <car>
Date:   Mon Jul 13 21:40:42 1998 +0000

    First CHeckin

Src/LinearSolvers/C_NodalMG/Notes.doc

commit abba5e1ed8c99d59d012c421d027f109cf4232fb
Author: car <car>
Date:   Mon Jul 13 18:17:39 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit bcb3ab2259ae975d9409ab4a941b6344a8a5fc31
Author: car <car>
Date:   Fri Jul 10 22:32:05 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit e8a0deeea75cfb6d2b44a16b8b00921f43a716d8
Author: car <car>
Date:   Fri Jul 10 21:56:16 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 8d52ae5f18fec55134f680e3b5dcf1dcd34facb7
Author: car <car>
Date:   Fri Jul 10 20:13:51 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 11ba2d0688a643e92d0d040c329bc6e2667d629d
Author: lijewski <lijewski>
Date:   Thu Jul 9 18:27:33 1998 +0000

    Added back in dest_comp argument to FillCoarsePatch().

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit a79d76c5ed2011f9a7d6da961d96b02e061750cd
Author: lijewski <lijewski>
Date:   Thu Jul 9 17:59:24 1998 +0000

    Assume dest_comp==0 in FillPatchIterator and FillCoarsePatch

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 3783cf499f9ac199245fc67131b9b55f3a8e8c1b
Author: car <car>
Date:   Thu Jul 9 00:53:37 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 02575940f1b7ffb2157a94d80ad5bce079e41001
Author: car <car>
Date:   Thu Jul 9 00:50:19 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 007d89bbea2baad2c094df354c334ac829d0a187
Author: lijewski <lijewski>
Date:   Wed Jul 8 22:26:37 1998 +0000

    Modest speedup in how we build PIRMMap.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit dcd43befce5f7c84bb62cc5da099fdf55c2cface
Author: lijewski <lijewski>
Date:   Wed Jul 8 21:56:21 1998 +0000

    Fixed very subtle bug in FillBoundary() caching mechanism.

Src/C_BaseLib/MultiFab.cpp

commit 73286732a57c1b6f1e6087a0d5d9fc39dcf3282b
Author: car <car>
Date:   Wed Jul 8 20:19:57 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 9794a496ed3611ed63643573eb8f2f03219940f2
Author: car <car>
Date:   Wed Jul 8 19:59:19 1998 +0000

    *** empty log message ***

Src/C_BaseLib/pBoxLib_2.dsp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit a8f19728a4f40c6f39162b3527c23710d2171eff
Author: lijewski <lijewski>
Date:   Wed Jul 8 19:17:51 1998 +0000

    Added updated version of self-intersection caching for FillBoundary().

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit ae4740d6f79aaf73160d55d66bea39b7bf0abfc1
Author: lijewski <lijewski>
Date:   Wed Jul 8 19:17:16 1998 +0000

    Added MultiFab::FlushSICache() in appropriate place.

Src/C_AMRLib/Amr.cpp

commit 9a3632319996d411b67088a789fe1b7e867b7084
Author: lijewski <lijewski>
Date:   Wed Jul 8 16:36:12 1998 +0000

    Added a sentinel value to m_procmap in DistributionMapping.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp

commit 78fc43e1c1b7e4d095fe3d99de637477f501db28
Author: lijewski <lijewski>
Date:   Wed Jul 8 16:33:56 1998 +0000

    Removed ProcessorMap() from FabArray.

Src/C_BaseLib/Geometry.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 2289e3ec70113ed1d986473dbf8a0e7fcf3b0995
Author: lijewski <lijewski>
Date:   Wed Jul 8 16:33:36 1998 +0000

    Removed ProcessorMap() from FabArray

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp

commit 0a4aaadc089f46ecfae9955567a2959997e674e0
Author: car <car>
Date:   Wed Jul 8 00:20:23 1998 +0000

    *** empty log message ***

Src/C_BaseLib/pBoxLib_2.dsp
Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit d28873e74df0928ea5dc9d9cfde44431cdc64281
Author: lijewski <lijewski>
Date:   Tue Jul 7 20:04:56 1998 +0000

    Added fpb_cache_size to geometry ParmParse in Setup().

Src/C_BaseLib/Geometry.cpp

commit 3d59f6db53ebde2b47d2282d26ad8d85136c0d7d
Author: lijewski <lijewski>
Date:   Tue Jul 7 19:43:28 1998 +0000

    Merged the four readFAB()s into one.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 7df4b362411e8556ea1a144e7cc277449e0efc5f
Author: lijewski <lijewski>
Date:   Tue Jul 7 17:25:11 1998 +0000

    Added BL_COPYRIGHT_NOTICE macro.
    Substituted spaces for TABs.
    Some generic code cleanup.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BoundCond.H
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp
Src/C_BoundaryLib/Mask.H
Src/C_BoundaryLib/Mask.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 0e01d1aee96b3d280ade8437f1ae0a8ad639ecc7
Author: car <car>
Date:   Tue Jul 7 15:41:52 1998 +0000

    Support for g++ 2.8.1

Tools/C_mk/Make.defs

commit 7186cd1cc733035165e0a2517dfac1b60d4bc257
Author: lijewski <lijewski>
Date:   Mon Jul 6 21:17:24 1998 +0000

    Got the sense of a #ifdef wrong.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/VisMF.cpp

commit d3da773e59f0a774943cf250bd7099447f420a65
Author: lijewski <lijewski>
Date:   Mon Jul 6 20:44:47 1998 +0000

    Now use pubsetbuf() by default instead of setbuf().
    BL_USE_SETBUF now means to use setbuf() instead of pubsetbuf().

Tools/C_mk/Make.OSF1
Tools/C_mk/Make.T3E

commit 459d20e3276eb14a511422a09fdd12a92d9b4bdd
Author: lijewski <lijewski>
Date:   Mon Jul 6 20:44:18 1998 +0000

    Now use pubsetbuf() instead of setbuf() by default.

Src/C_BaseLib/VisMF.cpp

commit 5b8c80317cb49b2f792654a0f564bf0185ff06c8
Author: lijewski <lijewski>
Date:   Mon Jul 6 20:44:00 1998 +0000

    Now use pubsetbuf() by default.

Src/C_AMRLib/Amr.cpp

commit cada317fc69798637b4115dbbc5952a2b620b65b
Author: lijewski <lijewski>
Date:   Mon Jul 6 18:05:03 1998 +0000

    Removed a setVal(0).
    Inverted a swith statement and a for loop.

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 434c5c69e320e3923039435f1c89cdf91af01591
Author: lijewski <lijewski>
Date:   Sat Jul 4 03:35:14 1998 +0000

    Fixed bug in FillCoarsePatch().

Src/C_AMRLib/AmrLevel.cpp

commit f58e9da9c926e374b5feaf28a1dae3c3925f8ea5
Author: car <car>
Date:   Thu Jul 2 20:17:06 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/interface.H

commit 8a837b3bc92ffc3727748f66fba70f0e637fcf43
Author: vince <vince>
Date:   Wed Jul 1 20:43:52 1998 +0000

    Added distinction between OSF1 versions 3 and 4.

Tools/C_mk/Make.OSF1
Tools/C_mk/Make.defs

commit 3a132e375641790b623af42799ac0740d056114f
Author: lijewski <lijewski>
Date:   Wed Jul 1 19:20:39 1998 +0000

    Removed FPMINBOX stuff as well as SerialFillPatch() gunk.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 4df6e72642fb0bc9258515571a08b79793925638
Author: lijewski <lijewski>
Date:   Tue Jun 30 23:43:45 1998 +0000

    More simplification to FillPatchIterator.

Src/C_AMRLib/AmrLevel.cpp

commit 2e28220e08879d6f147b403702a1ae05925e411b
Author: lijewski <lijewski>
Date:   Tue Jun 30 15:11:21 1998 +0000

    Make sure not to call SerialFillPatch if NProcs != 1.

Src/C_AMRLib/AmrLevel.cpp

commit 17484ca0af66241cd873a943c273a719197e5e8b
Author: lijewski <lijewski>
Date:   Tue Jun 30 04:33:56 1998 +0000

    Fixed bug in FillPatchIterator.
    Left in some fill patch debugging code.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 4f3e8ba67809b643dc090c24f8a4464a9bb0ff81
Author: lijewski <lijewski>
Date:   Tue Jun 30 04:08:16 1998 +0000

    A tad bit of cleanup.  More needed.

Src/C_AMRLib/Interpolater.cpp

commit 1cd8050ca2d2f88b7d058da73ad8e03b98e836ad
Author: car <car>
Date:   Mon Jun 29 17:03:29 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 4e51b918da634a34a28ac3119d03033269cceaac
Author: car <car>
Date:   Mon Jun 29 17:01:54 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit c5ed2f04341ebf44840e129042d277f8a0134cde
Author: car <car>
Date:   Mon Jun 29 16:44:27 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 522589b17c7a58b042bf6c2df911b3afd00644bb
Author: car <car>
Date:   Mon Jun 29 16:34:21 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit acf789a10b86df783dfe588c1c1744cf9e38c9af
Author: lijewski <lijewski>
Date:   Sat Jun 27 21:34:42 1998 +0000

    Some cleanup in FillPatch()
    FillCoarsePatch() is now more memory efficient.
    FillPatch() now sets course ghost cells outside of physical boundary.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 329113b6dc60d222d12d8d91bac10ad9ece9cd30
Author: car <car>
Date:   Fri Jun 26 20:09:31 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 6a79874822f9d798364523b78ba691761686f6d7
Author: car <car>
Date:   Fri Jun 26 19:54:02 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit b695555bb809e9b0b50c7e5bcc14daefafdb3d08
Author: car <car>
Date:   Thu Jun 25 21:54:33 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp

commit 5fbc9ef19bdae609667d23300f04574d3c992cd3
Author: car <car>
Date:   Thu Jun 25 21:26:58 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit b3743151376b29b69b8ef4144d1b71e605a78e9e
Author: car <car>
Date:   Thu Jun 25 16:34:37 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit ea451921df41c1d1bc392de4da90e198f9de5095
Author: car <car>
Date:   Thu Jun 25 15:54:12 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 4cce7c3b128b5ccb8cf9fb25fdf95074d582fa2c
Author: car <car>
Date:   Thu Jun 25 00:15:55 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit b1b26653a1392d1cf1f539205922ed5b67bb4d98
Author: car <car>
Date:   Wed Jun 24 23:46:21 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit ade3a0ef1ec57858f777b72e2923bcd4dcc38aa7
Author: car <car>
Date:   Wed Jun 24 20:49:06 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 4235eda301043d0343b4880f45522c2ec6d981a2
Author: car <car>
Date:   Wed Jun 24 17:34:36 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit c67a198fd430ede7cef3f8852a58ac9d2bf8f82e
Author: car <car>
Date:   Wed Jun 24 17:26:13 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit 7994afbbbb1a2cf3fa601aa5490636d2b68e589d
Author: car <car>
Date:   Tue Jun 23 23:57:52 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit ea66c56bd38d34d5213e9efa9f80b7f22a9e1443
Author: car <car>
Date:   Tue Jun 23 21:52:08 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit deca473695175c5ac6be40aba50b0e99ca9cb514
Author: car <car>
Date:   Sun Jun 21 22:10:35 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp

commit 1e6f48fdf3af3ef7c27e62c16e12c3df6ce4d4a8
Author: car <car>
Date:   Sun Jun 21 21:53:28 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 297e34e72608d47510e0073e12b575c6f5a72b3d
Author: lijewski <lijewski>
Date:   Sun Jun 21 18:02:39 1998 +0000

    Added additional assert()s re: AddBox() return values.

Src/C_BaseLib/Geometry.cpp
Src/C_BoundaryLib/FabSet.cpp

commit d8e143ffdec5f91079936452a48bcb40f81da331
Author: lijewski <lijewski>
Date:   Sun Jun 21 17:56:23 1998 +0000

    Added additional assert()s re: AddBox() return values.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit 4b4852854c915a0c945cc58d12bc6ef7b1422b3c
Author: lijewski <lijewski>
Date:   Sat Jun 20 16:16:09 1998 +0000

    Added copyright notice macro.

Src/C_AMRLib/Interpolater.H

commit ad5a1968f7cbdb7de33f17c54c17e8305f11b03f
Author: lijewski <lijewski>
Date:   Sat Jun 20 03:20:02 1998 +0000

    Fixed bug in mapPeriodic().

Src/C_AMRLib/TagBox.cpp

commit e60a3898d4a02076aa0da1fc0cd9aeae2f383a98
Author: car <car>
Date:   Fri Jun 19 22:47:15 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit b690fc7abda317a22f772b29a020f85c209af38a
Author: car <car>
Date:   Fri Jun 19 19:06:45 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 475223d4f8e8121b4c3e4ae9fec5a3c759a87fde
Author: car <car>
Date:   Fri Jun 19 18:18:21 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit cd36cc80c6becd95dca68349e68650f7b0899668
Author: car <car>
Date:   Fri Jun 19 18:18:20 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 43e1badb4e0459a737037fce43b1fdd580f1bde5
Author: lijewski <lijewski>
Date:   Thu Jun 18 23:45:52 1998 +0000

    Added another assert().

Src/C_BoundaryLib/FabSet.cpp

commit 4b62b801fd3549309b84739be7a89de805b8754d
Author: car <car>
Date:   Thu Jun 18 19:44:50 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 8abc89b589405f61b629598e9d21267a8d25abaa
Author: car <car>
Date:   Thu Jun 18 18:09:22 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit a4cfcc34e6eb6d2bbfce0e65f047841ed1b037e8
Author: car <car>
Date:   Thu Jun 18 17:54:29 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 6486b5da0e17423f4b6b4e9b10d5e04ea4fdfd31
Author: car <car>
Date:   Thu Jun 18 15:36:57 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 9cbaa9f73bbe6f20924e6eaa38d5e0ab32e5fc06
Author: lijewski <lijewski>
Date:   Thu Jun 18 04:12:41 1998 +0000

    Fixed a bug in the caching of FPBs.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit a7ffe122990c6ad885b4d5876843392a5ceb4bd4
Author: car <car>
Date:   Wed Jun 17 23:20:31 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 1b967c15927e3e04394b347be294cd9df4713b52
Author: car <car>
Date:   Wed Jun 17 19:15:52 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 2e523afd81ad6df3ecad1275a0620667cd7c7091
Author: car <car>
Date:   Wed Jun 17 18:16:57 1998 +0000

    2D Changes.2D Changes.

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 812b8d86e822387bac39147a363acab6058c778b
Author: car <car>
Date:   Wed Jun 17 18:15:55 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 7038ddfd411b3f0dce5b7a59fb355c304d8b522e
Author: car <car>
Date:   Wed Jun 17 17:23:25 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 88a4a19509a84705d4089fa85cbe13633862a380
Author: car <car>
Date:   Wed Jun 17 17:00:43 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 84879686ccd296e438da29ab8ebbe9bb23855edc
Author: car <car>
Date:   Tue Jun 16 23:30:05 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit 6579ceb48e8aa10386ccee388087ec06117a760b
Author: car <car>
Date:   Tue Jun 16 20:53:48 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/pBoxLib_2.dsp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 305766b357b44b52bd37ce840987204d55f2dd21
Author: lijewski <lijewski>
Date:   Tue Jun 16 18:02:04 1998 +0000

    Slight change regarding how we get MFCD from MultiFab.

Src/C_BaseLib/Geometry.cpp

commit 05f416afb7c5e4e7d79f1e0ba60268761739ddd4
Author: lijewski <lijewski>
Date:   Tue Jun 16 18:01:37 1998 +0000

    Removed call to FlushSICache().

Src/C_AMRLib/Amr.cpp

commit 73c54960c1b8ca320b47a9d134dbfd615813e299
Author: lijewski <lijewski>
Date:   Tue Jun 16 18:01:13 1998 +0000

    Removed the self-intersection cache.
    Doesn't look to have been really useful.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 17806c67378bb437400d7b7e065eedab47b392f7
Author: lijewski <lijewski>
Date:   Tue Jun 16 18:00:46 1998 +0000

    Made FabArrayCopyDescriptor::clear() really work.

Src/C_BaseLib/FabArray.H

commit 73517b11504a57c83c0f5b259a1e5e6789544d4d
Author: car <car>
Date:   Tue Jun 16 16:02:03 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 51cf3787dc9b72dbaba0daa8867dc01178e1e8f7
Author: car <car>
Date:   Tue Jun 16 16:01:06 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 62c546deb23a4b2393744a398106a3fbcc99f690
Author: car <car>
Date:   Tue Jun 16 15:59:43 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit b63539ae98ecaa5f185fc28c20f684fe1f1c5970
Author: car <car>
Date:   Tue Jun 16 15:41:38 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 421b290c5f5e468e9d774f1a2f1556c99cbf2158
Author: car <car>
Date:   Tue Jun 16 03:39:03 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit d880d98cc10b06bab9c0a6d0fd1fe7bad5d77d0f
Author: car <car>
Date:   Tue Jun 16 00:04:49 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 310fee123bfaf8bc89844b41403609a702d42731
Author: lijewski <lijewski>
Date:   Mon Jun 15 23:55:36 1998 +0000

    Added MultiGrid::FlushSICache().

Src/C_AMRLib/Amr.cpp

commit 7263d88fda53239acfe6bda7c8e36d530b38757a
Author: lijewski <lijewski>
Date:   Mon Jun 15 23:55:13 1998 +0000

    Decreased size of cache.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit ef25fff04a690610423d492b546536debd9ff0b0
Author: lijewski <lijewski>
Date:   Mon Jun 15 23:54:24 1998 +0000

    Added grid self-intersection cache for FillBoundary().

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit e3c441a779c0eb04ee27ff08ec9129c716a984a6
Author: lijewski <lijewski>
Date:   Mon Jun 15 23:53:44 1998 +0000

    Inlined operator==()s.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit aeb04c8786b5839fb8336264f53a0c46729b92be
Author: lijewski <lijewski>
Date:   Mon Jun 15 23:52:57 1998 +0000

    Simplified operator==() a tad.

Src/C_BaseLib/Array.H

commit e6dfcf9b0894e75ffab7d7e63f03e831c456eb01
Author: car <car>
Date:   Mon Jun 15 21:18:17 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit d71cba396249d71527cfae046073f71d0a0a9b2d
Author: lijewski <lijewski>
Date:   Mon Jun 15 20:06:16 1998 +0000

    Rearranged how FPB stuff is done.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit f769ce551cc84f8374bd50a44cf7cd11f26eb0d8
Author: car <car>
Date:   Mon Jun 15 16:07:17 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 6a38903106911a536d1fae3a44c9ade0386a211c
Author: lijewski <lijewski>
Date:   Mon Jun 15 15:13:25 1998 +0000

    Added fabarray_copy RunStat.

Src/C_BaseLib/FabArray.H

commit ab4564201577041b650133aa0e9eba8b16b42261
Author: lijewski <lijewski>
Date:   Sun Jun 14 22:05:38 1998 +0000

    Removed default size initializer on cache.

Src/C_BaseLib/Geometry.cpp

commit 48c4cad790ad4f88b930a0b301ee99fc26d1a2ca
Author: lijewski <lijewski>
Date:   Sun Jun 14 06:10:40 1998 +0000

    Fixed some bugs I introduced.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 779364e3052fcd59a4033912832bb1614f7714c4
Author: lijewski <lijewski>
Date:   Sat Jun 13 21:12:28 1998 +0000

    Added more RunStats.

Src/C_BoundaryLib/FabSet.cpp

commit 7630694b76263dbbf634a1455ea08cf55a75a4fc
Author: lijewski <lijewski>
Date:   Sat Jun 13 21:07:34 1998 +0000

    Added reflux RunStat.

Src/C_AMRLib/FluxRegister.cpp

commit 97b5b81ea0099a85e844bbe3462a36a811874ef4
Author: lijewski <lijewski>
Date:   Sat Jun 13 21:00:35 1998 +0000

    Use vector instead of List for cache.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 76632f51bb2f39aa411e9f35ea7daf038026e0fd
Author: lijewski <lijewski>
Date:   Sat Jun 13 21:00:09 1998 +0000

    Some performance mods and additional RunStats.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 9b9a823b656aca6c229f298fac08f62c402eb066
Author: lijewski <lijewski>
Date:   Sat Jun 13 17:28:58 1998 +0000

    Added theFPBmfcd() for cacheing FillPeriodicBoundary info.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 8ad2dbf6ba68648156d11bbf17ec7bb00aac44dd
Author: lijewski <lijewski>
Date:   Sat Jun 13 17:28:30 1998 +0000

    Now use MultiFab::theFPBmfcd()

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 3f0da15e7f7f8efed143bcd3a2f848e685c00653
Author: lijewski <lijewski>
Date:   Sat Jun 13 15:50:01 1998 +0000

    Geometry now caches PIRM stuff.

Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit f48c3fdf54933a99fb8ed38b5e43a4ad68380642
Author: lijewski <lijewski>
Date:   Sat Jun 13 15:49:43 1998 +0000

    Added a CacheSize() member.

Src/C_BaseLib/DistributionMapping.H

commit 0c91232aa61cce893ce29e1ba7ac11659fa8b29d
Author: lijewski <lijewski>
Date:   Sat Jun 13 15:49:08 1998 +0000

    Now cache PIRM stuff.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 00e9124d72155b93d40617b9f7eea08458c717f6
Author: lijewski <lijewski>
Date:   Sat Jun 13 15:48:11 1998 +0000

    Now flush PIRM cache at appropriate time.

Src/C_AMRLib/Amr.cpp

commit 51bb5ec6a3cd570e43bf5749e1774a925fe55ae6
Author: lijewski <lijewski>
Date:   Fri Jun 12 20:34:36 1998 +0000

    Moved FillBoundary() to MultiFab.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit cca0556395601a7d54c5178cb4f6467e97185734
Author: lijewski <lijewski>
Date:   Fri Jun 12 19:39:53 1998 +0000

    Now only use coalescing fab arena if BL_COALESCE_FABS.

Src/C_BaseLib/CArena.cpp

commit e12c6dbbfacb20d3caa58812bd725f05a13cce81
Author: lijewski <lijewski>
Date:   Fri Jun 12 16:47:08 1998 +0000

    Added BL_COALESCE_FABS.

Tools/C_mk/Make.T3E

commit 9b860d8e60047b613f4354939e5c2a90eb342063
Author: lijewski <lijewski>
Date:   Fri Jun 12 16:37:57 1998 +0000

    Unary + and - operators are now const.

Src/C_BaseLib/IntVect.H

commit 89b230199e736e2667e1661a0426a359e7055952
Author: lijewski <lijewski>
Date:   Fri Jun 12 16:25:18 1998 +0000

    Performance mods for second Reflux().

Src/C_AMRLib/FluxRegister.cpp

commit 8d03de2760511975d21af83bcc68f90f5e0b4e07
Author: lijewski <lijewski>
Date:   Fri Jun 12 00:11:14 1998 +0000

    Performance enhancement to first Reflux().

Src/C_AMRLib/FluxRegister.cpp

commit b90d7db247f59c109a790b0f7766c945ce28bd42
Author: lijewski <lijewski>
Date:   Thu Jun 11 22:37:45 1998 +0000

    Performance mods for mapPeriodic().

Src/C_AMRLib/TagBox.cpp

commit 558208994da77641ccbaa15232b3c55c792dd6c7
Author: lijewski <lijewski>
Date:   Thu Jun 11 21:24:25 1998 +0000

    Performance enhancement to CrseInit().

Src/C_AMRLib/FluxRegister.cpp

commit e55809379ffda85f1720dc4a052fba48839f1b57
Author: lijewski <lijewski>
Date:   Thu Jun 11 18:21:29 1998 +0000

    Some FillBoundary() optimizations (hacks?).

Src/C_BaseLib/FabArray.H

commit d119c97c2bcd9fe889e863c3232456f4971266cc
Author: lijewski <lijewski>
Date:   Thu Jun 11 17:23:10 1998 +0000

    Some performance enhancements to copyFrom() and plusFrom().

Src/C_BoundaryLib/FabSet.cpp

commit 9a19cdccd1605873d1fa1e03ed08d6400323c18c
Author: lijewski <lijewski>
Date:   Thu Jun 11 00:06:16 1998 +0000

    Fixed little bug I just introduced.

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 00078cf80f874994c34de77f3b63d06548b9fc7e
Author: car <car>
Date:   Wed Jun 10 23:30:13 1998 +0000

    windows fix

Src/C_BaseLib/FabArray.H

commit 65a2004078af80f40cee8e04196c917aef70ba2f
Author: lijewski <lijewski>
Date:   Wed Jun 10 22:24:32 1998 +0000

    Added RunStats to FillBoundary.

Src/C_BaseLib/FabArray.H

commit 16f2e824443ec3e78e65ae9849da6e9f07c09c60
Author: lijewski <lijewski>
Date:   Wed Jun 10 22:19:49 1998 +0000

    Use std::vector instead of Array.
    They're much more efficient when resize()d often.

Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit dcfcb8f1714432999a67022805d3e4e9877fb8d9
Author: lijewski <lijewski>
Date:   Wed Jun 10 22:18:58 1998 +0000

    Reverted out latest FillPeriodicFabArray mods.  Got to be a better way ...

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 097335334dd289705945393e829e1ca37c9f9c28
Author: lijewski <lijewski>
Date:   Wed Jun 10 19:40:49 1998 +0000

    Added second version of FillPeriodicFabArray().

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit b034f201fa33f926742f7a04d2051334a5f5c647
Author: lijewski <lijewski>
Date:   Wed Jun 10 19:20:00 1998 +0000

    Now use std::vector instead of Array<> in FabArrayCopyDescriptor.

Src/C_BaseLib/FabArray.H

commit 2d2c86ae8a738ccd4d19e2bdb5d6fd4e36ca0f8a
Author: lijewski <lijewski>
Date:   Wed Jun 10 18:23:01 1998 +0000

    Added test for periodicity in FillPeriodicFabArray().

Src/C_BaseLib/Geometry.cpp

commit e45ca4f1657370b4190cb1ceb3e75d0149d59b8c
Author: car <car>
Date:   Wed Jun 10 17:40:45 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 896adae9663807efaf58113ccad6759a91d00192
Author: car <car>
Date:   Wed Jun 10 17:29:00 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 2660bc84a2e4764021a6f019999f0378af381422
Author: lijewski <lijewski>
Date:   Tue Jun 9 23:04:48 1998 +0000

    Added fill_patch RunStats variable.

Src/C_AMRLib/AmrLevel.cpp

commit 9536294693807a36c235922b4c66280acfc6eecf
Author: lijewski <lijewski>
Date:   Tue Jun 9 21:41:39 1998 +0000

    Put ifdef USE_BSP around the sync in isValid().

Src/C_BaseLib/FabArray.H

commit 34cd0bc3919b0e058e000b0d6d671e66adc23fe6
Author: lijewski <lijewski>
Date:   Tue Jun 9 15:02:43 1998 +0000

    Enable BL_USE_SETBUF for OSF1.

Tools/C_mk/Make.OSF1

commit ae082ece64cc1142337df97fd02b4174f7c2d360
Author: lijewski <lijewski>
Date:   Thu Jun 4 17:12:38 1998 +0000

    Dealt with multifab copies taking nghost.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit f5a6cc8e58f681c85b316ae1b7ff4867dfd32bab
Author: lijewski <lijewski>
Date:   Thu Jun 4 00:16:32 1998 +0000

    MF-MF copy never mucks with ghost cells.

Src/C_BaseLib/FabArray.H

commit 5f4676a515289e902b0c3bb0764d3bba628d431a
Author: lijewski <lijewski>
Date:   Wed Jun 3 23:11:19 1998 +0000

    Reverted back to old version of copyFrom(MF) since we no longer
    support nghost argument to MF-MF copy.

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 1b61be54e86e1d39ffcb1f1ff7351180f5e97328
Author: lijewski <lijewski>
Date:   Wed Jun 3 23:10:38 1998 +0000

    No longer take nghost argument for MF-MF copy.

Src/C_BaseLib/FabArray.H

commit 477da0f7fe012673d969051e08cdc0c38c3c968f
Author: lijewski <lijewski>
Date:   Fri May 29 20:58:28 1998 +0000

    When !NDEBUG & BL_OSF1 we hide BaseFab::resize().
    What we do is call BaseFab::resize() and then setVal() with
    invalid floating-point values.
    Should help find erros quicker.

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp

commit 40a239b764bad703d74a675ec8ef13f04318d046
Author: lijewski <lijewski>
Date:   Fri May 29 19:46:52 1998 +0000

    Removed a couple unnecessary lines.

Src/C_AMRLib/TagBox.cpp

commit 6683a15815b31d9df33ce529e463c362c6fd5317
Author: lijewski <lijewski>
Date:   Fri May 29 18:01:37 1998 +0000

    Added toDouble(), toInteger() and toLong().

Src/C_BaseLib/aString.H

commit 805fe73c74e29a0b4761e039d197781af52ac65e
Author: lijewski <lijewski>
Date:   Thu May 28 21:34:29 1998 +0000

    Parallel copy() now generalized to accept num_comp, src_comp & dest_comp.

Src/C_BaseLib/FabArray.H

commit f2a4973e86318984f6c80104d3a50de2ed24d90d
Author: lijewski <lijewski>
Date:   Thu May 28 21:34:01 1998 +0000

    A little cleanup.

Src/C_BaseLib/MultiFab.cpp

commit 27f16269442e3ca642bf6f6a0c0c4b241f118c0e
Author: lijewski <lijewski>
Date:   Thu May 28 21:33:45 1998 +0000

    copyTo(MultiFab) & copyFrom(MultiFab) implemented in terms of FabArray copy

Src/C_BoundaryLib/FabSet.cpp

commit b47788850682a35f2034a2ec20cdbe85ebec06b2
Author: lijewski <lijewski>
Date:   Thu May 28 21:32:03 1998 +0000

    Some more cleanup.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit 7d4180504a0cff75b4f7a9dc29364127a132ef0f
Author: lijewski <lijewski>
Date:   Thu May 28 18:19:29 1998 +0000

    boxarray is now mutable so FabSet can change it in const member functions.

Src/C_BaseLib/FabArray.H

commit 809f7adbadb35b0ac26dce0843f69b7eda0880c3
Author: lijewski <lijewski>
Date:   Thu May 28 18:18:55 1998 +0000

    copyTo(MultiFab) is now implemented with FabArray::copy(FabArray).

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit db57b0ffdae080b83f916b2402d8b8785e7ba950
Author: lijewski <lijewski>
Date:   Thu May 28 02:50:44 1998 +0000

    Using different FabArray::copy() in copyTo().

Src/C_BoundaryLib/FabSet.H

commit 30c04f363a762cb5a23202463b679bf32f43076f
Author: lijewski <lijewski>
Date:   Thu May 28 00:11:22 1998 +0000

    Removed some assert()s that didn't really make sense.

Src/C_BoundaryLib/FabSet.H

commit 842e37c120c921a0085abfc61ed8e9c5f6a7c0e1
Author: vince <vince>
Date:   Wed May 27 22:46:11 1998 +0000

    Added Broadcast for MPI.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 4304a13afa5fcc392db4ffec990a6168a843d671
Author: lijewski <lijewski>
Date:   Tue May 26 22:58:40 1998 +0000

    Merged in new FillFab() routine.
    Not so fast-n-loose with FillBoxId copying.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit f0eae46b3757d6e8d08c3137a3de5f45a3cda594
Author: lijewski <lijewski>
Date:   Tue May 26 22:58:17 1998 +0000

    Merged in second FillFab() routine.
    Not so fast-n-loose with FillBoxId copying.

Src/C_BaseLib/Geometry.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 29d335cf2be752e1808d13a173b355f479fa8dca
Author: lijewski <lijewski>
Date:   Tue May 26 22:57:43 1998 +0000

    Added second FillFab() taking a destination Box.
    Merged common code in two AddBox()s into AddBoxDoIt().

Src/C_BaseLib/FabArray.H

commit e3325ed1d40f79b6dcaa5507bbae196f97d844e8
Author: lijewski <lijewski>
Date:   Tue May 26 17:08:54 1998 +0000

    Integrated in vector<FillBoxId>::iterator.

Src/C_AMRLib/FluxRegister.cpp

commit e74ba3766676db312b1d0899770a8bfd613a325e
Author: lijewski <lijewski>
Date:   Tue May 26 16:17:16 1998 +0000

    Oops.  Didn't check BSP.

Src/C_BaseLib/FabArray.H

commit 40745951f2388f6e84861cebc670400f51707bc2
Author: lijewski <lijewski>
Date:   Tue May 26 00:27:07 1998 +0000

    Now use the form of AddBox() in Reflux() taking FabArray grid index.

Src/C_AMRLib/FluxRegister.cpp

commit eed99680b045c454a5666b43e3f71c7471531ef7
Author: lijewski <lijewski>
Date:   Tue May 26 00:01:48 1998 +0000

    Optimized size of temp FAB used in CrseInit().

Src/C_AMRLib/FluxRegister.cpp

commit 3c7ceda8e9314101565ff2573972cb6ab1c9387b
Author: lijewski <lijewski>
Date:   Mon May 25 22:55:24 1998 +0000

    Optimized away the temp FAB in copyFrom() and plusFrom().

Src/C_BoundaryLib/FabSet.cpp

commit f8c117e4b7ba7cea674d94942d9f2756c865ff1d
Author: lijewski <lijewski>
Date:   Mon May 25 06:01:24 1998 +0000

    Fixed bug in FillBoundary().

Src/C_BaseLib/FabArray.H

commit 5a568f6e567899ff3e9a39760656648e1a9d6600
Author: lijewski <lijewski>
Date:   Mon May 25 05:06:25 1998 +0000

    Fixed some latent bugs in AddBox() calls.
    Did some simplification.

Src/C_AMRLib/FluxRegister.cpp

commit b17e1efa3c62007dd6694d87096ec289d6115f26
Author: lijewski <lijewski>
Date:   Mon May 25 05:01:10 1998 +0000

    Minor fixup.

Src/C_AMRLib/TagBox.cpp

commit eac12aa28099c47c4efd22432f55f45d17129c91
Author: lijewski <lijewski>
Date:   Mon May 25 05:00:19 1998 +0000

    Fixed some bugs in srccomp/destcomp in AddBox() calls.

Src/C_BoundaryLib/FabSet.cpp

commit b6a6cfa04b8e10d38b27eecee8b9c91aca3e348d
Author: lijewski <lijewski>
Date:   Fri May 22 23:52:27 1998 +0000

    Moved more FABs out of inner loops.  Using resize() instead.

Src/C_BaseLib/FabArray.H

commit 2fe7e36c68fb10246020eb576cd4506f252d3437
Author: lijewski <lijewski>
Date:   Fri May 22 23:31:31 1998 +0000

    Only communicate overlap in copyFrom() and linComb().

Src/C_BoundaryLib/FabSet.cpp

commit 62f5e80c81efd59e365c84c0b4e21c5c24bb33ed
Author: lijewski <lijewski>
Date:   Fri May 22 22:30:28 1998 +0000

    Removed a couple assert()s that didn't look OK.

Src/C_BoundaryLib/FabSet.cpp

commit 2a887085ad7107986197b3503f091bfdcd119c4e
Author: lijewski <lijewski>
Date:   Fri May 22 22:08:41 1998 +0000

    Moved some FAB constructors out of inner loops.  Use resize() instead.

Src/C_AMRLib/AmrLevel.cpp

commit ecc1f453b7556a515ef995c43a40585b41df4631
Author: lijewski <lijewski>
Date:   Fri May 22 22:03:14 1998 +0000

    Moved FAB construction out of inner loops.  Use resize() instead.

Src/C_BaseLib/FabArray.H

commit 4393d3bc48bec8b78afbb69d530ff81151d1158f
Author: lijewski <lijewski>
Date:   Fri May 22 21:52:49 1998 +0000

    Added copyTo(MultiFab).

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 045b3203e6975062a0e816042d2c9b5767b30108
Author: lijewski <lijewski>
Date:   Fri May 22 21:46:29 1998 +0000

    Moved some FABs out of inner loops.  Use resize() instead.

Src/C_BaseLib/Geometry.cpp

commit 266e4afb963a61a26e2b00f9a3c7e11ebbe6e828
Author: lijewski <lijewski>
Date:   Fri May 22 21:46:01 1998 +0000

    Added ncomp argument to resize().

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 02a2499619ac40ae141ff8c57bf551829121d023
Author: lijewski <lijewski>
Date:   Fri May 22 21:45:47 1998 +0000

    Moved some FAB constructors outside of loops.  Use resize() instead.

Src/C_AMRLib/FluxRegister.cpp

commit dc5321fd53f3f96288d59e3c9c1373fa1aea6b00
Author: lijewski <lijewski>
Date:   Fri May 22 17:47:11 1998 +0000

    Reverted out previous change; shouldn't have been checked in.

Src/C_AMRLib/DatasetClient.cpp

commit 0a0364f8c4e6ee6b56ce60f26c2906d7bbbd7425
Author: lijewski <lijewski>
Date:   Fri May 22 17:45:14 1998 +0000

    Now using setComplement() on FABs instead of setBndry() on MultiFabs.

Src/C_AMRLib/DatasetClient.cpp

commit 24eaf7d16e257d0cefc11e73c0289057b78e2c1a
Author: lijewski <lijewski>
Date:   Thu May 21 22:44:51 1998 +0000

    CXXOPTF=+K2

Tools/C_mk/Make.T3E

commit 12a182baa04a68f8e7b1cdc34ce7231c47f6d7fc
Author: car <car>
Date:   Thu May 21 21:28:43 1998 +0000

    assert foolishness

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 4c4e44fed2d8d44ce53542b0778023bdf2c13af4
Author: lijewski <lijewski>
Date:   Thu May 21 18:16:52 1998 +0000

    Added final newline in file to quiet KCC

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit bb8a6297234eab5b74eae97365723ecfa92d7f0b
Author: lijewski <lijewski>
Date:   Thu May 21 16:48:39 1998 +0000

    DependentFabArrayIterators now check for equality of processor maps.

Src/C_BaseLib/FabArray.H

commit 35dbc72e3c40e016854763e73a82a93d5a508ee8
Author: lijewski <lijewski>
Date:   Thu May 21 15:04:29 1998 +0000

    Removed DependentMultiFabIterator stuff from FillBoundary().

Src/C_AMRLib/StateData.cpp

commit 73640750c048a2cbdc785c22b95b50af3294c16e
Author: car <car>
Date:   Wed May 20 18:10:05 1998 +0000

    *** empty log message ***

Src/C_BaseLib/pBoxLib_2.dsp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 415b1bd51c9446d6e81536cae4c8f3673c1fc06f
Author: marc <marc>
Date:   Wed May 20 00:10:45 1998 +0000

    Make contains() const

Src/C_BaseLib/RealBox.H
Src/C_BaseLib/RealBox.cpp

commit 2285511c59d677551fad1ea21d38d867b3b53416
Author: marc <marc>
Date:   Tue May 19 21:08:35 1998 +0000

    Fix a couple of little errors.

Src/C_BaseLib/Geometry.cpp

commit 14d82a76c5568d6679f9a75612b6e6a8ca9ab83e
Author: lijewski <lijewski>
Date:   Tue May 19 20:27:03 1998 +0000

    Added no_ovlp argument to FillBoundary stuff for SyncRegister code.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 997dc7062627c80effd9971e549ea4728854d239
Author: lijewski <lijewski>
Date:   Tue May 19 17:10:52 1998 +0000

    Moved allocation of pshifts outside of all loops.

Src/C_BaseLib/Geometry.cpp

commit 8ae6e89d91a060b31af3451224d930dbc840d04b
Author: lijewski <lijewski>
Date:   Mon May 18 17:52:20 1998 +0000

    Some cleanup/simplification ...

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp

commit 0ccff42f46df50de43cd3ce9e1fb17113babaa54
Author: car <car>
Date:   Mon May 18 01:20:10 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 73136f067f1e8954b124cbb0099d5e69b0d53c61
Author: lijewski <lijewski>
Date:   Sun May 17 00:57:23 1998 +0000

    Added FillPeriodicBoundary() taking src_comp and num_comp.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 938932d4f0bc7f7d435ec9d4399330c80f03e58c
Author: car <car>
Date:   Fri May 15 22:31:29 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit 7c546102472b9624a5f8a3be0de5f7852f9bb56e
Author: car <car>
Date:   Fri May 15 22:28:48 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 4910eb18ba70096b013dded6b861df96db598d3c
Author: lijewski <lijewski>
Date:   Fri May 15 18:13:12 1998 +0000

    Fixed bugs in TagBoxArray::mapPeriodic() and TagBoxArray::coarsen().

Src/C_AMRLib/TagBox.cpp

commit 0211e7104de736d6e05828f5f33777be693287ba
Author: car <car>
Date:   Fri May 15 16:36:06 1998 +0000

    some 2D fixes

Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit edcaaf68f0f3197a32d842fec399f8c60f03e993
Author: car <car>
Date:   Fri May 15 16:16:22 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit 4fff2af87318afdaba7a9d565223e81f02d62558
Author: car <car>
Date:   Fri May 15 16:05:36 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit bbd9c6131bcecb00608e82b08f90155ea652d041
Author: car <car>
Date:   Fri May 15 00:32:20 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit ea58e78ff0f4e4183fc1a67aa1e09138dfb83c72
Author: car <car>
Date:   Fri May 15 00:31:48 1998 +0000

    3D only, sorry

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.cpp
Src/LinearSolvers/C_NodalMG/hgparallel.h
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 89344527f0781c9252228dc34841ed004d3c0d96
Author: vince <vince>
Date:   Thu May 14 22:23:04 1998 +0000

    Fixed minor bug due to TagBox changes.

Src/C_AMRLib/DatasetClient.cpp

commit ed129f3a991384f20f89bf62b2b3fe35e6f4e206
Author: almgren <almgren>
Date:   Thu May 14 22:08:50 1998 +0000

    Modified main.cpp. Amr.{H,cpp} to allow the user to specify a starting
    time for the calculation (strt_time, read in the inputs file like stop_time).

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 7325167a8d67186e6b302d51f246e718e9a537b0
Author: lijewski <lijewski>
Date:   Thu May 14 22:06:03 1998 +0000

    -O5 -> -O in FOPTF.  Compiler has problems with few routines.

Tools/C_mk/Make.OSF1

commit d0bcee9a5febd8514c5956b9758aba9f4f9a9ef6
Author: almgren <almgren>
Date:   Wed May 13 23:15:03 1998 +0000

    Changes necessary to pass stop_time through to the applications
    (NavierStokes, HyperClaw, e.g.) so that it can be used for time step
    control.  Also allow only one of max_step and stop_time to be set
    in inputs with the other not affecting the time step control.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H

commit 9f7c2a82232daab9f1b61c79ff1ff6dd6fc008a4
Author: almgren <almgren>
Date:   Wed May 13 18:57:09 1998 +0000

    Changed some ParmParse get's to query's and modified the plot test in Amr::init()
    so that it will make plt0000 if plot_int > 0 OR plot_per > 0.

Src/C_AMRLib/Amr.cpp

commit 442daa7b5e63cb14588e1ec9ac4f603b96345fb6
Author: lijewski <lijewski>
Date:   Tue May 12 22:12:42 1998 +0000

    Can now pass name of probin file to Fortran.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/PROB_AMR_F.H

commit f12fd16dad227a17c3087d42f50fc8d2ed5f5726
Author: car <car>
Date:   Tue May 12 19:38:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 86a8cf1aa1e5175962b91f33f8ca9c033a97655d
Author: car <car>
Date:   Tue May 12 15:36:58 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 7a7519751512c641fbeecb22395fb0bb36cc07c6
Author: lijewski <lijewski>
Date:   Mon May 11 17:45:46 1998 +0000

    -O2 -> -O for CXXOPTF when using g++.
    The former yields some nasty optimization bugs.

Tools/C_mk/Make.defs

commit 02404fcf90a9a2e1d870421d6433cb6915d5d1ab
Author: lijewski <lijewski>
Date:   Mon May 11 17:06:24 1998 +0000

    Removed some doc++ comments that didn't translate to html well.

Src/C_AMRLib/Derive.H
Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/StateDescriptor.H

commit 7ad339e6c6f5a1ff0f14364991626e7b6ad99b9f
Author: car <car>
Date:   Fri May 8 22:25:19 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 02e74468af9c2232ddb62acc30355ca1d30377f6
Author: car <car>
Date:   Fri May 8 17:47:03 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/interface.cpp

commit 86bff1dbe3df0bc33e6e4862c0b1c6102956df90
Author: lijewski <lijewski>
Date:   Fri May 8 15:58:50 1998 +0000

    Added more Doc++ comments.

Src/C_AMRLib/FluxRegister.H

commit 3daabeeda6935b050198ecc0bb91b1e8a66fc21a
Author: lijewski <lijewski>
Date:   Fri May 8 15:57:12 1998 +0000

    Updated Doc++ comments.

Src/C_BaseLib/Box.H

commit a543fb636b2b07d62a738f98b99e23358930cdac
Author: marc <marc>
Date:   Fri May 8 00:23:56 1998 +0000

    Fix up stuff in Reflux that was wrong for certain combinations of
    src_comp/dest_comp/etc.

Src/C_AMRLib/FluxRegister.cpp

commit f42be05ec8cb72da14fa2ff96e7642197d420ee5
Author: lijewski <lijewski>
Date:   Thu May 7 22:26:09 1998 +0000

    Added ResetWallClockTime().

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit c2e50d6c3f96855499cfa7981dac6f628d866698
Author: car <car>
Date:   Thu May 7 19:39:38 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit aa127c43c81579dd22b51f18e14ad7a472b740f2
Author: car <car>
Date:   Thu May 7 18:28:59 1998 +0000

    Microsoft VC++ bug with nested classes

Src/C_BaseLib/Geometry.H

commit 8e66035e94f7805e8f0eea7c45149ea05cfdabe3
Author: lijewski <lijewski>
Date:   Wed May 6 22:36:14 1998 +0000

    Added doc++ comments.

Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/RealBox.H
Src/C_BaseLib/RealBox.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/FabSet.H

commit 96a6be0aef77c841645d730d20e21e3b1c7ea5ca
Author: car <car>
Date:   Wed May 6 22:21:07 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 2a0447b292c785b132d735694aa1d02deb99b81e
Author: car <car>
Date:   Wed May 6 20:11:54 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 042f08fc0aaca7f500be693e9f7807e71224a072
Author: lijewski <lijewski>
Date:   Wed May 6 17:52:43 1998 +0000

    Gunk for doing doc++

Src/C_BoundaryLib/GNUmakefile

commit c314ea5979524c87706b22bcf52bd13138d3a04a
Author: lijewski <lijewski>
Date:   Wed May 6 17:50:44 1998 +0000

    Added doc++ comments.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/BCRec.H
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Derive.H
Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/LevelBld.H
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp
Src/C_AMRLib/TagBox.H

commit 4da161f2317d6adcb4c2b8bed4203406956e94a3
Author: lijewski <lijewski>
Date:   Wed May 6 17:50:30 1998 +0000

    Gunk for doing html and ps from Doc++ comments.

Src/C_AMRLib/GNUmakefile

commit c4c7094080429ad7cddcece84107506033bfc094
Author: car <car>
Date:   Wed May 6 03:33:49 1998 +0000

    *** empty log message ***

Src/C_AMRLib/.cvsignore
Src/C_BaseLib/.cvsignore
Src/C_BoundaryLib/.cvsignore
Src/LinearSolvers/C_CellMG/.cvsignore
Src/LinearSolvers/C_NodalMG/.cvsignore

commit 7a33c2d28a6be7ae83d636593163fc8069d268de
Author: car <car>
Date:   Tue May 5 00:25:29 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 779ffa56232870e248e3b39a4b1262d3e609be34
Author: lijewski <lijewski>
Date:   Mon May 4 23:13:13 1998 +0000

    Implemented ReduceBoolAnd() and ReduceBoolOr() for MPI.

Src/C_BaseLib/ParallelDescriptor.cpp

commit f7923952cfa21b74e91448752be7eb9abbe2e90e
Author: lijewski <lijewski>
Date:   Mon May 4 21:24:53 1998 +0000

    Added doc++ comments.

Src/C_BaseLib/Array.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/CArena.H
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/NormedFab.H
Src/C_BaseLib/OrderedFab.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/RunStats.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/VisMF.H

commit 31b397cc33c62fdc30667a28b075109fd1377c68
Author: car <car>
Date:   Mon May 4 17:36:56 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 3133bc231a2528d010f6b5c892729d75eab50ad0
Author: car <car>
Date:   Fri May 1 19:18:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 7dfae3d4c3a5017927669d5bf57e138e1b941df1
Author: car <car>
Date:   Fri May 1 18:23:58 1998 +0000

    *** empty log message ***

Src/C_BaseLib/GNUmakefile
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 6bdc6e942b23045ad199191cbd3b14498750b197
Author: lijewski <lijewski>
Date:   Fri May 1 17:12:32 1998 +0000

    Mods to FillFab() so g++ 2.8.1 will compile.

Src/C_BaseLib/FabArray.H

commit 09e18dbb6c31845225873da9a7fe3e4c1274bb1f
Author: lijewski <lijewski>
Date:   Thu Apr 30 18:04:33 1998 +0000

    Removed member template OpMin().

Src/C_BaseLib/Utility.H

commit 1637ab5b15aef54384b987b721df5ce22db52b84
Author: lijewski <lijewski>
Date:   Thu Apr 30 16:35:03 1998 +0000

    Mods to quiet g++ 2.8.1

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/ArithFab.H
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/Utility.cpp

commit 8eec662d54356745473741990bee19a9a53bef98
Author: lijewski <lijewski>
Date:   Thu Apr 30 15:51:19 1998 +0000

    Removed BL_AUTO_INSTANTIATE

Tools/C_mk/Make.OSF1
Tools/C_mk/Make.defs

commit 856bbdde82198f01ab360aaae1a4be97e29667eb
Author: lijewski <lijewski>
Date:   Wed Apr 29 23:12:37 1998 +0000

    fixed typo for GNUG workaround

Src/C_BaseLib/Geometry.H

commit 4abead740996163b37b52e0509d0ac9fce318ec7
Author: car <car>
Date:   Wed Apr 29 22:39:44 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 5884a75b7c9984551ae2eb9736f36f9e1a92b1ff
Author: lijewski <lijewski>
Date:   Wed Apr 29 20:06:10 1998 +0000

    Changed way GNUG workaround was coded.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 920b98a57bf26b430aed7ba7ad47f20196595721
Author: car <car>
Date:   Tue Apr 28 15:43:09 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 223211f8288421dfa2e70e1559a5ca01c8c6e811
Author: car <car>
Date:   Mon Apr 27 21:27:26 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 48d25fd663db95fdcbb17b686c350dae4834932a
Author: car <car>
Date:   Mon Apr 27 20:27:18 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 86d514b9333aca0da7f7ffeced04d8d9916253d6
Author: lijewski <lijewski>
Date:   Mon Apr 27 19:43:46 1998 +0000

    The BoxList argument to AddBox is now passed as a BoxList*.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 41998f167708da8abd3071eb75aafee095116a93
Author: lijewski <lijewski>
Date:   Mon Apr 27 19:43:19 1998 +0000

    The BoxList argument to AddBox is now passed as a BoxList*

Src/C_BaseLib/Geometry.cpp
Src/C_BoundaryLib/FabSet.cpp

commit 8b4a73c136b2252d2000e9d28c3de44a606c3eec
Author: lijewski <lijewski>
Date:   Mon Apr 27 19:42:54 1998 +0000

    The BoxList argument to AddBox is now passed as a pointer to make it
    easier to deal with the case where we aren't interested in the BoxList.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/TagBox.cpp

commit 537dfdce0cc1d4c4e30acef878daed6202e85a76
Author: car <car>
Date:   Mon Apr 27 17:37:40 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit fd2b7b4fdc1d59a3bc09b148c44d2589e7d6e137
Author: car <car>
Date:   Mon Apr 27 17:30:25 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 6bb3101efb4050986b225ece9bf817a04a404dd6
Author: lijewski <lijewski>
Date:   Mon Apr 27 16:31:42 1998 +0000

    Mods to work on non-standard conformant compilers.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 14416136c7817e9fb6bdf1947852c379a5d4aeda
Author: car <car>
Date:   Fri Apr 24 21:23:00 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/interface.cpp

commit 7bc1f484a28ccec35fd0f5903f390a94fb1269f7
Author: car <car>
Date:   Fri Apr 24 21:19:47 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/interface.cpp

commit e07a031177d103eb3223ab889c010260857251bc
Author: lijewski <lijewski>
Date:   Fri Apr 24 17:52:19 1998 +0000

    Now maintain NProcs() and MyProc() in static data members.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 9c5d007076675d5f5639858ee50c44b75d9411b7
Author: lijewski <lijewski>
Date:   Fri Apr 24 17:10:18 1998 +0000

    Collapsed a number of data members of FabComTag.

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H

commit 05d86397ef796da57c9db8838a22d53c882904ad
Author: lijewski <lijewski>
Date:   Fri Apr 24 16:28:57 1998 +0000

    Fixed typo.

Src/C_AMRLib/FluxRegister.cpp

commit 958170a51bc76d62152acd24d311601f38ead464
Author: lijewski <lijewski>
Date:   Fri Apr 24 16:23:58 1998 +0000

    Use query() instead of contains() to set amr.v

Src/C_AMRLib/Amr.cpp

commit e7cbe8c869950ca62cc1ebe359c6b77b16505749
Author: car <car>
Date:   Fri Apr 24 01:03:30 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/interface.cpp

commit 184b42b94aabc4302e7d3982210a20dcfb10076c
Author: lijewski <lijewski>
Date:   Fri Apr 24 00:11:38 1998 +0000

    Got CrseInit()/CrseInitFinish() working with MPI.

Src/C_AMRLib/FluxRegister.cpp

commit 97506424b51bc1a088f3027e26c3a79905d4d453
Author: car <car>
Date:   Thu Apr 23 22:37:48 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/interface.H

commit 72bcb0544026fe306348e2ccaaa757d462a9298b
Author: car <car>
Date:   Thu Apr 23 21:13:51 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 15cf84779e46fbedda76e02eb3e67d133f234cb9
Author: car <car>
Date:   Thu Apr 23 17:24:18 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 4f0a1fdc9ba91628b9664d9af931bfac1bef83f0
Author: lijewski <lijewski>
Date:   Thu Apr 23 16:37:32 1998 +0000

    MPI_Send() -> MPI_Ssend()

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/VisMF.cpp

commit 0dc2b0f7a67e6297900c3dc58d7a4a8f4dc3158e
Author: car <car>
Date:   Thu Apr 23 05:07:39 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit cc549725f601d3ef94df81b6984aa6d7189891d6
Author: car <car>
Date:   Thu Apr 23 04:48:44 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit 9c7eb639b3a877cdaade59aab021713f4c75f671
Author: car <car>
Date:   Thu Apr 23 04:46:04 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit be5cba063b9c6bba49550372936f36289d501b0c
Author: car <car>
Date:   Thu Apr 23 04:31:27 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit d7fa0d5b05a82669a6f6cccf3e4e3afe0574adfd
Author: car <car>
Date:   Thu Apr 23 04:13:12 1998 +0000

    *** empty log message ***

Src/C_AMRLib/Amr.cpp
Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 7db1d5cc7fa9f8793f6a44ba0bafd216ce53e667
Author: almgren <almgren>
Date:   Wed Apr 22 23:56:20 1998 +0000

    Removed the trace, debug and silent flags, and replaced them with
    the verbose flag. Also made verbose be defined by pp.contains("v")
    rather than pp.contains("verbose").  This is in keeping with how
    verbose is defined in the IAMR files.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 964861b3c4436f4ca45327765e02f61bc95b2c4d
Author: car <car>
Date:   Wed Apr 22 23:48:13 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/LinOp.H

commit 564e3a292908aa94ab7eee639b470e47cb41bd55
Author: marc <marc>
Date:   Wed Apr 22 23:39:31 1998 +0000

    Added info for periodic boundaries.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit b072e19262ec3d6585a00ec3e726ea8465b27f67
Author: car <car>
Date:   Wed Apr 22 23:39:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 6c15caa335b167bae3d7c60ebced363cbe1096cc
Author: car <car>
Date:   Wed Apr 22 22:51:24 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit a2783df5a9be469d53366e4ae50e4418474ff0f4
Author: lijewski <lijewski>
Date:   Wed Apr 22 22:40:37 1998 +0000

    Bug in TagBoxArray::collate(); used sizeof(IntVect) instead of BL_SPACEDIM.

Src/C_AMRLib/TagBox.cpp

commit 9e174c4a86be597195498c2cf71dcc04808f7041
Author: lijewski <lijewski>
Date:   Wed Apr 22 21:02:48 1998 +0000

    Wasn't erase()ing fabComTagList in MPI case.

Src/C_BaseLib/FabArray.H

commit 4d1458dc693bbbce3760d1e27d2e1e72783d28db
Author: car <car>
Date:   Wed Apr 22 19:58:20 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit c94c80536c0b25198fb976b7036ab07ca523dd1b
Author: lijewski <lijewski>
Date:   Wed Apr 22 19:39:06 1998 +0000

    Add setVal() to bad value when debugging on OSF1.

Src/C_BaseLib/FArrayBox.cpp

commit 2ce37c009ca9930f84af2564f134913ff0e8117c
Author: lijewski <lijewski>
Date:   Tue Apr 21 23:09:42 1998 +0000

    Added TRACER objects to all code making direct MPI calls.

Src/C_BaseLib/VisMF.cpp

commit 40493e15bc24859b598b1116601423a5bdd3d13f
Author: car <car>
Date:   Tue Apr 21 22:24:25 1998 +0000

    *** empty log message ***

Src/C_BaseLib/pBoxLib_2.dsp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit fbbed0fdaca707fe89c052b181ba04498af4d9ac
Author: almgren <almgren>
Date:   Tue Apr 21 22:22:41 1998 +0000

    Slight cleanup.

Src/LinearSolvers/C_NodalMG/proj.cpp

commit ee8fcab2b6ade4f870cff523058f4dc3b8613e06
Author: almgren <almgren>
Date:   Tue Apr 21 22:16:50 1998 +0000

    Modified proj.cpp to add init calls for m.length() = 3 before each test
    of the projection so that each test would have the right initial conditions.
    Also modified the timing routines so they would time the projections and
    not the initializations.

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 32a047481ec70bc25b4190a40bbc069d6ec79e23
Author: car <car>
Date:   Tue Apr 21 21:04:03 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/restrictor.H

commit 7faaecd4624943030a62bb06ebf6fe8195d5b254
Author: marc <marc>
Date:   Tue Apr 21 19:32:43 1998 +0000

    Limit optimization reduction to terrain file.  Possibly to remove
    this if we split up the terrain code further

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 3b9a6e77cdd0fe4b39f4c81e07645d07040be859
Author: car <car>
Date:   Tue Apr 21 16:40:04 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp

commit 75b62c164f5403a9f6af749969919de8503132ab
Author: lijewski <lijewski>
Date:   Tue Apr 21 05:21:08 1998 +0000

    Made parallel-aware.

Src/C_BaseLib/Tracer.cpp

commit b0333b1cf8f93fec60d3e29eddbc59eb2a436be3
Author: lijewski <lijewski>
Date:   Tue Apr 21 05:20:27 1998 +0000

    Commented out TRACER in StartParallel().

Src/C_BaseLib/ParallelDescriptor.cpp

commit 018dbc6008ebe705368b294e9890e00c6e0692cf
Author: car <car>
Date:   Tue Apr 21 02:01:36 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 0b9c3c984f6bcd9ef5e92d4ea936e828aa8d3232
Author: marc <marc>
Date:   Tue Apr 21 01:44:55 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 109a7c8d99bfe5a18e0e11e39bbe2a45f6d79713
Author: car <car>
Date:   Mon Apr 20 23:44:01 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp

commit c6944dee7961335fd4462d037341fba8c6aeeec3
Author: car <car>
Date:   Mon Apr 20 22:57:07 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/interface.H

commit 2f5098661ce89ac74aadfa1ebf9198f98666d1b5
Author: lijewski <lijewski>
Date:   Mon Apr 20 22:43:03 1998 +0000

    Added a few TRACER objects in functions making MPI calls.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit a90ccae964270446692d3bd8a21304270deb4a06
Author: lijewski <lijewski>
Date:   Mon Apr 20 22:34:09 1998 +0000

    Added a few TRACER objects for functions that make MPI calls.

Src/C_BaseLib/FabArray.H

commit 909974fb8248f082c4659f5d5c3ed08882e8b3a6
Author: lijewski <lijewski>
Date:   Mon Apr 20 22:18:29 1998 +0000

    Added TRACER objects to MPI calls.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 0186aa8854aed268a39948e038f2c34a4c0ce122
Author: car <car>
Date:   Mon Apr 20 22:17:10 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 4f4bcf73e6ba8437ac3a31b8b5bd3943adf05240
Author: lijewski <lijewski>
Date:   Mon Apr 20 22:16:38 1998 +0000

    Added fflush(stdout) after printf().

Src/C_BaseLib/Tracer.cpp

commit 8f0f988b36e9354d6b13506a8757a168d7b918b3
Author: car <car>
Date:   Mon Apr 20 20:24:56 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 12679c698478eb4ee599538391d8e1fe59fcd589
Author: car <car>
Date:   Mon Apr 20 19:14:08 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/boundary.cpp

commit 1bb07f853ccbb0a9238c7fc56de60f3ac5c28919
Author: car <car>
Date:   Mon Apr 20 19:14:07 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp

commit dff86a55f0ccac8bcf4c86fbe5dcf8b9133ad0d6
Author: lijewski <lijewski>
Date:   Mon Apr 20 04:18:54 1998 +0000

    The sense of an Assert() was backwards.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 330ba38cc92413f18b53b9394316d000905d03c3
Author: lijewski <lijewski>
Date:   Mon Apr 20 04:18:14 1998 +0000

    Fixed some MPI-specific bugs.

Src/C_BaseLib/VisMF.cpp

commit 69aac649455fc86b32f6d01f6ae4bfac798fb64f
Author: lijewski <lijewski>
Date:   Sun Apr 19 03:46:41 1998 +0000

    Added SetMessageHeaderSize(), ShareVar() and UnshareVar() in MPI as no-ops.

Src/C_BaseLib/ParallelDescriptor.cpp

commit e357907feb377d831e0ddf5d6b1ecbca26165d37
Author: lijewski <lijewski>
Date:   Sun Apr 19 03:46:05 1998 +0000

    MPI-specific code for FabArray::Copy(FAB).

Src/C_BaseLib/FabArray.H

commit e23034df536f9477aba111e2f29e57b1c5f9e0c0
Author: lijewski <lijewski>
Date:   Sat Apr 18 21:24:58 1998 +0000

    Added MPI-specific code for TagBoxArray::collate().

Src/C_AMRLib/TagBox.cpp

commit 59651f4c39dc176254067fa38b1077eb0da57819
Author: car <car>
Date:   Fri Apr 17 23:25:08 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit f16bade4715f43abd22bec03200c4d3e5adb00dc
Author: car <car>
Date:   Fri Apr 17 23:25:07 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit cc921c1f6b2d78573034da47af6c88773fb50e99
Author: lijewski <lijewski>
Date:   Fri Apr 17 22:22:06 1998 +0000

    Added three more integers to CommData.
    Wrote MPI-specific code for CollectData().

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 4962def3da2adc91bb7b0a4a842408c29768ede1
Author: lijewski <lijewski>
Date:   Fri Apr 17 22:21:31 1998 +0000

    Added three more integers to CommData.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit c7d90031f6a3c5f09ee2117cff7dd310e1da3a8f
Author: car <car>
Date:   Fri Apr 17 20:57:04 1998 +0000

    *** empty log message ***

Src/C_BaseLib/pBoxLib_2.dsp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit a0200c6d2fc02f0a1c40203e0abfb1bde4b16266
Author: car <car>
Date:   Fri Apr 17 19:22:41 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 7ed45149c087a9fd60b725888bea54be009dfb49
Author: lijewski <lijewski>
Date:   Fri Apr 17 18:14:12 1998 +0000

    Added fromproc() and id() to CommData.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit 6f1df7a930e3a9eb95db1c4c8ec3a093e85a1d28
Author: lijewski <lijewski>
Date:   Fri Apr 17 18:13:51 1998 +0000

    Added fromproc() and id() to CommData.
    Now use the combination of these two values to match up fab boxes
    and the data on those fab boxes that are sent separately.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 1802928b39c5fa771d2ad54a5b4f84f6e2a6bbbf
Author: car <car>
Date:   Fri Apr 17 16:40:11 1998 +0000

    check for non-existent test file

Src/LinearSolvers/C_NodalMG/proj.cpp

commit bcf531b09601a0f729d6b8705f4258b959d7222e
Author: marc <marc>
Date:   Fri Apr 17 00:30:48 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp

commit 6a9611cf33aaf6fc0da42ccedb9575d0908f6a30
Author: car <car>
Date:   Thu Apr 16 23:54:31 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 17423de807783dde0e6607fc77799a9cc54a86ce
Author: lijewski <lijewski>
Date:   Thu Apr 16 23:07:09 1998 +0000

    Merged in template<> mpi_data_type(T*)

Src/C_AMRLib/FluxRegister.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.cpp

commit 2ee12323d451fb459db57fb162c74f127fb58ccf
Author: car <car>
Date:   Thu Apr 16 22:50:12 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit b2a520b6e7868cb797098109acce68bd5162180e
Author: lijewski <lijewski>
Date:   Thu Apr 16 22:36:15 1998 +0000

    Moved CommData to ParallelDescriptor.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit d0f4fafb7b1ef5df478fd64ec970f3a2528369e7
Author: lijewski <lijewski>
Date:   Thu Apr 16 22:05:13 1998 +0000

    Now use CommData from ParallelDescriptor for MPI communication.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit 5515cf8dd82c59c22d2ade43ca895ccb79eb987f
Author: car <car>
Date:   Thu Apr 16 21:29:05 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit d8ee97aa071883eedbe28eeec1b0714a4c70aa0b
Author: lijewski <lijewski>
Date:   Thu Apr 16 20:31:47 1998 +0000

    Fixed minor nit found by dbs.

Src/C_BaseLib/IntVect.cpp

commit 62cef72d90b81f547446a8f6b959d5ecdb4cad60
Author: lijewski <lijewski>
Date:   Thu Apr 16 20:27:03 1998 +0000

    Some simplification in preparation for MPIification ...

Src/C_BaseLib/FabArray.H

commit e5e2d7e52aec6c0ec6fc688a430b0fbcd141cd89
Author: lijewski <lijewski>
Date:   Thu Apr 16 18:00:41 1998 +0000

    List<> -> vector<> ...

Src/C_BaseLib/FabArray.H

commit 4da74f5fc6f62b6737646f62fe5f4a6eb1d1838c
Author: car <car>
Date:   Thu Apr 16 16:15:48 1998 +0000

    *** empty log message ***

Src/C_BaseLib/pBoxLib_2.dsp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit ec4e872ddeac699273e8e4be1730df8e75a48d6c
Author: lijewski <lijewski>
Date:   Thu Apr 16 00:12:29 1998 +0000

    List<FillBoxId> -> vector<FillBoxId>.

Src/C_BoundaryLib/FabSet.cpp

commit e753ccd2177ee071fb17ea971eac0494474670d5
Author: marc <marc>
Date:   Wed Apr 15 23:47:53 1998 +0000

    reinstate files

Tools/C_util/DatasetClient.H
Tools/C_util/DatasetClient.cpp
Tools/C_util/README

commit 787b450d6fe7d8709f9238691a62409b5aada986
Author: car <car>
Date:   Wed Apr 15 23:42:26 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit aba086ff6ab102dd05ffc03c53d4709f811c8e87
Author: lijewski <lijewski>
Date:   Wed Apr 15 23:31:28 1998 +0000

    List<> -> vector<> ...

Src/C_AMRLib/TagBox.cpp

commit b023c86848d36eb34847fb5ec270159d8cb62147
Author: marc <marc>
Date:   Wed Apr 15 23:29:14 1998 +0000

    Oops! these were already in DataServices

Tools/C_util/README

commit db08156535b6d8705dd60917ac158ea5ace7e39a
Author: marc <marc>
Date:   Wed Apr 15 23:25:30 1998 +0000

    Clean up file

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/Make.package
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/Make.package

commit 9d18f79dec0de6a0a6a1ad1ddb54de3d905ddd08
Author: marc <marc>
Date:   Wed Apr 15 23:19:05 1998 +0000

    Clean up the file a little

Src/LinearSolvers/C_TensorMG/Test/GNUmakefile
Src/LinearSolvers/C_TensorMG/Test/Make.package
Tests/LinearSolvers/C_TensorMG/GNUmakefile
Tests/LinearSolvers/C_TensorMG/Make.package

commit 0118d847c6c94cefe328bc1ce2465a4f6efaa6e1
Author: marc <marc>
Date:   Wed Apr 15 23:17:40 1998 +0000

    Initial revision

Tools/C_util/ArrayView.H
Tools/C_util/README
Tools/C_util/TV_TempWrite.H
Tools/C_util/ViewMF/GNUmakefile
Tools/C_util/ViewMF/Make.package
Tools/C_util/ViewMF/main.cpp
Tools/C_util/WritePlotFile.H
Tools/C_util/WritePlotFile.cpp
Tools/C_util/preload.cpp

commit 392090f32793f530f69e4b243185d8aab0b45f5a
Author: lijewski <lijewski>
Date:   Wed Apr 15 22:49:54 1998 +0000

    List<FillBoxId> -> vector<FillBoxId>
    List<FabComTag> -> vector<FabComTag>.

Src/C_AMRLib/FluxRegister.cpp

commit 3e25f275a2c7f0f4896962fe7379dd08ff699ca0
Author: marc <marc>
Date:   Wed Apr 15 22:36:20 1998 +0000

    Move to util directory

Src/LinearSolvers/C_CellMG/Test/WritePlotFile.H
Src/LinearSolvers/C_CellMG/Test/WritePlotFile.cpp
Src/LinearSolvers/C_CellMG/Test/preload.cpp
Src/LinearSolvers/C_TensorMG/Test/WritePlotFile.H
Src/LinearSolvers/C_TensorMG/Test/WritePlotFile.cpp
Src/LinearSolvers/C_TensorMG/Test/preload.cpp
Tests/LinearSolvers/C_CellMG/WritePlotFile.H
Tests/LinearSolvers/C_CellMG/WritePlotFile.cpp
Tests/LinearSolvers/C_CellMG/preload.cpp
Tests/LinearSolvers/C_TensorMG/WritePlotFile.H
Tests/LinearSolvers/C_TensorMG/WritePlotFile.cpp
Tests/LinearSolvers/C_TensorMG/preload.cpp

commit 28799f46a0f78a7794b8f66fd11bd5e020cfdbef
Author: marc <marc>
Date:   Wed Apr 15 22:14:58 1998 +0000

    Update to properly extend to multiple components

Src/LinearSolvers/C_CellMG/Test/WritePlotFile.cpp
Tests/LinearSolvers/C_CellMG/WritePlotFile.cpp

commit 7c7d4cf87e105ad2e72440e6dcb188109e7cc9ba
Author: marc <marc>
Date:   Wed Apr 15 21:48:09 1998 +0000

    Enter changes necessary for multiprocessor solves.

Src/LinearSolvers/C_TensorMG/DivVis.H
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/MCBndryData.H
Src/LinearSolvers/C_TensorMG/MCBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit c1ef9edb340526c8b3eff59f3b64f480577d0f2c
Author: marc <marc>
Date:   Wed Apr 15 21:34:44 1998 +0000

    Add test files for multiprocessor version of tensor solve

Src/LinearSolvers/C_TensorMG/Test/GNUmakefile
Src/LinearSolvers/C_TensorMG/Test/Make.package
Src/LinearSolvers/C_TensorMG/Test/WritePlotFile.H
Src/LinearSolvers/C_TensorMG/Test/WritePlotFile.cpp
Src/LinearSolvers/C_TensorMG/Test/amrvis.defaults
Src/LinearSolvers/C_TensorMG/Test/inputs2D
Src/LinearSolvers/C_TensorMG/Test/inputs3D
Src/LinearSolvers/C_TensorMG/Test/inputs8
Src/LinearSolvers/C_TensorMG/Test/main_2D.F
Src/LinearSolvers/C_TensorMG/Test/testVI.cpp
Src/LinearSolvers/C_TensorMG/Test/vpramps.dat
Tests/LinearSolvers/C_TensorMG/GNUmakefile
Tests/LinearSolvers/C_TensorMG/Make.package
Tests/LinearSolvers/C_TensorMG/WritePlotFile.H
Tests/LinearSolvers/C_TensorMG/WritePlotFile.cpp
Tests/LinearSolvers/C_TensorMG/amrvis.defaults
Tests/LinearSolvers/C_TensorMG/inputs2D
Tests/LinearSolvers/C_TensorMG/inputs3D
Tests/LinearSolvers/C_TensorMG/inputs8
Tests/LinearSolvers/C_TensorMG/main_2D.F
Tests/LinearSolvers/C_TensorMG/testVI.cpp
Tests/LinearSolvers/C_TensorMG/vpramps.dat

commit 6bd8cade091d432c48501119d57d1d0a7f5ecd97
Author: marc <marc>
Date:   Wed Apr 15 21:28:32 1998 +0000

    Add a couple of test grids.

Src/LinearSolvers/C_TensorMG/Test/grids/gr.3_2x3x4
Src/LinearSolvers/C_TensorMG/Test/grids/gr2D
Tests/LinearSolvers/C_TensorMG/grids/gr.3_2x3x4
Tests/LinearSolvers/C_TensorMG/grids/gr2D

commit bcf3b46bb48cc850daa63202cb8105e2ab76d4f9
Author: marc <marc>
Date:   Wed Apr 15 21:25:55 1998 +0000

    Commit cosmetic and other changes to (nearly) complete the port to
    parallel.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BoundCond.H
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp
Src/C_BoundaryLib/Mask.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/MultiGrid.cpp
Src/LinearSolvers/C_CellMG/WriteMultiFab.H
Src/LinearSolvers/C_CellMG/WriteMultiFab.cpp

commit 0101b7781fd3476a39edebacd6f99a8de00efa77
Author: lijewski <lijewski>
Date:   Wed Apr 15 21:18:31 1998 +0000

    Finished with MPI-specific code for now.

Src/C_AMRLib/FluxRegister.cpp

commit 30ae225d948ff32063f1c63ef9b3eec1af5c99d9
Author: marc <marc>
Date:   Wed Apr 15 20:59:25 1998 +0000

    Convert test codes to multiple processors

Src/LinearSolvers/C_CellMG/Test/Make.package
Src/LinearSolvers/C_CellMG/Test/WritePlotFile.H
Src/LinearSolvers/C_CellMG/Test/WritePlotFile.cpp
Src/LinearSolvers/C_CellMG/Test/amrvis.defaults
Src/LinearSolvers/C_CellMG/Test/main.cpp
Tests/LinearSolvers/C_CellMG/Make.package
Tests/LinearSolvers/C_CellMG/WritePlotFile.H
Tests/LinearSolvers/C_CellMG/WritePlotFile.cpp
Tests/LinearSolvers/C_CellMG/amrvis.defaults
Tests/LinearSolvers/C_CellMG/main.cpp

commit ef34c7f5f435449b6a31c2532b12a05aebc4faf6
Author: marc <marc>
Date:   Wed Apr 15 20:50:28 1998 +0000

    Add input files checking periodic boundary conditions

Src/LinearSolvers/C_CellMG/Test/grids/in.2per_2x2_c
Src/LinearSolvers/C_CellMG/Test/grids/in.3per_2x3x4
Tests/LinearSolvers/C_CellMG/grids/in.2per_2x2_c
Tests/LinearSolvers/C_CellMG/grids/in.3per_2x3x4

commit f49fc08e0c1d2c3de965250fb1af7ecf35636ede
Author: lijewski <lijewski>
Date:   Wed Apr 15 18:04:11 1998 +0000

    More MPI-specific code.

Src/C_AMRLib/FluxRegister.cpp

commit 313f0ae9dd1e2232e5d382cc3a46deb82b7b0b48
Author: lijewski <lijewski>
Date:   Wed Apr 15 16:50:45 1998 +0000

    Some MPIification ....  More to come.

Src/C_AMRLib/FluxRegister.cpp

commit 32984e1036c8b3838853c0a61b99874dc141a383
Author: lijewski <lijewski>
Date:   Wed Apr 15 16:50:26 1998 +0000

    A tad bit of const'ification.

Src/C_AMRLib/TagBox.cpp

commit 56940968355d6528d39cf3a6fcbfff643adef737
Author: lijewski <lijewski>
Date:   Tue Apr 14 23:57:43 1998 +0000

    Changed a few names to more mnemonic ones ...

Src/C_AMRLib/TagBox.cpp

commit 170e1da5e5e2681159747a9e156a1a2f05163b4d
Author: lijewski <lijewski>
Date:   Tue Apr 14 23:01:50 1998 +0000

    Rearranged CrseInit() to facilitate MPI implementation.

Src/C_AMRLib/FluxRegister.cpp

commit 7846eec604e26c2accc75012b9aca8d28ddf5854
Author: lijewski <lijewski>
Date:   Tue Apr 14 21:01:45 1998 +0000

    Some more simplification and cleanup before doing MPI work.

Src/C_AMRLib/FluxRegister.cpp

commit e5b1627644a814fe2d47f62ed4385965b98d6346
Author: lijewski <lijewski>
Date:   Tue Apr 14 20:24:03 1998 +0000

    Now pass integer and Box in MPI as int[1+3*BL_SPACEDIM].

Src/C_AMRLib/TagBox.cpp

commit eb50ede5a8e71c617f9025a01959a17b989b4eb1
Author: lijewski <lijewski>
Date:   Tue Apr 14 19:38:49 1998 +0000

    Optimized a few setVal() calls.

Src/C_BaseLib/FabArray.H

commit d09ef4af3b1446d7f18accc9c62f77b1c870d693
Author: car <car>
Date:   Tue Apr 14 17:30:53 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi.cpp

commit 598323aa1821b86d3139260f1f722f1317e3f705
Author: car <car>
Date:   Tue Apr 14 17:07:24 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi.cpp

commit 265996dce789d49d629f40001711648ca31bc853
Author: lijewski <lijewski>
Date:   Tue Apr 14 16:51:39 1998 +0000

    Added some (as yet untested) MPI-specific code.

Src/C_AMRLib/TagBox.cpp

commit f7ba0a31e21e85f8bdd3f7ba46eb2cb38d6432fe
Author: lijewski <lijewski>
Date:   Tue Apr 14 16:50:53 1998 +0000

    Fixed some syntax errors in MPI-specific code.

Src/C_BaseLib/VisMF.cpp

commit 7eaf492854b2d5a05bfb88f4801bc0d476b47c2d
Author: lijewski <lijewski>
Date:   Mon Apr 13 21:50:13 1998 +0000

    Some more (as yet untested) MPI-specific code.

Src/C_BaseLib/VisMF.cpp

commit 7c814b7b1aaad1efb1d1a3deff5cdba8e127603b
Author: lijewski <lijewski>
Date:   Mon Apr 13 19:44:42 1998 +0000

    Added some (as yet) untested MPI-specific code.

Src/C_BaseLib/VisMF.cpp

commit 18c713475faa1f08aadca8d1f83d007949daf90e
Author: lijewski <lijewski>
Date:   Mon Apr 13 19:44:26 1998 +0000

    Added Abort(int) for MPI.
    Now check the return code of MPI calls.

Src/C_BaseLib/ParallelDescriptor.cpp

commit ea05fe6cf65f6fcb750af0938e6c7e2122b8367a
Author: lijewski <lijewski>
Date:   Mon Apr 13 19:44:04 1998 +0000

    Added Abort(int) for MPI use.

Src/C_BaseLib/ParallelDescriptor.H

commit 966a44f08bc5e7b14b64c7f9269a8eb405b827c9
Author: car <car>
Date:   Thu Apr 9 22:37:27 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp

commit 6ff233cdace6e699243f195b5f83b430b0f73042
Author: car <car>
Date:   Thu Apr 9 19:27:54 1998 +0000

    fixed makefiles

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/GNUmakefile.main
Src/LinearSolvers/C_NodalMG/Make.package

commit 33321ebf257cebc442b8887120403f15d0d0b572
Author: car <car>
Date:   Thu Apr 9 16:18:10 1998 +0000

    added serial Gather

Src/C_BaseLib/ParallelDescriptor.cpp

commit 29ec0b4872a99382c5025e0940336172c2b830c3
Author: lijewski <lijewski>
Date:   Wed Apr 8 23:42:52 1998 +0000

    Some more simplification.

Src/C_AMRLib/TagBox.cpp

commit a2005f6e4827d2073f1abf1f5647e07fd8355a94
Author: lijewski <lijewski>
Date:   Wed Apr 8 23:29:16 1998 +0000

    Some simplification.

Src/C_BaseLib/VisMF.cpp

commit 692ff903aedd718fb2cd5e2747c51ae3bd375729
Author: lijewski <lijewski>
Date:   Wed Apr 8 21:04:28 1998 +0000

    Added ParallelDescriptor::Gather().

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/RunStats.cpp

commit b51e452b24e25fe1da3003712b8d5c6eb29fd0b7
Author: car <car>
Date:   Wed Apr 8 19:45:20 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp

commit 0fee43962b7e164d169cdbd27dc3eab3a30d08da
Author: car <car>
Date:   Wed Apr 8 17:51:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 7ad78315ad1cc1a636d4be4f7b7837a0adebbedf
Author: lijewski <lijewski>
Date:   Tue Apr 7 23:10:18 1998 +0000

    Only compile in core of knapsack if BSP or MPI is being used.

Src/C_BaseLib/DistributionMapping.cpp

commit c42ceca619e9169b0ec6d7d7021312dd00b4071b
Author: lijewski <lijewski>
Date:   Tue Apr 7 22:24:44 1998 +0000

    More simplification.

Src/C_BaseLib/FabArray.H

commit 18828dfd65865198361daeaccb0c036fc3eceff0
Author: lijewski <lijewski>
Date:   Tue Apr 7 20:13:48 1998 +0000

    Simplified mergeUnique() a tad.

Src/C_AMRLib/TagBox.cpp

commit 6985108df97844650c8c2587c013c579fb4bf629
Author: car <car>
Date:   Tue Apr 7 20:03:17 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 767b57e72be37c77d8be34ca2df71f976fe27233
Author: car <car>
Date:   Tue Apr 7 19:43:54 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile.main
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 7b25059162e5fb24867ada3aca8236baaf52f346
Author: car <car>
Date:   Tue Apr 7 17:36:02 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 556b45bcad378427221e091611aeb14b49ccff42
Author: car <car>
Date:   Tue Apr 7 17:24:21 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 4647e605d2aa1a321f187fdf68d9d261c98997f9
Author: lijewski <lijewski>
Date:   Tue Apr 7 15:52:23 1998 +0000

    Some minor things found by KCC --strict_warnings.

Src/C_AMRLib/Derive.H
Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/FLUXREG_F.H
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/PROB_AMR_F.H
Src/C_AMRLib/StateDescriptor.H
Src/C_BaseLib/COORDSYS_F.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H

commit bcd1e7475d2f0ff5334a0c34a32b998aed9c42df
Author: car <car>
Date:   Mon Apr 6 22:43:19 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit 631768943c8aad2839958074b6caf65ca0f10903
Author: lijewski <lijewski>
Date:   Thu Apr 2 00:14:07 1998 +0000

    Removed cacheRemoteData data member; it was always true.
    Removed faName data member and the two access functions.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H

commit 6a6f5db6775304c7e495736fd00b409ddd998dfb
Author: lijewski <lijewski>
Date:   Thu Apr 2 00:13:02 1998 +0000

    Updated to reflect mods to FabArray.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit bc6e5cf43200c843706e2ae294f9139ff94db90f
Author: lijewski <lijewski>
Date:   Wed Apr 1 18:22:27 1998 +0000

    Removed commented out Synchronize() calls.

Src/C_BaseLib/FabArray.H

commit 4d76767748f04b89803338e9314448c9aa090085
Author: lijewski <lijewski>
Date:   Wed Apr 1 18:21:50 1998 +0000

    Merged in Barrier().

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp

commit 8bf34974f3f5e24bbe98c7600cce127a353c76fd
Author: lijewski <lijewski>
Date:   Wed Apr 1 17:52:37 1998 +0000

    Added Barrier() to the interface.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 5da597e9725998ade522789c151643d5d854108c
Author: car <car>
Date:   Wed Apr 1 17:38:35 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit a88344d39e43fe356d041f522c80580b5036b5bb
Author: lijewski <lijewski>
Date:   Wed Apr 1 17:34:25 1998 +0000

    Added Banner.html for doc++ users.

commit 34f21601c09afe51e276b7664f102aefa0b0620e
Author: car <car>
Date:   Wed Apr 1 17:01:55 1998 +0000

    *** empty log message ***

Src/C_BaseLib/test/tVisMF.cpp
Src/LinearSolvers/C_CellMG/Test/main.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Tests/C_BaseLib/tVisMF.cpp
Tests/LinearSolvers/C_CellMG/main.cpp

commit 09f6fbb6b238095dc66b235ad74eaf7b888be8e0
Author: lijewski <lijewski>
Date:   Wed Apr 1 16:55:04 1998 +0000

    Cleaned up code.
    Implemented Synchronize() for MPI using MPI_Barrier().

Src/C_BaseLib/ParallelDescriptor.cpp

commit fd9d4b8767526bdd70aafe429dc6a2ecf415f85e
Author: car <car>
Date:   Wed Apr 1 00:34:07 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/main.cpp
Src/LinearSolvers/C_TensorMG/Test/testVI.cpp
Tests/LinearSolvers/C_CellMG/main.cpp
Tests/LinearSolvers/C_TensorMG/testVI.cpp

commit dbf7eef80773688866ef21c5409fc25b46814338
Author: car <car>
Date:   Wed Apr 1 00:32:27 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/main.cpp
Src/LinearSolvers/C_TensorMG/Test/testVI.cpp
Tests/LinearSolvers/C_CellMG/main.cpp
Tests/LinearSolvers/C_TensorMG/testVI.cpp

commit effe4482e8d2c52baa8c7daa1d59f94cdb4c559d
Author: car <car>
Date:   Wed Apr 1 00:29:43 1998 +0000

    Made Start/EndParallel static

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/test/tVisMF.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Tests/C_BaseLib/tVisMF.cpp

commit 501126c3081c37821739ed8c34a697aa147ccf09
Author: marc <marc>
Date:   Wed Apr 1 00:27:32 1998 +0000

    Move forward declarations to fix Doc++ doc generation.

Src/C_BaseLib/MultiFab.H

commit db32bc53c3f404ae8f38161401f6455b6d596f33
Author: car <car>
Date:   Tue Mar 31 22:58:08 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 6f6868db0b09e2f644cb75bef18eed4f133a46d5
Author: car <car>
Date:   Tue Mar 31 20:43:12 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 8802d6ce0152cc6234e9c5373d86d3c46a0199fe
Author: car <car>
Date:   Tue Mar 31 18:43:52 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 9251f066547a179b1d14c69c2382bb7510857a20
Author: car <car>
Date:   Tue Mar 31 18:25:31 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit 679baf2c91d5c6dae1097e4df72b0360f56eb5f7
Author: lijewski <lijewski>
Date:   Tue Mar 31 00:23:59 1998 +0000

    Some reformatting ...

Src/C_AMRLib/FILCC_3D.F
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/MAKESLICE_3D.F
Src/C_BaseLib/COORDSYS_2D.F
Src/C_BaseLib/COORDSYS_3D.F

commit 423bef95a2313b969916a4ba11d84a40bc9fe25b
Author: lijewski <lijewski>
Date:   Mon Mar 30 21:57:32 1998 +0000

    Cleaned up the code for release.

Src/C_AMRLib/BCRec.H
Src/C_AMRLib/BCRec.cpp
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H

commit e6faecbcc1723d43513c5b52f7ef5f9abf0e0336
Author: lijewski <lijewski>
Date:   Mon Mar 30 20:45:51 1998 +0000

    Removed print() and two unimplemented CrseInit()s.

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 2e5ccce351605e8b01e8bd4a83d58d44deaeabcb
Author: lijewski <lijewski>
Date:   Mon Mar 30 20:23:45 1998 +0000

    Removed copyTo(MultiFab).

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 75ae0db1a89fcf0669c232266a0fe3088ecfc74d
Author: lijewski <lijewski>
Date:   Mon Mar 30 20:05:34 1998 +0000

    Removed I/O functions.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 67a14231d13b0d4a1a889d59d6b94c6910fe29f9
Author: lijewski <lijewski>
Date:   Mon Mar 30 20:04:18 1998 +0000

    Removed linInterp().

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit 6d0bcaafd93d7ecb19c8cf39393bf5706798f09f
Author: lijewski <lijewski>
Date:   Mon Mar 30 18:59:27 1998 +0000

    Removed linInterp().

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit cdfec93638f4f6efb5f8f9f12769f4cfd4a1f7da
Author: car <car>
Date:   Mon Mar 30 18:35:57 1998 +0000

    *** empty log message ***

Src/C_AMRLib/amrlib.dsp
Src/C_BaseLib/pBoxLib_2.dsp
Src/C_BoundaryLib/bndrylib.dsp
Src/LinearSolvers/C_CellMG/mglib.dsp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 3474716fcda8d2bc90f17c8e40caef8612fbffd4
Author: lijewski <lijewski>
Date:   Mon Mar 30 18:14:49 1998 +0000

    Removed operator<<().

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit cbfd49040eaee2c3ea913104f358530c91cd2dfa
Author: lijewski <lijewski>
Date:   Mon Mar 30 18:03:00 1998 +0000

    Removed MultiFab(istream).
    Removed readFrom() and writeOn().

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 80ce96576533c95076feb9918307323312b4b8aa
Author: lijewski <lijewski>
Date:   Mon Mar 30 17:28:57 1998 +0000

    Removed FillPatch().
    Removed FillCoarsePatch(FAB).
    Removed USEUNRAVELEDFILLPATCH define.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit afd277debb8c5a73a028e1d625292024e46ef7be
Author: car <car>
Date:   Sun Mar 29 16:46:11 1998 +0000

    *** empty log message ***

Src/C_AMRLib/amrlib.dsp
Src/C_BaseLib/pBoxLib_2.dsp
Src/C_BoundaryLib/bndrylib.dsp
Src/LinearSolvers/C_CellMG/mglib.dsp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 8f6861223b52ea34179fa3cd6ded89b2eb82b176
Author: car <car>
Date:   Sun Mar 29 16:25:55 1998 +0000

    *** empty log message ***

Src/C_AMRLib/amrlib.dsp
Src/C_BaseLib/pBoxLib_2.dsp
Src/C_BoundaryLib/bndrylib.dsp
Src/LinearSolvers/C_CellMG/mglib.dsp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 5b28850c79690d9b3ae704bb2e132243c89d1b18
Author: lijewski <lijewski>
Date:   Sat Mar 28 00:45:04 1998 +0000

    NEWFPMINBOX -> BL_NEWFPMINBOX

Src/C_AMRLib/AmrLevel.cpp

commit 72302898b276f59704c360a816981d364651b4f7
Author: lijewski <lijewski>
Date:   Fri Mar 27 23:53:20 1998 +0000

    Removed BL_PARALLEL_IO define.
    Removed USEOLDFILLPATCH define.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit c1119048349a6656814bc5229911966298e0ebbc
Author: vince <vince>
Date:   Fri Mar 27 18:34:00 1998 +0000

    Minor additions.

Tools/C_mk/Make.T3E

commit 8d2ee8f94a3e9b66b87f7e1f73c5f345107b19e7
Author: marc <marc>
Date:   Fri Mar 27 00:41:26 1998 +0000

    Remove extra copy of tridiag routine

Src/LinearSolvers/C_CellMG/ABec_2D.F

commit e989933a8fc150cc8344bc58d07306bce83b1f56
Author: lijewski <lijewski>
Date:   Fri Mar 27 00:06:39 1998 +0000

    Removed unused rangeType() and corresponding member data.

Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp

commit 09043219e1bcdceac254114ab7c1a8b9f6ac1b2d
Author: lijewski <lijewski>
Date:   Thu Mar 26 22:40:26 1998 +0000

    A useless commit ...

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit 54927ebd36f6d65358717f9c32b6fe95c0e4bc90
Author: marc <marc>
Date:   Thu Mar 26 22:24:04 1998 +0000

    Add PBOXLIB def

Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/test/GNUmakefile.tCArena
Src/C_BaseLib/test/GNUmakefile.test
Src/LinearSolvers/C_NodalMG/GNUmakefile.main
Src/LinearSolvers/C_TensorMG/MCBndryData.H
Src/LinearSolvers/C_TensorMG/MCBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp
Tests/C_BaseLib/GNUmakefile.tCArena
Tests/C_BaseLib/GNUmakefile.test
Tools/C_mk/Make.T3E
Tools/C_mk/Make.defs

commit efb5d9a489d249fdcbdcb4fbe7c85d53a3d4471d
Author: marc <marc>
Date:   Thu Mar 26 19:31:39 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/gr.2_19boxes
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_b
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_c
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_b
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_c
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3x2
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_big
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_b
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_c
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_d
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_e
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_small_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_small_b
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_b
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_c
Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_d
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_2boxes_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_2x3x4
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_big
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_b
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_c
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_shiftedUp
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_small_a
Src/LinearSolvers/C_CellMG/Test/grids/gr.3_stack_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_19boxes
Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_3x2
Src/LinearSolvers/C_CellMG/Test/grids/in.2_big
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_d
Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_e
Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_a
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_b
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_c
Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_d
Src/LinearSolvers/C_CellMG/Test/grids/in.3_2boxes_a
Src/LinearSolvers/C_CellMG/Test/grids/in.3_2x3x4
Src/LinearSolvers/C_CellMG/Test/grids/in.3_big
Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_a
Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_b
Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_c
Src/LinearSolvers/C_CellMG/Test/grids/in.3_shiftedUp
Src/LinearSolvers/C_CellMG/Test/grids/in.3_small_a
Src/LinearSolvers/C_CellMG/Test/grids/in.3_stack_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_19boxes
Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_c
Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_c
Tests/LinearSolvers/C_CellMG/grids/gr.2_3x2
Tests/LinearSolvers/C_CellMG/grids/gr.2_big
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_d
Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_e
Tests/LinearSolvers/C_CellMG/grids/gr.2_small_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_small_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_a
Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_b
Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_c
Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_d
Tests/LinearSolvers/C_CellMG/grids/gr.3_2boxes_a
Tests/LinearSolvers/C_CellMG/grids/gr.3_2x3x4
Tests/LinearSolvers/C_CellMG/grids/gr.3_big
Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/gr.3_shiftedUp
Tests/LinearSolvers/C_CellMG/grids/gr.3_small_a
Tests/LinearSolvers/C_CellMG/grids/gr.3_stack_a
Tests/LinearSolvers/C_CellMG/grids/in.2_19boxes
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_a
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_b
Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_c
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_a
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_b
Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_c
Tests/LinearSolvers/C_CellMG/grids/in.2_3x2
Tests/LinearSolvers/C_CellMG/grids/in.2_big
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_d
Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_e
Tests/LinearSolvers/C_CellMG/grids/in.2_small_a
Tests/LinearSolvers/C_CellMG/grids/in.2_small_b
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_a
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_b
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_c
Tests/LinearSolvers/C_CellMG/grids/in.2_stack_d
Tests/LinearSolvers/C_CellMG/grids/in.3_2boxes_a
Tests/LinearSolvers/C_CellMG/grids/in.3_2x3x4
Tests/LinearSolvers/C_CellMG/grids/in.3_big
Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_a
Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_b
Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_c
Tests/LinearSolvers/C_CellMG/grids/in.3_shiftedUp
Tests/LinearSolvers/C_CellMG/grids/in.3_small_a
Tests/LinearSolvers/C_CellMG/grids/in.3_stack_a

commit 54906dbca6fda685521cc67f1ea1a1fb92185c2d
Author: marc <marc>
Date:   Thu Mar 26 19:15:27 1998 +0000

    Add tensorMG to Parallel repo

Src/LinearSolvers/C_TensorMG/DV_2D.F
Src/LinearSolvers/C_TensorMG/DV_2D.mF
Src/LinearSolvers/C_TensorMG/DV_3D1.F
Src/LinearSolvers/C_TensorMG/DV_3D1.mF
Src/LinearSolvers/C_TensorMG/DV_3D2.F
Src/LinearSolvers/C_TensorMG/DV_3D2.mF
Src/LinearSolvers/C_TensorMG/DV_3D3.F
Src/LinearSolvers/C_TensorMG/DV_3D3.mF
Src/LinearSolvers/C_TensorMG/DV_3D4.F
Src/LinearSolvers/C_TensorMG/DV_3D4.mF
Src/LinearSolvers/C_TensorMG/DivVis.H
Src/LinearSolvers/C_TensorMG/DivVis.cpp
Src/LinearSolvers/C_TensorMG/DivVis_F.H
Src/LinearSolvers/C_TensorMG/MCBndryData.H
Src/LinearSolvers/C_TensorMG/MCBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_2D.F
Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F
Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_F.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp
Src/LinearSolvers/C_TensorMG/MCLO_2D.F
Src/LinearSolvers/C_TensorMG/MCLO_3D.F
Src/LinearSolvers/C_TensorMG/MCLO_F.H
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp
Src/LinearSolvers/C_TensorMG/Test/GNUmakefile
Src/LinearSolvers/C_TensorMG/Test/Make.package
Src/LinearSolvers/C_TensorMG/Test/Palette
Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.H
Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp
Src/LinearSolvers/C_TensorMG/Test/amrvis.defaults
Src/LinearSolvers/C_TensorMG/Test/doit
Src/LinearSolvers/C_TensorMG/Test/dotest
Src/LinearSolvers/C_TensorMG/Test/grids/gr16.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr16x8.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr32.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr32x8.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr64.dog
Src/LinearSolvers/C_TensorMG/Test/grids/gr8.dog
Src/LinearSolvers/C_TensorMG/Test/inputs
Src/LinearSolvers/C_TensorMG/Test/main_2D.F
Src/LinearSolvers/C_TensorMG/Test/main_3D.F
Src/LinearSolvers/C_TensorMG/Test/main_F.H
Src/LinearSolvers/C_TensorMG/Test/preload.cpp
Src/LinearSolvers/C_TensorMG/Test/probin
Src/LinearSolvers/C_TensorMG/Test/testVI.cpp
Src/LinearSolvers/C_TensorMG/Test/vpramps.dat
Src/LinearSolvers/C_TensorMG/visc2d.ma
Src/LinearSolvers/C_TensorMG/visc3d.ma
Tests/LinearSolvers/C_TensorMG/GNUmakefile
Tests/LinearSolvers/C_TensorMG/Make.package
Tests/LinearSolvers/C_TensorMG/Palette
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H
Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp
Tests/LinearSolvers/C_TensorMG/amrvis.defaults
Tests/LinearSolvers/C_TensorMG/doit
Tests/LinearSolvers/C_TensorMG/dotest
Tests/LinearSolvers/C_TensorMG/grids/gr16.dog
Tests/LinearSolvers/C_TensorMG/grids/gr16x8.dog
Tests/LinearSolvers/C_TensorMG/grids/gr32.dog
Tests/LinearSolvers/C_TensorMG/grids/gr32x8.dog
Tests/LinearSolvers/C_TensorMG/grids/gr64.dog
Tests/LinearSolvers/C_TensorMG/grids/gr8.dog
Tests/LinearSolvers/C_TensorMG/inputs
Tests/LinearSolvers/C_TensorMG/main_2D.F
Tests/LinearSolvers/C_TensorMG/main_3D.F
Tests/LinearSolvers/C_TensorMG/main_F.H
Tests/LinearSolvers/C_TensorMG/preload.cpp
Tests/LinearSolvers/C_TensorMG/probin
Tests/LinearSolvers/C_TensorMG/testVI.cpp
Tests/LinearSolvers/C_TensorMG/vpramps.dat

commit 51466191c70b6e0f1e4be55945cf84afd2ae2def
Author: marc <marc>
Date:   Thu Mar 26 18:58:17 1998 +0000

    Added test directory files

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Src/LinearSolvers/C_CellMG/Test/Make.package
Src/LinearSolvers/C_CellMG/Test/Palette
Src/LinearSolvers/C_CellMG/Test/amrvis.defaults
Src/LinearSolvers/C_CellMG/Test/main.cpp
Src/LinearSolvers/C_CellMG/Test/preload.cpp
Src/LinearSolvers/C_CellMG/Test/vpramps.dat
Tests/LinearSolvers/C_CellMG/GNUmakefile
Tests/LinearSolvers/C_CellMG/Make.package
Tests/LinearSolvers/C_CellMG/Palette
Tests/LinearSolvers/C_CellMG/amrvis.defaults
Tests/LinearSolvers/C_CellMG/main.cpp
Tests/LinearSolvers/C_CellMG/preload.cpp
Tests/LinearSolvers/C_CellMG/vpramps.dat

commit d2012999fb58b439a60f6e8dbbfaec0767d0ce25
Author: marc <marc>
Date:   Thu Mar 26 18:55:51 1998 +0000

    Incorporate changes from Bill's tensor solve directory

Src/LinearSolvers/C_CellMG/CG_2D.F
Src/LinearSolvers/C_CellMG/CG_3D.F

commit 9ea73fed1be32867a0a71a635db7fca0c84d7312
Author: almgren <almgren>
Date:   Thu Mar 26 17:51:58 1998 +0000

    Remove geom from setBndryConds call.

Src/C_BoundaryLib/InterpBndryData.cpp

commit 27aceb303de91d1d15f7416e9279ffc5a570dcc8
Author: almgren <almgren>
Date:   Thu Mar 26 17:51:33 1998 +0000

    Remove geom from the setBndryConds call.

Src/C_BoundaryLib/InterpBndryData.H

commit 494156ce680b792910a36b9b6c6b9a5fc9b2412b
Author: lijewski <lijewski>
Date:   Thu Mar 26 17:32:16 1998 +0000

    Added new convert() function.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 6dfbcb7295ad7412d9a11ca6531f377da1b24aca
Author: lijewski <lijewski>
Date:   Thu Mar 26 17:31:50 1998 +0000

    Uses new BoxArray::convert() function.

Src/C_AMRLib/AmrLevel.cpp

commit d60730e7b8a18b0a97f707f5e32862c1b36c044f
Author: lijewski <lijewski>
Date:   Wed Mar 25 21:32:18 1998 +0000

    First cut at parallelized AmrLevel::derive().  Needs to be checked out better.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 42f7b8c782cf8b9e12184a405a2afe72f34dff67
Author: car <car>
Date:   Wed Mar 25 20:59:54 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp

commit fa287ca43aab056bfcdd5f8344a9a6438a603e1a
Author: car <car>
Date:   Wed Mar 25 20:54:31 1998 +0000

    *** empty log message ***

Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/LinearSolvers/C_CellMG/WriteMultiFab.cpp

commit cbb89488c4064c612ec55c1df0af76ced40ee085
Author: car <car>
Date:   Wed Mar 25 19:20:50 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp

commit 69287608d46a6b3d28e275e048f17f5f4f060809
Author: car <car>
Date:   Wed Mar 25 19:17:47 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp

commit b80eb3e3c7460bd9523c66a7c247744c5a41645f
Author: car <car>
Date:   Wed Mar 25 19:03:06 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit c552012402c2bd395db846b09a428c16598d49b5
Author: car <car>
Date:   Wed Mar 25 18:23:08 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/pBoxLib_2.dsp

commit ed078c269f69e382ed28feab5f9132398aa67532
Author: car <car>
Date:   Tue Mar 24 23:45:14 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/.cvsignore
Src/LinearSolvers/C_CellMG/mglib.dsp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit d8c225f640708d95fc60f8f8289da557c6587851
Author: car <car>
Date:   Tue Mar 24 20:18:49 1998 +0000

    *** empty log message ***

Src/C_AMRLib/amrlib.dsp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BoundaryLib/bndrylib.dsp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hglib.dsp

commit 9971aec3582f9b51fde496bcf79d2209e384dc1b
Author: lijewski <lijewski>
Date:   Tue Mar 24 19:08:41 1998 +0000

    Commented out bunch of cout's in old FillPatch routines.

Src/C_AMRLib/AmrLevel.cpp

commit e1942293c0be7a47ae80aaa2e1af721d5db7a11d
Author: lijewski <lijewski>
Date:   Tue Mar 24 18:28:29 1998 +0000

    Some work in preparation for parallelizing FillDerive().

Src/C_AMRLib/AmrLevel.cpp

commit 993f07b149f3f4673b8928614528dcb5790e1109
Author: almgren <almgren>
Date:   Tue Mar 24 07:05:10 1998 +0000

    Moved this file from ../IAMRAll.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BoundCond.H
Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F
Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F
Src/C_BoundaryLib/INTERPBNDRYDATA_F.H
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/InterpBndryData.cpp
Src/C_BoundaryLib/LO_BCTYPES.H
Src/C_BoundaryLib/LO_UTIL.F
Src/C_BoundaryLib/Mask.H
Src/C_BoundaryLib/Mask.cpp
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp
Src/LinearSolvers/C_CellMG/ABec_2D.F
Src/LinearSolvers/C_CellMG/ABec_3D.F
Src/LinearSolvers/C_CellMG/ABec_F.H
Src/LinearSolvers/C_CellMG/ABec_UTIL.F
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_CellMG/CG_2D.F
Src/LinearSolvers/C_CellMG/CG_3D.F
Src/LinearSolvers/C_CellMG/CG_F.H
Src/LinearSolvers/C_CellMG/LO_2D.F
Src/LinearSolvers/C_CellMG/LO_3D.F
Src/LinearSolvers/C_CellMG/LO_F.H
Src/LinearSolvers/C_CellMG/LP_2D.F
Src/LinearSolvers/C_CellMG/LP_3D.F
Src/LinearSolvers/C_CellMG/LP_F.H
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/Laplacian.cpp
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MG_2D.F
Src/LinearSolvers/C_CellMG/MG_3D.F
Src/LinearSolvers/C_CellMG/MG_F.H
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_CellMG/WriteMultiFab.H
Src/LinearSolvers/C_CellMG/WriteMultiFab.cpp

commit 18dd515c42ab7847eb2f640c2b187ae27d403a89
Author: almgren <almgren>
Date:   Mon Mar 23 23:36:17 1998 +0000

    Moving this file from ../IAMRAll.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit d06c8e8ec64b18fb1909079f100118c6a57d8fe1
Author: lijewski <lijewski>
Date:   Mon Mar 23 21:03:17 1998 +0000

    Now maintain DeriveRec in List<DeriveRec> instead of List<DeriveRec*>

Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp

commit 9de50888e7e7ea480229214ec169ac4393f3402f
Author: lijewski <lijewski>
Date:   Mon Mar 23 21:02:56 1998 +0000

    Now maintain ErrorRec in List<ErrorRec> not List<ErrorRec*>

Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/ErrorList.cpp

commit b823cc551e8037d7eaf09d78517ced580412f9aa
Author: lijewski <lijewski>
Date:   Mon Mar 23 20:20:14 1998 +0000

    Removed default constructor and DeriveFuncSrc stuff.

Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp

commit e06890b6773064c664a03153c8ece3a885e47b75
Author: lijewski <lijewski>
Date:   Mon Mar 23 17:23:58 1998 +0000

    Cleaned up the code ...

Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp

commit 500f80b5d940ee5b35f34b9a2081e101ff33edcf
Author: car <car>
Date:   Thu Mar 19 19:02:47 1998 +0000

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Src/LinearSolvers/C_NodalMG/GNUmakefile.main
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Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
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commit ed2f3d02c3db7603aa902e140671ccccadc18548
Author: car <car>
Date:   Mon Mar 16 18:26:33 1998 +0000

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Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 78cad0cf04d5dadc1576576f9c0359691b7640d8
Author: car <car>
Date:   Sun Mar 15 23:44:53 1998 +0000

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commit 061a52241c3255ff6eb4f32993b8c31afd4822f5
Author: car <car>
Date:   Sun Mar 15 20:41:04 1998 +0000

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Src/LinearSolvers/C_NodalMG/amr_multi.cpp
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Src/LinearSolvers/C_NodalMG/cache.H
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
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Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp
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Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit d1c3ee873995175bf0d1d5a81a5c9f1a77f397fb
Author: car <car>
Date:   Fri Mar 13 23:10:31 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit cadf06710b601e167485c418c76d51922b8a4eb6
Author: car <car>
Date:   Fri Mar 13 22:18:43 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
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commit 3db41b0e97acff5837d93fd5f4e3ca97a9bca63e
Author: car <car>
Date:   Fri Mar 13 20:50:30 1998 +0000

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Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit c85294e902d5f40f0f0bc8ebf8870c0fd998bc45
Author: car <car>
Date:   Thu Mar 12 23:21:13 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/cache.H
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 6970820bc9a7f6d71d7c56dfdfea039162ab0307
Author: car <car>
Date:   Thu Mar 12 21:07:13 1998 +0000

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Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 8be5b29236e3468e034411c1ba575a046ae7555d
Author: car <car>
Date:   Wed Mar 11 21:31:05 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 8a60655758cf1c23673f083b6857ab613a18b0d5
Author: car <car>
Date:   Tue Mar 10 23:31:12 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 58ef77c733899e23ca2cf6133395e9bcace0fb83
Author: car <car>
Date:   Fri Mar 6 00:28:22 1998 +0000

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Src/LinearSolvers/C_NodalMG/cache.H
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp

commit ebb64b1d69c3142654d3890b90e2d785105a666b
Author: car <car>
Date:   Thu Mar 5 00:40:33 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 352d330720256f90bf32558458243afc0006b221
Author: car <car>
Date:   Wed Mar 4 22:44:31 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/cache.H
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 75b92dedf7566b09530d4f82e00257cb09744f88
Author: car <car>
Date:   Wed Mar 4 21:16:37 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F
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commit 21878921bdbbe06dd8304b87fe4a4d3883c955ba
Author: car <car>
Date:   Wed Mar 4 03:05:19 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
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commit 3cf9a5e9667aa56135deb03a46e35eb975f8cf2d
Author: car <car>
Date:   Wed Mar 4 02:31:23 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
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commit d3204a9d42cc08a726f6e0c8bcec78cc44299e7d
Author: car <car>
Date:   Wed Mar 4 00:55:42 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.F
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Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit ad21d479ebd8e34dfbe4aed8578993deb248d6c2
Author: car <car>
Date:   Tue Mar 3 23:19:47 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 84032fab90e533e6068e24bdb975500a16ec03b9
Author: car <car>
Date:   Mon Mar 2 17:57:04 1998 +0000

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Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/cache.H
Src/LinearSolvers/C_NodalMG/cache.cpp

commit 30a32794f0af360ed93f9e5b9840e8fabd692019
Author: car <car>
Date:   Sun Mar 1 22:17:46 1998 +0000

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Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 53a1e97f0def542902a922f992aaf076e1dadfee
Author: car <car>
Date:   Sun Mar 1 21:58:36 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F

commit 9fba3e2fb35260266b531312956e15edeb8ad08e
Author: car <car>
Date:   Sun Mar 1 21:51:51 1998 +0000

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Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit 6a52dfb6666a010b61c2873c79f5341c1a7e02d1
Author: car <car>
Date:   Sat Feb 28 17:56:51 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_avg3d.F
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commit 18ff5814921f13fa454e553ef4a5090b756925de
Author: car <car>
Date:   Fri Feb 27 22:49:06 1998 +0000

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Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 040c4955055a835aa1e2edb9b42f0cd4471383f4
Author: car <car>
Date:   Fri Feb 27 21:03:44 1998 +0000

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Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit 0398cf30094464180464c32a7b1dcbf5f43af0ef
Author: car <car>
Date:   Fri Feb 27 21:01:17 1998 +0000

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Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit a0565f3f87cbee8af57f78825fb2a549aac6d0f8
Author: car <car>
Date:   Fri Feb 27 20:59:27 1998 +0000

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Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit d7ab03739737010b94d4fb22d180406feef80901
Author: lijewski <lijewski>
Date:   Thu Feb 26 22:07:57 1998 +0000

    Made isStateVariable() static.

Src/C_AMRLib/AmrLevel.H

commit c38372b5d6f5474df5301bf23164cb6b000c7483
Author: car <car>
Date:   Wed Feb 25 23:24:16 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit 72ed30f6a11b06e4439257dc08e70818243a49cd
Author: car <car>
Date:   Wed Feb 25 22:27:33 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 04e17e6fff4a524e8873937a4145f5c2f3cfd77e
Author: car <car>
Date:   Wed Feb 25 21:05:04 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/cache.H
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 6a16fca94e170e366f74dca7c9b32af05fe885b2
Author: car <car>
Date:   Tue Feb 24 19:25:37 1998 +0000

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Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit e9b1951bda3b8fa68fa781f360c6ad0dda440175
Author: car <car>
Date:   Tue Feb 24 00:27:08 1998 +0000

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Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 62a1db5165620770bf04945b538a6076dcdffe9d
Author: car <car>
Date:   Mon Feb 23 22:55:47 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 20359df7d47d23fe26c73c10ab801c797161e8b6
Author: car <car>
Date:   Sun Feb 22 20:50:10 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
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Src/LinearSolvers/C_NodalMG/hglib.dsp
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commit 199545865962fd9e9b72326db5b4f1ad22e363d6
Author: car <car>
Date:   Sun Feb 22 19:24:25 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit 0e2eebe0744aabdf9613bf9b89865de8d4b7fc1b
Author: car <car>
Date:   Sun Feb 22 19:06:57 1998 +0000

    anal changes to fortran

Src/C_AMRLib/FILCC_2D.F
Src/C_AMRLib/FILCC_3D.F
Src/C_AMRLib/FLUXREG_2D.F
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/MAKESLICE_3D.F
Src/C_BaseLib/COORDSYS_2D.F
Src/C_BaseLib/COORDSYS_3D.F
Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F

commit 21a6a7678fee732eedec6b76472cf94fa408b81f
Author: car <car>
Date:   Sun Feb 22 17:29:22 1998 +0000

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Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.F
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Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit 4126cbd50d6a9e0af61cb7433c30b5a87116f78d
Author: car <car>
Date:   Sun Feb 22 04:16:19 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_multi3d.F
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commit e6bc0ed5fa4185457a26beb2ad6162c37bfc725a
Author: car <car>
Date:   Sun Feb 22 01:36:39 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit c7c57052a1d62e6ced9fe59c09b0a73930b28f4e
Author: car <car>
Date:   Sun Feb 22 01:35:39 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit eb32a57e2feb407515678c1b7cf1a3fc18ebb53b
Author: car <car>
Date:   Sun Feb 22 01:32:20 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 0a51bb21226c81586d647f8b8ad9e3b952575c20
Author: car <car>
Date:   Sun Feb 22 01:30:02 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 7c77304daba83b6ca60b4f868570c08232e6b1c5
Author: car <car>
Date:   Fri Feb 20 23:00:55 1998 +0000

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Src/C_BaseLib/FabArray.H
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit e3d53f27fcf21cec025d32de3d6c352d4b0ba05d
Author: car <car>
Date:   Fri Feb 20 22:53:09 1998 +0000

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Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 21c149ea3be4767d1b99e4c02afe32125e342f71
Author: car <car>
Date:   Fri Feb 20 21:49:27 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit d3bcb9cab2afcdf74b7dd8ee98b52b5f8cf0161d
Author: car <car>
Date:   Fri Feb 20 21:46:52 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit c769567ce01d62880f0dfd8d32514802c5a9f0b6
Author: car <car>
Date:   Fri Feb 20 21:42:58 1998 +0000

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Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit e40ee2c7831c132431b95f1aa3205ed59b89407b
Author: car <car>
Date:   Fri Feb 20 21:37:14 1998 +0000

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Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.F

commit 4c40f6be906b881eff9c35bff5f79e6e66db39e8
Author: car <car>
Date:   Fri Feb 20 21:07:11 1998 +0000

    changes

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit 16f8272630399bdb20ae851d25bec0bf7ebf47e8
Author: vince <vince>
Date:   Fri Feb 20 18:30:47 1998 +0000

    Optimized FillFab and fabCopyDescList.

Src/C_BaseLib/FabArray.H

commit 25c020128bd956dcf07eb6c1f0e78b9b162357ad
Author: car <car>
Date:   Thu Feb 19 23:26:40 1998 +0000

    fiddle:

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 914588858e15f1dcdc746f2ef14306535d8628cd
Author: lijewski <lijewski>
Date:   Thu Feb 19 18:10:46 1998 +0000

    Added default constructor to TagBoxMergeDesc.

Src/C_AMRLib/TagBox.cpp

commit 64833abe26920c9f796f1660f983b28f285b216f
Author: lijewski <lijewski>
Date:   Thu Feb 19 17:15:52 1998 +0000

    Added default constructor to FabComTag so that all values get set to
    some valid value; i.e. I wanted to shut up 3rd about reading unset
    values when BSP does a memcpy() of a FabComTag.

Src/C_BaseLib/ParallelDescriptor.H

commit 332e670a47e3e88973cf4a5dfa94e88e866b66ca
Author: car <car>
Date:   Thu Feb 19 01:51:35 1998 +0000

    fixes 2 d

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 64f3d2d2b8f0e83de0fa0e45bd06dd003bb7ece5
Author: car <car>
Date:   Wed Feb 18 23:09:55 1998 +0000

    fiddle

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/cache.H
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 60a41e742bc4a3ab78617a8aa94877ace0417e84
Author: vince <vince>
Date:   Wed Feb 18 21:38:11 1998 +0000

    Removed fortran apprentice flag.

Tools/C_mk/Make.T3E

commit 03bbc3c5d1060720fcdd181c664a1f88d0ae8ef0
Author: vince <vince>
Date:   Wed Feb 18 21:35:32 1998 +0000

    Removed unnecessary syncs.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BoundaryLib/FabSet.cpp

commit a6b3b7adbb1238c1b88cb85c2a92885bb3132a99
Author: lijewski <lijewski>
Date:   Wed Feb 18 21:34:37 1998 +0000

    Only FlushCache when at lbase==0

Src/C_AMRLib/Amr.cpp

commit a9fa8447e30df9f7cc15d70f2840c2a18c483ffe
Author: vince <vince>
Date:   Wed Feb 18 21:31:12 1998 +0000

    Removed unnecessary syncs and added functionality to support amrvis.

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/NormedFab.H
Src/C_BaseLib/Utility.cpp

commit b970099acba6d2b86dd3019b86fc2d6ab1c38284
Author: lijewski <lijewski>
Date:   Wed Feb 18 16:14:42 1998 +0000

    Had to remove parallel_sync RunStats stuff.
    Can't do that since RunStats::report() uses ParallelDescriptor::Synchronize()
    which leads to inconsistencies and weird numbers.

Src/C_BaseLib/ParallelDescriptor.cpp

commit d94013ece9266715ff2842b09e1b8a2a935b65fd
Author: car <car>
Date:   Tue Feb 17 23:02:16 1998 +0000

    nothing

Src/C_BaseLib/CoordSys.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit e2237736f5375680a911b371330f7c9b82863ba4
Author: lijewski <lijewski>
Date:   Tue Feb 17 22:42:04 1998 +0000

    Added a RunStats variable for parallel sync time.
    No longer need to include <Utility.H> in <ParallelDescritor.H>.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 6255667f18e56878cc262b6f42e82a773605afd4
Author: car <car>
Date:   Tue Feb 17 17:29:13 1998 +0000

    small changes

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 42df6f40c9b3b2579cbadc82eeeb1f02a74f8910
Author: lijewski <lijewski>
Date:   Fri Feb 13 21:13:07 1998 +0000

    Added rules for .f90 that exectly mirror those for .F files.
    Eventually we'd like to remove the need for FORTPREP (split77)
    for .f90 files.

Tools/C_mk/Make.rules

commit c65613de80f4e54028e7103f59e0ec2ac13ace26
Author: car <car>
Date:   Thu Feb 12 22:47:46 1998 +0000

    tweaks

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interpolator.cpp

commit c6deab694c84b0c67d250ef5cccc2df889c3f3ce
Author: wyc <wyc>
Date:   Thu Feb 12 22:37:13 1998 +0000

    fixed a bug in VisMF.H where there was ambiguity about which index was what
    in the clear(int,int) function.

Src/C_BaseLib/VisMF.H

commit 24c29e0d25d67d56ca3de3297198b2d64e79dea5
Author: vince <vince>
Date:   Thu Feb 12 22:16:24 1998 +0000

    Initialized m_pa.

Src/C_BaseLib/VisMF.cpp

commit 00571d09626ce3a98a5fe324d94dc3d521851f47
Author: lijewski <lijewski>
Date:   Thu Feb 12 18:13:27 1998 +0000

    Added calloc() and realloc() so can emulate malloc(3) functionality.

Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp

commit 133ad8afe411a42541a311819a77425275858d6b
Author: car <car>
Date:   Thu Feb 12 17:32:10 1998 +0000

    win32 changes

Src/C_BaseLib/Utility.cpp

commit c36759a831238ee7427d7d62b1b0c7a9a4d0db9c
Author: lijewski <lijewski>
Date:   Thu Feb 12 16:56:08 1998 +0000

    Fixed bug in getline().

Src/C_BaseLib/aString.cpp

commit e304a4e09dbd0a086ffcf5f1f8d967f6b62ec1d3
Author: car <car>
Date:   Wed Feb 11 21:41:12 1998 +0000

    Small changes.

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 277ec8c4dfd06731c7fd6faec309ff05ff6d5c4f
Author: car <car>
Date:   Tue Feb 10 15:15:33 1998 +0000

    win32 change

Src/C_BaseLib/CArena.H
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 7ee2df6eeaeb73a9d6009673c9db7e27ee0db33b
Author: lijewski <lijewski>
Date:   Mon Feb 9 22:45:58 1998 +0000

    Mods for T3E and g++.

Src/C_BaseLib/CArena.cpp

commit 15611985d70f567879568b465b10497ee49fdfd2
Author: lijewski <lijewski>
Date:   Mon Feb 9 22:02:14 1998 +0000

    Added a couple more insert() hints.

Src/C_BaseLib/CArena.cpp

commit 1e1fbf25e56da12fd1a1bd3fdc598784c74836ce
Author: lijewski <lijewski>
Date:   Mon Feb 9 22:01:27 1998 +0000

    Fixed using declaration: using std::list -> using std::set

Src/C_BaseLib/CArena.H

commit 31515f5379a847561769b1104fdfd5b34b7cca18
Author: lijewski <lijewski>
Date:   Mon Feb 9 20:46:52 1998 +0000

    We're now using the CArena stuff.

Src/C_BaseLib/Arena.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BArena.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/test/tCArena.cpp
Tests/C_BaseLib/tCArena.cpp

commit 71869768d73f85d47725d086fb58a64c1bb58ca2
Author: car <car>
Date:   Mon Feb 9 20:33:29 1998 +0000

    doodle

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 92090db6522a5207d7b2dbeac6e0a97c3555e313
Author: lijewski <lijewski>
Date:   Sun Feb 8 21:13:31 1998 +0000

    Increased the count on a few for loops to up test strength.

Src/C_BaseLib/test/tCArena.cpp
Tests/C_BaseLib/tCArena.cpp

commit 4c545e4a876ea148f8ad8b66b8b4a6a0167c0e84
Author: lijewski <lijewski>
Date:   Sun Feb 8 20:03:59 1998 +0000

    Free()d blocks are now coalesed with lo and hi neighbors.

Src/C_BaseLib/CArena.cpp

commit fa8220ec6b22c99f7cf11d8ae9985b3bd5a97033
Author: lijewski <lijewski>
Date:   Sun Feb 8 18:19:48 1998 +0000

    Test code for CArena

Src/C_BaseLib/test/GNUmakefile.tCArena
Src/C_BaseLib/test/tCArena.cpp
Tests/C_BaseLib/GNUmakefile.tCArena
Tests/C_BaseLib/tCArena.cpp

commit a6e042e77145dd8e45d6ad7fed1155df58bda17d
Author: lijewski <lijewski>
Date:   Sun Feb 8 18:19:28 1998 +0000

    A start at a rewrite using STL.
    Doesn't do compact()ing yet.

Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp

commit 7bc488840836e6651bb01828067c2710e3892bc1
Author: lijewski <lijewski>
Date:   Sun Feb 8 17:52:07 1998 +0000

    Added a function pointer to Word union.

Src/C_BaseLib/Arena.H

commit b7b6a26435c2ce7ce6211b6c1ea7c1fdddaf0375
Author: lijewski <lijewski>
Date:   Sat Feb 7 23:41:55 1998 +0000

    Still doesn't work.  Looks like I need to rewrite this.

Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp

commit 914719adf92a079b89ea7a0cf02a1688f35c394e
Author: lijewski <lijewski>
Date:   Fri Feb 6 23:44:09 1998 +0000

    Closer to working code.

Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp

commit 4e37176e7af7724850337bebd9e4dd9f264fbd00
Author: car <car>
Date:   Fri Feb 6 22:26:26 1998 +0000

    some fixes for win32

Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp
Src/C_BaseLib/pBoxLib_2.dsp

commit 466d7f721dd6c8eaf3993c699d81da49d0f7f184
Author: car <car>
Date:   Fri Feb 6 22:19:19 1998 +0000

    CleanUp

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 80d5bfbaed2b0599d96240f62afa723b084dd9cf
Author: vince <vince>
Date:   Fri Feb 6 22:09:13 1998 +0000

    Deleted warning for deprecated FArrayBox::setOrdering() and
    FArrayBox::getOrdering().  (amrvis needs these).

Src/C_BaseLib/FArrayBox.cpp

commit 08031b6e6aef590e6cd0011db5ecfce8a1848dc2
Author: lijewski <lijewski>
Date:   Fri Feb 6 18:22:03 1998 +0000

    Uses ::operator new and ::operator delete instead of new and delete.

Src/C_BaseLib/BArena.cpp

commit d2b47d8cc9473abe4036f7d838e8b9d4a1c84a75
Author: lijewski <lijewski>
Date:   Fri Feb 6 18:21:34 1998 +0000

    The initial cut.  Hasn't even been compiled.

Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp

commit 289c256767ed83fe616f671fb02349f958551f01
Author: car <car>
Date:   Fri Feb 6 16:53:10 1998 +0000

    Array bust

Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit ea263bbdb882b15f46b627d76dd003cf75db315e
Author: vince <vince>
Date:   Thu Feb 5 23:01:34 1998 +0000

    Changed VisMF to use an I/O granularity of a single component of a
    fab in a multifab and to not store data.

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/tVisMF.cpp

commit 12a8a67226460c56cacf386ce8d01afba274e4fd
Author: car <car>
Date:   Thu Feb 5 22:18:10 1998 +0000

    Frob

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/cache.H
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 48d4276946b5b321bf419c1a3b6b64188afc82b0
Author: vince <vince>
Date:   Thu Feb 5 22:15:55 1998 +0000

    Fixed a typo.

Src/C_BaseLib/COORDSYS_3D.F

commit ce8e8875aaa54119fc5223e0300bc22a452e5295
Author: lijewski <lijewski>
Date:   Thu Feb 5 17:02:28 1998 +0000

    Removed cout call when bumping collate space size.

Src/C_AMRLib/TagBox.cpp

commit 14ec52da85a4a0208ecc61d206cce6283dbf03a8
Author: car <car>
Date:   Thu Feb 5 00:38:19 1998 +0000

    Fiddling.

Src/C_AMRLib/amrlib.dsp
Src/C_BaseLib/pBoxLib_2.dsp
Src/C_BoundaryLib/bndrylib.dsp
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/restrictor.H

commit 45fb895cbbb28355927dcccd82b6c60086de6bee
Author: car <car>
Date:   Thu Feb 5 00:37:59 1998 +0000

    Fiddling

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 80293e5f80e68a315f1f8b4a5897f5b590b5c73a
Author: lijewski <lijewski>
Date:   Wed Feb 4 16:25:50 1998 +0000

    Fixes for Visual C++.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit bf9998d4c4db7f00c3a8a9de265ef8172d224ae2
Author: lijewski <lijewski>
Date:   Wed Feb 4 01:03:20 1998 +0000

    We're now reference-counted.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 5e109466e0da9ec7cd720e6eaab0d7b7ca29a40d
Author: lijewski <lijewski>
Date:   Tue Feb 3 19:33:53 1998 +0000

    In copy, check that the processor maps are equal, not the boxarrays.

Src/C_BaseLib/FabArray.H

commit 7553bebf1777d585d63cac104778816447d8e64e
Author: lijewski <lijewski>
Date:   Tue Feb 3 19:33:12 1998 +0000

    We now only flush the processor map cache in regrid if we're at
    the coarsest level.  Otherwise we can run into problems in LevelAdvance.

Src/C_AMRLib/Amr.cpp

commit a741ddf34570d42ea25dea51027cc931c8982fbc
Author: car <car>
Date:   Sat Jan 31 00:12:26 1998 +0000

    Minor Changes.

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit db51f51aeea00f50ae54dcd46e33e442c7bb6a53
Author: lijewski <lijewski>
Date:   Thu Jan 29 18:59:36 1998 +0000

    Lowered the size of ChunkSize.

Src/C_AMRLib/TagBox.H

commit 9ea937d02230e09230daea9ecc46f9a8f94fd56d
Author: car <car>
Date:   Wed Jan 28 22:54:23 1998 +0000

    Minor changes

Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 5f4de625b3196fc2dc35761db626339befabea2f
Author: car <car>
Date:   Wed Jan 28 22:29:15 1998 +0000

    A little more general, another stupid fill_patch fix.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 196bba89948a18ed325201eda957028d26a0b552
Author: car <car>
Date:   Wed Jan 28 22:11:15 1998 +0000

    Stupid fix in fill_patch.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 199d81602aa1069825f86af64bbf3e58da4f2196
Author: car <car>
Date:   Wed Jan 28 21:58:32 1998 +0000

    Thrashing.

Src/LinearSolvers/C_NodalMG/RegType.H
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/cache.H
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/hglib.dsp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.H
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit f2d1de6e75c0de276c0815f124737b7e6608e00f
Author: lijewski <lijewski>
Date:   Wed Jan 28 18:35:07 1998 +0000

    Latest mods to Cluster have now been ported to T3E.

Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 822e3a00d9e271118d6f584f2e9921aed4adef1f
Author: lijewski <lijewski>
Date:   Wed Jan 28 04:55:10 1998 +0000

    First cut at having the Cluster code work exclusively with a hardwired
    IntVect array built and maintained by the TagBox::collate() code.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 06eafb51535cb9abdc4f440fb6036431e157c79e
Author: car <car>
Date:   Tue Jan 27 00:15:05 1998 +0000

    Fixes cleanups.

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 43a7536450459ff4e1bae7b2caae11014a527cd1
Author: car <car>
Date:   Tue Jan 27 00:14:50 1998 +0000

    Fixes, cleanups.

Src/LinearSolvers/C_NodalMG/RegType.H
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/cache.H
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit 36374282171f75c1e5b4a28a6adeb8e70b78fe53
Author: car <car>
Date:   Mon Jan 26 23:27:00 1998 +0000

    No longer need cbasics.H, and updated .cvsignore to ignore louis's lib
    directory.

Src/LinearSolvers/C_NodalMG/.cvsignore
Src/LinearSolvers/C_NodalMG/cbasics.H

commit 8935fa74e5deccc5b00787fa45e2ff9e8d705fa6
Author: lijewski <lijewski>
Date:   Mon Jan 26 23:16:20 1998 +0000

    Removed unused function.

Src/C_AMRLib/Cluster.H

commit 1283da021cd32ef3581fcd626b6c4f0eff7b6832
Author: lijewski <lijewski>
Date:   Mon Jan 26 22:00:00 1998 +0000

    Cleaned up the code a bit.

Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp

commit d621d1ec8511a6451c3e0a710be1a052f8891a40
Author: lijewski <lijewski>
Date:   Mon Jan 26 21:57:18 1998 +0000

    We're now derived from BaseFab<char>
    Added tags() and tags(Array<int>) to support Fortran.

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 92cfb5d77a6ce97826b8a16ccba328c747852823
Author: car <car>
Date:   Mon Jan 26 20:56:19 1998 +0000

    Fixes.

Src/LinearSolvers/C_NodalMG/GNUmakefile.main

commit 0c8d38d2efd648d98d406865f649ac5809efeb09
Author: car <car>
Date:   Mon Jan 26 20:20:55 1998 +0000

    for loop index

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 3f9d86f2c7ef25aa91fb662bed03e15ee7c05105
Author: car <car>
Date:   Mon Jan 26 19:18:19 1998 +0000

    Changes for 2 D.

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 2807adec0d82d3286093e0af6835e14cd92533e1
Author: lijewski <lijewski>
Date:   Sat Jan 24 01:35:58 1998 +0000

    Forgot a 'endif' in the previous merge.

Src/C_AMRLib/INTERP_2D.F

commit 4755b9df6a7f81ae1ea2f51c8f8174d3c8cc194e
Author: lijewski <lijewski>
Date:   Fri Jan 23 22:48:38 1998 +0000

    bsp_put() -> bsp_hpput()
    bsp_get() -> bsp_hpget()

Src/C_BaseLib/ParallelDescriptor.H

commit 00ded7dab63a03132f215a5f995ed6f88043bbc5
Author: car <car>
Date:   Fri Jan 23 18:34:00 1998 +0000

    Changes.

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/cache.H
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 0f95128dc20326fbe55cbfeb48097973fce4d1de
Author: lijewski <lijewski>
Date:   Fri Jan 23 17:51:31 1998 +0000

    Reduced memory usage in colate().

Src/C_AMRLib/TagBox.cpp

commit f2e77a3fe0028db1bb5e80d8395894e7bdaa1c8f
Author: car <car>
Date:   Thu Jan 22 23:25:31 1998 +0000

    Const correctness...

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/interpolator.H
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit bcfe5b1079d12c7364d5fa5a454d059aa4e57c8e
Author: lijewski <lijewski>
Date:   Thu Jan 22 16:39:53 1998 +0000

    Added [] to delete in a few places.

Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/Interpolater.cpp

commit ea8a9a5689e9ae1a0e4b8c6a52f59aba5fa1ca52
Author: car <car>
Date:   Wed Jan 21 22:57:52 1998 +0000

    Caching removed.

Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 3a6802b773dc2e15ed9e50def231b79dc077d623
Author: car <car>
Date:   Wed Jan 21 22:57:38 1998 +0000

    Removed caching.

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 1515006855aba48d472f5bf09e7a74010edcdb91
Author: car <car>
Date:   Wed Jan 21 22:57:21 1998 +0000

    Removed caching

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/cache.H
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/restrictor.H

commit 4a6da3ee9b07976eca40502ea2d257af84afa368
Author: car <car>
Date:   Wed Jan 21 22:56:52 1998 +0000

    Removed include Files

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit 9ab04286ebba7f75ac30eba243160d3478ee1af5
Author: car <car>
Date:   Wed Jan 21 21:39:20 1998 +0000

    Removed more useless stuff.

Src/LinearSolvers/C_NodalMG/mall_info.cpp

commit 61d280f3f0c3429dbb20d0086dc702a443011e85
Author: car <car>
Date:   Wed Jan 21 21:35:50 1998 +0000

    Removed graphics.

Src/LinearSolvers/C_NodalMG/GNUmakefile.main
Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_graph.H
Src/LinearSolvers/C_NodalMG/amr_graph.cpp
Src/LinearSolvers/C_NodalMG/cont2d.F
Src/LinearSolvers/C_NodalMG/cont3d.F
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit e66b4a82793437cd2db8599549a8cc2c7a3c1603
Author: car <car>
Date:   Wed Jan 21 20:57:54 1998 +0000

    Changes for Parallel.

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_graph.H
Src/LinearSolvers/C_NodalMG/amr_graph.cpp
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp
Src/LinearSolvers/C_NodalMG/interpolator.H
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 04d5f5a28de9f57f9e6e051742c934797547395d
Author: vince <vince>
Date:   Wed Jan 21 19:32:12 1998 +0000

    Minor change for the cray.

Src/C_AMRLib/DatasetClient.cpp

commit cb75afca46ce7b18430e6d9f2813854612a297e8
Author: lijewski <lijewski>
Date:   Fri Jan 16 23:14:23 1998 +0000

    Merged in some fixes Ann added to _amr.

Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/Interpolater.cpp

commit 33eeb22fea7df2ad8dbe82cca743be21e64a084d
Author: lijewski <lijewski>
Date:   Fri Jan 16 22:53:01 1998 +0000

    Mods to compile with g++ 2.8.0

Src/C_BaseLib/DistributionMapping.cpp

commit 2d87fde7c686efb60dc38d11fb888b1553a2da45
Author: car <car>
Date:   Thu Jan 15 20:37:18 1998 +0000

    Changes for WIN32

Src/LinearSolvers/C_NodalMG/.cvsignore
Src/LinearSolvers/C_NodalMG/hglib.dsp

commit 6760927a889f6827ea3646e97574403e9c5d9032
Author: car <car>
Date:   Thu Jan 15 19:15:59 1998 +0000

    New files for WIN32 and cvs bookkeeping.
    Bug Fixes for WIN32.

Src/LinearSolvers/C_NodalMG/.cvsignore
Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hgproj.dsp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 0ab68793ee5ccf234611183c3db02a9d68569eba
Author: lijewski <lijewski>
Date:   Thu Jan 15 18:52:35 1998 +0000

    Removed references to Arena stuff ...
    The Arena junk still exists, it just isn't used or referenced anywhere.

Src/C_BaseLib/Make.package

commit f4b1741d6f30bd056dc5ac0fae090a137dde4956
Author: car <car>
Date:   Wed Jan 14 21:56:49 1998 +0000

    Don't need

Src/LinearSolvers/C_NodalMG/amr_grav2d.F
Src/LinearSolvers/C_NodalMG/amr_grav3d.F
Src/LinearSolvers/C_NodalMG/amr_gravity.H
Src/LinearSolvers/C_NodalMG/amr_gravity.cpp
Src/LinearSolvers/C_NodalMG/hg_elliptic.H
Src/LinearSolvers/C_NodalMG/hg_elliptic.cpp

commit f554eb86590e351feaaf108c5f95570a17fd66e9
Author: car <car>
Date:   Wed Jan 14 21:51:02 1998 +0000

    Parallel BoxLib_2 compatible first cut.
    Remove elliptic and other.

Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_NodalMG/GNUmakefile.main
Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/driver.cpp
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/poisson.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit a2662247c9141341c55a73a2ca83132f74e45c80
Author: car <car>
Date:   Mon Jan 12 21:21:46 1998 +0000

    Turned on browser.

Src/C_AMRLib/amrlib.dsp
Src/C_BaseLib/pBoxLib_2.dsp
Src/C_BoundaryLib/bndrylib.dsp

commit b9f7ca673b5f8efe52d003e64a4349a6cd8eb3d0
Author: vince <vince>
Date:   Thu Jan 8 23:06:04 1998 +0000

    Added ReduceBoolOr.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Utility.H

commit 00f672699c71006d5c77769a34285363ad1e9c82
Author: lijewski <lijewski>
Date:   Thu Jan 8 18:59:59 1998 +0000

    Now up-to-date with _amr.  Had to add in Steven's new stuff.

Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp

commit 603443b53d94e8518f8e0101e9cea7b6347aba57
Author: lijewski <lijewski>
Date:   Tue Jan 6 23:43:56 1998 +0000

    Brought into line with stuff in _amr.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp

commit 391c896479aac886fb2f0b53458e0971595acf1e
Author: car <car>
Date:   Tue Dec 23 19:22:34 1997 +0000

    VC++ changes.

Src/C_AMRLib/amrlib.dsp
Src/C_BoundaryLib/bndrylib.dsp

commit a1a0ac5a53aa194d881420f2854d2245f3d924e8
Author: car <car>
Date:   Tue Dec 23 05:15:52 1997 +0000

    Fix for win32.

Src/C_BoundaryLib/bndrylib.dsp

commit 9473074d92c11a725ce89060e0726e3cfc07441d
Author: car <car>
Date:   Tue Dec 23 05:15:15 1997 +0000

    Change for Win32.

Src/C_AMRLib/amrlib.dsp

commit 1249c6591b446e9c0902092644a64d75d90ee257
Author: car <car>
Date:   Mon Dec 22 23:12:04 1997 +0000

    Updates for Win32

Src/C_AMRLib/amrlib.dsp
Src/C_BaseLib/pBoxLib_2.dsp
Src/C_BoundaryLib/bndrylib.dsp

commit 61e8f6ffd62167301124c561045c3afdf3105f9b
Author: lijewski <lijewski>
Date:   Fri Dec 19 22:21:39 1997 +0000

    operator&() is now implemented in terms of operator&=().
    Likewise for the friend versions of surroundingNodes() and enclosedNodes().

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp

commit 5bdc6dfdaadf33eb1544ca2bb94ff62595c12d4f
Author: lijewski <lijewski>
Date:   Fri Dec 19 21:54:45 1997 +0000

    Removed List<T>::copy().  Just a memory leak waiting to happen.

Src/C_BaseLib/List.H

commit 681924cacad520171cc2d8f8f88d0808a19ebb7f
Author: lijewski <lijewski>
Date:   Fri Dec 19 19:08:55 1997 +0000

    Got rid of the ugly and dangerour (int*) cast.

Src/C_AMRLib/Interpolater.cpp

commit b1edb225eff063539eb70f4bc8b776944691064a
Author: lijewski <lijewski>
Date:   Fri Dec 19 18:43:51 1997 +0000

    getBCArray() now returns Array<int> not int*.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit fcf695131501679e53d72e44cb0fde25017848c1
Author: lijewski <lijewski>
Date:   Thu Dec 18 18:44:38 1997 +0000

    These are specialized versions of performCopy() and setVal().
    They're being checked in only for informational purposes at the moment.
    That is, they're aren't integrated into the code.
    Turns out, they don't buy you anything on the DEC Alpha.
    They do though on a vector machine such as the Cray.

Src/C_BaseLib/SPECIALIZE_2D.F
Src/C_BaseLib/SPECIALIZE_3D.F
Src/C_BaseLib/SPECIALIZE_F.H
Src/C_BaseLib/Specialize.cpp

commit f13ea356e3e9f1a8151468253dbfbf76aadf4814
Author: lijewski <lijewski>
Date:   Wed Dec 17 23:04:53 1997 +0000

    Now need <Utility.H>

Src/C_AMRLib/AmrLevel.cpp

commit f352fec4d8eb703e3e1b3afbd6a043a3dc931ccd
Author: lijewski <lijewski>
Date:   Wed Dec 17 23:04:32 1997 +0000

    Removed need for <Utility.H>

Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/Orientation.cpp
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/RealBox.cpp
Src/C_BaseLib/VisMF.cpp

commit 021cb575ad5915e0057c73aa06830e6b74f0b4e3
Author: lijewski <lijewski>
Date:   Wed Dec 17 18:09:33 1997 +0000

    Don't allow Mersenne prime as seed.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit a1c009ce34a57cebf12483cc121368bfd712d568
Author: vince <vince>
Date:   Tue Dec 16 23:34:14 1997 +0000

    Added pierre.nersc.gov (the T3E-600).

Tools/C_mk/Make.defs

commit 95f6693518a56f14211ab81a9825feee3fcc2228
Author: vince <vince>
Date:   Tue Dec 16 19:05:51 1997 +0000

    Changed the profile tool from apprentice (which is broken) to pat.

Tools/C_mk/Make.T3E

commit 1ed7f8b7e0c9f5d2c6fa62f8510a3a5a44648c6f
Author: lijewski <lijewski>
Date:   Tue Dec 16 16:44:54 1997 +0000

    I've made it clearer in the code that only processor #0 writes to
    or does anything useful with the plotfile or checkpoint file header.

Src/C_AMRLib/Amr.cpp

commit 7c9896f0ac62d8fbe932547f6ac1e4f34de79375
Author: car <car>
Date:   Tue Dec 16 15:27:47 1997 +0000

    Make a warning go away.

Src/C_BaseLib/RunStats.cpp

commit fa0ef937808dc73214eb9a10f457dd217bdb8358
Author: lijewski <lijewski>
Date:   Tue Dec 16 00:41:28 1997 +0000

    DIMV -> DIMENSION
    DIMV macro conflicted with the one in ArrayLim.H.

Src/C_AMRLib/MAKESLICE_3D.F

commit 17b3dbbf54051e26084d7f54aad368e3400aafc1
Author: lijewski <lijewski>
Date:   Mon Dec 15 17:00:52 1997 +0000

    utilrand() -> blutilrand().

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit e62ad3c067a13ec0a61485aad0bf0e2f19d5cb9b
Author: lijewski <lijewski>
Date:   Sun Dec 14 23:34:59 1997 +0000

    Added Random(), InitRandom() and Fortran entry points for Random().

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 302e9a2796342c636dca4b9499073f79fc15ce9a
Author: lijewski <lijewski>
Date:   Sun Dec 14 23:34:14 1997 +0000

    Added CVS ID in C comment.

Src/C_AMRLib/FLUXREG_F.H
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/MAKESLICE_F.H
Src/C_AMRLib/PROB_AMR_F.H
Src/C_BaseLib/COORDSYS_F.H

commit 647d2727d72d7bbfbf855e0b12ecd5e392f3c3fa
Author: lijewski <lijewski>
Date:   Sun Dec 14 01:05:52 1997 +0000

    Reverted out the merged of FAB stuff in BaseFab.
    It tickles a bug with the Cray CC compiler on the T3E.
    Quite pernicious.

Src/C_BaseLib/ArithFab.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/Make.package
Src/C_BaseLib/NormedFab.H
Src/C_BaseLib/OrderedFab.H

commit a37fa9cae782a4c4f8d753928ad0d7fe1120d1e7
Author: car <car>
Date:   Sat Dec 13 21:09:28 1997 +0000

    Compile rule changes.

Src/C_AMRLib/amrlib.dsp

commit 0a499e0803a493c0ca5adddc4eb347505878e82d
Author: lijewski <lijewski>
Date:   Sat Dec 13 19:53:07 1997 +0000

    Fixed some inconsistencies between declarations in the _F.H
    file and the definition/usage.

Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/Interpolater.cpp

commit 2ac9a7c7226b48c009e3e1c0917a40bf2c943fa6
Author: lijewski <lijewski>
Date:   Sat Dec 13 19:48:03 1997 +0000

    Mod to keep T3E quite re: usage of real*8

Src/C_AMRLib/FLUXREG_3D.F

commit 605213228d415d6bab0a44fb00eeb5948e564a6a
Author: lijewski <lijewski>
Date:   Fri Dec 12 23:23:40 1997 +0000

    Only the I/O processor tries to build the required directory tree.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp

commit 18788d705427dafc3064380d1b9ca1091168703b
Author: lijewski <lijewski>
Date:   Fri Dec 12 22:44:54 1997 +0000

    DIMS.H has been merged in.

Src/C_BaseLib/ArrayLim.H

commit c1c2ce6a09b6bca8ec3e5db780f4e0e70702fd0f
Author: lijewski <lijewski>
Date:   Fri Dec 12 22:42:42 1997 +0000

    DIMS.H has been merged into ArrayLim.H
    All .F files now have leading comment containing CVS ID.

Src/C_AMRLib/DIMS.H
Src/C_AMRLib/FILCC_2D.F
Src/C_AMRLib/FILCC_3D.F
Src/C_AMRLib/FLUXREG_2D.F
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/MAKESLICE_3D.F
Src/C_BaseLib/COORDSYS_2D.F
Src/C_BaseLib/COORDSYS_3D.F

commit e85bc2df3102bda72a4bd16ba4a1b0adffb28aae
Author: lijewski <lijewski>
Date:   Fri Dec 12 16:10:14 1997 +0000

    Now use f90 instead of f77.

Tools/C_mk/Make.OSF1

commit 935d811fa8891e5ccaec9fb350052eb3ff75a742
Author: car <car>
Date:   Fri Dec 12 00:17:15 1997 +0000

    Changes for VC++

Src/C_AMRLib/.cvsignore
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/MAKESLICE_3D.F
Src/C_AMRLib/amrlib.dsp

commit 96a8a983fc82bb0a21f3975d37a45b3a2d326138
Author: car <car>
Date:   Fri Dec 12 00:15:57 1997 +0000

    VC++ fixes.

Src/C_BaseLib/COORDSYS_3D.F
Src/C_BoundaryLib/.cvsignore
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/bndrylib.dsp

commit c6e44f8fa73ce93a38fe6c78e152bb53a7015be2
Author: car <car>
Date:   Fri Dec 12 00:14:57 1997 +0000

    Changles for VC++

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/pBoxLib_2.dsp

commit 16aa03f3b1f8b7235f5037208f44d468fbba0d35
Author: lijewski <lijewski>
Date:   Thu Dec 11 23:26:58 1997 +0000

    Removed all checks on the return value of new.
    We now rely on a set_new_handler() being installed.
    See Parallel/HCAll/main.cpp for details.
    Brought up-to-date with the serial version of BndryLib.

Src/C_BaseLib/COORDSYS_F.H
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/RealBox.H
Src/C_BaseLib/RealBox.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 174ae4a6f67c5648d78bde2487850264fc3ee234
Author: lijewski <lijewski>
Date:   Thu Dec 11 23:25:38 1997 +0000

    Removed all checks on the return value of new.
    We now rely on a set_new_handler() being installed.
    See Parallel/HCAll/main.cpp for details.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/BCRec.H
Src/C_AMRLib/BCRec.cpp
Src/C_AMRLib/BC_TYPES.H
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/DatasetClient.cpp
Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/ErrorList.cpp
Src/C_AMRLib/FLUXREG_F.H
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/LevelBld.H
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/Array.H
Src/C_BaseLib/BArena.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BoxAssoc.H
Src/C_BaseLib/BoxAssoc.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/List.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp
Src/C_BaseLib/Tracer.cpp
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp

commit 073b10ae7e3d6767e5b5cf7bc1a013461ce496d7
Author: lijewski <lijewski>
Date:   Thu Dec 11 06:14:02 1997 +0000

    A few more endls added.

Src/C_AMRLib/Amr.cpp

commit 611e3a3d57d80e13fc2f0708c1514d790d26b911
Author: lijewski <lijewski>
Date:   Thu Dec 11 06:07:47 1997 +0000

    Added some strategically placed endl's.
    The T3E iostream library doesn't flush on newline :-(

Src/C_AMRLib/Amr.cpp

commit 5df40bb4168d53c00db762cf974cc80d0d25b328
Author: lijewski <lijewski>
Date:   Thu Dec 11 05:01:08 1997 +0000

    Brought up-to-date with servial version of BndryLib stuff.

Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/RealBox.H
Src/C_BaseLib/RealBox.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit 2ff8299f66f1621d39f03fab4f4fbafb8fca7945
Author: lijewski <lijewski>
Date:   Wed Dec 10 22:04:42 1997 +0000

    Added DIMS==1 stuff.

Src/C_AMRLib/DIMS.H

commit 941c34764fdce5a833861ed1591a436c1ec63709
Author: lijewski <lijewski>
Date:   Wed Dec 10 21:56:01 1997 +0000

    Merged in mods from IAMRAll.
    Inlined all FabSetIterator gunk.

Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/RealBox.H
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit d622c9c131c70a12ccad7e91fdc09f1e0f34e321
Author: lijewski <lijewski>
Date:   Wed Dec 10 19:07:38 1997 +0000

    Moved from HCAll.

Src/C_BaseLib/COORDSYS_2D.F
Src/C_BaseLib/COORDSYS_3D.F
Src/C_BaseLib/COORDSYS_F.H
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/RealBox.H
Src/C_BaseLib/RealBox.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 5f003658c365112a12258ac3825e4f401e06213f
Author: lijewski <lijewski>
Date:   Tue Dec 9 23:29:59 1997 +0000

    ArithFab, NormedFab and OrderedFab have been merged into BaseFab.
    BaseFab is no longer a virtual baseclass of FArrayBox.
    Removed the maskLT-type operations.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/Make.package

commit bc51b60088e7011f61acc22c8f9d8b471bdca318
Author: lijewski <lijewski>
Date:   Tue Dec 9 21:54:52 1997 +0000

    TagBoxArray::numTags() now returns long.
    Merged in TagType typedef everywhere.
    TagBox::numTags(Box&) now calls TagBox::numTags().

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit b2f43254817e87dcd6021a324ef594ff706ba105
Author: lijewski <lijewski>
Date:   Tue Dec 9 17:46:20 1997 +0000

    Delayed some of the new's until after sync()s as much as possible.

Src/C_AMRLib/TagBox.cpp

commit d15fb5d669354198bdde126ea7d54d9413709509
Author: lijewski <lijewski>
Date:   Mon Dec 8 23:12:59 1997 +0000

    The define() functions now have a guard that checks to see if
    we're running in parallel or not.
    Also, the one that returns PArray<FArrayBox*>* now returns MultiFab*

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit ec10bf416228adf4d62f11e3f7a0b93ad46ad0f3
Author: lijewski <lijewski>
Date:   Sat Dec 6 01:04:47 1997 +0000

    Added in Marc's fix for non-nested grids.

Src/C_AMRLib/Amr.cpp

commit 5b31a6c2e087b856a33b7f7a520e424bcc7b8974
Author: lijewski <lijewski>
Date:   Fri Dec 5 22:07:31 1997 +0000

    Some consolidation.

Tools/C_mk/Make.T3E

commit 73822ae6714999728658448baccaf85b36fb90b4
Author: car <car>
Date:   Fri Dec 5 19:07:30 1997 +0000

    Give an argument to ::time()

Src/C_BaseLib/Utility.cpp

commit 041888b9739ec659c8e5a6cf0a69146730f0a9bb
Author: lijewski <lijewski>
Date:   Fri Dec 5 17:59:25 1997 +0000

    Merged couple more mods from IAMR.
    One was a setVal() in isValid() that had been removed -- it's needed in IAMR.

Src/C_AMRLib/AmrLevel.cpp

commit 06abebbad7523ba283fee6222e867f2be63123d6
Author: lijewski <lijewski>
Date:   Fri Dec 5 16:18:22 1997 +0000

    Added clear() and clear(int).

Src/C_BaseLib/VisMF.H

commit d814232dc3a7f7da34ce84fb069cfb1e9e990f94
Author: lijewski <lijewski>
Date:   Fri Dec 5 00:07:31 1997 +0000

    If not BL_USE_SETBUF setbuf -> pubsetbuf

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/VisMF.cpp

commit cbed681d37f6aa4355b2220152120eed9a520068
Author: lijewski <lijewski>
Date:   Thu Dec 4 22:57:08 1997 +0000

    Using .isNull() instead of == "".

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.cpp

commit a7482eb8f13bb825f8bb4185dcbca80adc30160c
Author: lijewski <lijewski>
Date:   Thu Dec 4 22:33:20 1997 +0000

    Fixed weird requirement that ParmParse must be init'd from command line.

Src/C_BaseLib/ParmParse.cpp

commit 40ee356ed8994303486ca644e4bec0be668a64e9
Author: lijewski <lijewski>
Date:   Thu Dec 4 21:32:06 1997 +0000

    Moved from amrlib.

Src/C_BaseLib/Make.package
Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp

commit 609c3231920fd66265b515ccd27aa3e819df4e9a
Author: lijewski <lijewski>
Date:   Thu Dec 4 21:31:52 1997 +0000

    Moved to pBoxLib_2

Src/C_AMRLib/RunStats.H
Src/C_AMRLib/RunStats.cpp

commit e91598b114acb9e481c054faa791e7a1a316b739
Author: lijewski <lijewski>
Date:   Thu Dec 4 20:58:48 1997 +0000

    Changed plotfile and checkpoint file formats slightly to facilitate
    reading and writing them to directories different from the one in
    which you're running.
    Merged more gunk from IAMRAll.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit d43432b60b1b500f976ff3c000471133691eb70f
Author: lijewski <lijewski>
Date:   Thu Dec 4 20:11:01 1997 +0000

    Mods to allow writing of plotfiles and checkpoint files in
    directories other than the one in which you're running.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 062fc873b23ccf26d68bea215849aca5319ae743
Author: lijewski <lijewski>
Date:   Wed Dec 3 23:26:11 1997 +0000

    chkfile -> chfile when not using BL_PARALLEL_IO.

Src/C_AMRLib/Amr.cpp

commit 6522fc97765ebc19f0e15e3713d1afd03f794145
Author: lijewski <lijewski>
Date:   Wed Dec 3 21:09:54 1997 +0000

    Cleaned up a tad.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit d5d40ca423116d44fabde4856d67ca109410580b
Author: vince <vince>
Date:   Wed Dec 3 19:24:54 1997 +0000

    Added a variable to distinguish between the NERSC T3E and the NAVO T3E.

Tools/C_mk/Make.defs

commit d9eec7e93e4b6e5256fa3e904614b04858e533f2
Author: lijewski <lijewski>
Date:   Wed Dec 3 03:26:57 1997 +0000

    Performance modification to performSetVal().

Src/C_BaseLib/BaseFab.H

commit b9d9755a1441e78a36b7d7252e284ac3d7fcaede
Author: lijewski <lijewski>
Date:   Tue Dec 2 23:59:29 1997 +0000

    Merged in from IAMRAll.

Src/C_AMRLib/FILCC_2D.F
Src/C_AMRLib/FILCC_3D.F
Src/C_AMRLib/FLUXREG_2D.F
Src/C_AMRLib/FLUXREG_3D.F

commit aca53b646f5b030c636c16c9248c287b5383eda7
Author: lijewski <lijewski>
Date:   Tue Dec 2 23:40:32 1997 +0000

    Merged with one from IAMRAll.

Src/C_AMRLib/FluxRegister.cpp

commit dcaba019a2fd0d31427420f46d3336a3a1e3d933
Author: lijewski <lijewski>
Date:   Tue Dec 2 23:05:28 1997 +0000

    Merged with IAMRAll.

Src/C_AMRLib/TagBox.cpp

commit 3cc8b18f0d6eb3ed26891ea45ec2f832e6fcbf28
Author: lijewski <lijewski>
Date:   Tue Dec 2 21:30:56 1997 +0000

    Updated from IAMRAll.

Src/C_AMRLib/StateData.cpp

commit a211f6340f445ba6a77b020c09761aaa8717764a
Author: lijewski <lijewski>
Date:   Tue Dec 2 21:15:47 1997 +0000

    Updated from IAMRAll.

Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp

commit b3e9cce89a07963e0ed3e3bcaf25f6ccc047480f
Author: lijewski <lijewski>
Date:   Tue Dec 2 19:12:17 1997 +0000

    ErrorType and ErrorFunc are now member of ErrorRec.

Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/ErrorList.cpp

commit bdc75be87999dab12a261d04ccc2d71a1518ea21
Author: lijewski <lijewski>
Date:   Tue Dec 2 00:08:55 1997 +0000

    Added virtual aString thePlotFileType() const.
    Removed an extraneous include directive.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 9a49fb840866a5c3dcb4888ab7cfcc763a04ba2d
Author: vince <vince>
Date:   Mon Dec 1 21:01:29 1997 +0000

    Moved BSP defines to the appropriate Make.machine file.

Tools/C_mk/Make.OSF1
Tools/C_mk/Make.T3E

commit b8498d60b70124f9e5da6a89a37d13cd5f59c4b2
Author: vince <vince>
Date:   Mon Dec 1 20:49:58 1997 +0000

    Added ifdefs for the T3E.

Src/C_BaseLib/CONSTANTS.H

commit bdbd2a0966e7027277119d5c831377780c7add9a
Author: lijewski <lijewski>
Date:   Mon Dec 1 18:23:11 1997 +0000

    Mods to compile with Cray compiler on T3E.

Src/C_BaseLib/DistributionMapping.cpp

commit bcf073c9c4f7686dcdb40526adc585921c249c04
Author: lijewski <lijewski>
Date:   Fri Nov 28 18:30:25 1997 +0000

    Removed maximum cache size mumbo-jumbo.
    The cache must now be flushed manually.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 6d2120e6876df2a34915fb4a49c942180001f7e2
Author: lijewski <lijewski>
Date:   Fri Nov 28 18:14:42 1997 +0000

    Call DistributionMapping::FlushCache() in regrid() after grid_places().

Src/C_AMRLib/Amr.cpp

commit 0a1c87390b127de07f8023f0159f87f4dc461a39
Author: lijewski <lijewski>
Date:   Fri Nov 28 17:27:37 1997 +0000

    Bypass the processor cache when using ROUNDROBIN.

Src/C_BaseLib/DistributionMapping.cpp

commit f93718ec08ebe1f09cd17646961f86b6e23b720c
Author: lijewski <lijewski>
Date:   Fri Nov 28 16:45:13 1997 +0000

    Added assert(rwtime > 0).
    Now that we're using wsecond() this shouldn't happen, but ...

Src/C_AMRLib/RunStats.cpp

commit a0c694a9f73c331d3e354c343f56aafe3a64f27d
Author: lijewski <lijewski>
Date:   Fri Nov 28 00:00:45 1997 +0000

    Am now caching processor maps.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 710697e5ad818b19abb8170f622298aaa0c04719
Author: lijewski <lijewski>
Date:   Wed Nov 26 20:51:36 1997 +0000

    CLUSTER -> Cluster

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp

commit dc7efde597f5e2f7be1d2b06a0f9b4b186843236
Author: nazgul <nazgul>
Date:   Wed Nov 26 20:46:17 1997 +0000

    Testing errors in divergence of a linear velocity field

Src/LinearSolvers/C_NodalMG/amr_graph.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit c5d04257975f57cda908e22201800e12cc88d6ec
Author: nazgul <nazgul>
Date:   Wed Nov 26 20:44:08 1997 +0000

    Grids for convergence test with single refined patch

Src/LinearSolvers/C_NodalMG/tests/gr2r1
Src/LinearSolvers/C_NodalMG/tests/gr2r2
Src/LinearSolvers/C_NodalMG/tests/gr2r3
Tests/LinearSolvers/C_NodalMG/test_grids/gr2r1
Tests/LinearSolvers/C_NodalMG/test_grids/gr2r2
Tests/LinearSolvers/C_NodalMG/test_grids/gr2r3

commit 875e4cf3add35beaed7a90cf0eb42230e3fb831e
Author: lijewski <lijewski>
Date:   Wed Nov 26 20:41:41 1997 +0000

    The return value of all "new"s is now checked.

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/ErrorList.cpp
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.cpp
Src/C_AMRLib/TagBox.cpp

commit 43c49db0947ea7a55dc0c8a1232fba1a2093192c
Author: lijewski <lijewski>
Date:   Wed Nov 26 19:18:46 1997 +0000

    BOX -> Box
    REAL -> Real
    TAGBOX -> TagBox
    INTVECT -> IntVect
    FARRAYBOX -> FArrayBox

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/BCRec.H
Src/C_AMRLib/BCRec.cpp
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/Derive.H
Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/FLUXREG_F.H
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/LevelBld.H
Src/C_AMRLib/MAKESLICE_F.H
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit d35e1c6a9cc6b6db290b737a0bbb5c2d4c88242b
Author: lijewski <lijewski>
Date:   Wed Nov 26 18:27:45 1997 +0000

    setTimeLevel() now takes three arguments.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit 909029aaab141527b8d9c59575ac5134efc8f654
Author: lijewski <lijewski>
Date:   Wed Nov 26 17:46:22 1997 +0000

    enum TimeCenter is now nested in StateDescriptor.

Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp

commit 10e5b26984d8391b48badf150356992e293db849
Author: lijewski <lijewski>
Date:   Wed Nov 26 06:26:45 1997 +0000

    Made wsecond() initializers explicitly extern.
    Don't want anyone to think they should be static :-)

Src/C_BaseLib/Utility.cpp

commit e173ec034764e9e29755b5e909030a1e2417b10d
Author: lijewski <lijewski>
Date:   Wed Nov 26 05:07:25 1997 +0000

    init() is now protected.
    The constructors call it if it hasn't already been called.

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp

commit ff669c441728a23f4ab81774d965e633679b9833
Author: lijewski <lijewski>
Date:   Wed Nov 26 04:22:34 1997 +0000

    Don't call knapsack code if on 1 cpu -- use roundrobin.
    Guarantee that all versions of wsecond() get initialized at program startup.

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 741d07df888ffa7adfa3dc0db507d3ec9f48221f
Author: lijewski <lijewski>
Date:   Wed Nov 26 04:21:46 1997 +0000

    init() is now protected.
    It's called by the constructor if it hasn't already been called.

Src/C_AMRLib/RunStats.H
Src/C_AMRLib/RunStats.cpp

commit 090da2f19dc49617370b4ecfb56fc80254bc071b
Author: lijewski <lijewski>
Date:   Tue Nov 25 22:17:51 1997 +0000

    Added four types of create functions.
    Call them through a static pointer to member function.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 966bcb45cc7c113576d08c8bfbd3989aa843d9f9
Author: car <car>
Date:   Tue Nov 25 19:55:15 1997 +0000

    Assertion for nprocessors > 1

Src/C_BaseLib/DistributionMapping.cpp

commit e343caa0f06827f5ad07b57e1aed6a9c06be2f14
Author: lijewski <lijewski>
Date:   Tue Nov 25 19:23:31 1997 +0000

    Regularized os.precision() mumbo-jumbo a tad.

Src/C_AMRLib/RunStats.cpp

commit 9e1091c89357c16a7905d2dce40c01aacab92524
Author: lijewski <lijewski>
Date:   Tue Nov 25 19:09:42 1997 +0000

    Different way to guarantee wall clock time gets initialized.

Src/C_BaseLib/Utility.cpp

commit 65fd1ea0ff17a71e0339ece4c461dfe68a17ea7a
Author: car <car>
Date:   Tue Nov 25 19:00:36 1997 +0000

    Improvements in DistributionMapping for Knapsack

Src/C_BaseLib/DistributionMapping.cpp

commit dbaffef3482714b2aa5279b0eccfb7fc6c22d7fa
Author: lijewski <lijewski>
Date:   Tue Nov 25 18:47:05 1997 +0000

    Added init() and strategy().
    Turned on knapsack().

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 2a4d5a0869b1b90cf48d31e4f4ce23a02e7c3e06
Author: lijewski <lijewski>
Date:   Tue Nov 25 17:08:25 1997 +0000

    Small changes ...

Src/C_BaseLib/DistributionMapping.cpp

commit 68fa915dfbc2338a1e6c57fa9a09c358d55e8db2
Author: car <car>
Date:   Tue Nov 25 14:49:30 1997 +0000

    Removed use of member template.

Src/C_BaseLib/DistributionMapping.cpp

commit 07c667a8064c45af21efc3b105b3c94482d8cb13
Author: lijewski <lijewski>
Date:   Mon Nov 24 23:45:51 1997 +0000

    Added initializer for wsecond().

Src/C_BaseLib/Utility.cpp

commit d713dc76066ff10d8180db70214104cb995a8a03
Author: car <car>
Date:   Mon Nov 24 22:05:10 1997 +0000

    Commiting some knapsack code, to see if it compiles on T3E.

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/GNUmakefile

commit 47c36e3f35abcc63b00f57b54cbfd534b088cf16
Author: lijewski <lijewski>
Date:   Mon Nov 24 21:04:37 1997 +0000

    Am now using Utility::wsecond() in place of ParallelDescriptor::second().

Src/C_AMRLib/RunStats.H
Src/C_AMRLib/RunStats.cpp

commit 30b300234dddd73ff35d87c877869e537e629290
Author: lijewski <lijewski>
Date:   Mon Nov 24 18:52:26 1997 +0000

    Merged in BL_COPYRIGHT_NOTICE macro.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Amr_auxil.H
Src/C_AMRLib/BCRec.H
Src/C_AMRLib/BCRec.cpp
Src/C_AMRLib/BC_TYPES.H
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/ErrorList.cpp
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/LevelBld.H
Src/C_AMRLib/RunStats.H
Src/C_AMRLib/RunStats.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 03a1edc77cfe304eb20a15dbb6c1f4403dab42eb
Author: lijewski <lijewski>
Date:   Mon Nov 24 18:40:53 1997 +0000

    Minor mod to output formatting.

Src/C_AMRLib/RunStats.cpp

commit 2d82e5ad5a4d6db9004cf9cff738e996bba85906
Author: lijewski <lijewski>
Date:   Sun Nov 23 21:42:50 1997 +0000

    Removed m_numpts stuff.  It's now in RunStats.

Src/C_BaseLib/FabArray.H

commit 927df7ff08765882c95dd7c3118e2e383683ef68
Author: lijewski <lijewski>
Date:   Sun Nov 23 21:42:31 1997 +0000

    NumPts() stuff from FabArray::AllocFabs() is now in here.

Src/C_AMRLib/RunStats.H
Src/C_AMRLib/RunStats.cpp

commit 4acbf7cb9f02a0106d17b0bd0b22b7d82c09e1e5
Author: lijewski <lijewski>
Date:   Sun Nov 23 18:19:59 1997 +0000

    We now return # of bytes written to disk.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 1ac4be59b81ef4dbef44a7adf63376379fa4a13d
Author: lijewski <lijewski>
Date:   Sun Nov 23 18:18:49 1997 +0000

    RunStats now accumulates bytes written to disk.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/RunStats.H
Src/C_AMRLib/RunStats.cpp
Src/C_AMRLib/StateData.cpp

commit 1223356c10c46af6ea34b84421af5108b5f7ad56
Author: lijewski <lijewski>
Date:   Sun Nov 23 00:12:08 1997 +0000

    Don't print out stats if the particular stat is 0.

Src/C_BaseLib/FabArray.H

commit 972bf74ed43f8cf8d61a0ed0cd0a2c13df086c14
Author: lijewski <lijewski>
Date:   Sun Nov 23 00:10:55 1997 +0000

    Merged in a saner RunStats.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/RunStats.H
Src/C_AMRLib/RunStats.cpp

commit d287254ecf1008f08a69bcf26ee8b8bc8b553854
Author: lijewski <lijewski>
Date:   Sat Nov 22 17:52:06 1997 +0000

    Moved FileOpenFailed() to Utility.
    Added CreateDirectoryFailed() to Utility.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 35f09d2306022d65900f0bc0f7f109fe2747bccd
Author: lijewski <lijewski>
Date:   Sat Nov 22 17:51:31 1997 +0000

    Moved FileOpenFailed() and CreateDirectoryFailed() to Utility.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp

commit 254c7f4c0205435dec780b6cac6e305655f3d874
Author: lijewski <lijewski>
Date:   Sat Nov 22 01:10:41 1997 +0000

    Merged in VisMF::FileOpenFailed().

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit d61c5cbf2174d79225ef99fa57f15535b1f0071d
Author: lijewski <lijewski>
Date:   Sat Nov 22 00:44:44 1997 +0000

    Merged in I/O statistics stuff.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 80b42b44834d0175d518a45e2e14b3478eaebe75
Author: lijewski <lijewski>
Date:   Sat Nov 22 00:44:22 1997 +0000

    Merged in I/O statistics.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 3a29dc686b6c227c96d1b1114799e0940f9e4c80
Author: lijewski <lijewski>
Date:   Fri Nov 21 20:33:25 1997 +0000

    Added typedef to describe first argument of bsp_fold().

Src/C_BaseLib/ParallelDescriptor.cpp

commit d7c140a2b36bf60ea5f45ed33ee9d407a5a4c3a3
Author: lijewski <lijewski>
Date:   Fri Nov 21 03:50:35 1997 +0000

    Now accumlate numPts() in m_numpts.

Src/C_BaseLib/FabArray.H

commit 273e77e9682043b051ce8fa8ab14ea43f32ec972
Author: lijewski <lijewski>
Date:   Fri Nov 21 03:50:10 1997 +0000

    Fixed a bug in RunStats.  Still needs work.
    The name of WritePlotFile RunStats variable didn't match that in inputs.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/RunStats.H
Src/C_AMRLib/RunStats.cpp

commit b6259f73d32732e0f2187202b66f00d0f892ecc8
Author: lijewski <lijewski>
Date:   Thu Nov 20 18:26:59 1997 +0000

    Small changes

Tools/C_mk/Make.OSF1
Tools/C_mk/Make.T3E

commit 14ea1a3b9bfee6907b4d30e11a5ddf1bf975db69
Author: lijewski <lijewski>
Date:   Thu Nov 20 18:14:32 1997 +0000

    Removed a `return' following a `stop' that compiler warned was unreachable.

Src/C_AMRLib/INTERP_3D.F

commit ebde3cbef4316373d3f53360e10de25a88312d56
Author: lijewski <lijewski>
Date:   Thu Nov 20 17:05:10 1997 +0000

    Small mod to compile on T3E.

Src/C_BaseLib/VisMF.cpp

commit d1144ac0f339e530ca652fa427ad8a7d75f740cd
Author: lijewski <lijewski>
Date:   Thu Nov 20 17:04:57 1997 +0000

    Small mod to get to compile on T3E.

Src/C_AMRLib/Amr.cpp

commit f93dce4316880b343263c358a1c8490f204d2931
Author: lijewski <lijewski>
Date:   Thu Nov 20 16:13:38 1997 +0000

    A small simplification.

Src/C_BaseLib/ParallelDescriptor.H

commit 3b1715cd2d8567bb8161758b1dcf21e051413a2a
Author: lijewski <lijewski>
Date:   Thu Nov 20 00:49:42 1997 +0000

    ParallelDescriptor::SetMessageHeaderSize() now takes int not int&.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/VisMF.cpp

commit 26f5efae06b0e670322d2d2ef0c8e55b222c93b7
Author: lijewski <lijewski>
Date:   Thu Nov 20 00:19:50 1997 +0000

    Added PrintStats() to FabArray.

Src/C_BaseLib/FabArray.H

commit 69d07d5b9af87d1a4313555ae1b6f5d918958d4d
Author: lijewski <lijewski>
Date:   Thu Nov 20 00:19:30 1997 +0000

    Prettified report() a tad.

Src/C_AMRLib/RunStats.cpp

commit 235c008475187c04dd7ae36eb8f520deded123b9
Author: lijewski <lijewski>
Date:   Wed Nov 19 17:31:19 1997 +0000

    Removed some unused arrays in FabArrayCopyDescriptor and general cleanup.

Src/C_BaseLib/FabArray.H

commit fc1aebf5a3a40ccded9a994bdc6f5c376c631b1d
Author: lijewski <lijewski>
Date:   Wed Nov 19 16:25:54 1997 +0000

    Added write_pltfile and write_chkfile RunStats.
    Moved some RunStats functions inline.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/RunStats.H
Src/C_AMRLib/RunStats.cpp

commit e93560b695d6d4509d99f56e101b34eb4955e7d0
Author: lijewski <lijewski>
Date:   Wed Nov 19 04:42:27 1997 +0000

    Simplified a tad bit of code.

Src/C_AMRLib/RunStats.cpp

commit 706190ebc65e593fd47687703c81e3752f7a4cf4
Author: lijewski <lijewski>
Date:   Wed Nov 19 00:01:26 1997 +0000

    Modified to deal with bsp_time() possible returning zero.

Src/C_AMRLib/RunStats.cpp

commit 411ed2fc60c77998ad4c5970761e3040f3a8296b
Author: car <car>
Date:   Tue Nov 18 21:45:28 1997 +0000

    Start some changes.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 88a4eaf6e05cdf6172364fe40dfb55d13e884cac
Author: lijewski <lijewski>
Date:   Tue Nov 18 19:30:19 1997 +0000

    Copied from Parallel/HCAll

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/Amr_auxil.H
Src/C_AMRLib/BCRec.H
Src/C_AMRLib/BCRec.cpp
Src/C_AMRLib/BC_TYPES.H
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/DIMS.H
Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp
Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/ErrorList.cpp
Src/C_AMRLib/FILCC_2D.F
Src/C_AMRLib/FILCC_3D.F
Src/C_AMRLib/FLUXREG_2D.F
Src/C_AMRLib/FLUXREG_3D.F
Src/C_AMRLib/FLUXREG_F.H
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/INTERP_2D.F
Src/C_AMRLib/INTERP_3D.F
Src/C_AMRLib/INTERP_F.H
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/LevelBld.H
Src/C_AMRLib/MAKESLICE_3D.F
Src/C_AMRLib/MAKESLICE_F.H
Src/C_AMRLib/PROB_AMR_F.H
Src/C_AMRLib/RunStats.H
Src/C_AMRLib/RunStats.cpp
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 7580dbc50250fc98c65d6287899469a168b556df
Author: lijewski <lijewski>
Date:   Tue Nov 18 18:51:53 1997 +0000

    PerFile -> PerFab

Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/tVisMF.cpp

commit b1b43805e1d22020c38aa4e7f205657818871126
Author: lijewski <lijewski>
Date:   Tue Nov 18 18:48:13 1997 +0000

    Fixed a bug.

Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/tVisMF.cpp

commit 2bed7fd7983f1060808bd0b38f3607313e42e485
Author: lijewski <lijewski>
Date:   Tue Nov 18 18:22:24 1997 +0000

    Mods to compile on NAVO T3E.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit b4c40aa369442e197db0fd969f3636726bedd8c8
Author: lijewski <lijewski>
Date:   Tue Nov 18 00:04:45 1997 +0000

    Added explicit to all single-argument constructors.
    Removed IntVect::operator const int *
    Wrote BoxList::contains(BoxArray).

Src/C_BaseLib/Array.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxAssoc.H
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/List.H
Src/C_BaseLib/Looping.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/Tracer.H
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/aString.H

commit da5f8ca65647b43377ab0c0250333b5fdc16b9a4
Author: lijewski <lijewski>
Date:   Mon Nov 17 21:09:30 1997 +0000

    Removed ToString().
    Got rid of GetTheChar().

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit be34251f063aae0ba8373b5b0065b3d93c923b47
Author: car <car>
Date:   Mon Nov 17 19:05:31 1997 +0000

    A little better way: just pass in a dummy mode variable in WIN32.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 02be1b6435f232df319cc65b3cfcc03b56bfcbba
Author: car <car>
Date:   Mon Nov 17 19:02:03 1997 +0000

    Fix for WIN32 not supporting mkdir.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit da2dca39383022b04afc87f7c728283a761f0b5a
Author: lijewski <lijewski>
Date:   Sat Nov 15 00:52:38 1997 +0000

    Added VisMF::Read().

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/tVisMF.cpp

commit a55ffec0d73f28c2ad91559bf836b35f719cb9ba
Author: vince <vince>
Date:   Fri Nov 14 21:43:35 1997 +0000

    Added better optimization flags.

Tools/C_mk/Make.T3E

commit 42f1aeaee1b13f53c6dba9329afa8d4224b6b43e
Author: lijewski <lijewski>
Date:   Fri Nov 14 20:22:40 1997 +0000

    The IO_Bufffer object needs to be created before the [io]fstream one!

Src/C_BaseLib/VisMF.cpp

commit 171470f55904913285ebfadbb1ee003299edbea4
Author: lijewski <lijewski>
Date:   Fri Nov 14 00:59:55 1997 +0000

    Removed Large_IO_Buffer() and replaced with Array<Setbuf_Char_type> usage.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 93d90f6eb05e1fd98ebda7e80c851c0348d47b54
Author: lijewski <lijewski>
Date:   Thu Nov 13 23:55:44 1997 +0000

    Made IO Buffer stuff public so Amr could use it as well.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 627d0ed0a2a41ba363d9626167273d917bc8ec81
Author: lijewski <lijewski>
Date:   Thu Nov 13 21:47:46 1997 +0000

    Removed ios::binary junk.
    Integrated in BL_USE_SETBUF and BL_SETBUF_CHAR_SIGNED.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit dcbcb4aa1f46879a8733fdff360e506e3e77866f
Author: lijewski <lijewski>
Date:   Thu Nov 13 21:41:23 1997 +0000

    Added BL_USE_SETBUF.

Tools/C_mk/Make.T3E

commit 8bf2453b733cc05f0dc021a7de03d5e2c32e9813
Author: lijewski <lijewski>
Date:   Thu Nov 13 21:28:01 1997 +0000

    Added -DBL_SETBUF_SIGNED_CHAR when using CC.

Tools/C_mk/Make.T3E

commit 36023a9e0532dc4dbb50e1375ea48066b3c583cf
Author: lijewski <lijewski>
Date:   Thu Nov 13 18:45:14 1997 +0000

    Now uniformly use BoxLib::Error() for error reporting.
    It now uses ParallelDescriptor::Abort() internally, when needed.

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/VisMF.cpp

commit 8fe14ed9529726e90c08c6bfd1bf68fa6c0bcab1
Author: lijewski <lijewski>
Date:   Thu Nov 13 16:38:54 1997 +0000

    Replaced abort() with BoxLib::Abort().

Src/C_BaseLib/ParallelDescriptor.H

commit 6f6535f7e59c6cb39deb231ee6499dfeec634d69
Author: lijewski <lijewski>
Date:   Thu Nov 13 16:34:00 1997 +0000

    Maxed out the precision when outputting the Header.
    Replaced BoxLib::Error() with ParallelDescriptor::Abort().

Src/C_BaseLib/VisMF.cpp

commit 3e4f7350c5ebdc3cacf3fc4433c1a2b7aff00419
Author: lijewski <lijewski>
Date:   Thu Nov 13 15:47:34 1997 +0000

    Bug in the relative path portion of CreateDirectory()

Src/C_BaseLib/Utility.cpp

commit 0e7688ec40ee9c57120f60205799349f4bc2e004
Author: vince <vince>
Date:   Thu Nov 13 01:14:43 1997 +0000

    Make definitions for the T3E.

Tools/C_mk/Make.T3E

commit 34c3ce53861205acf3f172113da3aed1cd192bcf
Author: lijewski <lijewski>
Date:   Thu Nov 13 01:05:12 1997 +0000

    Signatures of Abort() were not consistent in sequential/parallel code.

Src/C_BaseLib/ParallelDescriptor.H

commit 9deac822f6de4d5afa4c1ce513f5fe0989d37f6e
Author: nazgul <nazgul>
Date:   Wed Nov 12 22:10:30 1997 +0000

    fiddling with test problems

Src/LinearSolvers/C_NodalMG/proj.cpp

commit ea17c0a6c99aacaa2f5f90d2ac06e4c7ddbd54bd
Author: lijewski <lijewski>
Date:   Wed Nov 12 21:57:26 1997 +0000

    Added Utility:CreateDirectory() and a test case.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/test/GNUmakefile.test
Src/C_BaseLib/test/tDir.cpp
Tests/C_BaseLib/GNUmakefile.test
Tests/C_BaseLib/tDir.cpp

commit 974ebd6a6402d98bd84879e9d24a1cc2cb1143ea
Author: nazgul <nazgul>
Date:   Wed Nov 12 21:42:33 1997 +0000

    New tests for 3d terrain stencils

Src/LinearSolvers/C_NodalMG/tests/gt2t1
Src/LinearSolvers/C_NodalMG/tests/gt2t2
Src/LinearSolvers/C_NodalMG/tests/gt2t3
Tests/LinearSolvers/C_NodalMG/test_grids/gt2t1
Tests/LinearSolvers/C_NodalMG/test_grids/gt2t2
Tests/LinearSolvers/C_NodalMG/test_grids/gt2t3

commit d5405f554e8fa7292d1344340eb07c40e7707898
Author: nazgul <nazgul>
Date:   Wed Nov 12 21:39:29 1997 +0000

    Fix to problems with sigmas in terrain stencils?

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 6eafa3faf7a3a63e0442c7aac32bb7ef9df9fdce
Author: lijewski <lijewski>
Date:   Wed Nov 12 17:40:33 1997 +0000

    VisMF.cpp currently compiles on T3E.
    Added -nboxs flag to test case.

Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/tVisMF.cpp

commit c3b2b9decf9bed0c9cebc7a2a1f17827651a4e70
Author: lijewski <lijewski>
Date:   Wed Nov 12 04:12:24 1997 +0000

    Made the open modes I expect explicit.
    Now longer clean up previous output files in test case.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/tVisMF.cpp

commit 8477ccb607366879f486ff382f8e6a724229d993
Author: lijewski <lijewski>
Date:   Wed Nov 12 00:22:57 1997 +0000

    Added .cvsignore

Src/C_BaseLib/.cvsignore

commit 7b0886b7799558836552352318143a04261bea94
Author: lijewski <lijewski>
Date:   Wed Nov 12 00:16:56 1997 +0000

    Added some code to use large I/O buffers on T3E.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit b2a4849bd98ec80bc920200f1c98c648dafabfef
Author: lijewski <lijewski>
Date:   Tue Nov 11 22:18:59 1997 +0000

    Needed a ParallelDescriptor::Synchronize() between writing and reading.

Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/tVisMF.cpp

commit 1d2d9c7f876b9ae83a21881650a8f0e4119cb4c1
Author: lijewski <lijewski>
Date:   Tue Nov 11 21:38:37 1997 +0000

    Added a call to MultiFab::setBndry(0).

Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/tVisMF.cpp

commit 6efd06bd71aacccf2e7fe7e0ab8ab68daed64c99
Author: lijewski <lijewski>
Date:   Tue Nov 11 21:22:50 1997 +0000

    Consolidated some of the code into larger routine.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 05dd332fe75a4cb053c9de15d88b0de4b521c900
Author: vince <vince>
Date:   Tue Nov 11 21:04:52 1997 +0000

    Added sync argument:  FabArrayIterator<T>::isValid(bool bDoSync = true);

Src/C_BaseLib/Box.H
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Utility.cpp

commit 1cec386f02ec5642acf31469fe3f77a9d5b140dd
Author: lijewski <lijewski>
Date:   Tue Nov 11 21:02:19 1997 +0000

    Now the OneFilePerFab is working in Parallel.

Src/C_BaseLib/VisMF.cpp

commit ce90c46d9f36c971a0c99753ffe77e6765d5ba8d
Author: nazgul <nazgul>
Date:   Tue Nov 11 20:51:05 1997 +0000

    Added compiler options necessary to get optimization to work with
    KCC 3.1a and 3d terrain level solves.  (Cannot use higher than +K2).

Src/LinearSolvers/C_NodalMG/GNUmakefile.main

commit 7ea8288dc1d5e51f9d5caf8af9702155e569d23c
Author: lijewski <lijewski>
Date:   Tue Nov 11 20:29:56 1997 +0000

    Added -how flag.

Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/tVisMF.cpp

commit e1e01db38ee3abd6a9cf5f6d27d910d90dacb444
Author: lijewski <lijewski>
Date:   Tue Nov 11 19:20:05 1997 +0000

    Got the VisMF::OneFilePerCPU working in Parallel.
    Had to Change the signature of ParallelDescriptor::SendData().

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/test/GNUmakefile.test
Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/GNUmakefile.test
Tests/C_BaseLib/tVisMF.cpp

commit 69ba94f24fa738ddcdcbfe61b9885fc21d29f5fc
Author: lijewski <lijewski>
Date:   Tue Nov 11 01:18:13 1997 +0000

    Added some more parallel code.  Yet more to come.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/tVisMF.cpp

commit 4a85cfa5eb28722d7b729beb300a73fb11769a06
Author: lijewski <lijewski>
Date:   Mon Nov 10 22:41:21 1997 +0000

    Did the MultiFab loops using proper Parallel construct.
    All that remains is to do the reduction of the VisMF::Header.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 28b1d733eece835af8947f32f9deef7af6fb994e
Author: almgren <almgren>
Date:   Mon Nov 10 22:22:33 1997 +0000

    These files now have the correct subroutines for the 3-d multilevel terrain
    stencils (faces / edges / corners) for residual and divergence.  They are
    ifdef'ed for TERRAIN.

Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit 917a5935e1339560e318e7762442f5bf340fb02d
Author: lijewski <lijewski>
Date:   Mon Nov 10 22:14:47 1997 +0000

    Added length() member to VisMF.H
    Now test reading and writing both ways at once.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/tVisMF.cpp

commit e0511943b7c79a843f58a3bdf20a68794e3586aa
Author: car <car>
Date:   Mon Nov 10 21:36:17 1997 +0000

    Some changes for parallel file I/O.

Src/C_BaseLib/Box.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/pBoxLib_2.dsp

commit 42fc8aca600e7d443e836e807c733361a6a34f81
Author: lijewski <lijewski>
Date:   Mon Nov 10 21:29:48 1997 +0000

    Got working for -DUSE_NEW_HFILES macro.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit e9fda6fc2ba520eeef6937b9d5fa0fe55862609e
Author: lijewski <lijewski>
Date:   Mon Nov 10 21:17:10 1997 +0000

    Got OneFilePerFab working.  Parallel to come ....

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/tVisMF.cpp

commit 1f3f0335cc9c42666dcc88444a4ef099483238cd
Author: lijewski <lijewski>
Date:   Mon Nov 10 19:30:12 1997 +0000

    The OneFilePerCPU stuff seems to work.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp
Src/C_BaseLib/test/GNUmakefile.test
Src/C_BaseLib/test/tVisMF.cpp
Tests/C_BaseLib/GNUmakefile.test
Tests/C_BaseLib/tVisMF.cpp

commit 319f3a350a8b72b3e98e939024107c93036638f7
Author: lijewski <lijewski>
Date:   Mon Nov 10 17:54:40 1997 +0000

    BoxArray(istream&) wasn't implemented.
    Now can read the VisMF::Header that has been written to disk.

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit d90e806f32a69eacb746ce65e5aa5a5bd0002ce6
Author: lijewski <lijewski>
Date:   Mon Nov 10 03:55:46 1997 +0000

    Forgot about the ghost cells :-(

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 1cba5e03c9ab1744917afd85365f1713d946a920
Author: lijewski <lijewski>
Date:   Mon Nov 10 03:37:29 1997 +0000

    Wrote the stream extraction operators.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit c915e63bbd7e6df69b00621ca657334e050b0b1c
Author: lijewski <lijewski>
Date:   Sun Nov 9 20:31:40 1997 +0000

    OneFilePerCPU output is more or less done.  Now for the testing.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit d2639f853837afbfac5d509a4e247b69c6fd8ef9
Author: lijewski <lijewski>
Date:   Sun Nov 9 20:11:25 1997 +0000

    Just cosmetic guff.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 5c2d5d466f4e3b8e5ef92adc066d15897ec27c7d
Author: lijewski <lijewski>
Date:   Sun Nov 9 19:45:29 1997 +0000

    Slight cosmetic changes -- no more static stuff in .cpp file.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 0168fa96dd8c6b533f83b746594dfd07a59ab040
Author: lijewski <lijewski>
Date:   Sun Nov 9 00:58:56 1997 +0000

    Added some more code.  Lots more to follow.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 7450ac6ba2d45882ffd2d2e2cb0371873b53af3f
Author: lijewski <lijewski>
Date:   Sat Nov 8 23:24:16 1997 +0000

    Added VisMF stuff -- just getting started with it.

Src/C_BaseLib/Make.package
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit b6a549645833f8e7a91bd753baa11ebad0d6ab96
Author: jbb <jbb>
Date:   Sat Nov 8 01:42:02 1997 +0000

    Fixed nested comments

Src/C_BaseLib/Utility.H

commit 9e289e25a32fda9c0bf218d99f2b66a2320861ae
Author: almgren <almgren>
Date:   Thu Oct 30 22:44:32 1997 +0000

    Added subroutines hgfdiv, hgediv and hgcdiv for TERRAIN defined.

Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit 61c404f39f962c7079aa6908f789cb7385de8a89
Author: almgren <almgren>
Date:   Thu Oct 30 22:44:13 1997 +0000

    Cosmetic changes only.

Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit 6cd1d16687afdf6e5465cc44323f4c35c4d37cde
Author: vince <vince>
Date:   Tue Oct 21 22:00:52 1997 +0000

    Bug fixes for parallel multilevel IAMR (minus the nodal projection).
    Also other fixes and code cleanup.

Src/C_AMRLib/DatasetClient.cpp

commit 70e92eff9aac7b20539be29a390d0a5b616cf076
Author: vince <vince>
Date:   Tue Oct 21 21:55:53 1997 +0000

    Minor changes to AddBox interface.

Src/C_BaseLib/Box.H
Src/C_BaseLib/FabArray.H

commit 15b8ce2bab58de1b394fb1c2634e6aba90ecb577
Author: car <car>
Date:   Thu Oct 9 18:23:10 1997 +0000

    Added more access functions to the iterators: more STL like.

Src/C_BaseLib/FabArray.H

commit 7bff2a1aa5af7fbef7a9848b58034a1bf02c9c0b
Author: car <car>
Date:   Thu Sep 25 21:57:17 1997 +0000

    Small changes.

Src/C_BaseLib/pBoxLib_2.dsp

commit 949841b53c75d1a257cc5db73618a1155deb50c9
Author: lijewski <lijewski>
Date:   Wed Sep 24 22:06:41 1997 +0000

    Replaced most endl's with '\n'.

Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxAssoc.cpp
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/ParmParse.cpp

commit fea6a8fd2fd994433230de2174cdc937f9e4d4da
Author: lijewski <lijewski>
Date:   Wed Sep 24 04:24:50 1997 +0000

    Removed the BoxList intersect with BoxList function.
    It wasn't implemented properly.
    Will add a correct one if the need arises.
    Removed ostrstream usage from BoxLib.cpp.

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit 328fb178b241ca4a5ef2e36272078cbcada758d9
Author: car <car>
Date:   Wed Sep 24 03:01:20 1997 +0000

    Removed a strstream.h file inclusion, not needed.

Src/C_BaseLib/ParmParse.cpp

commit 2688be7c705eb08803aea6d09ef471eff637cceb
Author: lijewski <lijewski>
Date:   Tue Sep 23 19:25:39 1997 +0000

    Merged in BL_USE_NEW_HFILES.
    Removed many unnecessary #include directives.
    Removed a couple more instances of RASTER and CONTOUR usage.

Src/C_AMRLib/DatasetClient.cpp

commit 5e700a0626be21d946af44dde9b1b618535c7c9a
Author: nazgul <nazgul>
Date:   Tue Sep 23 18:13:44 1997 +0000

    Minor modifications occasioned by the 4 level test problem, and letting
    the convergence test see the norm of the coarse_source.

Src/LinearSolvers/C_NodalMG/amr_graph.cpp
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 41ba3fc0532f526083919b4f456c54fdf9a6efb6
Author: nazgul <nazgul>
Date:   Tue Sep 23 18:11:24 1997 +0000

    4 level test problem

Src/LinearSolvers/C_NodalMG/tests/gr4level
Tests/LinearSolvers/C_NodalMG/test_grids/gr4level

commit 0a58d792af5203d76118b7de867caf3ed626c901
Author: car <car>
Date:   Fri Sep 19 18:20:02 1997 +0000

    Quiet down a warning about conversion of long to bool.
    Update the Project file.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/pBoxLib_2.dsp

commit 29bcd0f20dd53cfb57133ed6472464de7189838c
Author: vince <vince>
Date:   Fri Sep 19 18:04:34 1997 +0000

    Bug fix for T3E (ReduceBoolAnd problems).

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Utility.H

commit c5fa29a9b4d3e3d87cb797108451e28b3e9956c4
Author: car <car>
Date:   Fri Sep 19 16:17:30 1997 +0000

    Change Comment.

Src/C_BaseLib/ArrayLim.H

commit 111550f24a68ea03c41d1098dd55de0b050e3340
Author: lijewski <lijewski>
Date:   Thu Sep 18 23:34:18 1997 +0000

    Only output continuation line count if > 19 of them.

Tools/C_scripts/strip72

commit e90fb1730737fa0b457463be6b821356ce3808a9
Author: lijewski <lijewski>
Date:   Thu Sep 18 22:09:24 1997 +0000

    Changed a few functions that took `const int' to take simply a `int'.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.H

commit c8450b894ea404e3bf808210f0ee49a2c324cdff
Author: lijewski <lijewski>
Date:   Thu Sep 18 21:22:19 1997 +0000

    Removed some lines that had been commented out.

Src/C_BaseLib/PArray.H

commit f225a6529dfa29d22f9c0b740debbf04f0dabed2
Author: lijewski <lijewski>
Date:   Thu Sep 18 20:12:42 1997 +0000

    Added BL_USE_NEW_HFILES macro.

Src/C_BaseLib/Arena.H
Src/C_BaseLib/Array.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/SPACE_F.H
Src/C_BaseLib/Tracer.cpp
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp

commit 86435a01bb3b77326b190f9d6e9e1da616314109
Author: car <car>
Date:   Thu Sep 18 18:25:19 1997 +0000

    Added some stuff.

Src/C_BaseLib/pBoxLib_2.dsp

commit 2dd0ee07696f36f5b6bf3400857e317ebfcefd6a
Author: car <car>
Date:   Thu Sep 18 18:18:01 1997 +0000

    Broke a comment.

Src/C_BaseLib/Utility.H

commit cb25311b3520630c59588f83a55157e4913dd78e
Author: car <car>
Date:   Thu Sep 18 18:03:33 1997 +0000

    C++ style comments can't be in fortran include files.

Src/C_BaseLib/CONSTANTS.H
Src/C_BaseLib/REAL.H
Src/C_BaseLib/SPACE_F.H
Src/C_BaseLib/Utility.H

commit 1f40f94399e7412e75333277525647f9bed65bdc
Author: lijewski <lijewski>
Date:   Wed Sep 17 22:51:11 1997 +0000

    Enforced all files having a copyright macro.
    Prepended all file inclusion macros with BL_

Src/C_BaseLib/Arena.H
Src/C_BaseLib/Array.H
Src/C_BaseLib/ArrayLim.H
Src/C_BaseLib/Assert.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/Boolean.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxAssoc.H
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/CONSTANTS.H
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FPC.H
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/List.H
Src/C_BaseLib/Looping.H
Src/C_BaseLib/Misc.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/REAL.H
Src/C_BaseLib/SPACE.H
Src/C_BaseLib/SPACE_F.H
Src/C_BaseLib/Tracer.H
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/aString.H

commit 99622cae738f6bbc75e357a7a772f552eba5f178
Author: lijewski <lijewski>
Date:   Wed Sep 17 22:22:49 1997 +0000

    Inlined the constructors.
    Prepended BL_ to file inclusion macros.

Src/C_BaseLib/BaseFab.H

commit 66551db6f06b7bfc85866db12c71673cd5e30304
Author: lijewski <lijewski>
Date:   Wed Sep 17 17:46:31 1997 +0000

    Inlined the constructors.
    Regularized the indentation.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 066bb95aeba8b0191008de0b02df29ed36dae9d2
Author: lijewski <lijewski>
Date:   Wed Sep 17 17:15:59 1997 +0000

    Inlined all the MultiFabIterator stuff.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit bac52e53c8d6289c982089535d698a2b0d43166e
Author: lijewski <lijewski>
Date:   Wed Sep 17 00:03:49 1997 +0000

    Now check assignments of Box::numPts() to integers.

Src/C_AMRLib/DatasetClient.cpp

commit 35b9afb0a67b852b8a53164aba70e5ffb155081d
Author: lijewski <lijewski>
Date:   Wed Sep 17 00:03:26 1997 +0000

    Check assignments of Box::numPts() to integers.

Src/C_BaseLib/FabArray.H

commit 847fc06b03eec118f13783e69ad0eeaa654fa99e
Author: lijewski <lijewski>
Date:   Tue Sep 16 22:28:14 1997 +0000

    Removed `inline' from class definitions.

Src/C_BaseLib/Array.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/List.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/Tuple.H

commit e03036067d3b0f437fa6dc36e9770ad34cb25f4f
Author: lijewski <lijewski>
Date:   Tue Sep 16 22:12:43 1997 +0000

    The previous virtual stuff that was removed consisted only of
    the stuff in FabArrayIterator.
    This mod removes all the virtual stuff from the three remaining Iterators
    in this module, as well as the virtual stuff from FabArrayCopyDescriptor.

Src/C_BaseLib/FabArray.H

commit ccc3769a13049b3460aaa750596c0c517633a30d
Author: lijewski <lijewski>
Date:   Tue Sep 16 21:11:34 1997 +0000

    Removed all virtual stuff.

Src/C_BaseLib/FabArray.H

commit 980dde8029d140ae76d2d05700648d63159e2d93
Author: lijewski <lijewski>
Date:   Tue Sep 16 19:18:11 1997 +0000

    Some cleanup and code simplification.
    Inlined more stuff.

Src/C_BaseLib/Array.H
Src/C_BaseLib/BLVERSION.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/FabArray.H

commit 673ec7d486b8830c16b6ef68674375adafd104ab
Author: lijewski <lijewski>
Date:   Tue Sep 16 16:04:59 1997 +0000

    Removed all DPtr stuff.

Src/C_BaseLib/AliasedDPtr.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/DPtr.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/SimpleDPtr.H

commit 3e687e8125c007bc433b3516f46555ebf67927ff
Author: lijewski <lijewski>
Date:   Tue Sep 16 03:30:36 1997 +0000

    Removed all aliasing stuff from BaseFab.

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/Looping.H

commit 536217df33fa117181fd3a1d19481209c7e841e8
Author: lijewski <lijewski>
Date:   Mon Sep 15 23:33:19 1997 +0000

    Removed aliasing stuff.
    Removed LPARX stuff.

Src/C_BaseLib/BArena.cpp
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/DPtr.H
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabArray.H

commit 18db379740d74a888d2946a9160a5cb99ae2c099
Author: lijewski <lijewski>
Date:   Mon Sep 15 22:24:10 1997 +0000

    From Guthamr release.

Tools/C_scripts/install-sh
Tools/C_scripts/mkdep
Tools/C_scripts/strip72

commit a8e7104301a3df86d54708c4964a4934017e3b8d
Author: lijewski <lijewski>
Date:   Mon Sep 15 21:53:51 1997 +0000

    Now assumes there is ../scripts directory.

Tools/C_mk/Make.defs

commit dcaa46f8a809e222b61ad27a01b4b511779f36ee
Author: lijewski <lijewski>
Date:   Mon Sep 15 20:46:01 1997 +0000

    Now assume things at ../mk

Tools/C_mk/Make.defs

commit 296a7d000fe41bc59e4b42fa1f3ba2b2a5ec2196
Author: lijewski <lijewski>
Date:   Mon Sep 15 20:45:43 1997 +0000

    Now assume ../mk existance.

Src/C_BaseLib/GNUmakefile

commit 1c282a382a7493b9332146ca3a08220cb1374021
Author: lijewski <lijewski>
Date:   Mon Sep 15 20:37:04 1997 +0000

    Moved from IARMAll directory.

Tools/C_mk/Make.OSF1
Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit 4b417c9677f32d29e5c8813d176d1f3085186baa
Author: lijewski <lijewski>
Date:   Mon Sep 15 19:45:24 1997 +0000

    Removed Tuple.cpp and rearranged some things.

Src/C_BaseLib/Make.package

commit 12c046f524fc5d203748dc36a37d2da7b206750a
Author: lijewski <lijewski>
Date:   Mon Sep 15 19:40:05 1997 +0000

    Brought some stuff up to the indentation style of previous boxlib.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/GNUmakefile
Src/C_BaseLib/Make.package
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit ad1c15eb80c200afabbd3559f95935d870fa1e63
Author: vince <vince>
Date:   Mon Sep 15 16:39:38 1997 +0000

    Added files.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 75deac98e0431fa3322aa21ab9f75e3513659f58
Author: lijewski <lijewski>
Date:   Fri Sep 12 17:59:59 1997 +0000

    Moved from IAMRAll directory.

Src/C_BaseLib/AliasedDPtr.H
Src/C_BaseLib/Arena.H
Src/C_BaseLib/Array.H
Src/C_BaseLib/ArrayLim.H
Src/C_BaseLib/Assert.H
Src/C_BaseLib/BArena.H
Src/C_BaseLib/BArena.cpp
Src/C_BaseLib/BLVERSION.H
Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/Boolean.H
Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp
Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxAssoc.H
Src/C_BaseLib/BoxAssoc.cpp
Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp
Src/C_BaseLib/CONSTANTS.H
Src/C_BaseLib/DPtr.H
Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FPC.H
Src/C_BaseLib/FPC.cpp
Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp
Src/C_BaseLib/IndexType.H
Src/C_BaseLib/IndexType.cpp
Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp
Src/C_BaseLib/List.H
Src/C_BaseLib/Looping.H
Src/C_BaseLib/Make.package
Src/C_BaseLib/Misc.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/Orientation.cpp
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/REAL.H
Src/C_BaseLib/SPACE.H
Src/C_BaseLib/SPACE_F.H
Src/C_BaseLib/SimpleDPtr.H
Src/C_BaseLib/Tracer.H
Src/C_BaseLib/Tracer.cpp
Src/C_BaseLib/Tuple.H
Src/C_BaseLib/UseCount.H
Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp

commit afb9a89932bb568e849656b2aca95cb63feb8549
Author: car <car>
Date:   Mon Aug 11 23:45:38 1997 +0000

    Fortran tweaks.

Src/C_AMRLib/DatasetClient.cpp

commit dd6443e646e9f29410d9c7ff897a43bbbc280159
Author: nazgul <nazgul>
Date:   Tue Aug 5 03:26:59 1997 +0000

    Yet more test grids.

Src/LinearSolvers/C_NodalMG/tests/gr2.0
Src/LinearSolvers/C_NodalMG/tests/gr2.1
Src/LinearSolvers/C_NodalMG/tests/gt010
Src/LinearSolvers/C_NodalMG/tests/gt012
Tests/LinearSolvers/C_NodalMG/test_grids/gr2.0
Tests/LinearSolvers/C_NodalMG/test_grids/gr2.1
Tests/LinearSolvers/C_NodalMG/test_grids/gt010
Tests/LinearSolvers/C_NodalMG/test_grids/gt012

commit 67e0489383acac4ceeea54af5758ff197f3da3d4
Author: nazgul <nazgul>
Date:   Tue Aug 5 03:24:54 1997 +0000

    Level project now works in the t27 stencil (no line solves yet).
    Line solves work in any direction in the v7 stencil.

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit bbb2dd4d390208db69facd61f2fa460ea3cb7571
Author: car <car>
Date:   Mon Jul 28 23:16:02 1997 +0000

    Make _OSF_... complient for KCC-3.2b

Src/C_AMRLib/DatasetClient.cpp

commit f157f5d78378df1e8cf0cfdc0dc8431dd9cc9e45
Author: nazgul <nazgul>
Date:   Sun Jul 27 06:11:46 1997 +0000

    A simple 16 cube

Src/LinearSolvers/C_NodalMG/tests/gt016
Tests/LinearSolvers/C_NodalMG/test_grids/gt016

commit 1f57183141ec47999aec76e91ea7c9bbcfcef59a
Author: vince <vince>
Date:   Thu Jul 24 20:31:14 1997 +0000

    Added more FillPatchIterators.

Src/C_AMRLib/DatasetClient.cpp

commit 3976a1d77302700e9b5717fe6712f60c2578f5ea
Author: nazgul <nazgul>
Date:   Sat Jul 12 06:10:39 1997 +0000

    2d 9-point terrain stencils now working fully.  line solves implemented,
    fixed bug in sync project.

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit c75230faf043996fcee66a2e1aa2cc265dd188b8
Author: nazgul <nazgul>
Date:   Fri Jul 11 22:02:56 1997 +0000

    2d 9-point terrain stencils appear to work for level and sync project,
    except that line solves are not yet implemented.

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/boundary.H
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit bbabf6d5f39a13d17f4ef25ec2f0d62be585c126
Author: nazgul <nazgul>
Date:   Thu Jul 3 21:44:21 1997 +0000

    test file for 2 small level 0 grids

Src/LinearSolvers/C_NodalMG/tests/gr0b
Tests/LinearSolvers/C_NodalMG/test_grids/gr0b

commit 197f0fa7276b0152fc83f02191a036cfcaaabf0d
Author: nazgul <nazgul>
Date:   Thu Jul 3 21:43:56 1997 +0000

    terrain now implemented for level project

Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 8722964b1385f26566d2c489c227c1c6d6fb9681
Author: nazgul <nazgul>
Date:   Fri Jun 27 21:54:00 1997 +0000

    integration form of restriction for terrain stencils
    declarations added

Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/cont3d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit ebbaf3120c60bc03aef836660a8c09146b7b7c59
Author: nazgul <nazgul>
Date:   Thu Jun 26 23:19:35 1997 +0000

    Beginnings of terrain additions.

Src/LinearSolvers/C_NodalMG/amr_multi.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 5b809cac28f31826f5a42f235aba46640dda8596
Author: nazgul <nazgul>
Date:   Thu Jun 26 23:17:46 1997 +0000

    Declarations added to fortran.
    Beginnings of terrain additions.

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/cont2d.F
Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 5829c65425db170a84df9b2ad5390f2e3a773f53
Author: nazgul <nazgul>
Date:   Thu Jun 26 23:05:43 1997 +0000

    Test grids which exceed the size the cg bottom solver can easily handle

Src/LinearSolvers/C_NodalMG/tests/gr1rick
Src/LinearSolvers/C_NodalMG/tests/gr1rick2
Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick
Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick2

commit 73897d51f8a7c0a69bac0a2b6c7372b6338e26bc
Author: nazgul <nazgul>
Date:   Tue Jun 10 21:50:31 1997 +0000

    Extend line solves to rz and dimension 0 in 2d.

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 7bae9431fcf243eecf446eedb0675699386ec75b
Author: nazgul <nazgul>
Date:   Tue Jun 10 00:50:17 1997 +0000

    Minor fixes:  forward line solve made vectorizable,
                  conjugate gradient failure made non-fatal, just prints
                   an error message (if pcode >= 2) and goes on.

Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 7acc39a95d9f35073c84419212b1d9285274b36e
Author: nazgul <nazgul>
Date:   Fri Jun 6 16:59:08 1997 +0000

    Full-level line solves, in dimension BL_SPACEDIM - 1, for stencils
    v5, v9 and v7, in Cartesian coordinates only.

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 2cb536d60338abae0b1fbf19629c168fc29b8fef
Author: nazgul <nazgul>
Date:   Fri Jun 6 16:49:29 1997 +0000

    Yet another test grid

Src/LinearSolvers/C_NodalMG/tests/gt05
Tests/LinearSolvers/C_NodalMG/test_grids/gt05

commit e7c2f6c4c99cd7c38f01326be4a9b208d3128c76
Author: nazgul <nazgul>
Date:   Mon Jun 2 20:56:14 1997 +0000

    Test for case where domain can't be coarsened but a grid (apparently) can.

Src/LinearSolvers/C_NodalMG/tests/gr2dave
Tests/LinearSolvers/C_NodalMG/test_grids/gr2dave

commit 588e910984fa921a0891b02b645817b0111e6f73
Author: nazgul <nazgul>
Date:   Mon Jun 2 20:55:51 1997 +0000

    Bug fix for case where domain can't be coarsened but a grid (apparently) can.

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 0221b7d7797f7fcccc64081bfa6664c66b0f5a18
Author: nazgul <nazgul>
Date:   Fri May 30 20:55:08 1997 +0000

    Fixed a routine that isn't used yet so that the file will compile.

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 180f1301d3af355a06bc8cee7813505b5ac5d487
Author: nazgul <nazgul>
Date:   Fri May 30 20:32:54 1997 +0000

    Corrections to handle (4,1) refinement correctly.

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/interface.H
Src/LinearSolvers/C_NodalMG/interface.cpp

commit 4842b6e5470bf7b21457af87a793e7d6e36e1ee3
Author: nazgul <nazgul>
Date:   Fri May 30 20:32:11 1997 +0000

    Adding (4,1) test grids.

Src/LinearSolvers/C_NodalMG/tests/gr.19s4.1
Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s4.1

commit 8206143d920174ac0ab88e14dc1e357510246696
Author: nazgul <nazgul>
Date:   Wed May 28 19:16:03 1997 +0000

    Adds changes to support IntVect refinement ratios.
    Minor: fixes bug where cell-based source average trashes some
    interface divergence values that were already calculated.

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_graph.H
Src/LinearSolvers/C_NodalMG/amr_graph.cpp
Src/LinearSolvers/C_NodalMG/amr_gravity.cpp
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/cont3d.F
Src/LinearSolvers/C_NodalMG/fill_patch.H
Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/interpolator.H
Src/LinearSolvers/C_NodalMG/interpolator.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp
Src/LinearSolvers/C_NodalMG/restrictor.H
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit bb56e75a5fff449325f871ed0c70285fd8f0f831
Author: nazgul <nazgul>
Date:   Wed May 28 19:12:32 1997 +0000

    Tests for variable refinement ratios.

Src/LinearSolvers/C_NodalMG/tests/gr.19s2.4
Src/LinearSolvers/C_NodalMG/tests/gt4s2.4.4
Src/LinearSolvers/C_NodalMG/tests/gt4s4
Src/LinearSolvers/C_NodalMG/tests/gt4s4.2.4
Src/LinearSolvers/C_NodalMG/tests/gt4s4.4.2
Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s2.4
Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2.4.4
Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4
Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4.2.4
Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4.4.2

commit c3ca852054668ca71425ea5c4950cac13b3a11e6
Author: nazgul <nazgul>
Date:   Wed May 14 20:33:27 1997 +0000

    line solve bug fix for degenerate case of 1-point line solves

Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit ccf827a86e46802ea327329177ff0cb1ab824a02
Author: nazgul <nazgul>
Date:   Thu May 8 15:18:17 1997 +0000

    Removed the function type(const PArray<MultiFab>& a).
    It was too prone to errors caused by partially-filled arrays.
    Use type(const FabArray<Real,Fab>& r) instead.

Src/LinearSolvers/C_NodalMG/amr_defs.H
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit d54a21c35d4f3cb5f27d0371773cdc75f00afef6
Author: nazgul <nazgul>
Date:   Wed May 7 22:24:26 1997 +0000

    fix type index bug

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 44bc484391ff0051173bbfcc8674a5f20ef5363b
Author: nazgul <nazgul>
Date:   Wed May 7 21:35:06 1997 +0000

    fix to sync source correction

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 8e8bc933eeba15314d227303c8e9b30cca05e59c
Author: nazgul <nazgul>
Date:   Wed May 7 21:29:19 1997 +0000

    sync source solvability correction

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.H
Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 93c2d649c1627732aedae0ffa64483674110b569
Author: nazgul <nazgul>
Date:   Wed May 7 01:37:55 1997 +0000

    adding line solve

Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 5bca72009eeb1c3d2f869563ae4261a411f18a97
Author: nazgul <nazgul>
Date:   Wed May 7 00:35:43 1997 +0000

    adding line solve

Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/hg_multi.H
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit c0c90778cefc358ca49b6132afc6e7ffde36d79c
Author: nazgul <nazgul>
Date:   Tue May 6 03:11:18 1997 +0000

    fix index bug

Src/LinearSolvers/C_NodalMG/amr_multi.cpp

commit bad568c5614578c49cbee45558f823110a6ab6e9
Author: nazgul <nazgul>
Date:   Mon May 5 22:18:35 1997 +0000

    Bug fix to build_index

Src/LinearSolvers/C_NodalMG/amr_multi.cpp

commit 37257f0bd58dd5c3099205e98974e1daa0fb6877
Author: nazgul <nazgul>
Date:   Fri May 2 22:06:26 1997 +0000

    Fixed memory leak in test program

Src/LinearSolvers/C_NodalMG/Make.package
Src/LinearSolvers/C_NodalMG/proj.cpp

commit c0b6bc499b3f85c4a7821027396d181cc57f7e6c
Author: nazgul <nazgul>
Date:   Fri May 2 17:35:14 1997 +0000

    Fixes for variable density now work.

Src/LinearSolvers/C_NodalMG/GNUmakefile.main
Src/LinearSolvers/C_NodalMG/Rewrite
Src/LinearSolvers/C_NodalMG/hg_multi1.cpp
Src/LinearSolvers/C_NodalMG/hg_multi2.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit 97e6e31d7d751d014563aabcec43b390fa0b0d1f
Author: nazgul <nazgul>
Date:   Wed Apr 30 22:04:33 1997 +0000

    Corrections for 3D.

Src/LinearSolvers/C_NodalMG/Rewrite
Src/LinearSolvers/C_NodalMG/amr_graph.H
Src/LinearSolvers/C_NodalMG/amr_graph.cpp
Src/LinearSolvers/C_NodalMG/amr_multi.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit e4f0a563c5d1dd000ec4903229699b9a1c2525f1
Author: nazgul <nazgul>
Date:   Wed Apr 30 20:28:51 1997 +0000

    adding GNUmakefile manually since import ignores it.

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 67746f0dc469437c4a66c7c74e478ac6223deef4
Author: nazgul <nazgul>
Date:   Wed Apr 30 20:03:52 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/amr_defs.H

commit 912dae00eccf22fa9f468469c07b3e03884eca74
Author: nazgul <nazgul>
Date:   Wed Apr 30 19:40:01 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/amr_graph.H
Src/LinearSolvers/C_NodalMG/amr_graph.cpp

commit 2593ad549b300c9030f9c96f2b92da94a607a040
Author: nazgul <nazgul>
Date:   Wed Apr 30 17:35:40 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp

commit eb88f1d8f9edbec08451464a1a58adc58c9a315c
Author: nazgul <nazgul>
Date:   Wed Apr 30 17:26:18 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/amr_multi.cpp

commit a153bb642f43c1f0dc43e9dda19224ca33bf0abd
Author: nazgul <nazgul>
Date:   Tue Apr 29 22:40:14 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/interface.cpp

commit fa663bf79c0f70141d03350f32c0ebf913e88c08
Author: nazgul <nazgul>
Date:   Tue Apr 29 20:41:56 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/fill_patch.cpp
Src/LinearSolvers/C_NodalMG/hg_multi3.cpp
Src/LinearSolvers/C_NodalMG/hg_projector.cpp
Src/LinearSolvers/C_NodalMG/proj.cpp

commit c686e8eb909d6bc9e1470687eba613f8979febe1
Author: nazgul <nazgul>
Date:   Tue Apr 29 20:38:16 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/fill_patch.H

commit 5e43618b9ba22ff0405611be875aed141fb2971a
Author: nazgul <nazgul>
Date:   Tue Apr 29 20:15:56 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit ba18f4dd9f6dfa86e00df173cf66154acc1ead2e
Author: nazgul <nazgul>
Date:   Tue Apr 29 18:29:40 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 94ffd818a9bf1ab6c86ec18e6e4565395f40ff4e
Author: nazgul <nazgul>
Date:   Mon Apr 28 21:51:56 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/amr_multi.H

commit a498100b0a43479409605ec9eaa464600fe1621b
Author: nazgul <nazgul>
Date:   Fri Apr 25 23:30:33 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/Make.package

commit 0f2561a87bce705882fc6124212c47013f79abea
Author: nazgul <nazgul>
Date:   Wed Apr 23 22:34:37 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/GNUmakefile.main

commit f686b4bc929214d97a8b0588608fe3b6731e46dc
Author: nazgul <nazgul>
Date:   Thu Mar 27 22:05:28 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_multi.H

commit 52d19b7261ae7399004472ae95a884a86413590c
Author: nazgul <nazgul>
Date:   Thu Mar 27 21:24:11 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_projector.H

commit 6b3d4c19412bdbce7f963ddded8121c512d600c1
Author: nazgul <nazgul>
Date:   Wed Mar 26 17:38:08 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/tests/gr2ann.p5
Src/LinearSolvers/C_NodalMG/tests/gr2ann.p6
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p5
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p6

commit 8ff71095cc689bc66f398bc1ee37ae130abe0c75
Author: nazgul <nazgul>
Date:   Tue Mar 25 18:58:20 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/amr_real2d.F
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/boundary.H

commit 1d73e974b0ad30060d63baa15439940bbbfff0a3
Author: nazgul <nazgul>
Date:   Fri Mar 21 20:13:36 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/amr_gravity.cpp
Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit a3cf04d3be4853c18b48d3189cb7d77c1e01860d
Author: nazgul <nazgul>
Date:   Fri Mar 21 20:09:06 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/cache.cpp
Src/LinearSolvers/C_NodalMG/interface.H

commit 92deacad1bee7c78f20a98ca485ca87363e4a677
Author: nazgul <nazgul>
Date:   Thu Mar 20 21:13:29 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/Rewrite

commit 2e93f82c5955ee9919b5c73c2a318745843ac9f0
Author: nazgul <nazgul>
Date:   Tue Mar 18 23:51:41 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/cache.H

commit 003ce6b53e5b81ecd219bc5a44af8d244e71f26a
Author: nazgul <nazgul>
Date:   Tue Mar 18 20:16:26 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/tests/gt3ann2
Tests/LinearSolvers/C_NodalMG/test_grids/gt3ann2

commit 007298ac68b21503d37eaf44a9cae210ad49c333
Author: nazgul <nazgul>
Date:   Tue Mar 11 21:41:59 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.F

commit 3c64577c7f70412dbff59ecc2e3f6e3af9daeb27
Author: nazgul <nazgul>
Date:   Mon Mar 3 18:05:45 1997 +0000

    Initial revision

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commit 0e784304318d972a12ff33b3ea641a81a402e790
Author: nazgul <nazgul>
Date:   Thu Feb 27 22:39:56 1997 +0000

    Initial revision

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commit 20def58b10e8becad27f7bff656cd10695829880
Author: nazgul <nazgul>
Date:   Wed Feb 26 20:41:58 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/interpolator.H
Src/LinearSolvers/C_NodalMG/interpolator.cpp

commit e2cac3e6437f670bdb29e607b8f777d3c23c1dd5
Author: nazgul <nazgul>
Date:   Tue Jan 28 18:30:30 1997 +0000

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Src/LinearSolvers/C_NodalMG/tests/gr3ann
Src/LinearSolvers/C_NodalMG/tests/gr3ann2
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Tests/LinearSolvers/C_NodalMG/test_grids/gr.19l3
Tests/LinearSolvers/C_NodalMG/test_grids/gr3ann
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commit ee9a62eadae53a655b766d757aaeb56b5ff725a3
Author: nazgul <nazgul>
Date:   Tue Sep 24 19:39:37 1996 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/mall_info.cpp

commit 928a1d7dde9f59786478d389194e2a0d314e6c8b
Author: nazgul <nazgul>
Date:   Sat Aug 31 00:51:34 1996 +0000

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Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 3931ee9d0cc9f7a1baeba373b1a4fa2dc915f118
Author: nazgul <nazgul>
Date:   Tue May 14 20:11:34 1996 +0000

    Initial revision

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Src/LinearSolvers/C_NodalMG/tests/gr3rick
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Tests/LinearSolvers/C_NodalMG/test_grids/gtjbb

commit 6830436830288f40cd9ae3c8829073031ee040db
Author: nazgul <nazgul>
Date:   Thu Apr 25 16:46:17 1996 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit 1f04efac2dc02158cf22a7c3d2f3f87082487dc6
Author: nazgul <nazgul>
Date:   Wed Mar 13 22:28:35 1996 +0000

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Src/LinearSolvers/C_NodalMG/cbasics.H
Src/LinearSolvers/C_NodalMG/tests/gr0a
Tests/LinearSolvers/C_NodalMG/test_grids/gr0a

commit f87f1b2d83b7fe9c512ddc0ca43ae9bcd434670f
Author: nazgul <nazgul>
Date:   Tue Nov 7 22:26:32 1995 +0000

    Initial revision

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Src/LinearSolvers/C_NodalMG/amr_grav3d.F
Src/LinearSolvers/C_NodalMG/cont2d.F
Src/LinearSolvers/C_NodalMG/cont3d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit c139797864292915ccc5ebea761e68615309b970
Author: nazgul <nazgul>
Date:   Mon Oct 30 22:35:09 1995 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/README

commit cfefdf25849ecf2ab5a5b2b6573a4f2bc43a21dd
Author: nazgul <nazgul>
Date:   Mon Sep 18 20:37:46 1995 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/poisson.cpp

commit d3a6d7bfeffcf89aa95b004c4aabb44f9243f13c
Author: nazgul <nazgul>
Date:   Mon Sep 18 18:20:14 1995 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_elliptic.cpp

commit e7ab65e98df0bd6814dab6ea6bb540296b1b4677
Author: nazgul <nazgul>
Date:   Thu Aug 24 21:25:02 1995 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/tests/gr2ann.l2
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l2

commit ef57898a17aac4dd83b5457c8f70d6b4c4e42a2e
Author: nazgul <nazgul>
Date:   Thu Aug 24 21:12:20 1995 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/tests/gr2ann.l1
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l1

commit 642554a3d74ed89dfdb89c9049612fbcfb061494
Author: nazgul <nazgul>
Date:   Thu Aug 24 21:02:50 1995 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/tests/gr2ann.l0
Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l0

commit 6603ce60473f65e14e871c323ac0c2fb4fda9df8
Author: nazgul <nazgul>
Date:   Fri Nov 4 23:35:41 1994 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/tests/gr.11
Src/LinearSolvers/C_NodalMG/tests/gr.15
Src/LinearSolvers/C_NodalMG/tests/gr.16
Src/LinearSolvers/C_NodalMG/tests/gr.19
Src/LinearSolvers/C_NodalMG/tests/gr.19s2
Src/LinearSolvers/C_NodalMG/tests/gr.19s4
Src/LinearSolvers/C_NodalMG/tests/gr.292.11
Src/LinearSolvers/C_NodalMG/tests/gr.292.25
Src/LinearSolvers/C_NodalMG/tests/gr.7
Src/LinearSolvers/C_NodalMG/tests/gr.8
Src/LinearSolvers/C_NodalMG/tests/gr.8a
Src/LinearSolvers/C_NodalMG/tests/gr0
Src/LinearSolvers/C_NodalMG/tests/gr1
Src/LinearSolvers/C_NodalMG/tests/gr1mike.thin
Src/LinearSolvers/C_NodalMG/tests/gr2
Src/LinearSolvers/C_NodalMG/tests/gr2a2
Src/LinearSolvers/C_NodalMG/tests/gr2a4
Src/LinearSolvers/C_NodalMG/tests/gr2ann
Src/LinearSolvers/C_NodalMG/tests/gr2ann.p1
Src/LinearSolvers/C_NodalMG/tests/gr2ann.p2
Src/LinearSolvers/C_NodalMG/tests/gr2ann.p3
Src/LinearSolvers/C_NodalMG/tests/gr2ann.p4
Src/LinearSolvers/C_NodalMG/tests/gr2b
Src/LinearSolvers/C_NodalMG/tests/gr2c
Src/LinearSolvers/C_NodalMG/tests/gr2cross
Src/LinearSolvers/C_NodalMG/tests/gr2d
Src/LinearSolvers/C_NodalMG/tests/gr2d2
Src/LinearSolvers/C_NodalMG/tests/gr2d4
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commit d9792e7e53274b898d907a0f08452bef75669031
Author: nazgul <nazgul>
Date:   Tue Oct 4 22:13:47 1994 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/amr_gravity.H

commit b06aef4481e3612148772e1a6e0aa59c3be684e4
Author: nazgul <nazgul>
Date:   Wed Mar 23 23:31:05 1994 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_elliptic.H

commit 1fc596b76899cdd13da6cd2998ba4f362c5b3130
Author: nazgul <nazgul>
Date:   Tue Oct 5 18:46:17 1993 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/driver.cpp

commit 93dbd8bb612ee031f19d5659b3b8aac4afb85511
Author: nazgul <nazgul>
Date:   Fri Mar 12 19:37:55 1993 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/RegType.H